diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2827165..3e9cbf5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [1.7.0] - 2022-12-31
+### Changed
+- Better robunsteness for the dependency installation script.
+- Functional enhancement for the basecalling, demultiplexing, and quality summary of ONT raw fast5 reads.
+- Version updates for multiple genome assemblers.
+- Functional enhancement for the mitochondrial genome assembly.
+- Functional enhancement for the mitochondrial gene annotation.
+- Functional enhancement for the nuclear gene annotation.
+- Functional enhancement for the TE annotation.
+- Functional enhancement for SGD_based orthology identification and tagging.
+- Removal of support for the long-read-assembler: Ra.
+- Removal of support for the long-read-polisher: MarginPolish.
 
 ## [1.6.0] - 2019-10-03
 ### Added
diff --git a/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.cds.fa.gz b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.cds.fa.gz
new file mode 100644
index 0000000..f612067
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diff --git a/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.fa.gz b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.fa.gz
new file mode 100644
index 0000000..bd55b3f
Binary files /dev/null and b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.fa.gz differ
diff --git a/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.gff3.gz b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.gff3.gz
new file mode 100644
index 0000000..980fc70
Binary files /dev/null and b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.gff3.gz differ
diff --git a/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.pep.fa.gz b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.pep.fa.gz
new file mode 100644
index 0000000..13cd425
Binary files /dev/null and b/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.pep.fa.gz differ
diff --git a/Example_Outputs/CPG_1a.nuclear_genome.tidy.cds.fa.gz b/Example_Outputs/CPG_1a.nuclear_genome.tidy.cds.fa.gz
new file mode 100644
index 0000000..d1577db
Binary files /dev/null and b/Example_Outputs/CPG_1a.nuclear_genome.tidy.cds.fa.gz differ
diff --git a/Example_Outputs/CPG_1a.nuclear_genome.tidy.fa.gz b/Example_Outputs/CPG_1a.nuclear_genome.tidy.fa.gz
new file mode 100644
index 0000000..cf3bf43
Binary files /dev/null and b/Example_Outputs/CPG_1a.nuclear_genome.tidy.fa.gz differ
diff --git a/Example_Outputs/CPG_1a.nuclear_genome.tidy.gff3.gz b/Example_Outputs/CPG_1a.nuclear_genome.tidy.gff3.gz
new file mode 100644
index 0000000..3fe1c06
Binary files /dev/null and b/Example_Outputs/CPG_1a.nuclear_genome.tidy.gff3.gz differ
diff --git a/Example_Outputs/CPG_1a.nuclear_genome.tidy.pep.fa.gz b/Example_Outputs/CPG_1a.nuclear_genome.tidy.pep.fa.gz
new file mode 100644
index 0000000..e66d072
Binary files /dev/null and b/Example_Outputs/CPG_1a.nuclear_genome.tidy.pep.fa.gz differ
diff --git a/Example_Outputs/SK1.assembly.final.fa.gz b/Example_Outputs/SK1.assembly.final.fa.gz
deleted file mode 100644
index e12192b..0000000
Binary files a/Example_Outputs/SK1.assembly.final.fa.gz and /dev/null differ
diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz
deleted file mode 100644
index 16363bc..0000000
Binary files a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz and /dev/null differ
diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz
deleted file mode 100644
index b15e8f6..0000000
Binary files a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz and /dev/null differ
diff --git a/Example_Outputs/SK1.assembly.final.filter.pdf b/Example_Outputs/SK1.assembly.final.filter.pdf
deleted file mode 100644
index c6a514a..0000000
Binary files a/Example_Outputs/SK1.assembly.final.filter.pdf and /dev/null differ
diff --git a/Example_Outputs/SK1.assembly.final.stats.txt b/Example_Outputs/SK1.assembly.final.stats.txt
deleted file mode 100644
index 2067a0d..0000000
--- a/Example_Outputs/SK1.assembly.final.stats.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-total sequence count: 34
-total sequence length: 12473902
-min sequence length: 12836
-max sequence length: 1480337
-mean sequence length: 366879.47
-median sequence length: 57378.00
-N50: 923760
-L50: 6
-N90: 328166
-L90: 14
-A%: 30.88
-T%: 30.81
-G%: 19.12
-C%: 19.14
-AT%: 61.69
-GC%: 38.27
-N%: 0.04
diff --git a/Example_Outputs/SK1.final.cds.fa.gz b/Example_Outputs/SK1.final.cds.fa.gz
deleted file mode 100644
index 68342e9..0000000
Binary files a/Example_Outputs/SK1.final.cds.fa.gz and /dev/null differ
diff --git a/Example_Outputs/SK1.final.gff3.gz b/Example_Outputs/SK1.final.gff3.gz
deleted file mode 100644
index 1cf9560..0000000
Binary files a/Example_Outputs/SK1.final.gff3.gz and /dev/null differ
diff --git a/Example_Outputs/SK1.final.manual_check.list b/Example_Outputs/SK1.final.manual_check.list
deleted file mode 100644
index b7fe7ad..0000000
--- a/Example_Outputs/SK1.final.manual_check.list
+++ /dev/null
@@ -1,243 +0,0 @@
-SK1_G0000020|SK1_G0000020.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0000680|SK1_G0000680.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0000780|SK1_G0000780.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0000920|SK1_G0000920.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0001070|SK1_G0001070.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0001180|SK1_G0001180.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0001230|SK1_G0001230.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0001430|SK1_G0001430.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0001610|SK1_G0001610.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0001760|SK1_G0001760.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0001860|SK1_G0001860.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0002650|SK1_G0002650.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0002840|SK1_G0002840.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0002870|SK1_G0002870.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0002930|SK1_G0002930.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0003780|SK1_G0003780.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0004160|SK1_G0004160.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0004500|SK1_G0004500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0004910|SK1_G0004910.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005420|SK1_G0005420.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005500|SK1_G0005500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005580|SK1_G0005580.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005780|SK1_G0005780.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005810|SK1_G0005810.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005820|SK1_G0005820.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0005840|SK1_G0005840.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0006000|SK1_G0006000.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0006160|SK1_G0006160.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0006410|SK1_G0006410.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0006460|SK1_G0006460.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
-SK1_G0006470|SK1_G0006470.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1
-SK1_G0006620|SK1_G0006620.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0007700|SK1_G0007700.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0007790|SK1_G0007790.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0008090|SK1_G0008090.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0008120|SK1_G0008120.mRNA.1	incorrect CDS length
-SK1_G0008130|SK1_G0008130.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0008140|SK1_G0008140.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0009330|SK1_G0009330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0009990|SK1_G0009990.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0010070|SK1_G0010070.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0010360|SK1_G0010360.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0011110|SK1_G0011110.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0011600|SK1_G0011600.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0012350|SK1_G0012350.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0012500|SK1_G0012500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0012710|SK1_G0012710.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0012720|SK1_G0012720.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0012900|SK1_G0012900.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0013380|SK1_G0013380.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0013400|SK1_G0013400.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0013690|SK1_G0013690.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
-SK1_G0013730|SK1_G0013730.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0013740|SK1_G0013740.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0013810|SK1_G0013810.mRNA.1	incorrect CDS length
-SK1_G0013830|SK1_G0013830.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0014550|SK1_G0014550.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0014600|SK1_G0014600.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0015000|SK1_G0015000.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0015140|SK1_G0015140.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0015530|SK1_G0015530.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0015560|SK1_G0015560.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0016490|SK1_G0016490.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0016620|SK1_G0016620.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0016840|SK1_G0016840.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0016850|SK1_G0016850.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0016950|SK1_G0016950.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0016960|SK1_G0016960.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0017430|SK1_G0017430.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0017510|SK1_G0017510.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0017770|SK1_G0017770.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0017780|SK1_G0017780.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0017790|SK1_G0017790.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0017940|SK1_G0017940.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0018170|SK1_G0018170.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0018550|SK1_G0018550.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0019100|SK1_G0019100.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0019390|SK1_G0019390.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0019500|SK1_G0019500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0020150|SK1_G0020150.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0021560|SK1_G0021560.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0021800|SK1_G0021800.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0022770|SK1_G0022770.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0022810|SK1_G0022810.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0022840|SK1_G0022840.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0022910|SK1_G0022910.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0022940|SK1_G0022940.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0023550|SK1_G0023550.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0023600|SK1_G0023600.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0023790|SK1_G0023790.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0023810|SK1_G0023810.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0023870|SK1_G0023870.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0024170|SK1_G0024170.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0024200|SK1_G0024200.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0024380|SK1_G0024380.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0024420|SK1_G0024420.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0024810|SK1_G0024810.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0025250|SK1_G0025250.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0025390|SK1_G0025390.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0025430|SK1_G0025430.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0025610|SK1_G0025610.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0025630|SK1_G0025630.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0025970|SK1_G0025970.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0026260|SK1_G0026260.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0026410|SK1_G0026410.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0026500|SK1_G0026500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0026540|SK1_G0026540.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0026690|SK1_G0026690.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0026890|SK1_G0026890.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0027180|SK1_G0027180.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0027630|SK1_G0027630.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0027660|SK1_G0027660.mRNA.1	incorrect CDS length
-SK1_G0027700|SK1_G0027700.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0027740|SK1_G0027740.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0027770|SK1_G0027770.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0027920|SK1_G0027920.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0028510|SK1_G0028510.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0029460|SK1_G0029460.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0029530|SK1_G0029530.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0029890|SK1_G0029890.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0030020|SK1_G0030020.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0031030|SK1_G0031030.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0031130|SK1_G0031130.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0031200|SK1_G0031200.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0031810|SK1_G0031810.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0032220|SK1_G0032220.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0032380|SK1_G0032380.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0033290|SK1_G0033290.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0033390|SK1_G0033390.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0033400|SK1_G0033400.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0034230|SK1_G0034230.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0034380|SK1_G0034380.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0034890|SK1_G0034890.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0035490|SK1_G0035490.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0035710|SK1_G0035710.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0035860|SK1_G0035860.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0036800|SK1_G0036800.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0036910|SK1_G0036910.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0038600|SK1_G0038600.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0038690|SK1_G0038690.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039140|SK1_G0039140.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039270|SK1_G0039270.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039290|SK1_G0039290.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039600|SK1_G0039600.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039640|SK1_G0039640.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039750|SK1_G0039750.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039810|SK1_G0039810.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0039930|SK1_G0039930.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0040190|SK1_G0040190.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0040200|SK1_G0040200.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0040500|SK1_G0040500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0041510|SK1_G0041510.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0041740|SK1_G0041740.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0041950|SK1_G0041950.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0042260|SK1_G0042260.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0042330|SK1_G0042330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0042570|SK1_G0042570.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0043650|SK1_G0043650.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0043680|SK1_G0043680.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0043700|SK1_G0043700.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0044000|SK1_G0044000.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0044010|SK1_G0044010.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0044280|SK1_G0044280.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0044330|SK1_G0044330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0044920|SK1_G0044920.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0045100|SK1_G0045100.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0045470|SK1_G0045470.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1
-SK1_G0045560|SK1_G0045560.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0045850|SK1_G0045850.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0046100|SK1_G0046100.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0046260|SK1_G0046260.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047240|SK1_G0047240.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047250|SK1_G0047250.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047330|SK1_G0047330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047360|SK1_G0047360.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047470|SK1_G0047470.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047880|SK1_G0047880.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0047890|SK1_G0047890.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0048580|SK1_G0048580.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0048590|SK1_G0048590.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0049250|SK1_G0049250.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0050130|SK1_G0050130.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0050980|SK1_G0050980.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0051140|SK1_G0051140.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0051210|SK1_G0051210.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0051540|SK1_G0051540.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0052240|SK1_G0052240.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0052480|SK1_G0052480.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0052490|SK1_G0052490.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0052630|SK1_G0052630.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0052670|SK1_G0052670.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0052680|SK1_G0052680.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0052700|SK1_G0052700.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0052730|SK1_G0052730.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0053030|SK1_G0053030.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0053120|SK1_G0053120.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0053650|SK1_G0053650.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0053830|SK1_G0053830.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0054270|SK1_G0054270.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0054370|SK1_G0054370.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0054560|SK1_G0054560.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055100|SK1_G0055100.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055160|SK1_G0055160.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055240|SK1_G0055240.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055500|SK1_G0055500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0055970|SK1_G0055970.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0056270|SK1_G0056270.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057280|SK1_G0057280.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057330|SK1_G0057330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057380|SK1_G0057380.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057410|SK1_G0057410.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057470|SK1_G0057470.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1
-SK1_G0057490|SK1_G0057490.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057500|SK1_G0057500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057510|SK1_G0057510.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057540|SK1_G0057540.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057750|SK1_G0057750.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057830|SK1_G0057830.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057860|SK1_G0057860.mRNA.1	incorrect CDS length
-SK1_G0057890|SK1_G0057890.mRNA.1	incorrect CDS length
-SK1_G0057930|SK1_G0057930.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057970|SK1_G0057970.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058000|SK1_G0058000.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058030|SK1_G0058030.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058070|SK1_G0058070.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058100|SK1_G0058100.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058110|SK1_G0058110.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058160|SK1_G0058160.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058200|SK1_G0058200.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
-SK1_G0058290|SK1_G0058290.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058300|SK1_G0058300.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058320|SK1_G0058320.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058330|SK1_G0058330.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058340|SK1_G0058340.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058350|SK1_G0058350.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 1
-SK1_G0058470|SK1_G0058470.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058550|SK1_G0058550.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058760|SK1_G0058760.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-cox2|cox2.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 3;incorrect CDS length
-orf474|orf474.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 3;incorrect CDS length
-orf90|orf90.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 3
-orf241|orf241.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 3;incorrect CDS length
-orf152|orf152.mRNA.1	incorrect CDS length
diff --git a/Example_Outputs/SK1.final.pep.fa.gz b/Example_Outputs/SK1.final.pep.fa.gz
deleted file mode 100644
index 0e4bacb..0000000
Binary files a/Example_Outputs/SK1.final.pep.fa.gz and /dev/null differ
diff --git a/Example_Outputs/SK1.final.trimmed_cds.fa.gz b/Example_Outputs/SK1.final.trimmed_cds.fa.gz
deleted file mode 100644
index 5dd77bb..0000000
Binary files a/Example_Outputs/SK1.final.trimmed_cds.fa.gz and /dev/null differ
diff --git a/LRSDAY_flowchart.png b/LRSDAY_flowchart.png
index 6d15d6d..f2566e9 100644
Binary files a/LRSDAY_flowchart.png and b/LRSDAY_flowchart.png differ
diff --git a/Manual.pdf b/Manual.pdf
deleted file mode 100644
index 3176c9e..0000000
Binary files a/Manual.pdf and /dev/null differ
diff --git a/Manual_20221231.docx b/Manual_20221231.docx
new file mode 100644
index 0000000..f557b82
Binary files /dev/null and b/Manual_20221231.docx differ
diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.Long_Reads_Preprocessing.sh b/Project_Template/00.Long_Reads/LRSDAY.00.Long_Reads_Preprocessing.sh
index 926db3f..c0347d6 100755
--- a/Project_Template/00.Long_Reads/LRSDAY.00.Long_Reads_Preprocessing.sh
+++ b/Project_Template/00.Long_Reads/LRSDAY.00.Long_Reads_Preprocessing.sh
@@ -1,19 +1,19 @@
 #!/bin/bash
 set -e -o pipefail
 #######################################
-# load environment variables for LRSDAY
+# load environment variables
 source ./../../env.sh
 
 #######################################
 # set project-specific variables
 
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-reads="./../00.Long_Reads/$prefix.filtered_subreads.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format).
-reads_type="pacbio-raw" # The long reads data type: "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected".
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.
+reads="./../00.Long_Reads/nanopore_basecalled_fastq_files/$prefix/$prefix.basecalled_reads.Q5.pass.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format).
+reads_type="nanopore-raw" # The long reads data type: "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected".
 run_filtering="yes" # Whether to filter and downsample the reads: "yes" or "no". Default = "yes".
 genome_size="12500000" # The haploid genome size (in bp) of sequenced organism. Default = "12500000" (i.e. 12.5 Mb for the budding yeast S. cereviaie genome). This is used to calculate targeted sequencing coverage after read filtering (see below). 
 post_filtering_coverage="60" # Targeted sequencing coverage after read filtering and downsampling. Default = "60" (i.e. 60x coverage).
-threads=4 # The number of threads to use. Default = "1".
+threads=24 # The number of threads to use. Default = "4".
 
 #######################################
 # process the pipeline
@@ -27,7 +27,7 @@ then
 	echo ""
 	echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
 	echo ""
-	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --target_bases $filtlong_target_bases $prefix.porechop.fastq.gz | gzip > $prefix.filtlong.fastq.gz
+	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --window_q_weight 5 --target_bases $filtlong_target_bases $prefix.porechop.fastq.gz | gzip > $prefix.filtlong.fastq.gz
     fi
 else
     if [[ "$run_filtering" == "yes" ]]
@@ -36,7 +36,7 @@ else
 	echo ""
 	echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
 	echo ""
-	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --target_bases $filtlong_target_bases $reads | gzip > $prefix.filtlong.fastq.gz
+	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --window_q_weight 5 --target_bases $filtlong_target_bases $reads | gzip > $prefix.filtlong.fastq.gz
     fi
 fi
 
diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.Nanopore_Reads_Basecalling.sh b/Project_Template/00.Long_Reads/LRSDAY.00.Nanopore_Reads_Basecalling.sh
new file mode 100755
index 0000000..4ce407f
--- /dev/null
+++ b/Project_Template/00.Long_Reads/LRSDAY.00.Nanopore_Reads_Basecalling.sh
@@ -0,0 +1,222 @@
+#!/bin/bash
+set -e -o pipefail
+#######################################
+# load environment variables
+source ./../../env.sh
+
+########################
+guppy_run_mode="cpu" # The running mode of Guppy basecalling: "gpu" or "cpu". Default = "cpu".
+if [[ $guppy_run_mode == "gpu" ]]
+then
+    # set CUDA environment for GPU
+    gpu_bin_path="/public/software/cuda-11.4/bin" # The path of CUDA's bin directory. Default = "/public/software/cuda-11.4/bin".
+    gpu_lib_path="/public/software/cuda-11.4/lib64" # The path of CUDA's lib directory. Default = "/public/software/cuda-11.4/lib64".
+    gpu_include_path="/public/software/cuda-11.4/include" # The path of CUDA's include directory. Default = "/public/software/cuda-11.4/include".
+fi
+##########################3
+export PATH=$gpu_bin_path:$PATH
+export LD_LIBRARY_PATH=$gpu_lib_path:$LD_LIBRARY_PATH
+export C_INCLUDE_PATH=$gpu_include_path:$C_INCLUDE_PATH
+export CPLUS_INCLUDE_PATH=$C_INCLUDE_PATH
+
+##k#####################################
+# set project-specific variables
+
+sample_id="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.              
+raw_fast5_dir="./nanopore_raw_fast5_files/$sample_id" # The directory containing the raw nanopore reads before basecalling. Default = "./raw_fast5/$sample_id".
+flowcell_version="FLO-MIN106" # The flowcell version of the nanopore run. Default = "FLO-MIN106".
+sequencing_kit_version="SQK-LSK108" # The sequencing kit version of the nanopore run. Default = "SQK-LSK109". 
+barcode_kit_version="EXP-NBD104" # The barcode kit version of the nanopore run if barcoding has been introduced during library preparation. Default = "EXP-NBD104". For the testing example, we have not applied barcoding. So this information will not be used when we set run_demultiplexing="no" below.
+
+run_basecalling="yes" # Whether to perform basecalling: "yes" or "no". Default = "yes". 
+run_demultiplexing="no" # Whether to perform demultiplexing: "yes" or "no". Default = "no". For the testing example, we have not applied barcoding. So no need to run this step. 
+run_nanoplotting="yes" # Whether to perform nanoplotting: "yes" or "no". Default = "yes". 
+
+threads=16 # The number of CPU threads to use. Default = 16.
+debug="no" # Whether to keep intermediate files for debugging: "yes" or "no". Default = "no".
+
+#############################
+# Normally no need to change the following parameter settings.
+basecalled_fast5_dir="./nanopore_basecalled_fast5_files/$sample_id" # The directory containing the basecalled fast5 reads. This directory will be automatically generated when running basecalling.
+basecalled_fastq_dir="./nanopore_basecalled_fastq_files/$sample_id" # The directory containing the basecalled fastq reads. This directory will be automatically generated when running basecalling.
+basecalled_qc_dir="./nanopore_basecalled_qc_files/$sample_id" # The directory containing nanoplot QC outputs. This directory will be automatically generated when running nanoplot.
+trim_strategy="dna" # Trimming strategy to apply: 'dna' or 'rna' or 'none' (to disable trimming). Default = "rna".
+gpu_device="auto" # Which GPU device to use. Default = "auto". 
+qual=5 # read quality filter for guppy basecalling. Default = 5.
+num_callers_in_cpu_mode=$threads # The number of callers for guppy basecalling in the CPU mode. Default = "$threads".
+num_callers_in_gpu_mode=$threads # The number of callers for guppy basecalling in the GPU mode. Default = "1".
+gpu_runners_per_device=1 # The number of GPU runners per device for guppy basecalling in the GPU mode. Default = "1".
+threads_per_caller=1 # The number of threads per caller for guppy basecalling. Default = "1".
+demultiplexing_threads=$threads # The number of threads to use for guppy demultiplexing. Default = "$threads".
+demultiplexed_fastq_dir="$basecalled_fastq_dir/demultiplexed_fastq" # The directory containing the demultiplexed basecalled nanopore reads. This directory will be automatically generated when running demultiplexing. 
+
+##############################
+
+wkdir=$(pwd)
+if [[ "$run_demultiplexing" == "yes" && "barcode_kit_version" == "" ]]
+then
+    echo "The variable run_demultiplexing has been set to \"yes\" but the barcode_kit_version variable has not been specified!"
+    echo "Please specified barcode_kit_version if you want to run demultiplexing."
+    exit;
+fi
+
+
+if [[ "$run_basecalling" == "yes" ]]
+then
+    echo "Check if $basecalled_fast5_dir is empty for running basecalling."
+    if [[ -d $basecalled_fast5_dir && "$(ls $basecalled_fast5_dir)" ]]
+    then
+	echo "Warning! The basecalled fast5 directory $basecalled_fast5_dir exists and it is not empty! Please empty its content if you want to run basecalling."
+	echo "Exit!!!"
+	exit
+    elif [[ -d $basecalled_fastq_dir && "$(ls $basecalled_fastq_dir)" ]]
+    then
+        echo "Warning! The basecalled fastq directory $basecalled_fastq_dir exists and it is not empty! Please empty its content if you want to run basecalling."
+        echo "Exit!!!"
+        exit
+    else
+	echo "Check passed!"
+	echo "Running basecalling .."
+	if [[ ! -d $basecalled_fast5_dir ]]
+	then
+	    mkdir -p $basecalled_fast5_dir
+	fi
+	if [[ ! -d $basecalled_fastq_dir ]]
+	then
+	    mkdir -p $basecalled_fastq_dir
+	fi
+
+	if [[ "$guppy_run_mode" == "gpu" ]]
+	then
+	    $guppy_gpu_dir/guppy_basecaller \
+		--flowcell $flowcell_version \
+		--kit $sequencing_kit_version \
+		--recursive \
+		--trim_strategy $trim_strategy \
+		--input_path $raw_fast5_dir \
+		--save_path $basecalled_fast5_dir \
+		--fast5_out \
+		--min_qscore $qual \
+		--device $gpu_device \
+		--num_callers $num_callers_in_gpu_mode \
+		--gpu_runners_per_device $gpu_runners_per_device \
+		--compress_fastq	    
+	else
+	    $guppy_cpu_dir/guppy_basecaller \
+		--flowcell $flowcell_version \
+		--kit $sequencing_kit_version \
+		--recursive \
+		--trim_strategy $trim_strategy \
+		--input_path $raw_fast5_dir \
+		--save_path $basecalled_fast5_dir \
+		--fast5_out \
+		--min_qscore $qual \
+		--num_callers $num_callers_in_cpu_mode \
+		--cpu_threads_per_caller $threads_per_caller \
+		--compress_fastq	    
+	fi
+	cat $basecalled_fast5_dir/pass/*.fastq.gz  > $basecalled_fastq_dir/$sample_id.basecalled_reads.Q${qual}.pass.fastq.gz
+	# cat $basecalled_fast5_dir/fail/*.fastq.gz  > $basecalled_fastq_dir/$sample_id.basecalled_reads.Q${qual}.fail.fastq.gz
+	if [[ $debug != "yes" ]]
+	then
+	    rm -r $basecalled_fast5_dir/pass
+	    rm -r $basecalled_fast5_dir/fail
+	fi
+    fi
+fi
+
+cd $wkdir
+if [[ "$run_demultiplexing" == "yes" ]]
+then
+    echo "Check if $basecalled_fastq_dir has basecalled reads for running demultiplexing."
+    if [[ "$(ls $basecalled_fastq_dir)" ]]
+    then
+	echo "Running demultiplexing."
+	if [[ "$guppy_run_mode" == "gpu" ]]
+	then
+	    $guppy_gpu_dir/guppy_barcoder \
+		--barcode_kits $barcode_kit_version \
+		--recursive \
+		--input_path $basecalled_fastq_dir \
+		--save_path $demultiplexed_fastq_dir \
+		--worker_threads $demultiplexing_threads
+	else
+	    $guppy_cpu_dir/guppy_barcoder \
+		--barcode_kits $barcode_kit_version \
+		--recursive \
+		--input_path $basecalled_fastq_dir \
+		--save_path $demultiplexed_fastq_dir \
+		--worker_threads $demultiplexing_threads
+	fi
+
+	cd $demultiplexed_fastq_dir
+	for b in barcode*
+	do 
+	    echo "for demultiplexing: barcode=$b"
+	    cat ./$b/*.fastq |gzip -c > $sample_id.basecalled_reads.Q${qual}.pass.$b.fastq.gz
+	done
+	cat ./unclassified/*.fastq |gzip -c > $sample_id.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz
+    else
+	echo "There is no reads in $basecalled_fastq_dir!"
+	echo "Please put the basecalled reads in $basecalled_fastq_dir for demultiplexing!"
+	echo "Exit!!!"
+	exit
+    fi
+fi
+
+set +oe pipefail 
+
+cd $wkdir
+if [[ "$run_nanoplotting" == "yes" ]]
+then
+    echo "Check if $basecalled_fastq_dir has basecalled reads for running nanoplotting."
+    if [[ "$(ls $basecalled_fastq_dir)" ]]
+    then
+	echo "Running nanoplotting."
+	mkdir -p $basecalled_qc_dir
+	fastq_input="$basecalled_fastq_dir/$sample_id.basecalled_reads.Q${qual}.pass.fastq.gz"
+	$nanoplot_dir/NanoPlot \
+	    --threads $threads \
+	    --fastq $fastq_input \
+	    --N50 \
+	    -o "$basecalled_qc_dir/${sample_id}_basecalled_reads_Q${qual}_pass_NanoPlot_out"
+    fi
+    if [[ "$run_demultiplexing" == "yes" ]]
+    then
+	cd $demultiplexed_fastq_dir
+	for b in barcode*
+	do
+	    echo "for nanoplotting: barcode=$b"
+	    fastq_input="./$sample_id.basecalled_reads.Q${qual}.pass.$b.fastq.gz"
+	    $nanoplot_dir/NanoPlot \
+		--threads $threads \
+		--fastq $fastq_input \
+		--N50 \
+		-o "./../../../$basecalled_qc_dir/${sample_id}_basecalled_reads_Q${qual}_pass_${b}_NanoPlot_out"
+	done
+	echo "for nanoplotting: unclassified"
+	fastq_input="./$sample_id.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz"
+	$nanoplot_dir/NanoPlot \
+            --threads $threads \
+            --fastq $fastq_input \
+            --N50 \
+            -o "./../../../$basecalled_qc_dir/${sample_id}_basecalled_reads_Q${qual}_pass_unclassified_NanoPlot_out" 
+    fi
+fi
+
+
+
+############################
+# checking bash exit status
+if [[ $? -eq 0 ]]
+then
+    echo "" 
+    echo "##########################################################################"
+    echo "" 
+    echo "LRSDAY message: This bash script has been successfully processed! :)"
+    echo ""
+    echo "##########################################################################"
+    echo ""
+    exit 0
+fi
+############################
diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.Nanopore_Reads_Basecalling_and_Demultiplexing.sh b/Project_Template/00.Long_Reads/LRSDAY.00.Nanopore_Reads_Basecalling_and_Demultiplexing.sh
deleted file mode 100755
index 6c1c640..0000000
--- a/Project_Template/00.Long_Reads/LRSDAY.00.Nanopore_Reads_Basecalling_and_Demultiplexing.sh
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/bin/bash
-set -e -o pipefail
-#######################################
-# load environment variables for LRSDAY
-source ./../../env.sh
-
-#######################################
-# set project-specific variables
-project_name="Project_Example" # LRSDAY Project name. Default = "Project_Example".
-run_basecalling="yes" # Whether to perform basecalling: "yes" or "no". Default = "yes". 
-run_demultiplexing="yes" # Whether to perform demultiplexing: "yes" or "no". Default = "yes". 
-run_nanoplotting="yes" # Whether to perform nanoplotting: "yes" or "no". Default = "yes". 
-
-flowcell_id="FAKXXXXX" # The flowcell ID of the nanopore run. Default = "FAKXXXXX".
-flowcell_version="FLO-MIN106" # The flowcell version of the nanopore run. Default = "FLO-MIN106".
-sequencing_kit_version="SQK-LSK108" # The sequencing kit version of the nanopore run. Default = "SQK-LSK108".
-barcode_kit_version="EXP-NBD103" # The barcode kit version of the nanopore run. Default = "EXP-NBD103".
-
-raw_reads_directory="$LRSDAY_HOME/$project_name/00.Long_Reads/nanopore_raw_fast5_files" # The directory containing the raw nanopore reads before basecalling
-basecalling_output_directory="$LRSDAY_HOME/$project_name/00.Long_Reads/nanopore_basecalled_fast5_files" # The directory containing the basecalled nanopore reads. This directory will be automatically generated when running basecalling.
-threads=8 # The number of threads to use. Default = 8.
-
-#############################
-# normally no need to change the following
-qual=5 # read quality filter for guppy basecalling
-num_callers=$threads # num_callers for guppy
-threads_per_caller=1 # threads_per_caller for guppy
-demultiplexing_threads=$threads # threads to use for demultiplexing
-demultiplexing_output_directory="$LRSDAY_HOME/$project_name/00.Long_Reads/nanopore_demultiplexed_fastq_files" # The directory containing the demultiplexed basecalled nanopore reads. This directory will be automatically generated when running demultiplexing. 
-
-if [[ "$run_basecalling" == "yes" ]]
-then
-    echo "Check if $basecalling_output_directory is empty for running basecalling."
-    if [[ "$(ls $basecalling_output_directory)" ]]
-    then
-	echo "Warning! The basecalling directory is not empty! Please empty its content if you want to run basecalling."
-	echo "Exit!!!"
-	exit
-    else
-	echo "Running basecalling."
-	$guppy_dir/guppy_basecaller \
-	    --flowcell $flowcell_version \
-	    --kit $sequencing_kit_version \
-	    --recursive \
-	    --input_path $raw_reads_directory \
-	    --save_path $basecalling_output_directory \
-	    --fast5_out \
-	    --qscore_filtering \
-	    --min_qscore $qual \
-	    --num_callers $num_callers \
-	    --cpu_threads_per_caller $threads_per_caller 
-	cd $basecalling_output_directory
-	cat ./pass/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.pass.fastq.gz
-	cat ./fail/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.fail.fastq.gz
-    fi
-fi
-
-if [[ "$run_demultiplexing" == "yes" ]]
-then
-    echo "Check if $basecalling_output_directory/pass has basecalled reads for running demultiplexing."
-    if [[ "$(ls $basecalling_output_directory/pass)" ]]
-    then
-	echo "Running demultiplexing."
-	$guppy_dir/guppy_barcoder \
-	    --barcode_kit $barcode_kit_version \
-	    --recursive \
-	    --input_path $basecalling_output_directory/pass \
-	    --save_path $demultiplexing_output_directory \
-	    --worker_threads $demultiplexing_threads
-	
-	cd $demultiplexing_output_directory
-	for b in barcode*
-	do 
-	    echo "for demultiplexing: barcode=$b"
-	    cat ./$b/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.pass.$b.fastq.gz
-	done
-	cat ./unclassified/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz
-    else
-	echo "There is no reads in $basecalling_output_directory/pass!"
-	echo "Please put the basecalled reads in $basecalling_output_directory/pass for demultiplexing!"
-	echo "Exit!!!"
-	exit
-    fi
-fi
-
-set +oe pipefail 
-
-if [[ "$run_nanoplotting" == "yes" ]]
-then
-    echo "Check if $basecalling_output_directory/pass has basecalled reads for running nanoplotting."
-    if [[ "$(ls $basecalling_output_directory/pass)" ]]
-    then
-	echo "Running nanoplotting."
-	cd $basecalling_output_directory
-	fastq_input="$project_name.basecalled_reads.Q${qual}.pass.fastq.gz"
-	source $nanoplot_dir/activate
-	$nanoplot_dir/NanoPlot \
-	    --threads $threads \
-	    --fastq $fastq_input \
-	    --N50 \
-	    -o "${project_name}_Q${qual}_pass_NanoPlot_out"
-    fi
-    if [[ "$run_demultiplexing" == "yes" ]]
-    then
-	cd $demultiplexing_output_directory
-	for b in barcode*
-	do
-	    echo "for nanoplotting: barcode=$b"
-	    fastq_input="$project_name.basecalled_reads.Q${qual}.pass.$b.fastq.gz"
-	    source $nanoplot_dir/activate
-	    $nanoplot_dir/NanoPlot \
-		--threads $threads \
-		--fastq $fastq_input \
-		--N50 \
-		-o "${project_name}_Q${qual}_pass_${b}_NanoPlot_out"
-	done
-	echo "for nanoplotting: unclassified"
-	fastq_input="$project_name.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz"
-	$nanoplot_dir/NanoPlot \
-            --threads $threads \
-            --fastq $fastq_input \
-            --N50 \
-            -o "${project_name}_Q${qual}_pass_unclassified_NanoPlot_out" 
-    fi
-fi
-
-
-
-############################
-# checking bash exit status
-if [[ $? -eq 0 ]]
-then
-    echo "" 
-    echo "LRSDAY message: This bash script has been successfully processed! :)"
-    echo ""
-    echo ""
-    exit 0
-fi
-############################
diff --git a/Project_Template/00.Short_Reads/.gitkeep b/Project_Template/00.Short_Reads/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/Project_Template/00.Short_Reads/LRSDAY.00.Retrieve_Sample_Illumina_Reads.sh b/Project_Template/00.Short_Reads/LRSDAY.00.Retrieve_Sample_Illumina_Reads.sh
deleted file mode 100755
index fe91af9..0000000
--- a/Project_Template/00.Short_Reads/LRSDAY.00.Retrieve_Sample_Illumina_Reads.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-set -e -o pipefail
-
-#######################################
-# load environment variables for LRSDAY
-source ./../../env.sh
-
-#######################################
-# set project-specific variables
-sra_id="SRR4074258" # the SRA Run ID for the reads that you want to retrieve, e.g. "SRR4074258 for S. cerevisiae strain SK1 generated by Yue et al. (2017) Nature Genetics"
-
-#######################################
-# process the pipeline
-echo "retrieve reads by the SRR_id: $sra_id ..."
-$sra_dir/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+$sn[_$rn]/$ri' \
-      --gzip --split-files -skip-technical --dumpbase --read-filter pass --clip $sra_id
-
-# if the fastq-dump doesn't work due to connection problems, please run the following two wget commands to directly download the reads.
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR407/008/SRR4074258/SRR4074258_1.fastq.gz 
-# ln -s SRR4074258_1.fastq.gz SRR4074258_pass_1.fastq.gz
-#  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR407/008/SRR4074258/SRR4074258_2.fastq.gz
-# ln -s SRR4074258_2.fastq.gz SRR4074258_pass_2.fastq.gz
-
-############################
-# checking bash exit status
-if [[ $? -eq 0 ]]
-then
-    echo ""
-    echo "LRSDAY message: This bash script has been successfully processed! :)"
-    echo ""
-    echo ""
-    exit 0
-fi
-############################
diff --git a/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh b/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh
index e471900..3dbdf41 100755
--- a/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh
+++ b/Project_Template/01.Long-read-based_Genome_Assembly/LRSDAY.01.Long-read-based_Genome_Assembly.sh
@@ -1,19 +1,20 @@
 #!/bin/bash
 set -e -o pipefail
 ##########################################
-# load environment variables for LRSDAY
+# load environment variables
 source ./../../env.sh
 PATH=$gnuplot_dir:$PATH
 
 ###########################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 long_reads="./../00.Long_Reads/$prefix.filtlong.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format).
-long_reads_type="pacbio-raw" # The long reads data type. Use "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected". Default = "pacbio-raw" for the testing example
+long_reads_type="nanopore-raw" # The long reads data type. Use "pacbio-raw" or "pacbio-corrected" or "pacbio-hifi" or "nanopore-raw" or "nanopore-corrected" or "nanopore-hq" (QV20 reads). Default = "nanopore-raw" for the testing example.
 genome_size="12.5m" # The estimated genome size with the format of <number>[g|m|k], e.g. 12.5m for 12.5 Mb. Default = "12.5m".
-assembler="canu" # The long-read assembler to use. Use "canu" or "flye" or "wtdbg2" or "smartdenovo" or "ra" or "shasta" or "canu-flye" or "canu-wtdbg2" or "canu-smartdenovo" or "canu-ra" or "canu-shasta". For "canu-flye", "canu-wtdbg2", "canu-smartdenovo", "canu-ra", or "canu-shasta", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/wtdbg2/smartdenovo/ra/shasta is used to assemble the genome. Default = "canu".
-customized_canu_parameters="" # When assembler="canu" or "canu-flye", "canu-wtdbg2", "canu-smartdenovo", "canu-ra", or "canu-shasta", users can set customized Canu assembly parameters here when needed. If users want to keep Canu's default parameters or when other assembler is used, simply leave it empty like customized_canu_parameters="". For example users could set customized_canu_parameters="correctedErrorRate=0.04" for high coverage (>60X) PacBio data and customized_canu_parameters="overlapper=mhap;utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. When assembling genomes with high heterozygosity, you can could set customized_canu_parameters="corOutCoverage=200;batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50" to avoid collasping haplotypes. As shown in these examples, more than one customized parameters can be set here as long as they are separeted by a semicolon and contained in a pair of double quotes (e.g. customized_canu_parameters="option1=XXX;option2=YYY;option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "" for the testing example.
-threads=4 # The number of threads to use. Default = 4.
+assembler="canu" # The long-read assembler to use. Use "canu" or "flye" or "wtdbg2" or "smartdenovo" or "shasta" or "canu-flye" or "canu-wtdbg2" or "canu-smartdenovo" or "canu-shasta". For "canu-flye", "canu-wtdbg2", "canu-smartdenovo", or "canu-shasta", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/wtdbg2/smartdenovo/shasta is used to assemble the genome. Default = "canu".
+customized_canu_parameters="" # When assembler="canu" or "canu-flye", "canu-wtdbg2", "canu-smartdenovo", or "canu-shasta", users can set customized Canu assembly parameters here when needed. If users want to keep Canu's default parameters or when other assembler is used, simply leave it empty like customized_canu_parameters="". For example users could set customized_canu_parameters="correctedErrorRate=0.04" for high coverage (>60X) PacBio data and customized_canu_parameters="overlapper=mhap;utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. When assembling genomes with high heterozygosity, you can could set customized_canu_parameters="corOutCoverage=200;batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50" to avoid collasping haplotypes. As shown in these examples, more than one customized parameters can be set here as long as they are separeted by a semicolon and contained in a pair of double quotes (e.g. customized_canu_parameters="option1=XXX;option2=YYY;option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "" for the testing example.
+threads=8 # The number of threads to use. Default = 8.
 vcf="yes" # Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Otherwise use "no". Default = "yes".
 dotplot="yes" # Use "yes" if prefer to plot genome-wide dotplot based on the comparison with the reference genome below. Otherwise use "no". Default = "yes".
 
@@ -23,11 +24,11 @@ then
     ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The file path of the raw reference genome. This is only needed when the option "dotplot" or "vcf" has been set as "yes".
 else
     parent1_tag="Parent1" # The name tag for parent1. Default = "Parent1".
-    parent1_short_reads="./../00.Short_Reads/$parent1_tag.illumina.fastq.gz" # The relative path to Illumina reads of parent1 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
+    parent1_short_reads="./../00.Short_Reads/$parent1_tag.fq.gz" # The relative path to Illumina reads of parent1 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
     parent1_ref_genome_raw="./../00.Reference_Genome/$parent1_tag.genome.raw.fa" # The relative path to the reference genome of parent1 of the hybrid. This is only needed when the options "canu_triobinning_mode" and "dotplot" (or "canu_triobinning_mode" and "vcf") have been set as "yes". When not available, it can be set to a general reference genome of the organism. 
 
     parent2_tag="Parent2" # The name tag for parent2. Default = "Parent2".
-    parent2_short_reads="./../00.Short_Reads/$parent2_tag.illumina.fastq.gz" # The relative path to Illumina reads of parent2 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
+    parent2_short_reads="./../00.Short_Reads/$parent2_tag.fq.gz" # The relative path to Illumina reads of parent2 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
     parent2_ref_genome_raw="./../00.Reference_Genome/$parent2_tag.genome.raw.fa" # The relative path to the reference genome of parent1 of the hybrid. This is only needed when the options "canu_triobinning_mode" and "dotplot" (or "canu_triobinning_mode" and "vcf") have been set as "yes". When not available, it can be set to a general reference genome of the organism. 
 fi
 
@@ -155,21 +156,33 @@ then
     fi
 elif [[ "$assembler" == "flye" ]]
 then
-    if [[ "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-raw" ]]
+    then
+	long_reads_type="pacbio-raw"
+    elif [[ "$long_reads_type" == "pacbio-corrected" ]]
     then
 	long_reads_type="pacbio-corr"
+    elif [[ "$long_reads_type" == "pacbio-hifi" ]]
+    then
+	long_reads_type="pacbio-hifi"
     elif [[ "$long_reads_type" == "nanopore-raw" ]]
     then
         long_reads_type="nano-raw"
     elif [[ "$long_reads_type" == "nanopore-corrected" ]]
     then
         long_reads_type="nano-corr"
+    elif [[ "$long_reads_type" == "nanopore-hq" ]]
+    then
+        long_reads_type="nano-hq"
     fi
+    source $miniconda3_dir/activate $build_dir/flye_conda_env
     $flye_dir/flye -o $out_dir \
 	-t $threads \
 	-g $genome_size \
+	--keep-haplotypes \
 	--${long_reads_type} $long_reads \
 	-i 2
+    source $miniconda3_dir/deactivate
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/assembly.fasta -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "wtdbg2" ]]
 then
@@ -188,33 +201,22 @@ then
     make -f $prefix.mak
     cd ..
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.dmo.cns  -o $prefix.assembly.$assembler.fa
-elif [[ "$assembler" == "ra" ]]
-then
-    mkdir $out_dir
-    cd $out_dir
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
-    then
-        long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
-    then
-        long_reads_type="ont"
-    fi
-    $ra_dir/ra -x $long_reads_type -t $threads ./../$long_reads > $prefix.assembly.$assembler.fa
-    cd ..
-    perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.assembly.$assembler.fa -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "shasta" ]]
 then
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-hifi" ]] 
     then
-        long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
+        long_reads_type="HiFi-Oct2021"
+    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "pacbio-raw" ]]
     then
-        long_reads_type="ont"
+        long_reads_type="Nanopore-Dec2019"
+    elif [[ "$long_reads_type" == "nanopore-corrected" || "$long_reads_type" == "pacbio-corrected" || "$long_reads_type" == "nanopore-hq" ]]
+    then
+	long_reads_type="R10-Slow-Nov2022"
     fi
-    perl $LRSDAY_HOME/scripts/fastq2fasta.pl -i $long_reads -o $prefix.long_reads.fasta
-    $shasta_dir/shasta --input $prefix.long_reads.fasta  --output $out_dir
+    perl $LRSDAY_HOME/scripts/fastq2fasta.pl -i $long_reads -o $prefix.long_reads.fa
+    $shasta_dir/shasta --input $prefix.long_reads.fa --assemblyDirectory $out_dir --config $long_reads_type
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/Assembly.fasta -o $prefix.assembly.$assembler.fa
-    rm $prefix.long_reads.fasta
+    rm $prefix.long_reads.fa
 elif [[ "$assembler" == "canu-flye" ]]
 then
     OLDIFS=$IFS;
@@ -230,18 +232,21 @@ then
 	gnuplot=$gnuplot_dir/gnuplot \
 	-${long_reads_type} $long_reads
     mv $prefix.customized_canu_parameters.spec ./$out_dir/canu
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" || "$long_reads_type" == "pacbio-hifi"  ]]
     then
 	long_reads_type="pacbio-corr"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
+    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" || "$long_reads_type" == "nanopore-hq" ]]
     then
         long_reads_type="nano-corr"
     fi
+    source $miniconda3_dir/activate $build_dir/flye_conda_env
     $flye_dir/flye -o $out_dir/flye \
 	-t $threads \
 	-g $genome_size \
+	--keep-haplotypes \
 	--${long_reads_type} $out_dir/canu/$prefix.correctedReads.fasta.gz \
 	-i 2
+    source $miniconda3_dir/deactivate
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/flye/assembly.fasta -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "canu-wtdbg2" ]]
 then
@@ -286,34 +291,6 @@ then
     make -f $prefix.mak
     cd ../..
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/smartdenovo/$prefix.dmo.cns  -o $prefix.assembly.$assembler.fa
-elif [[ "$assembler" == "canu-ra" ]]
-then
-    OLDIFS=$IFS;
-    IFS=";"
-    customized_canu_parameters_array=($customized_canu_parameters)
-    IFS=$OLDIFS;
-    printf "%s\n" "${customized_canu_parameters_array[@]}" > $prefix.customized_canu_parameters.spec
-
-    $canu_dir/canu -correct -p $prefix -d $out_dir/canu \
-	-s $prefix.customized_canu_parameters.spec \
-        useGrid=false \
-        maxThreads=$threads \
-        genomeSize=$genome_size \
-        gnuplot=$gnuplot_dir/gnuplot \
-        -${long_reads_type} $long_reads 
-    mv $prefix.customized_canu_parameters.spec ./$out_dir/canu
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
-    then
-	long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
-    then
-        long_reads_type="ont"
-    fi
-    mkdir -p $out_dir/ra
-    cd $out_dir/ra
-    $ra_dir/ra -x $long_reads_type -t $threads ./../canu/$prefix.correctedReads.fasta.gz > $prefix.assembly.$assembler.fa
-    cd ../..
-    perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/ra/$prefix.assembly.$assembler.fa -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "canu-shasta" ]]
 then
     OLDIFS=$IFS;
@@ -330,15 +307,14 @@ then
         gnuplot=$gnuplot_dir/gnuplot \
         -${long_reads_type} $long_reads 
     mv $prefix.customized_canu_parameters.spec ./$out_dir/canu
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-hifi" ]]
     then
-	long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
-    then
-        long_reads_type="ont"
+	long_reads_type="HiFi-Oct2021"
+    else
+	long_reads_type="R10-Slow-Nov2022"
     fi
     gunzip < $out_dir/canu/$prefix.correctedReads.fasta.gz > $out_dir/$prefix.correctedReads.fasta
-    $shasta_dir/shasta --input $out_dir/$prefix.correctedReads.fasta  --output $out_dir/shasta
+    $shasta_dir/shasta --input $out_dir/$prefix.correctedReads.fasta --assemblyDirectory $out_dir/shasta --config $long_reads_type
     rm $out_dir/$prefix.correctedReads.fasta
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/shasta/Assembly.fasta -o $prefix.assembly.$assembler.fa
 fi
@@ -441,9 +417,11 @@ fi
 # checking bash exit status
 if [[ $? -eq 0 ]]
 then
+    echo "#########################################################"
     echo ""
     echo "LRSDAY message: This bash script has been successfully processed! :)"
     echo ""
+    echo "#########################################################"
     echo ""
     exit 0
 fi
diff --git a/Project_Template/02.Long-read-based_Assembly_Polishing/LRSDAY.02.Long-read-based_Assembly_Polishing.sh b/Project_Template/02.Long-read-based_Assembly_Polishing/LRSDAY.02.Long-read-based_Assembly_Polishing.sh
index 49dece7..ac99721 100755
--- a/Project_Template/02.Long-read-based_Assembly_Polishing/LRSDAY.02.Long-read-based_Assembly_Polishing.sh
+++ b/Project_Template/02.Long-read-based_Assembly_Polishing/LRSDAY.02.Long-read-based_Assembly_Polishing.sh
@@ -7,17 +7,18 @@ source ./../../env.sh
 ###########################################
 # set project-specific variables
 
-prefix="SK1" # The file name prefix for the processing sample. Please avoid the character '.' in prefix. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 input_assembly="./../01.Long-read-based_Genome_Assembly/$prefix.assembly.raw.fa" # The file path of the input raw long-read-based assembly for polishing.
 long_reads_in_fastq="./../00.Long_Reads/$prefix.filtlong.fastq.gz" # The file path of the long-read fastq file. 
 
-polisher="quiver" # The long-read-based polisher to use: "quiver" (for PacBio RSII reads), "arrow" (for PacBio Sequel reads), "nanopolish" (for raw nanopore fast5 reads), "racon-medaka" (for basecalled nanopore fastq reads), or "marginpolish" (for basecalled nanopore fastq reads). Default = "quiver" for the testing example.
+polisher="racon-medaka" # The long-read-based polisher to use: "none" for (PacBio HiFi Reads), "arrow" (for PacBio Sequel reads), "quiver" (for PacBio RSII reads), "nanopolish" (for raw nanopore fast5 reads), "racon-medaka" (for basecalled nanopore fastq reads), or "marginpolish" (for basecalled nanopore fastq reads). Default = "racon-medaka" for the testing example.
 pacbio_bam_fofn_file="./../00.Long_Reads/pacbio_fofn_files/$prefix.merged.bam.fofn" # The file path to the fofn file containing the absolute path to the PacBio bam files. BAM file is the native output format for PacBio Sequel platform but this is not the case for the RSII platform. For RSII data, the bax2bam file conversion is needed. This can be done by running the LRSDAY.00.Retrieve_Sample_PacBio_Reads.sh script in the 00.Long_Reads directory. This is only needed when polisher="quiver" or "arrow".
 nanopore_basecalled_fast5_files="./../00.Long_Reads/nanopore_basecalled_fast5_files" # The file path to the directory containing the basecalled Oxford Nanopore FAST5 files. This option is only needed when polisher="nanopolish".
-guppy_basecalling_model="r941_flip235" # The guppy basecalling model to use for medaka. Supported values include: "r941_min_fast" for guppy (version_number >= 3.0.3) in fast mode, "r941_min_high" for guppy (version_number >= 3.0.3) in high accuracy mode, "r941_flip235" for guppy (2.3.5 <= version_number <3.0.3), "r941_flip213" for guppy (2.1.3 <= version_number <2.3.5), and "r941_trans" for albacore or guppy (version_number < 2.1.3). This option is only needed when polisher="racon-medaka".
-threads=1  # The number of threads to use. Default = "1".
+guppy_basecalling_model="r941_min_hac_g507" # The guppy basecalling model to use for medaka. Some supported values include: "r941_min_fast_g507" for guppy in fast mode for MinION R9.4.1 flowcell, "r941_min_hac_g507" for guppy in high accuracy mode for MinION R9.4.1 flowcell, "r941_prom_fast_g507" for guppy in fast mode for PromethION R9.4.1, "r941_prom_hac_g507" for guppy in high accuracy mode for PromethION R9.4.1. See here (https://github.com/nanoporetech/medaka/tree/master/medaka/data) for a complete list of supported models. This option is only needed when polisher="racon-medaka". Default = "r941_min_hac_g507".
+threads=8  # The number of threads to use. Default = "8".
 ploidy=1 # The ploidy status of the sequenced genome. Use "1" for haploid genome and "2" for diploid genome. Currently not supported when "polisher="racon-medaka". Default = "1" for the testing example.
-rounds_of_successive_polishing=1 # The number of total rounds of long-read-based assembly polishing. Default = "1" for the testing example.
+rounds_of_successive_polishing=3 # The number of total rounds of long-read-based assembly polishing. Default = "3".
 debug="no" # Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no"
 
 ###########################################
@@ -27,7 +28,10 @@ cp $input_assembly $prefix.assembly.tmp.fa
 
 mkdir tmp
 
-if [[ $polisher == "quiver" || $polisher == "arrow" ]]
+if [[ $polisher == "none" ]]
+then
+    cp $prefix.assembly.tmp.fa $prefix.assembly.long_read_polished.fa
+elif [[ $polisher == "quiver" || $polisher == "arrow" ]]
 then
     # perform correction using PacBio's pbalign-arrow pipeline
     source $miniconda2_dir/activate $build_dir/conda_pacbio_env
@@ -77,9 +81,9 @@ then
     $nanopolish_dir/nanopolish index -d $nanopore_basecalled_fast5_files $long_reads_in_fastq
     for i in $(seq 1 1 $rounds_of_successive_polishing)
     do
-	java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary -REFERENCE $prefix.assembly.tmp.fa -OUTPUT $prefix.assembly.tmp.dict
+	$java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary -REFERENCE $prefix.assembly.tmp.fa -OUTPUT $prefix.assembly.tmp.dict
 	$minimap2_dir/minimap2 -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
-	java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000  
+	$java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000  
 	$samtools_dir/samtools index $prefix.minimap2.round_${i}.bam
 	rm $prefix.minimap2.round_${i}.sam
 	python3 $nanopolish_dir/scripts/nanopolish_makerange.py $prefix.assembly.tmp.fa | $parallel_dir/parallel --results ${prefix}_nanopolish_round_${i}_results -P 1 \
@@ -94,7 +98,7 @@ then
     rm $prefix.assembly.tmp.fa
 elif [[ $polisher == "racon-medaka" ]]
 then
-    source $miniconda2_dir/activate $conda_medaka_dir/../../conda_medaka_env
+    source $miniconda3_dir/activate $medaka_dir/../../medaka_conda_env
     for i in $(seq 1 1 $rounds_of_successive_polishing)
     do
 	$minimap2_dir/minimap2 -t $threads -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
@@ -108,9 +112,9 @@ then
     done
     for i in $(seq 1 1 $rounds_of_successive_polishing)
     do
-	$conda_medaka_dir/medaka_consensus -i $long_reads_in_fastq -d $prefix.assembly.tmp.fa -o ${prefix}_medaka_out_round_${i} -t $threads -m $guppy_basecalling_model
+	$medaka_dir/medaka_consensus -i $long_reads_in_fastq -d $prefix.assembly.tmp.fa -o ${prefix}_medaka_out_round_${i} -t $threads -m $guppy_basecalling_model
 	rm $prefix.assembly.tmp.fa
-	rm $prefix.assembly.tmp.fa.mmi
+	rm $prefix.assembly.tmp.fa.map-ont.mmi
 	rm $prefix.assembly.tmp.fa.fai
         perl $LRSDAY_HOME/scripts/tidy_fasta_for_medaka.pl -i ${prefix}_medaka_out_round_${i}/consensus.fasta -o $prefix.assembly.medaka.round_${i}.fa 
 	cp $prefix.assembly.medaka.round_${i}.fa $prefix.assembly.tmp.fa
@@ -121,28 +125,28 @@ then
     done
     ln -s $prefix.assembly.medaka.round_${rounds_of_successive_polishing}.fa $prefix.assembly.long_read_polished.fa
     rm $prefix.assembly.tmp.fa
-    source $miniconda2_dir/deactivate
-elif [[ $polisher == "marginpolish" ]]
-then
-    source $miniconda2_dir/activate $conda_medaka_dir/../../conda_medaka_env
-    for i in $(seq 1 1 $rounds_of_successive_polishing)
-    do
-	$minimap2_dir/minimap2 -t $threads -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
-	java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000
-	$samtools_dir/samtools index $prefix.minimap2.round_${i}.bam
-	$marginpolish_dir/marginPolish $prefix.minimap2.round_${i}.bam $prefix.assembly.tmp.fa $marginpolish_dir/../params/allParams.np.json -t $threads -o ${prefix}.assembly.marginpolish.round_${i}
-	if [[ $debug == "no" ]]
-        then
-	    rm $prefix.minimap2.round_${i}.sam
-	    rm $prefix.minimap2.round_${i}.bam
-	    rm $prefix.minimap2.round_${i}.bam.bai
-	fi
-	rm $prefix.assembly.tmp.fa
-	cp $prefix.assembly.marginpolish.round_${i}.fa $prefix.assembly.tmp.fa
-    done
-    ln -s $prefix.assembly.marginpolish.round_${rounds_of_successive_polishing}.fa $prefix.assembly.long_read_polished.fa
-    rm $prefix.assembly.tmp.fa
-    source $miniconda2_dir/deactivate
+    source $miniconda3_dir/deactivate
+# elif [[ $polisher == "marginpolish" ]]
+# then
+#     source $miniconda3_dir/activate $conda_medaka_dir/../../conda_marginPolish_env
+#     for i in $(seq 1 1 $rounds_of_successive_polishing)
+#     do
+# 	$minimap2_dir/minimap2 -t $threads -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
+# 	$java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000
+# 	$samtools_dir/samtools index $prefix.minimap2.round_${i}.bam
+# 	$marginpolish_dir/marginPolish $prefix.minimap2.round_${i}.bam $prefix.assembly.tmp.fa $marginpolish_dir/../params/allParams.np.json -t $threads -o ${prefix}.assembly.marginpolish.round_${i}
+# 	if [[ $debug == "no" ]]
+#         then
+# 	    rm $prefix.minimap2.round_${i}.sam
+# 	    rm $prefix.minimap2.round_${i}.bam
+# 	    rm $prefix.minimap2.round_${i}.bam.bai
+# 	fi
+# 	rm $prefix.assembly.tmp.fa
+# 	cp $prefix.assembly.marginpolish.round_${i}.fa $prefix.assembly.tmp.fa
+#     done
+#     ln -s $prefix.assembly.marginpolish.round_${rounds_of_successive_polishing}.fa $prefix.assembly.long_read_polished.fa
+#     rm $prefix.assembly.tmp.fa
+#     source $miniconda3_dir/deactivate
 fi
 
 rm -r tmp
@@ -158,9 +162,11 @@ fi
 # checking bash exit status
 if [[ $? -eq 0 ]]
 then
+    echo "#########################################################"
     echo ""
     echo "LRSDAY message: This bash script has been successfully processed! :)"
     echo ""
+    echo "#########################################################"
     echo ""
     exit 0
 fi
diff --git a/Project_Template/03.Short-read-based_Assembly_Polishing/LRSDAY.03.Short-read-based_Assembly_Polishing.sh b/Project_Template/03.Short-read-based_Assembly_Polishing/LRSDAY.03.Short-read-based_Assembly_Polishing.sh
index ebfeacb..a82ed7d 100755
--- a/Project_Template/03.Short-read-based_Assembly_Polishing/LRSDAY.03.Short-read-based_Assembly_Polishing.sh
+++ b/Project_Template/03.Short-read-based_Assembly_Polishing/LRSDAY.03.Short-read-based_Assembly_Polishing.sh
@@ -7,20 +7,22 @@ source ./../../env.sh
 ###########################################
 # set project-specific variables
 
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a"  # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 input_assembly="./../02.Long-read-based_Assembly_Polishing/$prefix.assembly.long_read_polished.fa" # The file path of the input assembly before Illumina-based correction
 trim_illumina_reads="yes" # Whether to trim the input Illumina reads. Use "yes" if prefer to perform trimming, otherwise use "no". Default = "yes". 
-rounds_of_successive_polishing=1 # The number of total rounds of Illumina-read-based assembly polishing. Default = "1" for the testing example.
-threads=1 # The number of threads to use. Default = "1".
+rounds_of_successive_polishing=3 # The number of total rounds of Illumina-read-based assembly polishing. Default = "3" for the testing example.
+threads=8 # The number of threads to use. Default = "8".
 mode="PE" # Illumina sequencing mode, "PE" for paired-end sequencing and "SE" for single-end sequencing. Default = "PE".
-fixlist="snps,indels" # The types of errors for Illumina-read-based correction by Pilon; see Pilon's manual for more details. Default = "snps,indels".
 if [[ $mode == "PE" ]]
 then
-    reads_PE1="./../00.Short_Reads/SRR4074258_pass_1.fastq.gz" # Please replace the PE reads file name for your own project
-    reads_PE2="./../00.Short_Reads/SRR4074258_pass_2.fastq.gz" # Please replace the PE reads file name for your own project
+    reads_PE1="./../00.Short_Reads/$prefix.R1.fastq.gz" # Please replace the PE reads file name for your own project
+    reads_PE2="./../00.Short_Reads/$prefix.R2.fastq.gz" # Please replace the PE reads file name for your own project
 else
-    reads_SE="./../00.Short_Reads/sample_pass_1.fastq.gz" # Please replace the SE reads file name for your own project if you only have SE data
+    reads_SE="./../00.Short_Reads/$prefix.fastq.gz" # Please replace the SE reads file name for your own project if you only have SE data
 fi
+
+fixlist="snps,indels" # The types of errors for Illumina-read-based correction by Pilon; see Pilon's manual for more details. Default = "snps,indels".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ###########################################
@@ -29,11 +31,8 @@ debug="no" # Whether to keep intermediate files for debugging. Use "yes" if pref
 if [[ $mode == "PE" ]]
 then
     adapter="$trimmomatic_dir/adapters/TruSeq3-PE-2.fa" # adapter for PE reads
-    ln -s $reads_PE1 raw.R1.fq.gz;
-    ln -s $reads_PE2 raw.R2.fq.gz;
 else
     adpater="$trimmomatic_dir/adapters/TruSeq3-SE.fa" # adapter for SE reads
-    ln -s $reads_SE raw.fq.gz;
 fi
 
 cp  $input_assembly refseq.tmp.fa
@@ -45,22 +44,22 @@ if [[ $trim_illumina_reads == "yes" ]]
 then
     if [[ $mode == "PE" ]]
     then
-	java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar PE -threads $threads -phred33  raw.R1.fq.gz  raw.R2.fq.gz  trimmed.R1.fq.gz trimmed.unpaired.R1.fq.gz trimmed.R2.fq.gz trimmed.unpaired.R2.fq.gz ILLUMINACLIP:adapter.fa:2:30:10  SLIDINGWINDOW:5:20 MINLEN:36
-	rm trimmed.unpaired.R1.fq.gz
-	rm trimmed.unpaired.R2.fq.gz 
-	mv trimmed.R1.fq.gz clean.R1.fq.gz
-	mv trimmed.R2.fq.gz clean.R2.fq.gz
+	$java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar PE -threads $threads -phred33  $reads_PE1 $reads_PE2  $prefix.trimmed.R1.fq.gz $prefix.trimmed.unpaired.R1.fq.gz $prefix.trimmed.R2.fq.gz $prefix.trimmed.unpaired.R2.fq.gz ILLUMINACLIP:adapter.fa:2:30:10  SLIDINGWINDOW:5:20 MINLEN:36
+	rm $prefix.trimmed.unpaired.R1.fq.gz
+	rm $prefix.trimmed.unpaired.R2.fq.gz 
+	mv $prefix.trimmed.R1.fq.gz $prefix.clean.R1.fq.gz
+	mv $prefix.trimmed.R2.fq.gz $prefix.clean.R2.fq.gz
     else
-	java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar SE -threads $threads -phred33  raw.fq.gz  trimmed.fq.gz ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:36
-	mv trimmed.fq.gz clean.fq.gz
+	$java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar SE -threads $threads -phred33 $reads_SE  $prefix.trimmed.fq.gz ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:36
+	mv $prefix.trimmed.fq.gz $prefix.clean.fq.gz
     fi
 else
     if [[ $mode == "PE" ]]
     then
-	cp raw.R1.fq.gz clean.R1.fq.gz
-	cp raw.R2.fq.gz clean.R2.fq.gz
+	cp $prefix.raw.R1.fq.gz $prefix.clean.R1.fq.gz
+	cp $prefix.raw.R2.fq.gz $prefix.clean.R2.fq.gz
     else
-	cp raw.fq.gz clean.fq.gz
+	cp $prefix.raw.fq.gz $prefix.clean.fq.gz
     fi
 fi
 
@@ -71,30 +70,30 @@ do
 
     if [[ $mode == "PE" ]]
     then
-	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa clean.R1.fq.gz clean.R2.fq.gz >$prefix.round_${i}.sam
+	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa $prefix.clean.R1.fq.gz $prefix.clean.R2.fq.gz >$prefix.round_${i}.sam
     else
-	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa clean.fq.gz >$prefix.round_${i}.sam
+	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa $prefix.clean.fq.gz >$prefix.round_${i}.sam
     fi
 
     # index reference sequence
     $samtools_dir/samtools faidx refseq.tmp.fa
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary \
 	-REFERENCE refseq.tmp.fa \
 	-OUTPUT refseq.tmp.dict
 
     # sort bam file by picard-tools SortSam
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam \
 	-INPUT $prefix.round_${i}.sam \
 	-OUTPUT $prefix.round_${i}.sort.bam \
 	-SORT_ORDER coordinate
 
     # fixmate
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar FixMateInformation \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar FixMateInformation \
 	-INPUT $prefix.round_${i}.sort.bam \
 	-OUTPUT $prefix.round_${i}.fixmate.bam
 
     # add or replace read groups and sort
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar AddOrReplaceReadGroups \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar AddOrReplaceReadGroups \
 	-INPUT $prefix.round_${i}.fixmate.bam \
 	-OUTPUT $prefix.round_${i}.rdgrp.bam \
 	-SORT_ORDER coordinate \
@@ -106,7 +105,7 @@ do
 	-RGCN "RGCN"
 
     # remove duplicates
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar MarkDuplicates \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar MarkDuplicates \
 	-INPUT $prefix.round_${i}.rdgrp.bam \
 	-REMOVE_DUPLICATES true \
 	-METRICS_FILE $prefix.round_${i}.dedup.matrics \
@@ -117,13 +116,13 @@ do
 
     # GATK local realign
     # find realigner targets
-    java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
+    $java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
 	-R refseq.tmp.fa \
 	-T RealignerTargetCreator \
 	-I $prefix.round_${i}.dedup.bam \
 	-o $prefix.round_${i}.realn.intervals
     # run realigner
-    java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
+    $java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
 	-R refseq.tmp.fa \
 	-T IndelRealigner \
 	-I $prefix.round_${i}.dedup.bam \
@@ -136,7 +135,7 @@ do
     # for PE sequencing
     if [[ $mode == "PE" ]]
     then
-	java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
+	$java_dir/java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
 	    --genome refseq.tmp.fa \
 	    --frags $prefix.round_${i}.realn.bam \
 	    --fix $fixlist \
@@ -145,7 +144,7 @@ do
 	    --output $prefix.assembly.pilon.round_${i} \
 	    >$prefix.pilon.round_${i}.log
     else
-	java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
+	$java_dir/java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
 	    --genome refseq.tmp.fa \
 	    --unpaired $prefix.round_${i}.realn.bam \
 	    --fix $fixlist \
@@ -184,9 +183,11 @@ fi
 # checking bash exit status
 if [[ $? -eq 0 ]]
 then
+    echo "#########################################################"
     echo ""
     echo "LRSDAY message: This bash script has been successfully processed! :)"
     echo ""
+    echo "#########################################################"
     echo ""
     exit 0
 fi
diff --git a/Project_Template/04.Reference-guided_Assembly_Scaffolding/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh b/Project_Template/04.Reference-guided_Assembly_Scaffolding/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh
index bf74dc1..40fc8e1 100755
--- a/Project_Template/04.Reference-guided_Assembly_Scaffolding/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh
+++ b/Project_Template/04.Reference-guided_Assembly_Scaffolding/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh
@@ -3,18 +3,19 @@ set -e -o pipefail
 #######################################
 # load environment variables for LRSDAY
 source ./../../env.sh
-PATH=$gnuplot_dir:$hal_dir:$PATH
+PATH=$gnuplot_dir:$PATH
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for processing sample. Please avoid the character '.' in prefix. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 input_assembly="./../03.Short-read-based_Assembly_Polishing/$prefix.assembly.short_read_polished.fa" # The file path of the input genome assembly.
 ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The file path of the raw reference genome.
 ref_genome_noncore_masked="./../00.Reference_Genome/S288C.ASM205763v1.noncore_masked.fa" # The file path of the specially masked reference genome where subtelomeres and chromosome-ends were hard masked. When the subtelomere/chromosome-end information is unavailable for the organism that you are interested in, you can just put the path of the raw reference genome assembly here.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the raw reference genome file, if there are multiple reference mitochondrial genomes that you want to check, use a single ';' to separate them. e.g. "Sc_chrMT;Sp_chrMT". Default = "chrMT".
 gap_size=5000 # The number of Ns to insert between adjacent contigs during scaffolding. Default = "5000".
-scaffolder="ragout" # The reference-based assembly scaffolder to use: "ragout" or "ragoo". Default = "ragout". If the reference genome size is large (e.g. > 100 Mb), please use "ragoo" since extra dependency is needed for "ragout" to handle large genomes.
-threads=1 # The number of threads to use. Default = "1".
+scaffolder="ragtag" # The reference-based assembly scaffolder to use: "ragout" or "ragtag". Default = "ragtag". If the reference genome size is large (e.g. > 100 Mb), please use "ragtag" since extra dependency is needed for "ragout" to handle large genomes.
+threads=8 # The number of threads to use. Default = "8".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ######################################
@@ -26,28 +27,28 @@ sed -e '/^[^>]/s/[^ATGCatgc]/N/g' $ref_genome_noncore_masked > ref_genome_noncor
 
 if [[ $scaffolder == "ragout" ]]
 then
-    echo ".references = ref_genome" > ragout.recipe.txt
-    echo ".target = $prefix" >> ragout.recipe.txt
-    echo "ref_genome.fasta = ./ref_genome_noncore_masked.fa" >> ragout.recipe.txt
-    echo "$prefix.fasta = $input_assembly" >> ragout.recipe.txt
-    echo ".naming_ref = ref_genome" >> ragout.recipe.txt
-    source $miniconda2_dir/activate $build_dir/conda_ragout_env
-    python2 $ragout_dir/ragout -o ${prefix}_ragout_out --solid-scaffolds  -t $threads  ragout.recipe.txt
-    source $miniconda2_dir/deactivate
+    echo ".references = ref_genome" > $prefix.ragout.recipe.txt
+    echo ".target = $prefix" >>$prefix.ragout.recipe.txt
+    echo "ref_genome.fasta = ./ref_genome_noncore_masked.fa" >> $prefix.ragout.recipe.txt
+    echo "$prefix.fasta = $input_assembly" >> $prefix.ragout.recipe.txt
+    echo ".naming_ref = ref_genome" >> $prefix.ragout.recipe.txt
+    source $miniconda3_dir/activate $build_dir/ragout_conda_env
+    python3 $ragout_dir/ragout -o ${prefix}_ragout_out --solid-scaffolds --overwrite -t $threads  $prefix.ragout.recipe.txt
+    source $miniconda3_dir/deactivate
     cat ./${prefix}_ragout_out/${prefix}_scaffolds.fasta | sed "s/^>chr_/>/g" > ./${prefix}_ragout_out/${prefix}_scaffolds.renamed.fasta 
     cat ./${prefix}_ragout_out/${prefix}_scaffolds.renamed.fasta ./${prefix}_ragout_out/${prefix}_unplaced.fasta > ./${prefix}_ragout_out/${prefix}.ragout.raw.fa    
     perl $LRSDAY_HOME/scripts/adjust_assembly_by_ragoutAGP.pl -i $input_assembly -p $prefix -a ./${prefix}_ragout_out/${prefix}_scaffolds.agp -g $gap_size
-    ln -s ${prefix}.ragout.fa $prefix.assembly.ref_based_scaffolded.fa
-elif [[ $scaffolder == "ragoo" ]]
+    mv ${prefix}.ragout.fa $prefix.assembly.ref_based_scaffolded.fa
+elif [[ $scaffolder == "ragtag" ]]
 then
-    source $build_dir/py3_virtualenv_ragoo/bin/activate
-    python3 $ragoo_dir/ragoo.py -t $threads -g $gap_size  -C -m $minimap2_dir/minimap2 $input_assembly ref_genome_noncore_masked.fa
-    mv ragoo_output ${prefix}_ragoo_out
-    cp ${prefix}_ragoo_out/ragoo.fasta ${prefix}.ragoo.fa
-    ln -s ${prefix}.ragoo.fa $prefix.assembly.ref_based_scaffolded.fa
+    source $miniconda3_dir/activate $build_dir/ragtag_conda_env
+    $ragtag_dir/ragtag.py scaffold -t $threads -f 500 -g $gap_size -r -u -o ${prefix}_ragtag_out ref_genome_noncore_masked.fa $input_assembly 
+    source $miniconda3_dir/deactivate
+    cat ./${prefix}_ragtag_out/ragtag.scaffold.fasta  |sed "s/_RagTag$//g" > ${prefix}.ragtag.fa
+    mv ${prefix}.ragtag.fa $prefix.assembly.ref_based_scaffolded.fa 
 else
     echo "Unrecognized scaffolder: $scaffolder";
-    echo "Please set scaffolder=\"ragout\" or \"ragoo\".";
+    echo "Please set scaffolder=\"ragout\" or \"ragtag\".";
     echo "LRSDAY Exit!";
     exit;
 fi
@@ -66,20 +67,25 @@ perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.ref_based_sca
 $gnuplot_dir/gnuplot < $prefix.assembly.ref_based_scaffolded.filter_adjust.gp
 
 # generate dotplot for the mitochondrial genome only
-perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal -o ref.chrMT.fa
-perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.ref_based_scaffolded.fa -l $prefix.assembly.ref_based_scaffolded.mt_contig.list -m normal -o $prefix.assembly.ref_based_scaffolded.mt_contig.fa
-$mummer4_dir/nucmer --maxmatch --nosimplify  -p $prefix.assembly.ref_based_scaffolded.chrMT ref.chrMT.fa $prefix.assembly.ref_based_scaffolded.mt_contig.fa
-$mummer4_dir/delta-filter -m  $prefix.assembly.ref_based_scaffolded.chrMT.delta > $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter
-$mummer4_dir/mummerplot --large --postscript $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter -p $prefix.assembly.ref_based_scaffolded.chrMT.filter
-perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.ref_based_scaffolded.chrMT.filter.gp -o $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp -r ref.chrMT.fa -q $prefix.assembly.ref_based_scaffolded.mt_contig.fa
-$gnuplot_dir/gnuplot < $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp
+if [ -s $prefix.assembly.ref_based_scaffolded.mt_contig.list ]
+then
+    perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal -o ref.chrMT.fa
+    perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.ref_based_scaffolded.fa -l $prefix.assembly.ref_based_scaffolded.mt_contig.list -m normal -o $prefix.assembly.ref_based_scaffolded.mt_contig.fa
+    $mummer4_dir/nucmer --maxmatch --nosimplify  -p $prefix.assembly.ref_based_scaffolded.chrMT ref.chrMT.fa $prefix.assembly.ref_based_scaffolded.mt_contig.fa
+    $mummer4_dir/delta-filter -m  $prefix.assembly.ref_based_scaffolded.chrMT.delta > $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter
+    $mummer4_dir/mummerplot --large --postscript $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter -p $prefix.assembly.ref_based_scaffolded.chrMT.filter
+    perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.ref_based_scaffolded.chrMT.filter.gp -o $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp -r ref.chrMT.fa -q $prefix.assembly.ref_based_scaffolded.mt_contig.fa
+    $gnuplot_dir/gnuplot < $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp
+else 
+    echo "no chrMT contig detected, therefore no chrMT plotting will be performed."
+fi
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
     if [[ $scaffolder == "ragout" ]]
     then
-	rm ragout.recipe.txt
+	rm $prefix.ragout.recipe.txt
     fi
     rm ref_genome_noncore_masked.fa
     rm *.filter.fplot
@@ -89,8 +95,11 @@ then
     rm *.filter.gp
     rm *.filter_adjust.gp
     rm *.filter.ps
-    rm ref.chrMT.list
-    rm ref.chrMT.fa
+    if [ -e ref.chrMT.fa ]
+    then
+	rm ref.chrMT.list
+	rm ref.chrMT.fa
+    fi
 fi
 
 ############################
diff --git a/Project_Template/05.Centromere_Identity_Profiling/LRSDAY.05.Centromere_Identity_Profiling.sh b/Project_Template/05.Centromere_Identity_Profiling/LRSDAY.05.Centromere_Identity_Profiling.sh
index 663c004..25389d7 100755
--- a/Project_Template/05.Centromere_Identity_Profiling/LRSDAY.05.Centromere_Identity_Profiling.sh
+++ b/Project_Template/05.Centromere_Identity_Profiling/LRSDAY.05.Centromere_Identity_Profiling.sh
@@ -6,7 +6,8 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a"  # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 genome="./../04.Reference-guided_Assembly_Scaffolding/$prefix.assembly.ref_based_scaffolded.fa" # The file path of the input genome assembly
 query="$LRSDAY_HOME/data/S288C.centromere.fa" # S. cerevisiae S288C reference centromere sequences based on Yue et al. (2017) Nature Genetics. 
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
diff --git a/Project_Template/06.Mitochondrial_Genome_Assembly_Improvement/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh b/Project_Template/06.Mitochondrial_Genome_Assembly_Improvement/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh
index 97b06c0..2b793af 100755
--- a/Project_Template/06.Mitochondrial_Genome_Assembly_Improvement/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh
+++ b/Project_Template/06.Mitochondrial_Genome_Assembly_Improvement/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh
@@ -3,17 +3,18 @@ set -e
 ##########################################
 # load environment variables for LRSDAY
 source ./../../env.sh
-PATH=$bwa_dir:$samtools_dir:$gnuplot_dir:$canu_dir:$mummer_dir:$spades_dir:$prodigal_dir:$PATH
+PATH=$bwa_dir:$samtools_dir:$gnuplot_dir:$mummer4_dir:$spades_dir:$prodigal_dir:$PATH
 
 ###########################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a"  # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 genome="./../04.Reference-guided_Assembly_Scaffolding/$prefix.assembly.ref_based_scaffolded.fa" # The file path of the input genome assembly
 mt_contig_list="./../04.Reference-guided_Assembly_Scaffolding/$prefix.assembly.ref_based_scaffolded.mt_contig.list" # The mitochodnrial contig list generated by the module 04.Reference-guided_Assembly_Scaffolding.
 gene_start="$LRSDAY_HOME/data/ATP6.cds.fa" # A FASTA file containing the CDS sequence of the mitochodnrial gene to be used as the starting point of the mitochondrial assembly. This can be set to any gene as long as a fasta file containing the DNA sequence of the gene is provided.
 ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The file path of the raw reference genome 
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the raw reference genome file, if there are multiple reference mitochondrial genomes that you want to check, use a single ';' to separate them. e.g. "Sc_chrMT;Sp_chrMT". Default = "chrMT".
-threads=1 # The number of threads to use. Default = "1".
+threads=8 # The number of threads to use. Default = "8".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ##########################################
@@ -21,6 +22,9 @@ debug="no" # Whether to keep intermediate files for debugging. Use "yes" if pref
 $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $mt_contig_list -m reverse -o $prefix.assembly.non_mt_contig.fa
 $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $mt_contig_list -m normal -o $prefix.assembly.mt_contig.fa
 
+echo $chrMT_tag | sed -e "s/;/\n/g" > ref.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal  -o ref.chrMT.fa
+
 if [[ $(egrep -c "^>" "$prefix.assembly.mt_contig.fa") -eq 0 ]]
 then
     echo "no chrMT contig was found in the assembly, skip this step and just output the input assembly ..."
@@ -39,12 +43,13 @@ else
     perl $LRSDAY_HOME/scripts/break_contig_by_blast.pl -i $prefix.assembly.mt_contig.descaffold.fa -b $prefix.assembly.mt_contig.descaffold.tblastx.filtered.out -o $prefix.assembly.mt_contig.break_by_blast.fa
 
     # reassemble the mitochondrial genome using CAP3 to collapse smaller fragments
-    $cap_dir/cap3 $prefix.assembly.mt_contig.break_by_blast.fa -k 0 
+    $cap3_dir/cap3 $prefix.assembly.mt_contig.break_by_blast.fa -k 0 
     if [[ $(egrep -c "^>" "$prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs") -eq 0 ]]
     then
         cat $prefix.assembly.mt_contig.break_by_blast.fa | sed "s/>/>chrMT_/" > $prefix.assembly.mt_contig.for_clean.fa
     else
-        cat $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs| sed "s/>/>chrMT_/" > $prefix.assembly.mt_contig.for_clean.fa
+	cat $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs $prefix.assembly.mt_contig.break_by_blast.fa.cap.singlets > $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs_singlets
+        cat $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs_singlets| sed "s/>/>chrMT_/" > $prefix.assembly.mt_contig.for_clean.fa
     fi
 
     $circlator_dir/circlator clean --verbose $prefix.assembly.mt_contig.for_clean.fa  ${prefix}.assembly.mt_contig.for_fixstart.fa 
@@ -64,16 +69,15 @@ else
 
     $circlator_dir/circlator fixstart --verbose --genes_fa $gene_start --min_id 90 --ignore $prefix.assembly.for_fixstart.for_skip.list $prefix.assembly.mt_contig.for_fixstart.fa  $prefix.assembly.mt_contig.circlator
 
-    mv $prefix.assembly.mt_contig.circlator.fasta $prefix.assembly.mt_contig.circlator.fa
+    source $miniconda3_dir/activate $build_dir/ragtag_conda_env
+    $ragtag_dir/ragtag.py scaffold -t $threads -f 1 -u -o ${prefix}_chrMT_ragtag_out ref.chrMT.fa $prefix.assembly.mt_contig.circlator.fasta
+    cat ${prefix}_chrMT_ragtag_out/ragtag.scaffold.fasta |sed "s/>chrMT_RagTag/>${prefix}.chrMT/"|sed -r "s/N{100}//gi" >  ${prefix}.assembly.mt_contig.ragtag.fa
     cat $prefix.assembly.non_mt_contig.fa |egrep "^>"|egrep -v "^>chr" |sed "s/>//" > $prefix.assembly.non_primary_contig.list
     $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.non_mt_contig.fa -l $prefix.assembly.non_primary_contig.list -m reverse -o $prefix.assembly.primary_contig.fa
     $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.non_mt_contig.fa -l $prefix.assembly.non_primary_contig.list -m normal -o $prefix.assembly.non_primary_contig.fa
-    cat $prefix.assembly.primary_contig.fa $prefix.assembly.mt_contig.circlator.fa $prefix.assembly.non_primary_contig.fa > $prefix.assembly.mt_improved.fa
-
+    cat $prefix.assembly.primary_contig.fa $prefix.assembly.mt_contig.ragtag.fa $prefix.assembly.non_primary_contig.fa > $prefix.assembly.mt_improved.fa
     # generate dotplot for the mitochondrial genome only
-    echo $chrMT_tag | sed -e "s/;/\n/g" > ref.chrMT.list
-    perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal  -o ref.chrMT.fa
-    $mummer4_dir/nucmer -t $threads --maxmatch --nosimplify  -p $prefix.assembly.mt_improved.chrMT ref.chrMT.fa $prefix.assembly.mt_contig.circlator.fa
+    $mummer4_dir/nucmer -t $threads --maxmatch --nosimplify  -p $prefix.assembly.mt_improved.chrMT ref.chrMT.fa $prefix.assembly.mt_contig.ragtag.fa
     $mummer4_dir/delta-filter -m  $prefix.assembly.mt_improved.chrMT.delta > $prefix.assembly.mt_improved.chrMT.delta_filter
     $mummer4_dir/mummerplot --large --postscript $prefix.assembly.mt_improved.chrMT.delta_filter -p $prefix.assembly.mt_improved.chrMT.filter
     perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.mt_improved.chrMT.filter.gp -o $prefix.assembly.mt_improved.chrMT.filter_adjust.gp -r ref.chrMT.fa -q $prefix.assembly.mt_contig.final.fa
@@ -106,6 +110,10 @@ then
 	rm $prefix.assembly.for_fixstart.for_skip.fa
 	rm $prefix.assembly.for_fixstart.for_skip.list
     fi
+    if [ -d "${prefix}_chrMT_ragtag_out" ]
+    then
+	rm -r ${prefix}_chrMT_ragtag_out
+    fi
 fi
 
 ############################
diff --git a/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.1.sh b/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.1.sh
index f1a95ab..97b3e2a 100755
--- a/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.1.sh
+++ b/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.1.sh
@@ -6,7 +6,8 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 genome="./../06.Mitochondrial_Genome_Assembly_Improvement/$prefix.assembly.mt_improved.fa" # The file name of the input genome assembly.
 
 
diff --git a/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh b/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh
index 1d342a1..3d2eb44 100755
--- a/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh
+++ b/Project_Template/07.Supervised_Final_Assembly/LRSDAY.07.Supervised_Final_Assembly.2.sh
@@ -7,20 +7,23 @@ PATH=$gnuplot_dir:$PATH
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
 genome="./../06.Mitochondrial_Genome_Assembly_Improvement/$prefix.assembly.mt_improved.fa" # The file path of the input genome assembly.
-vcf="yes" # Whether to generate a vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome. Default = "yes".
 dotplot="yes" # Whether to plot genome-wide dotplot based on the comparison with the reference genome below. Use "yes" if prefer to plot, otherwise use "no". Default = "yes".
 ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The path of the raw reference genome, only needed when dotplot="yes" or vcf="yes".
-threads=1 # The number of threads to use. Default = 1.
+threads=8 # The number of threads to use. Default = 8.
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
 # process the pipeline
 # Please mark desiarable changes in the $prefix.modification.list file and comment the command lines for Step 1 before proceeding with Step 2.
+
+vcf="no" # Whether to generate a vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome. Default = "no".
 # Step 2:
-perl $LRSDAY_HOME/scripts/relabel_and_reorder_sequences.pl  -i $genome -m $prefix.assembly.modification.list -o $prefix.assembly.final.fa
+perl $LRSDAY_HOME/scripts/relabel_and_reorder_sequences.pl -i $genome -m $prefix.assembly.modification.list -o $prefix.assembly.relabel_and_reorder.fa
 # generate assembly statistics
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.relabel_and_reorder.fa -o $prefix.assembly.final.fa
 perl $LRSDAY_HOME/scripts/cal_assembly_stats.pl -i $prefix.assembly.final.fa -o $prefix.assembly.final.stats.txt
 
 # check project-specific variables
@@ -77,6 +80,8 @@ then
     rm *.delta
     rm *.delta_filter
     rm ref_genome.fa
+    rm $prefix.assembly.relabel_and_reorder.fa
+
     if [[ $vcf == "yes" ]] 
     then
 	rm ref_genome.fa.fai
diff --git a/Project_Template/08.Centromere_Annotation/LRSDAY.08.Centromere_Annotation.sh b/Project_Template/08.Centromere_Annotation/LRSDAY.08.Centromere_Annotation.sh
index 8a731c7..0951eff 100755
--- a/Project_Template/08.Centromere_Annotation/LRSDAY.08.Centromere_Annotation.sh
+++ b/Project_Template/08.Centromere_Annotation/LRSDAY.08.Centromere_Annotation.sh
@@ -6,20 +6,28 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example. 
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The path of the input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
 query="$LRSDAY_HOME/data/S288C.centromere.fa" # The S. cerevisiae S288C reference centromere sequences based on Yue et al. (2017) Nature Genetics.
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ######################################
 # process the pipeline
-$exonerate_dir/exonerate --showvulgar no --showcigar no --showalignment no --showtargetgff yes --bestn 1 $query $genome >$prefix.centromere.exonerate.gff
+
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+
+$exonerate_dir/exonerate --showvulgar no --showcigar no --showalignment no --showtargetgff yes --bestn 1 $query $prefix.assembly.nuclear_genome.tidy.fa  >$prefix.centromere.exonerate.gff
 perl $LRSDAY_HOME/scripts/exonerate_gff2gff3.pl  -i $prefix.centromere.exonerate.gff -o $prefix.centromere.gff3.tmp -t $prefix
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r $genome -i  $prefix.centromere.gff3.tmp -o  $prefix.centromere.gff3 -t $prefix
+perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r $prefix.assembly.nuclear_genome.tidy.fa -i $prefix.centromere.gff3.tmp -o $prefix.nuclear_genome.centromere.gff3 -t $prefix
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
+    rm $prefix.assembly.nuclear_genome.fa
+    rm $prefix.assembly.nuclear_genome.tidy.fa
     rm $prefix.centromere.exonerate.gff
     rm $prefix.centromere.gff3.tmp
 fi
diff --git a/Project_Template/09.Nuclear_Gene_Annotation/LRSDAY.09.Nuclear_Gene_Annotation.sh b/Project_Template/09.Nuclear_Gene_Annotation/LRSDAY.09.Nuclear_Gene_Annotation.sh
index 444ef7a..65cb69d 100755
--- a/Project_Template/09.Nuclear_Gene_Annotation/LRSDAY.09.Nuclear_Gene_Annotation.sh
+++ b/Project_Template/09.Nuclear_Gene_Annotation/LRSDAY.09.Nuclear_Gene_Annotation.sh
@@ -6,10 +6,11 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
-threads=1 # The number of threads to use. Default = "1".
+threads=8 # The number of threads to use. Default = "8".
 maker_opts="$LRSDAY_HOME/misc/maker_opts.customized.ctl" # The configuration file for MAKER. You can edit this file if you have native transciptome/EST data for the strain/species that you sequenced or if you want to adapt it to annotate other eukaryotic organisms. Otherwise, please keep it unchanged. Please note that if this file is in the same directory where this bash script is executed, the file name cannot be "maker_opts.ctl".
 EVM_weights="$LRSDAY_HOME/misc/EVM_weights.customized.txt" # The configuration file for EVM. A list of numeric weight values to be applied to each type of evidence.
 debug="no" # use "yes" if prefer to keep intermediate files, otherwise use "no".
@@ -24,17 +25,16 @@ echo "genome_assembly=$genome_assembly"
 # convert the genome assembly file to all uppercases
 
 echo $chrMT_tag | sed -e "s/;/\n/g" > $genome_tag.assembly.chrMT.list
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m reverse -o $genome_tag.assembly.nuclear_genome.fa
-#$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m normal -o $genome_tag.assembly.mitochondrial_genome.fa
-
-perl $LRSDAY_HOME/scripts/switch_letter_cases_in_fasta.pl -i $genome_tag.assembly.nuclear_genome.fa -o genome.uppercase.fa -c upper
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m reverse -o $genome_tag.assembly.nuclear_genome.fa
+# perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m normal -o $genome_tag.assembly.mitochondrial_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $genome_tag.assembly.nuclear_genome.fa -o $genome_tag.assembly.nuclear_genome.tidy.fa
 
 cp $maker_opts maker_opts.ctl
 cp $LRSDAY_HOME/misc/maker_exe.ctl .
 cp $LRSDAY_HOME/misc/maker_bopts.ctl .
 cp $LRSDAY_HOME/misc/maker_evm.ctl .
 
-$maker_dir/maker -fix_nucleotides -genome genome.uppercase.fa -cpus $threads -base $genome_tag
+$maker_dir/maker -fix_nucleotides -genome $genome_tag.assembly.nuclear_genome.tidy.fa -cpus $threads -base $genome_tag
 
 # $maker_dir/fasta_merge -d $genome_tag.maker.output/${genome_tag}_master_datastore_index.log -o $genome_tag.nuclear_genome.maker.fasta
 $maker_dir/gff3_merge -d $genome_tag.maker.output/${genome_tag}_master_datastore_index.log -n -g -o $genome_tag.nuclear_genome.maker.raw.gff3
@@ -64,7 +64,7 @@ cat $genome_tag.nuclear_genome.maker.raw.protein_coding_gene.gff3 $genome_tag.nu
 mkdir $genome_tag.nuclear_genome.EVM.output
 cd $genome_tag.nuclear_genome.EVM.output
 $EVM_HOME/EvmUtils/partition_EVM_inputs.pl \
-    --genome ./../genome.uppercase.fa \
+    --genome ./../$genome_tag.assembly.nuclear_genome.tidy.fa \
     --gene_predictions ./../$genome_tag.nuclear_genome.maker.combined.gff3 \
     --protein_alignments ./../$genome_tag.nuclear_genome.protein_evidence.gff3 \
     --transcript_alignments ./../$genome_tag.nuclear_genome.est_evidence.gff3 \
@@ -73,7 +73,7 @@ $EVM_HOME/EvmUtils/partition_EVM_inputs.pl \
     --partition_listing $genome_tag.nuclear_genome.partitions_list.out
 
 $EVM_HOME/EvmUtils/write_EVM_commands.pl \
-    --genome ./../genome.uppercase.fa \
+    --genome ./../$genome_tag.assembly.nuclear_genome.tidy.fa \
     --weights $EVM_weights  \
     --gene_predictions ./../$genome_tag.nuclear_genome.maker.combined.gff3 \
     --output_file_name $genome_tag.nuclear_genome.evm.out \
@@ -87,40 +87,51 @@ $EVM_HOME/EvmUtils/recombine_EVM_partial_outputs.pl \
 $EVM_HOME/EvmUtils/convert_EVM_outputs_to_GFF3.pl \
     --partitions $genome_tag.nuclear_genome.partitions_list.out \
     --output $genome_tag.nuclear_genome.evm.out \
-    --genome ./../genome.uppercase.fa
+    --genome ./../$genome_tag.assembly.nuclear_genome.tidy.fa
 
-perl $LRSDAY_HOME/scripts/collect_EVM_gff3.pl -p $genome_tag.nuclear_genome  -r ./../genome.uppercase.fa
+perl $LRSDAY_HOME/scripts/collect_EVM_gff3.pl -p $genome_tag.nuclear_genome  -r ./../$genome_tag.assembly.nuclear_genome.tidy.fa
 
 cat $genome_tag.nuclear_genome.EVM.raw.gff3 ./../$genome_tag.nuclear_genome.maker.raw.tRNA.gff3 > $genome_tag.nuclear_genome.EVM.raw.with_tRNA.gff3
 perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl \
     -i $genome_tag.nuclear_genome.EVM.raw.with_tRNA.gff3 \
-    -r ./../genome.uppercase.fa \
+    -r ./../$genome_tag.assembly.nuclear_genome.tidy.fa \
     -t $genome_tag \
     -o $genome_tag.nuclear_genome.EVM.gff3
-cp $genome_tag.nuclear_genome.EVM.gff3 ./../$genome_tag.nuclear_genome.EVM.gff3
+cp $genome_tag.nuclear_genome.EVM.gff3 ./../$genome_tag.nuclear_genome.gff3
 cd ..
 
 perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl \
-    -r $genome_assembly \
-    -g $genome_tag.nuclear_genome.EVM.gff3 \
-    -o $genome_tag.nuclear_genome.EVM.cds.fa
+    -r $genome_tag.assembly.nuclear_genome.tidy.fa \
+    -g $genome_tag.nuclear_genome.gff3 \
+    -o $genome_tag.nuclear_genome.cds.fa
 perl $LRSDAY_HOME/scripts/cds2protein.pl \
-    -i $genome_tag.nuclear_genome.EVM.cds.fa \
-    -p $genome_tag.nuclear_genome.EVM \
+    -i $genome_tag.nuclear_genome.cds.fa \
+    -p $genome_tag.nuclear_genome \
     -t 1
 
-perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $genome_tag.nuclear_genome.EVM.gff3 -o $genome_tag.nuclear_genome.EVM.PoFF.gff 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.EVM.trimmed_cds.fa -o $genome_tag.nuclear_genome.EVM.PoFF.ffn 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.EVM.pep.fa -o $genome_tag.nuclear_genome.EVM.PoFF.faa
 
 # filtered out snoRNA annotation since it is still an experimental features suffering from redundant annotations
-cp $genome_tag.nuclear_genome.EVM.gff3 $genome_tag.nuclear_genome.EVM.gff3.tmp
-cat $genome_tag.nuclear_genome.EVM.gff3.tmp | egrep -v "snoRNA" > $genome_tag.nuclear_genome.EVM.gff3
+cp $genome_tag.nuclear_genome.gff3 $genome_tag.nuclear_genome.gff3.tmp
+cat $genome_tag.nuclear_genome.gff3.tmp | egrep -v "snoRNA" > $genome_tag.nuclear_genome.snoRNA_filtered.gff3
+perl $LRSDAY_HOME/scripts/label_pseudogene_in_gff3.pl -i $genome_tag.nuclear_genome.snoRNA_filtered.gff3 -l $genome_tag.nuclear_genome.manual_check.list -o $genome_tag.nuclear_genome.gff3
+
+perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl \
+    -r $genome_tag.assembly.nuclear_genome.tidy.fa \
+    -g $genome_tag.nuclear_genome.gff3 \
+    -o $genome_tag.nuclear_genome.cds.fa
+perl $LRSDAY_HOME/scripts/cds2protein.pl \
+    -i $genome_tag.nuclear_genome.cds.fa \
+    -p $genome_tag.nuclear_genome \
+    -t 1
+
+perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $genome_tag.nuclear_genome.gff3 -o $genome_tag.nuclear_genome.PoFF.gff 
+perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.trimmed_cds.fa -o $genome_tag.nuclear_genome.PoFF.ffn 
+perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.pep.fa -o $genome_tag.nuclear_genome.PoFF.faa
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
-    rm genome.uppercase.fa
+    rm $genome_tag.assembly.nuclear_genome.fa
     rm $genome_tag.nuclear_genome.maker.raw.tRNA.gff3
     rm $genome_tag.nuclear_genome.maker.raw.protein_coding_gene.gff3
     rm $genome_tag.nuclear_genome.maker.raw.protein_coding_gene.single_exon_gene.gff3
@@ -129,9 +140,11 @@ then
     rm $genome_tag.nuclear_genome.est_evidence.for_gene_model_refinement.gff3
     rm $genome_tag.nuclear_genome.protein_evidence.complementary_gene_model.gff3
     rm $genome_tag.nuclear_genome.est_evidence.complementary_gene_model.gff3
-    rm $genome_tag.nuclear_genome.EVM.gff3.tmp
+    rm $genome_tag.nuclear_genome.gff3.tmp
     rm $genome_tag.nuclear_genome.maker.combined.gff3
+    rm $genome_tag.nuclear_genome.snoRNA_filtered.gff3
     rm -rf _Inline
+    rm *.ctl
 fi
 
 ############################
diff --git a/Project_Template/10.Mitochondrial_Gene_Annotation/LRSDAY.10.Mitochondrial_Gene_Annotation.sh b/Project_Template/10.Mitochondrial_Gene_Annotation/LRSDAY.10.Mitochondrial_Gene_Annotation.sh
index b37fec6..6e6be2e 100755
--- a/Project_Template/10.Mitochondrial_Gene_Annotation/LRSDAY.10.Mitochondrial_Gene_Annotation.sh
+++ b/Project_Template/10.Mitochondrial_Gene_Annotation/LRSDAY.10.Mitochondrial_Gene_Annotation.sh
@@ -18,8 +18,9 @@ export PATH="$flip_dir:$blast_dir:$muscle_dir:$umac_dir:$hmmer_dir:$erpin_dir:$t
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the input genome assembly, if there are multiple corresponding contigs/scaffolds, use a single ';' to separate them. e.g. "chrMT_1;chrMT_2". Default = "chrMT". 
 genetic_code_table=3 # The NCBI genetic code table (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) for the annotated mitochondrial genome. Default = 3 (i.e. Yeast Mitochondria)
 debug="no" # Whehter to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
@@ -27,32 +28,47 @@ debug="no" # Whehter to keep intermediate files for debugging. Use "yes" if pref
 ######################################
 # process the pipeline
 
+
 echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
 
-#$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m normal -o $prefix.assembly.mitochondrial_genome.fa
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m normal -o $prefix.assembly.mitochondrial_genome.fa
 
-mkdir tmp
+if [[ $(egrep -c "^>" "$prefix.assembly.mitochondrial_genome.fa") -eq 0 ]]
+then
+    echo "No mitochondrial genome assembly was detected! Skip mitochondrial genome annotation!"
+else
+    
+    perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.mitochondrial_genome.fa -o $prefix.assembly.mitochondrial_genome.tidy.fa
 
-$mfannot_dir/mfannot \
-    --genetic $genetic_code_table \
-    --outputfile $prefix.mitochondrial_genome.mfannot.out \
-    --logfile $prefix.mitochondrial_genome.mfannot.log \
-    --T $(pwd)/tmp \
-    $prefix.assembly.mitochondrial_genome.fa
+    mkdir tmp
 
-perl $LRSDAY_HOME/scripts/mfannot2gff3.pl -i $prefix.mitochondrial_genome.mfannot.out -o $prefix.mitochondrial_genome.mfannot.gff3 -m lite
-perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.mitochondrial_genome.fa -g $prefix.mitochondrial_genome.mfannot.gff3 -o $prefix.mitochondrial_genome.mfannot.cds.fa
-perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.mfannot.cds.fa -t $genetic_code_table -p $prefix.mitochondrial_genome.mfannot
+    $mfannot_dir/mfannot \
+	--genetic $genetic_code_table \
+	--outputfile $prefix.mitochondrial_genome.mfannot.out.txt \
+	--logfile $prefix.mitochondrial_genome.mfannot.log \
+	--T $(pwd)/tmp \
+	$prefix.assembly.mitochondrial_genome.tidy.fa
 
-perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $prefix.mitochondrial_genome.mfannot.gff3 -o $prefix.mitochondrial_genome.mfannot.PoFF.gff 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.mfannot.trimmed_cds.fa -o $prefix.mitochondrial_genome.mfannot.PoFF.ffn 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.mfannot.pep.fa -o $prefix.mitochondrial_genome.mfannot.PoFF.faa
+    $trnascan_dir/tRNAscan-SE -D -g $trnascan_dir/../gcode.ystmito $prefix.assembly.mitochondrial_genome.tidy.fa  -o $prefix.assembly.mitochondrial_genome.trnascan.out.txt
 
-# clean up intermediate files
-if [[ $debug == "no" ]]
-then
-    rm -r tmp
+
+    perl $LRSDAY_HOME/scripts/mfannot2gff3.pl -mfannot_out $prefix.mitochondrial_genome.mfannot.out.txt -trnascan_out $prefix.assembly.mitochondrial_genome.trnascan.out.txt -o $prefix.mitochondrial_genome.pre_sort.gff3 -m lite -t $prefix
+    perl $LRSDAY_HOME/scripts/sort_gff3.pl -i $prefix.mitochondrial_genome.pre_sort.gff3 -t $prefix -o $prefix.mitochondrial_genome.gff3 -r $prefix.assembly.mitochondrial_genome.tidy.fa
+
+    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.mitochondrial_genome.tidy.fa -g $prefix.mitochondrial_genome.gff3 -o $prefix.mitochondrial_genome.cds.fa
+    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.cds.fa -t $genetic_code_table -p $prefix.mitochondrial_genome
+
+    perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $prefix.mitochondrial_genome.gff3 -o $prefix.mitochondrial_genome.PoFF.gff 
+    perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.trimmed_cds.fa -o $prefix.mitochondrial_genome.PoFF.ffn 
+    perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.pep.fa -o $prefix.mitochondrial_genome.PoFF.faa
+
+    # clean up intermediate files
+    if [[ $debug == "no" ]]
+    then
+	rm -r tmp
+	rm -r $prefix.mitochondrial_genome.pre_sort.gff3
+	rm -r $prefix.assembly.mitochondrial_genome.fa
+    fi
 fi
 
 ############################
diff --git a/Project_Template/11.TE_Annotation/LRSDAY.11.TE_Annotation.sh b/Project_Template/11.TE_Annotation/LRSDAY.11.TE_Annotation.sh
index 7613f5e..44c2731 100755
--- a/Project_Template/11.TE_Annotation/LRSDAY.11.TE_Annotation.sh
+++ b/Project_Template/11.TE_Annotation/LRSDAY.11.TE_Annotation.sh
@@ -6,24 +6,32 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
-threads=1 # The number of threads to use. Default = "1".
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The path of the final input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
+threads=8 # The number of threads to use. Default = "8".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
 # process the pipeline
 
-ln -s $genome genome.fa
-$repeatmasker_dir/RepeatMasker -pa $threads -lib $LRSDAY_HOME/data/TY_lib.Yue_et_al_2017_NG.fa  genome.fa  -xsmall  -gff
-$reannotate_dir/REannotate_longname  -g -f $LRSDAY_HOME/data/fuzzy_defragmentation.txt  -k $clustalw_dir/clustalw2 -r 0.48764  -d 10000  -t genome.fa.out  genome.fa
+TE_lib="$LRSDAY_HOME/data/TE_lib.v20221221.tidy.fa"
+TE_lib_LTRonly="$LRSDAY_HOME/data/TE_lib.v20221221.LTRonly.tidy.fa"
+
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+ln -s $prefix.assembly.nuclear_genome.tidy.fa  $prefix.genome.fa
+
+$repeatmasker_dir/RepeatMasker -pa $threads -lib $TE_lib  $prefix.genome.fa  -xsmall  -gff
+$reannotate_dir/REannotate_longname  -g -f $LRSDAY_HOME/data/fuzzy_defragmentation.txt  -k $clustalw_dir/clustalw2 -r 0.48764  -d 10000  -t $prefix.genome.fa.out  $prefix.genome.fa
 mv REannotate_output ${prefix}_REannotate_out
 
 cd ${prefix}_REannotate_out 
 
 perl $LRSDAY_HOME/scripts/parse_REannotate_gff.pl -o $prefix.REannotate.raw.gff
 mv $prefix.REannotate.raw.gff $prefix.REannotate.gff
-perl $LRSDAY_HOME/scripts/parse_REannotate_out.pl -i genome.fa.REannotation -p $prefix.TY_REannotate -r ./../genome.fa
+perl $LRSDAY_HOME/scripts/parse_REannotate_out.pl -i $prefix.genome.fa.REannotation -p $prefix.TY_REannotate -r ./../$prefix.genome.fa
 
 cat $prefix.TY_REannotate.complete.raw.fa  |egrep ">" |egrep  '(TY1|TY2)' |sed "s/>//g" >$prefix.TY_REannotate.complete.TY1TY2.raw.list
 perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.TY_REannotate.complete.raw.fa -l $prefix.TY_REannotate.complete.TY1TY2.raw.list  -o $prefix.TY_REannotate.complete.TY1TY2.raw.fa
@@ -31,12 +39,13 @@ perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.TY_REannotate.compl
 cat $prefix.TY_REannotate.truncated.raw.fa  |egrep ">" |egrep  '(TY1|TY2)' |sed "s/>//g" >$prefix.TY_REannotate.truncated.TY1TY2.raw.list
 perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.TY_REannotate.truncated.raw.fa -l $prefix.TY_REannotate.truncated.TY1TY2.raw.list  -o $prefix.TY_REannotate.truncated.TY1TY2.raw.fa
 
-for i in {3..5}
+for i in TY3 TY4 TY5 TSU4
 do
-    cat $prefix.TY_REannotate.complete.raw.fa  |egrep ">" |egrep "TY${i}" |sed "s/>//g"  >$prefix.TY_REannotate.complete.TY${i}.final.list
-    cat $prefix.TY_REannotate.truncated.raw.fa  |egrep ">" |egrep "TY${i}" |sed "s/>//g"  >$prefix.TY_REannotate.truncated.TY${i}.final.list
+    cat $prefix.TY_REannotate.complete.raw.fa  |egrep ">" |egrep "$i" |sed "s/>//g"  >$prefix.TY_REannotate.complete.$i.final.list
+    cat $prefix.TY_REannotate.truncated.raw.fa  |egrep ">" |egrep "$i" |sed "s/>//g"  >$prefix.TY_REannotate.truncated.$i.final.list
 done
 
+
 TY2_query="$LRSDAY_HOME/data/TY2_specific_region.fa"
 
 
@@ -74,25 +83,25 @@ else
     cat $prefix.TY_REannotate.truncated.TY2.list |sed "s/TY1/TY2/g" >$prefix.TY_REannotate.truncated.TY2.final.list
 fi
 
-db="$LRSDAY_HOME/data/TY_lib.Yue_et_al_2017_NG.LTRonly.fa"
+LTR_query="$prefix.TY_REannotate.soloLTR.raw.fa"
+db=$TE_lib_LTRonly
 db_tag="soloLTR_db";
-if [ ! -s "$db" ]
+if [ ! -s "$LTR_query" ]
 then
-    echo "$db is empty, skip .."
+    echo "$LTR_query is empty, skip .."
     touch $prefix.TY_soloLTR.refined.nr.gff
 else
-    LTR_query="$prefix.TY_REannotate.soloLTR.raw.fa"
-    $blast_dir/makeblastdb  -in $db  -dbtype nucl -title $db_tag -hash_index -out $db_tag
-    $blast_dir/blastn  -task blastn -query $LTR_query -num_threads $threads -db $db_tag -outfmt 7 >$prefix.$db_tag.soloLTR.blastn.fmt7.out
-    perl $LRSDAY_HOME/scripts/trim_soloLTR_by_blast.pl -q $LTR_query -b  $prefix.$db_tag.soloLTR.blastn.fmt7.out -p $prefix  -i 70 -l 100
+    $blast_dir/makeblastdb -in $db -dbtype nucl -title $db_tag -hash_index -out $db_tag
+    $blast_dir/blastn -task blastn -query $LTR_query -num_threads $threads -db $db_tag -outfmt 7 >$prefix.$db_tag.soloLTR.blastn.fmt7.out
+    perl $LRSDAY_HOME/scripts/trim_soloLTR_by_blast.pl -q $LTR_query -b  $prefix.$db_tag.soloLTR.blastn.fmt7.out -p $prefix  -i 75 -l 100
     $bedtools_dir/bedtools sort  -i  $prefix.TY_REannotate.soloLTR.refined.gff > $prefix.TY_REannotate.soloLTR.refined.sorted.gff
-    perl $LRSDAY_HOME/scripts/rm_overlap_features_from_gff_simple.pl  -r ./../genome.fa  -i $prefix.TY_REannotate.soloLTR.refined.sorted.gff -o $prefix.TY_soloLTR.refined.nr.gff 
+    perl $LRSDAY_HOME/scripts/rm_overlap_features_from_gff_simple.pl  -r ./../$prefix.genome.fa  -i $prefix.TY_REannotate.soloLTR.refined.sorted.gff -o $prefix.TY_soloLTR.refined.nr.gff 
 fi
 
-for i in {1..5}
+for i in TY1 TY2 TY3 TY4 TY5 TSU4
 do
-    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.complete.TY${i}.final.list -o $prefix.TY_REannotate.complete.TY${i}.final.gff -t $prefix
-    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.truncated.TY${i}.final.list -o $prefix.TY_REannotate.truncated.TY${i}.final.gff -t $prefix
+    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.complete.$i.final.list -o $prefix.TY_REannotate.complete.$i.final.gff -t $prefix
+    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.truncated.$i.final.list -o $prefix.TY_REannotate.truncated.$i.final.gff -t $prefix
 done
 
 cat $prefix.TY_REannotate.*.final.gff > $prefix.TY.complete_plus_truncated.final.gff
@@ -102,17 +111,22 @@ $bedtools_dir/bedtools intersect -v -a $prefix.TY_soloLTR.refined.nr.gff -b $pre
 
 cat $prefix.TY.complete_plus_truncated.final.gff $prefix.TY.soloLTR.final.gff > $prefix.TY.all.final.gff
 
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r ./../genome.fa -i $prefix.TY.all.final.gff -o $prefix.TE.gff3 -t $prefix 
+#perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r ./../$prefix.genome.fa -i $prefix.TY.all.final.gff -o $prefix.TE.gff3 -t $prefix 
+perl $LRSDAY_HOME/scripts/tidy_TE_gff3.pl -r ./../$prefix.genome.fa -i $prefix.TY.all.final.gff -o ./../$prefix.nuclear_genome.TE.gff3 -t $prefix 
+
+
+if [[ $debug == "no" ]]
+then
+    rm $prefix.*.final.gff
+fi
 
-cp $prefix.TE.gff3 ./../
-cp $prefix.REannotate.gff ./../
-rm $prefix.*.final.gff
 cd ..
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
-    rm genome.fa*
+    rm $prefix.assembly.nuclear_genome*
+    rm $prefix.genome.fa*
 fi
 
 ############################
diff --git a/Project_Template/12.Core_X_Element_Annotation/LRSDAY.12.Core_X_Element_Annotation.sh b/Project_Template/12.Core_X_Element_Annotation/LRSDAY.12.Core_X_Element_Annotation.sh
index 5c4f6f6..15c64b4 100755
--- a/Project_Template/12.Core_X_Element_Annotation/LRSDAY.12.Core_X_Element_Annotation.sh
+++ b/Project_Template/12.Core_X_Element_Annotation/LRSDAY.12.Core_X_Element_Annotation.sh
@@ -6,25 +6,34 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
 # process the pipeline
 feature_type="X_element"
 length_cutoff_for_completeness=300
-$hmmer_dir/nhmmer -E 1 --tblout $prefix.$feature_type.nhmmer.out $LRSDAY_HOME/data/S288C.$feature_type.hmm $genome
-perl $LRSDAY_HOME/scripts/nhmer2seq.pl  -r $genome -i $prefix.$feature_type.nhmmer.out -e 0.0001 -p $prefix -ft $feature_type -l $length_cutoff_for_completeness
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $genome -o $prefix.$feature_type.gff3 -t $prefix
-perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $genome -g $prefix.$feature_type.gff3 -o $prefix.$feature_type.fa 
-$muscle_dir/muscle -in $prefix.$feature_type.fa -out $prefix.$feature_type.aln.fa
+
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+
+
+$hmmer_dir/nhmmer -E 1 --tblout $prefix.$feature_type.nhmmer.out $LRSDAY_HOME/data/S288C.$feature_type.hmm $prefix.assembly.nuclear_genome.tidy.fa
+perl $LRSDAY_HOME/scripts/nhmer2seq.pl -r $prefix.assembly.nuclear_genome.tidy.fa -i $prefix.$feature_type.nhmmer.out -e 0.0001 -p $prefix -ft $feature_type -l $length_cutoff_for_completeness
+perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $prefix.assembly.nuclear_genome.tidy.fa -o $prefix.nuclear_genome.$feature_type.gff3 -t $prefix
+perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $prefix.assembly.nuclear_genome.tidy.fa -g $prefix.nuclear_genome.$feature_type.gff3 -o $prefix.nuclear_genome.$feature_type.fa 
+$muscle_dir/muscle -in $prefix.nuclear_genome.$feature_type.fa -out $prefix.nuclear_genome.$feature_type.aln.fa
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
     rm $prefix.$feature_type.raw.gff3
     rm $prefix.$feature_type.raw.fa
+    rm $prefix.assembly.nuclear_genome.fa
+    rm $prefix.assembly.nuclear_genome.tidy.fa
 fi
 
 ############################
diff --git a/Project_Template/13.Y_Prime_Element_Annotation/LRSDAY.13.Y_Prime_Element_Annotation.sh b/Project_Template/13.Y_Prime_Element_Annotation/LRSDAY.13.Y_Prime_Element_Annotation.sh
index 52fcfd5..3c5b590 100755
--- a/Project_Template/13.Y_Prime_Element_Annotation/LRSDAY.13.Y_Prime_Element_Annotation.sh
+++ b/Project_Template/13.Y_Prime_Element_Annotation/LRSDAY.13.Y_Prime_Element_Annotation.sh
@@ -6,8 +6,9 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
@@ -16,13 +17,17 @@ feature_type="Y_prime_element"
 query="$LRSDAY_HOME/data/query.Y_prime_element.long.fa"
 length_cutoff_for_completeness=3500
 
-$ucsc_dir/blat -maxIntron=1000 $genome $query  $prefix.$feature_type.blat.psl
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+
+$ucsc_dir/blat -maxIntron=1000 $prefix.assembly.nuclear_genome.tidy.fa $query  $prefix.$feature_type.blat.psl
 $ucsc_dir/pslCDnaFilter  -minId=0.9 -minAlnSize=1000 -bestOverlap -filterWeirdOverlapped   $prefix.$feature_type.blat.psl  $prefix.$feature_type.blat.filtered.psl
 $ucsc_dir/pslScore  $prefix.$feature_type.blat.filtered.psl | sort -nk5 -r > $prefix.$feature_type.blat.filtered.pslScore.out
-perl $LRSDAY_HOME/scripts/psl2gff3.pl -i $prefix.$feature_type.blat.filtered.psl -o $prefix.$feature_type.raw.gff3 -ft $feature_type -t $prefix -r $genome -l $length_cutoff_for_completeness
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $genome -o $prefix.$feature_type.gff3 -t $prefix
-perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $genome -g $prefix.$feature_type.gff3 -o $prefix.$feature_type.fa
-$muscle_dir/muscle -in $prefix.$feature_type.fa -out $prefix.$feature_type.aln.fa
+perl $LRSDAY_HOME/scripts/psl2gff3.pl -i $prefix.$feature_type.blat.filtered.psl -o $prefix.$feature_type.raw.gff3 -ft $feature_type -t $prefix -r $prefix.assembly.nuclear_genome.tidy.fa  -l $length_cutoff_for_completeness
+perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $prefix.assembly.nuclear_genome.tidy.fa -o $prefix.nuclear_genome.$feature_type.gff3 -t $prefix
+perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $prefix.assembly.nuclear_genome.tidy.fa -g $prefix.nuclear_genome.$feature_type.gff3 -o $prefix.nuclear_genome.$feature_type.fa
+$muscle_dir/muscle -in $prefix.nuclear_genome.$feature_type.fa -out $prefix.nuclear_genome.$feature_type.aln.fa
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
@@ -31,6 +36,8 @@ then
     rm $prefix.Y_prime_element.blat.psl
     rm $prefix.Y_prime_element.blat.filtered.psl
     rm $prefix.Y_prime_element.blat.filtered.pslScore.out
+    rm $prefix.assembly.nuclear_genome.fa
+    rm $prefix.assembly.nuclear_genome.tidy.fa
 fi
 
  
diff --git a/Project_Template/14.Gene_Orthology_Identification/LRSDAY.14.Gene_Orthology_Identification.sh b/Project_Template/14.Gene_Orthology_Identification/LRSDAY.14.Gene_Orthology_Identification.sh
index 2fc5a3d..0fe8c04 100755
--- a/Project_Template/14.Gene_Orthology_Identification/LRSDAY.14.Gene_Orthology_Identification.sh
+++ b/Project_Template/14.Gene_Orthology_Identification/LRSDAY.14.Gene_Orthology_Identification.sh
@@ -6,16 +6,17 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-threads=1 # The number of threads to use. Default = "1".
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
 
-input_nuclear_gene_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.EVM.gff3" # The file path of the input nuclear gene gff3 file generated in the task 09.Nuclear_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the nuclear gene annotation. 
-query_nuclear_gene_PoFF_faa="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.EVM.PoFF.faa" # The file path of the PoFF.faa file generated in the task 09.Nuclear_Gene_Annotation.
-query_nuclear_gene_PoFF_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.EVM.PoFF.gff" # The file path of the PoFF.gff file generated in the task 09.Nuclear_Gene_Annotation.
+threads=8 # The number of threads to use. Default = "8".
 
-input_mitochondrial_gene_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.mfannot.gff3" # The file path of the input mitochondrial gene gff3 file generated in the task 10.Mitochondrial_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the mitochondrial gene annotation. 
-query_mitochondrial_gene_PoFF_faa="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.mfannot.PoFF.faa" # The file path of the PoFF.faa file generated in the task 10.Mitochondrial_Gene_Annotation.
-query_mitochondrial_gene_PoFF_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.mfannot.PoFF.gff" # The file path of the PoFF.gff file generated in the task 10.Mitochondrial_Gene_Annotation.
+input_nuclear_genome_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.gff3" # The file path of the input nuclear gene gff3 file generated in the task 09.Nuclear_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the nuclear gene annotation. 
+query_nuclear_genome_PoFF_faa="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.PoFF.faa" # The file path of the PoFF.faa file generated in the task 09.Nuclear_Gene_Annotation.Po
+query_nuclear_genome_PoFF_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.PoFF.gff" # The file path of the PoFF.gff file generated in the task 09.Nuclear_Gene_Annotation.
+
+input_mitochondrial_genome_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.gff3" # The file path of the input mitochondrial gene gff3 file generated in the task 10.Mitochondrial_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the mitochondrial gene annotation. 
+query_mitochondrial_genome_PoFF_faa="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.PoFF.faa" # The file path of the PoFF.faa file generated in the task 10.Mitochondrial_Gene_Annotation.
+query_mitochondrial_genome_PoFF_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.PoFF.gff" # The file path of the PoFF.gff file generated in the task 10.Mitochondrial_Gene_Annotation.
 
 ref_PoFF_faa="$LRSDAY_HOME/data/SGDref.PoFF.faa" # The file path of the reference proteome file in FASTA format: for S. cerevisiae and its close relatives, you can directly use the pre-shipped file: SGDref.PoFF.faa; if you work with other organisms, you can check ProteinOrtho's manual for details on how to prepare such file.
 ref_PoFF_gff="$LRSDAY_HOME/data/SGDref.PoFF.gff" # The path of the reference gene GFF file in GFF format: for S. cerevisiae and its close relatives, you can directly use the pre-shipped file: SGDref.PoFF.gff; if you work with other organisms, you can check ProteinOrtho's manual for details on how to prepare such file.
@@ -41,46 +42,45 @@ cp $ref_PoFF_faa ref.PoFF.faa
 cp $ref_PoFF_gff ref.PoFF.gff
 
 # process nuclear gene annotation
-if [[ ! -z $input_nuclear_gene_gff ]]
+if [[ ! -z $input_nuclear_genome_gff ]]
 then 
-    echo "The variable input_nuclear_gene_gff has been specified, so expecting input files specified for query_nuclear_gene_PoFF_faa and query_nuclear_gene_PoFF_gff"
-    test_file_existence $query_nuclear_gene_PoFF_faa
-    test_file_existence $query_nuclear_gene_PoFF_gff
-    cp $query_nuclear_gene_PoFF_faa query.nuclear_gene.PoFF.faa
-    cp $query_nuclear_gene_PoFF_gff query.nuclear_gene.PoFF.gff
-    output_nuclear_gene_gff="$prefix.nuclear_gene.orthology_map.gff3"
-    proteinortho_nuclear_gene_input="query.nuclear_gene.PoFF.faa ref.PoFF.faa"
-    perl $proteinortho_dir/proteinortho5.pl -cpus=$threads -blastpath=$blast_dir -singles -synteny -project="$prefix.nuclear_gene" $proteinortho_nuclear_gene_input  
-    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_nuclear_gene_gff -x $prefix.nuclear_gene.poff -r ref.PoFF.faa -q query.nuclear_gene.PoFF.faa -o $prefix.nuclear_gene.updated.gff3
+    echo "The variable input_nuclear_genome_gff has been specified, so expecting input files specified for query_nuclear_genome_PoFF_faa and query_nuclear_genome_PoFF_gff"
+    test_file_existence $query_nuclear_genome_PoFF_faa
+    test_file_existence $query_nuclear_genome_PoFF_gff
+    cp $query_nuclear_genome_PoFF_faa query.nuclear_genome.PoFF.faa
+    cp $query_nuclear_genome_PoFF_gff query.nuclear_genome.PoFF.gff
+    proteinortho_nuclear_genome_input="query.nuclear_genome.PoFF.faa ref.PoFF.faa"
+    $proteinortho_dir/proteinortho -cpus=$threads -p=blastp -binpath=$blast_dir -singles -synteny -project="$prefix.nuclear_genome" $proteinortho_nuclear_genome_input
+    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_nuclear_genome_gff -x $prefix.nuclear_genome.proteinortho.tsv -r ref.PoFF.faa -q query.nuclear_genome.PoFF.faa -o $prefix.nuclear_genome.SGD_orthology_mapped.gff3
+
 
     if [[ $debug == "no" ]]
     then
-	rm $prefix.nuclear_gene.ffadj-graph
-	rm $prefix.nuclear_gene.blast-graph
-	rm $prefix.nuclear_gene.proteinortho-graph
-	rm $prefix.nuclear_gene.poff-graph
+	rm $prefix.nuclear_genome.ffadj-graph
+	rm $prefix.nuclear_genome.blast-graph
+	rm $prefix.nuclear_genome.proteinortho-graph
+	rm $prefix.nuclear_genome.poff-graph
     fi
 fi
 
 # process mitochondrial gene annotation
-if [[ ! -z $input_mitochondrial_gene_gff ]]
+if [[ ! -z $input_mitochondrial_genome_gff ]]
 then 
-    echo "The variable input_mitochondrial_gene_gff has been specified, so expecting input files specified for query_mitochondrial_gene_PoFF_faa and query_mitochondrial_gene_PoFF_gff"
-    test_file_existence $query_mitochondrial_gene_PoFF_faa
-    test_file_existence $query_mitochondrial_gene_PoFF_gff
-    cp $query_mitochondrial_gene_PoFF_faa query.mitochondrial_gene.PoFF.faa
-    cp $query_mitochondrial_gene_PoFF_gff query.mitochondrial_gene.PoFF.gff
-    output_mitochondrial_gene_gff="$prefix.mitochondrial_gene.orthology_map.gff3"
-    proteinortho_mitochondrial_gene_input="query.mitochondrial_gene.PoFF.faa ref.PoFF.faa"
-    perl $proteinortho_dir/proteinortho5.pl -cpus=$threads -blastpath=$blast_dir -singles -synteny -project="$prefix.mitochondrial_gene"  $proteinortho_mitochondrial_gene_input  
-    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_mitochondrial_gene_gff -x $prefix.mitochondrial_gene.poff -r ref.PoFF.faa -q query.mitochondrial_gene.PoFF.faa -o $prefix.mitochondrial_gene.updated.gff3
+    echo "The variable input_mitochondrial_genome_gff has been specified, so expecting input files specified for query_mitochondrial_genome_PoFF_faa and query_mitochondrial_genome_PoFF_gff"
+    test_file_existence $query_mitochondrial_genome_PoFF_faa
+    test_file_existence $query_mitochondrial_genome_PoFF_gff
+    cp $query_mitochondrial_genome_PoFF_faa query.mitochondrial_genome.PoFF.faa
+    cp $query_mitochondrial_genome_PoFF_gff query.mitochondrial_genome.PoFF.gff
+    proteinortho_mitochondrial_genome_input="query.mitochondrial_genome.PoFF.faa ref.PoFF.faa"
+    perl $proteinortho_dir/proteinortho -cpus=$threads -p=blastp -binpath=$blast_dir -singles -synteny -project="$prefix.mitochondrial_genome"  $proteinortho_mitochondrial_genome_input  
+    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_mitochondrial_genome_gff -x $prefix.mitochondrial_genome.proteinortho.tsv -r ref.PoFF.faa -q query.mitochondrial_genome.PoFF.faa -o $prefix.mitochondrial_genome.SGD_orthology_mapped.gff3
 
     if [[ $debug == "no" ]]
     then
-	rm $prefix.mitochondrial_gene.ffadj-graph
-	rm $prefix.mitochondrial_gene.blast-graph
-	rm $prefix.mitochondrial_gene.proteinortho-graph
-	rm $prefix.mitochondrial_gene.poff-graph
+	rm $prefix.mitochondrial_genome.ffadj-graph
+	rm $prefix.mitochondrial_genome.blast-graph
+	rm $prefix.mitochondrial_genome.proteinortho-graph
+	rm $prefix.mitochondrial_genome.poff-graph
     fi
 fi
 
@@ -90,6 +90,7 @@ if [[ $debug == "no" ]]
 then
     rm query.*
     rm ref.*
+    rm proteinortho_cache_${prefix}.log
 fi
     
 ############################
diff --git a/Project_Template/15.Annotation_Integration/LRSDAY.15.Annotation_Integration.sh b/Project_Template/15.Annotation_Integration/LRSDAY.15.Annotation_Integration.sh
index 306f7e8..695d896 100755
--- a/Project_Template/15.Annotation_Integration/LRSDAY.15.Annotation_Integration.sh
+++ b/Project_Template/15.Annotation_Integration/LRSDAY.15.Annotation_Integration.sh
@@ -6,14 +6,15 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
-centromere_gff3="./../08.Centromere_Annotation/$prefix.centromere.gff3" # The path of the final centromere annotation gff3 generated by task 08.Centromere_Annotation_for_FinalAssembly, use "" if not existing.
-TE_gff3="./../11.TE_Annotation/$prefix.TE.gff3" # The file path of the TE annotation gff3 generated by task 11.TE_Annotation, use "" if not existing.
-X_element_gff3="./../12.Core_X_Element_Annotation/$prefix.X_element.gff3" # The file path of the X_element annotation gff3 generated by task 12.CoreX_Annotation, use "" if not existing.
-Y_prime_element_gff3="./../13.Y_Prime_Element_Annotation/$prefix.Y_prime_element.gff3" # The file path of the Y_prime_element annotation gff3 generated by task 13.Yprime_Annotation, use "" if not existing.
-nuclear_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.nuclear_gene.updated.gff3" # The file path of the nuclear gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 09.Nuclear_Gene_Annotation, use "" if not existing.
-mitochondrial_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.mitochondrial_gene.updated.gff3" # The file path of the mitochondrial gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 10.Mitochondrial_Gene_Annotation, use "" if not existing.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
+centromere_gff3="./../08.Centromere_Annotation/$prefix.nuclear_genome.centromere.gff3" # The path of the final centromere annotation gff3 generated by task 08.Centromere_Annotation_for_FinalAssembly, use "" if not existing.
+TE_gff3="./../11.TE_Annotation/$prefix.nuclear_genome.TE.gff3" # The file path of the TE annotation gff3 generated by task 11.TE_Annotation, use "" if not existing.
+X_element_gff3="./../12.Core_X_Element_Annotation/$prefix.nuclear_genome.X_element.gff3" # The file path of the X_element annotation gff3 generated by task 12.CoreX_Annotation, use "" if not existing.
+Y_prime_element_gff3="./../13.Y_Prime_Element_Annotation/$prefix.nuclear_genome.Y_prime_element.gff3" # The file path of the Y_prime_element annotation gff3 generated by task 13.Yprime_Annotation, use "" if not existing.
+nuclear_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.nuclear_genome.SGD_orthology_mapped.gff3" # The file path of the nuclear gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 09.Nuclear_Gene_Annotation, use "" if not existing.
+mitochondrial_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.mitochondrial_genome.SGD_orthology_mapped.gff3" # The file path of the mitochondrial gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 10.Mitochondrial_Gene_Annotation, use "" if not existing.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the input genome assembly, if there are multiple corresponding contigs/scaffolds, use a single ';' to separate them. e.g. "chrMT_1;chrMT_2". Default = "chrMT". 
 chrMT_genetic_code_table=3 # The NCBI genetic code table (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) for the annotated mitochondrial genome. Default = 3 (i.e. Yeast Mitochondria)
 
@@ -21,38 +22,52 @@ debug="no" # use "yes" if prefer to keep intermediate files, otherwise use "no".
 
 ######################################
 # process the pipeline
-cat $centromere_gff3 $TE_gff3 $X_element_gff3 $Y_prime_element_gff3 $nuclear_gene_gff3 $mitochondrial_gene_gff3  >$prefix.concatenated.gff3
-perl $LRSDAY_HOME/scripts/sort_gff3.pl -i $prefix.concatenated.gff3 -t $prefix -o $prefix.final.gff3 -r $genome
-perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $genome -g $prefix.final.gff3 -o $prefix.final.cds.fa
 
-cp $genome $prefix.assembly.final.fa
 echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m normal -o $prefix.assembly.mitochondrial_genome.fa
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m normal -o $prefix.mitochondrial_genome.fa
+
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.nuclear_genome.fa -o $prefix.nuclear_genome.tidy.fa
+
+cat $centromere_gff3 $TE_gff3 $X_element_gff3 $Y_prime_element_gff3 $nuclear_gene_gff3  >$prefix.nuclear_genome.concatenated.gff3
+perl $LRSDAY_HOME/scripts/sort_gff3.pl -i $prefix.nuclear_genome.concatenated.gff3 -t $prefix -o $prefix.nuclear_genome.tidy.gff3 -r $prefix.nuclear_genome.tidy.fa
 
 if [[ ! -z $nuclear_gene_gff3 ]]
 then
-    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.nuclear_genome.fa -g $prefix.final.gff3 -o $prefix.nuclear_genome.cds.fa
-    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.nuclear_genome.cds.fa -p $prefix.nuclear_genome -t 1
+    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.nuclear_genome.tidy.fa -g $prefix.nuclear_genome.tidy.gff3 -o $prefix.nuclear_genome.tidy.cds.fa
+    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.nuclear_genome.tidy.cds.fa -p $prefix.nuclear_genome.tidy -t 1
 fi
 
-if [[ ! -z $mitochondrial_gene_gff3 ]]
+if [[ $(egrep -c "^>" "$prefix.mitochondrial_genome.fa") -eq 0 ]]
 then
-    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.mitochondrial_genome.fa -g $prefix.final.gff3 -o $prefix.mitochondrial_genome.cds.fa
-    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.cds.fa -p $prefix.mitochondrial_genome -t $chrMT_genetic_code_table
-fi
+    echo "No mitochondrial genome assembly was detected! Skip final annotation aggregation for the mitochondrial genome!"
+else
+    perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.mitochondrial_genome.fa -o $prefix.mitochondrial_genome.tidy.fa
+    cp $mitochondrial_gene_gff3 $prefix.mitochondrial_genome.tidy.gff3
+    if [[ ! -z $mitochondrial_gene_gff3 ]]
+    then
+	perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.mitochondrial_genome.tidy.fa -g $prefix.mitochondrial_genome.tidy.gff3 -o $prefix.mitochondrial_genome.tidy.cds.fa
+	perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.tidy.cds.fa -p $prefix.mitochondrial_genome.tidy -t $chrMT_genetic_code_table
+    fi
 
-if [[ ! -z $nuclear_gene_gff3 && ! -z $mitochondrial_gene_gff3 ]]
-then
-    cat $prefix.nuclear_genome.trimmed_cds.fa $prefix.mitochondrial_genome.trimmed_cds.fa > $prefix.final.trimmed_cds.fa
-    cat $prefix.nuclear_genome.pep.fa $prefix.mitochondrial_genome.pep.fa >$prefix.final.pep.fa
-    cat $prefix.nuclear_genome.manual_check.list  $prefix.mitochondrial_genome.manual_check.list > $prefix.final.manual_check.list
 fi
 
+
+
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
-    rm $prefix.concatenated.gff3
+    rm $prefix.nuclear_genome.concatenated.gff3
+
+    if [[ -e $prefix.nuclear_genome.fa ]]
+    then
+	rm $prefix.nuclear_genome.fa
+    fi
+
+    if [[ -e $prefix.mitochondrial_genome.fa ]]
+    then
+	rm $prefix.mitochondrial_genome.fa
+    fi
 fi
 
 ############################
diff --git a/README.md b/README.md
index 3eebcb8..3bda02c 100644
--- a/README.md
+++ b/README.md
@@ -22,6 +22,7 @@ Jia-Xing Yue & Gianni Liti. (2018) Long-read sequencing data analysis for yeasts
 Jia-Xing Yue, Jing Li, Louise Aigrain, Johan Hallin, Karl Persson, Karen Oliver, Anders Bergström, Paul Coupland, Jonas Warringer, Marco Cosentino Lagomarsino, Gilles Fischer, Richard Durbin, Gianni Liti. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. *Nature Genetics*, 49:913-924.
 
 ## Release history
+* v1.7.0 Released on 2022/12/31
 * v1.6.0 Released on 2019/10/03
 * v1.5.0 Released on 2019/05/13
 * v1.4.0 Released on 2019/03/21
@@ -37,7 +38,7 @@ LRSDAY itself is distributed under the MIT license. A number of LRSDAY's depende
 
 ## Requirements
 ### Hardware, operating system and network
-This protocol is designed for a desktop or computing server running an x86-64-bit Linux operating system. Multithreaded processors are preferred to speed up the process since many steps can be configured to use multiple threads in parallel. For assembling and analyzing the budding yeast genomes (genome size = ~12.5 Mb), at least 16 Gb of RAM and 100 Gb of free disk space are recomended. When adapted for other eukaryotic organisms with larger genome sizes, the RAM and disk space consumption will scale up, majorly during *de novo* genome assembly (performed by [Canu](https://github.com/marbl/canu) by default. Plese refer to [Canu’s manual](http://canu.readthedocs.io/en/latest/) for suggested RAM and disk space consumption for assembling large genomes. Stable Internet connection is required for the installation and configuration of LRSDAY as well as for retrieving the test data.
+This protocol is designed for a desktop or computing server running an x86-64-bit Linux operating system. Multithreaded processors are preferred to speed up the process since many steps can be configured to use multiple threads in parallel. For assembling and analyzing the budding yeast genomes (genome size = ~12.5 Mb), at least 16 Gb of RAM and 100 Gb of free disk space are recomended. More disk space is needed if you want to use LRSDAY to do Nanopore basecalling. When adapted for other eukaryotic organisms with larger genome sizes, the RAM and disk space consumption will scale up, majorly during *de novo* genome assembly (performed by [Canu](https://github.com/marbl/canu) by default. Plese refer to [Canu’s manual](http://canu.readthedocs.io/en/latest/) for suggested RAM and disk space consumption for assembling large genomes. Stable Internet connection is required for the installation and configuration of LRSDAY as well as for retrieving the test data.
 
 
 ### Software or library requirements
@@ -53,7 +54,7 @@ This protocol is designed for a desktop or computing server running an x86-64-bi
 * perl v5.12 or newer (https://www.perl.org/)
 * python v2.7.9 or newer (https://www.python.org/)
 * python-devel
-* python v3.4 or newer (https://www.python.org/)
+* python v3.7 or newer (https://www.python.org/)
 * python3-devel
 * tar (https://www.gnu.org/software/tar/)
 * unzip (http://infozip.sourceforge.net/UnZip.html)
diff --git a/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz b/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz
index eee4cab..aa92adf 100644
Binary files a/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz and b/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz differ
diff --git a/data/SGDref.PoFF.faa.gz b/data/SGDref.PoFF.faa.gz
index bc36e84..0af577d 100644
Binary files a/data/SGDref.PoFF.faa.gz and b/data/SGDref.PoFF.faa.gz differ
diff --git a/data/SGDref.PoFF.ffn.gz b/data/SGDref.PoFF.ffn.gz
index a0c2124..6dca2f2 100644
Binary files a/data/SGDref.PoFF.ffn.gz and b/data/SGDref.PoFF.ffn.gz differ
diff --git a/data/SGDref.PoFF.gff b/data/SGDref.PoFF.gff
deleted file mode 100644
index ceece18..0000000
--- a/data/SGDref.PoFF.gff
+++ /dev/null
@@ -1,5816 +0,0 @@
-chrI	SGD	CDS	1807	2169	.	-	.	ID=YAL068C;Name=YAL068C;Alias=PAU8
-chrI	SGD	CDS	2480	2707	.	+	.	ID=YAL067W-A;Name=YAL067W-A;Alias=
-chrI	SGD	CDS	7235	9016	.	-	.	ID=YAL067C;Name=YAL067C;Alias=SEO1
-chrI	SGD	CDS	11565	11951	.	-	.	ID=YAL065C;Name=YAL065C;Alias=
-chrI	SGD	CDS	12046	12426	.	+	.	ID=YAL064W-B;Name=YAL064W-B;Alias=
-chrI	SGD	CDS	13363	13743	.	-	.	ID=YAL064C-A;Name=YAL064C-A;Alias=TDA8
-chrI	SGD	CDS	21566	21850	.	+	.	ID=YAL064W;Name=YAL064W;Alias=
-chrI	SGD	CDS	22395	22685	.	-	.	ID=YAL063C-A;Name=YAL063C-A;Alias=
-chrI	SGD	CDS	24000	27968	.	-	.	ID=YAL063C;Name=YAL063C;Alias=FLO9
-chrI	SGD	CDS	31567	32940	.	+	.	ID=YAL062W;Name=YAL062W;Alias=GDH3
-chrI	SGD	CDS	33448	34701	.	+	.	ID=YAL061W;Name=YAL061W;Alias=BDH2
-chrI	SGD	CDS	35155	36303	.	+	.	ID=YAL060W;Name=YAL060W;Alias=BDH1
-chrI	SGD	CDS	36509	37147	.	+	.	ID=YAL059W;Name=YAL059W;Alias=ECM1
-chrI	SGD	CDS	37464	38972	.	+	.	ID=YAL058W;Name=YAL058W;Alias=CNE1
-chrI	SGD	CDS	39259	41901	.	+	.	ID=YAL056W;Name=YAL056W;Alias=GPB2
-chrI	SGD	CDS	42177	42719	.	+	.	ID=YAL055W;Name=YAL055W;Alias=PEX22
-chrI	SGD	CDS	42881	45022	.	-	.	ID=YAL054C;Name=YAL054C;Alias=ACS1
-chrI	SGD	CDS	45899	48250	.	+	.	ID=YAL053W;Name=YAL053W;Alias=FLC2
-chrI	SGD	CDS	48564	51707	.	+	.	ID=YAL051W;Name=YAL051W;Alias=OAF1
-chrI	SGD	CDS	51855	52595	.	-	.	ID=YAL049C;Name=YAL049C;Alias=AIM2
-chrI	SGD	CDS	52801	54789	.	-	.	ID=YAL048C;Name=YAL048C;Alias=GEM1
-chrI	SGD	CDS	54989	56857	.	-	.	ID=YAL047C;Name=YAL047C;Alias=SPC72
-chrI	SGD	CDS	57029	57385	.	-	.	ID=YAL046C;Name=YAL046C;Alias=BOL3
-chrI	SGD	CDS	57518	57850	.	+	.	ID=YAL044W-A;Name=YAL044W-A;Alias=BOL1
-chrI	SGD	CDS	57950	58462	.	-	.	ID=YAL044C;Name=YAL044C;Alias=GCV3
-chrI	SGD	CDS	58695	61052	.	-	.	ID=YAL043C;Name=YAL043C;Alias=PTA1
-chrI	SGD	CDS	61316	62563	.	+	.	ID=YAL042W;Name=YAL042W;Alias=ERV46
-chrI	SGD	CDS	62840	65404	.	+	.	ID=YAL041W;Name=YAL041W;Alias=CDC24
-chrI	SGD	CDS	65778	67520	.	-	.	ID=YAL040C;Name=YAL040C;Alias=CLN3
-chrI	SGD	CDS	68716	69525	.	-	.	ID=YAL039C;Name=YAL039C;Alias=CYC3
-chrI	SGD	CDS	71786	73288	.	+	.	ID=YAL038W;Name=YAL038W;Alias=CDC19
-chrI	SGD	CDS	73426	73518	.	-	.	ID=YAL037C-A;Name=YAL037C-A;Alias=
-chrI	SGD	CDS	74020	74823	.	+	.	ID=YAL037W;Name=YAL037W;Alias=
-chrI	SGD	CDS	75043	76152	.	-	.	ID=YAL036C;Name=YAL036C;Alias=RBG1
-chrI	SGD	CDS	76427	79435	.	+	.	ID=YAL035W;Name=YAL035W;Alias=FUN12
-chrI	SGD	CDS	79718	80587	.	+	.	ID=YAL034W-A;Name=YAL034W-A;Alias=MTW1
-chrI	SGD	CDS	80710	81951	.	-	.	ID=YAL034C;Name=YAL034C;Alias=FUN19
-chrI	SGD	CDS	82706	83227	.	+	.	ID=YAL033W;Name=YAL033W;Alias=POP5
-chrI	SGD	CDS	83335	84474	.	-	.	ID=YAL032C;Name=YAL032C;Alias=PRP45
-chrI	SGD	CDS	84749	87031	.	-	.	ID=YAL031C;Name=YAL031C;Alias=GIP4
-chrI	SGD	CDS	87286	87752	.	+	.	ID=YAL030W;Name=YAL030W;Alias=SNC1
-chrI	SGD	CDS	87855	92270	.	-	.	ID=YAL029C;Name=YAL029C;Alias=MYO4
-chrI	SGD	CDS	92900	94486	.	+	.	ID=YAL028W;Name=YAL028W;Alias=FRT2
-chrI	SGD	CDS	94687	95472	.	+	.	ID=YAL027W;Name=YAL027W;Alias=SAW1
-chrI	SGD	CDS	95630	99697	.	-	.	ID=YAL026C;Name=YAL026C;Alias=DRS2
-chrI	SGD	CDS	100225	101145	.	-	.	ID=YAL025C;Name=YAL025C;Alias=MAK16
-chrI	SGD	CDS	101565	105872	.	-	.	ID=YAL024C;Name=YAL024C;Alias=LTE1
-chrI	SGD	CDS	106272	108551	.	-	.	ID=YAL023C;Name=YAL023C;Alias=PMT2
-chrI	SGD	CDS	108877	110430	.	-	.	ID=YAL022C;Name=YAL022C;Alias=FUN26
-chrI	SGD	CDS	110846	113359	.	-	.	ID=YAL021C;Name=YAL021C;Alias=CCR4
-chrI	SGD	CDS	113614	114615	.	-	.	ID=YAL020C;Name=YAL020C;Alias=ATS1
-chrI	SGD	CDS	114919	118314	.	+	.	ID=YAL019W;Name=YAL019W;Alias=FUN30
-chrI	SGD	CDS	118564	119541	.	-	.	ID=YAL018C;Name=YAL018C;Alias=LDS1
-chrI	SGD	CDS	120225	124295	.	+	.	ID=YAL017W;Name=YAL017W;Alias=PSK1
-chrI	SGD	CDS	124879	126786	.	+	.	ID=YAL016W;Name=YAL016W;Alias=TPD3
-chrI	SGD	CDS	126903	128102	.	-	.	ID=YAL015C;Name=YAL015C;Alias=NTG1
-chrI	SGD	CDS	128252	129019	.	-	.	ID=YAL014C;Name=YAL014C;Alias=SYN8
-chrI	SGD	CDS	129270	130487	.	+	.	ID=YAL013W;Name=YAL013W;Alias=DEP1
-chrI	SGD	CDS	130799	131983	.	+	.	ID=YAL012W;Name=YAL012W;Alias=CYS3
-chrI	SGD	CDS	132199	134076	.	+	.	ID=YAL011W;Name=YAL011W;Alias=SWC3
-chrI	SGD	CDS	134184	135665	.	-	.	ID=YAL010C;Name=YAL010C;Alias=MDM10
-chrI	SGD	CDS	135854	136633	.	+	.	ID=YAL009W;Name=YAL009W;Alias=SPO7
-chrI	SGD	CDS	136914	137510	.	+	.	ID=YAL008W;Name=YAL008W;Alias=FUN14
-chrI	SGD	CDS	137698	138345	.	-	.	ID=YAL007C;Name=YAL007C;Alias=ERP2
-chrI	SGD	CDS	139503	141431	.	-	.	ID=YAL005C;Name=YAL005C;Alias=SSA1
-chrI	SGD	CDS	142174	143160	.	+	.	ID=YAL003W;Name=YAL003W;Alias=EFB1
-chrI	SGD	CDS	143707	147531	.	+	.	ID=YAL002W;Name=YAL002W;Alias=VPS8
-chrI	SGD	CDS	147594	151166	.	-	.	ID=YAL001C;Name=YAL001C;Alias=TFC3
-chrI	SGD	CDS	152257	153876	.	+	.	ID=YAR002W;Name=YAR002W;Alias=NUP60
-chrI	SGD	CDS	154065	154724	.	-	.	ID=YAR002C-A;Name=YAR002C-A;Alias=ERP1
-chrI	SGD	CDS	155005	156285	.	+	.	ID=YAR003W;Name=YAR003W;Alias=SWD1
-chrI	SGD	CDS	156754	158619	.	-	.	ID=YAR007C;Name=YAR007C;Alias=RFA1
-chrI	SGD	CDS	158966	159793	.	+	.	ID=YAR008W;Name=YAR008W;Alias=SEN34
-chrI	SGD	CDS	166742	168871	.	-	.	ID=YAR014C;Name=YAR014C;Alias=BUD14
-chrI	SGD	CDS	169375	170295	.	+	.	ID=YAR015W;Name=YAR015W;Alias=ADE1
-chrI	SGD	CDS	170396	171703	.	-	.	ID=YAR018C;Name=YAR018C;Alias=KIN3
-chrI	SGD	CDS	172211	175135	.	-	.	ID=YAR019C;Name=YAR019C;Alias=CDC15
-chrI	SGD	CDS	176856	177023	.	-	.	ID=YAR020C;Name=YAR020C;Alias=PAU7
-chrI	SGD	CDS	179281	179820	.	-	.	ID=YAR023C;Name=YAR023C;Alias=
-chrI	SGD	CDS	183770	184477	.	+	.	ID=YAR027W;Name=YAR027W;Alias=UIP3
-chrI	SGD	CDS	184892	185596	.	+	.	ID=YAR028W;Name=YAR028W;Alias=
-chrI	SGD	CDS	186321	186545	.	+	.	ID=YAR029W;Name=YAR029W;Alias=
-chrI	SGD	CDS	186836	187732	.	+	.	ID=YAR031W;Name=YAR031W;Alias=PRM9
-chrI	SGD	CDS	188107	188811	.	+	.	ID=YAR033W;Name=YAR033W;Alias=MST28
-chrI	SGD	CDS	190193	192256	.	+	.	ID=YAR035W;Name=YAR035W;Alias=YAT1
-chrI	SGD	CDS	192337	192417	.	-	.	ID=YAR035C-A;Name=YAR035C-A;Alias=
-chrI	SGD	CDS	192619	196185	.	+	.	ID=YAR042W;Name=YAR042W;Alias=SWH1
-chrI	SGD	CDS	203403	208016	.	+	.	ID=YAR050W;Name=YAR050W;Alias=FLO1
-chrI	SGD	CDS	220198	220497	.	+	.	ID=YAR064W;Name=YAR064W;Alias=
-chrI	SGD	CDS	221049	221660	.	+	.	ID=YAR066W;Name=YAR066W;Alias=
-chrI	SGD	CDS	222406	222891	.	+	.	ID=YAR068W;Name=YAR068W;Alias=
-chrI	SGD	CDS	225460	226863	.	+	.	ID=YAR071W;Name=YAR071W;Alias=PHO11
-chrII	SGD	CDS	280	2658	.	-	.	ID=YBL113C;Name=YBL113C;Alias=
-chrII	SGD	CDS	2582	2899	.	-	.	ID=YBL112C;Name=YBL112C;Alias=
-chrII	SGD	CDS	2907	5009	.	-	.	ID=YBL111C;Name=YBL111C;Alias=
-chrII	SGD	CDS	7605	7733	.	-	.	ID=YBL108C-A;Name=YBL108C-A;Alias=PAU9
-chrII	SGD	CDS	9961	10551	.	-	.	ID=YBL107C;Name=YBL107C;Alias=MIX23
-chrII	SGD	CDS	10847	13879	.	-	.	ID=YBL106C;Name=YBL106C;Alias=SRO77
-chrII	SGD	CDS	14241	17696	.	-	.	ID=YBL105C;Name=YBL105C;Alias=PKC1
-chrII	SGD	CDS	18177	21293	.	-	.	ID=YBL104C;Name=YBL104C;Alias=SEA4
-chrII	SGD	CDS	22076	23536	.	-	.	ID=YBL103C;Name=YBL103C;Alias=RTG3
-chrII	SGD	CDS	24098	24745	.	+	.	ID=YBL102W;Name=YBL102W;Alias=SFT2
-chrII	SGD	CDS	24946	28299	.	-	.	ID=YBL101C;Name=YBL101C;Alias=ECM21
-chrII	SGD	CDS	28427	28546	.	+	.	ID=YBL100W-C;Name=YBL100W-C;Alias=
-chrII	SGD	CDS	37053	38690	.	+	.	ID=YBL099W;Name=YBL099W;Alias=ATP1
-chrII	SGD	CDS	39145	40527	.	+	.	ID=YBL098W;Name=YBL098W;Alias=BNA4
-chrII	SGD	CDS	40831	43095	.	+	.	ID=YBL097W;Name=YBL097W;Alias=BRN1
-chrII	SGD	CDS	43277	44089	.	+	.	ID=YBL095W;Name=YBL095W;Alias=MRX3
-chrII	SGD	CDS	44256	44918	.	-	.	ID=YBL093C;Name=YBL093C;Alias=ROX3
-chrII	SGD	CDS	45645	46370	.	+	.	ID=YBL092W;Name=YBL092W;Alias=RPL32
-chrII	SGD	CDS	46565	47180	.	-	.	ID=YBL091C-A;Name=YBL091C-A;Alias=SCS22
-chrII	SGD	CDS	47363	48628	.	-	.	ID=YBL091C;Name=YBL091C;Alias=MAP2
-chrII	SGD	CDS	48825	49358	.	+	.	ID=YBL090W;Name=YBL090W;Alias=MRP21
-chrII	SGD	CDS	49574	50953	.	+	.	ID=YBL089W;Name=YBL089W;Alias=AVT5
-chrII	SGD	CDS	51019	59382	.	-	.	ID=YBL088C;Name=YBL088C;Alias=TEL1
-chrII	SGD	CDS	59822	60739	.	-	.	ID=YBL087C;Name=YBL087C;Alias=RPL23A
-chrII	SGD	CDS	61202	62602	.	-	.	ID=YBL086C;Name=YBL086C;Alias=
-chrII	SGD	CDS	63876	66818	.	+	.	ID=YBL085W;Name=YBL085W;Alias=BOI1
-chrII	SGD	CDS	67169	69445	.	-	.	ID=YBL084C;Name=YBL084C;Alias=CDC27
-chrII	SGD	CDS	69751	71127	.	-	.	ID=YBL082C;Name=YBL082C;Alias=ALG3
-chrII	SGD	CDS	71866	72972	.	+	.	ID=YBL081W;Name=YBL081W;Alias=
-chrII	SGD	CDS	73070	74695	.	-	.	ID=YBL080C;Name=YBL080C;Alias=PET112
-chrII	SGD	CDS	75259	79767	.	+	.	ID=YBL079W;Name=YBL079W;Alias=NUP170
-chrII	SGD	CDS	80378	80731	.	-	.	ID=YBL078C;Name=YBL078C;Alias=ATG8
-chrII	SGD	CDS	81043	84261	.	-	.	ID=YBL076C;Name=YBL076C;Alias=ILS1
-chrII	SGD	CDS	84499	86448	.	-	.	ID=YBL075C;Name=YBL075C;Alias=SSA3
-chrII	SGD	CDS	86722	87789	.	-	.	ID=YBL074C;Name=YBL074C;Alias=AAR2
-chrII	SGD	CDS	88523	89440	.	-	.	ID=YBL072C;Name=YBL072C;Alias=RPS8A
-chrII	SGD	CDS	89458	89556	.	-	.	ID=YBL071C-B;Name=YBL071C-B;Alias=
-chrII	SGD	CDS	89978	90226	.	+	.	ID=YBL071W-A;Name=YBL071W-A;Alias=KTI11
-chrII	SGD	CDS	90741	92030	.	+	.	ID=YBL069W;Name=YBL069W;Alias=AST1
-chrII	SGD	CDS	92414	93394	.	+	.	ID=YBL068W;Name=YBL068W;Alias=PRS4
-chrII	SGD	CDS	93639	95882	.	-	.	ID=YBL067C;Name=YBL067C;Alias=UBP13
-chrII	SGD	CDS	96669	100115	.	-	.	ID=YBL066C;Name=YBL066C;Alias=SEF1
-chrII	SGD	CDS	100371	101156	.	-	.	ID=YBL064C;Name=YBL064C;Alias=PRX1
-chrII	SGD	CDS	101886	105221	.	+	.	ID=YBL063W;Name=YBL063W;Alias=KIP1
-chrII	SGD	CDS	105316	107406	.	-	.	ID=YBL061C;Name=YBL061C;Alias=SKT5
-chrII	SGD	CDS	107932	109995	.	+	.	ID=YBL060W;Name=YBL060W;Alias=YEL1
-chrII	SGD	CDS	110125	110539	.	-	.	ID=YBL059C-A;Name=YBL059C-A;Alias=CMC2
-chrII	SGD	CDS	110594	111244	.	+	.	ID=YBL059W;Name=YBL059W;Alias=
-chrII	SGD	CDS	111437	112708	.	+	.	ID=YBL058W;Name=YBL058W;Alias=SHP1
-chrII	SGD	CDS	112801	113427	.	-	.	ID=YBL057C;Name=YBL057C;Alias=PTH2
-chrII	SGD	CDS	113762	115168	.	+	.	ID=YBL056W;Name=YBL056W;Alias=PTC3
-chrII	SGD	CDS	115573	116829	.	-	.	ID=YBL055C;Name=YBL055C;Alias=
-chrII	SGD	CDS	117589	119166	.	+	.	ID=YBL054W;Name=YBL054W;Alias=TOD6
-chrII	SGD	CDS	119379	121874	.	-	.	ID=YBL052C;Name=YBL052C;Alias=SAS3
-chrII	SGD	CDS	122753	124759	.	-	.	ID=YBL051C;Name=YBL051C;Alias=PIN4
-chrII	SGD	CDS	125125	126119	.	+	.	ID=YBL050W;Name=YBL050W;Alias=SEC17
-chrII	SGD	CDS	126828	127244	.	+	.	ID=YBL049W;Name=YBL049W;Alias=MOH1
-chrII	SGD	CDS	127895	132040	.	-	.	ID=YBL047C;Name=YBL047C;Alias=EDE1
-chrII	SGD	CDS	132424	133749	.	+	.	ID=YBL046W;Name=YBL046W;Alias=PSY4
-chrII	SGD	CDS	134143	135516	.	-	.	ID=YBL045C;Name=YBL045C;Alias=COR1
-chrII	SGD	CDS	135998	136366	.	+	.	ID=YBL044W;Name=YBL044W;Alias=
-chrII	SGD	CDS	136688	137461	.	+	.	ID=YBL043W;Name=YBL043W;Alias=ECM13
-chrII	SGD	CDS	138341	140260	.	-	.	ID=YBL042C;Name=YBL042C;Alias=FUI1
-chrII	SGD	CDS	141247	141972	.	+	.	ID=YBL041W;Name=YBL041W;Alias=PRE7
-chrII	SGD	CDS	142112	142868	.	-	.	ID=YBL040C;Name=YBL040C;Alias=ERD2
-chrII	SGD	CDS	143393	143572	.	+	.	ID=YBL039W-B;Name=YBL039W-B;Alias=
-chrII	SGD	CDS	143989	145728	.	-	.	ID=YBL039C;Name=YBL039C;Alias=URA7
-chrII	SGD	CDS	146187	146885	.	+	.	ID=YBL038W;Name=YBL038W;Alias=MRPL16
-chrII	SGD	CDS	147209	150286	.	+	.	ID=YBL037W;Name=YBL037W;Alias=APL3
-chrII	SGD	CDS	150447	151220	.	-	.	ID=YBL036C;Name=YBL036C;Alias=
-chrII	SGD	CDS	151493	153610	.	-	.	ID=YBL035C;Name=YBL035C;Alias=POL12
-chrII	SGD	CDS	153848	158389	.	-	.	ID=YBL034C;Name=YBL034C;Alias=STU1
-chrII	SGD	CDS	158656	159693	.	-	.	ID=YBL033C;Name=YBL033C;Alias=RIB1
-chrII	SGD	CDS	160184	161329	.	+	.	ID=YBL032W;Name=YBL032W;Alias=HEK2
-chrII	SGD	CDS	161699	162715	.	+	.	ID=YBL031W;Name=YBL031W;Alias=SHE1
-chrII	SGD	CDS	163041	163997	.	-	.	ID=YBL030C;Name=YBL030C;Alias=PET9
-chrII	SGD	CDS	164488	164772	.	-	.	ID=YBL029C-A;Name=YBL029C-A;Alias=
-chrII	SGD	CDS	166134	167264	.	+	.	ID=YBL029W;Name=YBL029W;Alias=
-chrII	SGD	CDS	167518	167838	.	-	.	ID=YBL028C;Name=YBL028C;Alias=
-chrII	SGD	CDS	168423	169376	.	+	.	ID=YBL027W;Name=YBL027W;Alias=RPL19B
-chrII	SGD	CDS	170623	171038	.	+	.	ID=YBL026W;Name=YBL026W;Alias=LSM2
-chrII	SGD	CDS	171481	171918	.	+	.	ID=YBL025W;Name=YBL025W;Alias=RRN10
-chrII	SGD	CDS	172534	174588	.	+	.	ID=YBL024W;Name=YBL024W;Alias=NCL1
-chrII	SGD	CDS	174920	177526	.	-	.	ID=YBL023C;Name=YBL023C;Alias=MCM2
-chrII	SGD	CDS	177874	181275	.	-	.	ID=YBL022C;Name=YBL022C;Alias=PIM1
-chrII	SGD	CDS	181660	182094	.	-	.	ID=YBL021C;Name=YBL021C;Alias=HAP3
-chrII	SGD	CDS	182401	184125	.	+	.	ID=YBL020W;Name=YBL020W;Alias=RFT1
-chrII	SGD	CDS	184353	185915	.	+	.	ID=YBL019W;Name=YBL019W;Alias=APN2
-chrII	SGD	CDS	185998	186474	.	-	.	ID=YBL018C;Name=YBL018C;Alias=POP8
-chrII	SGD	CDS	186844	191583	.	-	.	ID=YBL017C;Name=YBL017C;Alias=PEP1
-chrII	SGD	CDS	192451	193512	.	+	.	ID=YBL016W;Name=YBL016W;Alias=FUS3
-chrII	SGD	CDS	194122	195702	.	+	.	ID=YBL015W;Name=YBL015W;Alias=ACH1
-chrII	SGD	CDS	199064	201748	.	-	.	ID=YBL014C;Name=YBL014C;Alias=RRN6
-chrII	SGD	CDS	202056	203261	.	+	.	ID=YBL013W;Name=YBL013W;Alias=FMT1
-chrII	SGD	CDS	203538	205817	.	+	.	ID=YBL011W;Name=YBL011W;Alias=SCT1
-chrII	SGD	CDS	206107	206949	.	-	.	ID=YBL010C;Name=YBL010C;Alias=
-chrII	SGD	CDS	207194	209224	.	+	.	ID=YBL009W;Name=YBL009W;Alias=ALK2
-chrII	SGD	CDS	209409	209648	.	+	.	ID=YBL008W-A;Name=YBL008W-A;Alias=
-chrII	SGD	CDS	209653	212175	.	+	.	ID=YBL008W;Name=YBL008W;Alias=HIR1
-chrII	SGD	CDS	212632	216366	.	-	.	ID=YBL007C;Name=YBL007C;Alias=SLA1
-chrII	SGD	CDS	216587	217129	.	-	.	ID=YBL006C;Name=YBL006C;Alias=LDB7
-chrII	SGD	CDS	217470	220400	.	+	.	ID=YBL005W;Name=YBL005W;Alias=PDR3
-chrII	SGD	CDS	227636	235117	.	+	.	ID=YBL004W;Name=YBL004W;Alias=UTP20
-chrII	SGD	CDS	235394	235792	.	-	.	ID=YBL003C;Name=YBL003C;Alias=HTA2
-chrII	SGD	CDS	236492	236887	.	+	.	ID=YBL002W;Name=YBL002W;Alias=HTB2
-chrII	SGD	CDS	237153	237467	.	-	.	ID=YBL001C;Name=YBL001C;Alias=ECM15
-chrII	SGD	CDS	238941	241283	.	-	.	ID=YBR001C;Name=YBR001C;Alias=NTH2
-chrII	SGD	CDS	241708	242568	.	-	.	ID=YBR002C;Name=YBR002C;Alias=RER2
-chrII	SGD	CDS	242809	244230	.	+	.	ID=YBR003W;Name=YBR003W;Alias=COQ1
-chrII	SGD	CDS	244366	245667	.	-	.	ID=YBR004C;Name=YBR004C;Alias=GPI18
-chrII	SGD	CDS	245906	246547	.	+	.	ID=YBR005W;Name=YBR005W;Alias=RCR1
-chrII	SGD	CDS	247010	248503	.	+	.	ID=YBR006W;Name=YBR006W;Alias=UGA2
-chrII	SGD	CDS	248806	251016	.	-	.	ID=YBR007C;Name=YBR007C;Alias=DSF2
-chrII	SGD	CDS	252563	254209	.	-	.	ID=YBR008C;Name=YBR008C;Alias=FLR1
-chrII	SGD	CDS	255373	255684	.	-	.	ID=YBR009C;Name=YBR009C;Alias=HHF1
-chrII	SGD	CDS	256331	256741	.	+	.	ID=YBR010W;Name=YBR010W;Alias=HHT1
-chrII	SGD	CDS	257112	257975	.	-	.	ID=YBR011C;Name=YBR011C;Alias=IPP1
-chrII	SGD	CDS	265492	265881	.	-	.	ID=YBR013C;Name=YBR013C;Alias=
-chrII	SGD	CDS	266725	267336	.	-	.	ID=YBR014C;Name=YBR014C;Alias=GRX7
-chrII	SGD	CDS	267710	269503	.	-	.	ID=YBR015C;Name=YBR015C;Alias=MNN2
-chrII	SGD	CDS	270247	270633	.	+	.	ID=YBR016W;Name=YBR016W;Alias=
-chrII	SGD	CDS	270947	273703	.	-	.	ID=YBR017C;Name=YBR017C;Alias=KAP104
-chrII	SGD	CDS	274427	275527	.	-	.	ID=YBR018C;Name=YBR018C;Alias=GAL7
-chrII	SGD	CDS	276253	278352	.	-	.	ID=YBR019C;Name=YBR019C;Alias=GAL10
-chrII	SGD	CDS	279021	280607	.	+	.	ID=YBR020W;Name=YBR020W;Alias=GAL1
-chrII	SGD	CDS	281443	283344	.	+	.	ID=YBR021W;Name=YBR021W;Alias=FUR4
-chrII	SGD	CDS	283738	284271	.	+	.	ID=YBR022W;Name=YBR022W;Alias=POA1
-chrII	SGD	CDS	284428	287925	.	-	.	ID=YBR023C;Name=YBR023C;Alias=CHS3
-chrII	SGD	CDS	289445	290350	.	+	.	ID=YBR024W;Name=YBR024W;Alias=SCO2
-chrII	SGD	CDS	290681	291865	.	-	.	ID=YBR025C;Name=YBR025C;Alias=OLA1
-chrII	SGD	CDS	292877	294019	.	-	.	ID=YBR026C;Name=YBR026C;Alias=ETR1
-chrII	SGD	CDS	294425	296002	.	-	.	ID=YBR028C;Name=YBR028C;Alias=YPK3
-chrII	SGD	CDS	296369	297742	.	-	.	ID=YBR029C;Name=YBR029C;Alias=CDS1
-chrII	SGD	CDS	298292	299950	.	+	.	ID=YBR030W;Name=YBR030W;Alias=RKM3
-chrII	SGD	CDS	300166	301254	.	+	.	ID=YBR031W;Name=YBR031W;Alias=RPL4A
-chrII	SGD	CDS	301944	304703	.	+	.	ID=YBR033W;Name=YBR033W;Alias=EDS1
-chrII	SGD	CDS	304930	305976	.	-	.	ID=YBR034C;Name=YBR034C;Alias=HMT1
-chrII	SGD	CDS	306269	306955	.	-	.	ID=YBR035C;Name=YBR035C;Alias=PDX3
-chrII	SGD	CDS	309081	310313	.	-	.	ID=YBR036C;Name=YBR036C;Alias=CSG2
-chrII	SGD	CDS	310565	311452	.	-	.	ID=YBR037C;Name=YBR037C;Alias=SCO1
-chrII	SGD	CDS	311898	314789	.	+	.	ID=YBR038W;Name=YBR038W;Alias=CHS2
-chrII	SGD	CDS	315575	316510	.	+	.	ID=YBR039W;Name=YBR039W;Alias=ATP3
-chrII	SGD	CDS	316968	317864	.	+	.	ID=YBR040W;Name=YBR040W;Alias=FIG1
-chrII	SGD	CDS	318266	320275	.	+	.	ID=YBR041W;Name=YBR041W;Alias=FAT1
-chrII	SGD	CDS	320416	321609	.	-	.	ID=YBR042C;Name=YBR042C;Alias=CST26
-chrII	SGD	CDS	321876	323945	.	-	.	ID=YBR043C;Name=YBR043C;Alias=QDR3
-chrII	SGD	CDS	324341	326059	.	-	.	ID=YBR044C;Name=YBR044C;Alias=TCM62
-chrII	SGD	CDS	328173	330092	.	-	.	ID=YBR045C;Name=YBR045C;Alias=GIP1
-chrII	SGD	CDS	330507	331511	.	-	.	ID=YBR046C;Name=YBR046C;Alias=ZTA1
-chrII	SGD	CDS	331833	332360	.	+	.	ID=YBR047W;Name=YBR047W;Alias=FMP23
-chrII	SGD	CDS	332831	333812	.	+	.	ID=YBR048W;Name=YBR048W;Alias=RPS11B
-chrII	SGD	CDS	334386	336818	.	-	.	ID=YBR049C;Name=YBR049C;Alias=REB1
-chrII	SGD	CDS	337183	338199	.	-	.	ID=YBR050C;Name=YBR050C;Alias=REG2
-chrII	SGD	CDS	338720	339352	.	-	.	ID=YBR052C;Name=YBR052C;Alias=RFS1
-chrII	SGD	CDS	339675	340751	.	-	.	ID=YBR053C;Name=YBR053C;Alias=
-chrII	SGD	CDS	343101	344135	.	+	.	ID=YBR054W;Name=YBR054W;Alias=YRO2
-chrII	SGD	CDS	344602	347301	.	-	.	ID=YBR055C;Name=YBR055C;Alias=PRP6
-chrII	SGD	CDS	347879	349384	.	+	.	ID=YBR056W;Name=YBR056W;Alias=
-chrII	SGD	CDS	351255	351455	.	+	.	ID=YBR056W-A;Name=YBR056W-A;Alias=
-chrII	SGD	CDS	352193	353293	.	-	.	ID=YBR057C;Name=YBR057C;Alias=MUM2
-chrII	SGD	CDS	353672	356017	.	-	.	ID=YBR058C;Name=YBR058C;Alias=UBP14
-chrII	SGD	CDS	356324	356566	.	-	.	ID=YBR058C-A;Name=YBR058C-A;Alias=TSC3
-chrII	SGD	CDS	356861	360187	.	-	.	ID=YBR059C;Name=YBR059C;Alias=AKL1
-chrII	SGD	CDS	360652	362514	.	-	.	ID=YBR060C;Name=YBR060C;Alias=ORC2
-chrII	SGD	CDS	364787	365719	.	-	.	ID=YBR061C;Name=YBR061C;Alias=TRM7
-chrII	SGD	CDS	365976	366600	.	-	.	ID=YBR062C;Name=YBR062C;Alias=
-chrII	SGD	CDS	366970	368184	.	-	.	ID=YBR063C;Name=YBR063C;Alias=
-chrII	SGD	CDS	368584	369678	.	-	.	ID=YBR065C;Name=YBR065C;Alias=ECM2
-chrII	SGD	CDS	370037	370699	.	-	.	ID=YBR066C;Name=YBR066C;Alias=NRG2
-chrII	SGD	CDS	372103	372735	.	-	.	ID=YBR067C;Name=YBR067C;Alias=TIP1
-chrII	SGD	CDS	373861	375690	.	-	.	ID=YBR068C;Name=YBR068C;Alias=BAP2
-chrII	SGD	CDS	376574	378433	.	-	.	ID=YBR069C;Name=YBR069C;Alias=TAT1
-chrII	SGD	CDS	379221	379934	.	-	.	ID=YBR070C;Name=YBR070C;Alias=ALG14
-chrII	SGD	CDS	380411	381046	.	+	.	ID=YBR071W;Name=YBR071W;Alias=
-chrII	SGD	CDS	382030	382674	.	+	.	ID=YBR072W;Name=YBR072W;Alias=HSP26
-chrII	SGD	CDS	382860	383021	.	-	.	ID=YBR072C-A;Name=YBR072C-A;Alias=
-chrII	SGD	CDS	383112	385988	.	+	.	ID=YBR073W;Name=YBR073W;Alias=RDH54
-chrII	SGD	CDS	386286	389216	.	+	.	ID=YBR074W;Name=YBR074W;Alias=PFF1
-chrII	SGD	CDS	390227	391291	.	+	.	ID=YBR076W;Name=YBR076W;Alias=ECM8
-chrII	SGD	CDS	391805	392293	.	-	.	ID=YBR077C;Name=YBR077C;Alias=SLM4
-chrII	SGD	CDS	393123	394742	.	+	.	ID=YBR078W;Name=YBR078W;Alias=ECM33
-chrII	SGD	CDS	395383	398277	.	-	.	ID=YBR079C;Name=YBR079C;Alias=RPG1
-chrII	SGD	CDS	398614	400890	.	-	.	ID=YBR080C;Name=YBR080C;Alias=SEC18
-chrII	SGD	CDS	401253	405251	.	-	.	ID=YBR081C;Name=YBR081C;Alias=SPT7
-chrII	SGD	CDS	406628	407169	.	-	.	ID=YBR082C;Name=YBR082C;Alias=UBC4
-chrII	SGD	CDS	409169	410629	.	+	.	ID=YBR083W;Name=YBR083W;Alias=TEC1
-chrII	SGD	CDS	411054	413981	.	+	.	ID=YBR084W;Name=YBR084W;Alias=MIS1
-chrII	SGD	CDS	414186	415261	.	-	.	ID=YBR084C-A;Name=YBR084C-A;Alias=RPL19A
-chrII	SGD	CDS	415983	416906	.	+	.	ID=YBR085W;Name=YBR085W;Alias=AAC3
-chrII	SGD	CDS	418907	419164	.	-	.	ID=YBR085C-A;Name=YBR085C-A;Alias=
-chrII	SGD	CDS	420201	423041	.	-	.	ID=YBR086C;Name=YBR086C;Alias=IST2
-chrII	SGD	CDS	423765	424829	.	+	.	ID=YBR087W;Name=YBR087W;Alias=RFC5
-chrII	SGD	CDS	424990	425766	.	-	.	ID=YBR088C;Name=YBR088C;Alias=POL30
-chrII	SGD	CDS	426190	426873	.	-	.	ID=YBR089C-A;Name=YBR089C-A;Alias=NHP6B
-chrII	SGD	CDS	426333	427058	.	-	.	ID=YBR090C;Name=YBR090C;Alias=
-chrII	SGD	CDS	427155	427484	.	-	.	ID=YBR091C;Name=YBR091C;Alias=TIM12
-chrII	SGD	CDS	427698	429101	.	-	.	ID=YBR092C;Name=YBR092C;Alias=PHO3
-chrII	SGD	CDS	429548	430951	.	-	.	ID=YBR093C;Name=YBR093C;Alias=PHO5
-chrII	SGD	CDS	432036	434297	.	+	.	ID=YBR094W;Name=YBR094W;Alias=PBY1
-chrII	SGD	CDS	434406	435698	.	-	.	ID=YBR095C;Name=YBR095C;Alias=RXT2
-chrII	SGD	CDS	436021	436713	.	+	.	ID=YBR096W;Name=YBR096W;Alias=
-chrII	SGD	CDS	436951	441315	.	+	.	ID=YBR097W;Name=YBR097W;Alias=VPS15
-chrII	SGD	CDS	441515	443590	.	+	.	ID=YBR098W;Name=YBR098W;Alias=MMS4
-chrII	SGD	CDS	443821	444693	.	-	.	ID=YBR101C;Name=YBR101C;Alias=FES1
-chrII	SGD	CDS	445062	447323	.	-	.	ID=YBR102C;Name=YBR102C;Alias=EXO84
-chrII	SGD	CDS	447709	449316	.	+	.	ID=YBR103W;Name=YBR103W;Alias=SIF2
-chrII	SGD	CDS	449667	450656	.	+	.	ID=YBR104W;Name=YBR104W;Alias=YMC2
-chrII	SGD	CDS	450881	451969	.	-	.	ID=YBR105C;Name=YBR105C;Alias=VID24
-chrII	SGD	CDS	452658	453224	.	+	.	ID=YBR106W;Name=YBR106W;Alias=PHO88
-chrII	SGD	CDS	453793	454530	.	-	.	ID=YBR107C;Name=YBR107C;Alias=IML3
-chrII	SGD	CDS	454822	457665	.	+	.	ID=YBR108W;Name=YBR108W;Alias=AIM3
-chrII	SGD	CDS	457919	458362	.	-	.	ID=YBR109C;Name=YBR109C;Alias=CMD1
-chrII	SGD	CDS	458872	460221	.	+	.	ID=YBR110W;Name=YBR110W;Alias=ALG1
-chrII	SGD	CDS	461178	461873	.	-	.	ID=YBR111C;Name=YBR111C;Alias=YSA1
-chrII	SGD	CDS	462139	462579	.	+	.	ID=YBR111W-A;Name=YBR111W-A;Alias=SUS1
-chrII	SGD	CDS	462870	465770	.	-	.	ID=YBR112C;Name=YBR112C;Alias=CYC8
-chrII	SGD	CDS	467248	469620	.	+	.	ID=YBR114W;Name=YBR114W;Alias=RAD16
-chrII	SGD	CDS	469748	473926	.	-	.	ID=YBR115C;Name=YBR115C;Alias=LYS2
-chrII	SGD	CDS	474392	476437	.	-	.	ID=YBR117C;Name=YBR117C;Alias=TKL2
-chrII	SGD	CDS	477671	479047	.	+	.	ID=YBR118W;Name=YBR118W;Alias=TEF2
-chrII	SGD	CDS	479338	480323	.	+	.	ID=YBR119W;Name=YBR119W;Alias=MUD1
-chrII	SGD	CDS	480435	480923	.	-	.	ID=YBR120C;Name=YBR120C;Alias=CBP6
-chrII	SGD	CDS	481364	483367	.	-	.	ID=YBR121C;Name=YBR121C;Alias=GRS1
-chrII	SGD	CDS	483970	484503	.	-	.	ID=YBR122C;Name=YBR122C;Alias=MRPL36
-chrII	SGD	CDS	484742	486691	.	-	.	ID=YBR123C;Name=YBR123C;Alias=TFC1
-chrII	SGD	CDS	487199	488380	.	-	.	ID=YBR125C;Name=YBR125C;Alias=PTC4
-chrII	SGD	CDS	488905	490392	.	-	.	ID=YBR126C;Name=YBR126C;Alias=TPS1
-chrII	SGD	CDS	490850	491056	.	+	.	ID=YBR126W-A;Name=YBR126W-A;Alias=MEO1
-chrII	SGD	CDS	491269	492822	.	-	.	ID=YBR127C;Name=YBR127C;Alias=VMA2
-chrII	SGD	CDS	493081	494115	.	-	.	ID=YBR128C;Name=YBR128C;Alias=ATG14
-chrII	SGD	CDS	494353	495339	.	-	.	ID=YBR129C;Name=YBR129C;Alias=OPY1
-chrII	SGD	CDS	495592	496869	.	-	.	ID=YBR130C;Name=YBR130C;Alias=SHE3
-chrII	SGD	CDS	497163	499277	.	+	.	ID=YBR131W;Name=YBR131W;Alias=CCZ1
-chrII	SGD	CDS	499652	501442	.	-	.	ID=YBR132C;Name=YBR132C;Alias=AGP2
-chrII	SGD	CDS	501804	504287	.	-	.	ID=YBR133C;Name=YBR133C;Alias=HSL7
-chrII	SGD	CDS	504854	505306	.	+	.	ID=YBR135W;Name=YBR135W;Alias=CKS1
-chrII	SGD	CDS	505668	512774	.	+	.	ID=YBR136W;Name=YBR136W;Alias=MEC1
-chrII	SGD	CDS	513044	513583	.	+	.	ID=YBR137W;Name=YBR137W;Alias=
-chrII	SGD	CDS	513762	515336	.	-	.	ID=YBR138C;Name=YBR138C;Alias=
-chrII	SGD	CDS	515664	517190	.	+	.	ID=YBR139W;Name=YBR139W;Alias=
-chrII	SGD	CDS	517350	526628	.	-	.	ID=YBR140C;Name=YBR140C;Alias=IRA1
-chrII	SGD	CDS	527025	528038	.	-	.	ID=YBR141C;Name=YBR141C;Alias=BMT2
-chrII	SGD	CDS	528317	530638	.	+	.	ID=YBR142W;Name=YBR142W;Alias=MAK5
-chrII	SGD	CDS	530869	532182	.	-	.	ID=YBR143C;Name=YBR143C;Alias=SUP45
-chrII	SGD	CDS	533762	534817	.	+	.	ID=YBR145W;Name=YBR145W;Alias=ADH5
-chrII	SGD	CDS	535260	536096	.	+	.	ID=YBR146W;Name=YBR146W;Alias=MRPS9
-chrII	SGD	CDS	536575	537465	.	+	.	ID=YBR147W;Name=YBR147W;Alias=RTC2
-chrII	SGD	CDS	537876	539705	.	+	.	ID=YBR148W;Name=YBR148W;Alias=YSW1
-chrII	SGD	CDS	539987	541021	.	+	.	ID=YBR149W;Name=YBR149W;Alias=ARA1
-chrII	SGD	CDS	541209	544493	.	-	.	ID=YBR150C;Name=YBR150C;Alias=TBS1
-chrII	SGD	CDS	545028	545978	.	+	.	ID=YBR151W;Name=YBR151W;Alias=APD1
-chrII	SGD	CDS	546376	547251	.	+	.	ID=YBR152W;Name=YBR152W;Alias=SPP381
-chrII	SGD	CDS	547460	548194	.	+	.	ID=YBR153W;Name=YBR153W;Alias=RIB7
-chrII	SGD	CDS	548362	549009	.	-	.	ID=YBR154C;Name=YBR154C;Alias=RPB5
-chrII	SGD	CDS	549771	550928	.	+	.	ID=YBR155W;Name=YBR155W;Alias=CNS1
-chrII	SGD	CDS	551104	553200	.	-	.	ID=YBR156C;Name=YBR156C;Alias=SLI15
-chrII	SGD	CDS	553543	554310	.	-	.	ID=YBR157C;Name=YBR157C;Alias=ICS2
-chrII	SGD	CDS	556549	558198	.	+	.	ID=YBR158W;Name=YBR158W;Alias=AMN1
-chrII	SGD	CDS	558685	559728	.	+	.	ID=YBR159W;Name=YBR159W;Alias=IFA38
-chrII	SGD	CDS	560078	560974	.	+	.	ID=YBR160W;Name=YBR160W;Alias=CDC28
-chrII	SGD	CDS	561634	562764	.	+	.	ID=YBR161W;Name=YBR161W;Alias=CSH1
-chrII	SGD	CDS	563203	564570	.	-	.	ID=YBR162C;Name=YBR162C;Alias=TOS1
-chrII	SGD	CDS	565231	565428	.	+	.	ID=YBR162W-A;Name=YBR162W-A;Alias=YSY6
-chrII	SGD	CDS	565723	567480	.	+	.	ID=YBR163W;Name=YBR163W;Alias=EXO5
-chrII	SGD	CDS	567875	568426	.	-	.	ID=YBR164C;Name=YBR164C;Alias=ARL1
-chrII	SGD	CDS	568852	569685	.	+	.	ID=YBR165W;Name=YBR165W;Alias=UBS1
-chrII	SGD	CDS	569842	571200	.	-	.	ID=YBR166C;Name=YBR166C;Alias=TYR1
-chrII	SGD	CDS	571468	571890	.	-	.	ID=YBR167C;Name=YBR167C;Alias=POP7
-chrII	SGD	CDS	572371	573612	.	+	.	ID=YBR168W;Name=YBR168W;Alias=PEX32
-chrII	SGD	CDS	573915	575996	.	-	.	ID=YBR169C;Name=YBR169C;Alias=SSE2
-chrII	SGD	CDS	576344	578086	.	-	.	ID=YBR170C;Name=YBR170C;Alias=NPL4
-chrII	SGD	CDS	578364	578984	.	+	.	ID=YBR171W;Name=YBR171W;Alias=SEC66
-chrII	SGD	CDS	579150	581372	.	-	.	ID=YBR172C;Name=YBR172C;Alias=SMY2
-chrII	SGD	CDS	581726	582172	.	-	.	ID=YBR173C;Name=YBR173C;Alias=UMP1
-chrII	SGD	CDS	582408	583355	.	+	.	ID=YBR175W;Name=YBR175W;Alias=SWD3
-chrII	SGD	CDS	583720	584658	.	+	.	ID=YBR176W;Name=YBR176W;Alias=ECM31
-chrII	SGD	CDS	584807	586162	.	-	.	ID=YBR177C;Name=YBR177C;Alias=EHT1
-chrII	SGD	CDS	586547	589114	.	-	.	ID=YBR179C;Name=YBR179C;Alias=FZO1
-chrII	SGD	CDS	589741	591459	.	+	.	ID=YBR180W;Name=YBR180W;Alias=DTR1
-chrII	SGD	CDS	591712	592774	.	-	.	ID=YBR181C;Name=YBR181C;Alias=RPS6B
-chrII	SGD	CDS	593506	594864	.	-	.	ID=YBR182C;Name=YBR182C;Alias=SMP1
-chrII	SGD	CDS	595361	595555	.	-	.	ID=YBR182C-A;Name=YBR182C-A;Alias=
-chrII	SGD	CDS	596115	597065	.	+	.	ID=YBR183W;Name=YBR183W;Alias=YPC1
-chrII	SGD	CDS	597363	598934	.	+	.	ID=YBR184W;Name=YBR184W;Alias=
-chrII	SGD	CDS	599123	599959	.	-	.	ID=YBR185C;Name=YBR185C;Alias=MBA1
-chrII	SGD	CDS	600553	602360	.	+	.	ID=YBR186W;Name=YBR186W;Alias=PCH2
-chrII	SGD	CDS	602634	603476	.	+	.	ID=YBR187W;Name=YBR187W;Alias=GDT1
-chrII	SGD	CDS	603685	604107	.	-	.	ID=YBR188C;Name=YBR188C;Alias=NTC20
-chrII	SGD	CDS	604508	605508	.	+	.	ID=YBR189W;Name=YBR189W;Alias=RPS9B
-chrII	SGD	CDS	606270	607140	.	+	.	ID=YBR191W;Name=YBR191W;Alias=RPL21A
-chrII	SGD	CDS	607652	608785	.	+	.	ID=YBR192W;Name=YBR192W;Alias=RIM2
-chrII	SGD	CDS	609082	609753	.	-	.	ID=YBR193C;Name=YBR193C;Alias=MED8
-chrII	SGD	CDS	610038	610409	.	+	.	ID=YBR194W;Name=YBR194W;Alias=AIM4
-chrII	SGD	CDS	610614	611882	.	-	.	ID=YBR195C;Name=YBR195C;Alias=MSI1
-chrII	SGD	CDS	612236	613900	.	-	.	ID=YBR196C;Name=YBR196C;Alias=PGI1
-chrII	SGD	CDS	614024	614173	.	-	.	ID=YBR196C-A;Name=YBR196C-A;Alias=
-chrII	SGD	CDS	614526	614630	.	-	.	ID=YBR196C-B;Name=YBR196C-B;Alias=
-chrII	SGD	CDS	615203	615856	.	-	.	ID=YBR197C;Name=YBR197C;Alias=
-chrII	SGD	CDS	616127	618523	.	-	.	ID=YBR198C;Name=YBR198C;Alias=TAF5
-chrII	SGD	CDS	618909	620303	.	+	.	ID=YBR199W;Name=YBR199W;Alias=KTR4
-chrII	SGD	CDS	620872	622527	.	+	.	ID=YBR200W;Name=YBR200W;Alias=BEM1
-chrII	SGD	CDS	622983	623147	.	+	.	ID=YBR200W-A;Name=YBR200W-A;Alias=
-chrII	SGD	CDS	623576	624211	.	+	.	ID=YBR201W;Name=YBR201W;Alias=DER1
-chrII	SGD	CDS	624493	624696	.	-	.	ID=YBR201C-A;Name=YBR201C-A;Alias=
-chrII	SGD	CDS	625772	628309	.	+	.	ID=YBR202W;Name=YBR202W;Alias=MCM7
-chrII	SGD	CDS	629168	631942	.	+	.	ID=YBR203W;Name=YBR203W;Alias=COS111
-chrII	SGD	CDS	632254	633381	.	-	.	ID=YBR204C;Name=YBR204C;Alias=LDH1
-chrII	SGD	CDS	633622	634836	.	+	.	ID=YBR205W;Name=YBR205W;Alias=KTR3
-chrII	SGD	CDS	635146	636543	.	+	.	ID=YBR207W;Name=YBR207W;Alias=FTH1
-chrII	SGD	CDS	636703	642210	.	-	.	ID=YBR208C;Name=YBR208C;Alias=DUR1%2C2
-chrII	SGD	CDS	645550	645978	.	+	.	ID=YBR210W;Name=YBR210W;Alias=ERV15
-chrII	SGD	CDS	646158	647132	.	-	.	ID=YBR211C;Name=YBR211C;Alias=AME1
-chrII	SGD	CDS	647886	649904	.	+	.	ID=YBR212W;Name=YBR212W;Alias=NGR1
-chrII	SGD	CDS	650368	651192	.	+	.	ID=YBR213W;Name=YBR213W;Alias=MET8
-chrII	SGD	CDS	651415	652998	.	+	.	ID=YBR214W;Name=YBR214W;Alias=SDS24
-chrII	SGD	CDS	653356	655317	.	+	.	ID=YBR215W;Name=YBR215W;Alias=HPC2
-chrII	SGD	CDS	655576	657600	.	-	.	ID=YBR216C;Name=YBR216C;Alias=YBP1
-chrII	SGD	CDS	657832	658392	.	+	.	ID=YBR217W;Name=YBR217W;Alias=ATG12
-chrII	SGD	CDS	658707	662249	.	-	.	ID=YBR218C;Name=YBR218C;Alias=PYC2
-chrII	SGD	CDS	662499	663303	.	-	.	ID=YBR219C;Name=YBR219C;Alias=
-chrII	SGD	CDS	662995	664677	.	-	.	ID=YBR220C;Name=YBR220C;Alias=
-chrII	SGD	CDS	665153	666253	.	-	.	ID=YBR221C;Name=YBR221C;Alias=PDB1
-chrII	SGD	CDS	666538	666642	.	+	.	ID=YBR221W-A;Name=YBR221W-A;Alias=
-chrII	SGD	CDS	666720	668351	.	-	.	ID=YBR222C;Name=YBR222C;Alias=PCS60
-chrII	SGD	CDS	668663	670297	.	-	.	ID=YBR223C;Name=YBR223C;Alias=TDP1
-chrII	SGD	CDS	670627	673329	.	+	.	ID=YBR225W;Name=YBR225W;Alias=
-chrII	SGD	CDS	673572	675134	.	-	.	ID=YBR227C;Name=YBR227C;Alias=MCX1
-chrII	SGD	CDS	675313	676227	.	+	.	ID=YBR228W;Name=YBR228W;Alias=SLX1
-chrII	SGD	CDS	676357	679221	.	-	.	ID=YBR229C;Name=YBR229C;Alias=ROT2
-chrII	SGD	CDS	679549	680050	.	-	.	ID=YBR230C;Name=YBR230C;Alias=OM14
-chrII	SGD	CDS	680362	680562	.	+	.	ID=YBR230W-A;Name=YBR230W-A;Alias=
-chrII	SGD	CDS	682179	683090	.	-	.	ID=YBR231C;Name=YBR231C;Alias=SWC5
-chrII	SGD	CDS	683428	684669	.	+	.	ID=YBR233W;Name=YBR233W;Alias=PBP2
-chrII	SGD	CDS	684977	685261	.	+	.	ID=YBR233W-A;Name=YBR233W-A;Alias=DAD3
-chrII	SGD	CDS	685438	686592	.	-	.	ID=YBR234C;Name=YBR234C;Alias=ARC40
-chrII	SGD	CDS	686901	690263	.	+	.	ID=YBR235W;Name=YBR235W;Alias=VHC1
-chrII	SGD	CDS	690383	691693	.	-	.	ID=YBR236C;Name=YBR236C;Alias=ABD1
-chrII	SGD	CDS	691969	694518	.	+	.	ID=YBR237W;Name=YBR237W;Alias=PRP5
-chrII	SGD	CDS	695107	697302	.	-	.	ID=YBR238C;Name=YBR238C;Alias=
-chrII	SGD	CDS	698354	699943	.	-	.	ID=YBR239C;Name=YBR239C;Alias=ERT1
-chrII	SGD	CDS	700490	701842	.	-	.	ID=YBR240C;Name=YBR240C;Alias=THI2
-chrII	SGD	CDS	702589	704055	.	-	.	ID=YBR241C;Name=YBR241C;Alias=
-chrII	SGD	CDS	704670	705386	.	+	.	ID=YBR242W;Name=YBR242W;Alias=
-chrII	SGD	CDS	705447	706793	.	-	.	ID=YBR243C;Name=YBR243C;Alias=ALG7
-chrII	SGD	CDS	707528	708016	.	+	.	ID=YBR244W;Name=YBR244W;Alias=GPX2
-chrII	SGD	CDS	708150	711539	.	-	.	ID=YBR245C;Name=YBR245C;Alias=ISW1
-chrII	SGD	CDS	711591	712754	.	+	.	ID=YBR246W;Name=YBR246W;Alias=RRT2
-chrII	SGD	CDS	713004	714455	.	-	.	ID=YBR247C;Name=YBR247C;Alias=ENP1
-chrII	SGD	CDS	714807	716465	.	-	.	ID=YBR248C;Name=YBR248C;Alias=HIS7
-chrII	SGD	CDS	716882	717994	.	-	.	ID=YBR249C;Name=YBR249C;Alias=ARO4
-chrII	SGD	CDS	719033	720604	.	+	.	ID=YBR250W;Name=YBR250W;Alias=SPO23
-chrII	SGD	CDS	721390	722313	.	+	.	ID=YBR251W;Name=YBR251W;Alias=MRPS5
-chrII	SGD	CDS	722611	723054	.	+	.	ID=YBR252W;Name=YBR252W;Alias=DUT1
-chrII	SGD	CDS	723270	723635	.	+	.	ID=YBR253W;Name=YBR253W;Alias=SRB6
-chrII	SGD	CDS	723736	724263	.	-	.	ID=YBR254C;Name=YBR254C;Alias=TRS20
-chrII	SGD	CDS	724456	726540	.	+	.	ID=YBR255W;Name=YBR255W;Alias=MTC4
-chrII	SGD	CDS	726618	727074	.	-	.	ID=YBR255C-A;Name=YBR255C-A;Alias=RCF3
-chrII	SGD	CDS	727386	728102	.	-	.	ID=YBR256C;Name=YBR256C;Alias=RIB5
-chrII	SGD	CDS	728885	729724	.	+	.	ID=YBR257W;Name=YBR257W;Alias=POP4
-chrII	SGD	CDS	729734	730162	.	-	.	ID=YBR258C;Name=YBR258C;Alias=SHG1
-chrII	SGD	CDS	730387	732453	.	+	.	ID=YBR259W;Name=YBR259W;Alias=
-chrII	SGD	CDS	732639	734639	.	-	.	ID=YBR260C;Name=YBR260C;Alias=RGD1
-chrII	SGD	CDS	734832	735530	.	-	.	ID=YBR261C;Name=YBR261C;Alias=TAE1
-chrII	SGD	CDS	735720	736040	.	-	.	ID=YBR262C;Name=YBR262C;Alias=MIC12
-chrII	SGD	CDS	736264	737736	.	+	.	ID=YBR263W;Name=YBR263W;Alias=SHM1
-chrII	SGD	CDS	737770	738369	.	-	.	ID=YBR264C;Name=YBR264C;Alias=YPT10
-chrII	SGD	CDS	738582	739544	.	+	.	ID=YBR265W;Name=YBR265W;Alias=TSC10
-chrII	SGD	CDS	739841	741022	.	+	.	ID=YBR267W;Name=YBR267W;Alias=REI1
-chrII	SGD	CDS	741299	741616	.	+	.	ID=YBR268W;Name=YBR268W;Alias=MRPL37
-chrII	SGD	CDS	742160	742576	.	-	.	ID=YBR269C;Name=YBR269C;Alias=SDH8
-chrII	SGD	CDS	742761	744398	.	-	.	ID=YBR270C;Name=YBR270C;Alias=BIT2
-chrII	SGD	CDS	744852	746111	.	+	.	ID=YBR271W;Name=YBR271W;Alias=EFM2
-chrII	SGD	CDS	746361	747803	.	-	.	ID=YBR272C;Name=YBR272C;Alias=HSM3
-chrII	SGD	CDS	748061	749371	.	-	.	ID=YBR273C;Name=YBR273C;Alias=UBX7
-chrII	SGD	CDS	749594	751177	.	+	.	ID=YBR274W;Name=YBR274W;Alias=CHK1
-chrII	SGD	CDS	751356	757106	.	-	.	ID=YBR275C;Name=YBR275C;Alias=RIF1
-chrII	SGD	CDS	757620	760043	.	-	.	ID=YBR276C;Name=YBR276C;Alias=PPS1
-chrII	SGD	CDS	760294	760899	.	+	.	ID=YBR278W;Name=YBR278W;Alias=DPB3
-chrII	SGD	CDS	761257	762594	.	+	.	ID=YBR279W;Name=YBR279W;Alias=PAF1
-chrII	SGD	CDS	762784	764697	.	-	.	ID=YBR280C;Name=YBR280C;Alias=SAF1
-chrII	SGD	CDS	764970	767606	.	-	.	ID=YBR281C;Name=YBR281C;Alias=DUG2
-chrII	SGD	CDS	768240	768680	.	+	.	ID=YBR282W;Name=YBR282W;Alias=MRPL27
-chrII	SGD	CDS	768943	770415	.	-	.	ID=YBR283C;Name=YBR283C;Alias=SSH1
-chrII	SGD	CDS	771239	773632	.	+	.	ID=YBR284W;Name=YBR284W;Alias=
-chrII	SGD	CDS	773922	774356	.	+	.	ID=YBR285W;Name=YBR285W;Alias=
-chrII	SGD	CDS	774700	776313	.	+	.	ID=YBR286W;Name=YBR286W;Alias=APE3
-chrII	SGD	CDS	776571	777854	.	+	.	ID=YBR287W;Name=YBR287W;Alias=
-chrII	SGD	CDS	778012	779463	.	-	.	ID=YBR288C;Name=YBR288C;Alias=APM3
-chrII	SGD	CDS	779667	782384	.	+	.	ID=YBR289W;Name=YBR289W;Alias=SNF5
-chrII	SGD	CDS	782591	783556	.	+	.	ID=YBR290W;Name=YBR290W;Alias=BSD2
-chrII	SGD	CDS	783673	784572	.	-	.	ID=YBR291C;Name=YBR291C;Alias=CTP1
-chrII	SGD	CDS	787006	788430	.	+	.	ID=YBR293W;Name=YBR293W;Alias=VBA2
-chrII	SGD	CDS	789235	791814	.	+	.	ID=YBR294W;Name=YBR294W;Alias=SUL1
-chrII	SGD	CDS	792849	796499	.	+	.	ID=YBR295W;Name=YBR295W;Alias=PCA1
-chrII	SGD	CDS	796798	798522	.	-	.	ID=YBR296C;Name=YBR296C;Alias=PHO89
-chrII	SGD	CDS	800123	800242	.	-	.	ID=YBR296C-A;Name=YBR296C-A;Alias=
-chrII	SGD	CDS	800523	801929	.	+	.	ID=YBR297W;Name=YBR297W;Alias=MAL33
-chrII	SGD	CDS	802631	804475	.	-	.	ID=YBR298C;Name=YBR298C;Alias=MAL31
-chrII	SGD	CDS	805035	805256	.	-	.	ID=YBR298C-A;Name=YBR298C-A;Alias=
-chrII	SGD	CDS	805351	807105	.	+	.	ID=YBR299W;Name=YBR299W;Alias=MAL32
-chrII	SGD	CDS	809057	809419	.	+	.	ID=YBR301W;Name=YBR301W;Alias=PAU24
-chrII	SGD	CDS	810340	811479	.	-	.	ID=YBR302C;Name=YBR302C;Alias=COS2
-chrIII	SGD	CDS	6479	8326	.	-	.	ID=YCL073C;Name=YCL073C;Alias=GEX1
-chrIII	SGD	CDS	9706	11082	.	+	.	ID=YCL069W;Name=YCL069W;Alias=VBA3
-chrIII	SGD	CDS	11503	12285	.	-	.	ID=YCL068C;Name=YCL068C;Alias=
-chrIII	SGD	CDS	12386	13018	.	-	.	ID=YCL067C;Name=YCL067C;Alias=HMLALPHA2
-chrIII	SGD	CDS	13282	13809	.	+	.	ID=YCL066W;Name=YCL066W;Alias=HMLALPHA1
-chrIII	SGD	CDS	15798	16880	.	-	.	ID=YCL064C;Name=YCL064C;Alias=CHA1
-chrIII	SGD	CDS	17290	18561	.	+	.	ID=YCL063W;Name=YCL063W;Alias=VAC17
-chrIII	SGD	CDS	18816	22106	.	-	.	ID=YCL061C;Name=YCL061C;Alias=MRC1
-chrIII	SGD	CDS	22429	23379	.	-	.	ID=YCL059C;Name=YCL059C;Alias=KRR1
-chrIII	SGD	CDS	23523	23981	.	-	.	ID=YCL058C;Name=YCL058C;Alias=FYV5
-chrIII	SGD	CDS	23584	23925	.	+	.	ID=YCL058W-A;Name=YCL058W-A;Alias=ADF1
-chrIII	SGD	CDS	24032	24325	.	-	.	ID=YCL057C-A;Name=YCL057C-A;Alias=MIC10
-chrIII	SGD	CDS	24768	26906	.	+	.	ID=YCL057W;Name=YCL057W;Alias=PRD1
-chrIII	SGD	CDS	26925	27359	.	-	.	ID=YCL056C;Name=YCL056C;Alias=PEX34
-chrIII	SGD	CDS	27929	28936	.	+	.	ID=YCL055W;Name=YCL055W;Alias=KAR4
-chrIII	SGD	CDS	30910	30996	.	+	.	ID=YCL054W-A;Name=YCL054W-A;Alias=RDT1
-chrIII	SGD	CDS	31449	33974	.	+	.	ID=YCL054W;Name=YCL054W;Alias=SPB1
-chrIII	SGD	CDS	34143	35393	.	-	.	ID=YCL052C;Name=YCL052C;Alias=PBN1
-chrIII	SGD	CDS	35865	37616	.	+	.	ID=YCL051W;Name=YCL051W;Alias=LRE1
-chrIII	SGD	CDS	37836	38801	.	-	.	ID=YCL050C;Name=YCL050C;Alias=APA1
-chrIII	SGD	CDS	39786	40724	.	-	.	ID=YCL049C;Name=YCL049C;Alias=
-chrIII	SGD	CDS	41488	41727	.	+	.	ID=YCL048W-A;Name=YCL048W-A;Alias=
-chrIII	SGD	CDS	42165	43556	.	+	.	ID=YCL048W;Name=YCL048W;Alias=SPS22
-chrIII	SGD	CDS	43661	44437	.	-	.	ID=YCL047C;Name=YCL047C;Alias=POF1
-chrIII	SGD	CDS	44623	46905	.	-	.	ID=YCL045C;Name=YCL045C;Alias=EMC1
-chrIII	SGD	CDS	47111	48364	.	-	.	ID=YCL044C;Name=YCL044C;Alias=MGR1
-chrIII	SGD	CDS	48653	50221	.	-	.	ID=YCL043C;Name=YCL043C;Alias=PDI1
-chrIII	SGD	CDS	50584	50943	.	+	.	ID=YCL042W;Name=YCL042W;Alias=
-chrIII	SGD	CDS	50838	52340	.	+	.	ID=YCL040W;Name=YCL040W;Alias=GLK1
-chrIII	SGD	CDS	52645	54882	.	+	.	ID=YCL039W;Name=YCL039W;Alias=GID7
-chrIII	SGD	CDS	54941	56527	.	-	.	ID=YCL038C;Name=YCL038C;Alias=ATG22
-chrIII	SGD	CDS	57374	58678	.	-	.	ID=YCL037C;Name=YCL037C;Alias=SRO9
-chrIII	SGD	CDS	59026	60726	.	+	.	ID=YCL036W;Name=YCL036W;Alias=GFD2
-chrIII	SGD	CDS	60841	61173	.	-	.	ID=YCL035C;Name=YCL035C;Alias=GRX1
-chrIII	SGD	CDS	61658	62722	.	+	.	ID=YCL034W;Name=YCL034W;Alias=LSB5
-chrIII	SGD	CDS	62776	63282	.	-	.	ID=YCL033C;Name=YCL033C;Alias=MXR2
-chrIII	SGD	CDS	63441	64481	.	+	.	ID=YCL032W;Name=YCL032W;Alias=STE50
-chrIII	SGD	CDS	64675	65568	.	-	.	ID=YCL031C;Name=YCL031C;Alias=RRP7
-chrIII	SGD	CDS	65934	68333	.	-	.	ID=YCL030C;Name=YCL030C;Alias=HIS4
-chrIII	SGD	CDS	68599	69921	.	-	.	ID=YCL029C;Name=YCL029C;Alias=BIK1
-chrIII	SGD	CDS	70150	71367	.	+	.	ID=YCL028W;Name=YCL028W;Alias=RNQ1
-chrIII	SGD	CDS	71803	73341	.	+	.	ID=YCL027W;Name=YCL027W;Alias=FUS1
-chrIII	SGD	CDS	73405	73986	.	-	.	ID=YCL026C-B;Name=YCL026C-B;Alias=HBN1
-chrIII	SGD	CDS	74704	75285	.	-	.	ID=YCL026C-A;Name=YCL026C-A;Alias=FRM2
-chrIII	SGD	CDS	76018	77919	.	-	.	ID=YCL025C;Name=YCL025C;Alias=AGP1
-chrIII	SGD	CDS	79162	82275	.	+	.	ID=YCL024W;Name=YCL024W;Alias=KCC4
-chrIII	SGD	CDS	83620	83997	.	+	.	ID=YCL021W-A;Name=YCL021W-A;Alias=
-chrIII	SGD	CDS	91324	92418	.	+	.	ID=YCL018W;Name=YCL018W;Alias=LEU2
-chrIII	SGD	CDS	92777	94270	.	-	.	ID=YCL017C;Name=YCL017C;Alias=NFS1
-chrIII	SGD	CDS	94621	95763	.	-	.	ID=YCL016C;Name=YCL016C;Alias=DCC1
-chrIII	SGD	CDS	96281	101191	.	+	.	ID=YCL014W;Name=YCL014W;Alias=BUD3
-chrIII	SGD	CDS	101317	101788	.	-	.	ID=YCL012C;Name=YCL012C;Alias=
-chrIII	SGD	CDS	102075	103358	.	-	.	ID=YCL011C;Name=YCL011C;Alias=GBP2
-chrIII	SGD	CDS	103571	104350	.	-	.	ID=YCL010C;Name=YCL010C;Alias=SGF29
-chrIII	SGD	CDS	104619	105548	.	-	.	ID=YCL009C;Name=YCL009C;Alias=ILV6
-chrIII	SGD	CDS	105696	106853	.	-	.	ID=YCL008C;Name=YCL008C;Alias=STP22
-chrIII	SGD	CDS	107023	107417	.	+	.	ID=YCL005W-A;Name=YCL005W-A;Alias=VMA9
-chrIII	SGD	CDS	108021	108791	.	+	.	ID=YCL005W;Name=YCL005W;Alias=LDB16
-chrIII	SGD	CDS	109105	110670	.	+	.	ID=YCL004W;Name=YCL004W;Alias=PGS1
-chrIII	SGD	CDS	110808	111675	.	-	.	ID=YCL002C;Name=YCL002C;Alias=
-chrIII	SGD	CDS	111916	112482	.	+	.	ID=YCL001W;Name=YCL001W;Alias=RER1
-chrIII	SGD	CDS	113080	113541	.	+	.	ID=YCL001W-A;Name=YCL001W-A;Alias=
-chrIII	SGD	CDS	113770	114024	.	+	.	ID=YCL001W-B;Name=YCL001W-B;Alias=
-chrIII	SGD	CDS	117380	118348	.	-	.	ID=YCR002C;Name=YCR002C;Alias=CDC10
-chrIII	SGD	CDS	118620	119171	.	+	.	ID=YCR003W;Name=YCR003W;Alias=MRPL32
-chrIII	SGD	CDS	119575	120318	.	-	.	ID=YCR004C;Name=YCR004C;Alias=YCP4
-chrIII	SGD	CDS	120946	122328	.	-	.	ID=YCR005C;Name=YCR005C;Alias=CIT2
-chrIII	SGD	CDS	126011	126730	.	-	.	ID=YCR007C;Name=YCR007C;Alias=
-chrIII	SGD	CDS	128470	130281	.	+	.	ID=YCR008W;Name=YCR008W;Alias=SAT4
-chrIII	SGD	CDS	130745	131542	.	-	.	ID=YCR009C;Name=YCR009C;Alias=RVS161
-chrIII	SGD	CDS	132273	133124	.	-	.	ID=YCR010C;Name=YCR010C;Alias=ADY2
-chrIII	SGD	CDS	133724	136873	.	-	.	ID=YCR011C;Name=YCR011C;Alias=ADP1
-chrIII	SGD	CDS	137746	138996	.	+	.	ID=YCR012W;Name=YCR012W;Alias=PGK1
-chrIII	SGD	CDS	139185	140933	.	-	.	ID=YCR014C;Name=YCR014C;Alias=POL4
-chrIII	SGD	CDS	141217	142170	.	-	.	ID=YCR015C;Name=YCR015C;Alias=CTO1
-chrIII	SGD	CDS	143634	144506	.	+	.	ID=YCR016W;Name=YCR016W;Alias=
-chrIII	SGD	CDS	144773	147634	.	-	.	ID=YCR017C;Name=YCR017C;Alias=CWH43
-chrIII	SGD	CDS	148238	148903	.	-	.	ID=YCR018C;Name=YCR018C;Alias=SRD1
-chrIII	SGD	CDS	152837	153928	.	+	.	ID=YCR019W;Name=YCR019W;Alias=MAK32
-chrIII	SGD	CDS	154012	154659	.	-	.	ID=YCR020C;Name=YCR020C;Alias=PET18
-chrIII	SGD	CDS	154830	155096	.	-	.	ID=YCR020C-A;Name=YCR020C-A;Alias=MAK31
-chrIII	SGD	CDS	155320	155556	.	+	.	ID=YCR020W-B;Name=YCR020W-B;Alias=HTL1
-chrIII	SGD	CDS	156109	157107	.	-	.	ID=YCR021C;Name=YCR021C;Alias=HSP30
-chrIII	SGD	CDS	158538	160373	.	-	.	ID=YCR023C;Name=YCR023C;Alias=
-chrIII	SGD	CDS	160744	162222	.	-	.	ID=YCR024C;Name=YCR024C;Alias=SLM5
-chrIII	SGD	CDS	162599	162865	.	-	.	ID=YCR024C-B;Name=YCR024C-B;Alias=
-chrIII	SGD	CDS	162945	163067	.	-	.	ID=YCR024C-A;Name=YCR024C-A;Alias=PMP1
-chrIII	SGD	CDS	164111	166339	.	-	.	ID=YCR026C;Name=YCR026C;Alias=NPP1
-chrIII	SGD	CDS	167370	167999	.	-	.	ID=YCR027C;Name=YCR027C;Alias=RHB1
-chrIII	SGD	CDS	170886	172424	.	-	.	ID=YCR028C;Name=YCR028C;Alias=FEN2
-chrIII	SGD	CDS	172950	173440	.	-	.	ID=YCR028C-A;Name=YCR028C-A;Alias=RIM1
-chrIII	SGD	CDS	173826	176438	.	-	.	ID=YCR030C;Name=YCR030C;Alias=SYP1
-chrIII	SGD	CDS	177500	178220	.	-	.	ID=YCR031C;Name=YCR031C;Alias=RPS14A
-chrIII	SGD	CDS	179520	186023	.	+	.	ID=YCR032W;Name=YCR032W;Alias=BPH1
-chrIII	SGD	CDS	186489	190169	.	+	.	ID=YCR033W;Name=YCR033W;Alias=SNT1
-chrIII	SGD	CDS	190592	191635	.	+	.	ID=YCR034W;Name=YCR034W;Alias=ELO2
-chrIII	SGD	CDS	191834	193018	.	-	.	ID=YCR035C;Name=YCR035C;Alias=RRP43
-chrIII	SGD	CDS	193297	194298	.	+	.	ID=YCR036W;Name=YCR036W;Alias=RBK1
-chrIII	SGD	CDS	194414	197185	.	-	.	ID=YCR037C;Name=YCR037C;Alias=PHO87
-chrIII	SGD	CDS	197621	199549	.	-	.	ID=YCR038C;Name=YCR038C;Alias=BUD5
-chrIII	SGD	CDS	199546	200178	.	-	.	ID=YCR039C;Name=YCR039C;Alias=MATALPHA2
-chrIII	SGD	CDS	200442	200969	.	+	.	ID=YCR040W;Name=YCR040W;Alias=MATALPHA1
-chrIII	SGD	CDS	200911	201243	.	+	.	ID=YCR041W;Name=YCR041W;Alias=
-chrIII	SGD	CDS	201174	205397	.	-	.	ID=YCR042C;Name=YCR042C;Alias=TAF2
-chrIII	SGD	CDS	206261	206644	.	-	.	ID=YCR043C;Name=YCR043C;Alias=
-chrIII	SGD	CDS	206877	207950	.	-	.	ID=YCR044C;Name=YCR044C;Alias=PER1
-chrIII	SGD	CDS	208135	209610	.	-	.	ID=YCR045C;Name=YCR045C;Alias=RRT12
-chrIII	SGD	CDS	209914	210423	.	-	.	ID=YCR046C;Name=YCR046C;Alias=IMG1
-chrIII	SGD	CDS	210718	211545	.	-	.	ID=YCR047C;Name=YCR047C;Alias=BUD23
-chrIII	SGD	CDS	211929	213761	.	+	.	ID=YCR048W;Name=YCR048W;Alias=ARE1
-chrIII	SGD	CDS	213464	213772	.	-	.	ID=YCR050C;Name=YCR050C;Alias=
-chrIII	SGD	CDS	214071	214739	.	+	.	ID=YCR051W;Name=YCR051W;Alias=
-chrIII	SGD	CDS	214994	216445	.	+	.	ID=YCR052W;Name=YCR052W;Alias=RSC6
-chrIII	SGD	CDS	216697	218241	.	+	.	ID=YCR053W;Name=YCR053W;Alias=THR4
-chrIII	SGD	CDS	218376	220067	.	-	.	ID=YCR054C;Name=YCR054C;Alias=CTR86
-chrIII	SGD	CDS	220457	223228	.	-	.	ID=YCR057C;Name=YCR057C;Alias=PWP2
-chrIII	SGD	CDS	223454	224230	.	-	.	ID=YCR059C;Name=YCR059C;Alias=YIH1
-chrIII	SGD	CDS	224399	224734	.	+	.	ID=YCR060W;Name=YCR060W;Alias=TAH1
-chrIII	SGD	CDS	225563	227458	.	+	.	ID=YCR061W;Name=YCR061W;Alias=
-chrIII	SGD	CDS	228318	228791	.	+	.	ID=YCR063W;Name=YCR063W;Alias=BUD31
-chrIII	SGD	CDS	229310	231004	.	+	.	ID=YCR065W;Name=YCR065W;Alias=HCM1
-chrIII	SGD	CDS	231500	232963	.	+	.	ID=YCR066W;Name=YCR066W;Alias=RAD18
-chrIII	SGD	CDS	233125	236322	.	-	.	ID=YCR067C;Name=YCR067C;Alias=SED4
-chrIII	SGD	CDS	237214	238776	.	+	.	ID=YCR068W;Name=YCR068W;Alias=ATG15
-chrIII	SGD	CDS	239055	240011	.	+	.	ID=YCR069W;Name=YCR069W;Alias=CPR4
-chrIII	SGD	CDS	240103	240543	.	-	.	ID=YCR071C;Name=YCR071C;Alias=IMG2
-chrIII	SGD	CDS	240805	242352	.	-	.	ID=YCR072C;Name=YCR072C;Alias=RSA4
-chrIII	SGD	CDS	242588	246583	.	-	.	ID=YCR073C;Name=YCR073C;Alias=SSK22
-chrIII	SGD	CDS	246963	247910	.	+	.	ID=YCR073W-A;Name=YCR073W-A;Alias=SOL2
-chrIII	SGD	CDS	248033	248815	.	-	.	ID=YCR075C;Name=YCR075C;Alias=ERS1
-chrIII	SGD	CDS	248975	249202	.	+	.	ID=YCR075W-A;Name=YCR075W-A;Alias=EGO2
-chrIII	SGD	CDS	249293	250045	.	-	.	ID=YCR076C;Name=YCR076C;Alias=FUB1
-chrIII	SGD	CDS	250238	252628	.	-	.	ID=YCR077C;Name=YCR077C;Alias=PAT1
-chrIII	SGD	CDS	252845	254173	.	+	.	ID=YCR079W;Name=YCR079W;Alias=PTC6
-chrIII	SGD	CDS	254371	258654	.	+	.	ID=YCR081W;Name=YCR081W;Alias=SRB8
-chrIII	SGD	CDS	258883	259269	.	+	.	ID=YCR082W;Name=YCR082W;Alias=AHC2
-chrIII	SGD	CDS	259578	259961	.	+	.	ID=YCR083W;Name=YCR083W;Alias=TRX3
-chrIII	SGD	CDS	260311	262452	.	-	.	ID=YCR084C;Name=YCR084C;Alias=TUP1
-chrIII	SGD	CDS	263392	263964	.	+	.	ID=YCR086W;Name=YCR086W;Alias=CSM1
-chrIII	SGD	CDS	264006	264467	.	-	.	ID=YCR087C-A;Name=YCR087C-A;Alias=
-chrIII	SGD	CDS	265068	266846	.	+	.	ID=YCR088W;Name=YCR088W;Alias=ABP1
-chrIII	SGD	CDS	267434	272263	.	+	.	ID=YCR089W;Name=YCR089W;Alias=FIG2
-chrIII	SGD	CDS	272315	272863	.	-	.	ID=YCR090C;Name=YCR090C;Alias=
-chrIII	SGD	CDS	274404	276566	.	+	.	ID=YCR091W;Name=YCR091W;Alias=KIN82
-chrIII	SGD	CDS	276764	279820	.	-	.	ID=YCR092C;Name=YCR092C;Alias=MSH3
-chrIII	SGD	CDS	280117	286443	.	+	.	ID=YCR093W;Name=YCR093W;Alias=CDC39
-chrIII	SGD	CDS	286762	287937	.	+	.	ID=YCR094W;Name=YCR094W;Alias=CDC50
-chrIII	SGD	CDS	288170	289258	.	-	.	ID=YCR095C;Name=YCR095C;Alias=OCA4
-chrIII	SGD	CDS	289639	289797	.	+	.	ID=YCR095W-A;Name=YCR095W-A;Alias=
-chrIII	SGD	CDS	293179	293538	.	-	.	ID=YCR096C;Name=YCR096C;Alias=HMRA2
-chrIII	SGD	CDS	293835	294321	.	+	.	ID=YCR097W;Name=YCR097W;Alias=HMRA1
-chrIII	SGD	CDS	297049	298605	.	-	.	ID=YCR098C;Name=YCR098C;Alias=GIT1
-chrIII	SGD	CDS	300832	301299	.	-	.	ID=YCR099C;Name=YCR099C;Alias=
-chrIII	SGD	CDS	301271	302221	.	-	.	ID=YCR100C;Name=YCR100C;Alias=
-chrIII	SGD	CDS	302482	303030	.	-	.	ID=YCR101C;Name=YCR101C;Alias=
-chrIII	SGD	CDS	304361	305467	.	-	.	ID=YCR102C;Name=YCR102C;Alias=
-chrIII	SGD	CDS	307801	308175	.	+	.	ID=YCR104W;Name=YCR104W;Alias=PAU3
-chrIII	SGD	CDS	309070	310155	.	+	.	ID=YCR105W;Name=YCR105W;Alias=ADH7
-chrIII	SGD	CDS	310958	313456	.	+	.	ID=YCR106W;Name=YCR106W;Alias=RDS1
-chrIII	SGD	CDS	313890	314981	.	+	.	ID=YCR107W;Name=YCR107W;Alias=AAD3
-chrIII	SGD	CDS	315997	316188	.	-	.	ID=YCR108C;Name=YCR108C;Alias=
-chrIV	SGD	CDS	1802	2953	.	+	.	ID=YDL248W;Name=YDL248W;Alias=COS7
-chrIV	SGD	CDS	5985	7814	.	+	.	ID=YDL247W;Name=YDL247W;Alias=MPH2
-chrIV	SGD	CDS	8683	9756	.	-	.	ID=YDL246C;Name=YDL246C;Alias=SOR2
-chrIV	SGD	CDS	11657	13360	.	-	.	ID=YDL245C;Name=YDL245C;Alias=HXT15
-chrIV	SGD	CDS	16204	17226	.	+	.	ID=YDL244W;Name=YDL244W;Alias=THI13
-chrIV	SGD	CDS	17577	18566	.	-	.	ID=YDL243C;Name=YDL243C;Alias=AAD4
-chrIV	SGD	CDS	20635	21006	.	+	.	ID=YDL241W;Name=YDL241W;Alias=
-chrIV	SGD	CDS	22823	25876	.	+	.	ID=YDL240W;Name=YDL240W;Alias=LRG1
-chrIV	SGD	CDS	26403	28775	.	-	.	ID=YDL239C;Name=YDL239C;Alias=ADY3
-chrIV	SGD	CDS	28985	30454	.	-	.	ID=YDL238C;Name=YDL238C;Alias=GUD1
-chrIV	SGD	CDS	30657	31829	.	+	.	ID=YDL237W;Name=YDL237W;Alias=AIM6
-chrIV	SGD	CDS	32296	33234	.	+	.	ID=YDL236W;Name=YDL236W;Alias=PHO13
-chrIV	SGD	CDS	33415	33918	.	-	.	ID=YDL235C;Name=YDL235C;Alias=YPD1
-chrIV	SGD	CDS	34237	36477	.	-	.	ID=YDL234C;Name=YDL234C;Alias=GYP7
-chrIV	SGD	CDS	36797	38173	.	+	.	ID=YDL233W;Name=YDL233W;Alias=MFG1
-chrIV	SGD	CDS	38487	38597	.	+	.	ID=YDL232W;Name=YDL232W;Alias=OST4
-chrIV	SGD	CDS	38867	42244	.	-	.	ID=YDL231C;Name=YDL231C;Alias=BRE4
-chrIV	SGD	CDS	42700	43707	.	+	.	ID=YDL230W;Name=YDL230W;Alias=PTP1
-chrIV	SGD	CDS	44065	45906	.	+	.	ID=YDL229W;Name=YDL229W;Alias=SSB1
-chrIV	SGD	CDS	46271	48031	.	-	.	ID=YDL227C;Name=YDL227C;Alias=HO
-chrIV	SGD	CDS	51115	52173	.	-	.	ID=YDL226C;Name=YDL226C;Alias=GCS1
-chrIV	SGD	CDS	52445	54100	.	+	.	ID=YDL225W;Name=YDL225W;Alias=SHS1
-chrIV	SGD	CDS	54397	56346	.	-	.	ID=YDL224C;Name=YDL224C;Alias=WHI4
-chrIV	SGD	CDS	57265	60405	.	-	.	ID=YDL223C;Name=YDL223C;Alias=HBT1
-chrIV	SGD	CDS	60872	61801	.	-	.	ID=YDL222C;Name=YDL222C;Alias=FMP45
-chrIV	SGD	CDS	62244	65018	.	-	.	ID=YDL220C;Name=YDL220C;Alias=CDC13
-chrIV	SGD	CDS	65242	65765	.	+	.	ID=YDL219W;Name=YDL219W;Alias=DTD1
-chrIV	SGD	CDS	66493	67446	.	+	.	ID=YDL218W;Name=YDL218W;Alias=
-chrIV	SGD	CDS	67983	68606	.	-	.	ID=YDL217C;Name=YDL217C;Alias=TIM22
-chrIV	SGD	CDS	68997	70319	.	-	.	ID=YDL216C;Name=YDL216C;Alias=RRI1
-chrIV	SGD	CDS	70640	73918	.	-	.	ID=YDL215C;Name=YDL215C;Alias=GDH2
-chrIV	SGD	CDS	74446	76545	.	-	.	ID=YDL214C;Name=YDL214C;Alias=PRR2
-chrIV	SGD	CDS	77289	77966	.	-	.	ID=YDL213C;Name=YDL213C;Alias=NOP6
-chrIV	SGD	CDS	78426	79058	.	+	.	ID=YDL212W;Name=YDL212W;Alias=SHR3
-chrIV	SGD	CDS	79294	80412	.	-	.	ID=YDL211C;Name=YDL211C;Alias=
-chrIV	SGD	CDS	84270	85985	.	+	.	ID=YDL210W;Name=YDL210W;Alias=UGA4
-chrIV	SGD	CDS	86207	87226	.	-	.	ID=YDL209C;Name=YDL209C;Alias=CWC2
-chrIV	SGD	CDS	87512	87982	.	+	.	ID=YDL208W;Name=YDL208W;Alias=NHP2
-chrIV	SGD	CDS	88248	89864	.	+	.	ID=YDL207W;Name=YDL207W;Alias=GLE1
-chrIV	SGD	CDS	90176	92464	.	+	.	ID=YDL206W;Name=YDL206W;Alias=
-chrIV	SGD	CDS	92762	93745	.	-	.	ID=YDL205C;Name=YDL205C;Alias=HEM3
-chrIV	SGD	CDS	94605	95786	.	+	.	ID=YDL204W;Name=YDL204W;Alias=RTN2
-chrIV	SGD	CDS	96082	97953	.	-	.	ID=YDL203C;Name=YDL203C;Alias=ACK1
-chrIV	SGD	CDS	98475	99224	.	+	.	ID=YDL202W;Name=YDL202W;Alias=MRPL11
-chrIV	SGD	CDS	99561	100421	.	+	.	ID=YDL201W;Name=YDL201W;Alias=TRM8
-chrIV	SGD	CDS	100501	101067	.	-	.	ID=YDL200C;Name=YDL200C;Alias=MGT1
-chrIV	SGD	CDS	101290	103353	.	-	.	ID=YDL199C;Name=YDL199C;Alias=
-chrIV	SGD	CDS	103649	104551	.	-	.	ID=YDL198C;Name=YDL198C;Alias=GGC1
-chrIV	SGD	CDS	104917	106494	.	-	.	ID=YDL197C;Name=YDL197C;Alias=ASF2
-chrIV	SGD	CDS	107208	111029	.	+	.	ID=YDL195W;Name=YDL195W;Alias=SEC31
-chrIV	SGD	CDS	111580	114234	.	+	.	ID=YDL194W;Name=YDL194W;Alias=SNF3
-chrIV	SGD	CDS	114672	115799	.	+	.	ID=YDL193W;Name=YDL193W;Alias=NUS1
-chrIV	SGD	CDS	116321	116866	.	+	.	ID=YDL192W;Name=YDL192W;Alias=ARF1
-chrIV	SGD	CDS	117664	118517	.	+	.	ID=YDL191W;Name=YDL191W;Alias=RPL35A
-chrIV	SGD	CDS	118707	121592	.	-	.	ID=YDL190C;Name=YDL190C;Alias=UFD2
-chrIV	SGD	CDS	122078	123589	.	+	.	ID=YDL189W;Name=YDL189W;Alias=RBS1
-chrIV	SGD	CDS	123865	124998	.	-	.	ID=YDL188C;Name=YDL188C;Alias=PPH22
-chrIV	SGD	CDS	125616	126449	.	+	.	ID=YDL186W;Name=YDL186W;Alias=
-chrIV	SGD	CDS	126787	130002	.	+	.	ID=YDL185W;Name=YDL185W;Alias=VMA1
-chrIV	SGD	CDS	130407	130484	.	-	.	ID=YDL184C;Name=YDL184C;Alias=RPL41A
-chrIV	SGD	CDS	130871	131833	.	-	.	ID=YDL183C;Name=YDL183C;Alias=
-chrIV	SGD	CDS	133437	134723	.	+	.	ID=YDL182W;Name=YDL182W;Alias=LYS20
-chrIV	SGD	CDS	135179	135436	.	+	.	ID=YDL181W;Name=YDL181W;Alias=INH1
-chrIV	SGD	CDS	135896	137539	.	+	.	ID=YDL180W;Name=YDL180W;Alias=
-chrIV	SGD	CDS	138291	139205	.	+	.	ID=YDL179W;Name=YDL179W;Alias=PCL9
-chrIV	SGD	CDS	139522	141114	.	+	.	ID=YDL178W;Name=YDL178W;Alias=DLD2
-chrIV	SGD	CDS	141209	141721	.	-	.	ID=YDL177C;Name=YDL177C;Alias=
-chrIV	SGD	CDS	142097	144223	.	+	.	ID=YDL176W;Name=YDL176W;Alias=
-chrIV	SGD	CDS	144484	145518	.	-	.	ID=YDL175C;Name=YDL175C;Alias=AIR2
-chrIV	SGD	CDS	145826	147589	.	-	.	ID=YDL174C;Name=YDL174C;Alias=DLD1
-chrIV	SGD	CDS	148191	149078	.	+	.	ID=YDL173W;Name=YDL173W;Alias=PAR32
-chrIV	SGD	CDS	149203	155640	.	-	.	ID=YDL171C;Name=YDL171C;Alias=GLT1
-chrIV	SGD	CDS	156318	157904	.	+	.	ID=YDL170W;Name=YDL170W;Alias=UGA3
-chrIV	SGD	CDS	158064	158735	.	-	.	ID=YDL169C;Name=YDL169C;Alias=UGX2
-chrIV	SGD	CDS	159604	160764	.	+	.	ID=YDL168W;Name=YDL168W;Alias=SFA1
-chrIV	SGD	CDS	160995	163154	.	-	.	ID=YDL167C;Name=YDL167C;Alias=NRP1
-chrIV	SGD	CDS	163449	164042	.	-	.	ID=YDL166C;Name=YDL166C;Alias=FAP7
-chrIV	SGD	CDS	164290	164865	.	+	.	ID=YDL165W;Name=YDL165W;Alias=CDC36
-chrIV	SGD	CDS	164987	167254	.	-	.	ID=YDL164C;Name=YDL164C;Alias=CDC9
-chrIV	SGD	CDS	167714	169078	.	+	.	ID=YDL161W;Name=YDL161W;Alias=ENT1
-chrIV	SGD	CDS	169366	169608	.	-	.	ID=YDL160C-A;Name=YDL160C-A;Alias=MHF2
-chrIV	SGD	CDS	170410	171930	.	-	.	ID=YDL160C;Name=YDL160C;Alias=DHH1
-chrIV	SGD	CDS	172182	172313	.	+	.	ID=YDL159W-A;Name=YDL159W-A;Alias=
-chrIV	SGD	CDS	172481	174028	.	+	.	ID=YDL159W;Name=YDL159W;Alias=STE7
-chrIV	SGD	CDS	174232	174588	.	-	.	ID=YDL157C;Name=YDL157C;Alias=
-chrIV	SGD	CDS	174918	176486	.	+	.	ID=YDL156W;Name=YDL156W;Alias=CMR1
-chrIV	SGD	CDS	176773	178056	.	+	.	ID=YDL155W;Name=YDL155W;Alias=CLB3
-chrIV	SGD	CDS	178334	181039	.	+	.	ID=YDL154W;Name=YDL154W;Alias=MSH5
-chrIV	SGD	CDS	181186	183018	.	-	.	ID=YDL153C;Name=YDL153C;Alias=SAS10
-chrIV	SGD	CDS	183343	184611	.	+	.	ID=YDL150W;Name=YDL150W;Alias=RPC53
-chrIV	SGD	CDS	184925	187918	.	+	.	ID=YDL149W;Name=YDL149W;Alias=ATG9
-chrIV	SGD	CDS	188154	190586	.	-	.	ID=YDL148C;Name=YDL148C;Alias=NOP14
-chrIV	SGD	CDS	190924	192261	.	+	.	ID=YDL147W;Name=YDL147W;Alias=RPN5
-chrIV	SGD	CDS	192750	194225	.	+	.	ID=YDL146W;Name=YDL146W;Alias=LDB17
-chrIV	SGD	CDS	194571	198176	.	-	.	ID=YDL145C;Name=YDL145C;Alias=COP1
-chrIV	SGD	CDS	198662	199732	.	-	.	ID=YDL144C;Name=YDL144C;Alias=
-chrIV	SGD	CDS	199996	201582	.	+	.	ID=YDL143W;Name=YDL143W;Alias=CCT4
-chrIV	SGD	CDS	201719	202570	.	-	.	ID=YDL142C;Name=YDL142C;Alias=CRD1
-chrIV	SGD	CDS	203039	205111	.	+	.	ID=YDL141W;Name=YDL141W;Alias=BPL1
-chrIV	SGD	CDS	205360	210561	.	-	.	ID=YDL140C;Name=YDL140C;Alias=RPO21
-chrIV	SGD	CDS	211375	212046	.	-	.	ID=YDL139C;Name=YDL139C;Alias=SCM3
-chrIV	SGD	CDS	213351	215642	.	+	.	ID=YDL138W;Name=YDL138W;Alias=RGT2
-chrIV	SGD	CDS	216158	217074	.	+	.	ID=YDL137W;Name=YDL137W;Alias=ARF2
-chrIV	SGD	CDS	217600	218367	.	+	.	ID=YDL136W;Name=YDL136W;Alias=RPL35B
-chrIV	SGD	CDS	218680	219288	.	-	.	ID=YDL135C;Name=YDL135C;Alias=RDI1
-chrIV	SGD	CDS	219662	220771	.	-	.	ID=YDL134C;Name=YDL134C;Alias=PPH21
-chrIV	SGD	CDS	221724	221801	.	-	.	ID=YDL133C-A;Name=YDL133C-A;Alias=RPL41B
-chrIV	SGD	CDS	222427	223740	.	+	.	ID=YDL133W;Name=YDL133W;Alias=SRF1
-chrIV	SGD	CDS	224304	226751	.	+	.	ID=YDL132W;Name=YDL132W;Alias=CDC53
-chrIV	SGD	CDS	227393	228715	.	+	.	ID=YDL131W;Name=YDL131W;Alias=LYS21
-chrIV	SGD	CDS	229171	229431	.	+	.	ID=YDL130W-A;Name=YDL130W-A;Alias=STF1
-chrIV	SGD	CDS	229906	230527	.	+	.	ID=YDL130W;Name=YDL130W;Alias=RPP1B
-chrIV	SGD	CDS	231024	231899	.	+	.	ID=YDL129W;Name=YDL129W;Alias=
-chrIV	SGD	CDS	232652	233887	.	+	.	ID=YDL128W;Name=YDL128W;Alias=VCX1
-chrIV	SGD	CDS	234927	235853	.	+	.	ID=YDL127W;Name=YDL127W;Alias=PCL2
-chrIV	SGD	CDS	236157	238664	.	-	.	ID=YDL126C;Name=YDL126C;Alias=CDC48
-chrIV	SGD	CDS	239019	239606	.	-	.	ID=YDL125C;Name=YDL125C;Alias=HNT1
-chrIV	SGD	CDS	240259	241197	.	+	.	ID=YDL124W;Name=YDL124W;Alias=
-chrIV	SGD	CDS	241418	241840	.	+	.	ID=YDL123W;Name=YDL123W;Alias=SNA4
-chrIV	SGD	CDS	242552	244981	.	+	.	ID=YDL122W;Name=YDL122W;Alias=UBP1
-chrIV	SGD	CDS	245133	245582	.	-	.	ID=YDL121C;Name=YDL121C;Alias=
-chrIV	SGD	CDS	245923	246447	.	+	.	ID=YDL120W;Name=YDL120W;Alias=YFH1
-chrIV	SGD	CDS	246689	247612	.	-	.	ID=YDL119C;Name=YDL119C;Alias=HEM25
-chrIV	SGD	CDS	248581	251238	.	+	.	ID=YDL117W;Name=YDL117W;Alias=CYK3
-chrIV	SGD	CDS	251566	253746	.	+	.	ID=YDL116W;Name=YDL116W;Alias=NUP84
-chrIV	SGD	CDS	253995	255126	.	-	.	ID=YDL115C;Name=YDL115C;Alias=IWR1
-chrIV	SGD	CDS	255604	256530	.	+	.	ID=YDL114W;Name=YDL114W;Alias=
-chrIV	SGD	CDS	256633	258555	.	-	.	ID=YDL113C;Name=YDL113C;Alias=ATG20
-chrIV	SGD	CDS	258915	263225	.	+	.	ID=YDL112W;Name=YDL112W;Alias=TRM3
-chrIV	SGD	CDS	263313	264110	.	-	.	ID=YDL111C;Name=YDL111C;Alias=RRP42
-chrIV	SGD	CDS	264512	264964	.	-	.	ID=YDL110C;Name=YDL110C;Alias=TMA17
-chrIV	SGD	CDS	265258	267201	.	-	.	ID=YDL109C;Name=YDL109C;Alias=
-chrIV	SGD	CDS	267698	268699	.	+	.	ID=YDL108W;Name=YDL108W;Alias=KIN28
-chrIV	SGD	CDS	268921	269976	.	+	.	ID=YDL107W;Name=YDL107W;Alias=MSS2
-chrIV	SGD	CDS	270222	271901	.	-	.	ID=YDL106C;Name=YDL106C;Alias=PHO2
-chrIV	SGD	CDS	272389	273597	.	+	.	ID=YDL105W;Name=YDL105W;Alias=NSE4
-chrIV	SGD	CDS	273653	274876	.	-	.	ID=YDL104C;Name=YDL104C;Alias=QRI7
-chrIV	SGD	CDS	275148	276581	.	-	.	ID=YDL103C;Name=YDL103C;Alias=QRI1
-chrIV	SGD	CDS	276872	280165	.	+	.	ID=YDL102W;Name=YDL102W;Alias=POL3
-chrIV	SGD	CDS	280307	281848	.	-	.	ID=YDL101C;Name=YDL101C;Alias=DUN1
-chrIV	SGD	CDS	282112	283176	.	-	.	ID=YDL100C;Name=YDL100C;Alias=GET3
-chrIV	SGD	CDS	283419	284444	.	+	.	ID=YDL099W;Name=YDL099W;Alias=BUG1
-chrIV	SGD	CDS	284581	285165	.	-	.	ID=YDL098C;Name=YDL098C;Alias=SNU23
-chrIV	SGD	CDS	285391	286695	.	-	.	ID=YDL097C;Name=YDL097C;Alias=RPN6
-chrIV	SGD	CDS	287059	289512	.	+	.	ID=YDL095W;Name=YDL095W;Alias=PMT1
-chrIV	SGD	CDS	289909	292140	.	+	.	ID=YDL093W;Name=YDL093W;Alias=PMT5
-chrIV	SGD	CDS	292781	293221	.	+	.	ID=YDL092W;Name=YDL092W;Alias=SRP14
-chrIV	SGD	CDS	293392	294759	.	-	.	ID=YDL091C;Name=YDL091C;Alias=UBX3
-chrIV	SGD	CDS	295034	296329	.	-	.	ID=YDL090C;Name=YDL090C;Alias=RAM1
-chrIV	SGD	CDS	296820	298274	.	+	.	ID=YDL089W;Name=YDL089W;Alias=NUR1
-chrIV	SGD	CDS	298417	300003	.	-	.	ID=YDL088C;Name=YDL088C;Alias=ASM4
-chrIV	SGD	CDS	300214	300999	.	-	.	ID=YDL087C;Name=YDL087C;Alias=LUC7
-chrIV	SGD	CDS	301413	302234	.	+	.	ID=YDL086W;Name=YDL086W;Alias=
-chrIV	SGD	CDS	302464	302670	.	-	.	ID=YDL085C-A;Name=YDL085C-A;Alias=
-chrIV	SGD	CDS	303211	304848	.	+	.	ID=YDL085W;Name=YDL085W;Alias=NDE2
-chrIV	SGD	CDS	305237	306577	.	+	.	ID=YDL084W;Name=YDL084W;Alias=SUB2
-chrIV	SGD	CDS	306926	307789	.	-	.	ID=YDL083C;Name=YDL083C;Alias=RPS16B
-chrIV	SGD	CDS	308424	309388	.	+	.	ID=YDL082W;Name=YDL082W;Alias=RPL13A
-chrIV	SGD	CDS	309802	310122	.	-	.	ID=YDL081C;Name=YDL081C;Alias=RPP1A
-chrIV	SGD	CDS	310642	312471	.	-	.	ID=YDL080C;Name=YDL080C;Alias=THI3
-chrIV	SGD	CDS	312951	314748	.	-	.	ID=YDL079C;Name=YDL079C;Alias=MRK1
-chrIV	SGD	CDS	315357	316388	.	-	.	ID=YDL078C;Name=YDL078C;Alias=MDH3
-chrIV	SGD	CDS	316971	320120	.	-	.	ID=YDL077C;Name=YDL077C;Alias=VAM6
-chrIV	SGD	CDS	320668	321552	.	-	.	ID=YDL076C;Name=YDL076C;Alias=RXT3
-chrIV	SGD	CDS	322226	322988	.	+	.	ID=YDL075W;Name=YDL075W;Alias=RPL31A
-chrIV	SGD	CDS	324047	326149	.	-	.	ID=YDL074C;Name=YDL074C;Alias=BRE1
-chrIV	SGD	CDS	326613	329567	.	+	.	ID=YDL073W;Name=YDL073W;Alias=AHK1
-chrIV	SGD	CDS	329836	330447	.	-	.	ID=YDL072C;Name=YDL072C;Alias=YET3
-chrIV	SGD	CDS	331024	332940	.	+	.	ID=YDL070W;Name=YDL070W;Alias=BDF2
-chrIV	SGD	CDS	333121	333810	.	-	.	ID=YDL069C;Name=YDL069C;Alias=CBS1
-chrIV	SGD	CDS	334217	334396	.	-	.	ID=YDL067C;Name=YDL067C;Alias=COX9
-chrIV	SGD	CDS	334835	336121	.	+	.	ID=YDL066W;Name=YDL066W;Alias=IDP1
-chrIV	SGD	CDS	336249	337277	.	-	.	ID=YDL065C;Name=YDL065C;Alias=PEX19
-chrIV	SGD	CDS	337487	338070	.	+	.	ID=YDL064W;Name=YDL064W;Alias=UBC9
-chrIV	SGD	CDS	338272	340134	.	-	.	ID=YDL063C;Name=YDL063C;Alias=SYO1
-chrIV	SGD	CDS	340628	341219	.	-	.	ID=YDL061C;Name=YDL061C;Alias=RPS29B
-chrIV	SGD	CDS	341619	343985	.	+	.	ID=YDL060W;Name=YDL060W;Alias=TSR1
-chrIV	SGD	CDS	344237	344953	.	-	.	ID=YDL059C;Name=YDL059C;Alias=RAD59
-chrIV	SGD	CDS	345665	351037	.	+	.	ID=YDL058W;Name=YDL058W;Alias=USO1
-chrIV	SGD	CDS	351434	352420	.	+	.	ID=YDL057W;Name=YDL057W;Alias=
-chrIV	SGD	CDS	352877	355378	.	+	.	ID=YDL056W;Name=YDL056W;Alias=MBP1
-chrIV	SGD	CDS	355674	356759	.	-	.	ID=YDL055C;Name=YDL055C;Alias=PSA1
-chrIV	SGD	CDS	359825	361285	.	-	.	ID=YDL054C;Name=YDL054C;Alias=MCH1
-chrIV	SGD	CDS	361699	362256	.	-	.	ID=YDL053C;Name=YDL053C;Alias=PBP4
-chrIV	SGD	CDS	362672	363583	.	-	.	ID=YDL052C;Name=YDL052C;Alias=SLC1
-chrIV	SGD	CDS	363952	364779	.	+	.	ID=YDL051W;Name=YDL051W;Alias=LHP1
-chrIV	SGD	CDS	365068	365874	.	-	.	ID=YDL049C;Name=YDL049C;Alias=KNH1
-chrIV	SGD	CDS	366739	368211	.	-	.	ID=YDL048C;Name=YDL048C;Alias=STP4
-chrIV	SGD	CDS	369771	370706	.	+	.	ID=YDL047W;Name=YDL047W;Alias=SIT4
-chrIV	SGD	CDS	371240	371761	.	+	.	ID=YDL046W;Name=YDL046W;Alias=NPC2
-chrIV	SGD	CDS	372248	372535	.	+	.	ID=YDL045W-A;Name=YDL045W-A;Alias=MRP10
-chrIV	SGD	CDS	372688	373608	.	-	.	ID=YDL045C;Name=YDL045C;Alias=FAD1
-chrIV	SGD	CDS	373967	375289	.	-	.	ID=YDL044C;Name=YDL044C;Alias=MTF2
-chrIV	SGD	CDS	375680	376480	.	-	.	ID=YDL043C;Name=YDL043C;Alias=PRP11
-chrIV	SGD	CDS	376757	378445	.	-	.	ID=YDL042C;Name=YDL042C;Alias=SIR2
-chrIV	SGD	CDS	378874	381438	.	-	.	ID=YDL040C;Name=YDL040C;Alias=NAT1
-chrIV	SGD	CDS	381985	384081	.	-	.	ID=YDL039C;Name=YDL039C;Alias=PRM7
-chrIV	SGD	CDS	384601	385587	.	-	.	ID=YDL037C;Name=YDL037C;Alias=BSC1
-chrIV	SGD	CDS	387513	388901	.	-	.	ID=YDL036C;Name=YDL036C;Alias=PUS9
-chrIV	SGD	CDS	389172	392057	.	-	.	ID=YDL035C;Name=YDL035C;Alias=GPR1
-chrIV	SGD	CDS	392659	393912	.	-	.	ID=YDL033C;Name=YDL033C;Alias=SLM3
-chrIV	SGD	CDS	394217	397204	.	+	.	ID=YDL031W;Name=YDL031W;Alias=DBP10
-chrIV	SGD	CDS	397537	399129	.	+	.	ID=YDL030W;Name=YDL030W;Alias=PRP9
-chrIV	SGD	CDS	399340	400638	.	+	.	ID=YDL029W;Name=YDL029W;Alias=ARP2
-chrIV	SGD	CDS	400997	403291	.	-	.	ID=YDL028C;Name=YDL028C;Alias=MPS1
-chrIV	SGD	CDS	403695	404957	.	-	.	ID=YDL027C;Name=YDL027C;Alias=MRX9
-chrIV	SGD	CDS	405344	407206	.	-	.	ID=YDL025C;Name=YDL025C;Alias=RTK1
-chrIV	SGD	CDS	408451	409857	.	-	.	ID=YDL024C;Name=YDL024C;Alias=DIA3
-chrIV	SGD	CDS	409808	410056	.	-	.	ID=YDL022C-A;Name=YDL022C-A;Alias=
-chrIV	SGD	CDS	411825	413000	.	+	.	ID=YDL022W;Name=YDL022W;Alias=GPD1
-chrIV	SGD	CDS	413953	414888	.	+	.	ID=YDL021W;Name=YDL021W;Alias=GPM2
-chrIV	SGD	CDS	415113	416708	.	-	.	ID=YDL020C;Name=YDL020C;Alias=RPN4
-chrIV	SGD	CDS	417663	421514	.	-	.	ID=YDL019C;Name=YDL019C;Alias=OSH2
-chrIV	SGD	CDS	422833	423510	.	-	.	ID=YDL018C;Name=YDL018C;Alias=ERP3
-chrIV	SGD	CDS	424209	425732	.	+	.	ID=YDL017W;Name=YDL017W;Alias=CDC7
-chrIV	SGD	CDS	426002	426934	.	-	.	ID=YDL015C;Name=YDL015C;Alias=TSC13
-chrIV	SGD	CDS	427364	428347	.	+	.	ID=YDL014W;Name=YDL014W;Alias=NOP1
-chrIV	SGD	CDS	429067	430926	.	+	.	ID=YDL013W;Name=YDL013W;Alias=SLX5
-chrIV	SGD	CDS	431108	431517	.	-	.	ID=YDL012C;Name=YDL012C;Alias=
-chrIV	SGD	CDS	432330	433025	.	+	.	ID=YDL010W;Name=YDL010W;Alias=GRX6
-chrIV	SGD	CDS	432925	433248	.	-	.	ID=YDL009C;Name=YDL009C;Alias=
-chrIV	SGD	CDS	433497	433994	.	+	.	ID=YDL008W;Name=YDL008W;Alias=APC11
-chrIV	SGD	CDS	436567	436824	.	-	.	ID=YDL007C-A;Name=YDL007C-A;Alias=
-chrIV	SGD	CDS	438047	439360	.	+	.	ID=YDL007W;Name=YDL007W;Alias=RPT2
-chrIV	SGD	CDS	439909	440754	.	+	.	ID=YDL006W;Name=YDL006W;Alias=PTC1
-chrIV	SGD	CDS	441014	442309	.	-	.	ID=YDL005C;Name=YDL005C;Alias=MED2
-chrIV	SGD	CDS	443029	443511	.	+	.	ID=YDL004W;Name=YDL004W;Alias=ATP16
-chrIV	SGD	CDS	444683	446383	.	+	.	ID=YDL003W;Name=YDL003W;Alias=MCD1
-chrIV	SGD	CDS	446967	447578	.	-	.	ID=YDL002C;Name=YDL002C;Alias=NHP10
-chrIV	SGD	CDS	447984	449276	.	+	.	ID=YDL001W;Name=YDL001W;Alias=RMD1
-chrIV	SGD	CDS	450220	452475	.	-	.	ID=YDR001C;Name=YDR001C;Alias=NTH1
-chrIV	SGD	CDS	453045	453650	.	+	.	ID=YDR002W;Name=YDR002W;Alias=YRB1
-chrIV	SGD	CDS	454122	454754	.	+	.	ID=YDR003W;Name=YDR003W;Alias=RCR2
-chrIV	SGD	CDS	454782	454904	.	+	.	ID=YDR003W-A;Name=YDR003W-A;Alias=
-chrIV	SGD	CDS	455201	456583	.	+	.	ID=YDR004W;Name=YDR004W;Alias=RAD57
-chrIV	SGD	CDS	456836	458103	.	-	.	ID=YDR005C;Name=YDR005C;Alias=MAF1
-chrIV	SGD	CDS	458542	461247	.	-	.	ID=YDR006C;Name=YDR006C;Alias=SOK1
-chrIV	SGD	CDS	461842	462516	.	+	.	ID=YDR007W;Name=YDR007W;Alias=TRP1
-chrIV	SGD	CDS	463434	464996	.	+	.	ID=YDR009W;Name=YDR009W;Alias=GAL3
-chrIV	SGD	CDS	465919	470424	.	+	.	ID=YDR011W;Name=YDR011W;Alias=SNQ2
-chrIV	SGD	CDS	471853	472941	.	+	.	ID=YDR012W;Name=YDR012W;Alias=RPL4B
-chrIV	SGD	CDS	473157	473783	.	+	.	ID=YDR013W;Name=YDR013W;Alias=PSF1
-chrIV	SGD	CDS	474046	475989	.	+	.	ID=YDR014W;Name=YDR014W;Alias=RAD61
-chrIV	SGD	CDS	477797	478285	.	+	.	ID=YDR014W-A;Name=YDR014W-A;Alias=HED1
-chrIV	SGD	CDS	478474	478758	.	-	.	ID=YDR016C;Name=YDR016C;Alias=DAD1
-chrIV	SGD	CDS	479115	482267	.	-	.	ID=YDR017C;Name=YDR017C;Alias=KCS1
-chrIV	SGD	CDS	482670	483860	.	-	.	ID=YDR018C;Name=YDR018C;Alias=
-chrIV	SGD	CDS	484163	485365	.	-	.	ID=YDR019C;Name=YDR019C;Alias=GCV1
-chrIV	SGD	CDS	485746	486444	.	-	.	ID=YDR020C;Name=YDR020C;Alias=DAS2
-chrIV	SGD	CDS	486804	488003	.	+	.	ID=YDR021W;Name=YDR021W;Alias=FAL1
-chrIV	SGD	CDS	488072	488662	.	-	.	ID=YDR022C;Name=YDR022C;Alias=ATG31
-chrIV	SGD	CDS	489508	490896	.	+	.	ID=YDR023W;Name=YDR023W;Alias=SES1
-chrIV	SGD	CDS	491515	492324	.	+	.	ID=YDR025W;Name=YDR025W;Alias=RPS11A
-chrIV	SGD	CDS	492556	494268	.	-	.	ID=YDR026C;Name=YDR026C;Alias=NSI1
-chrIV	SGD	CDS	494649	497318	.	-	.	ID=YDR027C;Name=YDR027C;Alias=VPS54
-chrIV	SGD	CDS	497835	500879	.	-	.	ID=YDR028C;Name=YDR028C;Alias=REG1
-chrIV	SGD	CDS	501753	503273	.	-	.	ID=YDR030C;Name=YDR030C;Alias=RAD28
-chrIV	SGD	CDS	503498	503863	.	+	.	ID=YDR031W;Name=YDR031W;Alias=MIX14
-chrIV	SGD	CDS	504099	504695	.	-	.	ID=YDR032C;Name=YDR032C;Alias=PST2
-chrIV	SGD	CDS	508147	509109	.	+	.	ID=YDR033W;Name=YDR033W;Alias=MRH1
-chrIV	SGD	CDS	509737	512109	.	-	.	ID=YDR034C;Name=YDR034C;Alias=LYS14
-chrIV	SGD	CDS	520516	520692	.	-	.	ID=YDR034C-A;Name=YDR034C-A;Alias=
-chrIV	SGD	CDS	521314	521469	.	+	.	ID=YDR034W-B;Name=YDR034W-B;Alias=
-chrIV	SGD	CDS	521816	522928	.	+	.	ID=YDR035W;Name=YDR035W;Alias=ARO3
-chrIV	SGD	CDS	523211	524713	.	-	.	ID=YDR036C;Name=YDR036C;Alias=EHD3
-chrIV	SGD	CDS	525440	527215	.	+	.	ID=YDR037W;Name=YDR037W;Alias=KRS1
-chrIV	SGD	CDS	527422	530697	.	-	.	ID=YDR038C;Name=YDR038C;Alias=ENA5
-chrIV	SGD	CDS	531307	534582	.	-	.	ID=YDR039C;Name=YDR039C;Alias=ENA2
-chrIV	SGD	CDS	535192	538467	.	-	.	ID=YDR040C;Name=YDR040C;Alias=ENA1
-chrIV	SGD	CDS	539803	540414	.	+	.	ID=YDR041W;Name=YDR041W;Alias=RSM10
-chrIV	SGD	CDS	540601	541203	.	-	.	ID=YDR042C;Name=YDR042C;Alias=
-chrIV	SGD	CDS	542674	543369	.	-	.	ID=YDR043C;Name=YDR043C;Alias=NRG1
-chrIV	SGD	CDS	546642	547628	.	+	.	ID=YDR044W;Name=YDR044W;Alias=HEM13
-chrIV	SGD	CDS	547978	548310	.	-	.	ID=YDR045C;Name=YDR045C;Alias=RPC11
-chrIV	SGD	CDS	548762	550576	.	-	.	ID=YDR046C;Name=YDR046C;Alias=BAP3
-chrIV	SGD	CDS	551860	552948	.	+	.	ID=YDR047W;Name=YDR047W;Alias=HEM12
-chrIV	SGD	CDS	553254	555152	.	+	.	ID=YDR049W;Name=YDR049W;Alias=VMS1
-chrIV	SGD	CDS	555726	556472	.	-	.	ID=YDR050C;Name=YDR050C;Alias=TPI1
-chrIV	SGD	CDS	557056	558060	.	-	.	ID=YDR051C;Name=YDR051C;Alias=DET1
-chrIV	SGD	CDS	558511	560625	.	-	.	ID=YDR052C;Name=YDR052C;Alias=DBF4
-chrIV	SGD	CDS	561440	562327	.	-	.	ID=YDR054C;Name=YDR054C;Alias=CDC34
-chrIV	SGD	CDS	563527	564861	.	+	.	ID=YDR055W;Name=YDR055W;Alias=PST1
-chrIV	SGD	CDS	565023	565640	.	-	.	ID=YDR056C;Name=YDR056C;Alias=EMC10
-chrIV	SGD	CDS	565927	567555	.	+	.	ID=YDR057W;Name=YDR057W;Alias=YOS9
-chrIV	SGD	CDS	567723	568703	.	-	.	ID=YDR058C;Name=YDR058C;Alias=TGL2
-chrIV	SGD	CDS	569234	569770	.	-	.	ID=YDR059C;Name=YDR059C;Alias=UBC5
-chrIV	SGD	CDS	570649	573726	.	+	.	ID=YDR060W;Name=YDR060W;Alias=MAK21
-chrIV	SGD	CDS	574164	575783	.	+	.	ID=YDR061W;Name=YDR061W;Alias=
-chrIV	SGD	CDS	576474	578159	.	+	.	ID=YDR062W;Name=YDR062W;Alias=LCB2
-chrIV	SGD	CDS	578663	579112	.	+	.	ID=YDR063W;Name=YDR063W;Alias=AIM7
-chrIV	SGD	CDS	579458	580452	.	+	.	ID=YDR064W;Name=YDR064W;Alias=RPS13
-chrIV	SGD	CDS	580687	581784	.	+	.	ID=YDR065W;Name=YDR065W;Alias=RRG1
-chrIV	SGD	CDS	581908	582498	.	-	.	ID=YDR066C;Name=YDR066C;Alias=RTR2
-chrIV	SGD	CDS	582791	583465	.	-	.	ID=YDR067C;Name=YDR067C;Alias=OCA6
-chrIV	SGD	CDS	583713	584645	.	+	.	ID=YDR068W;Name=YDR068W;Alias=DOS2
-chrIV	SGD	CDS	584939	587719	.	-	.	ID=YDR069C;Name=YDR069C;Alias=DOA4
-chrIV	SGD	CDS	588098	588379	.	-	.	ID=YDR070C;Name=YDR070C;Alias=FMP16
-chrIV	SGD	CDS	588827	589402	.	-	.	ID=YDR071C;Name=YDR071C;Alias=PAA1
-chrIV	SGD	CDS	589761	591344	.	-	.	ID=YDR072C;Name=YDR072C;Alias=IPT1
-chrIV	SGD	CDS	592439	592948	.	+	.	ID=YDR073W;Name=YDR073W;Alias=SNF11
-chrIV	SGD	CDS	593893	596583	.	+	.	ID=YDR074W;Name=YDR074W;Alias=TPS2
-chrIV	SGD	CDS	597156	598082	.	+	.	ID=YDR075W;Name=YDR075W;Alias=PPH3
-chrIV	SGD	CDS	598468	599688	.	+	.	ID=YDR076W;Name=YDR076W;Alias=RAD55
-chrIV	SGD	CDS	600793	601809	.	+	.	ID=YDR077W;Name=YDR077W;Alias=SED1
-chrIV	SGD	CDS	602198	602869	.	-	.	ID=YDR078C;Name=YDR078C;Alias=SHU2
-chrIV	SGD	CDS	603064	603399	.	+	.	ID=YDR079W;Name=YDR079W;Alias=PET100
-chrIV	SGD	CDS	603593	603811	.	-	.	ID=YDR079C-A;Name=YDR079C-A;Alias=TFB5
-chrIV	SGD	CDS	604008	606986	.	+	.	ID=YDR080W;Name=YDR080W;Alias=VPS41
-chrIV	SGD	CDS	607304	610081	.	-	.	ID=YDR081C;Name=YDR081C;Alias=PDC2
-chrIV	SGD	CDS	610441	611925	.	+	.	ID=YDR082W;Name=YDR082W;Alias=STN1
-chrIV	SGD	CDS	612073	613251	.	+	.	ID=YDR083W;Name=YDR083W;Alias=RRP8
-chrIV	SGD	CDS	613405	614004	.	-	.	ID=YDR084C;Name=YDR084C;Alias=TVP23
-chrIV	SGD	CDS	614288	616150	.	-	.	ID=YDR085C;Name=YDR085C;Alias=AFR1
-chrIV	SGD	CDS	616928	617170	.	-	.	ID=YDR086C;Name=YDR086C;Alias=SSS1
-chrIV	SGD	CDS	617470	618306	.	-	.	ID=YDR087C;Name=YDR087C;Alias=RRP1
-chrIV	SGD	CDS	618497	619645	.	-	.	ID=YDR088C;Name=YDR088C;Alias=SLU7
-chrIV	SGD	CDS	622112	624721	.	+	.	ID=YDR089W;Name=YDR089W;Alias=VTC5
-chrIV	SGD	CDS	625066	625998	.	-	.	ID=YDR090C;Name=YDR090C;Alias=
-chrIV	SGD	CDS	626708	628534	.	-	.	ID=YDR091C;Name=YDR091C;Alias=RLI1
-chrIV	SGD	CDS	629876	630605	.	+	.	ID=YDR092W;Name=YDR092W;Alias=UBC13
-chrIV	SGD	CDS	631282	636120	.	+	.	ID=YDR093W;Name=YDR093W;Alias=DNF2
-chrIV	SGD	CDS	637139	639823	.	+	.	ID=YDR096W;Name=YDR096W;Alias=GIS1
-chrIV	SGD	CDS	640109	643837	.	-	.	ID=YDR097C;Name=YDR097C;Alias=MSH6
-chrIV	SGD	CDS	644178	644930	.	-	.	ID=YDR098C;Name=YDR098C;Alias=GRX3
-chrIV	SGD	CDS	652781	654428	.	+	.	ID=YDR099W;Name=YDR099W;Alias=BMH2
-chrIV	SGD	CDS	655013	655444	.	+	.	ID=YDR100W;Name=YDR100W;Alias=TVP15
-chrIV	SGD	CDS	655686	657467	.	-	.	ID=YDR101C;Name=YDR101C;Alias=ARX1
-chrIV	SGD	CDS	658350	661103	.	+	.	ID=YDR103W;Name=YDR103W;Alias=STE5
-chrIV	SGD	CDS	661173	664910	.	-	.	ID=YDR104C;Name=YDR104C;Alias=SPO71
-chrIV	SGD	CDS	665349	666770	.	-	.	ID=YDR105C;Name=YDR105C;Alias=TMS1
-chrIV	SGD	CDS	667004	667858	.	+	.	ID=YDR106W;Name=YDR106W;Alias=ARP10
-chrIV	SGD	CDS	669016	671034	.	-	.	ID=YDR107C;Name=YDR107C;Alias=TMN2
-chrIV	SGD	CDS	671269	673365	.	+	.	ID=YDR108W;Name=YDR108W;Alias=TRS85
-chrIV	SGD	CDS	673520	675667	.	-	.	ID=YDR109C;Name=YDR109C;Alias=
-chrIV	SGD	CDS	676102	677802	.	+	.	ID=YDR110W;Name=YDR110W;Alias=FOB1
-chrIV	SGD	CDS	678241	679764	.	-	.	ID=YDR111C;Name=YDR111C;Alias=ALT2
-chrIV	SGD	CDS	680496	681617	.	-	.	ID=YDR113C;Name=YDR113C;Alias=PDS1
-chrIV	SGD	CDS	681924	682226	.	-	.	ID=YDR114C;Name=YDR114C;Alias=
-chrIV	SGD	CDS	682175	682492	.	+	.	ID=YDR115W;Name=YDR115W;Alias=MRX14
-chrIV	SGD	CDS	682724	683581	.	-	.	ID=YDR116C;Name=YDR116C;Alias=MRPL1
-chrIV	SGD	CDS	683946	685643	.	-	.	ID=YDR117C;Name=YDR117C;Alias=TMA64
-chrIV	SGD	CDS	685882	687840	.	+	.	ID=YDR118W;Name=YDR118W;Alias=APC4
-chrIV	SGD	CDS	688227	690533	.	+	.	ID=YDR119W;Name=YDR119W;Alias=VBA4
-chrIV	SGD	CDS	691014	691214	.	+	.	ID=YDR119W-A;Name=YDR119W-A;Alias=COX26
-chrIV	SGD	CDS	691549	693261	.	-	.	ID=YDR120C;Name=YDR120C;Alias=TRM1
-chrIV	SGD	CDS	693585	694175	.	+	.	ID=YDR121W;Name=YDR121W;Alias=DPB4
-chrIV	SGD	CDS	694700	697894	.	+	.	ID=YDR122W;Name=YDR122W;Alias=KIN1
-chrIV	SGD	CDS	698554	699468	.	-	.	ID=YDR123C;Name=YDR123C;Alias=INO2
-chrIV	SGD	CDS	700315	701289	.	+	.	ID=YDR124W;Name=YDR124W;Alias=
-chrIV	SGD	CDS	701397	702758	.	-	.	ID=YDR125C;Name=YDR125C;Alias=ECM18
-chrIV	SGD	CDS	703234	704244	.	+	.	ID=YDR126W;Name=YDR126W;Alias=SWF1
-chrIV	SGD	CDS	704484	709250	.	+	.	ID=YDR127W;Name=YDR127W;Alias=ARO1
-chrIV	SGD	CDS	709549	712995	.	+	.	ID=YDR128W;Name=YDR128W;Alias=MTC5
-chrIV	SGD	CDS	713340	715379	.	-	.	ID=YDR129C;Name=YDR129C;Alias=SAC6
-chrIV	SGD	CDS	715747	716622	.	-	.	ID=YDR130C;Name=YDR130C;Alias=FIN1
-chrIV	SGD	CDS	716790	718460	.	-	.	ID=YDR131C;Name=YDR131C;Alias=
-chrIV	SGD	CDS	718816	720303	.	-	.	ID=YDR132C;Name=YDR132C;Alias=
-chrIV	SGD	CDS	723004	727551	.	-	.	ID=YDR135C;Name=YDR135C;Alias=YCF1
-chrIV	SGD	CDS	728259	730250	.	+	.	ID=YDR137W;Name=YDR137W;Alias=RGP1
-chrIV	SGD	CDS	730578	732836	.	+	.	ID=YDR138W;Name=YDR138W;Alias=HPR1
-chrIV	SGD	CDS	733618	733924	.	-	.	ID=YDR139C;Name=YDR139C;Alias=RUB1
-chrIV	SGD	CDS	734138	734803	.	+	.	ID=YDR140W;Name=YDR140W;Alias=MTQ2
-chrIV	SGD	CDS	734901	739997	.	-	.	ID=YDR141C;Name=YDR141C;Alias=DOP1
-chrIV	SGD	CDS	740473	741600	.	-	.	ID=YDR142C;Name=YDR142C;Alias=PEX7
-chrIV	SGD	CDS	742042	743874	.	-	.	ID=YDR143C;Name=YDR143C;Alias=SAN1
-chrIV	SGD	CDS	744311	746101	.	-	.	ID=YDR144C;Name=YDR144C;Alias=MKC7
-chrIV	SGD	CDS	746738	748357	.	+	.	ID=YDR145W;Name=YDR145W;Alias=TAF12
-chrIV	SGD	CDS	748613	750742	.	-	.	ID=YDR146C;Name=YDR146C;Alias=SWI5
-chrIV	SGD	CDS	751631	753235	.	+	.	ID=YDR147W;Name=YDR147W;Alias=EKI1
-chrIV	SGD	CDS	753675	755066	.	-	.	ID=YDR148C;Name=YDR148C;Alias=KGD2
-chrIV	SGD	CDS	755628	763874	.	+	.	ID=YDR150W;Name=YDR150W;Alias=NUM1
-chrIV	SGD	CDS	764178	765155	.	-	.	ID=YDR151C;Name=YDR151C;Alias=CTH1
-chrIV	SGD	CDS	765706	766503	.	+	.	ID=YDR152W;Name=YDR152W;Alias=GIR2
-chrIV	SGD	CDS	766736	767971	.	-	.	ID=YDR153C;Name=YDR153C;Alias=ENT5
-chrIV	SGD	CDS	768512	769000	.	-	.	ID=YDR155C;Name=YDR155C;Alias=CPR1
-chrIV	SGD	CDS	769525	769938	.	+	.	ID=YDR156W;Name=YDR156W;Alias=RPA14
-chrIV	SGD	CDS	770357	771454	.	+	.	ID=YDR158W;Name=YDR158W;Alias=HOM2
-chrIV	SGD	CDS	771877	775782	.	+	.	ID=YDR159W;Name=YDR159W;Alias=SAC3
-chrIV	SGD	CDS	776163	778721	.	+	.	ID=YDR160W;Name=YDR160W;Alias=SSY1
-chrIV	SGD	CDS	779043	780206	.	+	.	ID=YDR161W;Name=YDR161W;Alias=ACL4
-chrIV	SGD	CDS	780390	781100	.	-	.	ID=YDR162C;Name=YDR162C;Alias=NBP2
-chrIV	SGD	CDS	781423	781950	.	+	.	ID=YDR163W;Name=YDR163W;Alias=CWC15
-chrIV	SGD	CDS	782041	784215	.	-	.	ID=YDR164C;Name=YDR164C;Alias=SEC1
-chrIV	SGD	CDS	784871	786205	.	+	.	ID=YDR165W;Name=YDR165W;Alias=TRM82
-chrIV	SGD	CDS	786306	789221	.	-	.	ID=YDR166C;Name=YDR166C;Alias=SEC5
-chrIV	SGD	CDS	789449	790069	.	+	.	ID=YDR167W;Name=YDR167W;Alias=TAF10
-chrIV	SGD	CDS	790328	791848	.	+	.	ID=YDR168W;Name=YDR168W;Alias=CDC37
-chrIV	SGD	CDS	792348	793889	.	-	.	ID=YDR169C;Name=YDR169C;Alias=STB3
-chrIV	SGD	CDS	794574	794723	.	-	.	ID=YDR169C-A;Name=YDR169C-A;Alias=
-chrIV	SGD	CDS	796193	802222	.	-	.	ID=YDR170C;Name=YDR170C;Alias=SEC7
-chrIV	SGD	CDS	806621	807748	.	+	.	ID=YDR171W;Name=YDR171W;Alias=HSP42
-chrIV	SGD	CDS	808324	810381	.	+	.	ID=YDR172W;Name=YDR172W;Alias=SUP35
-chrIV	SGD	CDS	810565	811632	.	-	.	ID=YDR173C;Name=YDR173C;Alias=ARG82
-chrIV	SGD	CDS	812110	812850	.	+	.	ID=YDR174W;Name=YDR174W;Alias=HMO1
-chrIV	SGD	CDS	813193	814152	.	-	.	ID=YDR175C;Name=YDR175C;Alias=RSM24
-chrIV	SGD	CDS	814452	816560	.	+	.	ID=YDR176W;Name=YDR176W;Alias=NGG1
-chrIV	SGD	CDS	816878	817525	.	+	.	ID=YDR177W;Name=YDR177W;Alias=UBC1
-chrIV	SGD	CDS	817950	818495	.	+	.	ID=YDR178W;Name=YDR178W;Alias=SDH4
-chrIV	SGD	CDS	818708	819196	.	-	.	ID=YDR179C;Name=YDR179C;Alias=CSN9
-chrIV	SGD	CDS	819433	820824	.	+	.	ID=YDR179W-A;Name=YDR179W-A;Alias=NVJ3
-chrIV	SGD	CDS	821295	825776	.	+	.	ID=YDR180W;Name=YDR180W;Alias=SCC2
-chrIV	SGD	CDS	825910	827355	.	-	.	ID=YDR181C;Name=YDR181C;Alias=SAS4
-chrIV	SGD	CDS	827582	829057	.	+	.	ID=YDR182W;Name=YDR182W;Alias=CDC1
-chrIV	SGD	CDS	829151	829354	.	+	.	ID=YDR182W-A;Name=YDR182W-A;Alias=
-chrIV	SGD	CDS	829585	830277	.	+	.	ID=YDR183W;Name=YDR183W;Alias=PLP1
-chrIV	SGD	CDS	830629	831513	.	-	.	ID=YDR184C;Name=YDR184C;Alias=ATC1
-chrIV	SGD	CDS	831934	832473	.	-	.	ID=YDR185C;Name=YDR185C;Alias=UPS3
-chrIV	SGD	CDS	832859	835492	.	-	.	ID=YDR186C;Name=YDR186C;Alias=SND1
-chrIV	SGD	CDS	836421	838061	.	+	.	ID=YDR188W;Name=YDR188W;Alias=CCT6
-chrIV	SGD	CDS	838392	840392	.	+	.	ID=YDR189W;Name=YDR189W;Alias=SLY1
-chrIV	SGD	CDS	840604	841995	.	-	.	ID=YDR190C;Name=YDR190C;Alias=RVB1
-chrIV	SGD	CDS	842337	843449	.	+	.	ID=YDR191W;Name=YDR191W;Alias=HST4
-chrIV	SGD	CDS	843569	844861	.	-	.	ID=YDR192C;Name=YDR192C;Alias=NUP42
-chrIV	SGD	CDS	845952	847946	.	-	.	ID=YDR194C;Name=YDR194C;Alias=MSS116
-chrIV	SGD	CDS	848071	848223	.	+	.	ID=YDR194W-A;Name=YDR194W-A;Alias=
-chrIV	SGD	CDS	848599	850200	.	+	.	ID=YDR195W;Name=YDR195W;Alias=REF2
-chrIV	SGD	CDS	850274	850999	.	-	.	ID=YDR196C;Name=YDR196C;Alias=CAB5
-chrIV	SGD	CDS	851228	852397	.	+	.	ID=YDR197W;Name=YDR197W;Alias=CBS2
-chrIV	SGD	CDS	852533	853972	.	-	.	ID=YDR198C;Name=YDR198C;Alias=RKM2
-chrIV	SGD	CDS	854279	856093	.	-	.	ID=YDR200C;Name=YDR200C;Alias=VPS64
-chrIV	SGD	CDS	856317	856814	.	+	.	ID=YDR201W;Name=YDR201W;Alias=SPC19
-chrIV	SGD	CDS	856898	857953	.	-	.	ID=YDR202C;Name=YDR202C;Alias=RAV2
-chrIV	SGD	CDS	858137	859144	.	+	.	ID=YDR204W;Name=YDR204W;Alias=COQ4
-chrIV	SGD	CDS	859346	861520	.	+	.	ID=YDR205W;Name=YDR205W;Alias=MSC2
-chrIV	SGD	CDS	862054	864708	.	+	.	ID=YDR206W;Name=YDR206W;Alias=EBS1
-chrIV	SGD	CDS	865012	867522	.	-	.	ID=YDR207C;Name=YDR207C;Alias=UME6
-chrIV	SGD	CDS	868224	870563	.	+	.	ID=YDR208W;Name=YDR208W;Alias=MSS4
-chrIV	SGD	CDS	871074	871301	.	+	.	ID=YDR210W;Name=YDR210W;Alias=
-chrIV	SGD	CDS	884727	886865	.	+	.	ID=YDR211W;Name=YDR211W;Alias=GCD6
-chrIV	SGD	CDS	887232	888911	.	+	.	ID=YDR212W;Name=YDR212W;Alias=TCP1
-chrIV	SGD	CDS	889751	892492	.	+	.	ID=YDR213W;Name=YDR213W;Alias=UPC2
-chrIV	SGD	CDS	892875	893927	.	+	.	ID=YDR214W;Name=YDR214W;Alias=AHA1
-chrIV	SGD	CDS	895035	899006	.	+	.	ID=YDR216W;Name=YDR216W;Alias=ADR1
-chrIV	SGD	CDS	899551	903480	.	-	.	ID=YDR217C;Name=YDR217C;Alias=RAD9
-chrIV	SGD	CDS	903781	905052	.	-	.	ID=YDR218C;Name=YDR218C;Alias=SPR28
-chrIV	SGD	CDS	905455	906852	.	-	.	ID=YDR219C;Name=YDR219C;Alias=MFB1
-chrIV	SGD	CDS	907330	909438	.	+	.	ID=YDR221W;Name=YDR221W;Alias=GTB1
-chrIV	SGD	CDS	910054	911301	.	+	.	ID=YDR222W;Name=YDR222W;Alias=
-chrIV	SGD	CDS	912099	913502	.	+	.	ID=YDR223W;Name=YDR223W;Alias=CRF1
-chrIV	SGD	CDS	914317	914712	.	-	.	ID=YDR224C;Name=YDR224C;Alias=HTB1
-chrIV	SGD	CDS	915530	915928	.	+	.	ID=YDR225W;Name=YDR225W;Alias=HTA1
-chrIV	SGD	CDS	916486	917154	.	+	.	ID=YDR226W;Name=YDR226W;Alias=ADK1
-chrIV	SGD	CDS	917571	921647	.	+	.	ID=YDR227W;Name=YDR227W;Alias=SIR4
-chrIV	SGD	CDS	921926	923806	.	-	.	ID=YDR228C;Name=YDR228C;Alias=PCF11
-chrIV	SGD	CDS	924785	926146	.	+	.	ID=YDR229W;Name=YDR229W;Alias=IVY1
-chrIV	SGD	CDS	926293	926910	.	-	.	ID=YDR231C;Name=YDR231C;Alias=COX20
-chrIV	SGD	CDS	927452	929098	.	+	.	ID=YDR232W;Name=YDR232W;Alias=HEM1
-chrIV	SGD	CDS	929470	930357	.	-	.	ID=YDR233C;Name=YDR233C;Alias=RTN1
-chrIV	SGD	CDS	931129	933210	.	+	.	ID=YDR234W;Name=YDR234W;Alias=LYS4
-chrIV	SGD	CDS	933504	935138	.	+	.	ID=YDR235W;Name=YDR235W;Alias=PRP42
-chrIV	SGD	CDS	935236	935892	.	-	.	ID=YDR236C;Name=YDR236C;Alias=FMN1
-chrIV	SGD	CDS	936615	937493	.	+	.	ID=YDR237W;Name=YDR237W;Alias=MRPL7
-chrIV	SGD	CDS	937895	940816	.	-	.	ID=YDR238C;Name=YDR238C;Alias=SEC26
-chrIV	SGD	CDS	941057	943420	.	-	.	ID=YDR239C;Name=YDR239C;Alias=
-chrIV	SGD	CDS	943674	945152	.	-	.	ID=YDR240C;Name=YDR240C;Alias=SNU56
-chrIV	SGD	CDS	946807	948456	.	+	.	ID=YDR242W;Name=YDR242W;Alias=AMD2
-chrIV	SGD	CDS	948518	950284	.	-	.	ID=YDR243C;Name=YDR243C;Alias=PRP28
-chrIV	SGD	CDS	950563	952401	.	+	.	ID=YDR244W;Name=YDR244W;Alias=PEX5
-chrIV	SGD	CDS	952800	953981	.	+	.	ID=YDR245W;Name=YDR245W;Alias=MNN10
-chrIV	SGD	CDS	954288	954947	.	+	.	ID=YDR246W;Name=YDR246W;Alias=TRS23
-chrIV	SGD	CDS	955133	955333	.	+	.	ID=YDR246W-A;Name=YDR246W-A;Alias=
-chrIV	SGD	CDS	956013	957398	.	+	.	ID=YDR247W;Name=YDR247W;Alias=VHS1
-chrIV	SGD	CDS	957758	958339	.	-	.	ID=YDR248C;Name=YDR248C;Alias=
-chrIV	SGD	CDS	958681	959802	.	-	.	ID=YDR249C;Name=YDR249C;Alias=
-chrIV	SGD	CDS	960614	963106	.	+	.	ID=YDR251W;Name=YDR251W;Alias=PAM1
-chrIV	SGD	CDS	963412	963861	.	+	.	ID=YDR252W;Name=YDR252W;Alias=BTT1
-chrIV	SGD	CDS	963990	964565	.	-	.	ID=YDR253C;Name=YDR253C;Alias=MET32
-chrIV	SGD	CDS	965113	966489	.	+	.	ID=YDR254W;Name=YDR254W;Alias=CHL4
-chrIV	SGD	CDS	966557	967822	.	-	.	ID=YDR255C;Name=YDR255C;Alias=RMD5
-chrIV	SGD	CDS	968133	969680	.	-	.	ID=YDR256C;Name=YDR256C;Alias=CTA1
-chrIV	SGD	CDS	969990	971474	.	-	.	ID=YDR257C;Name=YDR257C;Alias=RKM4
-chrIV	SGD	CDS	971808	974243	.	-	.	ID=YDR258C;Name=YDR258C;Alias=HSP78
-chrIV	SGD	CDS	974631	975782	.	-	.	ID=YDR259C;Name=YDR259C;Alias=YAP6
-chrIV	SGD	CDS	976717	977229	.	-	.	ID=YDR260C;Name=YDR260C;Alias=SWM1
-chrIV	SGD	CDS	977521	979209	.	-	.	ID=YDR261C;Name=YDR261C;Alias=EXG2
-chrIV	SGD	CDS	993134	993952	.	+	.	ID=YDR262W;Name=YDR262W;Alias=
-chrIV	SGD	CDS	994242	995534	.	-	.	ID=YDR263C;Name=YDR263C;Alias=DIN7
-chrIV	SGD	CDS	996029	998323	.	-	.	ID=YDR264C;Name=YDR264C;Alias=AKR1
-chrIV	SGD	CDS	998864	999877	.	+	.	ID=YDR265W;Name=YDR265W;Alias=PEX10
-chrIV	SGD	CDS	1000104	1002023	.	-	.	ID=YDR266C;Name=YDR266C;Alias=HEL2
-chrIV	SGD	CDS	1002510	1003502	.	-	.	ID=YDR267C;Name=YDR267C;Alias=CIA1
-chrIV	SGD	CDS	1004004	1005143	.	+	.	ID=YDR268W;Name=YDR268W;Alias=MSW1
-chrIV	SGD	CDS	1005675	1008689	.	+	.	ID=YDR270W;Name=YDR270W;Alias=CCC2
-chrIV	SGD	CDS	1009010	1009834	.	+	.	ID=YDR272W;Name=YDR272W;Alias=GLO2
-chrIV	SGD	CDS	1010176	1011273	.	+	.	ID=YDR273W;Name=YDR273W;Alias=DON1
-chrIV	SGD	CDS	1012252	1012959	.	+	.	ID=YDR275W;Name=YDR275W;Alias=BSC2
-chrIV	SGD	CDS	1013476	1013643	.	-	.	ID=YDR276C;Name=YDR276C;Alias=PMP3
-chrIV	SGD	CDS	1014401	1015702	.	-	.	ID=YDR277C;Name=YDR277C;Alias=MTH1
-chrIV	SGD	CDS	1019368	1020420	.	+	.	ID=YDR279W;Name=YDR279W;Alias=RNH202
-chrIV	SGD	CDS	1020747	1021664	.	+	.	ID=YDR280W;Name=YDR280W;Alias=RRP45
-chrIV	SGD	CDS	1022007	1022321	.	-	.	ID=YDR281C;Name=YDR281C;Alias=PHM6
-chrIV	SGD	CDS	1023511	1024755	.	-	.	ID=YDR282C;Name=YDR282C;Alias=MRX10
-chrIV	SGD	CDS	1025070	1030049	.	-	.	ID=YDR283C;Name=YDR283C;Alias=GCN2
-chrIV	SGD	CDS	1030550	1031419	.	-	.	ID=YDR284C;Name=YDR284C;Alias=DPP1
-chrIV	SGD	CDS	1032436	1035063	.	+	.	ID=YDR285W;Name=YDR285W;Alias=ZIP1
-chrIV	SGD	CDS	1035231	1035575	.	-	.	ID=YDR286C;Name=YDR286C;Alias=
-chrIV	SGD	CDS	1035995	1036873	.	+	.	ID=YDR287W;Name=YDR287W;Alias=INM2
-chrIV	SGD	CDS	1037195	1038106	.	+	.	ID=YDR288W;Name=YDR288W;Alias=NSE3
-chrIV	SGD	CDS	1038280	1039509	.	-	.	ID=YDR289C;Name=YDR289C;Alias=RTT103
-chrIV	SGD	CDS	1039728	1042961	.	+	.	ID=YDR291W;Name=YDR291W;Alias=HRQ1
-chrIV	SGD	CDS	1043146	1045011	.	-	.	ID=YDR292C;Name=YDR292C;Alias=SRP101
-chrIV	SGD	CDS	1045640	1049392	.	-	.	ID=YDR293C;Name=YDR293C;Alias=SSD1
-chrIV	SGD	CDS	1050459	1052228	.	-	.	ID=YDR294C;Name=YDR294C;Alias=DPL1
-chrIV	SGD	CDS	1052623	1054647	.	-	.	ID=YDR295C;Name=YDR295C;Alias=HDA2
-chrIV	SGD	CDS	1055212	1055892	.	+	.	ID=YDR296W;Name=YDR296W;Alias=MHR1
-chrIV	SGD	CDS	1056551	1057600	.	+	.	ID=YDR297W;Name=YDR297W;Alias=SUR2
-chrIV	SGD	CDS	1058176	1058814	.	-	.	ID=YDR298C;Name=YDR298C;Alias=ATP5
-chrIV	SGD	CDS	1059627	1061231	.	+	.	ID=YDR299W;Name=YDR299W;Alias=BFR2
-chrIV	SGD	CDS	1061505	1062791	.	-	.	ID=YDR300C;Name=YDR300C;Alias=PRO1
-chrIV	SGD	CDS	1063352	1067425	.	+	.	ID=YDR301W;Name=YDR301W;Alias=CFT1
-chrIV	SGD	CDS	1067731	1068390	.	+	.	ID=YDR302W;Name=YDR302W;Alias=GPI11
-chrIV	SGD	CDS	1068729	1071386	.	-	.	ID=YDR303C;Name=YDR303C;Alias=RSC3
-chrIV	SGD	CDS	1071880	1072557	.	-	.	ID=YDR304C;Name=YDR304C;Alias=CPR5
-chrIV	SGD	CDS	1072746	1073488	.	-	.	ID=YDR305C;Name=YDR305C;Alias=HNT2
-chrIV	SGD	CDS	1073735	1075171	.	-	.	ID=YDR306C;Name=YDR306C;Alias=
-chrIV	SGD	CDS	1075865	1077853	.	+	.	ID=YDR307W;Name=YDR307W;Alias=PMT7
-chrIV	SGD	CDS	1078027	1078449	.	-	.	ID=YDR308C;Name=YDR308C;Alias=SRB7
-chrIV	SGD	CDS	1079048	1080199	.	-	.	ID=YDR309C;Name=YDR309C;Alias=GIC2
-chrIV	SGD	CDS	1081128	1084316	.	-	.	ID=YDR310C;Name=YDR310C;Alias=SUM1
-chrIV	SGD	CDS	1085065	1086993	.	+	.	ID=YDR311W;Name=YDR311W;Alias=TFB1
-chrIV	SGD	CDS	1087581	1088942	.	+	.	ID=YDR312W;Name=YDR312W;Alias=SSF2
-chrIV	SGD	CDS	1089219	1090079	.	-	.	ID=YDR313C;Name=YDR313C;Alias=PIB1
-chrIV	SGD	CDS	1090433	1092511	.	-	.	ID=YDR314C;Name=YDR314C;Alias=RAD34
-chrIV	SGD	CDS	1092741	1093586	.	-	.	ID=YDR315C;Name=YDR315C;Alias=IPK1
-chrIV	SGD	CDS	1093763	1095178	.	+	.	ID=YDR316W;Name=YDR316W;Alias=OMS1
-chrIV	SGD	CDS	1102184	1103428	.	+	.	ID=YDR317W;Name=YDR317W;Alias=HIM1
-chrIV	SGD	CDS	1103758	1104947	.	+	.	ID=YDR318W;Name=YDR318W;Alias=MCM21
-chrIV	SGD	CDS	1105003	1105827	.	-	.	ID=YDR319C;Name=YDR319C;Alias=YFT2
-chrIV	SGD	CDS	1106095	1108101	.	-	.	ID=YDR320C;Name=YDR320C;Alias=SWA2
-chrIV	SGD	CDS	1108280	1108498	.	-	.	ID=YDR320C-A;Name=YDR320C-A;Alias=DAD4
-chrIV	SGD	CDS	1108702	1109847	.	+	.	ID=YDR321W;Name=YDR321W;Alias=ASP1
-chrIV	SGD	CDS	1110589	1111692	.	+	.	ID=YDR322W;Name=YDR322W;Alias=MRPL35
-chrIV	SGD	CDS	1112003	1112293	.	-	.	ID=YDR322C-A;Name=YDR322C-A;Alias=TIM11
-chrIV	SGD	CDS	1112480	1114027	.	-	.	ID=YDR323C;Name=YDR323C;Alias=PEP7
-chrIV	SGD	CDS	1114433	1116763	.	-	.	ID=YDR324C;Name=YDR324C;Alias=UTP4
-chrIV	SGD	CDS	1117126	1120233	.	+	.	ID=YDR325W;Name=YDR325W;Alias=YCG1
-chrIV	SGD	CDS	1120609	1124925	.	-	.	ID=YDR326C;Name=YDR326C;Alias=YSP2
-chrIV	SGD	CDS	1125434	1126018	.	-	.	ID=YDR328C;Name=YDR328C;Alias=SKP1
-chrIV	SGD	CDS	1126270	1127595	.	-	.	ID=YDR329C;Name=YDR329C;Alias=PEX3
-chrIV	SGD	CDS	1127872	1129374	.	+	.	ID=YDR330W;Name=YDR330W;Alias=UBX5
-chrIV	SGD	CDS	1129588	1130823	.	+	.	ID=YDR331W;Name=YDR331W;Alias=GPI8
-chrIV	SGD	CDS	1131001	1133070	.	+	.	ID=YDR332W;Name=YDR332W;Alias=IRC3
-chrIV	SGD	CDS	1133260	1135431	.	-	.	ID=YDR333C;Name=YDR333C;Alias=RQC1
-chrIV	SGD	CDS	1135932	1140476	.	+	.	ID=YDR334W;Name=YDR334W;Alias=SWR1
-chrIV	SGD	CDS	1141168	1144842	.	+	.	ID=YDR335W;Name=YDR335W;Alias=MSN5
-chrIV	SGD	CDS	1145092	1146036	.	+	.	ID=YDR336W;Name=YDR336W;Alias=MRX8
-chrIV	SGD	CDS	1146319	1147179	.	+	.	ID=YDR337W;Name=YDR337W;Alias=MRPS28
-chrIV	SGD	CDS	1147379	1149466	.	-	.	ID=YDR338C;Name=YDR338C;Alias=
-chrIV	SGD	CDS	1149951	1150520	.	-	.	ID=YDR339C;Name=YDR339C;Alias=FCF1
-chrIV	SGD	CDS	1151803	1153626	.	-	.	ID=YDR341C;Name=YDR341C;Alias=
-chrIV	SGD	CDS	1154216	1155928	.	-	.	ID=YDR342C;Name=YDR342C;Alias=HXT7
-chrIV	SGD	CDS	1159608	1161320	.	-	.	ID=YDR343C;Name=YDR343C;Alias=HXT6
-chrIV	SGD	CDS	1162957	1164660	.	-	.	ID=YDR345C;Name=YDR345C;Alias=HXT3
-chrIV	SGD	CDS	1167214	1168659	.	-	.	ID=YDR346C;Name=YDR346C;Alias=SVF1
-chrIV	SGD	CDS	1169178	1170143	.	+	.	ID=YDR347W;Name=YDR347W;Alias=MRP1
-chrIV	SGD	CDS	1170326	1171825	.	-	.	ID=YDR348C;Name=YDR348C;Alias=PAL1
-chrIV	SGD	CDS	1172386	1174176	.	-	.	ID=YDR349C;Name=YDR349C;Alias=YPS7
-chrIV	SGD	CDS	1176120	1178174	.	-	.	ID=YDR350C;Name=YDR350C;Alias=ATP22
-chrIV	SGD	CDS	1178666	1181260	.	+	.	ID=YDR351W;Name=YDR351W;Alias=SBE2
-chrIV	SGD	CDS	1181801	1182754	.	+	.	ID=YDR352W;Name=YDR352W;Alias=YPQ2
-chrIV	SGD	CDS	1183299	1184258	.	+	.	ID=YDR353W;Name=YDR353W;Alias=TRR1
-chrIV	SGD	CDS	1184747	1185889	.	+	.	ID=YDR354W;Name=YDR354W;Alias=TRP4
-chrIV	SGD	CDS	1186107	1188941	.	+	.	ID=YDR356W;Name=YDR356W;Alias=SPC110
-chrIV	SGD	CDS	1189199	1189567	.	-	.	ID=YDR357C;Name=YDR357C;Alias=CNL1
-chrIV	SGD	CDS	1190059	1191732	.	+	.	ID=YDR358W;Name=YDR358W;Alias=GGA1
-chrIV	SGD	CDS	1191936	1194884	.	-	.	ID=YDR359C;Name=YDR359C;Alias=EAF1
-chrIV	SGD	CDS	1195412	1196263	.	-	.	ID=YDR361C;Name=YDR361C;Alias=BCP1
-chrIV	SGD	CDS	1196679	1198697	.	-	.	ID=YDR362C;Name=YDR362C;Alias=TFC6
-chrIV	SGD	CDS	1199183	1200553	.	+	.	ID=YDR363W;Name=YDR363W;Alias=ESC2
-chrIV	SGD	CDS	1202128	1202397	.	+	.	ID=YDR363W-A;Name=YDR363W-A;Alias=SEM1
-chrIV	SGD	CDS	1202843	1204210	.	-	.	ID=YDR364C;Name=YDR364C;Alias=CDC40
-chrIV	SGD	CDS	1204497	1206383	.	-	.	ID=YDR365C;Name=YDR365C;Alias=ESF1
-chrIV	SGD	CDS	1212438	1212836	.	-	.	ID=YDR366C;Name=YDR366C;Alias=
-chrIV	SGD	CDS	1212848	1213614	.	+	.	ID=YDR367W;Name=YDR367W;Alias=KEI1
-chrIV	SGD	CDS	1213904	1214842	.	+	.	ID=YDR368W;Name=YDR368W;Alias=YPR1
-chrIV	SGD	CDS	1215016	1217580	.	-	.	ID=YDR369C;Name=YDR369C;Alias=XRS2
-chrIV	SGD	CDS	1217782	1219110	.	-	.	ID=YDR370C;Name=YDR370C;Alias=DXO1
-chrIV	SGD	CDS	1219413	1220948	.	+	.	ID=YDR371W;Name=YDR371W;Alias=CTS2
-chrIV	SGD	CDS	1221112	1222149	.	-	.	ID=YDR372C;Name=YDR372C;Alias=VPS74
-chrIV	SGD	CDS	1222759	1223331	.	+	.	ID=YDR373W;Name=YDR373W;Alias=FRQ1
-chrIV	SGD	CDS	1223474	1224394	.	-	.	ID=YDR374C;Name=YDR374C;Alias=PHO92
-chrIV	SGD	CDS	1224757	1225026	.	+	.	ID=YDR374W-A;Name=YDR374W-A;Alias=WIP1
-chrIV	SGD	CDS	1225166	1226536	.	-	.	ID=YDR375C;Name=YDR375C;Alias=BCS1
-chrIV	SGD	CDS	1226822	1228303	.	+	.	ID=YDR376W;Name=YDR376W;Alias=ARH1
-chrIV	SGD	CDS	1228611	1228916	.	+	.	ID=YDR377W;Name=YDR377W;Alias=ATP17
-chrIV	SGD	CDS	1229349	1229609	.	-	.	ID=YDR378C;Name=YDR378C;Alias=LSM6
-chrIV	SGD	CDS	1230167	1233196	.	+	.	ID=YDR379W;Name=YDR379W;Alias=RGA2
-chrIV	SGD	CDS	1233278	1233517	.	-	.	ID=YDR379C-A;Name=YDR379C-A;Alias=SDH6
-chrIV	SGD	CDS	1234218	1236125	.	+	.	ID=YDR380W;Name=YDR380W;Alias=ARO10
-chrIV	SGD	CDS	1236558	1238004	.	+	.	ID=YDR381W;Name=YDR381W;Alias=YRA1
-chrIV	SGD	CDS	1238312	1238850	.	-	.	ID=YDR381C-A;Name=YDR381C-A;Alias=
-chrIV	SGD	CDS	1239492	1239824	.	+	.	ID=YDR382W;Name=YDR382W;Alias=RPP2B
-chrIV	SGD	CDS	1239960	1240676	.	-	.	ID=YDR383C;Name=YDR383C;Alias=NKP1
-chrIV	SGD	CDS	1241204	1242031	.	-	.	ID=YDR384C;Name=YDR384C;Alias=ATO3
-chrIV	SGD	CDS	1243230	1245758	.	+	.	ID=YDR385W;Name=YDR385W;Alias=EFT2
-chrIV	SGD	CDS	1246084	1247982	.	+	.	ID=YDR386W;Name=YDR386W;Alias=MUS81
-chrIV	SGD	CDS	1248154	1249821	.	-	.	ID=YDR387C;Name=YDR387C;Alias=CIN10
-chrIV	SGD	CDS	1250186	1251634	.	+	.	ID=YDR388W;Name=YDR388W;Alias=RVS167
-chrIV	SGD	CDS	1252537	1254501	.	+	.	ID=YDR389W;Name=YDR389W;Alias=SAC7
-chrIV	SGD	CDS	1254937	1256847	.	-	.	ID=YDR390C;Name=YDR390C;Alias=UBA2
-chrIV	SGD	CDS	1257358	1258056	.	-	.	ID=YDR391C;Name=YDR391C;Alias=
-chrIV	SGD	CDS	1258696	1259709	.	+	.	ID=YDR392W;Name=YDR392W;Alias=SPT3
-chrIV	SGD	CDS	1259901	1261271	.	+	.	ID=YDR393W;Name=YDR393W;Alias=SHE9
-chrIV	SGD	CDS	1261681	1262967	.	+	.	ID=YDR394W;Name=YDR394W;Alias=RPT3
-chrIV	SGD	CDS	1263324	1266158	.	+	.	ID=YDR395W;Name=YDR395W;Alias=SXM1
-chrIV	SGD	CDS	1266366	1266898	.	-	.	ID=YDR397C;Name=YDR397C;Alias=NCB2
-chrIV	SGD	CDS	1267471	1269402	.	+	.	ID=YDR398W;Name=YDR398W;Alias=UTP5
-chrIV	SGD	CDS	1270068	1270733	.	+	.	ID=YDR399W;Name=YDR399W;Alias=HPT1
-chrIV	SGD	CDS	1271063	1272085	.	+	.	ID=YDR400W;Name=YDR400W;Alias=URH1
-chrIV	SGD	CDS	1272234	1273703	.	-	.	ID=YDR402C;Name=YDR402C;Alias=DIT2
-chrIV	SGD	CDS	1274602	1276212	.	+	.	ID=YDR403W;Name=YDR403W;Alias=DIT1
-chrIV	SGD	CDS	1276654	1277169	.	-	.	ID=YDR404C;Name=YDR404C;Alias=RPB7
-chrIV	SGD	CDS	1277646	1278437	.	+	.	ID=YDR405W;Name=YDR405W;Alias=MRP20
-chrIV	SGD	CDS	1279210	1283799	.	+	.	ID=YDR406W;Name=YDR406W;Alias=PDR15
-chrIV	SGD	CDS	1284069	1287938	.	-	.	ID=YDR407C;Name=YDR407C;Alias=TRS120
-chrIV	SGD	CDS	1288215	1288859	.	-	.	ID=YDR408C;Name=YDR408C;Alias=ADE8
-chrIV	SGD	CDS	1289406	1292120	.	+	.	ID=YDR409W;Name=YDR409W;Alias=SIZ1
-chrIV	SGD	CDS	1292372	1293091	.	-	.	ID=YDR410C;Name=YDR410C;Alias=STE14
-chrIV	SGD	CDS	1293369	1294394	.	-	.	ID=YDR411C;Name=YDR411C;Alias=DFM1
-chrIV	SGD	CDS	1294693	1295400	.	+	.	ID=YDR412W;Name=YDR412W;Alias=RRP17
-chrIV	SGD	CDS	1295598	1296686	.	-	.	ID=YDR414C;Name=YDR414C;Alias=ERD1
-chrIV	SGD	CDS	1297037	1298161	.	-	.	ID=YDR415C;Name=YDR415C;Alias=
-chrIV	SGD	CDS	1298432	1301011	.	+	.	ID=YDR416W;Name=YDR416W;Alias=SYF1
-chrIV	SGD	CDS	1301616	1302113	.	+	.	ID=YDR418W;Name=YDR418W;Alias=RPL12B
-chrIV	SGD	CDS	1303174	1305072	.	+	.	ID=YDR419W;Name=YDR419W;Alias=RAD30
-chrIV	SGD	CDS	1306267	1311675	.	+	.	ID=YDR420W;Name=YDR420W;Alias=HKR1
-chrIV	SGD	CDS	1312040	1314892	.	+	.	ID=YDR421W;Name=YDR421W;Alias=ARO80
-chrIV	SGD	CDS	1315326	1317773	.	-	.	ID=YDR422C;Name=YDR422C;Alias=SIP1
-chrIV	SGD	CDS	1318046	1319275	.	-	.	ID=YDR423C;Name=YDR423C;Alias=CAD1
-chrIV	SGD	CDS	1319387	1319841	.	-	.	ID=YDR424C;Name=YDR424C;Alias=DYN2
-chrIV	SGD	CDS	1320064	1321941	.	+	.	ID=YDR425W;Name=YDR425W;Alias=SNX41
-chrIV	SGD	CDS	1322205	1323386	.	+	.	ID=YDR427W;Name=YDR427W;Alias=RPN9
-chrIV	SGD	CDS	1323454	1324239	.	-	.	ID=YDR428C;Name=YDR428C;Alias=BNA7
-chrIV	SGD	CDS	1324477	1325301	.	-	.	ID=YDR429C;Name=YDR429C;Alias=TIF35
-chrIV	SGD	CDS	1325501	1328470	.	-	.	ID=YDR430C;Name=YDR430C;Alias=CYM1
-chrIV	SGD	CDS	1328783	1330027	.	+	.	ID=YDR432W;Name=YDR432W;Alias=NPL3
-chrIV	SGD	CDS	1331237	1332841	.	+	.	ID=YDR434W;Name=YDR434W;Alias=GPI17
-chrIV	SGD	CDS	1332983	1333969	.	-	.	ID=YDR435C;Name=YDR435C;Alias=PPM1
-chrIV	SGD	CDS	1334821	1336953	.	+	.	ID=YDR436W;Name=YDR436W;Alias=PPZ2
-chrIV	SGD	CDS	1337352	1337774	.	+	.	ID=YDR437W;Name=YDR437W;Alias=GPI19
-chrIV	SGD	CDS	1338274	1339386	.	+	.	ID=YDR438W;Name=YDR438W;Alias=THI74
-chrIV	SGD	CDS	1339676	1340719	.	+	.	ID=YDR439W;Name=YDR439W;Alias=LRS4
-chrIV	SGD	CDS	1342493	1344241	.	+	.	ID=YDR440W;Name=YDR440W;Alias=DOT1
-chrIV	SGD	CDS	1344517	1345062	.	-	.	ID=YDR441C;Name=YDR441C;Alias=APT2
-chrIV	SGD	CDS	1345676	1349938	.	-	.	ID=YDR443C;Name=YDR443C;Alias=SSN2
-chrIV	SGD	CDS	1350290	1352353	.	+	.	ID=YDR444W;Name=YDR444W;Alias=
-chrIV	SGD	CDS	1353725	1354633	.	+	.	ID=YDR446W;Name=YDR446W;Alias=ECM11
-chrIV	SGD	CDS	1354829	1355553	.	-	.	ID=YDR447C;Name=YDR447C;Alias=RPS17B
-chrIV	SGD	CDS	1356065	1357369	.	+	.	ID=YDR448W;Name=YDR448W;Alias=ADA2
-chrIV	SGD	CDS	1357580	1358902	.	-	.	ID=YDR449C;Name=YDR449C;Alias=UTP6
-chrIV	SGD	CDS	1359923	1360798	.	+	.	ID=YDR450W;Name=YDR450W;Alias=RPS18A
-chrIV	SGD	CDS	1361120	1362181	.	-	.	ID=YDR451C;Name=YDR451C;Alias=YHP1
-chrIV	SGD	CDS	1362878	1364902	.	+	.	ID=YDR452W;Name=YDR452W;Alias=PPN1
-chrIV	SGD	CDS	1365072	1365662	.	-	.	ID=YDR453C;Name=YDR453C;Alias=TSA2
-chrIV	SGD	CDS	1366264	1366827	.	-	.	ID=YDR454C;Name=YDR454C;Alias=GUK1
-chrIV	SGD	CDS	1367485	1369386	.	+	.	ID=YDR456W;Name=YDR456W;Alias=NHX1
-chrIV	SGD	CDS	1369790	1379596	.	+	.	ID=YDR457W;Name=YDR457W;Alias=TOM1
-chrIV	SGD	CDS	1380055	1382046	.	-	.	ID=YDR458C;Name=YDR458C;Alias=HEH2
-chrIV	SGD	CDS	1382319	1383443	.	-	.	ID=YDR459C;Name=YDR459C;Alias=PFA5
-chrIV	SGD	CDS	1383811	1384776	.	+	.	ID=YDR460W;Name=YDR460W;Alias=TFB3
-chrIV	SGD	CDS	1385176	1385286	.	+	.	ID=YDR461W;Name=YDR461W;Alias=MFA1
-chrIV	SGD	CDS	1385524	1385766	.	-	.	ID=YDR461C-A;Name=YDR461C-A;Alias=
-chrIV	SGD	CDS	1386073	1386516	.	+	.	ID=YDR462W;Name=YDR462W;Alias=MRPL28
-chrIV	SGD	CDS	1386816	1388375	.	+	.	ID=YDR463W;Name=YDR463W;Alias=STP1
-chrIV	SGD	CDS	1388872	1393179	.	+	.	ID=YDR464W;Name=YDR464W;Alias=SPP41
-chrIV	SGD	CDS	1393336	1394574	.	-	.	ID=YDR465C;Name=YDR465C;Alias=RMT2
-chrIV	SGD	CDS	1395121	1397817	.	+	.	ID=YDR466W;Name=YDR466W;Alias=PKH3
-chrIV	SGD	CDS	1398026	1398700	.	-	.	ID=YDR468C;Name=YDR468C;Alias=TLG1
-chrIV	SGD	CDS	1399015	1399542	.	+	.	ID=YDR469W;Name=YDR469W;Alias=SDC1
-chrIV	SGD	CDS	1399706	1401214	.	-	.	ID=YDR470C;Name=YDR470C;Alias=UGO1
-chrIV	SGD	CDS	1401770	1402564	.	+	.	ID=YDR471W;Name=YDR471W;Alias=RPL27B
-chrIV	SGD	CDS	1403322	1404173	.	+	.	ID=YDR472W;Name=YDR472W;Alias=TRS31
-chrIV	SGD	CDS	1404445	1405854	.	-	.	ID=YDR473C;Name=YDR473C;Alias=PRP3
-chrIV	SGD	CDS	1407464	1410094	.	-	.	ID=YDR475C;Name=YDR475C;Alias=JIP4
-chrIV	SGD	CDS	1410453	1411127	.	-	.	ID=YDR476C;Name=YDR476C;Alias=
-chrIV	SGD	CDS	1412373	1414274	.	+	.	ID=YDR477W;Name=YDR477W;Alias=SNF1
-chrIV	SGD	CDS	1414575	1415171	.	+	.	ID=YDR478W;Name=YDR478W;Alias=SNM1
-chrIV	SGD	CDS	1415210	1416874	.	-	.	ID=YDR479C;Name=YDR479C;Alias=PEX29
-chrIV	SGD	CDS	1417399	1418370	.	+	.	ID=YDR480W;Name=YDR480W;Alias=DIG2
-chrIV	SGD	CDS	1418550	1420250	.	-	.	ID=YDR481C;Name=YDR481C;Alias=PHO8
-chrIV	SGD	CDS	1420431	1420838	.	-	.	ID=YDR482C;Name=YDR482C;Alias=CWC21
-chrIV	SGD	CDS	1421157	1422485	.	+	.	ID=YDR483W;Name=YDR483W;Alias=KRE2
-chrIV	SGD	CDS	1422763	1424688	.	+	.	ID=YDR484W;Name=YDR484W;Alias=VPS52
-chrIV	SGD	CDS	1424820	1427207	.	-	.	ID=YDR485C;Name=YDR485C;Alias=VPS72
-chrIV	SGD	CDS	1427431	1428120	.	-	.	ID=YDR486C;Name=YDR486C;Alias=VPS60
-chrIV	SGD	CDS	1428354	1428980	.	-	.	ID=YDR487C;Name=YDR487C;Alias=RIB3
-chrIV	SGD	CDS	1429188	1430789	.	-	.	ID=YDR488C;Name=YDR488C;Alias=PAC11
-chrIV	SGD	CDS	1431012	1431896	.	+	.	ID=YDR489W;Name=YDR489W;Alias=SLD5
-chrIV	SGD	CDS	1431968	1434268	.	-	.	ID=YDR490C;Name=YDR490C;Alias=PKH1
-chrIV	SGD	CDS	1434924	1435874	.	+	.	ID=YDR492W;Name=YDR492W;Alias=IZH1
-chrIV	SGD	CDS	1436217	1436588	.	+	.	ID=YDR493W;Name=YDR493W;Alias=MZM1
-chrIV	SGD	CDS	1436930	1438015	.	+	.	ID=YDR494W;Name=YDR494W;Alias=RSM28
-chrIV	SGD	CDS	1438115	1441150	.	-	.	ID=YDR495C;Name=YDR495C;Alias=VPS3
-chrIV	SGD	CDS	1441433	1443403	.	-	.	ID=YDR496C;Name=YDR496C;Alias=PUF6
-chrIV	SGD	CDS	1443713	1445467	.	-	.	ID=YDR497C;Name=YDR497C;Alias=ITR1
-chrIV	SGD	CDS	1445843	1446994	.	-	.	ID=YDR498C;Name=YDR498C;Alias=SEC20
-chrIV	SGD	CDS	1447830	1450073	.	+	.	ID=YDR499W;Name=YDR499W;Alias=LCD1
-chrIV	SGD	CDS	1450198	1450853	.	-	.	ID=YDR500C;Name=YDR500C;Alias=RPL37B
-chrIV	SGD	CDS	1451353	1452918	.	+	.	ID=YDR501W;Name=YDR501W;Alias=PLM2
-chrIV	SGD	CDS	1453310	1454464	.	-	.	ID=YDR502C;Name=YDR502C;Alias=SAM2
-chrIV	SGD	CDS	1455042	1455866	.	-	.	ID=YDR503C;Name=YDR503C;Alias=LPP1
-chrIV	SGD	CDS	1456311	1456694	.	-	.	ID=YDR504C;Name=YDR504C;Alias=SPG3
-chrIV	SGD	CDS	1456695	1459220	.	-	.	ID=YDR505C;Name=YDR505C;Alias=PSP1
-chrIV	SGD	CDS	1459728	1461554	.	-	.	ID=YDR506C;Name=YDR506C;Alias=GMC1
-chrIV	SGD	CDS	1462358	1465786	.	-	.	ID=YDR507C;Name=YDR507C;Alias=GIN4
-chrIV	SGD	CDS	1466453	1468444	.	-	.	ID=YDR508C;Name=YDR508C;Alias=GNP1
-chrIV	SGD	CDS	1469400	1469705	.	+	.	ID=YDR510W;Name=YDR510W;Alias=SMT3
-chrIV	SGD	CDS	1470017	1470418	.	+	.	ID=YDR511W;Name=YDR511W;Alias=SDH7
-chrIV	SGD	CDS	1470500	1471063	.	-	.	ID=YDR512C;Name=YDR512C;Alias=EMI1
-chrIV	SGD	CDS	1471017	1471448	.	+	.	ID=YDR513W;Name=YDR513W;Alias=GRX2
-chrIV	SGD	CDS	1471548	1472999	.	-	.	ID=YDR514C;Name=YDR514C;Alias=
-chrIV	SGD	CDS	1473429	1474772	.	+	.	ID=YDR515W;Name=YDR515W;Alias=SLF1
-chrIV	SGD	CDS	1474974	1476476	.	-	.	ID=YDR516C;Name=YDR516C;Alias=EMI2
-chrIV	SGD	CDS	1477239	1478357	.	+	.	ID=YDR517W;Name=YDR517W;Alias=GRH1
-chrIV	SGD	CDS	1478608	1480161	.	+	.	ID=YDR518W;Name=YDR518W;Alias=EUG1
-chrIV	SGD	CDS	1480425	1480832	.	+	.	ID=YDR519W;Name=YDR519W;Alias=FPR2
-chrIV	SGD	CDS	1481085	1483403	.	-	.	ID=YDR520C;Name=YDR520C;Alias=URC2
-chrIV	SGD	CDS	1483795	1485303	.	-	.	ID=YDR522C;Name=YDR522C;Alias=SPS2
-chrIV	SGD	CDS	1485566	1487038	.	-	.	ID=YDR523C;Name=YDR523C;Alias=SPS1
-chrIV	SGD	CDS	1487542	1488990	.	-	.	ID=YDR524C;Name=YDR524C;Alias=AGE1
-chrIV	SGD	CDS	1489403	1489492	.	+	.	ID=YDR524W-C;Name=YDR524W-C;Alias=
-chrIV	SGD	CDS	1489598	1489798	.	-	.	ID=YDR524C-B;Name=YDR524C-B;Alias=
-chrIV	SGD	CDS	1490596	1490835	.	+	.	ID=YDR525W-A;Name=YDR525W-A;Alias=SNA2
-chrIV	SGD	CDS	1491094	1492413	.	+	.	ID=YDR527W;Name=YDR527W;Alias=RBA50
-chrIV	SGD	CDS	1494586	1495857	.	+	.	ID=YDR528W;Name=YDR528W;Alias=HLR1
-chrIV	SGD	CDS	1496165	1496548	.	-	.	ID=YDR529C;Name=YDR529C;Alias=QCR7
-chrIV	SGD	CDS	1496791	1497768	.	-	.	ID=YDR530C;Name=YDR530C;Alias=APA2
-chrIV	SGD	CDS	1498232	1499335	.	+	.	ID=YDR531W;Name=YDR531W;Alias=CAB1
-chrIV	SGD	CDS	1499396	1500553	.	-	.	ID=YDR532C;Name=YDR532C;Alias=KRE28
-chrIV	SGD	CDS	1501447	1502160	.	-	.	ID=YDR533C;Name=YDR533C;Alias=HSP31
-chrIV	SGD	CDS	1503314	1504900	.	-	.	ID=YDR534C;Name=YDR534C;Alias=FIT1
-chrIV	SGD	CDS	1508005	1509714	.	+	.	ID=YDR536W;Name=YDR536W;Alias=STL1
-chrIV	SGD	CDS	1510902	1511630	.	+	.	ID=YDR538W;Name=YDR538W;Alias=PAD1
-chrIV	SGD	CDS	1512094	1513605	.	+	.	ID=YDR539W;Name=YDR539W;Alias=FDC1
-chrIV	SGD	CDS	1517136	1517675	.	-	.	ID=YDR540C;Name=YDR540C;Alias=IRC4
-chrIV	SGD	CDS	1519664	1520698	.	-	.	ID=YDR541C;Name=YDR541C;Alias=
-chrIV	SGD	CDS	1523249	1523611	.	+	.	ID=YDR542W;Name=YDR542W;Alias=PAU10
-chrIV	SGD	CDS	1526321	1531711	.	+	.	ID=YDR545W;Name=YDR545W;Alias=YRF1-1
-chrV	SGD	CDS	264	4097	.	-	.	ID=YEL077C;Name=YEL077C;Alias=
-chrV	SGD	CDS	4185	5114	.	-	.	ID=YEL076C-A;Name=YEL076C-A;Alias=
-chrV	SGD	CDS	4464	5114	.	-	.	ID=YEL076C;Name=YEL076C;Alias=
-chrV	SGD	CDS	5345	5713	.	-	.	ID=YEL075C;Name=YEL075C;Alias=
-chrV	SGD	CDS	7230	7553	.	-	.	ID=YEL073C;Name=YEL073C;Alias=
-chrV	SGD	CDS	13720	14415	.	+	.	ID=YEL072W;Name=YEL072W;Alias=RMD6
-chrV	SGD	CDS	16355	17845	.	+	.	ID=YEL071W;Name=YEL071W;Alias=DLD3
-chrV	SGD	CDS	19589	21097	.	+	.	ID=YEL070W;Name=YEL070W;Alias=DSF1
-chrV	SGD	CDS	21537	23231	.	-	.	ID=YEL069C;Name=YEL069C;Alias=HXT13
-chrV	SGD	CDS	25646	25978	.	-	.	ID=YEL068C;Name=YEL068C;Alias=
-chrV	SGD	CDS	26189	26776	.	-	.	ID=YEL067C;Name=YEL067C;Alias=
-chrV	SGD	CDS	26667	27206	.	+	.	ID=YEL066W;Name=YEL066W;Alias=HPA3
-chrV	SGD	CDS	27657	29543	.	+	.	ID=YEL065W;Name=YEL065W;Alias=SIT1
-chrV	SGD	CDS	29797	31239	.	-	.	ID=YEL064C;Name=YEL064C;Alias=AVT2
-chrV	SGD	CDS	31694	33466	.	-	.	ID=YEL063C;Name=YEL063C;Alias=CAN1
-chrV	SGD	CDS	34407	36254	.	+	.	ID=YEL062W;Name=YEL062W;Alias=NPR2
-chrV	SGD	CDS	36535	39537	.	-	.	ID=YEL061C;Name=YEL061C;Alias=CIN8
-chrV	SGD	CDS	40046	41953	.	-	.	ID=YEL060C;Name=YEL060C;Alias=PRB1
-chrV	SGD	CDS	42400	42624	.	-	.	ID=YEL059C-A;Name=YEL059C-A;Alias=SOM1
-chrV	SGD	CDS	43252	44925	.	+	.	ID=YEL058W;Name=YEL058W;Alias=PCM1
-chrV	SGD	CDS	45020	45721	.	-	.	ID=YEL057C;Name=YEL057C;Alias=SDD1
-chrV	SGD	CDS	47168	48373	.	+	.	ID=YEL056W;Name=YEL056W;Alias=HAT2
-chrV	SGD	CDS	48471	51539	.	-	.	ID=YEL055C;Name=YEL055C;Alias=POL5
-chrV	SGD	CDS	52721	53218	.	-	.	ID=YEL054C;Name=YEL054C;Alias=RPL12A
-chrV	SGD	CDS	53901	56102	.	-	.	ID=YEL053C;Name=YEL053C;Alias=MAK10
-chrV	SGD	CDS	56571	58100	.	+	.	ID=YEL052W;Name=YEL052W;Alias=AFG1
-chrV	SGD	CDS	58378	59148	.	+	.	ID=YEL051W;Name=YEL051W;Alias=VMA8
-chrV	SGD	CDS	59670	60851	.	-	.	ID=YEL050C;Name=YEL050C;Alias=RML2
-chrV	SGD	CDS	63728	64090	.	+	.	ID=YEL049W;Name=YEL049W;Alias=PAU2
-chrV	SGD	CDS	64709	65167	.	-	.	ID=YEL048C;Name=YEL048C;Alias=TCA17
-chrV	SGD	CDS	65385	66797	.	-	.	ID=YEL047C;Name=YEL047C;Alias=FRD1
-chrV	SGD	CDS	67629	68792	.	-	.	ID=YEL046C;Name=YEL046C;Alias=GLY1
-chrV	SGD	CDS	69757	70257	.	+	.	ID=YEL044W;Name=YEL044W;Alias=IES6
-chrV	SGD	CDS	70478	73348	.	+	.	ID=YEL043W;Name=YEL043W;Alias=
-chrV	SGD	CDS	73771	75327	.	+	.	ID=YEL042W;Name=YEL042W;Alias=GDA1
-chrV	SGD	CDS	75944	77431	.	+	.	ID=YEL041W;Name=YEL041W;Alias=YEF1
-chrV	SGD	CDS	78053	79456	.	+	.	ID=YEL040W;Name=YEL040W;Alias=UTR2
-chrV	SGD	CDS	79636	79977	.	-	.	ID=YEL039C;Name=YEL039C;Alias=CYC7
-chrV	SGD	CDS	80462	81145	.	+	.	ID=YEL038W;Name=YEL038W;Alias=UTR4
-chrV	SGD	CDS	81407	82603	.	-	.	ID=YEL037C;Name=YEL037C;Alias=RAD23
-chrV	SGD	CDS	83050	84552	.	-	.	ID=YEL036C;Name=YEL036C;Alias=ANP1
-chrV	SGD	CDS	85045	85545	.	-	.	ID=YEL035C;Name=YEL035C;Alias=UTR5
-chrV	SGD	CDS	85676	86149	.	+	.	ID=YEL034W;Name=YEL034W;Alias=HYP2
-chrV	SGD	CDS	86179	86598	.	+	.	ID=YEL033W;Name=YEL033W;Alias=MTC7
-chrV	SGD	CDS	86937	89852	.	+	.	ID=YEL032W;Name=YEL032W;Alias=MCM3
-chrV	SGD	CDS	90258	93905	.	+	.	ID=YEL031W;Name=YEL031W;Alias=SPF1
-chrV	SGD	CDS	94644	96578	.	+	.	ID=YEL030W;Name=YEL030W;Alias=ECM10
-chrV	SGD	CDS	96858	97796	.	-	.	ID=YEL029C;Name=YEL029C;Alias=BUD16
-chrV	SGD	CDS	100769	101251	.	+	.	ID=YEL027W;Name=YEL027W;Alias=VMA3
-chrV	SGD	CDS	101943	102323	.	+	.	ID=YEL026W;Name=YEL026W;Alias=SNU13
-chrV	SGD	CDS	102581	106147	.	-	.	ID=YEL025C;Name=YEL025C;Alias=
-chrV	SGD	CDS	107260	107907	.	+	.	ID=YEL024W;Name=YEL024W;Alias=RIP1
-chrV	SGD	CDS	108504	110552	.	-	.	ID=YEL023C;Name=YEL023C;Alias=
-chrV	SGD	CDS	111421	115800	.	+	.	ID=YEL022W;Name=YEL022W;Alias=GEA2
-chrV	SGD	CDS	116167	116970	.	+	.	ID=YEL021W;Name=YEL021W;Alias=URA3
-chrV	SGD	CDS	117211	117474	.	+	.	ID=YEL020W-A;Name=YEL020W-A;Alias=TIM9
-chrV	SGD	CDS	118617	120299	.	-	.	ID=YEL020C;Name=YEL020C;Alias=PXP1
-chrV	SGD	CDS	120498	121301	.	-	.	ID=YEL019C;Name=YEL019C;Alias=MMS21
-chrV	SGD	CDS	121471	122310	.	+	.	ID=YEL018W;Name=YEL018W;Alias=EAF5
-chrV	SGD	CDS	122798	122929	.	-	.	ID=YEL017C-A;Name=YEL017C-A;Alias=PMP2
-chrV	SGD	CDS	123657	124670	.	+	.	ID=YEL017W;Name=YEL017W;Alias=GTT3
-chrV	SGD	CDS	124737	126218	.	-	.	ID=YEL016C;Name=YEL016C;Alias=NPP2
-chrV	SGD	CDS	126629	128284	.	+	.	ID=YEL015W;Name=YEL015W;Alias=EDC3
-chrV	SGD	CDS	128825	130561	.	+	.	ID=YEL013W;Name=YEL013W;Alias=VAC8
-chrV	SGD	CDS	131772	132551	.	+	.	ID=YEL012W;Name=YEL012W;Alias=UBC8
-chrV	SGD	CDS	133120	135234	.	+	.	ID=YEL011W;Name=YEL011W;Alias=GLC3
-chrV	SGD	CDS	138918	139763	.	-	.	ID=YEL009C;Name=YEL009C;Alias=GCN4
-chrV	SGD	CDS	141892	143892	.	+	.	ID=YEL007W;Name=YEL007W;Alias=MIT1
-chrV	SGD	CDS	144327	145334	.	+	.	ID=YEL006W;Name=YEL006W;Alias=YEA6
-chrV	SGD	CDS	145907	146755	.	-	.	ID=YEL005C;Name=YEL005C;Alias=VAB2
-chrV	SGD	CDS	146951	147979	.	+	.	ID=YEL004W;Name=YEL004W;Alias=YEA4
-chrV	SGD	CDS	148176	148599	.	+	.	ID=YEL003W;Name=YEL003W;Alias=GIM4
-chrV	SGD	CDS	148722	150014	.	-	.	ID=YEL002C;Name=YEL002C;Alias=WBP1
-chrV	SGD	CDS	150301	150978	.	-	.	ID=YEL001C;Name=YEL001C;Alias=IRC22
-chrV	SGD	CDS	153520	155808	.	+	.	ID=YER001W;Name=YER001W;Alias=MNN1
-chrV	SGD	CDS	156803	157498	.	+	.	ID=YER002W;Name=YER002W;Alias=NOP16
-chrV	SGD	CDS	157736	159118	.	-	.	ID=YER003C;Name=YER003C;Alias=PMI40
-chrV	SGD	CDS	159580	160275	.	+	.	ID=YER004W;Name=YER004W;Alias=FMP52
-chrV	SGD	CDS	160550	162442	.	+	.	ID=YER005W;Name=YER005W;Alias=YND1
-chrV	SGD	CDS	162723	164285	.	+	.	ID=YER006W;Name=YER006W;Alias=NUG1
-chrV	SGD	CDS	164527	166083	.	+	.	ID=YER007W;Name=YER007W;Alias=PAC2
-chrV	SGD	CDS	166237	166885	.	-	.	ID=YER007C-A;Name=YER007C-A;Alias=TMA20
-chrV	SGD	CDS	167808	171818	.	-	.	ID=YER008C;Name=YER008C;Alias=SEC3
-chrV	SGD	CDS	172115	172492	.	+	.	ID=YER009W;Name=YER009W;Alias=NTF2
-chrV	SGD	CDS	172634	173338	.	-	.	ID=YER010C;Name=YER010C;Alias=
-chrV	SGD	CDS	175248	176012	.	+	.	ID=YER011W;Name=YER011W;Alias=TIR1
-chrV	SGD	CDS	177835	178431	.	+	.	ID=YER012W;Name=YER012W;Alias=PRE1
-chrV	SGD	CDS	178841	182278	.	+	.	ID=YER013W;Name=YER013W;Alias=PRP22
-chrV	SGD	CDS	182600	184219	.	+	.	ID=YER014W;Name=YER014W;Alias=HEM14
-chrV	SGD	CDS	183731	184700	.	-	.	ID=YER014C-A;Name=YER014C-A;Alias=BUD25
-chrV	SGD	CDS	184541	186775	.	+	.	ID=YER015W;Name=YER015W;Alias=FAA2
-chrV	SGD	CDS	188277	189311	.	+	.	ID=YER016W;Name=YER016W;Alias=BIM1
-chrV	SGD	CDS	189503	191788	.	-	.	ID=YER017C;Name=YER017C;Alias=AFG3
-chrV	SGD	CDS	191959	192624	.	-	.	ID=YER018C;Name=YER018C;Alias=SPC25
-chrV	SGD	CDS	192797	194230	.	+	.	ID=YER019W;Name=YER019W;Alias=ISC1
-chrV	SGD	CDS	194273	194539	.	-	.	ID=YER019C-A;Name=YER019C-A;Alias=SBH2
-chrV	SGD	CDS	195168	196517	.	+	.	ID=YER020W;Name=YER020W;Alias=GPA2
-chrV	SGD	CDS	196948	198519	.	+	.	ID=YER021W;Name=YER021W;Alias=RPN3
-chrV	SGD	CDS	198812	200875	.	+	.	ID=YER022W;Name=YER022W;Alias=SRB4
-chrV	SGD	CDS	201076	201936	.	+	.	ID=YER023W;Name=YER023W;Alias=PRO3
-chrV	SGD	CDS	202192	204963	.	+	.	ID=YER024W;Name=YER024W;Alias=YAT2
-chrV	SGD	CDS	205251	206834	.	+	.	ID=YER025W;Name=YER025W;Alias=GCD11
-chrV	SGD	CDS	207644	208474	.	-	.	ID=YER026C;Name=YER026C;Alias=CHO1
-chrV	SGD	CDS	208979	210232	.	-	.	ID=YER027C;Name=YER027C;Alias=GAL83
-chrV	SGD	CDS	210692	211876	.	-	.	ID=YER028C;Name=YER028C;Alias=MIG3
-chrV	SGD	CDS	212587	213177	.	-	.	ID=YER029C;Name=YER029C;Alias=SMB1
-chrV	SGD	CDS	213437	213898	.	+	.	ID=YER030W;Name=YER030W;Alias=CHZ1
-chrV	SGD	CDS	214076	214747	.	-	.	ID=YER031C;Name=YER031C;Alias=YPT31
-chrV	SGD	CDS	215063	217693	.	+	.	ID=YER032W;Name=YER032W;Alias=FIR1
-chrV	SGD	CDS	218057	221287	.	-	.	ID=YER033C;Name=YER033C;Alias=ZRG8
-chrV	SGD	CDS	221846	222403	.	+	.	ID=YER034W;Name=YER034W;Alias=
-chrV	SGD	CDS	222639	223076	.	+	.	ID=YER035W;Name=YER035W;Alias=EDC2
-chrV	SGD	CDS	223367	225199	.	-	.	ID=YER036C;Name=YER036C;Alias=ARB1
-chrV	SGD	CDS	225889	226854	.	+	.	ID=YER037W;Name=YER037W;Alias=PHM8
-chrV	SGD	CDS	226858	228252	.	-	.	ID=YER038C;Name=YER038C;Alias=KRE29
-chrV	SGD	CDS	228451	228831	.	+	.	ID=YER038W-A;Name=YER038W-A;Alias=FMP49
-chrV	SGD	CDS	228456	229205	.	-	.	ID=YER039C;Name=YER039C;Alias=HVG1
-chrV	SGD	CDS	229263	229481	.	-	.	ID=YER039C-A;Name=YER039C-A;Alias=
-chrV	SGD	CDS	229795	231987	.	+	.	ID=YER040W;Name=YER040W;Alias=GLN3
-chrV	SGD	CDS	232461	234740	.	+	.	ID=YER041W;Name=YER041W;Alias=YEN1
-chrV	SGD	CDS	234937	235491	.	+	.	ID=YER042W;Name=YER042W;Alias=MXR1
-chrV	SGD	CDS	235770	237119	.	-	.	ID=YER043C;Name=YER043C;Alias=SAH1
-chrV	SGD	CDS	237570	238016	.	-	.	ID=YER044C;Name=YER044C;Alias=ERG28
-chrV	SGD	CDS	238460	239774	.	-	.	ID=YER044C-A;Name=YER044C-A;Alias=MEI4
-chrV	SGD	CDS	240032	241501	.	-	.	ID=YER045C;Name=YER045C;Alias=ACA1
-chrV	SGD	CDS	243180	243611	.	+	.	ID=YER046W;Name=YER046W;Alias=SPO73
-chrV	SGD	CDS	243810	246503	.	-	.	ID=YER047C;Name=YER047C;Alias=SAP1
-chrV	SGD	CDS	246982	248157	.	-	.	ID=YER048C;Name=YER048C;Alias=CAJ1
-chrV	SGD	CDS	250718	251002	.	+	.	ID=YER048W-A;Name=YER048W-A;Alias=ISD11
-chrV	SGD	CDS	251728	253662	.	+	.	ID=YER049W;Name=YER049W;Alias=TPA1
-chrV	SGD	CDS	253971	254387	.	-	.	ID=YER050C;Name=YER050C;Alias=RSM18
-chrV	SGD	CDS	254656	256134	.	+	.	ID=YER051W;Name=YER051W;Alias=JHD1
-chrV	SGD	CDS	256375	257958	.	-	.	ID=YER052C;Name=YER052C;Alias=HOM3
-chrV	SGD	CDS	258737	259639	.	-	.	ID=YER053C;Name=YER053C;Alias=PIC2
-chrV	SGD	CDS	260933	261046	.	-	.	ID=YER053C-A;Name=YER053C-A;Alias=
-chrV	SGD	CDS	262052	263698	.	-	.	ID=YER054C;Name=YER054C;Alias=GIP2
-chrV	SGD	CDS	264892	265785	.	-	.	ID=YER055C;Name=YER055C;Alias=HIS1
-chrV	SGD	CDS	266512	268113	.	-	.	ID=YER056C;Name=YER056C;Alias=FCY2
-chrV	SGD	CDS	269423	270185	.	-	.	ID=YER056C-A;Name=YER056C-A;Alias=RPL34A
-chrV	SGD	CDS	270737	271126	.	-	.	ID=YER057C;Name=YER057C;Alias=HMF1
-chrV	SGD	CDS	271768	272091	.	+	.	ID=YER058W;Name=YER058W;Alias=PET117
-chrV	SGD	CDS	272624	273886	.	+	.	ID=YER059W;Name=YER059W;Alias=PCL6
-chrV	SGD	CDS	274567	276153	.	+	.	ID=YER060W;Name=YER060W;Alias=FCY21
-chrV	SGD	CDS	276572	278164	.	+	.	ID=YER060W-A;Name=YER060W-A;Alias=FCY22
-chrV	SGD	CDS	278298	279626	.	-	.	ID=YER061C;Name=YER061C;Alias=CEM1
-chrV	SGD	CDS	279930	280682	.	-	.	ID=YER062C;Name=YER062C;Alias=GPP2
-chrV	SGD	CDS	281710	282366	.	+	.	ID=YER063W;Name=YER063W;Alias=THO1
-chrV	SGD	CDS	282705	284222	.	-	.	ID=YER064C;Name=YER064C;Alias=VHR2
-chrV	SGD	CDS	285241	286914	.	-	.	ID=YER065C;Name=YER065C;Alias=ICL1
-chrV	SGD	CDS	290242	290799	.	+	.	ID=YER066W;Name=YER066W;Alias=RRT13
-chrV	SGD	CDS	292066	292551	.	+	.	ID=YER067W;Name=YER067W;Alias=RGI1
-chrV	SGD	CDS	293050	294813	.	+	.	ID=YER068W;Name=YER068W;Alias=MOT2
-chrV	SGD	CDS	295410	298001	.	+	.	ID=YER069W;Name=YER069W;Alias=ARG5%2C6
-chrV	SGD	CDS	298950	301616	.	+	.	ID=YER070W;Name=YER070W;Alias=RNR1
-chrV	SGD	CDS	301947	302327	.	-	.	ID=YER071C;Name=YER071C;Alias=TDA2
-chrV	SGD	CDS	302806	303195	.	+	.	ID=YER072W;Name=YER072W;Alias=VTC1
-chrV	SGD	CDS	304030	305592	.	+	.	ID=YER073W;Name=YER073W;Alias=ALD5
-chrV	SGD	CDS	306323	307196	.	+	.	ID=YER074W;Name=YER074W;Alias=RPS24A
-chrV	SGD	CDS	307653	308123	.	+	.	ID=YER074W-A;Name=YER074W-A;Alias=YOS1
-chrV	SGD	CDS	308413	311199	.	-	.	ID=YER075C;Name=YER075C;Alias=PTP3
-chrV	SGD	CDS	312590	313498	.	-	.	ID=YER076C;Name=YER076C;Alias=
-chrV	SGD	CDS	314534	316600	.	-	.	ID=YER077C;Name=YER077C;Alias=MRX1
-chrV	SGD	CDS	316807	318342	.	-	.	ID=YER078C;Name=YER078C;Alias=ICP55
-chrV	SGD	CDS	318646	318810	.	+	.	ID=YER078W-A;Name=YER078W-A;Alias=
-chrV	SGD	CDS	318920	319552	.	+	.	ID=YER079W;Name=YER079W;Alias=
-chrV	SGD	CDS	319963	321846	.	+	.	ID=YER080W;Name=YER080W;Alias=AIM9
-chrV	SGD	CDS	322686	324095	.	+	.	ID=YER081W;Name=YER081W;Alias=SER3
-chrV	SGD	CDS	324272	325936	.	-	.	ID=YER082C;Name=YER082C;Alias=UTP7
-chrV	SGD	CDS	326174	327031	.	-	.	ID=YER083C;Name=YER083C;Alias=GET2
-chrV	SGD	CDS	327065	327451	.	+	.	ID=YER084W;Name=YER084W;Alias=
-chrV	SGD	CDS	327619	328140	.	-	.	ID=YER085C;Name=YER085C;Alias=
-chrV	SGD	CDS	328477	330207	.	+	.	ID=YER086W;Name=YER086W;Alias=ILV1
-chrV	SGD	CDS	330576	332306	.	+	.	ID=YER087W;Name=YER087W;Alias=AIM10
-chrV	SGD	CDS	332582	332830	.	-	.	ID=YER087C-B;Name=YER087C-B;Alias=SBH1
-chrV	SGD	CDS	333176	335188	.	-	.	ID=YER088C;Name=YER088C;Alias=DOT6
-chrV	SGD	CDS	335946	337340	.	-	.	ID=YER089C;Name=YER089C;Alias=PTC2
-chrV	SGD	CDS	337949	339472	.	+	.	ID=YER090W;Name=YER090W;Alias=TRP2
-chrV	SGD	CDS	339864	342167	.	-	.	ID=YER091C;Name=YER091C;Alias=MET6
-chrV	SGD	CDS	342855	343232	.	+	.	ID=YER092W;Name=YER092W;Alias=IES5
-chrV	SGD	CDS	343320	347612	.	-	.	ID=YER093C;Name=YER093C;Alias=TSC11
-chrV	SGD	CDS	347912	348400	.	-	.	ID=YER093C-A;Name=YER093C-A;Alias=AIM11
-chrV	SGD	CDS	348729	349346	.	-	.	ID=YER094C;Name=YER094C;Alias=PUP3
-chrV	SGD	CDS	349980	351182	.	+	.	ID=YER095W;Name=YER095W;Alias=RAD51
-chrV	SGD	CDS	351698	353236	.	+	.	ID=YER096W;Name=YER096W;Alias=SHC1
-chrV	SGD	CDS	355466	357730	.	+	.	ID=YER098W;Name=YER098W;Alias=UBP9
-chrV	SGD	CDS	358105	359061	.	-	.	ID=YER099C;Name=YER099C;Alias=PRS2
-chrV	SGD	CDS	359562	360314	.	+	.	ID=YER100W;Name=YER100W;Alias=UBC6
-chrV	SGD	CDS	360502	361794	.	-	.	ID=YER101C;Name=YER101C;Alias=AST2
-chrV	SGD	CDS	362733	363702	.	+	.	ID=YER102W;Name=YER102W;Alias=RPS8B
-chrV	SGD	CDS	364589	366517	.	+	.	ID=YER103W;Name=YER103W;Alias=SSA4
-chrV	SGD	CDS	366802	367428	.	+	.	ID=YER104W;Name=YER104W;Alias=RTT105
-chrV	SGD	CDS	367838	372013	.	-	.	ID=YER105C;Name=YER105C;Alias=NUP157
-chrV	SGD	CDS	372326	373234	.	+	.	ID=YER106W;Name=YER106W;Alias=MAM1
-chrV	SGD	CDS	373448	374545	.	-	.	ID=YER107C;Name=YER107C;Alias=GLE2
-chrV	SGD	CDS	378762	382103	.	-	.	ID=YER110C;Name=YER110C;Alias=KAP123
-chrV	SGD	CDS	382595	385876	.	-	.	ID=YER111C;Name=YER111C;Alias=SWI4
-chrV	SGD	CDS	387232	387795	.	+	.	ID=YER112W;Name=YER112W;Alias=LSM4
-chrV	SGD	CDS	387932	390052	.	-	.	ID=YER113C;Name=YER113C;Alias=TMN3
-chrV	SGD	CDS	390590	393712	.	-	.	ID=YER114C;Name=YER114C;Alias=BOI2
-chrV	SGD	CDS	394292	394867	.	-	.	ID=YER115C;Name=YER115C;Alias=SPR6
-chrV	SGD	CDS	395348	396172	.	-	.	ID=YER116C;Name=YER116C;Alias=SLX8
-chrV	SGD	CDS	396769	397653	.	+	.	ID=YER117W;Name=YER117W;Alias=RPL23B
-chrV	SGD	CDS	397952	399055	.	-	.	ID=YER118C;Name=YER118C;Alias=SHO1
-chrV	SGD	CDS	399496	400842	.	-	.	ID=YER119C;Name=YER119C;Alias=AVT6
-chrV	SGD	CDS	401135	401869	.	+	.	ID=YER120W;Name=YER120W;Alias=SCS2
-chrV	SGD	CDS	402375	402719	.	+	.	ID=YER121W;Name=YER121W;Alias=
-chrV	SGD	CDS	402871	404352	.	-	.	ID=YER122C;Name=YER122C;Alias=GLO3
-chrV	SGD	CDS	404813	406387	.	+	.	ID=YER123W;Name=YER123W;Alias=YCK3
-chrV	SGD	CDS	407342	409063	.	-	.	ID=YER124C;Name=YER124C;Alias=DSE1
-chrV	SGD	CDS	410189	412618	.	+	.	ID=YER125W;Name=YER125W;Alias=RSP5
-chrV	SGD	CDS	413394	414179	.	-	.	ID=YER126C;Name=YER126C;Alias=NSA2
-chrV	SGD	CDS	414481	415554	.	+	.	ID=YER127W;Name=YER127W;Alias=LCP5
-chrV	SGD	CDS	415859	416470	.	+	.	ID=YER128W;Name=YER128W;Alias=VFA1
-chrV	SGD	CDS	417281	420709	.	+	.	ID=YER129W;Name=YER129W;Alias=SAK1
-chrV	SGD	CDS	421115	422446	.	-	.	ID=YER130C;Name=YER130C;Alias=COM2
-chrV	SGD	CDS	423591	424311	.	+	.	ID=YER131W;Name=YER131W;Alias=RPS26B
-chrV	SGD	CDS	425188	430449	.	-	.	ID=YER132C;Name=YER132C;Alias=PMD1
-chrV	SGD	CDS	432495	433958	.	+	.	ID=YER133W;Name=YER133W;Alias=GLC7
-chrV	SGD	CDS	437267	437803	.	-	.	ID=YER134C;Name=YER134C;Alias=
-chrV	SGD	CDS	439616	440971	.	+	.	ID=YER136W;Name=YER136W;Alias=GDI1
-chrV	SGD	CDS	441373	441819	.	-	.	ID=YER137C;Name=YER137C;Alias=
-chrV	SGD	CDS	449474	449578	.	+	.	ID=YER138W-A;Name=YER138W-A;Alias=
-chrV	SGD	CDS	450563	451243	.	-	.	ID=YER139C;Name=YER139C;Alias=RTR1
-chrV	SGD	CDS	451565	453235	.	+	.	ID=YER140W;Name=YER140W;Alias=EMP65
-chrV	SGD	CDS	453459	454919	.	+	.	ID=YER141W;Name=YER141W;Alias=COX15
-chrV	SGD	CDS	455146	456036	.	-	.	ID=YER142C;Name=YER142C;Alias=MAG1
-chrV	SGD	CDS	456319	457605	.	+	.	ID=YER143W;Name=YER143W;Alias=DDI1
-chrV	SGD	CDS	457806	460223	.	-	.	ID=YER144C;Name=YER144C;Alias=UBP5
-chrV	SGD	CDS	460526	461740	.	-	.	ID=YER145C;Name=YER145C;Alias=FTR1
-chrV	SGD	CDS	462585	462866	.	+	.	ID=YER146W;Name=YER146W;Alias=LSM5
-chrV	SGD	CDS	462968	464842	.	-	.	ID=YER147C;Name=YER147C;Alias=SCC4
-chrV	SGD	CDS	465303	466025	.	+	.	ID=YER148W;Name=YER148W;Alias=SPT15
-chrV	SGD	CDS	466208	467470	.	-	.	ID=YER149C;Name=YER149C;Alias=PEA2
-chrV	SGD	CDS	468370	468816	.	+	.	ID=YER150W;Name=YER150W;Alias=SPI1
-chrV	SGD	CDS	469686	472424	.	-	.	ID=YER151C;Name=YER151C;Alias=UBP3
-chrV	SGD	CDS	472657	473988	.	-	.	ID=YER152C;Name=YER152C;Alias=
-chrV	SGD	CDS	474041	474805	.	-	.	ID=YER153C;Name=YER153C;Alias=PET122
-chrV	SGD	CDS	475020	476228	.	+	.	ID=YER154W;Name=YER154W;Alias=OXA1
-chrV	SGD	CDS	476345	482848	.	-	.	ID=YER155C;Name=YER155C;Alias=BEM2
-chrV	SGD	CDS	483325	484341	.	-	.	ID=YER156C;Name=YER156C;Alias=
-chrV	SGD	CDS	484788	487193	.	+	.	ID=YER157W;Name=YER157W;Alias=COG3
-chrV	SGD	CDS	488857	490578	.	-	.	ID=YER158C;Name=YER158C;Alias=
-chrV	SGD	CDS	491530	491958	.	-	.	ID=YER159C;Name=YER159C;Alias=BUR6
-chrV	SGD	CDS	499347	500348	.	-	.	ID=YER161C;Name=YER161C;Alias=SPT2
-chrV	SGD	CDS	500630	502894	.	-	.	ID=YER162C;Name=YER162C;Alias=RAD4
-chrV	SGD	CDS	503084	503782	.	-	.	ID=YER163C;Name=YER163C;Alias=GCG1
-chrV	SGD	CDS	505392	509798	.	+	.	ID=YER164W;Name=YER164W;Alias=CHD1
-chrV	SGD	CDS	510373	512106	.	+	.	ID=YER165W;Name=YER165W;Alias=PAB1
-chrV	SGD	CDS	512744	517459	.	+	.	ID=YER166W;Name=YER166W;Alias=DNF1
-chrV	SGD	CDS	518216	520771	.	+	.	ID=YER167W;Name=YER167W;Alias=BCK2
-chrV	SGD	CDS	521029	522669	.	-	.	ID=YER168C;Name=YER168C;Alias=CCA1
-chrV	SGD	CDS	523369	525759	.	+	.	ID=YER169W;Name=YER169W;Alias=RPH1
-chrV	SGD	CDS	525974	526651	.	+	.	ID=YER170W;Name=YER170W;Alias=ADK2
-chrV	SGD	CDS	527082	529418	.	+	.	ID=YER171W;Name=YER171W;Alias=RAD3
-chrV	SGD	CDS	529530	536021	.	-	.	ID=YER172C;Name=YER172C;Alias=BRR2
-chrV	SGD	CDS	536300	538279	.	+	.	ID=YER173W;Name=YER173W;Alias=RAD24
-chrV	SGD	CDS	538434	539168	.	-	.	ID=YER174C;Name=YER174C;Alias=GRX4
-chrV	SGD	CDS	539464	540363	.	-	.	ID=YER175C;Name=YER175C;Alias=TMT1
-chrV	SGD	CDS	540650	540814	.	+	.	ID=YER175W-A;Name=YER175W-A;Alias=
-chrV	SGD	CDS	541690	545055	.	+	.	ID=YER176W;Name=YER176W;Alias=ECM32
-chrV	SGD	CDS	545611	546414	.	+	.	ID=YER177W;Name=YER177W;Alias=BMH1
-chrV	SGD	CDS	546817	548079	.	+	.	ID=YER178W;Name=YER178W;Alias=PDA1
-chrV	SGD	CDS	548421	549517	.	+	.	ID=YER179W;Name=YER179W;Alias=DMC1
-chrV	SGD	CDS	549724	550527	.	-	.	ID=YER180C;Name=YER180C;Alias=ISC10
-chrV	SGD	CDS	550865	551122	.	-	.	ID=YER180C-A;Name=YER180C-A;Alias=SLO1
-chrV	SGD	CDS	552525	553259	.	+	.	ID=YER182W;Name=YER182W;Alias=FMP10
-chrV	SGD	CDS	553334	553969	.	-	.	ID=YER183C;Name=YER183C;Alias=FAU1
-chrV	SGD	CDS	556296	558680	.	-	.	ID=YER184C;Name=YER184C;Alias=TOG1
-chrV	SGD	CDS	559454	560365	.	+	.	ID=YER185W;Name=YER185W;Alias=PUG1
-chrV	SGD	CDS	561705	562625	.	-	.	ID=YER186C;Name=YER186C;Alias=
-chrV	SGD	CDS	566230	566655	.	+	.	ID=YER187W;Name=YER187W;Alias=
-chrV	SGD	CDS	569608	569907	.	-	.	ID=YER188C-A;Name=YER188C-A;Alias=
-chrV	SGD	CDS	571155	571523	.	+	.	ID=YER189W;Name=YER189W;Alias=
-chrV	SGD	CDS	571480	576525	.	+	.	ID=YER190W;Name=YER190W;Alias=YRF1-2
-chrV	SGD	CDS	575680	576162	.	-	.	ID=YER190C-B;Name=YER190C-B;Alias=
-chrVI	SGD	CDS	53	535	.	+	.	ID=YFL068W;Name=YFL068W;Alias=
-chrVI	SGD	CDS	836	1363	.	+	.	ID=YFL067W;Name=YFL067W;Alias=
-chrVI	SGD	CDS	1437	2615	.	-	.	ID=YFL066C;Name=YFL066C;Alias=
-chrVI	SGD	CDS	3030	3338	.	-	.	ID=YFL065C;Name=YFL065C;Alias=
-chrVI	SGD	CDS	3322	3846	.	-	.	ID=YFL064C;Name=YFL064C;Alias=
-chrVI	SGD	CDS	6426	7565	.	+	.	ID=YFL062W;Name=YFL062W;Alias=COS4
-chrVI	SGD	CDS	9545	10222	.	+	.	ID=YFL061W;Name=YFL061W;Alias=DDI2
-chrVI	SGD	CDS	10301	10969	.	-	.	ID=YFL060C;Name=YFL060C;Alias=SNO3
-chrVI	SGD	CDS	11363	12259	.	+	.	ID=YFL059W;Name=YFL059W;Alias=SNZ3
-chrVI	SGD	CDS	12929	13951	.	+	.	ID=YFL058W;Name=YFL058W;Alias=THI5
-chrVI	SGD	CDS	17004	18680	.	+	.	ID=YFL055W;Name=YFL055W;Alias=AGP3
-chrVI	SGD	CDS	20847	22787	.	-	.	ID=YFL054C;Name=YFL054C;Alias=AQY3
-chrVI	SGD	CDS	23423	25198	.	+	.	ID=YFL053W;Name=YFL053W;Alias=DAK2
-chrVI	SGD	CDS	28232	29629	.	+	.	ID=YFL052W;Name=YFL052W;Alias=ZNF1
-chrVI	SGD	CDS	30058	30540	.	-	.	ID=YFL051C;Name=YFL051C;Alias=
-chrVI	SGD	CDS	33272	35848	.	-	.	ID=YFL050C;Name=YFL050C;Alias=ALR2
-chrVI	SGD	CDS	36803	38674	.	+	.	ID=YFL049W;Name=YFL049W;Alias=SWP82
-chrVI	SGD	CDS	38843	40180	.	-	.	ID=YFL048C;Name=YFL048C;Alias=EMP47
-chrVI	SGD	CDS	40421	42565	.	+	.	ID=YFL047W;Name=YFL047W;Alias=RGD2
-chrVI	SGD	CDS	42815	43438	.	+	.	ID=YFL046W;Name=YFL046W;Alias=FMP32
-chrVI	SGD	CDS	43628	44392	.	-	.	ID=YFL045C;Name=YFL045C;Alias=SEC53
-chrVI	SGD	CDS	44655	45560	.	-	.	ID=YFL044C;Name=YFL044C;Alias=OTU1
-chrVI	SGD	CDS	45720	47744	.	-	.	ID=YFL042C;Name=YFL042C;Alias=LAM5
-chrVI	SGD	CDS	48734	48925	.	+	.	ID=YFL041W-A;Name=YFL041W-A;Alias=
-chrVI	SGD	CDS	49139	51007	.	+	.	ID=YFL041W;Name=YFL041W;Alias=FET5
-chrVI	SGD	CDS	51350	52972	.	+	.	ID=YFL040W;Name=YFL040W;Alias=
-chrVI	SGD	CDS	53260	54696	.	-	.	ID=YFL039C;Name=YFL039C;Alias=ACT1
-chrVI	SGD	CDS	55366	55986	.	-	.	ID=YFL038C;Name=YFL038C;Alias=YPT1
-chrVI	SGD	CDS	56336	57709	.	+	.	ID=YFL037W;Name=YFL037W;Alias=TUB2
-chrVI	SGD	CDS	58782	62837	.	+	.	ID=YFL036W;Name=YFL036W;Alias=RPO41
-chrVI	SGD	CDS	63016	63993	.	-	.	ID=YFL034C-B;Name=YFL034C-B;Alias=MOB2
-chrVI	SGD	CDS	64243	64932	.	-	.	ID=YFL034C-A;Name=YFL034C-A;Alias=RPL22B
-chrVI	SGD	CDS	65477	68698	.	+	.	ID=YFL034W;Name=YFL034W;Alias=MIL1
-chrVI	SGD	CDS	69115	74427	.	-	.	ID=YFL033C;Name=YFL033C;Alias=RIM15
-chrVI	SGD	CDS	75179	76147	.	+	.	ID=YFL031W;Name=YFL031W;Alias=HAC1
-chrVI	SGD	CDS	76831	77988	.	+	.	ID=YFL030W;Name=YFL030W;Alias=AGX1
-chrVI	SGD	CDS	78055	79161	.	-	.	ID=YFL029C;Name=YFL029C;Alias=CAK1
-chrVI	SGD	CDS	79344	80213	.	-	.	ID=YFL028C;Name=YFL028C;Alias=CAF16
-chrVI	SGD	CDS	80419	81912	.	-	.	ID=YFL027C;Name=YFL027C;Alias=GYP8
-chrVI	SGD	CDS	82580	83875	.	+	.	ID=YFL026W;Name=YFL026W;Alias=STE2
-chrVI	SGD	CDS	84145	87234	.	-	.	ID=YFL025C;Name=YFL025C;Alias=BST1
-chrVI	SGD	CDS	87847	90345	.	-	.	ID=YFL024C;Name=YFL024C;Alias=EPL1
-chrVI	SGD	CDS	90986	93376	.	+	.	ID=YFL023W;Name=YFL023W;Alias=BUD27
-chrVI	SGD	CDS	93499	95010	.	-	.	ID=YFL022C;Name=YFL022C;Alias=FRS2
-chrVI	SGD	CDS	95966	97498	.	+	.	ID=YFL021W;Name=YFL021W;Alias=GAT1
-chrVI	SGD	CDS	99231	99599	.	-	.	ID=YFL020C;Name=YFL020C;Alias=PAU5
-chrVI	SGD	CDS	101628	103127	.	-	.	ID=YFL018C;Name=YFL018C;Alias=LPD1
-chrVI	SGD	CDS	103699	103932	.	+	.	ID=YFL017W-A;Name=YFL017W-A;Alias=SMX2
-chrVI	SGD	CDS	103983	104462	.	-	.	ID=YFL017C;Name=YFL017C;Alias=GNA1
-chrVI	SGD	CDS	104701	106236	.	-	.	ID=YFL016C;Name=YFL016C;Alias=MDJ1
-chrVI	SGD	CDS	107256	107585	.	+	.	ID=YFL014W;Name=YFL014W;Alias=HSP12
-chrVI	SGD	CDS	107852	109930	.	-	.	ID=YFL013C;Name=YFL013C;Alias=IES1
-chrVI	SGD	CDS	110647	111093	.	+	.	ID=YFL012W;Name=YFL012W;Alias=
-chrVI	SGD	CDS	112345	113985	.	+	.	ID=YFL011W;Name=YFL011W;Alias=HXT10
-chrVI	SGD	CDS	114990	115274	.	+	.	ID=YFL010W-A;Name=YFL010W-A;Alias=AUA1
-chrVI	SGD	CDS	115108	115743	.	-	.	ID=YFL010C;Name=YFL010C;Alias=WWM1
-chrVI	SGD	CDS	116145	118484	.	+	.	ID=YFL009W;Name=YFL009W;Alias=CDC4
-chrVI	SGD	CDS	119429	123106	.	+	.	ID=YFL008W;Name=YFL008W;Alias=SMC1
-chrVI	SGD	CDS	123479	129910	.	+	.	ID=YFL007W;Name=YFL007W;Alias=BLM10
-chrVI	SGD	CDS	130334	130981	.	+	.	ID=YFL005W;Name=YFL005W;Alias=SEC4
-chrVI	SGD	CDS	131810	134296	.	+	.	ID=YFL004W;Name=YFL004W;Alias=VTC2
-chrVI	SGD	CDS	134521	137157	.	-	.	ID=YFL003C;Name=YFL003C;Alias=MSH4
-chrVI	SGD	CDS	145114	146934	.	-	.	ID=YFL002C;Name=YFL002C;Alias=SPB4
-chrVI	SGD	CDS	147131	148459	.	+	.	ID=YFL001W;Name=YFL001W;Alias=DEG1
-chrVI	SGD	CDS	149110	149724	.	+	.	ID=YFR001W;Name=YFR001W;Alias=LOC1
-chrVI	SGD	CDS	150016	152535	.	+	.	ID=YFR002W;Name=YFR002W;Alias=NIC96
-chrVI	SGD	CDS	152657	153124	.	-	.	ID=YFR003C;Name=YFR003C;Alias=YPI1
-chrVI	SGD	CDS	153393	154313	.	+	.	ID=YFR004W;Name=YFR004W;Alias=RPN11
-chrVI	SGD	CDS	154527	155873	.	-	.	ID=YFR005C;Name=YFR005C;Alias=SAD1
-chrVI	SGD	CDS	156145	157752	.	+	.	ID=YFR006W;Name=YFR006W;Alias=
-chrVI	SGD	CDS	159299	160360	.	+	.	ID=YFR007W;Name=YFR007W;Alias=YFH7
-chrVI	SGD	CDS	160535	161200	.	+	.	ID=YFR008W;Name=YFR008W;Alias=FAR7
-chrVI	SGD	CDS	162488	164746	.	+	.	ID=YFR009W;Name=YFR009W;Alias=GCN20
-chrVI	SGD	CDS	165067	166566	.	+	.	ID=YFR010W;Name=YFR010W;Alias=UBP6
-chrVI	SGD	CDS	166746	167258	.	-	.	ID=YFR011C;Name=YFR011C;Alias=MIC19
-chrVI	SGD	CDS	167888	168496	.	+	.	ID=YFR012W;Name=YFR012W;Alias=DCV1
-chrVI	SGD	CDS	169224	169310	.	+	.	ID=YFR012W-A;Name=YFR012W-A;Alias=
-chrVI	SGD	CDS	169922	172285	.	+	.	ID=YFR013W;Name=YFR013W;Alias=IOC3
-chrVI	SGD	CDS	172537	173877	.	-	.	ID=YFR014C;Name=YFR014C;Alias=CMK1
-chrVI	SGD	CDS	174265	176391	.	-	.	ID=YFR015C;Name=YFR015C;Alias=GSY1
-chrVI	SGD	CDS	177042	180743	.	-	.	ID=YFR016C;Name=YFR016C;Alias=
-chrVI	SGD	CDS	182274	182861	.	-	.	ID=YFR017C;Name=YFR017C;Alias=IGD1
-chrVI	SGD	CDS	183131	184222	.	-	.	ID=YFR018C;Name=YFR018C;Alias=
-chrVI	SGD	CDS	184502	191338	.	+	.	ID=YFR019W;Name=YFR019W;Alias=FAB1
-chrVI	SGD	CDS	192737	193435	.	+	.	ID=YFR020W;Name=YFR020W;Alias=CSS2
-chrVI	SGD	CDS	194812	196314	.	+	.	ID=YFR021W;Name=YFR021W;Alias=ATG18
-chrVI	SGD	CDS	196833	199034	.	+	.	ID=YFR022W;Name=YFR022W;Alias=ROG3
-chrVI	SGD	CDS	199874	201709	.	+	.	ID=YFR023W;Name=YFR023W;Alias=PES4
-chrVI	SGD	CDS	201960	203433	.	-	.	ID=YFR024C-A;Name=YFR024C-A;Alias=LSB3
-chrVI	SGD	CDS	203743	204750	.	-	.	ID=YFR025C;Name=YFR025C;Alias=HIS2
-chrVI	SGD	CDS	205748	206257	.	-	.	ID=YFR026C;Name=YFR026C;Alias=ULI1
-chrVI	SGD	CDS	207452	208297	.	+	.	ID=YFR027W;Name=YFR027W;Alias=ECO1
-chrVI	SGD	CDS	208413	210068	.	-	.	ID=YFR028C;Name=YFR028C;Alias=CDC14
-chrVI	SGD	CDS	210937	212973	.	+	.	ID=YFR029W;Name=YFR029W;Alias=PTR3
-chrVI	SGD	CDS	213312	216419	.	+	.	ID=YFR030W;Name=YFR030W;Alias=MET10
-chrVI	SGD	CDS	216594	220106	.	-	.	ID=YFR031C;Name=YFR031C;Alias=SMC2
-chrVI	SGD	CDS	220507	221418	.	-	.	ID=YFR031C-A;Name=YFR031C-A;Alias=RPL2A
-chrVI	SGD	CDS	222090	222959	.	-	.	ID=YFR032C;Name=YFR032C;Alias=RRT5
-chrVI	SGD	CDS	223258	223771	.	-	.	ID=YFR032C-A;Name=YFR032C-A;Alias=RPL29
-chrVI	SGD	CDS	223710	223973	.	-	.	ID=YFR032C-B;Name=YFR032C-B;Alias=
-chrVI	SGD	CDS	224326	224769	.	-	.	ID=YFR033C;Name=YFR033C;Alias=QCR6
-chrVI	SGD	CDS	225020	225958	.	-	.	ID=YFR034C;Name=YFR034C;Alias=PHO4
-chrVI	SGD	CDS	226121	226465	.	-	.	ID=YFR035C;Name=YFR035C;Alias=
-chrVI	SGD	CDS	226963	227337	.	+	.	ID=YFR036W;Name=YFR036W;Alias=CDC26
-chrVI	SGD	CDS	227513	229186	.	-	.	ID=YFR037C;Name=YFR037C;Alias=RSC8
-chrVI	SGD	CDS	229380	231941	.	+	.	ID=YFR038W;Name=YFR038W;Alias=IRC5
-chrVI	SGD	CDS	232012	233544	.	-	.	ID=YFR039C;Name=YFR039C;Alias=OSW7
-chrVI	SGD	CDS	234242	237250	.	+	.	ID=YFR040W;Name=YFR040W;Alias=SAP155
-chrVI	SGD	CDS	237368	238255	.	-	.	ID=YFR041C;Name=YFR041C;Alias=ERJ5
-chrVI	SGD	CDS	238458	239060	.	+	.	ID=YFR042W;Name=YFR042W;Alias=KEG1
-chrVI	SGD	CDS	239114	239827	.	-	.	ID=YFR043C;Name=YFR043C;Alias=IRC6
-chrVI	SGD	CDS	239992	241437	.	-	.	ID=YFR044C;Name=YFR044C;Alias=DUG1
-chrVI	SGD	CDS	241998	242999	.	+	.	ID=YFR045W;Name=YFR045W;Alias=
-chrVI	SGD	CDS	243074	244159	.	-	.	ID=YFR046C;Name=YFR046C;Alias=CNN1
-chrVI	SGD	CDS	244279	245166	.	-	.	ID=YFR047C;Name=YFR047C;Alias=BNA6
-chrVI	SGD	CDS	246146	248134	.	+	.	ID=YFR048W;Name=YFR048W;Alias=RMD8
-chrVI	SGD	CDS	248523	248894	.	+	.	ID=YFR049W;Name=YFR049W;Alias=YMR31
-chrVI	SGD	CDS	249066	249866	.	-	.	ID=YFR050C;Name=YFR050C;Alias=PRE4
-chrVI	SGD	CDS	250163	251803	.	-	.	ID=YFR051C;Name=YFR051C;Alias=RET2
-chrVI	SGD	CDS	252505	253329	.	+	.	ID=YFR052W;Name=YFR052W;Alias=RPN12
-chrVI	SGD	CDS	253592	255049	.	-	.	ID=YFR053C;Name=YFR053C;Alias=HXK1
-chrVI	SGD	CDS	264204	265226	.	+	.	ID=YFR055W;Name=YFR055W;Alias=IRC7
-chrVI	SGD	CDS	269061	269516	.	+	.	ID=YFR057W;Name=YFR057W;Alias=
-chrVII	SGD	CDS	2790	3932	.	+	.	ID=YGL263W;Name=YGL263W;Alias=COS12
-chrVII	SGD	CDS	5312	5839	.	+	.	ID=YGL262W;Name=YGL262W;Alias=
-chrVII	SGD	CDS	6290	6652	.	-	.	ID=YGL261C;Name=YGL261C;Alias=PAU11
-chrVII	SGD	CDS	6860	7090	.	+	.	ID=YGL260W;Name=YGL260W;Alias=
-chrVII	SGD	CDS	8470	8967	.	+	.	ID=YGL259W;Name=YGL259W;Alias=YPS5
-chrVII	SGD	CDS	9162	9395	.	+	.	ID=YGL258W-A;Name=YGL258W-A;Alias=
-chrVII	SGD	CDS	11110	11730	.	+	.	ID=YGL258W;Name=YGL258W;Alias=VEL1
-chrVII	SGD	CDS	12481	14157	.	-	.	ID=YGL257C;Name=YGL257C;Alias=MNT2
-chrVII	SGD	CDS	15159	16307	.	+	.	ID=YGL256W;Name=YGL256W;Alias=ADH4
-chrVII	SGD	CDS	20978	22108	.	+	.	ID=YGL255W;Name=YGL255W;Alias=ZRT1
-chrVII	SGD	CDS	22304	23203	.	+	.	ID=YGL254W;Name=YGL254W;Alias=FZF1
-chrVII	SGD	CDS	23935	25395	.	+	.	ID=YGL253W;Name=YGL253W;Alias=HXK2
-chrVII	SGD	CDS	25718	27484	.	-	.	ID=YGL252C;Name=YGL252C;Alias=RTG2
-chrVII	SGD	CDS	27921	31636	.	-	.	ID=YGL251C;Name=YGL251C;Alias=HFM1
-chrVII	SGD	CDS	31910	32635	.	+	.	ID=YGL250W;Name=YGL250W;Alias=RMR1
-chrVII	SGD	CDS	33098	35212	.	+	.	ID=YGL249W;Name=YGL249W;Alias=ZIP2
-chrVII	SGD	CDS	35653	36762	.	+	.	ID=YGL248W;Name=YGL248W;Alias=PDE1
-chrVII	SGD	CDS	36933	37526	.	+	.	ID=YGL247W;Name=YGL247W;Alias=BRR6
-chrVII	SGD	CDS	37617	38780	.	-	.	ID=YGL246C;Name=YGL246C;Alias=RAI1
-chrVII	SGD	CDS	39023	41149	.	+	.	ID=YGL245W;Name=YGL245W;Alias=GUS1
-chrVII	SGD	CDS	41498	43174	.	+	.	ID=YGL244W;Name=YGL244W;Alias=RTF1
-chrVII	SGD	CDS	43307	44509	.	+	.	ID=YGL243W;Name=YGL243W;Alias=TAD1
-chrVII	SGD	CDS	44652	45197	.	-	.	ID=YGL242C;Name=YGL242C;Alias=
-chrVII	SGD	CDS	45445	48459	.	+	.	ID=YGL241W;Name=YGL241W;Alias=KAP114
-chrVII	SGD	CDS	48613	49365	.	+	.	ID=YGL240W;Name=YGL240W;Alias=DOC1
-chrVII	SGD	CDS	49552	52434	.	+	.	ID=YGL238W;Name=YGL238W;Alias=CSE1
-chrVII	SGD	CDS	52731	53528	.	-	.	ID=YGL237C;Name=YGL237C;Alias=HAP2
-chrVII	SGD	CDS	53787	55796	.	-	.	ID=YGL236C;Name=YGL236C;Alias=MTO1
-chrVII	SGD	CDS	55279	55815	.	+	.	ID=YGL235W;Name=YGL235W;Alias=
-chrVII	SGD	CDS	56482	58890	.	+	.	ID=YGL234W;Name=YGL234W;Alias=ADE5%2C7
-chrVII	SGD	CDS	59122	61854	.	+	.	ID=YGL233W;Name=YGL233W;Alias=SEC15
-chrVII	SGD	CDS	62075	63002	.	+	.	ID=YGL232W;Name=YGL232W;Alias=TAN1
-chrVII	SGD	CDS	63048	63620	.	-	.	ID=YGL231C;Name=YGL231C;Alias=EMC4
-chrVII	SGD	CDS	63772	64215	.	-	.	ID=YGL230C;Name=YGL230C;Alias=
-chrVII	SGD	CDS	64503	66959	.	-	.	ID=YGL229C;Name=YGL229C;Alias=SAP4
-chrVII	SGD	CDS	67598	69331	.	+	.	ID=YGL228W;Name=YGL228W;Alias=SHE10
-chrVII	SGD	CDS	69671	72547	.	+	.	ID=YGL227W;Name=YGL227W;Alias=VID30
-chrVII	SGD	CDS	72749	73158	.	-	.	ID=YGL226C-A;Name=YGL226C-A;Alias=OST5
-chrVII	SGD	CDS	73340	73711	.	+	.	ID=YGL226W;Name=YGL226W;Alias=MTC3
-chrVII	SGD	CDS	76894	77907	.	+	.	ID=YGL225W;Name=YGL225W;Alias=VRG4
-chrVII	SGD	CDS	78015	78857	.	-	.	ID=YGL224C;Name=YGL224C;Alias=SDT1
-chrVII	SGD	CDS	79112	80365	.	-	.	ID=YGL223C;Name=YGL223C;Alias=COG1
-chrVII	SGD	CDS	80659	81186	.	-	.	ID=YGL222C;Name=YGL222C;Alias=EDC1
-chrVII	SGD	CDS	81426	82292	.	-	.	ID=YGL221C;Name=YGL221C;Alias=NIF3
-chrVII	SGD	CDS	82374	82736	.	+	.	ID=YGL220W;Name=YGL220W;Alias=BOL2
-chrVII	SGD	CDS	82878	84257	.	-	.	ID=YGL219C;Name=YGL219C;Alias=MDM34
-chrVII	SGD	CDS	84885	87302	.	+	.	ID=YGL216W;Name=YGL216W;Alias=KIP3
-chrVII	SGD	CDS	87981	89339	.	+	.	ID=YGL215W;Name=YGL215W;Alias=CLG1
-chrVII	SGD	CDS	90054	91247	.	-	.	ID=YGL213C;Name=YGL213C;Alias=SKI8
-chrVII	SGD	CDS	91432	92382	.	+	.	ID=YGL212W;Name=YGL212W;Alias=VAM7
-chrVII	SGD	CDS	92512	93591	.	+	.	ID=YGL211W;Name=YGL211W;Alias=NCS6
-chrVII	SGD	CDS	93792	94460	.	+	.	ID=YGL210W;Name=YGL210W;Alias=YPT32
-chrVII	SGD	CDS	95858	97006	.	+	.	ID=YGL209W;Name=YGL209W;Alias=MIG2
-chrVII	SGD	CDS	97338	98585	.	+	.	ID=YGL208W;Name=YGL208W;Alias=SIP2
-chrVII	SGD	CDS	98969	102076	.	+	.	ID=YGL207W;Name=YGL207W;Alias=SPT16
-chrVII	SGD	CDS	102543	107504	.	-	.	ID=YGL206C;Name=YGL206C;Alias=CHC1
-chrVII	SGD	CDS	108158	110404	.	+	.	ID=YGL205W;Name=YGL205W;Alias=POX1
-chrVII	SGD	CDS	111700	112005	.	-	.	ID=YGL204C;Name=YGL204C;Alias=
-chrVII	SGD	CDS	112475	114664	.	-	.	ID=YGL203C;Name=YGL203C;Alias=KEX1
-chrVII	SGD	CDS	116059	117561	.	+	.	ID=YGL202W;Name=YGL202W;Alias=ARO8
-chrVII	SGD	CDS	117854	120907	.	-	.	ID=YGL201C;Name=YGL201C;Alias=MCM6
-chrVII	SGD	CDS	122694	123305	.	-	.	ID=YGL200C;Name=YGL200C;Alias=EMP24
-chrVII	SGD	CDS	123591	124298	.	+	.	ID=YGL198W;Name=YGL198W;Alias=YIP4
-chrVII	SGD	CDS	124698	129161	.	+	.	ID=YGL197W;Name=YGL197W;Alias=MDS3
-chrVII	SGD	CDS	129883	131169	.	+	.	ID=YGL196W;Name=YGL196W;Alias=DSD1
-chrVII	SGD	CDS	131525	139543	.	+	.	ID=YGL195W;Name=YGL195W;Alias=GCN1
-chrVII	SGD	CDS	139719	139961	.	-	.	ID=YGL194C-A;Name=YGL194C-A;Alias=
-chrVII	SGD	CDS	140368	141726	.	-	.	ID=YGL194C;Name=YGL194C;Alias=HOS2
-chrVII	SGD	CDS	141916	142227	.	-	.	ID=YGL193C;Name=YGL193C;Alias=
-chrVII	SGD	CDS	142246	144048	.	+	.	ID=YGL192W;Name=YGL192W;Alias=IME4
-chrVII	SGD	CDS	144808	145197	.	+	.	ID=YGL191W;Name=YGL191W;Alias=COX13
-chrVII	SGD	CDS	145809	147389	.	-	.	ID=YGL190C;Name=YGL190C;Alias=CDC55
-chrVII	SGD	CDS	148229	148966	.	-	.	ID=YGL189C;Name=YGL189C;Alias=RPS26A
-chrVII	SGD	CDS	148824	148964	.	-	.	ID=YGL188C-A;Name=YGL188C-A;Alias=
-chrVII	SGD	CDS	149704	150525	.	-	.	ID=YGL187C;Name=YGL187C;Alias=COX4
-chrVII	SGD	CDS	151037	152776	.	-	.	ID=YGL186C;Name=YGL186C;Alias=TPN1
-chrVII	SGD	CDS	153167	154306	.	-	.	ID=YGL185C;Name=YGL185C;Alias=
-chrVII	SGD	CDS	154615	156012	.	-	.	ID=YGL184C;Name=YGL184C;Alias=STR3
-chrVII	SGD	CDS	156543	157285	.	-	.	ID=YGL183C;Name=YGL183C;Alias=MND1
-chrVII	SGD	CDS	157906	159096	.	+	.	ID=YGL181W;Name=YGL181W;Alias=GTS1
-chrVII	SGD	CDS	160065	162758	.	+	.	ID=YGL180W;Name=YGL180W;Alias=ATG1
-chrVII	SGD	CDS	163409	165091	.	-	.	ID=YGL179C;Name=YGL179C;Alias=TOS3
-chrVII	SGD	CDS	167352	170571	.	+	.	ID=YGL178W;Name=YGL178W;Alias=MPT5
-chrVII	SGD	CDS	171415	173079	.	-	.	ID=YGL176C;Name=YGL176C;Alias=
-chrVII	SGD	CDS	173285	174322	.	-	.	ID=YGL175C;Name=YGL175C;Alias=SAE2
-chrVII	SGD	CDS	174545	175345	.	+	.	ID=YGL174W;Name=YGL174W;Alias=BUD13
-chrVII	SGD	CDS	175527	180113	.	-	.	ID=YGL173C;Name=YGL173C;Alias=XRN1
-chrVII	SGD	CDS	180700	182118	.	+	.	ID=YGL172W;Name=YGL172W;Alias=NUP49
-chrVII	SGD	CDS	182390	184084	.	+	.	ID=YGL171W;Name=YGL171W;Alias=ROK1
-chrVII	SGD	CDS	184153	185394	.	-	.	ID=YGL170C;Name=YGL170C;Alias=SPO74
-chrVII	SGD	CDS	186059	187339	.	+	.	ID=YGL169W;Name=YGL169W;Alias=SUA5
-chrVII	SGD	CDS	187464	187796	.	+	.	ID=YGL168W;Name=YGL168W;Alias=HUR1
-chrVII	SGD	CDS	187616	190468	.	-	.	ID=YGL167C;Name=YGL167C;Alias=PMR1
-chrVII	SGD	CDS	191129	191806	.	+	.	ID=YGL166W;Name=YGL166W;Alias=CUP2
-chrVII	SGD	CDS	191978	193300	.	-	.	ID=YGL164C;Name=YGL164C;Alias=YRB30
-chrVII	SGD	CDS	193707	196403	.	-	.	ID=YGL163C;Name=YGL163C;Alias=RAD54
-chrVII	SGD	CDS	198138	199037	.	+	.	ID=YGL162W;Name=YGL162W;Alias=SUT1
-chrVII	SGD	CDS	199210	200142	.	-	.	ID=YGL161C;Name=YGL161C;Alias=YIP5
-chrVII	SGD	CDS	200561	202273	.	+	.	ID=YGL160W;Name=YGL160W;Alias=AIM14
-chrVII	SGD	CDS	202721	203833	.	+	.	ID=YGL159W;Name=YGL159W;Alias=
-chrVII	SGD	CDS	207033	208571	.	+	.	ID=YGL158W;Name=YGL158W;Alias=RCK1
-chrVII	SGD	CDS	209006	210049	.	+	.	ID=YGL157W;Name=YGL157W;Alias=ARI1
-chrVII	SGD	CDS	210416	213667	.	+	.	ID=YGL156W;Name=YGL156W;Alias=AMS1
-chrVII	SGD	CDS	214081	215211	.	+	.	ID=YGL155W;Name=YGL155W;Alias=CDC43
-chrVII	SGD	CDS	215278	216096	.	-	.	ID=YGL154C;Name=YGL154C;Alias=LYS5
-chrVII	SGD	CDS	216273	217298	.	+	.	ID=YGL153W;Name=YGL153W;Alias=PEX14
-chrVII	SGD	CDS	217524	220922	.	+	.	ID=YGL151W;Name=YGL151W;Alias=NUT1
-chrVII	SGD	CDS	221104	225573	.	-	.	ID=YGL150C;Name=YGL150C;Alias=INO80
-chrVII	SGD	CDS	226399	227529	.	+	.	ID=YGL148W;Name=YGL148W;Alias=ARO2
-chrVII	SGD	CDS	227754	228329	.	-	.	ID=YGL147C;Name=YGL147C;Alias=RPL9A
-chrVII	SGD	CDS	228751	229686	.	-	.	ID=YGL146C;Name=YGL146C;Alias=RRT6
-chrVII	SGD	CDS	230243	232348	.	+	.	ID=YGL145W;Name=YGL145W;Alias=TIP20
-chrVII	SGD	CDS	232450	234507	.	-	.	ID=YGL144C;Name=YGL144C;Alias=ROG1
-chrVII	SGD	CDS	234717	235958	.	-	.	ID=YGL143C;Name=YGL143C;Alias=MRF1
-chrVII	SGD	CDS	236269	238119	.	-	.	ID=YGL142C;Name=YGL142C;Alias=GPI10
-chrVII	SGD	CDS	238353	241085	.	+	.	ID=YGL141W;Name=YGL141W;Alias=HUL5
-chrVII	SGD	CDS	241353	245012	.	-	.	ID=YGL140C;Name=YGL140C;Alias=
-chrVII	SGD	CDS	245716	248124	.	+	.	ID=YGL139W;Name=YGL139W;Alias=FLC3
-chrVII	SGD	CDS	248494	249531	.	-	.	ID=YGL138C;Name=YGL138C;Alias=
-chrVII	SGD	CDS	249869	252738	.	+	.	ID=YGL137W;Name=YGL137W;Alias=SEC27
-chrVII	SGD	CDS	252897	253859	.	-	.	ID=YGL136C;Name=YGL136C;Alias=MRM2
-chrVII	SGD	CDS	254641	255294	.	+	.	ID=YGL135W;Name=YGL135W;Alias=RPL1B
-chrVII	SGD	CDS	255663	256964	.	+	.	ID=YGL134W;Name=YGL134W;Alias=PCL10
-chrVII	SGD	CDS	257707	261501	.	+	.	ID=YGL133W;Name=YGL133W;Alias=ITC1
-chrVII	SGD	CDS	261648	265859	.	-	.	ID=YGL131C;Name=YGL131C;Alias=SNT2
-chrVII	SGD	CDS	266145	267524	.	+	.	ID=YGL130W;Name=YGL130W;Alias=CEG1
-chrVII	SGD	CDS	267723	269075	.	-	.	ID=YGL129C;Name=YGL129C;Alias=RSM23
-chrVII	SGD	CDS	269293	270144	.	-	.	ID=YGL128C;Name=YGL128C;Alias=CWC23
-chrVII	SGD	CDS	270392	270775	.	-	.	ID=YGL127C;Name=YGL127C;Alias=SOH1
-chrVII	SGD	CDS	270997	272139	.	+	.	ID=YGL126W;Name=YGL126W;Alias=SCS3
-chrVII	SGD	CDS	272520	274322	.	+	.	ID=YGL125W;Name=YGL125W;Alias=MET13
-chrVII	SGD	CDS	274780	276714	.	-	.	ID=YGL124C;Name=YGL124C;Alias=MON1
-chrVII	SGD	CDS	277617	278381	.	+	.	ID=YGL123W;Name=YGL123W;Alias=RPS2
-chrVII	SGD	CDS	278946	280523	.	-	.	ID=YGL122C;Name=YGL122C;Alias=NAB2
-chrVII	SGD	CDS	280777	281157	.	-	.	ID=YGL121C;Name=YGL121C;Alias=GPG1
-chrVII	SGD	CDS	281634	283937	.	-	.	ID=YGL120C;Name=YGL120C;Alias=PRP43
-chrVII	SGD	CDS	284442	285947	.	+	.	ID=YGL119W;Name=YGL119W;Alias=COQ8
-chrVII	SGD	CDS	288512	289309	.	+	.	ID=YGL117W;Name=YGL117W;Alias=
-chrVII	SGD	CDS	289809	291641	.	+	.	ID=YGL116W;Name=YGL116W;Alias=CDC20
-chrVII	SGD	CDS	292033	293001	.	+	.	ID=YGL115W;Name=YGL115W;Alias=SNF4
-chrVII	SGD	CDS	293460	295637	.	+	.	ID=YGL114W;Name=YGL114W;Alias=
-chrVII	SGD	CDS	295932	297938	.	+	.	ID=YGL113W;Name=YGL113W;Alias=SLD3
-chrVII	SGD	CDS	298178	299728	.	-	.	ID=YGL112C;Name=YGL112C;Alias=TAF6
-chrVII	SGD	CDS	299978	301369	.	+	.	ID=YGL111W;Name=YGL111W;Alias=NSA1
-chrVII	SGD	CDS	301537	303411	.	-	.	ID=YGL110C;Name=YGL110C;Alias=CUE3
-chrVII	SGD	CDS	303649	304071	.	-	.	ID=YGL108C;Name=YGL108C;Alias=
-chrVII	SGD	CDS	304333	306273	.	-	.	ID=YGL107C;Name=YGL107C;Alias=RMD9
-chrVII	SGD	CDS	306560	307009	.	+	.	ID=YGL106W;Name=YGL106W;Alias=MLC1
-chrVII	SGD	CDS	307437	308567	.	+	.	ID=YGL105W;Name=YGL105W;Alias=ARC1
-chrVII	SGD	CDS	308713	310173	.	-	.	ID=YGL104C;Name=YGL104C;Alias=VPS73
-chrVII	SGD	CDS	310967	311927	.	+	.	ID=YGL103W;Name=YGL103W;Alias=RPL28
-chrVII	SGD	CDS	312193	312840	.	+	.	ID=YGL101W;Name=YGL101W;Alias=
-chrVII	SGD	CDS	313234	314283	.	+	.	ID=YGL100W;Name=YGL100W;Alias=SEH1
-chrVII	SGD	CDS	314631	316553	.	+	.	ID=YGL099W;Name=YGL099W;Alias=LSG1
-chrVII	SGD	CDS	317342	318079	.	+	.	ID=YGL098W;Name=YGL098W;Alias=USE1
-chrVII	SGD	CDS	321782	323230	.	+	.	ID=YGL097W;Name=YGL097W;Alias=SRM1
-chrVII	SGD	CDS	325331	326161	.	+	.	ID=YGL096W;Name=YGL096W;Alias=TOS8
-chrVII	SGD	CDS	328874	330607	.	-	.	ID=YGL095C;Name=YGL095C;Alias=VPS45
-chrVII	SGD	CDS	331118	334465	.	-	.	ID=YGL094C;Name=YGL094C;Alias=PAN2
-chrVII	SGD	CDS	334886	337639	.	+	.	ID=YGL093W;Name=YGL093W;Alias=SPC105
-chrVII	SGD	CDS	337906	341859	.	+	.	ID=YGL092W;Name=YGL092W;Alias=NUP145
-chrVII	SGD	CDS	342056	343042	.	-	.	ID=YGL091C;Name=YGL091C;Alias=NBP35
-chrVII	SGD	CDS	343319	344584	.	+	.	ID=YGL090W;Name=YGL090W;Alias=LIF1
-chrVII	SGD	CDS	344791	345153	.	-	.	ID=YGL089C;Name=YGL089C;Alias=MF%28ALPHA%292
-chrVII	SGD	CDS	346406	346904	.	-	.	ID=YGL087C;Name=YGL087C;Alias=MMS2
-chrVII	SGD	CDS	347119	349368	.	+	.	ID=YGL086W;Name=YGL086W;Alias=MAD1
-chrVII	SGD	CDS	349616	350440	.	+	.	ID=YGL085W;Name=YGL085W;Alias=LCL3
-chrVII	SGD	CDS	350616	352298	.	-	.	ID=YGL084C;Name=YGL084C;Alias=GUP1
-chrVII	SGD	CDS	353058	355472	.	+	.	ID=YGL083W;Name=YGL083W;Alias=SCY1
-chrVII	SGD	CDS	355827	356972	.	+	.	ID=YGL082W;Name=YGL082W;Alias=
-chrVII	SGD	CDS	357377	358339	.	+	.	ID=YGL081W;Name=YGL081W;Alias=
-chrVII	SGD	CDS	358636	359028	.	+	.	ID=YGL080W;Name=YGL080W;Alias=MPC1
-chrVII	SGD	CDS	359444	360100	.	+	.	ID=YGL079W;Name=YGL079W;Alias=KXD1
-chrVII	SGD	CDS	360288	361859	.	-	.	ID=YGL078C;Name=YGL078C;Alias=DBP3
-chrVII	SGD	CDS	362225	363916	.	-	.	ID=YGL077C;Name=YGL077C;Alias=HNM1
-chrVII	SGD	CDS	364335	365996	.	-	.	ID=YGL076C;Name=YGL076C;Alias=RPL7A
-chrVII	SGD	CDS	366925	368088	.	-	.	ID=YGL075C;Name=YGL075C;Alias=MPS2
-chrVII	SGD	CDS	368753	371254	.	+	.	ID=YGL073W;Name=YGL073W;Alias=HSF1
-chrVII	SGD	CDS	372012	374084	.	+	.	ID=YGL071W;Name=YGL071W;Alias=AFT1
-chrVII	SGD	CDS	374459	374827	.	-	.	ID=YGL070C;Name=YGL070C;Alias=RPB9
-chrVII	SGD	CDS	375087	375671	.	+	.	ID=YGL068W;Name=YGL068W;Alias=MNP1
-chrVII	SGD	CDS	376101	377255	.	+	.	ID=YGL067W;Name=YGL067W;Alias=NPY1
-chrVII	SGD	CDS	377609	379582	.	+	.	ID=YGL066W;Name=YGL066W;Alias=SGF73
-chrVII	SGD	CDS	379760	381271	.	-	.	ID=YGL065C;Name=YGL065C;Alias=ALG2
-chrVII	SGD	CDS	381523	383208	.	-	.	ID=YGL064C;Name=YGL064C;Alias=MRH4
-chrVII	SGD	CDS	383654	384766	.	+	.	ID=YGL063W;Name=YGL063W;Alias=PUS2
-chrVII	SGD	CDS	385196	388732	.	+	.	ID=YGL062W;Name=YGL062W;Alias=PYC1
-chrVII	SGD	CDS	388968	389711	.	-	.	ID=YGL061C;Name=YGL061C;Alias=DUO1
-chrVII	SGD	CDS	390065	391990	.	+	.	ID=YGL060W;Name=YGL060W;Alias=YBP2
-chrVII	SGD	CDS	392223	393698	.	+	.	ID=YGL059W;Name=YGL059W;Alias=PKP2
-chrVII	SGD	CDS	393986	394504	.	+	.	ID=YGL058W;Name=YGL058W;Alias=RAD6
-chrVII	SGD	CDS	394966	395829	.	-	.	ID=YGL057C;Name=YGL057C;Alias=GEP7
-chrVII	SGD	CDS	396035	397618	.	-	.	ID=YGL056C;Name=YGL056C;Alias=SDS23
-chrVII	SGD	CDS	398628	400160	.	+	.	ID=YGL055W;Name=YGL055W;Alias=OLE1
-chrVII	SGD	CDS	400871	401287	.	-	.	ID=YGL054C;Name=YGL054C;Alias=ERV14
-chrVII	SGD	CDS	402589	403302	.	+	.	ID=YGL053W;Name=YGL053W;Alias=PRM8
-chrVII	SGD	CDS	403687	404391	.	+	.	ID=YGL051W;Name=YGL051W;Alias=MST27
-chrVII	SGD	CDS	405776	406597	.	+	.	ID=YGL050W;Name=YGL050W;Alias=TYW3
-chrVII	SGD	CDS	406860	409604	.	-	.	ID=YGL049C;Name=YGL049C;Alias=TIF4632
-chrVII	SGD	CDS	410069	411286	.	-	.	ID=YGL048C;Name=YGL048C;Alias=RPT6
-chrVII	SGD	CDS	411552	412160	.	+	.	ID=YGL047W;Name=YGL047W;Alias=ALG13
-chrVII	SGD	CDS	414102	415730	.	+	.	ID=YGL045W;Name=YGL045W;Alias=RIM8
-chrVII	SGD	CDS	416146	417036	.	-	.	ID=YGL044C;Name=YGL044C;Alias=RNA15
-chrVII	SGD	CDS	417483	418412	.	+	.	ID=YGL043W;Name=YGL043W;Alias=DST1
-chrVII	SGD	CDS	418704	418886	.	-	.	ID=YGL041C-B;Name=YGL041C-B;Alias=
-chrVII	SGD	CDS	418825	419289	.	+	.	ID=YGL041W-A;Name=YGL041W-A;Alias=
-chrVII	SGD	CDS	419527	420555	.	-	.	ID=YGL040C;Name=YGL040C;Alias=HEM2
-chrVII	SGD	CDS	423961	425007	.	+	.	ID=YGL039W;Name=YGL039W;Alias=
-chrVII	SGD	CDS	425362	426804	.	-	.	ID=YGL038C;Name=YGL038C;Alias=OCH1
-chrVII	SGD	CDS	427297	427947	.	-	.	ID=YGL037C;Name=YGL037C;Alias=PNC1
-chrVII	SGD	CDS	428601	431330	.	+	.	ID=YGL036W;Name=YGL036W;Alias=
-chrVII	SGD	CDS	431548	433062	.	-	.	ID=YGL035C;Name=YGL035C;Alias=MIG1
-chrVII	SGD	CDS	435625	436401	.	+	.	ID=YGL033W;Name=YGL033W;Alias=HOP2
-chrVII	SGD	CDS	436570	436833	.	-	.	ID=YGL032C;Name=YGL032C;Alias=AGA2
-chrVII	SGD	CDS	437467	438397	.	-	.	ID=YGL031C;Name=YGL031C;Alias=RPL24A
-chrVII	SGD	CDS	439091	439638	.	+	.	ID=YGL030W;Name=YGL030W;Alias=RPL30
-chrVII	SGD	CDS	440063	440425	.	+	.	ID=YGL029W;Name=YGL029W;Alias=CGR1
-chrVII	SGD	CDS	441281	442909	.	-	.	ID=YGL028C;Name=YGL028C;Alias=SCW11
-chrVII	SGD	CDS	443642	446143	.	-	.	ID=YGL027C;Name=YGL027C;Alias=CWH41
-chrVII	SGD	CDS	446412	448535	.	-	.	ID=YGL026C;Name=YGL026C;Alias=TRP5
-chrVII	SGD	CDS	448764	449957	.	-	.	ID=YGL025C;Name=YGL025C;Alias=PGD1
-chrVII	SGD	CDS	450197	452104	.	-	.	ID=YGL023C;Name=YGL023C;Alias=PIB2
-chrVII	SGD	CDS	452404	454560	.	+	.	ID=YGL022W;Name=YGL022W;Alias=STT3
-chrVII	SGD	CDS	454785	457067	.	+	.	ID=YGL021W;Name=YGL021W;Alias=ALK1
-chrVII	SGD	CDS	457163	457870	.	-	.	ID=YGL020C;Name=YGL020C;Alias=GET1
-chrVII	SGD	CDS	458156	458992	.	+	.	ID=YGL019W;Name=YGL019W;Alias=CKB1
-chrVII	SGD	CDS	459110	459664	.	-	.	ID=YGL018C;Name=YGL018C;Alias=JAC1
-chrVII	SGD	CDS	459854	461365	.	+	.	ID=YGL017W;Name=YGL017W;Alias=ATE1
-chrVII	SGD	CDS	461666	464911	.	+	.	ID=YGL016W;Name=YGL016W;Alias=KAP122
-chrVII	SGD	CDS	465043	465435	.	-	.	ID=YGL015C;Name=YGL015C;Alias=
-chrVII	SGD	CDS	466141	468807	.	+	.	ID=YGL014W;Name=YGL014W;Alias=PUF4
-chrVII	SGD	CDS	469092	472298	.	-	.	ID=YGL013C;Name=YGL013C;Alias=PDR1
-chrVII	SGD	CDS	472855	474276	.	+	.	ID=YGL012W;Name=YGL012W;Alias=ERG4
-chrVII	SGD	CDS	474489	475247	.	-	.	ID=YGL011C;Name=YGL011C;Alias=SCL1
-chrVII	SGD	CDS	475545	476069	.	+	.	ID=YGL010W;Name=YGL010W;Alias=MPO1
-chrVII	SGD	CDS	476313	478652	.	-	.	ID=YGL009C;Name=YGL009C;Alias=LEU1
-chrVII	SGD	CDS	479910	482666	.	-	.	ID=YGL008C;Name=YGL008C;Alias=PMA1
-chrVII	SGD	CDS	482941	483027	.	-	.	ID=YGL007C-A;Name=YGL007C-A;Alias=
-chrVII	SGD	CDS	485423	485533	.	+	.	ID=YGL006W-A;Name=YGL006W-A;Alias=
-chrVII	SGD	CDS	485921	489442	.	+	.	ID=YGL006W;Name=YGL006W;Alias=PMC1
-chrVII	SGD	CDS	489708	490547	.	-	.	ID=YGL005C;Name=YGL005C;Alias=COG7
-chrVII	SGD	CDS	490703	491956	.	-	.	ID=YGL004C;Name=YGL004C;Alias=RPN14
-chrVII	SGD	CDS	492474	494174	.	-	.	ID=YGL003C;Name=YGL003C;Alias=CDH1
-chrVII	SGD	CDS	494517	495167	.	+	.	ID=YGL002W;Name=YGL002W;Alias=ERP6
-chrVII	SGD	CDS	495453	496502	.	-	.	ID=YGL001C;Name=YGL001C;Alias=ERG26
-chrVII	SGD	CDS	497133	498034	.	-	.	ID=YGR001C;Name=YGR001C;Alias=EFM5
-chrVII	SGD	CDS	498476	499906	.	-	.	ID=YGR002C;Name=YGR002C;Alias=SWC4
-chrVII	SGD	CDS	500132	502366	.	+	.	ID=YGR003W;Name=YGR003W;Alias=CUL3
-chrVII	SGD	CDS	502938	504326	.	+	.	ID=YGR004W;Name=YGR004W;Alias=PEX31
-chrVII	SGD	CDS	504657	505859	.	-	.	ID=YGR005C;Name=YGR005C;Alias=TFG2
-chrVII	SGD	CDS	506070	506825	.	+	.	ID=YGR006W;Name=YGR006W;Alias=PRP18
-chrVII	SGD	CDS	506969	507940	.	+	.	ID=YGR007W;Name=YGR007W;Alias=ECT1
-chrVII	SGD	CDS	508110	508364	.	-	.	ID=YGR008C;Name=YGR008C;Alias=STF2
-chrVII	SGD	CDS	509047	511002	.	-	.	ID=YGR009C;Name=YGR009C;Alias=SEC9
-chrVII	SGD	CDS	511545	512732	.	+	.	ID=YGR010W;Name=YGR010W;Alias=NMA2
-chrVII	SGD	CDS	513159	514340	.	+	.	ID=YGR012W;Name=YGR012W;Alias=MCY1
-chrVII	SGD	CDS	514554	516416	.	+	.	ID=YGR013W;Name=YGR013W;Alias=SNU71
-chrVII	SGD	CDS	516943	520863	.	+	.	ID=YGR014W;Name=YGR014W;Alias=MSB2
-chrVII	SGD	CDS	521090	522076	.	-	.	ID=YGR015C;Name=YGR015C;Alias=
-chrVII	SGD	CDS	522261	522833	.	+	.	ID=YGR016W;Name=YGR016W;Alias=
-chrVII	SGD	CDS	523787	524680	.	+	.	ID=YGR017W;Name=YGR017W;Alias=
-chrVII	SGD	CDS	524365	524694	.	-	.	ID=YGR018C;Name=YGR018C;Alias=
-chrVII	SGD	CDS	525229	526644	.	+	.	ID=YGR019W;Name=YGR019W;Alias=UGA1
-chrVII	SGD	CDS	526973	527329	.	-	.	ID=YGR020C;Name=YGR020C;Alias=VMA7
-chrVII	SGD	CDS	527632	528504	.	+	.	ID=YGR021W;Name=YGR021W;Alias=
-chrVII	SGD	CDS	529264	530919	.	+	.	ID=YGR023W;Name=YGR023W;Alias=MTL1
-chrVII	SGD	CDS	531883	532596	.	-	.	ID=YGR024C;Name=YGR024C;Alias=THG1
-chrVII	SGD	CDS	532985	533821	.	+	.	ID=YGR026W;Name=YGR026W;Alias=
-chrVII	SGD	CDS	534132	534785	.	-	.	ID=YGR027C;Name=YGR027C;Alias=RPS25A
-chrVII	SGD	CDS	542203	543291	.	+	.	ID=YGR028W;Name=YGR028W;Alias=MSP1
-chrVII	SGD	CDS	543553	544205	.	+	.	ID=YGR029W;Name=YGR029W;Alias=ERV1
-chrVII	SGD	CDS	545681	546157	.	-	.	ID=YGR030C;Name=YGR030C;Alias=POP6
-chrVII	SGD	CDS	546441	547469	.	+	.	ID=YGR031W;Name=YGR031W;Alias=IMO32
-chrVII	SGD	CDS	546809	547300	.	-	.	ID=YGR031C-A;Name=YGR031C-A;Alias=NAG1
-chrVII	SGD	CDS	548264	553951	.	+	.	ID=YGR032W;Name=YGR032W;Alias=GSC2
-chrVII	SGD	CDS	554248	554967	.	-	.	ID=YGR033C;Name=YGR033C;Alias=TIM21
-chrVII	SGD	CDS	555812	556672	.	+	.	ID=YGR034W;Name=YGR034W;Alias=RPL26B
-chrVII	SGD	CDS	557072	557422	.	-	.	ID=YGR035C;Name=YGR035C;Alias=
-chrVII	SGD	CDS	557565	557786	.	+	.	ID=YGR035W-A;Name=YGR035W-A;Alias=
-chrVII	SGD	CDS	558149	558868	.	-	.	ID=YGR036C;Name=YGR036C;Alias=CAX4
-chrVII	SGD	CDS	559731	559994	.	-	.	ID=YGR037C;Name=YGR037C;Alias=ACB1
-chrVII	SGD	CDS	560682	561350	.	+	.	ID=YGR038W;Name=YGR038W;Alias=ORM1
-chrVII	SGD	CDS	575398	576504	.	+	.	ID=YGR040W;Name=YGR040W;Alias=KSS1
-chrVII	SGD	CDS	577487	579130	.	+	.	ID=YGR041W;Name=YGR041W;Alias=BUD9
-chrVII	SGD	CDS	579476	580291	.	+	.	ID=YGR042W;Name=YGR042W;Alias=MTE1
-chrVII	SGD	CDS	580435	581436	.	-	.	ID=YGR043C;Name=YGR043C;Alias=NQM1
-chrVII	SGD	CDS	582990	583892	.	-	.	ID=YGR044C;Name=YGR044C;Alias=RME1
-chrVII	SGD	CDS	584895	586052	.	+	.	ID=YGR046W;Name=YGR046W;Alias=TAM41
-chrVII	SGD	CDS	586392	589469	.	-	.	ID=YGR047C;Name=YGR047C;Alias=TFC4
-chrVII	SGD	CDS	589826	590911	.	+	.	ID=YGR048W;Name=YGR048W;Alias=UFD1
-chrVII	SGD	CDS	591314	591877	.	+	.	ID=YGR049W;Name=YGR049W;Alias=SCM4
-chrVII	SGD	CDS	592086	592442	.	-	.	ID=YGR050C;Name=YGR050C;Alias=
-chrVII	SGD	CDS	593596	594705	.	+	.	ID=YGR052W;Name=YGR052W;Alias=FMP48
-chrVII	SGD	CDS	594986	595837	.	-	.	ID=YGR053C;Name=YGR053C;Alias=
-chrVII	SGD	CDS	596693	598621	.	+	.	ID=YGR054W;Name=YGR054W;Alias=
-chrVII	SGD	CDS	599417	601141	.	+	.	ID=YGR055W;Name=YGR055W;Alias=MUP1
-chrVII	SGD	CDS	601661	604447	.	+	.	ID=YGR056W;Name=YGR056W;Alias=RSC1
-chrVII	SGD	CDS	604773	605501	.	-	.	ID=YGR057C;Name=YGR057C;Alias=LST7
-chrVII	SGD	CDS	606136	607143	.	+	.	ID=YGR058W;Name=YGR058W;Alias=PEF1
-chrVII	SGD	CDS	607563	609101	.	+	.	ID=YGR059W;Name=YGR059W;Alias=SPR3
-chrVII	SGD	CDS	610564	611493	.	+	.	ID=YGR060W;Name=YGR060W;Alias=ERG25
-chrVII	SGD	CDS	611889	615965	.	-	.	ID=YGR061C;Name=YGR061C;Alias=ADE6
-chrVII	SGD	CDS	616328	617278	.	-	.	ID=YGR062C;Name=YGR062C;Alias=COX18
-chrVII	SGD	CDS	617516	617824	.	-	.	ID=YGR063C;Name=YGR063C;Alias=SPT4
-chrVII	SGD	CDS	618077	619858	.	-	.	ID=YGR065C;Name=YGR065C;Alias=VHT1
-chrVII	SGD	CDS	620921	621799	.	-	.	ID=YGR066C;Name=YGR066C;Alias=
-chrVII	SGD	CDS	622372	624786	.	-	.	ID=YGR067C;Name=YGR067C;Alias=
-chrVII	SGD	CDS	625324	627084	.	-	.	ID=YGR068C;Name=YGR068C;Alias=ART5
-chrVII	SGD	CDS	627806	631273	.	+	.	ID=YGR070W;Name=YGR070W;Alias=ROM1
-chrVII	SGD	CDS	631481	634063	.	-	.	ID=YGR071C;Name=YGR071C;Alias=ENV11
-chrVII	SGD	CDS	634304	635467	.	+	.	ID=YGR072W;Name=YGR072W;Alias=UPF3
-chrVII	SGD	CDS	635712	636152	.	+	.	ID=YGR074W;Name=YGR074W;Alias=SMD1
-chrVII	SGD	CDS	636147	636875	.	-	.	ID=YGR075C;Name=YGR075C;Alias=PRP38
-chrVII	SGD	CDS	637104	637577	.	-	.	ID=YGR076C;Name=YGR076C;Alias=MRPL25
-chrVII	SGD	CDS	637744	639513	.	-	.	ID=YGR077C;Name=YGR077C;Alias=PEX8
-chrVII	SGD	CDS	639772	640371	.	-	.	ID=YGR078C;Name=YGR078C;Alias=PAC10
-chrVII	SGD	CDS	640720	641832	.	+	.	ID=YGR079W;Name=YGR079W;Alias=
-chrVII	SGD	CDS	642010	643008	.	+	.	ID=YGR080W;Name=YGR080W;Alias=TWF1
-chrVII	SGD	CDS	643148	643780	.	-	.	ID=YGR081C;Name=YGR081C;Alias=SLX9
-chrVII	SGD	CDS	644044	644595	.	+	.	ID=YGR082W;Name=YGR082W;Alias=TOM20
-chrVII	SGD	CDS	644860	646815	.	-	.	ID=YGR083C;Name=YGR083C;Alias=GCD2
-chrVII	SGD	CDS	647123	648142	.	-	.	ID=YGR084C;Name=YGR084C;Alias=MRP13
-chrVII	SGD	CDS	648383	648907	.	-	.	ID=YGR085C;Name=YGR085C;Alias=RPL11B
-chrVII	SGD	CDS	649598	650617	.	-	.	ID=YGR086C;Name=YGR086C;Alias=PIL1
-chrVII	SGD	CDS	651290	652981	.	-	.	ID=YGR087C;Name=YGR087C;Alias=PDC6
-chrVII	SGD	CDS	654634	656322	.	+	.	ID=YGR088W;Name=YGR088W;Alias=CTT1
-chrVII	SGD	CDS	656960	659770	.	+	.	ID=YGR089W;Name=YGR089W;Alias=NNF2
-chrVII	SGD	CDS	662358	666071	.	+	.	ID=YGR090W;Name=YGR090W;Alias=UTP22
-chrVII	SGD	CDS	666341	667825	.	+	.	ID=YGR091W;Name=YGR091W;Alias=PRP31
-chrVII	SGD	CDS	668189	669907	.	+	.	ID=YGR092W;Name=YGR092W;Alias=DBF2
-chrVII	SGD	CDS	670388	671911	.	+	.	ID=YGR093W;Name=YGR093W;Alias=DRN1
-chrVII	SGD	CDS	672186	675500	.	+	.	ID=YGR094W;Name=YGR094W;Alias=VAS1
-chrVII	SGD	CDS	675671	676342	.	-	.	ID=YGR095C;Name=YGR095C;Alias=RRP46
-chrVII	SGD	CDS	676621	677565	.	+	.	ID=YGR096W;Name=YGR096W;Alias=TPC1
-chrVII	SGD	CDS	678695	682135	.	+	.	ID=YGR097W;Name=YGR097W;Alias=ASK10
-chrVII	SGD	CDS	682566	687458	.	-	.	ID=YGR098C;Name=YGR098C;Alias=ESP1
-chrVII	SGD	CDS	687899	689965	.	+	.	ID=YGR099W;Name=YGR099W;Alias=TEL2
-chrVII	SGD	CDS	690245	693097	.	+	.	ID=YGR100W;Name=YGR100W;Alias=MDR1
-chrVII	SGD	CDS	693363	694403	.	+	.	ID=YGR101W;Name=YGR101W;Alias=PCP1
-chrVII	SGD	CDS	694584	695135	.	-	.	ID=YGR102C;Name=YGR102C;Alias=GTF1
-chrVII	SGD	CDS	695417	697234	.	+	.	ID=YGR103W;Name=YGR103W;Alias=NOP7
-chrVII	SGD	CDS	697445	698368	.	-	.	ID=YGR104C;Name=YGR104C;Alias=SRB5
-chrVII	SGD	CDS	698599	698832	.	+	.	ID=YGR105W;Name=YGR105W;Alias=VMA21
-chrVII	SGD	CDS	698989	699786	.	-	.	ID=YGR106C;Name=YGR106C;Alias=VOA1
-chrVII	SGD	CDS	703636	705051	.	+	.	ID=YGR108W;Name=YGR108W;Alias=CLB1
-chrVII	SGD	CDS	705359	706501	.	-	.	ID=YGR109C;Name=YGR109C;Alias=CLB6
-chrVII	SGD	CDS	713709	715046	.	+	.	ID=YGR110W;Name=YGR110W;Alias=CLD1
-chrVII	SGD	CDS	715828	717030	.	+	.	ID=YGR111W;Name=YGR111W;Alias=
-chrVII	SGD	CDS	717358	718527	.	+	.	ID=YGR112W;Name=YGR112W;Alias=SHY1
-chrVII	SGD	CDS	718893	719924	.	+	.	ID=YGR113W;Name=YGR113W;Alias=DAM1
-chrVII	SGD	CDS	720409	724764	.	+	.	ID=YGR116W;Name=YGR116W;Alias=SPT6
-chrVII	SGD	CDS	725049	726479	.	-	.	ID=YGR117C;Name=YGR117C;Alias=
-chrVII	SGD	CDS	726974	727730	.	+	.	ID=YGR118W;Name=YGR118W;Alias=RPS23A
-chrVII	SGD	CDS	728046	729671	.	-	.	ID=YGR119C;Name=YGR119C;Alias=NUP57
-chrVII	SGD	CDS	730033	730821	.	-	.	ID=YGR120C;Name=YGR120C;Alias=COG2
-chrVII	SGD	CDS	731449	732927	.	-	.	ID=YGR121C;Name=YGR121C;Alias=MEP1
-chrVII	SGD	CDS	733412	733627	.	+	.	ID=YGR121W-A;Name=YGR121W-A;Alias=
-chrVII	SGD	CDS	733935	735143	.	+	.	ID=YGR122W;Name=YGR122W;Alias=
-chrVII	SGD	CDS	736662	738203	.	-	.	ID=YGR123C;Name=YGR123C;Alias=PPT1
-chrVII	SGD	CDS	739944	741662	.	+	.	ID=YGR124W;Name=YGR124W;Alias=ASN2
-chrVII	SGD	CDS	742325	745435	.	+	.	ID=YGR125W;Name=YGR125W;Alias=
-chrVII	SGD	CDS	745835	746527	.	+	.	ID=YGR126W;Name=YGR126W;Alias=
-chrVII	SGD	CDS	746798	747736	.	+	.	ID=YGR127W;Name=YGR127W;Alias=
-chrVII	SGD	CDS	747950	750091	.	-	.	ID=YGR128C;Name=YGR128C;Alias=UTP8
-chrVII	SGD	CDS	750400	751047	.	+	.	ID=YGR129W;Name=YGR129W;Alias=SYF2
-chrVII	SGD	CDS	751394	753844	.	-	.	ID=YGR130C;Name=YGR130C;Alias=
-chrVII	SGD	CDS	754726	755250	.	+	.	ID=YGR131W;Name=YGR131W;Alias=FHN1
-chrVII	SGD	CDS	755589	756452	.	-	.	ID=YGR132C;Name=YGR132C;Alias=PHB1
-chrVII	SGD	CDS	756896	757447	.	+	.	ID=YGR133W;Name=YGR133W;Alias=PEX4
-chrVII	SGD	CDS	757770	761138	.	+	.	ID=YGR134W;Name=YGR134W;Alias=CAF130
-chrVII	SGD	CDS	761392	762168	.	+	.	ID=YGR135W;Name=YGR135W;Alias=PRE9
-chrVII	SGD	CDS	762428	763153	.	+	.	ID=YGR136W;Name=YGR136W;Alias=LSB1
-chrVII	SGD	CDS	763762	765606	.	-	.	ID=YGR138C;Name=YGR138C;Alias=TPO2
-chrVII	SGD	CDS	767429	770299	.	+	.	ID=YGR140W;Name=YGR140W;Alias=CBF2
-chrVII	SGD	CDS	770569	771972	.	+	.	ID=YGR141W;Name=YGR141W;Alias=VPS62
-chrVII	SGD	CDS	772454	773686	.	+	.	ID=YGR142W;Name=YGR142W;Alias=BTN2
-chrVII	SGD	CDS	775193	777508	.	+	.	ID=YGR143W;Name=YGR143W;Alias=SKN1
-chrVII	SGD	CDS	780399	781379	.	+	.	ID=YGR144W;Name=YGR144W;Alias=THI4
-chrVII	SGD	CDS	781767	783890	.	+	.	ID=YGR145W;Name=YGR145W;Alias=ENP2
-chrVII	SGD	CDS	784223	784858	.	-	.	ID=YGR146C;Name=YGR146C;Alias=ECL1
-chrVII	SGD	CDS	785276	785437	.	-	.	ID=YGR146C-A;Name=YGR146C-A;Alias=
-chrVII	SGD	CDS	786054	786920	.	-	.	ID=YGR147C;Name=YGR147C;Alias=NAT2
-chrVII	SGD	CDS	787312	788178	.	-	.	ID=YGR148C;Name=YGR148C;Alias=RPL24B
-chrVII	SGD	CDS	789031	790329	.	+	.	ID=YGR149W;Name=YGR149W;Alias=GPC1
-chrVII	SGD	CDS	790459	793053	.	-	.	ID=YGR150C;Name=YGR150C;Alias=CCM1
-chrVII	SGD	CDS	794674	795492	.	-	.	ID=YGR152C;Name=YGR152C;Alias=RSR1
-chrVII	SGD	CDS	796092	796745	.	+	.	ID=YGR153W;Name=YGR153W;Alias=
-chrVII	SGD	CDS	796798	797868	.	-	.	ID=YGR154C;Name=YGR154C;Alias=GTO1
-chrVII	SGD	CDS	798543	800066	.	+	.	ID=YGR155W;Name=YGR155W;Alias=CYS4
-chrVII	SGD	CDS	800546	801823	.	+	.	ID=YGR156W;Name=YGR156W;Alias=PTI1
-chrVII	SGD	CDS	802440	805049	.	+	.	ID=YGR157W;Name=YGR157W;Alias=CHO2
-chrVII	SGD	CDS	805269	806021	.	-	.	ID=YGR158C;Name=YGR158C;Alias=MTR3
-chrVII	SGD	CDS	806412	807656	.	-	.	ID=YGR159C;Name=YGR159C;Alias=NSR1
-chrVII	SGD	CDS	808629	809420	.	-	.	ID=YGR161C;Name=YGR161C;Alias=RTS3
-chrVII	SGD	CDS	810227	810505	.	+	.	ID=YGR161W-C;Name=YGR161W-C;Alias=
-chrVII	SGD	CDS	824059	826917	.	+	.	ID=YGR162W;Name=YGR162W;Alias=TIF4631
-chrVII	SGD	CDS	827552	828577	.	+	.	ID=YGR163W;Name=YGR163W;Alias=GTR2
-chrVII	SGD	CDS	829116	830153	.	+	.	ID=YGR165W;Name=YGR165W;Alias=MRPS35
-chrVII	SGD	CDS	830515	832197	.	+	.	ID=YGR166W;Name=YGR166W;Alias=TRS65
-chrVII	SGD	CDS	832456	833157	.	+	.	ID=YGR167W;Name=YGR167W;Alias=CLC1
-chrVII	SGD	CDS	833352	834482	.	-	.	ID=YGR168C;Name=YGR168C;Alias=
-chrVII	SGD	CDS	834689	835903	.	-	.	ID=YGR169C;Name=YGR169C;Alias=PUS6
-chrVII	SGD	CDS	836387	836665	.	-	.	ID=YGR169C-A;Name=YGR169C-A;Alias=LSO2
-chrVII	SGD	CDS	837142	840558	.	+	.	ID=YGR170W;Name=YGR170W;Alias=PSD2
-chrVII	SGD	CDS	840824	842551	.	-	.	ID=YGR171C;Name=YGR171C;Alias=MSM1
-chrVII	SGD	CDS	842845	843591	.	-	.	ID=YGR172C;Name=YGR172C;Alias=YIP1
-chrVII	SGD	CDS	843854	844960	.	+	.	ID=YGR173W;Name=YGR173W;Alias=RBG2
-chrVII	SGD	CDS	845893	846405	.	-	.	ID=YGR174C;Name=YGR174C;Alias=CBP4
-chrVII	SGD	CDS	846655	846741	.	+	.	ID=YGR174W-A;Name=YGR174W-A;Alias=
-chrVII	SGD	CDS	846933	848423	.	-	.	ID=YGR175C;Name=YGR175C;Alias=ERG1
-chrVII	SGD	CDS	848829	850436	.	-	.	ID=YGR177C;Name=YGR177C;Alias=ATF2
-chrVII	SGD	CDS	851047	853215	.	-	.	ID=YGR178C;Name=YGR178C;Alias=PBP1
-chrVII	SGD	CDS	853675	854895	.	-	.	ID=YGR179C;Name=YGR179C;Alias=OKP1
-chrVII	SGD	CDS	855264	856301	.	-	.	ID=YGR180C;Name=YGR180C;Alias=RNR4
-chrVII	SGD	CDS	858287	858604	.	+	.	ID=YGR181W;Name=YGR181W;Alias=TIM13
-chrVII	SGD	CDS	859063	859476	.	-	.	ID=YGR183C;Name=YGR183C;Alias=QCR9
-chrVII	SGD	CDS	859901	865753	.	-	.	ID=YGR184C;Name=YGR184C;Alias=UBR1
-chrVII	SGD	CDS	866336	867520	.	-	.	ID=YGR185C;Name=YGR185C;Alias=TYS1
-chrVII	SGD	CDS	867774	869981	.	+	.	ID=YGR186W;Name=YGR186W;Alias=TFG1
-chrVII	SGD	CDS	870232	871416	.	-	.	ID=YGR187C;Name=YGR187C;Alias=HGH1
-chrVII	SGD	CDS	872044	875109	.	-	.	ID=YGR188C;Name=YGR188C;Alias=BUB1
-chrVII	SGD	CDS	876669	878192	.	-	.	ID=YGR189C;Name=YGR189C;Alias=CRH1
-chrVII	SGD	CDS	880420	882231	.	+	.	ID=YGR191W;Name=YGR191W;Alias=HIP1
-chrVII	SGD	CDS	882812	883810	.	-	.	ID=YGR192C;Name=YGR192C;Alias=TDH3
-chrVII	SGD	CDS	884509	885741	.	-	.	ID=YGR193C;Name=YGR193C;Alias=PDX1
-chrVII	SGD	CDS	886073	887875	.	-	.	ID=YGR194C;Name=YGR194C;Alias=XKS1
-chrVII	SGD	CDS	888882	889622	.	+	.	ID=YGR195W;Name=YGR195W;Alias=SKI6
-chrVII	SGD	CDS	889733	892186	.	-	.	ID=YGR196C;Name=YGR196C;Alias=FYV8
-chrVII	SGD	CDS	892497	894140	.	-	.	ID=YGR197C;Name=YGR197C;Alias=SNG1
-chrVII	SGD	CDS	894693	897146	.	+	.	ID=YGR198W;Name=YGR198W;Alias=YPP1
-chrVII	SGD	CDS	897502	899781	.	+	.	ID=YGR199W;Name=YGR199W;Alias=PMT6
-chrVII	SGD	CDS	899904	902270	.	-	.	ID=YGR200C;Name=YGR200C;Alias=ELP2
-chrVII	SGD	CDS	902520	903197	.	-	.	ID=YGR201C;Name=YGR201C;Alias=
-chrVII	SGD	CDS	903474	904748	.	-	.	ID=YGR202C;Name=YGR202C;Alias=PCT1
-chrVII	SGD	CDS	905237	905683	.	+	.	ID=YGR203W;Name=YGR203W;Alias=YCH1
-chrVII	SGD	CDS	905934	908774	.	+	.	ID=YGR204W;Name=YGR204W;Alias=ADE3
-chrVII	SGD	CDS	909061	909174	.	-	.	ID=YGR204C-A;Name=YGR204C-A;Alias=
-chrVII	SGD	CDS	909213	910085	.	+	.	ID=YGR205W;Name=YGR205W;Alias=TDA10
-chrVII	SGD	CDS	910432	910737	.	+	.	ID=YGR206W;Name=YGR206W;Alias=MVB12
-chrVII	SGD	CDS	910843	911628	.	-	.	ID=YGR207C;Name=YGR207C;Alias=CIR1
-chrVII	SGD	CDS	911883	912812	.	+	.	ID=YGR208W;Name=YGR208W;Alias=SER2
-chrVII	SGD	CDS	912913	913227	.	-	.	ID=YGR209C;Name=YGR209C;Alias=TRX2
-chrVII	SGD	CDS	913503	914738	.	-	.	ID=YGR210C;Name=YGR210C;Alias=
-chrVII	SGD	CDS	915241	916701	.	+	.	ID=YGR211W;Name=YGR211W;Alias=ZPR1
-chrVII	SGD	CDS	917040	918446	.	+	.	ID=YGR212W;Name=YGR212W;Alias=SLI1
-chrVII	SGD	CDS	918512	919465	.	-	.	ID=YGR213C;Name=YGR213C;Alias=RTA1
-chrVII	SGD	CDS	920575	921788	.	+	.	ID=YGR214W;Name=YGR214W;Alias=RPS0A
-chrVII	SGD	CDS	922175	922507	.	+	.	ID=YGR215W;Name=YGR215W;Alias=RSM27
-chrVII	SGD	CDS	922633	924462	.	-	.	ID=YGR216C;Name=YGR216C;Alias=GPI1
-chrVII	SGD	CDS	924696	930815	.	+	.	ID=YGR217W;Name=YGR217W;Alias=CCH1
-chrVII	SGD	CDS	932541	935795	.	+	.	ID=YGR218W;Name=YGR218W;Alias=CRM1
-chrVII	SGD	CDS	936074	936883	.	-	.	ID=YGR220C;Name=YGR220C;Alias=MRPL9
-chrVII	SGD	CDS	937124	938992	.	-	.	ID=YGR221C;Name=YGR221C;Alias=TOS2
-chrVII	SGD	CDS	939923	940804	.	+	.	ID=YGR222W;Name=YGR222W;Alias=PET54
-chrVII	SGD	CDS	940869	942215	.	-	.	ID=YGR223C;Name=YGR223C;Alias=HSV2
-chrVII	SGD	CDS	942806	944647	.	+	.	ID=YGR224W;Name=YGR224W;Alias=AZR1
-chrVII	SGD	CDS	945145	947019	.	+	.	ID=YGR225W;Name=YGR225W;Alias=AMA1
-chrVII	SGD	CDS	947420	948997	.	+	.	ID=YGR227W;Name=YGR227W;Alias=DIE2
-chrVII	SGD	CDS	949382	950899	.	-	.	ID=YGR229C;Name=YGR229C;Alias=SMI1
-chrVII	SGD	CDS	951894	952307	.	+	.	ID=YGR230W;Name=YGR230W;Alias=BNS1
-chrVII	SGD	CDS	952548	953480	.	-	.	ID=YGR231C;Name=YGR231C;Alias=PHB2
-chrVII	SGD	CDS	953960	954646	.	+	.	ID=YGR232W;Name=YGR232W;Alias=NAS6
-chrVII	SGD	CDS	954674	958210	.	-	.	ID=YGR233C;Name=YGR233C;Alias=PHO81
-chrVII	SGD	CDS	959904	961103	.	+	.	ID=YGR234W;Name=YGR234W;Alias=YHB1
-chrVII	SGD	CDS	961360	962061	.	-	.	ID=YGR235C;Name=YGR235C;Alias=MIC26
-chrVII	SGD	CDS	962530	962817	.	-	.	ID=YGR236C;Name=YGR236C;Alias=SPG1
-chrVII	SGD	CDS	963298	965655	.	-	.	ID=YGR237C;Name=YGR237C;Alias=
-chrVII	SGD	CDS	966039	968687	.	-	.	ID=YGR238C;Name=YGR238C;Alias=KEL2
-chrVII	SGD	CDS	969187	970053	.	-	.	ID=YGR239C;Name=YGR239C;Alias=PEX21
-chrVII	SGD	CDS	970771	973734	.	-	.	ID=YGR240C;Name=YGR240C;Alias=PFK1
-chrVII	SGD	CDS	974577	974777	.	-	.	ID=YGR240C-A;Name=YGR240C-A;Alias=
-chrVII	SGD	CDS	974875	976581	.	-	.	ID=YGR241C;Name=YGR241C;Alias=YAP1802
-chrVII	SGD	CDS	977336	977776	.	+	.	ID=YGR243W;Name=YGR243W;Alias=MPC3
-chrVII	SGD	CDS	978036	979319	.	-	.	ID=YGR244C;Name=YGR244C;Alias=LSC2
-chrVII	SGD	CDS	979765	982068	.	-	.	ID=YGR245C;Name=YGR245C;Alias=SDA1
-chrVII	SGD	CDS	982482	984272	.	-	.	ID=YGR246C;Name=YGR246C;Alias=BRF1
-chrVII	SGD	CDS	984966	985685	.	+	.	ID=YGR247W;Name=YGR247W;Alias=CPD1
-chrVII	SGD	CDS	985972	986739	.	+	.	ID=YGR248W;Name=YGR248W;Alias=SOL4
-chrVII	SGD	CDS	988049	989419	.	+	.	ID=YGR249W;Name=YGR249W;Alias=MGA1
-chrVII	SGD	CDS	991176	993521	.	-	.	ID=YGR250C;Name=YGR250C;Alias=RIE1
-chrVII	SGD	CDS	995639	996229	.	+	.	ID=YGR251W;Name=YGR251W;Alias=NOP19
-chrVII	SGD	CDS	996869	998188	.	+	.	ID=YGR252W;Name=YGR252W;Alias=GCN5
-chrVII	SGD	CDS	998358	999140	.	-	.	ID=YGR253C;Name=YGR253C;Alias=PUP2
-chrVII	SGD	CDS	1000927	1002240	.	+	.	ID=YGR254W;Name=YGR254W;Alias=ENO1
-chrVII	SGD	CDS	1002523	1003962	.	-	.	ID=YGR255C;Name=YGR255C;Alias=COQ6
-chrVII	SGD	CDS	1004624	1006102	.	+	.	ID=YGR256W;Name=YGR256W;Alias=GND2
-chrVII	SGD	CDS	1006205	1007305	.	-	.	ID=YGR257C;Name=YGR257C;Alias=MTM1
-chrVII	SGD	CDS	1007671	1010766	.	-	.	ID=YGR258C;Name=YGR258C;Alias=RAD2
-chrVII	SGD	CDS	1012485	1014089	.	+	.	ID=YGR260W;Name=YGR260W;Alias=TNA1
-chrVII	SGD	CDS	1014321	1016750	.	-	.	ID=YGR261C;Name=YGR261C;Alias=APL6
-chrVII	SGD	CDS	1016974	1017759	.	-	.	ID=YGR262C;Name=YGR262C;Alias=BUD32
-chrVII	SGD	CDS	1017967	1019241	.	-	.	ID=YGR263C;Name=YGR263C;Alias=SAY1
-chrVII	SGD	CDS	1019598	1021853	.	-	.	ID=YGR264C;Name=YGR264C;Alias=MES1
-chrVII	SGD	CDS	1022656	1024761	.	+	.	ID=YGR266W;Name=YGR266W;Alias=
-chrVII	SGD	CDS	1025004	1025735	.	-	.	ID=YGR267C;Name=YGR267C;Alias=FOL2
-chrVII	SGD	CDS	1026057	1026653	.	-	.	ID=YGR268C;Name=YGR268C;Alias=HUA1
-chrVII	SGD	CDS	1027370	1031509	.	+	.	ID=YGR270W;Name=YGR270W;Alias=YTA7
-chrVII	SGD	CDS	1031791	1037694	.	+	.	ID=YGR271W;Name=YGR271W;Alias=SLH1
-chrVII	SGD	CDS	1037800	1038501	.	-	.	ID=YGR271C-A;Name=YGR271C-A;Alias=EFG1
-chrVII	SGD	CDS	1038715	1039239	.	-	.	ID=YGR273C;Name=YGR273C;Alias=
-chrVII	SGD	CDS	1039895	1043095	.	-	.	ID=YGR274C;Name=YGR274C;Alias=TAF1
-chrVII	SGD	CDS	1043276	1043749	.	+	.	ID=YGR275W;Name=YGR275W;Alias=RTT102
-chrVII	SGD	CDS	1043819	1045480	.	-	.	ID=YGR276C;Name=YGR276C;Alias=RNH70
-chrVII	SGD	CDS	1045644	1046561	.	-	.	ID=YGR277C;Name=YGR277C;Alias=CAB4
-chrVII	SGD	CDS	1046731	1048464	.	+	.	ID=YGR278W;Name=YGR278W;Alias=CWC22
-chrVII	SGD	CDS	1048798	1049958	.	-	.	ID=YGR279C;Name=YGR279C;Alias=SCW4
-chrVII	SGD	CDS	1050910	1051725	.	-	.	ID=YGR280C;Name=YGR280C;Alias=PXR1
-chrVII	SGD	CDS	1052824	1057257	.	+	.	ID=YGR281W;Name=YGR281W;Alias=YOR1
-chrVII	SGD	CDS	1057783	1058724	.	-	.	ID=YGR282C;Name=YGR282C;Alias=BGL2
-chrVII	SGD	CDS	1059015	1060040	.	-	.	ID=YGR283C;Name=YGR283C;Alias=
-chrVII	SGD	CDS	1060658	1061590	.	-	.	ID=YGR284C;Name=YGR284C;Alias=ERV29
-chrVII	SGD	CDS	1061852	1063153	.	-	.	ID=YGR285C;Name=YGR285C;Alias=ZUO1
-chrVII	SGD	CDS	1063813	1064940	.	-	.	ID=YGR286C;Name=YGR286C;Alias=BIO2
-chrVII	SGD	CDS	1067222	1068991	.	-	.	ID=YGR287C;Name=YGR287C;Alias=IMA1
-chrVII	SGD	CDS	1070293	1071714	.	+	.	ID=YGR288W;Name=YGR288W;Alias=MAL13
-chrVII	SGD	CDS	1073963	1075813	.	-	.	ID=YGR289C;Name=YGR289C;Alias=MAL11
-chrVII	SGD	CDS	1076599	1078353	.	+	.	ID=YGR292W;Name=YGR292W;Alias=MAL12
-chrVII	SGD	CDS	1080306	1080668	.	+	.	ID=YGR294W;Name=YGR294W;Alias=PAU12
-chrVII	SGD	CDS	1081584	1082729	.	-	.	ID=YGR295C;Name=YGR295C;Alias=COS6
-chrVII	SGD	CDS	1084864	1090591	.	+	.	ID=YGR296W;Name=YGR296W;Alias=YRF1-3
-chrVIII	SGD	CDS	445	3311	.	-	.	ID=YHL050C;Name=YHL050C;Alias=
-chrVIII	SGD	CDS	3726	4541	.	-	.	ID=YHL049C;Name=YHL049C;Alias=
-chrVIII	SGD	CDS	5663	5797	.	-	.	ID=YHL048C-A;Name=YHL048C-A;Alias=
-chrVIII	SGD	CDS	6401	7546	.	+	.	ID=YHL048W;Name=YHL048W;Alias=COS8
-chrVIII	SGD	CDS	8351	10213	.	-	.	ID=YHL047C;Name=YHL047C;Alias=ARN2
-chrVIII	SGD	CDS	11923	12285	.	-	.	ID=YHL046C;Name=YHL046C;Alias=PAU13
-chrVIII	SGD	CDS	13565	14272	.	+	.	ID=YHL044W;Name=YHL044W;Alias=
-chrVIII	SGD	CDS	14901	15413	.	+	.	ID=YHL043W;Name=YHL043W;Alias=ECM34
-chrVIII	SGD	CDS	15667	16119	.	+	.	ID=YHL042W;Name=YHL042W;Alias=
-chrVIII	SGD	CDS	19088	20971	.	-	.	ID=YHL040C;Name=YHL040C;Alias=ARN1
-chrVIII	SGD	CDS	21783	23540	.	+	.	ID=YHL039W;Name=YHL039W;Alias=EFM1
-chrVIII	SGD	CDS	23617	25509	.	-	.	ID=YHL038C;Name=YHL038C;Alias=CBP2
-chrVIII	SGD	CDS	26241	27881	.	+	.	ID=YHL036W;Name=YHL036W;Alias=MUP3
-chrVIII	SGD	CDS	27978	32756	.	-	.	ID=YHL035C;Name=YHL035C;Alias=VMR1
-chrVIII	SGD	CDS	33193	34077	.	-	.	ID=YHL034C;Name=YHL034C;Alias=SBP1
-chrVIII	SGD	CDS	35255	36025	.	-	.	ID=YHL033C;Name=YHL033C;Alias=RPL8A
-chrVIII	SGD	CDS	36379	38508	.	-	.	ID=YHL032C;Name=YHL032C;Alias=GUT1
-chrVIII	SGD	CDS	38815	39486	.	-	.	ID=YHL031C;Name=YHL031C;Alias=GOS1
-chrVIII	SGD	CDS	40084	45690	.	+	.	ID=YHL030W;Name=YHL030W;Alias=ECM29
-chrVIII	SGD	CDS	45929	47968	.	-	.	ID=YHL029C;Name=YHL029C;Alias=OCA5
-chrVIII	SGD	CDS	48763	50580	.	+	.	ID=YHL028W;Name=YHL028W;Alias=WSC4
-chrVIII	SGD	CDS	51111	52988	.	+	.	ID=YHL027W;Name=YHL027W;Alias=RIM101
-chrVIII	SGD	CDS	53219	54166	.	-	.	ID=YHL026C;Name=YHL026C;Alias=
-chrVIII	SGD	CDS	54851	55849	.	+	.	ID=YHL025W;Name=YHL025W;Alias=SNF6
-chrVIII	SGD	CDS	56649	58790	.	+	.	ID=YHL024W;Name=YHL024W;Alias=RIM4
-chrVIII	SGD	CDS	59123	62563	.	-	.	ID=YHL023C;Name=YHL023C;Alias=NPR3
-chrVIII	SGD	CDS	62961	64157	.	-	.	ID=YHL022C;Name=YHL022C;Alias=SPO11
-chrVIII	SGD	CDS	64462	65859	.	-	.	ID=YHL021C;Name=YHL021C;Alias=AIM17
-chrVIII	SGD	CDS	66242	67456	.	-	.	ID=YHL020C;Name=YHL020C;Alias=OPI1
-chrVIII	SGD	CDS	67731	69548	.	-	.	ID=YHL019C;Name=YHL019C;Alias=APM2
-chrVIII	SGD	CDS	69708	70070	.	+	.	ID=YHL018W;Name=YHL018W;Alias=
-chrVIII	SGD	CDS	70276	71874	.	+	.	ID=YHL017W;Name=YHL017W;Alias=
-chrVIII	SGD	CDS	72037	74244	.	-	.	ID=YHL016C;Name=YHL016C;Alias=DUR3
-chrVIII	SGD	CDS	74699	74782	.	+	.	ID=YHL015W-A;Name=YHL015W-A;Alias=
-chrVIII	SGD	CDS	75412	75777	.	+	.	ID=YHL015W;Name=YHL015W;Alias=RPS20
-chrVIII	SGD	CDS	76097	77314	.	-	.	ID=YHL014C;Name=YHL014C;Alias=YLF2
-chrVIII	SGD	CDS	77430	78353	.	-	.	ID=YHL013C;Name=YHL013C;Alias=OTU2
-chrVIII	SGD	CDS	78936	80417	.	+	.	ID=YHL012W;Name=YHL012W;Alias=
-chrVIII	SGD	CDS	80654	81616	.	-	.	ID=YHL011C;Name=YHL011C;Alias=PRS3
-chrVIII	SGD	CDS	81964	83721	.	-	.	ID=YHL010C;Name=YHL010C;Alias=ETP1
-chrVIII	SGD	CDS	84068	85060	.	-	.	ID=YHL009C;Name=YHL009C;Alias=YAP3
-chrVIII	SGD	CDS	92627	94510	.	-	.	ID=YHL008C;Name=YHL008C;Alias=
-chrVIII	SGD	CDS	95118	97937	.	-	.	ID=YHL007C;Name=YHL007C;Alias=STE20
-chrVIII	SGD	CDS	98343	98795	.	-	.	ID=YHL006C;Name=YHL006C;Alias=SHU1
-chrVIII	SGD	CDS	99219	100403	.	+	.	ID=YHL004W;Name=YHL004W;Alias=MRP4
-chrVIII	SGD	CDS	100648	101883	.	-	.	ID=YHL003C;Name=YHL003C;Alias=LAG1
-chrVIII	SGD	CDS	102612	103970	.	+	.	ID=YHL002W;Name=YHL002W;Alias=HSE1
-chrVIII	SGD	CDS	104277	105091	.	+	.	ID=YHL001W;Name=YHL001W;Alias=RPL14B
-chrVIII	SGD	CDS	106055	107368	.	+	.	ID=YHR001W;Name=YHR001W;Alias=OSH7
-chrVIII	SGD	CDS	107826	108122	.	+	.	ID=YHR001W-A;Name=YHR001W-A;Alias=QCR10
-chrVIII	SGD	CDS	108812	109885	.	+	.	ID=YHR002W;Name=YHR002W;Alias=LEU5
-chrVIII	SGD	CDS	110028	111317	.	-	.	ID=YHR003C;Name=YHR003C;Alias=TCD1
-chrVIII	SGD	CDS	111754	113094	.	-	.	ID=YHR004C;Name=YHR004C;Alias=NEM1
-chrVIII	SGD	CDS	113499	114917	.	-	.	ID=YHR005C;Name=YHR005C;Alias=GPA1
-chrVIII	SGD	CDS	115620	115901	.	-	.	ID=YHR005C-A;Name=YHR005C-A;Alias=TIM10
-chrVIII	SGD	CDS	117814	119439	.	+	.	ID=YHR006W;Name=YHR006W;Alias=STP2
-chrVIII	SGD	CDS	120091	121683	.	-	.	ID=YHR007C;Name=YHR007C;Alias=ERG11
-chrVIII	SGD	CDS	122550	122765	.	-	.	ID=YHR007C-A;Name=YHR007C-A;Alias=
-chrVIII	SGD	CDS	122889	123590	.	-	.	ID=YHR008C;Name=YHR008C;Alias=SOD2
-chrVIII	SGD	CDS	124109	125680	.	-	.	ID=YHR009C;Name=YHR009C;Alias=TDA3
-chrVIII	SGD	CDS	126521	127492	.	+	.	ID=YHR010W;Name=YHR010W;Alias=RPL27A
-chrVIII	SGD	CDS	127780	129120	.	+	.	ID=YHR011W;Name=YHR011W;Alias=DIA4
-chrVIII	SGD	CDS	129481	130448	.	+	.	ID=YHR012W;Name=YHR012W;Alias=VPS29
-chrVIII	SGD	CDS	130730	131446	.	-	.	ID=YHR013C;Name=YHR013C;Alias=ARD1
-chrVIII	SGD	CDS	132047	132922	.	+	.	ID=YHR014W;Name=YHR014W;Alias=SPO13
-chrVIII	SGD	CDS	134554	136533	.	+	.	ID=YHR015W;Name=YHR015W;Alias=MIP6
-chrVIII	SGD	CDS	136881	138455	.	-	.	ID=YHR016C;Name=YHR016C;Alias=YSC84
-chrVIII	SGD	CDS	138694	139851	.	+	.	ID=YHR017W;Name=YHR017W;Alias=YSC83
-chrVIII	SGD	CDS	140011	141402	.	-	.	ID=YHR018C;Name=YHR018C;Alias=ARG4
-chrVIII	SGD	CDS	141894	143558	.	-	.	ID=YHR019C;Name=YHR019C;Alias=DED81
-chrVIII	SGD	CDS	143996	146062	.	+	.	ID=YHR020W;Name=YHR020W;Alias=
-chrVIII	SGD	CDS	147871	148669	.	-	.	ID=YHR021C;Name=YHR021C;Alias=RPS27B
-chrVIII	SGD	CDS	149225	149680	.	+	.	ID=YHR021W-A;Name=YHR021W-A;Alias=ECM12
-chrVIII	SGD	CDS	149575	150345	.	-	.	ID=YHR022C;Name=YHR022C;Alias=
-chrVIII	SGD	CDS	151217	151306	.	-	.	ID=YHR022C-A;Name=YHR022C-A;Alias=
-chrVIII	SGD	CDS	151666	157452	.	+	.	ID=YHR023W;Name=YHR023W;Alias=MYO1
-chrVIII	SGD	CDS	157744	159192	.	-	.	ID=YHR024C;Name=YHR024C;Alias=MAS2
-chrVIII	SGD	CDS	159438	160511	.	+	.	ID=YHR025W;Name=YHR025W;Alias=THR1
-chrVIII	SGD	CDS	160844	161485	.	+	.	ID=YHR026W;Name=YHR026W;Alias=VMA16
-chrVIII	SGD	CDS	161730	164711	.	-	.	ID=YHR027C;Name=YHR027C;Alias=RPN1
-chrVIII	SGD	CDS	164978	167434	.	-	.	ID=YHR028C;Name=YHR028C;Alias=DAP2
-chrVIII	SGD	CDS	167677	168561	.	-	.	ID=YHR029C;Name=YHR029C;Alias=YHI9
-chrVIII	SGD	CDS	168890	170344	.	-	.	ID=YHR030C;Name=YHR030C;Alias=SLT2
-chrVIII	SGD	CDS	170799	172970	.	-	.	ID=YHR031C;Name=YHR031C;Alias=RRM3
-chrVIII	SGD	CDS	173344	175089	.	+	.	ID=YHR032W;Name=YHR032W;Alias=ERC1
-chrVIII	SGD	CDS	175548	176819	.	+	.	ID=YHR033W;Name=YHR033W;Alias=
-chrVIII	SGD	CDS	176965	177999	.	-	.	ID=YHR034C;Name=YHR034C;Alias=PIH1
-chrVIII	SGD	CDS	178219	180111	.	+	.	ID=YHR035W;Name=YHR035W;Alias=NEL1
-chrVIII	SGD	CDS	180345	181760	.	+	.	ID=YHR036W;Name=YHR036W;Alias=BRL1
-chrVIII	SGD	CDS	181977	183704	.	+	.	ID=YHR037W;Name=YHR037W;Alias=PUT2
-chrVIII	SGD	CDS	184066	184758	.	+	.	ID=YHR038W;Name=YHR038W;Alias=RRF1
-chrVIII	SGD	CDS	184875	186809	.	-	.	ID=YHR039C;Name=YHR039C;Alias=MSC7
-chrVIII	SGD	CDS	187173	187679	.	-	.	ID=YHR039C-A;Name=YHR039C-A;Alias=VMA10
-chrVIII	SGD	CDS	187924	189024	.	+	.	ID=YHR040W;Name=YHR040W;Alias=BCD1
-chrVIII	SGD	CDS	189131	189864	.	-	.	ID=YHR041C;Name=YHR041C;Alias=SRB2
-chrVIII	SGD	CDS	190543	192618	.	+	.	ID=YHR042W;Name=YHR042W;Alias=NCP1
-chrVIII	SGD	CDS	192805	193545	.	-	.	ID=YHR043C;Name=YHR043C;Alias=DOG2
-chrVIII	SGD	CDS	194068	194808	.	-	.	ID=YHR044C;Name=YHR044C;Alias=DOG1
-chrVIII	SGD	CDS	195551	197233	.	+	.	ID=YHR045W;Name=YHR045W;Alias=
-chrVIII	SGD	CDS	197398	198285	.	-	.	ID=YHR046C;Name=YHR046C;Alias=INM1
-chrVIII	SGD	CDS	198740	201310	.	-	.	ID=YHR047C;Name=YHR047C;Alias=AAP1
-chrVIII	SGD	CDS	204607	206151	.	+	.	ID=YHR048W;Name=YHR048W;Alias=YHK8
-chrVIII	SGD	CDS	206462	207193	.	+	.	ID=YHR049W;Name=YHR049W;Alias=FSH1
-chrVIII	SGD	CDS	207654	209303	.	+	.	ID=YHR050W;Name=YHR050W;Alias=SMF2
-chrVIII	SGD	CDS	209475	209645	.	+	.	ID=YHR050W-A;Name=YHR050W-A;Alias=
-chrVIII	SGD	CDS	209705	210151	.	+	.	ID=YHR051W;Name=YHR051W;Alias=COX6
-chrVIII	SGD	CDS	210848	211978	.	+	.	ID=YHR052W;Name=YHR052W;Alias=CIC1
-chrVIII	SGD	CDS	212535	212720	.	-	.	ID=YHR053C;Name=YHR053C;Alias=CUP1-1
-chrVIII	SGD	CDS	213185	214249	.	-	.	ID=YHR054C;Name=YHR054C;Alias=
-chrVIII	SGD	CDS	214533	214718	.	-	.	ID=YHR055C;Name=YHR055C;Alias=CUP1-2
-chrVIII	SGD	CDS	215183	217834	.	-	.	ID=YHR056C;Name=YHR056C;Alias=RSC30
-chrVIII	SGD	CDS	218226	218843	.	-	.	ID=YHR057C;Name=YHR057C;Alias=CPR2
-chrVIII	SGD	CDS	218997	219884	.	-	.	ID=YHR058C;Name=YHR058C;Alias=MED6
-chrVIII	SGD	CDS	220108	220500	.	+	.	ID=YHR059W;Name=YHR059W;Alias=FYV4
-chrVIII	SGD	CDS	220725	221270	.	+	.	ID=YHR060W;Name=YHR060W;Alias=VMA22
-chrVIII	SGD	CDS	221534	222478	.	-	.	ID=YHR061C;Name=YHR061C;Alias=GIC1
-chrVIII	SGD	CDS	222877	223758	.	-	.	ID=YHR062C;Name=YHR062C;Alias=RPP1
-chrVIII	SGD	CDS	224030	225169	.	-	.	ID=YHR063C;Name=YHR063C;Alias=PAN5
-chrVIII	SGD	CDS	225525	227141	.	-	.	ID=YHR064C;Name=YHR064C;Alias=SSZ1
-chrVIII	SGD	CDS	227532	229037	.	-	.	ID=YHR065C;Name=YHR065C;Alias=RRP3
-chrVIII	SGD	CDS	229335	230696	.	+	.	ID=YHR066W;Name=YHR066W;Alias=SSF1
-chrVIII	SGD	CDS	230970	231812	.	+	.	ID=YHR067W;Name=YHR067W;Alias=HTD2
-chrVIII	SGD	CDS	232133	233296	.	+	.	ID=YHR068W;Name=YHR068W;Alias=DYS1
-chrVIII	SGD	CDS	233579	234658	.	-	.	ID=YHR069C;Name=YHR069C;Alias=RRP4
-chrVIII	SGD	CDS	234881	236380	.	+	.	ID=YHR070W;Name=YHR070W;Alias=TRM5
-chrVIII	SGD	CDS	237004	237693	.	+	.	ID=YHR071W;Name=YHR071W;Alias=PCL5
-chrVIII	SGD	CDS	239098	241293	.	+	.	ID=YHR072W;Name=YHR072W;Alias=ERG7
-chrVIII	SGD	CDS	241664	241840	.	+	.	ID=YHR072W-A;Name=YHR072W-A;Alias=NOP10
-chrVIII	SGD	CDS	242582	245572	.	+	.	ID=YHR073W;Name=YHR073W;Alias=OSH3
-chrVIII	SGD	CDS	246193	248337	.	+	.	ID=YHR074W;Name=YHR074W;Alias=QNS1
-chrVIII	SGD	CDS	248439	249641	.	-	.	ID=YHR075C;Name=YHR075C;Alias=PPE1
-chrVIII	SGD	CDS	251101	252225	.	+	.	ID=YHR076W;Name=YHR076W;Alias=PTC7
-chrVIII	SGD	CDS	252374	255756	.	-	.	ID=YHR077C;Name=YHR077C;Alias=NMD2
-chrVIII	SGD	CDS	256360	258018	.	+	.	ID=YHR078W;Name=YHR078W;Alias=
-chrVIII	SGD	CDS	258244	261591	.	-	.	ID=YHR079C;Name=YHR079C;Alias=IRE1
-chrVIII	SGD	CDS	262192	262553	.	-	.	ID=YHR079C-A;Name=YHR079C-A;Alias=SAE3
-chrVIII	SGD	CDS	262801	266838	.	-	.	ID=YHR080C;Name=YHR080C;Alias=LAM4
-chrVIII	SGD	CDS	267538	268092	.	+	.	ID=YHR081W;Name=YHR081W;Alias=LRP1
-chrVIII	SGD	CDS	268459	271548	.	-	.	ID=YHR082C;Name=YHR082C;Alias=KSP1
-chrVIII	SGD	CDS	272627	273616	.	+	.	ID=YHR083W;Name=YHR083W;Alias=SAM35
-chrVIII	SGD	CDS	274174	276240	.	+	.	ID=YHR084W;Name=YHR084W;Alias=STE12
-chrVIII	SGD	CDS	276764	277768	.	+	.	ID=YHR085W;Name=YHR085W;Alias=IPI1
-chrVIII	SGD	CDS	278153	279724	.	+	.	ID=YHR086W;Name=YHR086W;Alias=NAM8
-chrVIII	SGD	CDS	280231	280392	.	+	.	ID=YHR086W-A;Name=YHR086W-A;Alias=
-chrVIII	SGD	CDS	280820	281155	.	+	.	ID=YHR087W;Name=YHR087W;Alias=RTC3
-chrVIII	SGD	CDS	281495	282382	.	+	.	ID=YHR088W;Name=YHR088W;Alias=RPF1
-chrVIII	SGD	CDS	282681	283298	.	-	.	ID=YHR089C;Name=YHR089C;Alias=GAR1
-chrVIII	SGD	CDS	283777	284625	.	-	.	ID=YHR090C;Name=YHR090C;Alias=YNG2
-chrVIII	SGD	CDS	284839	286770	.	-	.	ID=YHR091C;Name=YHR091C;Alias=MSR1
-chrVIII	SGD	CDS	287081	288811	.	-	.	ID=YHR092C;Name=YHR092C;Alias=HXT4
-chrVIII	SGD	CDS	290913	292625	.	-	.	ID=YHR094C;Name=YHR094C;Alias=HXT1
-chrVIII	SGD	CDS	294669	296447	.	-	.	ID=YHR096C;Name=YHR096C;Alias=HXT5
-chrVIII	SGD	CDS	297385	298609	.	-	.	ID=YHR097C;Name=YHR097C;Alias=
-chrVIII	SGD	CDS	299145	301934	.	-	.	ID=YHR098C;Name=YHR098C;Alias=SFB3
-chrVIII	SGD	CDS	302761	313995	.	+	.	ID=YHR099W;Name=YHR099W;Alias=TRA1
-chrVIII	SGD	CDS	314116	314673	.	-	.	ID=YHR100C;Name=YHR100C;Alias=GEP4
-chrVIII	SGD	CDS	314874	315968	.	-	.	ID=YHR101C;Name=YHR101C;Alias=BIG1
-chrVIII	SGD	CDS	316572	319814	.	+	.	ID=YHR102W;Name=YHR102W;Alias=KIC1
-chrVIII	SGD	CDS	320414	322972	.	+	.	ID=YHR103W;Name=YHR103W;Alias=SBE22
-chrVIII	SGD	CDS	323409	324392	.	+	.	ID=YHR104W;Name=YHR104W;Alias=GRE3
-chrVIII	SGD	CDS	324766	325410	.	+	.	ID=YHR105W;Name=YHR105W;Alias=YPT35
-chrVIII	SGD	CDS	325598	326626	.	+	.	ID=YHR106W;Name=YHR106W;Alias=TRR2
-chrVIII	SGD	CDS	326813	328036	.	-	.	ID=YHR107C;Name=YHR107C;Alias=CDC12
-chrVIII	SGD	CDS	328303	330060	.	+	.	ID=YHR108W;Name=YHR108W;Alias=GGA2
-chrVIII	SGD	CDS	330310	332067	.	+	.	ID=YHR109W;Name=YHR109W;Alias=CTM1
-chrVIII	SGD	CDS	332282	332920	.	+	.	ID=YHR110W;Name=YHR110W;Alias=ERP5
-chrVIII	SGD	CDS	333072	334394	.	+	.	ID=YHR111W;Name=YHR111W;Alias=UBA4
-chrVIII	SGD	CDS	334527	335663	.	-	.	ID=YHR112C;Name=YHR112C;Alias=
-chrVIII	SGD	CDS	336337	337809	.	+	.	ID=YHR113W;Name=YHR113W;Alias=APE4
-chrVIII	SGD	CDS	338083	339984	.	+	.	ID=YHR114W;Name=YHR114W;Alias=BZZ1
-chrVIII	SGD	CDS	340109	341359	.	-	.	ID=YHR115C;Name=YHR115C;Alias=DMA1
-chrVIII	SGD	CDS	341665	342120	.	+	.	ID=YHR116W;Name=YHR116W;Alias=COX23
-chrVIII	SGD	CDS	342349	344268	.	+	.	ID=YHR117W;Name=YHR117W;Alias=TOM71
-chrVIII	SGD	CDS	344321	345628	.	-	.	ID=YHR118C;Name=YHR118C;Alias=ORC6
-chrVIII	SGD	CDS	346043	349285	.	+	.	ID=YHR119W;Name=YHR119W;Alias=SET1
-chrVIII	SGD	CDS	349574	352453	.	+	.	ID=YHR120W;Name=YHR120W;Alias=MSH1
-chrVIII	SGD	CDS	352756	353319	.	+	.	ID=YHR121W;Name=YHR121W;Alias=LSM12
-chrVIII	SGD	CDS	353625	354320	.	+	.	ID=YHR122W;Name=YHR122W;Alias=CIA2
-chrVIII	SGD	CDS	354815	356081	.	+	.	ID=YHR123W;Name=YHR123W;Alias=EPT1
-chrVIII	SGD	CDS	356561	358444	.	+	.	ID=YHR124W;Name=YHR124W;Alias=NDT80
-chrVIII	SGD	CDS	359702	360181	.	-	.	ID=YHR126C;Name=YHR126C;Alias=ANS1
-chrVIII	SGD	CDS	360913	361644	.	+	.	ID=YHR127W;Name=YHR127W;Alias=
-chrVIII	SGD	CDS	362115	362765	.	+	.	ID=YHR128W;Name=YHR128W;Alias=FUR1
-chrVIII	SGD	CDS	362999	364153	.	-	.	ID=YHR129C;Name=YHR129C;Alias=ARP1
-chrVIII	SGD	CDS	365340	367892	.	-	.	ID=YHR131C;Name=YHR131C;Alias=
-chrVIII	SGD	CDS	368502	369794	.	-	.	ID=YHR132C;Name=YHR132C;Alias=ECM14
-chrVIII	SGD	CDS	370054	370449	.	+	.	ID=YHR132W-A;Name=YHR132W-A;Alias=IGO2
-chrVIII	SGD	CDS	370722	371597	.	-	.	ID=YHR133C;Name=YHR133C;Alias=NSG1
-chrVIII	SGD	CDS	371749	372558	.	+	.	ID=YHR134W;Name=YHR134W;Alias=WSS1
-chrVIII	SGD	CDS	372694	374310	.	-	.	ID=YHR135C;Name=YHR135C;Alias=YCK1
-chrVIII	SGD	CDS	374654	375100	.	-	.	ID=YHR136C;Name=YHR136C;Alias=SPL2
-chrVIII	SGD	CDS	375709	377250	.	+	.	ID=YHR137W;Name=YHR137W;Alias=ARO9
-chrVIII	SGD	CDS	377355	377699	.	-	.	ID=YHR138C;Name=YHR138C;Alias=
-chrVIII	SGD	CDS	378219	379199	.	-	.	ID=YHR139C;Name=YHR139C;Alias=SPS100
-chrVIII	SGD	CDS	380572	381291	.	+	.	ID=YHR140W;Name=YHR140W;Alias=
-chrVIII	SGD	CDS	381990	382751	.	-	.	ID=YHR141C;Name=YHR141C;Alias=RPL42B
-chrVIII	SGD	CDS	383538	384488	.	+	.	ID=YHR142W;Name=YHR142W;Alias=CHS7
-chrVIII	SGD	CDS	385510	386487	.	+	.	ID=YHR143W;Name=YHR143W;Alias=DSE2
-chrVIII	SGD	CDS	387233	387445	.	+	.	ID=YHR143W-A;Name=YHR143W-A;Alias=RPC10
-chrVIII	SGD	CDS	387788	388726	.	-	.	ID=YHR144C;Name=YHR144C;Alias=DCD1
-chrVIII	SGD	CDS	390300	391697	.	+	.	ID=YHR146W;Name=YHR146W;Alias=CRP1
-chrVIII	SGD	CDS	392639	393283	.	-	.	ID=YHR147C;Name=YHR147C;Alias=MRPL6
-chrVIII	SGD	CDS	393534	394085	.	+	.	ID=YHR148W;Name=YHR148W;Alias=IMP3
-chrVIII	SGD	CDS	394455	396659	.	-	.	ID=YHR149C;Name=YHR149C;Alias=SKG6
-chrVIII	SGD	CDS	397251	398990	.	+	.	ID=YHR150W;Name=YHR150W;Alias=PEX28
-chrVIII	SGD	CDS	399268	400848	.	-	.	ID=YHR151C;Name=YHR151C;Alias=MTC6
-chrVIII	SGD	CDS	401434	401955	.	+	.	ID=YHR152W;Name=YHR152W;Alias=SPO12
-chrVIII	SGD	CDS	402086	402682	.	-	.	ID=YHR153C;Name=YHR153C;Alias=SPO16
-chrVIII	SGD	CDS	402966	406178	.	+	.	ID=YHR154W;Name=YHR154W;Alias=RTT107
-chrVIII	SGD	CDS	407103	410789	.	+	.	ID=YHR155W;Name=YHR155W;Alias=LAM1
-chrVIII	SGD	CDS	411384	412406	.	-	.	ID=YHR156C;Name=YHR156C;Alias=LIN1
-chrVIII	SGD	CDS	412907	413455	.	+	.	ID=YHR157W;Name=YHR157W;Alias=REC104
-chrVIII	SGD	CDS	413685	417179	.	-	.	ID=YHR158C;Name=YHR158C;Alias=KEL1
-chrVIII	SGD	CDS	417549	419063	.	+	.	ID=YHR159W;Name=YHR159W;Alias=TDA11
-chrVIII	SGD	CDS	419221	420072	.	-	.	ID=YHR160C;Name=YHR160C;Alias=PEX18
-chrVIII	SGD	CDS	420373	422286	.	-	.	ID=YHR161C;Name=YHR161C;Alias=YAP1801
-chrVIII	SGD	CDS	423072	423461	.	+	.	ID=YHR162W;Name=YHR162W;Alias=MPC2
-chrVIII	SGD	CDS	423724	424473	.	+	.	ID=YHR163W;Name=YHR163W;Alias=SOL3
-chrVIII	SGD	CDS	424610	429178	.	-	.	ID=YHR164C;Name=YHR164C;Alias=DNA2
-chrVIII	SGD	CDS	429707	436948	.	-	.	ID=YHR165C;Name=YHR165C;Alias=PRP8
-chrVIII	SGD	CDS	437170	439050	.	-	.	ID=YHR166C;Name=YHR166C;Alias=CDC23
-chrVIII	SGD	CDS	439342	440127	.	+	.	ID=YHR167W;Name=YHR167W;Alias=THP2
-chrVIII	SGD	CDS	440377	441933	.	+	.	ID=YHR168W;Name=YHR168W;Alias=MTG2
-chrVIII	SGD	CDS	442181	443476	.	+	.	ID=YHR169W;Name=YHR169W;Alias=DBP8
-chrVIII	SGD	CDS	443828	445384	.	+	.	ID=YHR170W;Name=YHR170W;Alias=NMD3
-chrVIII	SGD	CDS	445713	447605	.	+	.	ID=YHR171W;Name=YHR171W;Alias=ATG7
-chrVIII	SGD	CDS	448335	450806	.	+	.	ID=YHR172W;Name=YHR172W;Alias=SPC97
-chrVIII	SGD	CDS	450815	451153	.	-	.	ID=YHR173C;Name=YHR173C;Alias=
-chrVIII	SGD	CDS	451327	452640	.	+	.	ID=YHR174W;Name=YHR174W;Alias=ENO2
-chrVIII	SGD	CDS	452872	453441	.	+	.	ID=YHR175W;Name=YHR175W;Alias=CTR2
-chrVIII	SGD	CDS	453558	453707	.	+	.	ID=YHR175W-A;Name=YHR175W-A;Alias=
-chrVIII	SGD	CDS	454229	455527	.	+	.	ID=YHR176W;Name=YHR176W;Alias=FMO1
-chrVIII	SGD	CDS	456591	457952	.	+	.	ID=YHR177W;Name=YHR177W;Alias=
-chrVIII	SGD	CDS	459299	461530	.	+	.	ID=YHR178W;Name=YHR178W;Alias=STB5
-chrVIII	SGD	CDS	462502	463704	.	+	.	ID=YHR179W;Name=YHR179W;Alias=OYE2
-chrVIII	SGD	CDS	467228	467914	.	+	.	ID=YHR181W;Name=YHR181W;Alias=SVP26
-chrVIII	SGD	CDS	468219	470576	.	+	.	ID=YHR182W;Name=YHR182W;Alias=
-chrVIII	SGD	CDS	470960	472429	.	+	.	ID=YHR183W;Name=YHR183W;Alias=GND1
-chrVIII	SGD	CDS	472744	474459	.	+	.	ID=YHR184W;Name=YHR184W;Alias=SSP1
-chrVIII	SGD	CDS	474627	475340	.	-	.	ID=YHR185C;Name=YHR185C;Alias=PFS1
-chrVIII	SGD	CDS	475999	480672	.	-	.	ID=YHR186C;Name=YHR186C;Alias=KOG1
-chrVIII	SGD	CDS	480990	481919	.	+	.	ID=YHR187W;Name=YHR187W;Alias=IKI1
-chrVIII	SGD	CDS	482005	483837	.	-	.	ID=YHR188C;Name=YHR188C;Alias=GPI16
-chrVIII	SGD	CDS	484028	484600	.	+	.	ID=YHR189W;Name=YHR189W;Alias=PTH1
-chrVIII	SGD	CDS	484845	486179	.	+	.	ID=YHR190W;Name=YHR190W;Alias=ERG9
-chrVIII	SGD	CDS	486230	486631	.	-	.	ID=YHR191C;Name=YHR191C;Alias=CTF8
-chrVIII	SGD	CDS	486826	487662	.	+	.	ID=YHR192W;Name=YHR192W;Alias=LNP1
-chrVIII	SGD	CDS	487712	488236	.	-	.	ID=YHR193C;Name=YHR193C;Alias=EGD2
-chrVIII	SGD	CDS	488657	490396	.	+	.	ID=YHR194W;Name=YHR194W;Alias=MDM31
-chrVIII	SGD	CDS	490747	491712	.	+	.	ID=YHR195W;Name=YHR195W;Alias=NVJ1
-chrVIII	SGD	CDS	491931	493658	.	+	.	ID=YHR196W;Name=YHR196W;Alias=UTP9
-chrVIII	SGD	CDS	493896	496187	.	+	.	ID=YHR197W;Name=YHR197W;Alias=RIX1
-chrVIII	SGD	CDS	496315	497280	.	-	.	ID=YHR198C;Name=YHR198C;Alias=AIM18
-chrVIII	SGD	CDS	497490	498422	.	-	.	ID=YHR199C;Name=YHR199C;Alias=AIM46
-chrVIII	SGD	CDS	498571	498859	.	-	.	ID=YHR199C-A;Name=YHR199C-A;Alias=NBL1
-chrVIII	SGD	CDS	499079	499885	.	+	.	ID=YHR200W;Name=YHR200W;Alias=RPN10
-chrVIII	SGD	CDS	499950	501143	.	-	.	ID=YHR201C;Name=YHR201C;Alias=PPX1
-chrVIII	SGD	CDS	502388	504196	.	+	.	ID=YHR202W;Name=YHR202W;Alias=
-chrVIII	SGD	CDS	504476	505530	.	-	.	ID=YHR203C;Name=YHR203C;Alias=RPS4B
-chrVIII	SGD	CDS	506319	508709	.	+	.	ID=YHR204W;Name=YHR204W;Alias=MNL1
-chrVIII	SGD	CDS	509363	511837	.	+	.	ID=YHR205W;Name=YHR205W;Alias=SCH9
-chrVIII	SGD	CDS	512732	514600	.	+	.	ID=YHR206W;Name=YHR206W;Alias=SKN7
-chrVIII	SGD	CDS	514905	516485	.	-	.	ID=YHR207C;Name=YHR207C;Alias=SET5
-chrVIII	SGD	CDS	517532	518713	.	+	.	ID=YHR208W;Name=YHR208W;Alias=BAT1
-chrVIII	SGD	CDS	519437	520312	.	+	.	ID=YHR209W;Name=YHR209W;Alias=CRG1
-chrVIII	SGD	CDS	520712	521737	.	-	.	ID=YHR210C;Name=YHR210C;Alias=
-chrVIII	SGD	CDS	525392	528619	.	+	.	ID=YHR211W;Name=YHR211W;Alias=FLO5
-chrVIII	SGD	CDS	538742	538945	.	+	.	ID=YHR212W-A;Name=YHR212W-A;Alias=
-chrVIII	SGD	CDS	539151	539747	.	+	.	ID=YHR213W;Name=YHR213W;Alias=
-chrVIII	SGD	CDS	540549	540782	.	+	.	ID=YHR213W-A;Name=YHR213W-A;Alias=
-chrVIII	SGD	CDS	540800	541099	.	+	.	ID=YHR213W-B;Name=YHR213W-B;Alias=
-chrVIII	SGD	CDS	541651	542262	.	+	.	ID=YHR214W;Name=YHR214W;Alias=
-chrVIII	SGD	CDS	550648	550941	.	-	.	ID=YHR214C-D;Name=YHR214C-D;Alias=
-chrVIII	SGD	CDS	551200	551499	.	-	.	ID=YHR214C-E;Name=YHR214C-E;Alias=
-chrVIII	SGD	CDS	552099	553502	.	+	.	ID=YHR215W;Name=YHR215W;Alias=PHO12
-chrVIII	SGD	CDS	554396	555967	.	+	.	ID=YHR216W;Name=YHR216W;Alias=IMD2
-chrVIII	SGD	CDS	558014	559924	.	+	.	ID=YHR218W;Name=YHR218W;Alias=
-chrVIII	SGD	CDS	560173	562047	.	+	.	ID=YHR219W;Name=YHR219W;Alias=
-chrIX	SGD	CDS	483	6147	.	-	.	ID=YIL177C;Name=YIL177C;Alias=
-chrIX	SGD	CDS	8793	9155	.	-	.	ID=YIL176C;Name=YIL176C;Alias=PAU14
-chrIX	SGD	CDS	11492	16141	.	+	.	ID=YIL173W;Name=YIL173W;Alias=VTH1
-chrIX	SGD	CDS	16784	18553	.	-	.	ID=YIL172C;Name=YIL172C;Alias=IMA3
-chrIX	SGD	CDS	23119	26106	.	-	.	ID=YIL169C;Name=YIL169C;Alias=CSS1
-chrIX	SGD	CDS	30938	32566	.	-	.	ID=YIL166C;Name=YIL166C;Alias=
-chrIX	SGD	CDS	33718	34077	.	-	.	ID=YIL165C;Name=YIL165C;Alias=
-chrIX	SGD	CDS	34087	34686	.	-	.	ID=YIL164C;Name=YIL164C;Alias=NIT1
-chrIX	SGD	CDS	36899	37252	.	-	.	ID=YIL163C;Name=YIL163C;Alias=
-chrIX	SGD	CDS	37385	38983	.	+	.	ID=YIL162W;Name=YIL162W;Alias=SUC2
-chrIX	SGD	CDS	39433	40140	.	+	.	ID=YIL161W;Name=YIL161W;Alias=
-chrIX	SGD	CDS	40191	41444	.	-	.	ID=YIL160C;Name=YIL160C;Alias=POT1
-chrIX	SGD	CDS	41825	45952	.	+	.	ID=YIL159W;Name=YIL159W;Alias=BNR1
-chrIX	SGD	CDS	46201	46815	.	+	.	ID=YIL158W;Name=YIL158W;Alias=AIM20
-chrIX	SGD	CDS	46949	47542	.	-	.	ID=YIL157C;Name=YIL157C;Alias=COA1
-chrIX	SGD	CDS	47690	47973	.	+	.	ID=YIL156W-B;Name=YIL156W-B;Alias=
-chrIX	SGD	CDS	48091	51306	.	+	.	ID=YIL156W;Name=YIL156W;Alias=UBP7
-chrIX	SGD	CDS	51759	53708	.	-	.	ID=YIL155C;Name=YIL155C;Alias=GUT2
-chrIX	SGD	CDS	53981	55021	.	-	.	ID=YIL154C;Name=YIL154C;Alias=IMP2%27
-chrIX	SGD	CDS	55198	56379	.	+	.	ID=YIL153W;Name=YIL153W;Alias=RRD1
-chrIX	SGD	CDS	56545	57252	.	+	.	ID=YIL152W;Name=YIL152W;Alias=
-chrIX	SGD	CDS	57338	60694	.	-	.	ID=YIL151C;Name=YIL151C;Alias=ESL1
-chrIX	SGD	CDS	61013	62728	.	-	.	ID=YIL150C;Name=YIL150C;Alias=MCM10
-chrIX	SGD	CDS	63028	68067	.	-	.	ID=YIL149C;Name=YIL149C;Alias=MLP2
-chrIX	SGD	CDS	68708	69528	.	+	.	ID=YIL148W;Name=YIL148W;Alias=RPL40A
-chrIX	SGD	CDS	69791	73453	.	-	.	ID=YIL147C;Name=YIL147C;Alias=SLN1
-chrIX	SGD	CDS	74184	75773	.	-	.	ID=YIL146C;Name=YIL146C;Alias=ATG32
-chrIX	SGD	CDS	76354	77283	.	-	.	ID=YIL145C;Name=YIL145C;Alias=PAN6
-chrIX	SGD	CDS	78074	80149	.	+	.	ID=YIL144W;Name=YIL144W;Alias=NDC80
-chrIX	SGD	CDS	80510	83041	.	-	.	ID=YIL143C;Name=YIL143C;Alias=SSL2
-chrIX	SGD	CDS	83302	84885	.	+	.	ID=YIL142W;Name=YIL142W;Alias=CCT2
-chrIX	SGD	CDS	85366	87837	.	+	.	ID=YIL140W;Name=YIL140W;Alias=AXL2
-chrIX	SGD	CDS	87979	88716	.	-	.	ID=YIL139C;Name=YIL139C;Alias=REV7
-chrIX	SGD	CDS	89230	89715	.	-	.	ID=YIL138C;Name=YIL138C;Alias=TPM2
-chrIX	SGD	CDS	89948	92788	.	-	.	ID=YIL137C;Name=YIL137C;Alias=TMA108
-chrIX	SGD	CDS	93619	94800	.	+	.	ID=YIL136W;Name=YIL136W;Alias=OM45
-chrIX	SGD	CDS	95065	96375	.	-	.	ID=YIL135C;Name=YIL135C;Alias=VHS2
-chrIX	SGD	CDS	96522	96725	.	-	.	ID=YIL134C-A;Name=YIL134C-A;Alias=
-chrIX	SGD	CDS	97395	98330	.	+	.	ID=YIL134W;Name=YIL134W;Alias=FLX1
-chrIX	SGD	CDS	98527	99416	.	-	.	ID=YIL133C;Name=YIL133C;Alias=RPL16A
-chrIX	SGD	CDS	99860	100501	.	-	.	ID=YIL132C;Name=YIL132C;Alias=CSM2
-chrIX	SGD	CDS	100781	102235	.	-	.	ID=YIL131C;Name=YIL131C;Alias=FKH1
-chrIX	SGD	CDS	102782	105676	.	+	.	ID=YIL130W;Name=YIL130W;Alias=ASG1
-chrIX	SGD	CDS	106107	113237	.	-	.	ID=YIL129C;Name=YIL129C;Alias=TAO3
-chrIX	SGD	CDS	113806	116904	.	+	.	ID=YIL128W;Name=YIL128W;Alias=MET18
-chrIX	SGD	CDS	117024	117644	.	-	.	ID=YIL127C;Name=YIL127C;Alias=RRT14
-chrIX	SGD	CDS	117992	122071	.	+	.	ID=YIL126W;Name=YIL126W;Alias=STH1
-chrIX	SGD	CDS	122689	125733	.	+	.	ID=YIL125W;Name=YIL125W;Alias=KGD1
-chrIX	SGD	CDS	126204	127097	.	+	.	ID=YIL124W;Name=YIL124W;Alias=AYR1
-chrIX	SGD	CDS	127662	129581	.	+	.	ID=YIL123W;Name=YIL123W;Alias=SIM1
-chrIX	SGD	CDS	130610	131665	.	+	.	ID=YIL122W;Name=YIL122W;Alias=POG1
-chrIX	SGD	CDS	132244	133872	.	+	.	ID=YIL121W;Name=YIL121W;Alias=QDR2
-chrIX	SGD	CDS	134417	136108	.	+	.	ID=YIL120W;Name=YIL120W;Alias=QDR1
-chrIX	SGD	CDS	136654	137877	.	-	.	ID=YIL119C;Name=YIL119C;Alias=RPI1
-chrIX	SGD	CDS	139752	140447	.	+	.	ID=YIL118W;Name=YIL118W;Alias=RHO3
-chrIX	SGD	CDS	140613	141569	.	-	.	ID=YIL117C;Name=YIL117C;Alias=PRM5
-chrIX	SGD	CDS	142928	144085	.	+	.	ID=YIL116W;Name=YIL116W;Alias=HIS5
-chrIX	SGD	CDS	144327	148709	.	-	.	ID=YIL115C;Name=YIL115C;Alias=NUP159
-chrIX	SGD	CDS	149143	149988	.	-	.	ID=YIL114C;Name=YIL114C;Alias=POR2
-chrIX	SGD	CDS	150559	151188	.	+	.	ID=YIL113W;Name=YIL113W;Alias=SDP1
-chrIX	SGD	CDS	151595	154846	.	+	.	ID=YIL112W;Name=YIL112W;Alias=HOS4
-chrIX	SGD	CDS	155222	155765	.	+	.	ID=YIL111W;Name=YIL111W;Alias=COX5B
-chrIX	SGD	CDS	156045	157178	.	+	.	ID=YIL110W;Name=YIL110W;Alias=HPM1
-chrIX	SGD	CDS	157385	160165	.	-	.	ID=YIL109C;Name=YIL109C;Alias=SEC24
-chrIX	SGD	CDS	160887	162977	.	+	.	ID=YIL108W;Name=YIL108W;Alias=
-chrIX	SGD	CDS	163278	165761	.	-	.	ID=YIL107C;Name=YIL107C;Alias=PFK26
-chrIX	SGD	CDS	166415	167444	.	+	.	ID=YIL106W;Name=YIL106W;Alias=MOB1
-chrIX	SGD	CDS	167581	169641	.	-	.	ID=YIL105C;Name=YIL105C;Alias=SLM1
-chrIX	SGD	CDS	167664	167804	.	+	.	ID=YIL105W-A;Name=YIL105W-A;Alias=
-chrIX	SGD	CDS	169982	171505	.	-	.	ID=YIL104C;Name=YIL104C;Alias=SHQ1
-chrIX	SGD	CDS	171751	173028	.	+	.	ID=YIL103W;Name=YIL103W;Alias=DPH1
-chrIX	SGD	CDS	173365	173592	.	-	.	ID=YIL102C-A;Name=YIL102C-A;Alias=
-chrIX	SGD	CDS	174582	174887	.	-	.	ID=YIL102C;Name=YIL102C;Alias=
-chrIX	SGD	CDS	175307	177250	.	-	.	ID=YIL101C;Name=YIL101C;Alias=XBP1
-chrIX	SGD	CDS	178004	179653	.	+	.	ID=YIL099W;Name=YIL099W;Alias=SGA1
-chrIX	SGD	CDS	179772	180239	.	-	.	ID=YIL098C;Name=YIL098C;Alias=FMC1
-chrIX	SGD	CDS	180427	181977	.	+	.	ID=YIL097W;Name=YIL097W;Alias=FYV10
-chrIX	SGD	CDS	182117	183127	.	-	.	ID=YIL096C;Name=YIL096C;Alias=BMT5
-chrIX	SGD	CDS	183937	186369	.	+	.	ID=YIL095W;Name=YIL095W;Alias=PRK1
-chrIX	SGD	CDS	186517	187632	.	-	.	ID=YIL094C;Name=YIL094C;Alias=LYS12
-chrIX	SGD	CDS	187990	188784	.	-	.	ID=YIL093C;Name=YIL093C;Alias=RSM25
-chrIX	SGD	CDS	189066	190967	.	+	.	ID=YIL092W;Name=YIL092W;Alias=
-chrIX	SGD	CDS	191030	193195	.	-	.	ID=YIL091C;Name=YIL091C;Alias=UTP25
-chrIX	SGD	CDS	193595	195070	.	+	.	ID=YIL090W;Name=YIL090W;Alias=ICE2
-chrIX	SGD	CDS	195599	196216	.	+	.	ID=YIL089W;Name=YIL089W;Alias=
-chrIX	SGD	CDS	197931	199403	.	-	.	ID=YIL088C;Name=YIL088C;Alias=AVT7
-chrIX	SGD	CDS	199646	200119	.	-	.	ID=YIL087C;Name=YIL087C;Alias=AIM19
-chrIX	SGD	CDS	200490	202043	.	-	.	ID=YIL085C;Name=YIL085C;Alias=KTR7
-chrIX	SGD	CDS	202276	203259	.	-	.	ID=YIL084C;Name=YIL084C;Alias=SDS3
-chrIX	SGD	CDS	203556	204653	.	-	.	ID=YIL083C;Name=YIL083C;Alias=CAB2
-chrIX	SGD	CDS	210923	212005	.	-	.	ID=YIL079C;Name=YIL079C;Alias=AIR1
-chrIX	SGD	CDS	212499	214703	.	+	.	ID=YIL078W;Name=YIL078W;Alias=THS1
-chrIX	SGD	CDS	214991	215953	.	-	.	ID=YIL077C;Name=YIL077C;Alias=
-chrIX	SGD	CDS	216658	217548	.	+	.	ID=YIL076W;Name=YIL076W;Alias=SEC28
-chrIX	SGD	CDS	217863	220700	.	-	.	ID=YIL075C;Name=YIL075C;Alias=RPN2
-chrIX	SGD	CDS	221081	222490	.	-	.	ID=YIL074C;Name=YIL074C;Alias=SER33
-chrIX	SGD	CDS	222937	225954	.	-	.	ID=YIL073C;Name=YIL073C;Alias=SPO22
-chrIX	SGD	CDS	226602	228419	.	+	.	ID=YIL072W;Name=YIL072W;Alias=HOP1
-chrIX	SGD	CDS	228660	229994	.	-	.	ID=YIL071C;Name=YIL071C;Alias=PCI8
-chrIX	SGD	CDS	230272	231072	.	-	.	ID=YIL070C;Name=YIL070C;Alias=MAM33
-chrIX	SGD	CDS	231553	232369	.	-	.	ID=YIL069C;Name=YIL069C;Alias=RPS24B
-chrIX	SGD	CDS	233057	235474	.	-	.	ID=YIL068C;Name=YIL068C;Alias=SEC6
-chrIX	SGD	CDS	235724	237760	.	-	.	ID=YIL067C;Name=YIL067C;Alias=
-chrIX	SGD	CDS	238099	240708	.	-	.	ID=YIL066C;Name=YIL066C;Alias=RNR3
-chrIX	SGD	CDS	241308	241775	.	-	.	ID=YIL065C;Name=YIL065C;Alias=FIS1
-chrIX	SGD	CDS	241943	242716	.	+	.	ID=YIL064W;Name=YIL064W;Alias=EFM4
-chrIX	SGD	CDS	242761	243744	.	-	.	ID=YIL063C;Name=YIL063C;Alias=YRB2
-chrIX	SGD	CDS	243998	244462	.	-	.	ID=YIL062C;Name=YIL062C;Alias=ARC15
-chrIX	SGD	CDS	244657	245559	.	-	.	ID=YIL061C;Name=YIL061C;Alias=SNP1
-chrIX	SGD	CDS	246392	246826	.	+	.	ID=YIL060W;Name=YIL060W;Alias=
-chrIX	SGD	CDS	247902	248396	.	-	.	ID=YIL057C;Name=YIL057C;Alias=RGI2
-chrIX	SGD	CDS	249991	251913	.	+	.	ID=YIL056W;Name=YIL056W;Alias=VHR1
-chrIX	SGD	CDS	252042	253925	.	-	.	ID=YIL055C;Name=YIL055C;Alias=
-chrIX	SGD	CDS	254543	254860	.	+	.	ID=YIL054W;Name=YIL054W;Alias=
-chrIX	SGD	CDS	255115	255867	.	+	.	ID=YIL053W;Name=YIL053W;Alias=GPP1
-chrIX	SGD	CDS	256226	257063	.	-	.	ID=YIL052C;Name=YIL052C;Alias=RPL34B
-chrIX	SGD	CDS	257843	258280	.	-	.	ID=YIL051C;Name=YIL051C;Alias=MMF1
-chrIX	SGD	CDS	258913	259770	.	+	.	ID=YIL050W;Name=YIL050W;Alias=PCL7
-chrIX	SGD	CDS	260158	260919	.	+	.	ID=YIL049W;Name=YIL049W;Alias=DFG10
-chrIX	SGD	CDS	261437	264892	.	+	.	ID=YIL048W;Name=YIL048W;Alias=NEO1
-chrIX	SGD	CDS	265115	267823	.	-	.	ID=YIL047C;Name=YIL047C;Alias=SYG1
-chrIX	SGD	CDS	268309	268473	.	+	.	ID=YIL046W-A;Name=YIL046W-A;Alias=
-chrIX	SGD	CDS	268651	270573	.	+	.	ID=YIL046W;Name=YIL046W;Alias=MET30
-chrIX	SGD	CDS	271161	272777	.	+	.	ID=YIL045W;Name=YIL045W;Alias=PIG2
-chrIX	SGD	CDS	272950	273846	.	-	.	ID=YIL044C;Name=YIL044C;Alias=AGE2
-chrIX	SGD	CDS	274072	274926	.	-	.	ID=YIL043C;Name=YIL043C;Alias=CBR1
-chrIX	SGD	CDS	275108	276292	.	-	.	ID=YIL042C;Name=YIL042C;Alias=PKP1
-chrIX	SGD	CDS	276525	277505	.	+	.	ID=YIL041W;Name=YIL041W;Alias=GVP36
-chrIX	SGD	CDS	277723	278139	.	+	.	ID=YIL040W;Name=YIL040W;Alias=APQ12
-chrIX	SGD	CDS	278426	279847	.	+	.	ID=YIL039W;Name=YIL039W;Alias=TED1
-chrIX	SGD	CDS	280142	282652	.	-	.	ID=YIL038C;Name=YIL038C;Alias=NOT3
-chrIX	SGD	CDS	283029	284999	.	-	.	ID=YIL037C;Name=YIL037C;Alias=PRM2
-chrIX	SGD	CDS	285666	287429	.	+	.	ID=YIL036W;Name=YIL036W;Alias=CST6
-chrIX	SGD	CDS	287790	288908	.	-	.	ID=YIL035C;Name=YIL035C;Alias=CKA1
-chrIX	SGD	CDS	289226	290089	.	-	.	ID=YIL034C;Name=YIL034C;Alias=CAP2
-chrIX	SGD	CDS	290419	291669	.	-	.	ID=YIL033C;Name=YIL033C;Alias=BCY1
-chrIX	SGD	CDS	292633	295737	.	+	.	ID=YIL031W;Name=YIL031W;Alias=ULP2
-chrIX	SGD	CDS	296050	300009	.	-	.	ID=YIL030C;Name=YIL030C;Alias=SSM4
-chrIX	SGD	CDS	300829	301257	.	-	.	ID=YIL029C;Name=YIL029C;Alias=
-chrIX	SGD	CDS	303679	304104	.	-	.	ID=YIL027C;Name=YIL027C;Alias=EMC5
-chrIX	SGD	CDS	304477	307929	.	-	.	ID=YIL026C;Name=YIL026C;Alias=IRR1
-chrIX	SGD	CDS	308602	309171	.	-	.	ID=YIL024C;Name=YIL024C;Alias=
-chrIX	SGD	CDS	309386	310426	.	-	.	ID=YIL023C;Name=YIL023C;Alias=YKE4
-chrIX	SGD	CDS	311165	312460	.	+	.	ID=YIL022W;Name=YIL022W;Alias=TIM44
-chrIX	SGD	CDS	312905	313861	.	+	.	ID=YIL021W;Name=YIL021W;Alias=RPB3
-chrIX	SGD	CDS	314035	314820	.	-	.	ID=YIL020C;Name=YIL020C;Alias=HIS6
-chrIX	SGD	CDS	315093	316133	.	+	.	ID=YIL019W;Name=YIL019W;Alias=FAF1
-chrIX	SGD	CDS	316768	317932	.	+	.	ID=YIL018W;Name=YIL018W;Alias=RPL2B
-chrIX	SGD	CDS	318200	320965	.	-	.	ID=YIL017C;Name=YIL017C;Alias=VID28
-chrIX	SGD	CDS	321454	321933	.	+	.	ID=YIL016W;Name=YIL016W;Alias=SNL1
-chrIX	SGD	CDS	322342	324105	.	+	.	ID=YIL015W;Name=YIL015W;Alias=BAR1
-chrIX	SGD	CDS	325212	325526	.	-	.	ID=YIL014C-A;Name=YIL014C-A;Alias=
-chrIX	SGD	CDS	326103	327995	.	+	.	ID=YIL014W;Name=YIL014W;Alias=MNT3
-chrIX	SGD	CDS	328207	332442	.	-	.	ID=YIL013C;Name=YIL013C;Alias=PDR11
-chrIX	SGD	CDS	333727	334536	.	+	.	ID=YIL011W;Name=YIL011W;Alias=TIR3
-chrIX	SGD	CDS	334882	335529	.	+	.	ID=YIL010W;Name=YIL010W;Alias=DOT5
-chrIX	SGD	CDS	335666	336212	.	-	.	ID=YIL009C-A;Name=YIL009C-A;Alias=EST3
-chrIX	SGD	CDS	339344	341428	.	+	.	ID=YIL009W;Name=YIL009W;Alias=FAA3
-chrIX	SGD	CDS	342536	342835	.	+	.	ID=YIL008W;Name=YIL008W;Alias=URM1
-chrIX	SGD	CDS	342994	343656	.	-	.	ID=YIL007C;Name=YIL007C;Alias=NAS2
-chrIX	SGD	CDS	344062	345183	.	+	.	ID=YIL006W;Name=YIL006W;Alias=YIA6
-chrIX	SGD	CDS	345692	347797	.	+	.	ID=YIL005W;Name=YIL005W;Alias=EPS1
-chrIX	SGD	CDS	347946	348505	.	-	.	ID=YIL004C;Name=YIL004C;Alias=BET1
-chrIX	SGD	CDS	349122	350003	.	+	.	ID=YIL003W;Name=YIL003W;Alias=CFD1
-chrIX	SGD	CDS	350301	350510	.	+	.	ID=YIL002W-A;Name=YIL002W-A;Alias=
-chrIX	SGD	CDS	350591	353431	.	-	.	ID=YIL002C;Name=YIL002C;Alias=INP51
-chrIX	SGD	CDS	353940	355481	.	+	.	ID=YIL001W;Name=YIL001W;Alias=
-chrIX	SGD	CDS	356143	356895	.	-	.	ID=YIR001C;Name=YIR001C;Alias=SGN1
-chrIX	SGD	CDS	357415	360396	.	-	.	ID=YIR002C;Name=YIR002C;Alias=MPH1
-chrIX	SGD	CDS	360885	362924	.	+	.	ID=YIR003W;Name=YIR003W;Alias=AIM21
-chrIX	SGD	CDS	363221	364519	.	+	.	ID=YIR004W;Name=YIR004W;Alias=DJP1
-chrIX	SGD	CDS	364889	365335	.	+	.	ID=YIR005W;Name=YIR005W;Alias=IST3
-chrIX	SGD	CDS	365466	369908	.	-	.	ID=YIR006C;Name=YIR006C;Alias=PAN1
-chrIX	SGD	CDS	370704	372998	.	+	.	ID=YIR007W;Name=YIR007W;Alias=EGH1
-chrIX	SGD	CDS	373077	374306	.	-	.	ID=YIR008C;Name=YIR008C;Alias=PRI1
-chrIX	SGD	CDS	374525	374860	.	+	.	ID=YIR009W;Name=YIR009W;Alias=MSL1
-chrIX	SGD	CDS	375431	377161	.	+	.	ID=YIR010W;Name=YIR010W;Alias=DSN1
-chrIX	SGD	CDS	377287	378246	.	-	.	ID=YIR011C;Name=YIR011C;Alias=STS1
-chrIX	SGD	CDS	378486	379781	.	+	.	ID=YIR012W;Name=YIR012W;Alias=SQT1
-chrIX	SGD	CDS	380019	380384	.	-	.	ID=YIR013C;Name=YIR013C;Alias=GAT4
-chrIX	SGD	CDS	381086	381814	.	+	.	ID=YIR014W;Name=YIR014W;Alias=
-chrIX	SGD	CDS	381948	382382	.	+	.	ID=YIR015W;Name=YIR015W;Alias=RPR2
-chrIX	SGD	CDS	382628	383425	.	+	.	ID=YIR016W;Name=YIR016W;Alias=
-chrIX	SGD	CDS	383556	384119	.	-	.	ID=YIR017C;Name=YIR017C;Alias=MET28
-chrIX	SGD	CDS	384609	385346	.	+	.	ID=YIR018W;Name=YIR018W;Alias=YAP5
-chrIX	SGD	CDS	385564	385701	.	-	.	ID=YIR018C-A;Name=YIR018C-A;Alias=
-chrIX	SGD	CDS	389572	393675	.	-	.	ID=YIR019C;Name=YIR019C;Alias=FLO11
-chrIX	SGD	CDS	394255	394557	.	-	.	ID=YIR020C;Name=YIR020C;Alias=
-chrIX	SGD	CDS	397294	398385	.	+	.	ID=YIR021W;Name=YIR021W;Alias=MRS1
-chrIX	SGD	CDS	398514	398726	.	+	.	ID=YIR021W-A;Name=YIR021W-A;Alias=
-chrIX	SGD	CDS	398733	399236	.	+	.	ID=YIR022W;Name=YIR022W;Alias=SEC11
-chrIX	SGD	CDS	399777	402689	.	+	.	ID=YIR023W;Name=YIR023W;Alias=DAL81
-chrIX	SGD	CDS	402841	403491	.	-	.	ID=YIR024C;Name=YIR024C;Alias=INA22
-chrIX	SGD	CDS	403659	404765	.	+	.	ID=YIR025W;Name=YIR025W;Alias=MND2
-chrIX	SGD	CDS	404873	405967	.	-	.	ID=YIR026C;Name=YIR026C;Alias=YVH1
-chrIX	SGD	CDS	406260	407642	.	-	.	ID=YIR027C;Name=YIR027C;Alias=DAL1
-chrIX	SGD	CDS	408468	410375	.	+	.	ID=YIR028W;Name=YIR028W;Alias=DAL4
-chrIX	SGD	CDS	410807	411838	.	+	.	ID=YIR029W;Name=YIR029W;Alias=DAL2
-chrIX	SGD	CDS	412036	412770	.	-	.	ID=YIR030C;Name=YIR030C;Alias=DCG1
-chrIX	SGD	CDS	413015	414679	.	-	.	ID=YIR031C;Name=YIR031C;Alias=DAL7
-chrIX	SGD	CDS	415030	415617	.	-	.	ID=YIR032C;Name=YIR032C;Alias=DAL3
-chrIX	SGD	CDS	416124	419465	.	+	.	ID=YIR033W;Name=YIR033W;Alias=MGA2
-chrIX	SGD	CDS	419615	420736	.	-	.	ID=YIR034C;Name=YIR034C;Alias=LYS1
-chrIX	SGD	CDS	421026	421790	.	-	.	ID=YIR035C;Name=YIR035C;Alias=
-chrIX	SGD	CDS	422074	422865	.	-	.	ID=YIR036C;Name=YIR036C;Alias=IRC24
-chrIX	SGD	CDS	423128	423619	.	+	.	ID=YIR037W;Name=YIR037W;Alias=HYR1
-chrIX	SGD	CDS	423809	424513	.	-	.	ID=YIR038C;Name=YIR038C;Alias=GTT1
-chrIX	SGD	CDS	430498	432111	.	-	.	ID=YIR039C;Name=YIR039C;Alias=YPS6
-chrIX	SGD	CDS	433929	434303	.	+	.	ID=YIR041W;Name=YIR041W;Alias=PAU15
-chrIX	SGD	CDS	435273	435983	.	-	.	ID=YIR042C;Name=YIR042C;Alias=
-chrX	SGD	CDS	466	6130	.	-	.	ID=YJL225C;Name=YJL225C;Alias=
-chrX	SGD	CDS	8776	9138	.	-	.	ID=YJL223C;Name=YJL223C;Alias=PAU1
-chrX	SGD	CDS	11475	16124	.	+	.	ID=YJL222W;Name=YJL222W;Alias=VTH2
-chrX	SGD	CDS	16767	18536	.	-	.	ID=YJL221C;Name=YJL221C;Alias=IMA4
-chrX	SGD	CDS	19497	21200	.	+	.	ID=YJL219W;Name=YJL219W;Alias=HXT9
-chrX	SGD	CDS	21973	22563	.	+	.	ID=YJL218W;Name=YJL218W;Alias=
-chrX	SGD	CDS	23133	23729	.	+	.	ID=YJL217W;Name=YJL217W;Alias=REE1
-chrX	SGD	CDS	24341	26086	.	-	.	ID=YJL216C;Name=YJL216C;Alias=IMA5
-chrX	SGD	CDS	26887	28596	.	+	.	ID=YJL214W;Name=YJL214W;Alias=HXT8
-chrX	SGD	CDS	32163	33158	.	+	.	ID=YJL213W;Name=YJL213W;Alias=
-chrX	SGD	CDS	33850	36249	.	-	.	ID=YJL212C;Name=YJL212C;Alias=OPT1
-chrX	SGD	CDS	36919	37734	.	+	.	ID=YJL210W;Name=YJL210W;Alias=PEX2
-chrX	SGD	CDS	38005	39969	.	+	.	ID=YJL209W;Name=YJL209W;Alias=CBP1
-chrX	SGD	CDS	40194	41183	.	-	.	ID=YJL208C;Name=YJL208C;Alias=NUC1
-chrX	SGD	CDS	41389	47433	.	-	.	ID=YJL207C;Name=YJL207C;Alias=LAA1
-chrX	SGD	CDS	47659	49935	.	-	.	ID=YJL206C;Name=YJL206C;Alias=
-chrX	SGD	CDS	50139	50443	.	-	.	ID=YJL205C;Name=YJL205C;Alias=NCE101
-chrX	SGD	CDS	50629	53151	.	-	.	ID=YJL204C;Name=YJL204C;Alias=RCY1
-chrX	SGD	CDS	53341	54183	.	+	.	ID=YJL203W;Name=YJL203W;Alias=PRP21
-chrX	SGD	CDS	54379	56178	.	+	.	ID=YJL201W;Name=YJL201W;Alias=ECM25
-chrX	SGD	CDS	56444	58813	.	-	.	ID=YJL200C;Name=YJL200C;Alias=ACO2
-chrX	SGD	CDS	60844	63489	.	+	.	ID=YJL198W;Name=YJL198W;Alias=PHO90
-chrX	SGD	CDS	63805	67569	.	+	.	ID=YJL197W;Name=YJL197W;Alias=UBP12
-chrX	SGD	CDS	67850	68782	.	-	.	ID=YJL196C;Name=YJL196C;Alias=ELO1
-chrX	SGD	CDS	69338	70879	.	+	.	ID=YJL194W;Name=YJL194W;Alias=CDC6
-chrX	SGD	CDS	71366	72574	.	+	.	ID=YJL193W;Name=YJL193W;Alias=
-chrX	SGD	CDS	72710	73414	.	-	.	ID=YJL192C;Name=YJL192C;Alias=SOP4
-chrX	SGD	CDS	73787	74611	.	+	.	ID=YJL191W;Name=YJL191W;Alias=RPS14B
-chrX	SGD	CDS	74910	75302	.	-	.	ID=YJL190C;Name=YJL190C;Alias=RPS22A
-chrX	SGD	CDS	75933	76474	.	+	.	ID=YJL189W;Name=YJL189W;Alias=RPL39
-chrX	SGD	CDS	76803	79262	.	-	.	ID=YJL187C;Name=YJL187C;Alias=SWE1
-chrX	SGD	CDS	80155	81915	.	+	.	ID=YJL186W;Name=YJL186W;Alias=MNN5
-chrX	SGD	CDS	82095	82976	.	-	.	ID=YJL185C;Name=YJL185C;Alias=ATG36
-chrX	SGD	CDS	83448	83819	.	+	.	ID=YJL184W;Name=YJL184W;Alias=GON7
-chrX	SGD	CDS	84068	85336	.	+	.	ID=YJL183W;Name=YJL183W;Alias=MNN11
-chrX	SGD	CDS	85660	87495	.	+	.	ID=YJL181W;Name=YJL181W;Alias=RBH1
-chrX	SGD	CDS	87583	88560	.	-	.	ID=YJL180C;Name=YJL180C;Alias=ATP12
-chrX	SGD	CDS	88787	89116	.	+	.	ID=YJL179W;Name=YJL179W;Alias=PFD1
-chrX	SGD	CDS	89282	90097	.	-	.	ID=YJL178C;Name=YJL178C;Alias=ATG27
-chrX	SGD	CDS	90786	91657	.	+	.	ID=YJL177W;Name=YJL177W;Alias=RPL17B
-chrX	SGD	CDS	92053	94530	.	-	.	ID=YJL176C;Name=YJL176C;Alias=SWI3
-chrX	SGD	CDS	95092	95922	.	+	.	ID=YJL174W;Name=YJL174W;Alias=KRE9
-chrX	SGD	CDS	96161	96529	.	-	.	ID=YJL173C;Name=YJL173C;Alias=RFA3
-chrX	SGD	CDS	97737	99467	.	+	.	ID=YJL172W;Name=YJL172W;Alias=CPS1
-chrX	SGD	CDS	99704	100894	.	-	.	ID=YJL171C;Name=YJL171C;Alias=TOH1
-chrX	SGD	CDS	101150	101779	.	-	.	ID=YJL170C;Name=YJL170C;Alias=ASG7
-chrX	SGD	CDS	102227	104428	.	-	.	ID=YJL168C;Name=YJL168C;Alias=SET2
-chrX	SGD	CDS	105014	106072	.	+	.	ID=YJL167W;Name=YJL167W;Alias=ERG20
-chrX	SGD	CDS	106434	106718	.	+	.	ID=YJL166W;Name=YJL166W;Alias=QCR8
-chrX	SGD	CDS	106894	109461	.	-	.	ID=YJL165C;Name=YJL165C;Alias=HAL5
-chrX	SGD	CDS	109966	111159	.	-	.	ID=YJL164C;Name=YJL164C;Alias=TPK1
-chrX	SGD	CDS	111666	113333	.	-	.	ID=YJL163C;Name=YJL163C;Alias=
-chrX	SGD	CDS	113878	115629	.	-	.	ID=YJL162C;Name=YJL162C;Alias=JJJ2
-chrX	SGD	CDS	117245	117787	.	+	.	ID=YJL161W;Name=YJL161W;Alias=FMP33
-chrX	SGD	CDS	117962	118825	.	-	.	ID=YJL160C;Name=YJL160C;Alias=PIR5
-chrX	SGD	CDS	120449	121690	.	+	.	ID=YJL159W;Name=YJL159W;Alias=HSP150
-chrX	SGD	CDS	122265	122948	.	-	.	ID=YJL158C;Name=YJL158C;Alias=CIS3
-chrX	SGD	CDS	123836	126328	.	-	.	ID=YJL157C;Name=YJL157C;Alias=FAR1
-chrX	SGD	CDS	126853	128952	.	-	.	ID=YJL156C;Name=YJL156C;Alias=SSY5
-chrX	SGD	CDS	129285	130643	.	-	.	ID=YJL155C;Name=YJL155C;Alias=FBP26
-chrX	SGD	CDS	131101	133935	.	-	.	ID=YJL154C;Name=YJL154C;Alias=VPS35
-chrX	SGD	CDS	134332	135933	.	-	.	ID=YJL153C;Name=YJL153C;Alias=INO1
-chrX	SGD	CDS	136372	136773	.	-	.	ID=YJL151C;Name=YJL151C;Alias=SNA3
-chrX	SGD	CDS	137379	139370	.	+	.	ID=YJL149W;Name=YJL149W;Alias=DAS1
-chrX	SGD	CDS	140437	141138	.	+	.	ID=YJL148W;Name=YJL148W;Alias=RPA34
-chrX	SGD	CDS	141419	142567	.	-	.	ID=YJL147C;Name=YJL147C;Alias=MRX5
-chrX	SGD	CDS	143292	144701	.	+	.	ID=YJL146W;Name=YJL146W;Alias=IDS2
-chrX	SGD	CDS	145160	146044	.	+	.	ID=YJL145W;Name=YJL145W;Alias=SFH5
-chrX	SGD	CDS	146359	146673	.	+	.	ID=YJL144W;Name=YJL144W;Alias=
-chrX	SGD	CDS	147101	147577	.	+	.	ID=YJL143W;Name=YJL143W;Alias=TIM17
-chrX	SGD	CDS	147967	150390	.	-	.	ID=YJL141C;Name=YJL141C;Alias=YAK1
-chrX	SGD	CDS	150961	151626	.	+	.	ID=YJL140W;Name=YJL140W;Alias=RPB4
-chrX	SGD	CDS	151713	152999	.	-	.	ID=YJL139C;Name=YJL139C;Alias=YUR1
-chrX	SGD	CDS	153504	154691	.	-	.	ID=YJL138C;Name=YJL138C;Alias=TIF2
-chrX	SGD	CDS	154985	156127	.	-	.	ID=YJL137C;Name=YJL137C;Alias=GLG2
-chrX	SGD	CDS	156169	156252	.	+	.	ID=YJL136W-A;Name=YJL136W-A;Alias=
-chrX	SGD	CDS	156550	157273	.	-	.	ID=YJL136C;Name=YJL136C;Alias=RPS21B
-chrX	SGD	CDS	158188	159417	.	+	.	ID=YJL134W;Name=YJL134W;Alias=LCB3
-chrX	SGD	CDS	159623	159847	.	-	.	ID=YJL133C-A;Name=YJL133C-A;Alias=
-chrX	SGD	CDS	160619	161563	.	+	.	ID=YJL133W;Name=YJL133W;Alias=MRS3
-chrX	SGD	CDS	161914	164166	.	+	.	ID=YJL132W;Name=YJL132W;Alias=
-chrX	SGD	CDS	164278	165348	.	-	.	ID=YJL131C;Name=YJL131C;Alias=AIM23
-chrX	SGD	CDS	165723	172752	.	-	.	ID=YJL130C;Name=YJL130C;Alias=URA2
-chrX	SGD	CDS	173599	177306	.	-	.	ID=YJL129C;Name=YJL129C;Alias=TRK1
-chrX	SGD	CDS	178097	180103	.	-	.	ID=YJL128C;Name=YJL128C;Alias=PBS2
-chrX	SGD	CDS	181551	181709	.	-	.	ID=YJL127C-B;Name=YJL127C-B;Alias=
-chrX	SGD	CDS	182298	184220	.	-	.	ID=YJL127C;Name=YJL127C;Alias=SPT10
-chrX	SGD	CDS	184501	185424	.	+	.	ID=YJL126W;Name=YJL126W;Alias=NIT2
-chrX	SGD	CDS	185528	186679	.	-	.	ID=YJL125C;Name=YJL125C;Alias=GCD14
-chrX	SGD	CDS	187126	187644	.	-	.	ID=YJL124C;Name=YJL124C;Alias=LSM1
-chrX	SGD	CDS	188004	189440	.	-	.	ID=YJL123C;Name=YJL123C;Alias=MTC1
-chrX	SGD	CDS	189716	190243	.	+	.	ID=YJL122W;Name=YJL122W;Alias=ALB1
-chrX	SGD	CDS	190374	191090	.	-	.	ID=YJL121C;Name=YJL121C;Alias=RPE1
-chrX	SGD	CDS	191639	192298	.	+	.	ID=YJL118W;Name=YJL118W;Alias=
-chrX	SGD	CDS	192531	193466	.	+	.	ID=YJL117W;Name=YJL117W;Alias=PHO86
-chrX	SGD	CDS	193860	194873	.	-	.	ID=YJL116C;Name=YJL116C;Alias=NCA3
-chrX	SGD	CDS	196287	197126	.	+	.	ID=YJL115W;Name=YJL115W;Alias=ASF1
-chrX	SGD	CDS	205305	207449	.	+	.	ID=YJL112W;Name=YJL112W;Alias=MDV1
-chrX	SGD	CDS	207877	209529	.	+	.	ID=YJL111W;Name=YJL111W;Alias=CCT7
-chrX	SGD	CDS	209922	211577	.	-	.	ID=YJL110C;Name=YJL110C;Alias=GZF3
-chrX	SGD	CDS	212000	217309	.	-	.	ID=YJL109C;Name=YJL109C;Alias=UTP10
-chrX	SGD	CDS	217705	218856	.	-	.	ID=YJL108C;Name=YJL108C;Alias=PRM10
-chrX	SGD	CDS	218853	220016	.	-	.	ID=YJL107C;Name=YJL107C;Alias=
-chrX	SGD	CDS	221390	223327	.	+	.	ID=YJL106W;Name=YJL106W;Alias=IME2
-chrX	SGD	CDS	225055	226737	.	+	.	ID=YJL105W;Name=YJL105W;Alias=SET4
-chrX	SGD	CDS	227327	227776	.	+	.	ID=YJL104W;Name=YJL104W;Alias=PAM16
-chrX	SGD	CDS	229025	230881	.	-	.	ID=YJL103C;Name=YJL103C;Alias=GSM1
-chrX	SGD	CDS	231301	233760	.	+	.	ID=YJL102W;Name=YJL102W;Alias=MEF2
-chrX	SGD	CDS	234320	236356	.	-	.	ID=YJL101C;Name=YJL101C;Alias=GSH1
-chrX	SGD	CDS	237263	239086	.	+	.	ID=YJL100W;Name=YJL100W;Alias=LSB6
-chrX	SGD	CDS	239414	241654	.	+	.	ID=YJL099W;Name=YJL099W;Alias=CHS6
-chrX	SGD	CDS	242082	245258	.	+	.	ID=YJL098W;Name=YJL098W;Alias=SAP185
-chrX	SGD	CDS	245591	246244	.	+	.	ID=YJL097W;Name=YJL097W;Alias=PHS1
-chrX	SGD	CDS	246490	246975	.	+	.	ID=YJL096W;Name=YJL096W;Alias=MRPL49
-chrX	SGD	CDS	247255	251691	.	+	.	ID=YJL095W;Name=YJL095W;Alias=BCK1
-chrX	SGD	CDS	251821	254442	.	-	.	ID=YJL094C;Name=YJL094C;Alias=KHA1
-chrX	SGD	CDS	254737	256812	.	-	.	ID=YJL093C;Name=YJL093C;Alias=TOK1
-chrX	SGD	CDS	257423	260947	.	+	.	ID=YJL092W;Name=YJL092W;Alias=SRS2
-chrX	SGD	CDS	261080	262552	.	-	.	ID=YJL091C;Name=YJL091C;Alias=GWT1
-chrX	SGD	CDS	262757	265051	.	-	.	ID=YJL090C;Name=YJL090C;Alias=DPB11
-chrX	SGD	CDS	265926	268415	.	+	.	ID=YJL089W;Name=YJL089W;Alias=SIP4
-chrX	SGD	CDS	268799	269815	.	+	.	ID=YJL088W;Name=YJL088W;Alias=ARG3
-chrX	SGD	CDS	270002	272485	.	-	.	ID=YJL087C;Name=YJL087C;Alias=TRL1
-chrX	SGD	CDS	272827	274698	.	+	.	ID=YJL085W;Name=YJL085W;Alias=EXO70
-chrX	SGD	CDS	274862	278002	.	-	.	ID=YJL084C;Name=YJL084C;Alias=ALY2
-chrX	SGD	CDS	278841	280655	.	+	.	ID=YJL083W;Name=YJL083W;Alias=TAX4
-chrX	SGD	CDS	281185	283380	.	+	.	ID=YJL082W;Name=YJL082W;Alias=IML2
-chrX	SGD	CDS	283802	285271	.	-	.	ID=YJL081C;Name=YJL081C;Alias=ARP4
-chrX	SGD	CDS	285558	289226	.	-	.	ID=YJL080C;Name=YJL080C;Alias=SCP160
-chrX	SGD	CDS	289875	290774	.	-	.	ID=YJL079C;Name=YJL079C;Alias=PRY1
-chrX	SGD	CDS	291336	293981	.	-	.	ID=YJL078C;Name=YJL078C;Alias=PRY3
-chrX	SGD	CDS	294047	294145	.	+	.	ID=YJL077W-B;Name=YJL077W-B;Alias=
-chrX	SGD	CDS	294666	295061	.	-	.	ID=YJL077C;Name=YJL077C;Alias=ICS3
-chrX	SGD	CDS	294799	294885	.	+	.	ID=YJL077W-A;Name=YJL077W-A;Alias=
-chrX	SGD	CDS	295245	298814	.	+	.	ID=YJL076W;Name=YJL076W;Alias=NET1
-chrX	SGD	CDS	299157	302849	.	-	.	ID=YJL074C;Name=YJL074C;Alias=SMC3
-chrX	SGD	CDS	303181	305118	.	+	.	ID=YJL073W;Name=YJL073W;Alias=JEM1
-chrX	SGD	CDS	305221	305862	.	-	.	ID=YJL072C;Name=YJL072C;Alias=PSF2
-chrX	SGD	CDS	306132	307856	.	+	.	ID=YJL071W;Name=YJL071W;Alias=ARG2
-chrX	SGD	CDS	307971	310637	.	-	.	ID=YJL070C;Name=YJL070C;Alias=
-chrX	SGD	CDS	310922	312706	.	-	.	ID=YJL069C;Name=YJL069C;Alias=UTP18
-chrX	SGD	CDS	313016	313915	.	-	.	ID=YJL068C;Name=YJL068C;Alias=
-chrX	SGD	CDS	314114	314872	.	-	.	ID=YJL066C;Name=YJL066C;Alias=MPM1
-chrX	SGD	CDS	315054	315557	.	-	.	ID=YJL065C;Name=YJL065C;Alias=DLS1
-chrX	SGD	CDS	315759	316475	.	-	.	ID=YJL063C;Name=YJL063C;Alias=MRPL8
-chrX	SGD	CDS	316723	316980	.	+	.	ID=YJL062W-A;Name=YJL062W-A;Alias=COA3
-chrX	SGD	CDS	317284	319776	.	+	.	ID=YJL062W;Name=YJL062W;Alias=LAS21
-chrX	SGD	CDS	320016	322157	.	+	.	ID=YJL061W;Name=YJL061W;Alias=NUP82
-chrX	SGD	CDS	323386	324720	.	+	.	ID=YJL060W;Name=YJL060W;Alias=BNA3
-chrX	SGD	CDS	324964	326190	.	+	.	ID=YJL059W;Name=YJL059W;Alias=YHC3
-chrX	SGD	CDS	326242	327873	.	-	.	ID=YJL058C;Name=YJL058C;Alias=BIT61
-chrX	SGD	CDS	328118	330121	.	-	.	ID=YJL057C;Name=YJL057C;Alias=IKS1
-chrX	SGD	CDS	330431	333073	.	-	.	ID=YJL056C;Name=YJL056C;Alias=ZAP1
-chrX	SGD	CDS	333357	334094	.	+	.	ID=YJL055W;Name=YJL055W;Alias=
-chrX	SGD	CDS	334265	335701	.	+	.	ID=YJL054W;Name=YJL054W;Alias=TIM54
-chrX	SGD	CDS	335898	337037	.	+	.	ID=YJL053W;Name=YJL053W;Alias=PEP8
-chrX	SGD	CDS	337884	338003	.	-	.	ID=YJL052C-A;Name=YJL052C-A;Alias=
-chrX	SGD	CDS	338271	339269	.	+	.	ID=YJL052W;Name=YJL052W;Alias=TDH1
-chrX	SGD	CDS	339787	342255	.	+	.	ID=YJL051W;Name=YJL051W;Alias=IRC8
-chrX	SGD	CDS	342522	345743	.	+	.	ID=YJL050W;Name=YJL050W;Alias=MTR4
-chrX	SGD	CDS	345973	347325	.	+	.	ID=YJL049W;Name=YJL049W;Alias=CHM7
-chrX	SGD	CDS	347447	348637	.	-	.	ID=YJL048C;Name=YJL048C;Alias=UBX6
-chrX	SGD	CDS	349044	349178	.	-	.	ID=YJL047C-A;Name=YJL047C-A;Alias=
-chrX	SGD	CDS	349580	352108	.	-	.	ID=YJL047C;Name=YJL047C;Alias=RTT101
-chrX	SGD	CDS	352386	353615	.	+	.	ID=YJL046W;Name=YJL046W;Alias=AIM22
-chrX	SGD	CDS	356024	357928	.	+	.	ID=YJL045W;Name=YJL045W;Alias=
-chrX	SGD	CDS	358300	359676	.	-	.	ID=YJL044C;Name=YJL044C;Alias=GYP6
-chrX	SGD	CDS	360130	360903	.	+	.	ID=YJL043W;Name=YJL043W;Alias=
-chrX	SGD	CDS	361249	365445	.	+	.	ID=YJL042W;Name=YJL042W;Alias=MHP1
-chrX	SGD	CDS	365784	368373	.	+	.	ID=YJL041W;Name=YJL041W;Alias=NSP1
-chrX	SGD	CDS	368748	373799	.	-	.	ID=YJL039C;Name=YJL039C;Alias=NUP192
-chrX	SGD	CDS	375115	375774	.	-	.	ID=YJL038C;Name=YJL038C;Alias=LOH1
-chrX	SGD	CDS	376662	377336	.	+	.	ID=YJL037W;Name=YJL037W;Alias=IRC18
-chrX	SGD	CDS	378825	380096	.	+	.	ID=YJL036W;Name=YJL036W;Alias=SNX4
-chrX	SGD	CDS	380249	381001	.	-	.	ID=YJL035C;Name=YJL035C;Alias=TAD2
-chrX	SGD	CDS	381327	383375	.	+	.	ID=YJL034W;Name=YJL034W;Alias=KAR2
-chrX	SGD	CDS	383837	386149	.	+	.	ID=YJL033W;Name=YJL033W;Alias=HCA4
-chrX	SGD	CDS	386368	387438	.	-	.	ID=YJL031C;Name=YJL031C;Alias=BET4
-chrX	SGD	CDS	387657	388247	.	+	.	ID=YJL030W;Name=YJL030W;Alias=MAD2
-chrX	SGD	CDS	388385	390853	.	-	.	ID=YJL029C;Name=YJL029C;Alias=VPS53
-chrX	SGD	CDS	391311	391646	.	+	.	ID=YJL028W;Name=YJL028W;Alias=
-chrX	SGD	CDS	391833	392249	.	-	.	ID=YJL027C;Name=YJL027C;Alias=
-chrX	SGD	CDS	392404	393603	.	+	.	ID=YJL026W;Name=YJL026W;Alias=RNR2
-chrX	SGD	CDS	393967	395511	.	+	.	ID=YJL025W;Name=YJL025W;Alias=RRN7
-chrX	SGD	CDS	395931	396592	.	-	.	ID=YJL024C;Name=YJL024C;Alias=APS3
-chrX	SGD	CDS	397355	398398	.	-	.	ID=YJL023C;Name=YJL023C;Alias=PET130
-chrX	SGD	CDS	398937	402410	.	-	.	ID=YJL020C;Name=YJL020C;Alias=BBC1
-chrX	SGD	CDS	402897	404945	.	+	.	ID=YJL019W;Name=YJL019W;Alias=MPS3
-chrX	SGD	CDS	405588	407273	.	+	.	ID=YJL016W;Name=YJL016W;Alias=TPH3
-chrX	SGD	CDS	407558	409162	.	+	.	ID=YJL014W;Name=YJL014W;Alias=CCT3
-chrX	SGD	CDS	409493	411040	.	-	.	ID=YJL013C;Name=YJL013C;Alias=MAD3
-chrX	SGD	CDS	411234	413399	.	-	.	ID=YJL012C;Name=YJL012C;Alias=VTC4
-chrX	SGD	CDS	414285	414770	.	-	.	ID=YJL011C;Name=YJL011C;Alias=RPC17
-chrX	SGD	CDS	417562	419562	.	-	.	ID=YJL010C;Name=YJL010C;Alias=NOP9
-chrX	SGD	CDS	419957	421663	.	-	.	ID=YJL008C;Name=YJL008C;Alias=CCT8
-chrX	SGD	CDS	423138	424109	.	-	.	ID=YJL006C;Name=YJL006C;Alias=CTK2
-chrX	SGD	CDS	425157	431237	.	+	.	ID=YJL005W;Name=YJL005W;Alias=CYR1
-chrX	SGD	CDS	431589	432200	.	-	.	ID=YJL004C;Name=YJL004C;Alias=SYS1
-chrX	SGD	CDS	432644	433000	.	+	.	ID=YJL003W;Name=YJL003W;Alias=COX16
-chrX	SGD	CDS	433221	434651	.	-	.	ID=YJL002C;Name=YJL002C;Alias=OST1
-chrX	SGD	CDS	435163	435926	.	+	.	ID=YJL001W;Name=YJL001W;Alias=PRE3
-chrX	SGD	CDS	436802	438610	.	+	.	ID=YJR001W;Name=YJR001W;Alias=AVT1
-chrX	SGD	CDS	438865	440646	.	+	.	ID=YJR002W;Name=YJR002W;Alias=MPP10
-chrX	SGD	CDS	440994	442553	.	-	.	ID=YJR003C;Name=YJR003C;Alias=MRX12
-chrX	SGD	CDS	442909	444861	.	-	.	ID=YJR004C;Name=YJR004C;Alias=SAG1
-chrX	SGD	CDS	445923	448025	.	+	.	ID=YJR005W;Name=YJR005W;Alias=APL1
-chrX	SGD	CDS	448477	448758	.	-	.	ID=YJR005C-A;Name=YJR005C-A;Alias=LSO1
-chrX	SGD	CDS	449202	450665	.	+	.	ID=YJR006W;Name=YJR006W;Alias=POL31
-chrX	SGD	CDS	451020	451934	.	+	.	ID=YJR007W;Name=YJR007W;Alias=SUI2
-chrX	SGD	CDS	452430	453446	.	+	.	ID=YJR008W;Name=YJR008W;Alias=MHO1
-chrX	SGD	CDS	453683	454681	.	-	.	ID=YJR009C;Name=YJR009C;Alias=TDH2
-chrX	SGD	CDS	456239	457774	.	+	.	ID=YJR010W;Name=YJR010W;Alias=MET3
-chrX	SGD	CDS	458077	458361	.	-	.	ID=YJR010C-A;Name=YJR010C-A;Alias=SPC1
-chrX	SGD	CDS	458641	459426	.	-	.	ID=YJR011C;Name=YJR011C;Alias=
-chrX	SGD	CDS	459795	460418	.	-	.	ID=YJR012C;Name=YJR012C;Alias=
-chrX	SGD	CDS	460382	461593	.	+	.	ID=YJR013W;Name=YJR013W;Alias=GPI14
-chrX	SGD	CDS	461829	462425	.	+	.	ID=YJR014W;Name=YJR014W;Alias=TMA22
-chrX	SGD	CDS	462721	464253	.	+	.	ID=YJR015W;Name=YJR015W;Alias=
-chrX	SGD	CDS	464451	466208	.	-	.	ID=YJR016C;Name=YJR016C;Alias=ILV3
-chrX	SGD	CDS	466521	467033	.	-	.	ID=YJR017C;Name=YJR017C;Alias=ESS1
-chrX	SGD	CDS	467232	468281	.	-	.	ID=YJR019C;Name=YJR019C;Alias=TES1
-chrX	SGD	CDS	468555	469579	.	-	.	ID=YJR021C;Name=YJR021C;Alias=REC107
-chrX	SGD	CDS	469784	470113	.	+	.	ID=YJR022W;Name=YJR022W;Alias=LSM8
-chrX	SGD	CDS	470230	470964	.	-	.	ID=YJR024C;Name=YJR024C;Alias=MDE1
-chrX	SGD	CDS	471138	471671	.	-	.	ID=YJR025C;Name=YJR025C;Alias=BNA1
-chrX	SGD	CDS	483959	486196	.	-	.	ID=YJR030C;Name=YJR030C;Alias=RBH2
-chrX	SGD	CDS	486586	490812	.	-	.	ID=YJR031C;Name=YJR031C;Alias=GEA1
-chrX	SGD	CDS	491081	492262	.	+	.	ID=YJR032W;Name=YJR032W;Alias=CPR7
-chrX	SGD	CDS	492378	496451	.	-	.	ID=YJR033C;Name=YJR033C;Alias=RAV1
-chrX	SGD	CDS	496683	497009	.	+	.	ID=YJR034W;Name=YJR034W;Alias=PET191
-chrX	SGD	CDS	497355	500612	.	+	.	ID=YJR035W;Name=YJR035W;Alias=RAD26
-chrX	SGD	CDS	500713	503391	.	-	.	ID=YJR036C;Name=YJR036C;Alias=HUL4
-chrX	SGD	CDS	503936	507301	.	+	.	ID=YJR039W;Name=YJR039W;Alias=
-chrX	SGD	CDS	507746	510085	.	+	.	ID=YJR040W;Name=YJR040W;Alias=GEF1
-chrX	SGD	CDS	510239	513763	.	-	.	ID=YJR041C;Name=YJR041C;Alias=URB2
-chrX	SGD	CDS	514055	516289	.	+	.	ID=YJR042W;Name=YJR042W;Alias=NUP85
-chrX	SGD	CDS	516461	517513	.	-	.	ID=YJR043C;Name=YJR043C;Alias=POL32
-chrX	SGD	CDS	518763	519185	.	-	.	ID=YJR044C;Name=YJR044C;Alias=VPS55
-chrX	SGD	CDS	519638	521602	.	-	.	ID=YJR045C;Name=YJR045C;Alias=SSC1
-chrX	SGD	CDS	522048	523862	.	+	.	ID=YJR046W;Name=YJR046W;Alias=TAH11
-chrX	SGD	CDS	524908	525381	.	-	.	ID=YJR047C;Name=YJR047C;Alias=ANB1
-chrX	SGD	CDS	526335	526664	.	+	.	ID=YJR048W;Name=YJR048W;Alias=CYC1
-chrX	SGD	CDS	526884	528476	.	-	.	ID=YJR049C;Name=YJR049C;Alias=UTR1
-chrX	SGD	CDS	528697	529404	.	+	.	ID=YJR050W;Name=YJR050W;Alias=ISY1
-chrX	SGD	CDS	529861	531366	.	+	.	ID=YJR051W;Name=YJR051W;Alias=OSM1
-chrX	SGD	CDS	532062	533759	.	+	.	ID=YJR052W;Name=YJR052W;Alias=RAD7
-chrX	SGD	CDS	534027	535751	.	+	.	ID=YJR053W;Name=YJR053W;Alias=BFA1
-chrX	SGD	CDS	536056	537549	.	+	.	ID=YJR054W;Name=YJR054W;Alias=KCH1
-chrX	SGD	CDS	538772	539266	.	+	.	ID=YJR055W;Name=YJR055W;Alias=HIT1
-chrX	SGD	CDS	541792	542502	.	-	.	ID=YJR056C;Name=YJR056C;Alias=
-chrX	SGD	CDS	544062	544712	.	+	.	ID=YJR057W;Name=YJR057W;Alias=CDC8
-chrX	SGD	CDS	544732	545175	.	-	.	ID=YJR058C;Name=YJR058C;Alias=APS2
-chrX	SGD	CDS	545787	548243	.	+	.	ID=YJR059W;Name=YJR059W;Alias=PTK2
-chrX	SGD	CDS	548759	549814	.	+	.	ID=YJR060W;Name=YJR060W;Alias=CBF1
-chrX	SGD	CDS	550511	553318	.	+	.	ID=YJR061W;Name=YJR061W;Alias=
-chrX	SGD	CDS	553476	554849	.	-	.	ID=YJR062C;Name=YJR062C;Alias=NTA1
-chrX	SGD	CDS	555195	555572	.	+	.	ID=YJR063W;Name=YJR063W;Alias=RPA12
-chrX	SGD	CDS	555914	557602	.	+	.	ID=YJR064W;Name=YJR064W;Alias=CCT5
-chrX	SGD	CDS	557809	559158	.	-	.	ID=YJR065C;Name=YJR065C;Alias=ARP3
-chrX	SGD	CDS	559416	566828	.	+	.	ID=YJR066W;Name=YJR066W;Alias=TOR1
-chrX	SGD	CDS	567019	567444	.	-	.	ID=YJR067C;Name=YJR067C;Alias=YAE1
-chrX	SGD	CDS	567643	568704	.	+	.	ID=YJR068W;Name=YJR068W;Alias=RFC2
-chrX	SGD	CDS	568806	569399	.	-	.	ID=YJR069C;Name=YJR069C;Alias=HAM1
-chrX	SGD	CDS	569621	570598	.	-	.	ID=YJR070C;Name=YJR070C;Alias=LIA1
-chrX	SGD	CDS	570967	572124	.	-	.	ID=YJR072C;Name=YJR072C;Alias=NPA3
-chrX	SGD	CDS	572315	572935	.	-	.	ID=YJR073C;Name=YJR073C;Alias=OPI3
-chrX	SGD	CDS	573095	573751	.	+	.	ID=YJR074W;Name=YJR074W;Alias=MOG1
-chrX	SGD	CDS	573981	575171	.	+	.	ID=YJR075W;Name=YJR075W;Alias=HOC1
-chrX	SGD	CDS	575354	576601	.	-	.	ID=YJR076C;Name=YJR076C;Alias=CDC11
-chrX	SGD	CDS	577255	578190	.	-	.	ID=YJR077C;Name=YJR077C;Alias=MIR1
-chrX	SGD	CDS	578860	580221	.	+	.	ID=YJR078W;Name=YJR078W;Alias=BNA2
-chrX	SGD	CDS	580205	581239	.	+	.	ID=YJR079W;Name=YJR079W;Alias=
-chrX	SGD	CDS	580432	581616	.	-	.	ID=YJR080C;Name=YJR080C;Alias=AIM24
-chrX	SGD	CDS	581914	582255	.	-	.	ID=YJR082C;Name=YJR082C;Alias=EAF6
-chrX	SGD	CDS	582608	583537	.	-	.	ID=YJR083C;Name=YJR083C;Alias=ACF4
-chrX	SGD	CDS	583733	585004	.	+	.	ID=YJR084W;Name=YJR084W;Alias=
-chrX	SGD	CDS	585120	585437	.	-	.	ID=YJR085C;Name=YJR085C;Alias=
-chrX	SGD	CDS	586068	586400	.	+	.	ID=YJR086W;Name=YJR086W;Alias=STE18
-chrX	SGD	CDS	586495	587373	.	-	.	ID=YJR088C;Name=YJR088C;Alias=EMC2
-chrX	SGD	CDS	587718	590582	.	+	.	ID=YJR089W;Name=YJR089W;Alias=BIR1
-chrX	SGD	CDS	590872	594327	.	-	.	ID=YJR090C;Name=YJR090C;Alias=GRR1
-chrX	SGD	CDS	595061	598336	.	-	.	ID=YJR091C;Name=YJR091C;Alias=JSN1
-chrX	SGD	CDS	598735	603078	.	+	.	ID=YJR092W;Name=YJR092W;Alias=BUD4
-chrX	SGD	CDS	603220	604203	.	-	.	ID=YJR093C;Name=YJR093C;Alias=FIP1
-chrX	SGD	CDS	604569	605651	.	-	.	ID=YJR094C;Name=YJR094C;Alias=IME1
-chrX	SGD	CDS	608305	608858	.	+	.	ID=YJR094W-A;Name=YJR094W-A;Alias=RPL43B
-chrX	SGD	CDS	609773	610741	.	+	.	ID=YJR095W;Name=YJR095W;Alias=SFC1
-chrX	SGD	CDS	611195	612043	.	+	.	ID=YJR096W;Name=YJR096W;Alias=
-chrX	SGD	CDS	612413	612931	.	+	.	ID=YJR097W;Name=YJR097W;Alias=JJJ3
-chrX	SGD	CDS	613186	615156	.	-	.	ID=YJR098C;Name=YJR098C;Alias=
-chrX	SGD	CDS	615576	616286	.	+	.	ID=YJR099W;Name=YJR099W;Alias=YUH1
-chrX	SGD	CDS	616351	617334	.	-	.	ID=YJR100C;Name=YJR100C;Alias=AIM25
-chrX	SGD	CDS	618234	619034	.	+	.	ID=YJR101W;Name=YJR101W;Alias=RSM26
-chrX	SGD	CDS	619157	619765	.	-	.	ID=YJR102C;Name=YJR102C;Alias=VPS25
-chrX	SGD	CDS	620754	622490	.	+	.	ID=YJR103W;Name=YJR103W;Alias=URA8
-chrX	SGD	CDS	622550	623014	.	-	.	ID=YJR104C;Name=YJR104C;Alias=SOD1
-chrX	SGD	CDS	623581	624603	.	+	.	ID=YJR105W;Name=YJR105W;Alias=ADO1
-chrX	SGD	CDS	624838	627015	.	+	.	ID=YJR106W;Name=YJR106W;Alias=ECM27
-chrX	SGD	CDS	627340	628326	.	+	.	ID=YJR107W;Name=YJR107W;Alias=LIH1
-chrX	SGD	CDS	628712	629083	.	+	.	ID=YJR108W;Name=YJR108W;Alias=ABM1
-chrX	SGD	CDS	629585	632941	.	-	.	ID=YJR109C;Name=YJR109C;Alias=CPA2
-chrX	SGD	CDS	633615	635681	.	+	.	ID=YJR110W;Name=YJR110W;Alias=YMR1
-chrX	SGD	CDS	635855	636706	.	-	.	ID=YJR111C;Name=YJR111C;Alias=PXP2
-chrX	SGD	CDS	637030	637635	.	+	.	ID=YJR112W;Name=YJR112W;Alias=NNF1
-chrX	SGD	CDS	637790	638168	.	+	.	ID=YJR112W-A;Name=YJR112W-A;Alias=
-chrX	SGD	CDS	638232	638975	.	-	.	ID=YJR113C;Name=YJR113C;Alias=RSM7
-chrX	SGD	CDS	639942	640451	.	+	.	ID=YJR115W;Name=YJR115W;Alias=
-chrX	SGD	CDS	640825	641664	.	+	.	ID=YJR116W;Name=YJR116W;Alias=TDA4
-chrX	SGD	CDS	642007	643368	.	+	.	ID=YJR117W;Name=YJR117W;Alias=STE24
-chrX	SGD	CDS	643490	644101	.	-	.	ID=YJR118C;Name=YJR118C;Alias=ILM1
-chrX	SGD	CDS	644304	646490	.	-	.	ID=YJR119C;Name=YJR119C;Alias=JHD2
-chrX	SGD	CDS	647126	647476	.	+	.	ID=YJR120W;Name=YJR120W;Alias=
-chrX	SGD	CDS	647607	649142	.	+	.	ID=YJR121W;Name=YJR121W;Alias=ATP2
-chrX	SGD	CDS	649776	651269	.	+	.	ID=YJR122W;Name=YJR122W;Alias=IBA57
-chrX	SGD	CDS	651901	652578	.	+	.	ID=YJR123W;Name=YJR123W;Alias=RPS5
-chrX	SGD	CDS	652892	654238	.	-	.	ID=YJR124C;Name=YJR124C;Alias=
-chrX	SGD	CDS	654737	655963	.	-	.	ID=YJR125C;Name=YJR125C;Alias=ENT3
-chrX	SGD	CDS	656254	658689	.	-	.	ID=YJR126C;Name=YJR126C;Alias=VPS70
-chrX	SGD	CDS	658917	663059	.	-	.	ID=YJR127C;Name=YJR127C;Alias=RSF2
-chrX	SGD	CDS	664000	665019	.	-	.	ID=YJR129C;Name=YJR129C;Alias=EFM3
-chrX	SGD	CDS	665218	667137	.	-	.	ID=YJR130C;Name=YJR130C;Alias=STR2
-chrX	SGD	CDS	667644	669293	.	+	.	ID=YJR131W;Name=YJR131W;Alias=MNS1
-chrX	SGD	CDS	669522	672668	.	+	.	ID=YJR132W;Name=YJR132W;Alias=NMD5
-chrX	SGD	CDS	672991	673620	.	+	.	ID=YJR133W;Name=YJR133W;Alias=XPT1
-chrX	SGD	CDS	673729	675852	.	-	.	ID=YJR134C;Name=YJR134C;Alias=SGM1
-chrX	SGD	CDS	676059	676778	.	-	.	ID=YJR135C;Name=YJR135C;Alias=MCM22
-chrX	SGD	CDS	676971	677234	.	+	.	ID=YJR135W-A;Name=YJR135W-A;Alias=TIM8
-chrX	SGD	CDS	677441	678706	.	-	.	ID=YJR136C;Name=YJR136C;Alias=TTI2
-chrX	SGD	CDS	678957	683285	.	-	.	ID=YJR137C;Name=YJR137C;Alias=MET5
-chrX	SGD	CDS	684567	689321	.	+	.	ID=YJR138W;Name=YJR138W;Alias=IML1
-chrX	SGD	CDS	689445	690524	.	-	.	ID=YJR139C;Name=YJR139C;Alias=HOM6
-chrX	SGD	CDS	690750	695696	.	-	.	ID=YJR140C;Name=YJR140C;Alias=HIR3
-chrX	SGD	CDS	695906	696949	.	+	.	ID=YJR141W;Name=YJR141W;Alias=IPA1
-chrX	SGD	CDS	697141	698169	.	+	.	ID=YJR142W;Name=YJR142W;Alias=
-chrX	SGD	CDS	698326	700614	.	-	.	ID=YJR143C;Name=YJR143C;Alias=PMT4
-chrX	SGD	CDS	700882	701691	.	+	.	ID=YJR144W;Name=YJR144W;Alias=MGM101
-chrX	SGD	CDS	702027	703068	.	-	.	ID=YJR145C;Name=YJR145C;Alias=RPS4A
-chrX	SGD	CDS	703885	704238	.	+	.	ID=YJR146W;Name=YJR146W;Alias=
-chrX	SGD	CDS	704196	705272	.	+	.	ID=YJR147W;Name=YJR147W;Alias=HMS2
-chrX	SGD	CDS	705744	706874	.	+	.	ID=YJR148W;Name=YJR148W;Alias=BAT2
-chrX	SGD	CDS	707160	708374	.	+	.	ID=YJR149W;Name=YJR149W;Alias=
-chrX	SGD	CDS	708811	709707	.	-	.	ID=YJR150C;Name=YJR150C;Alias=DAN1
-chrX	SGD	CDS	712255	715740	.	-	.	ID=YJR151C;Name=YJR151C;Alias=DAN4
-chrX	SGD	CDS	717580	717630	.	+	.	ID=YJR151W-A;Name=YJR151W-A;Alias=
-chrX	SGD	CDS	719666	721297	.	+	.	ID=YJR152W;Name=YJR152W;Alias=DAL5
-chrX	SGD	CDS	722815	723900	.	+	.	ID=YJR153W;Name=YJR153W;Alias=PGU1
-chrX	SGD	CDS	725784	726824	.	+	.	ID=YJR154W;Name=YJR154W;Alias=
-chrX	SGD	CDS	727405	728271	.	+	.	ID=YJR155W;Name=YJR155W;Alias=AAD10
-chrX	SGD	CDS	728574	729596	.	-	.	ID=YJR156C;Name=YJR156C;Alias=THI11
-chrX	SGD	CDS	732440	734143	.	+	.	ID=YJR158W;Name=YJR158W;Alias=HXT16
-chrX	SGD	CDS	736044	737117	.	+	.	ID=YJR159W;Name=YJR159W;Alias=SOR1
-chrX	SGD	CDS	738008	739816	.	-	.	ID=YJR160C;Name=YJR160C;Alias=MPH3
-chrX	SGD	CDS	742848	743999	.	-	.	ID=YJR161C;Name=YJR161C;Alias=COS5
-chrXI	SGD	CDS	1810	2181	.	-	.	ID=YKL224C;Name=YKL224C;Alias=PAU16
-chrXI	SGD	CDS	3503	5620	.	-	.	ID=YKL222C;Name=YKL222C;Alias=
-chrXI	SGD	CDS	6107	7528	.	+	.	ID=YKL221W;Name=YKL221W;Alias=MCH2
-chrXI	SGD	CDS	9091	11226	.	-	.	ID=YKL220C;Name=YKL220C;Alias=FRE2
-chrXI	SGD	CDS	14485	15708	.	+	.	ID=YKL219W;Name=YKL219W;Alias=COS9
-chrXI	SGD	CDS	17359	18339	.	-	.	ID=YKL218C;Name=YKL218C;Alias=SRY1
-chrXI	SGD	CDS	22234	24084	.	+	.	ID=YKL217W;Name=YKL217W;Alias=JEN1
-chrXI	SGD	CDS	25215	26159	.	+	.	ID=YKL216W;Name=YKL216W;Alias=URA1
-chrXI	SGD	CDS	26827	30687	.	-	.	ID=YKL215C;Name=YKL215C;Alias=OXP1
-chrXI	SGD	CDS	31082	31693	.	-	.	ID=YKL214C;Name=YKL214C;Alias=YRA2
-chrXI	SGD	CDS	31960	34107	.	-	.	ID=YKL213C;Name=YKL213C;Alias=DOA1
-chrXI	SGD	CDS	34543	36414	.	+	.	ID=YKL212W;Name=YKL212W;Alias=SAC1
-chrXI	SGD	CDS	36699	38153	.	-	.	ID=YKL211C;Name=YKL211C;Alias=TRP3
-chrXI	SGD	CDS	39163	42237	.	+	.	ID=YKL210W;Name=YKL210W;Alias=UBA1
-chrXI	SGD	CDS	42423	46295	.	-	.	ID=YKL209C;Name=YKL209C;Alias=STE6
-chrXI	SGD	CDS	47157	47972	.	+	.	ID=YKL208W;Name=YKL208W;Alias=CBT1
-chrXI	SGD	CDS	48194	48955	.	+	.	ID=YKL207W;Name=YKL207W;Alias=EMC3
-chrXI	SGD	CDS	49006	49809	.	-	.	ID=YKL206C;Name=YKL206C;Alias=ADD66
-chrXI	SGD	CDS	50051	53353	.	+	.	ID=YKL205W;Name=YKL205W;Alias=LOS1
-chrXI	SGD	CDS	53704	55602	.	+	.	ID=YKL204W;Name=YKL204W;Alias=EAP1
-chrXI	SGD	CDS	55935	63359	.	-	.	ID=YKL203C;Name=YKL203C;Alias=TOR2
-chrXI	SGD	CDS	63930	67466	.	-	.	ID=YKL201C;Name=YKL201C;Alias=MNN4
-chrXI	SGD	CDS	68232	70220	.	-	.	ID=YKL198C;Name=YKL198C;Alias=PTK1
-chrXI	SGD	CDS	70734	73865	.	-	.	ID=YKL197C;Name=YKL197C;Alias=PEX1
-chrXI	SGD	CDS	74932	75534	.	-	.	ID=YKL196C;Name=YKL196C;Alias=YKT6
-chrXI	SGD	CDS	75821	77032	.	+	.	ID=YKL195W;Name=YKL195W;Alias=MIA40
-chrXI	SGD	CDS	77258	78646	.	-	.	ID=YKL194C;Name=YKL194C;Alias=MST1
-chrXI	SGD	CDS	78866	79882	.	-	.	ID=YKL193C;Name=YKL193C;Alias=SDS22
-chrXI	SGD	CDS	80160	80537	.	-	.	ID=YKL192C;Name=YKL192C;Alias=ACP1
-chrXI	SGD	CDS	81035	82639	.	+	.	ID=YKL191W;Name=YKL191W;Alias=DPH2
-chrXI	SGD	CDS	82947	83550	.	+	.	ID=YKL190W;Name=YKL190W;Alias=CNB1
-chrXI	SGD	CDS	84704	85903	.	+	.	ID=YKL189W;Name=YKL189W;Alias=HYM1
-chrXI	SGD	CDS	86225	88786	.	-	.	ID=YKL188C;Name=YKL188C;Alias=PXA2
-chrXI	SGD	CDS	89284	91536	.	-	.	ID=YKL187C;Name=YKL187C;Alias=FAT3
-chrXI	SGD	CDS	92744	93465	.	-	.	ID=YKL186C;Name=YKL186C;Alias=MTR2
-chrXI	SGD	CDS	94499	96265	.	+	.	ID=YKL185W;Name=YKL185W;Alias=ASH1
-chrXI	SGD	CDS	96757	98157	.	+	.	ID=YKL184W;Name=YKL184W;Alias=SPE1
-chrXI	SGD	CDS	98395	98607	.	-	.	ID=YKL183C-A;Name=YKL183C-A;Alias=
-chrXI	SGD	CDS	98721	99641	.	+	.	ID=YKL183W;Name=YKL183W;Alias=LOT5
-chrXI	SGD	CDS	100671	106826	.	+	.	ID=YKL182W;Name=YKL182W;Alias=FAS1
-chrXI	SGD	CDS	107316	108599	.	+	.	ID=YKL181W;Name=YKL181W;Alias=PRS1
-chrXI	SGD	CDS	109269	110129	.	+	.	ID=YKL180W;Name=YKL180W;Alias=RPL17A
-chrXI	SGD	CDS	110464	112503	.	-	.	ID=YKL179C;Name=YKL179C;Alias=COY1
-chrXI	SGD	CDS	113215	114627	.	-	.	ID=YKL178C;Name=YKL178C;Alias=STE3
-chrXI	SGD	CDS	115500	117986	.	-	.	ID=YKL176C;Name=YKL176C;Alias=LST4
-chrXI	SGD	CDS	118793	120304	.	+	.	ID=YKL175W;Name=YKL175W;Alias=ZRT3
-chrXI	SGD	CDS	120380	122236	.	-	.	ID=YKL174C;Name=YKL174C;Alias=TPO5
-chrXI	SGD	CDS	122517	125543	.	+	.	ID=YKL173W;Name=YKL173W;Alias=SNU114
-chrXI	SGD	CDS	125759	127042	.	+	.	ID=YKL172W;Name=YKL172W;Alias=EBP2
-chrXI	SGD	CDS	127475	130261	.	+	.	ID=YKL171W;Name=YKL171W;Alias=NNK1
-chrXI	SGD	CDS	130634	131050	.	+	.	ID=YKL170W;Name=YKL170W;Alias=MRPL38
-chrXI	SGD	CDS	131288	133462	.	-	.	ID=YKL168C;Name=YKL168C;Alias=KKQ8
-chrXI	SGD	CDS	133721	134134	.	-	.	ID=YKL167C;Name=YKL167C;Alias=MRP49
-chrXI	SGD	CDS	134509	135705	.	-	.	ID=YKL166C;Name=YKL166C;Alias=TPK3
-chrXI	SGD	CDS	137932	140691	.	-	.	ID=YKL165C;Name=YKL165C;Alias=MCD4
-chrXI	SGD	CDS	141794	142819	.	-	.	ID=YKL164C;Name=YKL164C;Alias=PIR1
-chrXI	SGD	CDS	144401	145378	.	+	.	ID=YKL163W;Name=YKL163W;Alias=PIR3
-chrXI	SGD	CDS	147630	148838	.	-	.	ID=YKL162C;Name=YKL162C;Alias=
-chrXI	SGD	CDS	149386	150687	.	-	.	ID=YKL161C;Name=YKL161C;Alias=KDX1
-chrXI	SGD	CDS	153269	153706	.	+	.	ID=YKL160W;Name=YKL160W;Alias=ELF1
-chrXI	SGD	CDS	153816	154451	.	-	.	ID=YKL159C;Name=YKL159C;Alias=RCN1
-chrXI	SGD	CDS	154991	158232	.	+	.	ID=YKL157W;Name=YKL157W;Alias=APE2
-chrXI	SGD	CDS	158613	159212	.	+	.	ID=YKL156W;Name=YKL156W;Alias=RPS27A
-chrXI	SGD	CDS	159456	161342	.	-	.	ID=YKL155C;Name=YKL155C;Alias=RSM22
-chrXI	SGD	CDS	161601	162335	.	+	.	ID=YKL154W;Name=YKL154W;Alias=SRP102
-chrXI	SGD	CDS	163642	164385	.	-	.	ID=YKL152C;Name=YKL152C;Alias=GPM1
-chrXI	SGD	CDS	164917	165930	.	-	.	ID=YKL151C;Name=YKL151C;Alias=NNR2
-chrXI	SGD	CDS	166400	167452	.	+	.	ID=YKL150W;Name=YKL150W;Alias=MCR1
-chrXI	SGD	CDS	167612	168829	.	-	.	ID=YKL149C;Name=YKL149C;Alias=DBR1
-chrXI	SGD	CDS	169207	171129	.	-	.	ID=YKL148C;Name=YKL148C;Alias=SDH1
-chrXI	SGD	CDS	171783	173861	.	+	.	ID=YKL146W;Name=YKL146W;Alias=AVT3
-chrXI	SGD	CDS	174213	175616	.	+	.	ID=YKL145W;Name=YKL145W;Alias=RPT1
-chrXI	SGD	CDS	175843	176481	.	-	.	ID=YKL144C;Name=YKL144C;Alias=RPC25
-chrXI	SGD	CDS	176781	178172	.	+	.	ID=YKL143W;Name=YKL143W;Alias=LTV1
-chrXI	SGD	CDS	178515	179174	.	+	.	ID=YKL142W;Name=YKL142W;Alias=MRP8
-chrXI	SGD	CDS	179667	180263	.	+	.	ID=YKL141W;Name=YKL141W;Alias=SDH3
-chrXI	SGD	CDS	180779	182425	.	+	.	ID=YKL140W;Name=YKL140W;Alias=TGL1
-chrXI	SGD	CDS	182958	184544	.	+	.	ID=YKL139W;Name=YKL139W;Alias=CTK1
-chrXI	SGD	CDS	184803	185012	.	-	.	ID=YKL138C-A;Name=YKL138C-A;Alias=HSK3
-chrXI	SGD	CDS	185286	185681	.	-	.	ID=YKL138C;Name=YKL138C;Alias=MRPL31
-chrXI	SGD	CDS	185957	186292	.	+	.	ID=YKL137W;Name=YKL137W;Alias=CMC1
-chrXI	SGD	CDS	186460	188640	.	-	.	ID=YKL135C;Name=YKL135C;Alias=APL2
-chrXI	SGD	CDS	189124	191442	.	-	.	ID=YKL134C;Name=YKL134C;Alias=OCT1
-chrXI	SGD	CDS	191679	193070	.	-	.	ID=YKL133C;Name=YKL133C;Alias=
-chrXI	SGD	CDS	193574	194866	.	-	.	ID=YKL132C;Name=YKL132C;Alias=RMA1
-chrXI	SGD	CDS	195288	196028	.	-	.	ID=YKL130C;Name=YKL130C;Alias=SHE2
-chrXI	SGD	CDS	196349	200167	.	-	.	ID=YKL129C;Name=YKL129C;Alias=MYO3
-chrXI	SGD	CDS	200884	201771	.	-	.	ID=YKL128C;Name=YKL128C;Alias=PMU1
-chrXI	SGD	CDS	203541	205253	.	+	.	ID=YKL127W;Name=YKL127W;Alias=PGM1
-chrXI	SGD	CDS	205707	207749	.	+	.	ID=YKL126W;Name=YKL126W;Alias=YPK1
-chrXI	SGD	CDS	208247	210130	.	+	.	ID=YKL125W;Name=YKL125W;Alias=RRN3
-chrXI	SGD	CDS	210593	212332	.	+	.	ID=YKL124W;Name=YKL124W;Alias=SSH4
-chrXI	SGD	CDS	212495	212998	.	-	.	ID=YKL122C;Name=YKL122C;Alias=SRP21
-chrXI	SGD	CDS	214142	216700	.	+	.	ID=YKL121W;Name=YKL121W;Alias=DGR2
-chrXI	SGD	CDS	217344	218318	.	+	.	ID=YKL120W;Name=YKL120W;Alias=OAC1
-chrXI	SGD	CDS	218570	219217	.	-	.	ID=YKL119C;Name=YKL119C;Alias=VPH2
-chrXI	SGD	CDS	220324	220974	.	+	.	ID=YKL117W;Name=YKL117W;Alias=SBA1
-chrXI	SGD	CDS	221344	222900	.	-	.	ID=YKL116C;Name=YKL116C;Alias=PRR1
-chrXI	SGD	CDS	223352	224455	.	-	.	ID=YKL114C;Name=YKL114C;Alias=APN1
-chrXI	SGD	CDS	224727	225875	.	-	.	ID=YKL113C;Name=YKL113C;Alias=RAD27
-chrXI	SGD	CDS	226570	228765	.	+	.	ID=YKL112W;Name=YKL112W;Alias=ABF1
-chrXI	SGD	CDS	228939	229880	.	-	.	ID=YKL110C;Name=YKL110C;Alias=KTI12
-chrXI	SGD	CDS	232227	233891	.	+	.	ID=YKL109W;Name=YKL109W;Alias=HAP4
-chrXI	SGD	CDS	234426	235787	.	+	.	ID=YKL108W;Name=YKL108W;Alias=SLD2
-chrXI	SGD	CDS	236141	237070	.	+	.	ID=YKL107W;Name=YKL107W;Alias=
-chrXI	SGD	CDS	237147	237266	.	-	.	ID=YKL106C-A;Name=YKL106C-A;Alias=
-chrXI	SGD	CDS	237536	238891	.	+	.	ID=YKL106W;Name=YKL106W;Alias=AAT1
-chrXI	SGD	CDS	239185	242583	.	-	.	ID=YKL105C;Name=YKL105C;Alias=SEG2
-chrXI	SGD	CDS	243220	245373	.	-	.	ID=YKL104C;Name=YKL104C;Alias=GFA1
-chrXI	SGD	CDS	246138	247682	.	-	.	ID=YKL103C;Name=YKL103C;Alias=APE1
-chrXI	SGD	CDS	248920	253476	.	+	.	ID=YKL101W;Name=YKL101W;Alias=HSL1
-chrXI	SGD	CDS	253697	255460	.	-	.	ID=YKL100C;Name=YKL100C;Alias=YPF1
-chrXI	SGD	CDS	255720	256472	.	-	.	ID=YKL099C;Name=YKL099C;Alias=UTP11
-chrXI	SGD	CDS	256770	257843	.	+	.	ID=YKL098W;Name=YKL098W;Alias=MTC2
-chrXI	SGD	CDS	259073	259222	.	-	.	ID=YKL096C-B;Name=YKL096C-B;Alias=
-chrXI	SGD	CDS	259253	259531	.	+	.	ID=YKL096W-A;Name=YKL096W-A;Alias=CWP2
-chrXI	SGD	CDS	261132	261851	.	+	.	ID=YKL096W;Name=YKL096W;Alias=CWP1
-chrXI	SGD	CDS	262277	263113	.	+	.	ID=YKL095W;Name=YKL095W;Alias=YJU2
-chrXI	SGD	CDS	263349	264290	.	+	.	ID=YKL094W;Name=YKL094W;Alias=YJU3
-chrXI	SGD	CDS	264789	265808	.	+	.	ID=YKL093W;Name=YKL093W;Alias=MBR1
-chrXI	SGD	CDS	266145	269459	.	-	.	ID=YKL092C;Name=YKL092C;Alias=BUD2
-chrXI	SGD	CDS	269718	270650	.	-	.	ID=YKL091C;Name=YKL091C;Alias=
-chrXI	SGD	CDS	271878	273209	.	+	.	ID=YKL090W;Name=YKL090W;Alias=CUE2
-chrXI	SGD	CDS	273394	275043	.	+	.	ID=YKL089W;Name=YKL089W;Alias=MIF2
-chrXI	SGD	CDS	275283	276998	.	+	.	ID=YKL088W;Name=YKL088W;Alias=CAB3
-chrXI	SGD	CDS	277189	277863	.	-	.	ID=YKL087C;Name=YKL087C;Alias=CYT2
-chrXI	SGD	CDS	278281	278664	.	+	.	ID=YKL086W;Name=YKL086W;Alias=SRX1
-chrXI	SGD	CDS	279123	280127	.	+	.	ID=YKL085W;Name=YKL085W;Alias=MDH1
-chrXI	SGD	CDS	280509	280859	.	+	.	ID=YKL084W;Name=YKL084W;Alias=HOT13
-chrXI	SGD	CDS	281025	282329	.	-	.	ID=YKL082C;Name=YKL082C;Alias=RRP14
-chrXI	SGD	CDS	282891	284455	.	+	.	ID=YKL081W;Name=YKL081W;Alias=TEF4
-chrXI	SGD	CDS	285030	286208	.	+	.	ID=YKL080W;Name=YKL080W;Alias=VMA5
-chrXI	SGD	CDS	286603	288573	.	+	.	ID=YKL079W;Name=YKL079W;Alias=SMY1
-chrXI	SGD	CDS	288845	291052	.	+	.	ID=YKL078W;Name=YKL078W;Alias=DHR2
-chrXI	SGD	CDS	291453	292631	.	+	.	ID=YKL077W;Name=YKL077W;Alias=
-chrXI	SGD	CDS	292956	294308	.	-	.	ID=YKL075C;Name=YKL075C;Alias=
-chrXI	SGD	CDS	294610	296193	.	-	.	ID=YKL074C;Name=YKL074C;Alias=MUD2
-chrXI	SGD	CDS	296430	299075	.	+	.	ID=YKL073W;Name=YKL073W;Alias=LHS1
-chrXI	SGD	CDS	299582	301882	.	+	.	ID=YKL072W;Name=YKL072W;Alias=STB6
-chrXI	SGD	CDS	305114	305884	.	+	.	ID=YKL071W;Name=YKL071W;Alias=
-chrXI	SGD	CDS	306211	306720	.	+	.	ID=YKL070W;Name=YKL070W;Alias=
-chrXI	SGD	CDS	307285	307827	.	+	.	ID=YKL069W;Name=YKL069W;Alias=
-chrXI	SGD	CDS	309206	309442	.	+	.	ID=YKL068W-A;Name=YKL068W-A;Alias=
-chrXI	SGD	CDS	310199	313078	.	+	.	ID=YKL068W;Name=YKL068W;Alias=NUP100
-chrXI	SGD	CDS	314812	315273	.	+	.	ID=YKL067W;Name=YKL067W;Alias=YNK1
-chrXI	SGD	CDS	315954	316175	.	+	.	ID=YKL065W-A;Name=YKL065W-A;Alias=
-chrXI	SGD	CDS	316437	317057	.	-	.	ID=YKL065C;Name=YKL065C;Alias=YET1
-chrXI	SGD	CDS	317764	320673	.	+	.	ID=YKL064W;Name=YKL064W;Alias=MNR2
-chrXI	SGD	CDS	321015	321518	.	-	.	ID=YKL063C;Name=YKL063C;Alias=
-chrXI	SGD	CDS	323228	325120	.	+	.	ID=YKL062W;Name=YKL062W;Alias=MSN4
-chrXI	SGD	CDS	325771	326112	.	+	.	ID=YKL061W;Name=YKL061W;Alias=BLI1
-chrXI	SGD	CDS	326408	327487	.	-	.	ID=YKL060C;Name=YKL060C;Alias=FBA1
-chrXI	SGD	CDS	328118	329443	.	-	.	ID=YKL059C;Name=YKL059C;Alias=MPE1
-chrXI	SGD	CDS	330166	330534	.	+	.	ID=YKL058W;Name=YKL058W;Alias=TOA2
-chrXI	SGD	CDS	330856	333969	.	-	.	ID=YKL057C;Name=YKL057C;Alias=NUP120
-chrXI	SGD	CDS	334412	334915	.	-	.	ID=YKL056C;Name=YKL056C;Alias=TMA19
-chrXI	SGD	CDS	335321	336157	.	-	.	ID=YKL055C;Name=YKL055C;Alias=OAR1
-chrXI	SGD	CDS	336537	338753	.	-	.	ID=YKL054C;Name=YKL054C;Alias=DEF1
-chrXI	SGD	CDS	339182	339442	.	-	.	ID=YKL053C-A;Name=YKL053C-A;Alias=MDM35
-chrXI	SGD	CDS	339668	340546	.	-	.	ID=YKL052C;Name=YKL052C;Alias=ASK1
-chrXI	SGD	CDS	341312	342373	.	+	.	ID=YKL051W;Name=YKL051W;Alias=SFK1
-chrXI	SGD	CDS	342852	345620	.	-	.	ID=YKL050C;Name=YKL050C;Alias=
-chrXI	SGD	CDS	346075	346764	.	-	.	ID=YKL049C;Name=YKL049C;Alias=CSE4
-chrXI	SGD	CDS	347214	349136	.	-	.	ID=YKL048C;Name=YKL048C;Alias=ELM1
-chrXI	SGD	CDS	349463	351013	.	+	.	ID=YKL047W;Name=YKL047W;Alias=ANR2
-chrXI	SGD	CDS	351275	352624	.	-	.	ID=YKL046C;Name=YKL046C;Alias=DCW1
-chrXI	SGD	CDS	353493	355079	.	+	.	ID=YKL045W;Name=YKL045W;Alias=PRI2
-chrXI	SGD	CDS	356322	356642	.	+	.	ID=YKL044W;Name=YKL044W;Alias=MMO1
-chrXI	SGD	CDS	356748	357848	.	+	.	ID=YKL043W;Name=YKL043W;Alias=PHD1
-chrXI	SGD	CDS	358475	359566	.	+	.	ID=YKL042W;Name=YKL042W;Alias=SPC42
-chrXI	SGD	CDS	360143	360817	.	+	.	ID=YKL041W;Name=YKL041W;Alias=VPS24
-chrXI	SGD	CDS	361058	361828	.	-	.	ID=YKL040C;Name=YKL040C;Alias=NFU1
-chrXI	SGD	CDS	362622	364193	.	+	.	ID=YKL039W;Name=YKL039W;Alias=PTM1
-chrXI	SGD	CDS	365605	369117	.	+	.	ID=YKL038W;Name=YKL038W;Alias=RGT1
-chrXI	SGD	CDS	369365	369721	.	+	.	ID=YKL037W;Name=YKL037W;Alias=AIM26
-chrXI	SGD	CDS	369891	371390	.	+	.	ID=YKL035W;Name=YKL035W;Alias=UGP1
-chrXI	SGD	CDS	371829	374105	.	+	.	ID=YKL034W;Name=YKL034W;Alias=TUL1
-chrXI	SGD	CDS	374505	375215	.	+	.	ID=YKL033W-A;Name=YKL033W-A;Alias=
-chrXI	SGD	CDS	375456	378572	.	+	.	ID=YKL033W;Name=YKL033W;Alias=TTI1
-chrXI	SGD	CDS	380065	381858	.	-	.	ID=YKL032C;Name=YKL032C;Alias=IXR1
-chrXI	SGD	CDS	382716	384725	.	-	.	ID=YKL029C;Name=YKL029C;Alias=MAE1
-chrXI	SGD	CDS	385758	387206	.	+	.	ID=YKL028W;Name=YKL028W;Alias=TFA1
-chrXI	SGD	CDS	387562	388905	.	+	.	ID=YKL027W;Name=YKL027W;Alias=TCD2
-chrXI	SGD	CDS	389380	389883	.	-	.	ID=YKL026C;Name=YKL026C;Alias=GPX1
-chrXI	SGD	CDS	390240	392279	.	-	.	ID=YKL025C;Name=YKL025C;Alias=PAN3
-chrXI	SGD	CDS	392526	393140	.	-	.	ID=YKL024C;Name=YKL024C;Alias=URA6
-chrXI	SGD	CDS	393146	393373	.	-	.	ID=YKL023C-A;Name=YKL023C-A;Alias=
-chrXI	SGD	CDS	393721	394554	.	+	.	ID=YKL023W;Name=YKL023W;Alias=
-chrXI	SGD	CDS	394726	397248	.	-	.	ID=YKL022C;Name=YKL022C;Alias=CDC16
-chrXI	SGD	CDS	397344	398750	.	-	.	ID=YKL021C;Name=YKL021C;Alias=MAK11
-chrXI	SGD	CDS	398832	402080	.	-	.	ID=YKL020C;Name=YKL020C;Alias=SPT23
-chrXI	SGD	CDS	402568	403518	.	+	.	ID=YKL019W;Name=YKL019W;Alias=RAM2
-chrXI	SGD	CDS	403580	403879	.	-	.	ID=YKL018C-A;Name=YKL018C-A;Alias=
-chrXI	SGD	CDS	404102	405091	.	+	.	ID=YKL018W;Name=YKL018W;Alias=SWD2
-chrXI	SGD	CDS	405190	407241	.	-	.	ID=YKL017C;Name=YKL017C;Alias=HCS1
-chrXI	SGD	CDS	407465	407989	.	-	.	ID=YKL016C;Name=YKL016C;Alias=ATP7
-chrXI	SGD	CDS	408544	411483	.	+	.	ID=YKL015W;Name=YKL015W;Alias=PUT3
-chrXI	SGD	CDS	411619	416913	.	-	.	ID=YKL014C;Name=YKL014C;Alias=URB1
-chrXI	SGD	CDS	417508	418023	.	-	.	ID=YKL013C;Name=YKL013C;Alias=ARC19
-chrXI	SGD	CDS	418310	420061	.	+	.	ID=YKL012W;Name=YKL012W;Alias=PRP40
-chrXI	SGD	CDS	420155	421216	.	-	.	ID=YKL011C;Name=YKL011C;Alias=CCE1
-chrXI	SGD	CDS	421424	425875	.	-	.	ID=YKL010C;Name=YKL010C;Alias=UFD4
-chrXI	SGD	CDS	426242	426952	.	+	.	ID=YKL009W;Name=YKL009W;Alias=MRT4
-chrXI	SGD	CDS	427295	428551	.	-	.	ID=YKL008C;Name=YKL008C;Alias=LAC1
-chrXI	SGD	CDS	429302	430108	.	+	.	ID=YKL007W;Name=YKL007W;Alias=CAP1
-chrXI	SGD	CDS	430198	430632	.	-	.	ID=YKL006C-A;Name=YKL006C-A;Alias=SFT1
-chrXI	SGD	CDS	431906	432720	.	+	.	ID=YKL006W;Name=YKL006W;Alias=RPL14A
-chrXI	SGD	CDS	433093	434877	.	-	.	ID=YKL005C;Name=YKL005C;Alias=BYE1
-chrXI	SGD	CDS	435580	436785	.	+	.	ID=YKL004W;Name=YKL004W;Alias=AUR1
-chrXI	SGD	CDS	437097	437492	.	-	.	ID=YKL003C;Name=YKL003C;Alias=MRP17
-chrXI	SGD	CDS	437778	438544	.	+	.	ID=YKL002W;Name=YKL002W;Alias=DID4
-chrXI	SGD	CDS	438777	439385	.	-	.	ID=YKL001C;Name=YKL001C;Alias=MET14
-chrXI	SGD	CDS	440608	442722	.	-	.	ID=YKR001C;Name=YKR001C;Alias=VPS1
-chrXI	SGD	CDS	443232	444938	.	+	.	ID=YKR002W;Name=YKR002W;Alias=PAP1
-chrXI	SGD	CDS	445381	446727	.	+	.	ID=YKR003W;Name=YKR003W;Alias=OSH6
-chrXI	SGD	CDS	446799	448036	.	-	.	ID=YKR004C;Name=YKR004C;Alias=ECM9
-chrXI	SGD	CDS	448521	450167	.	-	.	ID=YKR005C;Name=YKR005C;Alias=
-chrXI	SGD	CDS	450423	451217	.	-	.	ID=YKR006C;Name=YKR006C;Alias=MRPL13
-chrXI	SGD	CDS	451434	451988	.	+	.	ID=YKR007W;Name=YKR007W;Alias=MEH1
-chrXI	SGD	CDS	452201	454078	.	+	.	ID=YKR008W;Name=YKR008W;Alias=RSC4
-chrXI	SGD	CDS	454352	457054	.	-	.	ID=YKR009C;Name=YKR009C;Alias=FOX2
-chrXI	SGD	CDS	458924	461239	.	-	.	ID=YKR010C;Name=YKR010C;Alias=TOF2
-chrXI	SGD	CDS	461635	462696	.	-	.	ID=YKR011C;Name=YKR011C;Alias=
-chrXI	SGD	CDS	463959	464948	.	+	.	ID=YKR013W;Name=YKR013W;Alias=PRY2
-chrXI	SGD	CDS	465367	466071	.	-	.	ID=YKR014C;Name=YKR014C;Alias=YPT52
-chrXI	SGD	CDS	466961	468667	.	-	.	ID=YKR015C;Name=YKR015C;Alias=
-chrXI	SGD	CDS	469717	471339	.	+	.	ID=YKR016W;Name=YKR016W;Alias=MIC60
-chrXI	SGD	CDS	471694	473349	.	-	.	ID=YKR017C;Name=YKR017C;Alias=HEL1
-chrXI	SGD	CDS	473723	475900	.	-	.	ID=YKR018C;Name=YKR018C;Alias=
-chrXI	SGD	CDS	476216	478063	.	-	.	ID=YKR019C;Name=YKR019C;Alias=IRS4
-chrXI	SGD	CDS	478338	478832	.	+	.	ID=YKR020W;Name=YKR020W;Alias=VPS51
-chrXI	SGD	CDS	479234	481981	.	+	.	ID=YKR021W;Name=YKR021W;Alias=ALY1
-chrXI	SGD	CDS	482171	483139	.	-	.	ID=YKR022C;Name=YKR022C;Alias=NTR2
-chrXI	SGD	CDS	483419	485011	.	+	.	ID=YKR023W;Name=YKR023W;Alias=
-chrXI	SGD	CDS	485144	487372	.	-	.	ID=YKR024C;Name=YKR024C;Alias=DBP7
-chrXI	SGD	CDS	487770	488618	.	+	.	ID=YKR025W;Name=YKR025W;Alias=RPC37
-chrXI	SGD	CDS	488738	489655	.	-	.	ID=YKR026C;Name=YKR026C;Alias=GCN3
-chrXI	SGD	CDS	491364	493661	.	+	.	ID=YKR027W;Name=YKR027W;Alias=BCH2
-chrXI	SGD	CDS	494257	497358	.	+	.	ID=YKR028W;Name=YKR028W;Alias=SAP190
-chrXI	SGD	CDS	497578	499833	.	-	.	ID=YKR029C;Name=YKR029C;Alias=SET3
-chrXI	SGD	CDS	500282	501103	.	+	.	ID=YKR030W;Name=YKR030W;Alias=GMH1
-chrXI	SGD	CDS	501344	506395	.	-	.	ID=YKR031C;Name=YKR031C;Alias=SPO14
-chrXI	SGD	CDS	506898	507707	.	+	.	ID=YKR034W;Name=YKR034W;Alias=DAL80
-chrXI	SGD	CDS	507939	508553	.	+	.	ID=YKR035W-A;Name=YKR035W-A;Alias=DID2
-chrXI	SGD	CDS	508702	510633	.	-	.	ID=YKR036C;Name=YKR036C;Alias=CAF4
-chrXI	SGD	CDS	510910	511797	.	-	.	ID=YKR037C;Name=YKR037C;Alias=SPC34
-chrXI	SGD	CDS	511999	513159	.	-	.	ID=YKR038C;Name=YKR038C;Alias=KAE1
-chrXI	SGD	CDS	515063	516871	.	+	.	ID=YKR039W;Name=YKR039W;Alias=GAP1
-chrXI	SGD	CDS	518198	518950	.	+	.	ID=YKR041W;Name=YKR041W;Alias=
-chrXI	SGD	CDS	519527	520624	.	+	.	ID=YKR042W;Name=YKR042W;Alias=UTH1
-chrXI	SGD	CDS	520897	521712	.	-	.	ID=YKR043C;Name=YKR043C;Alias=SHB17
-chrXI	SGD	CDS	522015	523346	.	+	.	ID=YKR044W;Name=YKR044W;Alias=UIP5
-chrXI	SGD	CDS	523418	523969	.	-	.	ID=YKR045C;Name=YKR045C;Alias=
-chrXI	SGD	CDS	524223	525074	.	-	.	ID=YKR046C;Name=YKR046C;Alias=PET10
-chrXI	SGD	CDS	525387	526640	.	-	.	ID=YKR048C;Name=YKR048C;Alias=NAP1
-chrXI	SGD	CDS	526830	527231	.	-	.	ID=YKR049C;Name=YKR049C;Alias=FMP46
-chrXI	SGD	CDS	527815	530484	.	+	.	ID=YKR050W;Name=YKR050W;Alias=TRK2
-chrXI	SGD	CDS	530946	532202	.	+	.	ID=YKR051W;Name=YKR051W;Alias=
-chrXI	SGD	CDS	532550	533464	.	-	.	ID=YKR052C;Name=YKR052C;Alias=MRS4
-chrXI	SGD	CDS	534067	535281	.	-	.	ID=YKR053C;Name=YKR053C;Alias=YSR3
-chrXI	SGD	CDS	535647	547925	.	-	.	ID=YKR054C;Name=YKR054C;Alias=DYN1
-chrXI	SGD	CDS	548216	549091	.	+	.	ID=YKR055W;Name=YKR055W;Alias=RHO4
-chrXI	SGD	CDS	549448	551367	.	+	.	ID=YKR056W;Name=YKR056W;Alias=TRM2
-chrXI	SGD	CDS	551657	552242	.	+	.	ID=YKR057W;Name=YKR057W;Alias=RPS21A
-chrXI	SGD	CDS	552770	554620	.	+	.	ID=YKR058W;Name=YKR058W;Alias=GLG1
-chrXI	SGD	CDS	554987	556174	.	+	.	ID=YKR059W;Name=YKR059W;Alias=TIF1
-chrXI	SGD	CDS	556518	557342	.	+	.	ID=YKR060W;Name=YKR060W;Alias=UTP30
-chrXI	SGD	CDS	557677	558954	.	+	.	ID=YKR061W;Name=YKR061W;Alias=KTR2
-chrXI	SGD	CDS	559666	560652	.	+	.	ID=YKR062W;Name=YKR062W;Alias=TFA2
-chrXI	SGD	CDS	560789	562297	.	-	.	ID=YKR063C;Name=YKR063C;Alias=LAS1
-chrXI	SGD	CDS	562547	565138	.	+	.	ID=YKR064W;Name=YKR064W;Alias=OAF3
-chrXI	SGD	CDS	565299	565892	.	-	.	ID=YKR065C;Name=YKR065C;Alias=PAM17
-chrXI	SGD	CDS	566113	567198	.	-	.	ID=YKR066C;Name=YKR066C;Alias=CCP1
-chrXI	SGD	CDS	567918	570149	.	+	.	ID=YKR067W;Name=YKR067W;Alias=GPT2
-chrXI	SGD	CDS	570328	570909	.	-	.	ID=YKR068C;Name=YKR068C;Alias=BET3
-chrXI	SGD	CDS	571612	573393	.	+	.	ID=YKR069W;Name=YKR069W;Alias=MET1
-chrXI	SGD	CDS	573574	574632	.	+	.	ID=YKR070W;Name=YKR070W;Alias=
-chrXI	SGD	CDS	574934	575980	.	-	.	ID=YKR071C;Name=YKR071C;Alias=DRE2
-chrXI	SGD	CDS	576435	578123	.	-	.	ID=YKR072C;Name=YKR072C;Alias=SIS2
-chrXI	SGD	CDS	579209	579676	.	+	.	ID=YKR074W;Name=YKR074W;Alias=AIM29
-chrXI	SGD	CDS	579827	580750	.	-	.	ID=YKR075C;Name=YKR075C;Alias=
-chrXI	SGD	CDS	582283	583395	.	+	.	ID=YKR076W;Name=YKR076W;Alias=ECM4
-chrXI	SGD	CDS	583653	584744	.	+	.	ID=YKR077W;Name=YKR077W;Alias=MSA2
-chrXI	SGD	CDS	584952	586709	.	+	.	ID=YKR078W;Name=YKR078W;Alias=
-chrXI	SGD	CDS	586789	589305	.	-	.	ID=YKR079C;Name=YKR079C;Alias=TRZ1
-chrXI	SGD	CDS	590395	591357	.	+	.	ID=YKR080W;Name=YKR080W;Alias=MTD1
-chrXI	SGD	CDS	591506	592540	.	-	.	ID=YKR081C;Name=YKR081C;Alias=RPF2
-chrXI	SGD	CDS	592825	596298	.	+	.	ID=YKR082W;Name=YKR082W;Alias=NUP133
-chrXI	SGD	CDS	596421	596822	.	-	.	ID=YKR083C;Name=YKR083C;Alias=DAD2
-chrXI	SGD	CDS	597055	598890	.	-	.	ID=YKR084C;Name=YKR084C;Alias=HBS1
-chrXI	SGD	CDS	599094	599681	.	-	.	ID=YKR085C;Name=YKR085C;Alias=MRPL20
-chrXI	SGD	CDS	599857	603072	.	+	.	ID=YKR086W;Name=YKR086W;Alias=PRP16
-chrXI	SGD	CDS	603195	604232	.	-	.	ID=YKR087C;Name=YKR087C;Alias=OMA1
-chrXI	SGD	CDS	604405	605418	.	-	.	ID=YKR088C;Name=YKR088C;Alias=TVP38
-chrXI	SGD	CDS	605633	608365	.	-	.	ID=YKR089C;Name=YKR089C;Alias=TGL4
-chrXI	SGD	CDS	608946	611066	.	+	.	ID=YKR090W;Name=YKR090W;Alias=PXL1
-chrXI	SGD	CDS	611525	612265	.	+	.	ID=YKR091W;Name=YKR091W;Alias=SRL3
-chrXI	SGD	CDS	612665	613885	.	-	.	ID=YKR092C;Name=YKR092C;Alias=SRP40
-chrXI	SGD	CDS	615730	617535	.	+	.	ID=YKR093W;Name=YKR093W;Alias=PTR2
-chrXI	SGD	CDS	617996	618750	.	-	.	ID=YKR094C;Name=YKR094C;Alias=RPL40B
-chrXI	SGD	CDS	619805	625432	.	+	.	ID=YKR095W;Name=YKR095W;Alias=MLP1
-chrXI	SGD	CDS	625864	626205	.	+	.	ID=YKR095W-A;Name=YKR095W-A;Alias=PCC1
-chrXI	SGD	CDS	626793	630380	.	+	.	ID=YKR096W;Name=YKR096W;Alias=ESL2
-chrXI	SGD	CDS	631152	632801	.	+	.	ID=YKR097W;Name=YKR097W;Alias=PCK1
-chrXI	SGD	CDS	633026	635179	.	-	.	ID=YKR098C;Name=YKR098C;Alias=UBP11
-chrXI	SGD	CDS	635851	638286	.	+	.	ID=YKR099W;Name=YKR099W;Alias=BAS1
-chrXI	SGD	CDS	638901	639968	.	-	.	ID=YKR100C;Name=YKR100C;Alias=SKG1
-chrXI	SGD	CDS	640540	642504	.	+	.	ID=YKR101W;Name=YKR101W;Alias=SIR1
-chrXI	SGD	CDS	646356	649865	.	+	.	ID=YKR102W;Name=YKR102W;Alias=FLO10
-chrXI	SGD	CDS	653080	656736	.	+	.	ID=YKR103W;Name=YKR103W;Alias=NFT1
-chrXI	SGD	CDS	656836	657756	.	+	.	ID=YKR104W;Name=YKR104W;Alias=
-chrXI	SGD	CDS	658716	660464	.	-	.	ID=YKR105C;Name=YKR105C;Alias=VBA5
-chrXI	SGD	CDS	661442	663289	.	+	.	ID=YKR106W;Name=YKR106W;Alias=GEX2
-chrXII	SGD	CDS	585	4301	.	-	.	ID=YLL067C;Name=YLL067C;Alias=
-chrXII	SGD	CDS	5605	5775	.	+	.	ID=YLL066W-B;Name=YLL066W-B;Alias=
-chrXII	SGD	CDS	6120	9836	.	-	.	ID=YLL066C;Name=YLL066C;Alias=
-chrXII	SGD	CDS	13083	13445	.	-	.	ID=YLL064C;Name=YLL064C;Alias=PAU18
-chrXII	SGD	CDS	14648	16072	.	-	.	ID=YLL063C;Name=YLL063C;Alias=AYT1
-chrXII	SGD	CDS	16639	17613	.	-	.	ID=YLL062C;Name=YLL062C;Alias=MHT1
-chrXII	SGD	CDS	17956	19707	.	+	.	ID=YLL061W;Name=YLL061W;Alias=MMP1
-chrXII	SGD	CDS	21138	21839	.	-	.	ID=YLL060C;Name=YLL060C;Alias=GTT2
-chrXII	SGD	CDS	23569	25296	.	+	.	ID=YLL058W;Name=YLL058W;Alias=
-chrXII	SGD	CDS	25756	26994	.	-	.	ID=YLL057C;Name=YLL057C;Alias=JLP1
-chrXII	SGD	CDS	27409	28305	.	-	.	ID=YLL056C;Name=YLL056C;Alias=
-chrXII	SGD	CDS	30109	31704	.	+	.	ID=YLL055W;Name=YLL055W;Alias=YCT1
-chrXII	SGD	CDS	32673	35204	.	-	.	ID=YLL054C;Name=YLL054C;Alias=
-chrXII	SGD	CDS	35503	35961	.	-	.	ID=YLL053C;Name=YLL053C;Alias=
-chrXII	SGD	CDS	35912	36361	.	-	.	ID=YLL052C;Name=YLL052C;Alias=AQY2
-chrXII	SGD	CDS	37333	39471	.	-	.	ID=YLL051C;Name=YLL051C;Alias=FRE6
-chrXII	SGD	CDS	39804	40414	.	-	.	ID=YLL050C;Name=YLL050C;Alias=COF1
-chrXII	SGD	CDS	40666	41205	.	+	.	ID=YLL049W;Name=YLL049W;Alias=LDB18
-chrXII	SGD	CDS	41280	46265	.	-	.	ID=YLL048C;Name=YLL048C;Alias=YBT1
-chrXII	SGD	CDS	46714	47463	.	-	.	ID=YLL046C;Name=YLL046C;Alias=RNP1
-chrXII	SGD	CDS	47859	48629	.	-	.	ID=YLL045C;Name=YLL045C;Alias=RPL8B
-chrXII	SGD	CDS	49938	51947	.	+	.	ID=YLL043W;Name=YLL043W;Alias=FPS1
-chrXII	SGD	CDS	52087	52590	.	-	.	ID=YLL042C;Name=YLL042C;Alias=ATG10
-chrXII	SGD	CDS	53131	53931	.	-	.	ID=YLL041C;Name=YLL041C;Alias=SDH2
-chrXII	SGD	CDS	54211	63645	.	-	.	ID=YLL040C;Name=YLL040C;Alias=VPS13
-chrXII	SGD	CDS	64062	65207	.	-	.	ID=YLL039C;Name=YLL039C;Alias=UBI4
-chrXII	SGD	CDS	65775	66518	.	-	.	ID=YLL038C;Name=YLL038C;Alias=ENT4
-chrXII	SGD	CDS	66745	68256	.	-	.	ID=YLL036C;Name=YLL036C;Alias=PRP19
-chrXII	SGD	CDS	68580	70478	.	+	.	ID=YLL035W;Name=YLL035W;Alias=GRC3
-chrXII	SGD	CDS	70633	73146	.	-	.	ID=YLL034C;Name=YLL034C;Alias=RIX7
-chrXII	SGD	CDS	73409	74101	.	+	.	ID=YLL033W;Name=YLL033W;Alias=IRC19
-chrXII	SGD	CDS	74270	76747	.	-	.	ID=YLL032C;Name=YLL032C;Alias=
-chrXII	SGD	CDS	77152	80205	.	-	.	ID=YLL031C;Name=YLL031C;Alias=GPI13
-chrXII	SGD	CDS	81461	83710	.	+	.	ID=YLL029W;Name=YLL029W;Alias=FRA1
-chrXII	SGD	CDS	84804	86564	.	+	.	ID=YLL028W;Name=YLL028W;Alias=TPO1
-chrXII	SGD	CDS	87403	88155	.	+	.	ID=YLL027W;Name=YLL027W;Alias=ISA1
-chrXII	SGD	CDS	88623	91349	.	+	.	ID=YLL026W;Name=YLL026W;Alias=HSP104
-chrXII	SGD	CDS	94747	95121	.	+	.	ID=YLL025W;Name=YLL025W;Alias=PAU17
-chrXII	SGD	CDS	95566	97485	.	-	.	ID=YLL024C;Name=YLL024C;Alias=SSA2
-chrXII	SGD	CDS	97997	98836	.	-	.	ID=YLL023C;Name=YLL023C;Alias=POM33
-chrXII	SGD	CDS	99044	100201	.	-	.	ID=YLL022C;Name=YLL022C;Alias=HIF1
-chrXII	SGD	CDS	100947	105347	.	+	.	ID=YLL021W;Name=YLL021W;Alias=SPA2
-chrXII	SGD	CDS	105686	107899	.	-	.	ID=YLL019C;Name=YLL019C;Alias=KNS1
-chrXII	SGD	CDS	108676	108972	.	-	.	ID=YLL018C-A;Name=YLL018C-A;Alias=COX19
-chrXII	SGD	CDS	109902	111575	.	-	.	ID=YLL018C;Name=YLL018C;Alias=DPS1
-chrXII	SGD	CDS	116432	121111	.	+	.	ID=YLL015W;Name=YLL015W;Alias=BPT1
-chrXII	SGD	CDS	121322	121648	.	+	.	ID=YLL014W;Name=YLL014W;Alias=EMC6
-chrXII	SGD	CDS	122075	124714	.	-	.	ID=YLL013C;Name=YLL013C;Alias=PUF3
-chrXII	SGD	CDS	125534	127255	.	+	.	ID=YLL012W;Name=YLL012W;Alias=YEH1
-chrXII	SGD	CDS	127523	128992	.	+	.	ID=YLL011W;Name=YLL011W;Alias=SOF1
-chrXII	SGD	CDS	129330	130613	.	-	.	ID=YLL010C;Name=YLL010C;Alias=PSR1
-chrXII	SGD	CDS	131205	131414	.	-	.	ID=YLL009C;Name=YLL009C;Alias=COX17
-chrXII	SGD	CDS	131729	133987	.	+	.	ID=YLL008W;Name=YLL008W;Alias=DRS1
-chrXII	SGD	CDS	134302	136299	.	-	.	ID=YLL007C;Name=YLL007C;Alias=LMO1
-chrXII	SGD	CDS	136345	136521	.	+	.	ID=YLL006W-A;Name=YLL006W-A;Alias=
-chrXII	SGD	CDS	136586	137866	.	+	.	ID=YLL006W;Name=YLL006W;Alias=MMM1
-chrXII	SGD	CDS	137940	140546	.	-	.	ID=YLL005C;Name=YLL005C;Alias=SPO75
-chrXII	SGD	CDS	141073	142923	.	+	.	ID=YLL004W;Name=YLL004W;Alias=ORC3
-chrXII	SGD	CDS	143201	146041	.	+	.	ID=YLL003W;Name=YLL003W;Alias=SFI1
-chrXII	SGD	CDS	146291	147601	.	+	.	ID=YLL002W;Name=YLL002W;Alias=RTT109
-chrXII	SGD	CDS	147890	150163	.	+	.	ID=YLL001W;Name=YLL001W;Alias=DNM1
-chrXII	SGD	CDS	151389	153977	.	-	.	ID=YLR001C;Name=YLR001C;Alias=
-chrXII	SGD	CDS	154343	156334	.	-	.	ID=YLR002C;Name=YLR002C;Alias=NOC3
-chrXII	SGD	CDS	156855	157730	.	-	.	ID=YLR003C;Name=YLR003C;Alias=CMS1
-chrXII	SGD	CDS	157934	159505	.	-	.	ID=YLR004C;Name=YLR004C;Alias=THI73
-chrXII	SGD	CDS	160049	161434	.	+	.	ID=YLR005W;Name=YLR005W;Alias=SSL1
-chrXII	SGD	CDS	161755	163893	.	-	.	ID=YLR006C;Name=YLR006C;Alias=SSK1
-chrXII	SGD	CDS	164392	165402	.	+	.	ID=YLR007W;Name=YLR007W;Alias=NSE1
-chrXII	SGD	CDS	165577	166083	.	-	.	ID=YLR008C;Name=YLR008C;Alias=PAM18
-chrXII	SGD	CDS	166537	167136	.	+	.	ID=YLR009W;Name=YLR009W;Alias=RLP24
-chrXII	SGD	CDS	167320	167802	.	-	.	ID=YLR010C;Name=YLR010C;Alias=TEN1
-chrXII	SGD	CDS	169103	169678	.	+	.	ID=YLR011W;Name=YLR011W;Alias=LOT6
-chrXII	SGD	CDS	169982	170281	.	-	.	ID=YLR012C;Name=YLR012C;Alias=
-chrXII	SGD	CDS	171339	171764	.	+	.	ID=YLR013W;Name=YLR013W;Alias=GAT3
-chrXII	SGD	CDS	172268	174982	.	-	.	ID=YLR014C;Name=YLR014C;Alias=PPR1
-chrXII	SGD	CDS	175227	176744	.	+	.	ID=YLR015W;Name=YLR015W;Alias=BRE2
-chrXII	SGD	CDS	176802	177416	.	-	.	ID=YLR016C;Name=YLR016C;Alias=PML1
-chrXII	SGD	CDS	177608	178621	.	+	.	ID=YLR017W;Name=YLR017W;Alias=MEU1
-chrXII	SGD	CDS	178707	179606	.	-	.	ID=YLR018C;Name=YLR018C;Alias=POM34
-chrXII	SGD	CDS	180288	181481	.	+	.	ID=YLR019W;Name=YLR019W;Alias=PSR2
-chrXII	SGD	CDS	181789	183405	.	-	.	ID=YLR020C;Name=YLR020C;Alias=YEH2
-chrXII	SGD	CDS	183623	184162	.	+	.	ID=YLR021W;Name=YLR021W;Alias=IRC25
-chrXII	SGD	CDS	184174	184926	.	-	.	ID=YLR022C;Name=YLR022C;Alias=SDO1
-chrXII	SGD	CDS	185498	187129	.	-	.	ID=YLR023C;Name=YLR023C;Alias=IZH3
-chrXII	SGD	CDS	187663	193281	.	-	.	ID=YLR024C;Name=YLR024C;Alias=UBR2
-chrXII	SGD	CDS	194452	195174	.	+	.	ID=YLR025W;Name=YLR025W;Alias=SNF7
-chrXII	SGD	CDS	195450	196472	.	-	.	ID=YLR026C;Name=YLR026C;Alias=SED5
-chrXII	SGD	CDS	196829	198085	.	-	.	ID=YLR027C;Name=YLR027C;Alias=AAT2
-chrXII	SGD	CDS	199540	201315	.	-	.	ID=YLR028C;Name=YLR028C;Alias=ADE16
-chrXII	SGD	CDS	201976	202590	.	-	.	ID=YLR029C;Name=YLR029C;Alias=RPL15A
-chrXII	SGD	CDS	203290	204081	.	+	.	ID=YLR030W;Name=YLR030W;Alias=
-chrXII	SGD	CDS	204225	204785	.	+	.	ID=YLR031W;Name=YLR031W;Alias=
-chrXII	SGD	CDS	204991	208500	.	+	.	ID=YLR032W;Name=YLR032W;Alias=RAD5
-chrXII	SGD	CDS	208761	210269	.	+	.	ID=YLR033W;Name=YLR033W;Alias=RSC58
-chrXII	SGD	CDS	210512	211933	.	-	.	ID=YLR034C;Name=YLR034C;Alias=SMF3
-chrXII	SGD	CDS	212369	214456	.	-	.	ID=YLR035C;Name=YLR035C;Alias=MLH2
-chrXII	SGD	CDS	221521	222132	.	-	.	ID=YLR036C;Name=YLR036C;Alias=
-chrXII	SGD	CDS	222685	223059	.	-	.	ID=YLR037C;Name=YLR037C;Alias=PAU23
-chrXII	SGD	CDS	224921	225172	.	-	.	ID=YLR038C;Name=YLR038C;Alias=COX12
-chrXII	SGD	CDS	225426	228596	.	-	.	ID=YLR039C;Name=YLR039C;Alias=RIC1
-chrXII	SGD	CDS	228908	229582	.	-	.	ID=YLR040C;Name=YLR040C;Alias=AFB1
-chrXII	SGD	CDS	229966	230451	.	-	.	ID=YLR042C;Name=YLR042C;Alias=
-chrXII	SGD	CDS	231702	232013	.	-	.	ID=YLR043C;Name=YLR043C;Alias=TRX1
-chrXII	SGD	CDS	232390	234081	.	-	.	ID=YLR044C;Name=YLR044C;Alias=PDC1
-chrXII	SGD	CDS	235037	237703	.	-	.	ID=YLR045C;Name=YLR045C;Alias=STU2
-chrXII	SGD	CDS	238001	238813	.	-	.	ID=YLR046C;Name=YLR046C;Alias=
-chrXII	SGD	CDS	239347	241407	.	-	.	ID=YLR047C;Name=YLR047C;Alias=FRE8
-chrXII	SGD	CDS	242232	243349	.	+	.	ID=YLR048W;Name=YLR048W;Alias=RPS0B
-chrXII	SGD	CDS	243886	245172	.	-	.	ID=YLR049C;Name=YLR049C;Alias=
-chrXII	SGD	CDS	245587	246072	.	-	.	ID=YLR050C;Name=YLR050C;Alias=
-chrXII	SGD	CDS	246324	246977	.	-	.	ID=YLR051C;Name=YLR051C;Alias=FCF2
-chrXII	SGD	CDS	247201	247953	.	+	.	ID=YLR052W;Name=YLR052W;Alias=IES3
-chrXII	SGD	CDS	248100	248426	.	-	.	ID=YLR053C;Name=YLR053C;Alias=
-chrXII	SGD	CDS	248717	250978	.	-	.	ID=YLR054C;Name=YLR054C;Alias=OSW2
-chrXII	SGD	CDS	251272	253080	.	-	.	ID=YLR055C;Name=YLR055C;Alias=SPT8
-chrXII	SGD	CDS	253861	254958	.	+	.	ID=YLR056W;Name=YLR056W;Alias=ERG3
-chrXII	SGD	CDS	255306	257855	.	+	.	ID=YLR057W;Name=YLR057W;Alias=MNL2
-chrXII	SGD	CDS	257992	259401	.	-	.	ID=YLR058C;Name=YLR058C;Alias=SHM2
-chrXII	SGD	CDS	259738	260547	.	-	.	ID=YLR059C;Name=YLR059C;Alias=REX2
-chrXII	SGD	CDS	260979	262766	.	+	.	ID=YLR060W;Name=YLR060W;Alias=FRS1
-chrXII	SGD	CDS	263194	263948	.	+	.	ID=YLR061W;Name=YLR061W;Alias=RPL22A
-chrXII	SGD	CDS	264157	265254	.	+	.	ID=YLR063W;Name=YLR063W;Alias=BMT6
-chrXII	SGD	CDS	265456	266277	.	+	.	ID=YLR064W;Name=YLR064W;Alias=PER33
-chrXII	SGD	CDS	266373	266918	.	-	.	ID=YLR065C;Name=YLR065C;Alias=ENV10
-chrXII	SGD	CDS	267169	267723	.	+	.	ID=YLR066W;Name=YLR066W;Alias=SPC3
-chrXII	SGD	CDS	267813	270710	.	-	.	ID=YLR067C;Name=YLR067C;Alias=PET309
-chrXII	SGD	CDS	271008	271463	.	+	.	ID=YLR068W;Name=YLR068W;Alias=FYV7
-chrXII	SGD	CDS	271630	273915	.	-	.	ID=YLR069C;Name=YLR069C;Alias=MEF1
-chrXII	SGD	CDS	274141	275211	.	-	.	ID=YLR070C;Name=YLR070C;Alias=XYL2
-chrXII	SGD	CDS	275378	278626	.	-	.	ID=YLR071C;Name=YLR071C;Alias=RGR1
-chrXII	SGD	CDS	278862	280943	.	+	.	ID=YLR072W;Name=YLR072W;Alias=LAM6
-chrXII	SGD	CDS	281019	281621	.	-	.	ID=YLR073C;Name=YLR073C;Alias=RFU1
-chrXII	SGD	CDS	281956	282456	.	-	.	ID=YLR074C;Name=YLR074C;Alias=BUD20
-chrXII	SGD	CDS	282927	283592	.	+	.	ID=YLR075W;Name=YLR075W;Alias=RPL10
-chrXII	SGD	CDS	283872	285623	.	+	.	ID=YLR077W;Name=YLR077W;Alias=FMP25
-chrXII	SGD	CDS	285736	286559	.	-	.	ID=YLR078C;Name=YLR078C;Alias=BOS1
-chrXII	SGD	CDS	286820	287674	.	+	.	ID=YLR079W;Name=YLR079W;Alias=SIC1
-chrXII	SGD	CDS	287916	289250	.	+	.	ID=YLR080W;Name=YLR080W;Alias=EMP46
-chrXII	SGD	CDS	290212	291936	.	+	.	ID=YLR081W;Name=YLR081W;Alias=GAL2
-chrXII	SGD	CDS	292394	293572	.	-	.	ID=YLR082C;Name=YLR082C;Alias=SRL2
-chrXII	SGD	CDS	294091	296094	.	-	.	ID=YLR083C;Name=YLR083C;Alias=EMP70
-chrXII	SGD	CDS	296589	300251	.	-	.	ID=YLR084C;Name=YLR084C;Alias=RAX2
-chrXII	SGD	CDS	300673	301989	.	-	.	ID=YLR085C;Name=YLR085C;Alias=ARP6
-chrXII	SGD	CDS	302243	306499	.	+	.	ID=YLR086W;Name=YLR086W;Alias=SMC4
-chrXII	SGD	CDS	306855	315731	.	-	.	ID=YLR087C;Name=YLR087C;Alias=CSF1
-chrXII	SGD	CDS	316107	317951	.	+	.	ID=YLR088W;Name=YLR088W;Alias=GAA1
-chrXII	SGD	CDS	318237	320015	.	-	.	ID=YLR089C;Name=YLR089C;Alias=ALT1
-chrXII	SGD	CDS	320701	322080	.	+	.	ID=YLR090W;Name=YLR090W;Alias=XDJ1
-chrXII	SGD	CDS	322297	323178	.	+	.	ID=YLR091W;Name=YLR091W;Alias=GEP5
-chrXII	SGD	CDS	323544	326225	.	+	.	ID=YLR092W;Name=YLR092W;Alias=SUL2
-chrXII	SGD	CDS	326513	327415	.	-	.	ID=YLR093C;Name=YLR093C;Alias=NYV1
-chrXII	SGD	CDS	327730	329238	.	-	.	ID=YLR094C;Name=YLR094C;Alias=GIS3
-chrXII	SGD	CDS	329677	332115	.	-	.	ID=YLR095C;Name=YLR095C;Alias=IOC2
-chrXII	SGD	CDS	332590	336033	.	+	.	ID=YLR096W;Name=YLR096W;Alias=KIN2
-chrXII	SGD	CDS	336231	337265	.	-	.	ID=YLR097C;Name=YLR097C;Alias=HRT3
-chrXII	SGD	CDS	337527	339473	.	-	.	ID=YLR098C;Name=YLR098C;Alias=CHA4
-chrXII	SGD	CDS	339744	340928	.	-	.	ID=YLR099C;Name=YLR099C;Alias=ICT1
-chrXII	SGD	CDS	341325	341588	.	+	.	ID=YLR099W-A;Name=YLR099W-A;Alias=MIM2
-chrXII	SGD	CDS	341810	342853	.	+	.	ID=YLR100W;Name=YLR100W;Alias=ERG27
-chrXII	SGD	CDS	342970	343767	.	-	.	ID=YLR102C;Name=YLR102C;Alias=APC9
-chrXII	SGD	CDS	343989	345941	.	-	.	ID=YLR103C;Name=YLR103C;Alias=CDC45
-chrXII	SGD	CDS	346585	346980	.	+	.	ID=YLR104W;Name=YLR104W;Alias=LCL2
-chrXII	SGD	CDS	347047	348180	.	-	.	ID=YLR105C;Name=YLR105C;Alias=SEN2
-chrXII	SGD	CDS	349006	363738	.	-	.	ID=YLR106C;Name=YLR106C;Alias=MDN1
-chrXII	SGD	CDS	364116	365330	.	+	.	ID=YLR107W;Name=YLR107W;Alias=REX3
-chrXII	SGD	CDS	366667	368124	.	-	.	ID=YLR108C;Name=YLR108C;Alias=
-chrXII	SGD	CDS	368781	369311	.	+	.	ID=YLR109W;Name=YLR109W;Alias=AHP1
-chrXII	SGD	CDS	369697	370098	.	-	.	ID=YLR110C;Name=YLR110C;Alias=CCW12
-chrXII	SGD	CDS	371620	372927	.	+	.	ID=YLR113W;Name=YLR113W;Alias=HOG1
-chrXII	SGD	CDS	374944	377238	.	-	.	ID=YLR114C;Name=YLR114C;Alias=AVL9
-chrXII	SGD	CDS	377985	380564	.	+	.	ID=YLR115W;Name=YLR115W;Alias=CFT2
-chrXII	SGD	CDS	380822	382252	.	+	.	ID=YLR116W;Name=YLR116W;Alias=MSL5
-chrXII	SGD	CDS	382471	384534	.	-	.	ID=YLR117C;Name=YLR117C;Alias=CLF1
-chrXII	SGD	CDS	384725	385408	.	-	.	ID=YLR118C;Name=YLR118C;Alias=
-chrXII	SGD	CDS	385534	386175	.	+	.	ID=YLR119W;Name=YLR119W;Alias=SRN2
-chrXII	SGD	CDS	386511	388220	.	-	.	ID=YLR120C;Name=YLR120C;Alias=YPS1
-chrXII	SGD	CDS	388744	390270	.	-	.	ID=YLR121C;Name=YLR121C;Alias=YPS3
-chrXII	SGD	CDS	393484	393894	.	+	.	ID=YLR125W;Name=YLR125W;Alias=
-chrXII	SGD	CDS	394765	395520	.	-	.	ID=YLR126C;Name=YLR126C;Alias=
-chrXII	SGD	CDS	395758	398319	.	-	.	ID=YLR127C;Name=YLR127C;Alias=APC2
-chrXII	SGD	CDS	398530	399433	.	+	.	ID=YLR128W;Name=YLR128W;Alias=DCN1
-chrXII	SGD	CDS	399657	402488	.	+	.	ID=YLR129W;Name=YLR129W;Alias=DIP2
-chrXII	SGD	CDS	402794	404062	.	-	.	ID=YLR130C;Name=YLR130C;Alias=ZRT2
-chrXII	SGD	CDS	404510	406822	.	-	.	ID=YLR131C;Name=YLR131C;Alias=ACE2
-chrXII	SGD	CDS	407283	408155	.	-	.	ID=YLR132C;Name=YLR132C;Alias=USB1
-chrXII	SGD	CDS	408445	410193	.	+	.	ID=YLR133W;Name=YLR133W;Alias=CKI1
-chrXII	SGD	CDS	410723	412414	.	+	.	ID=YLR134W;Name=YLR134W;Alias=PDC5
-chrXII	SGD	CDS	413281	415527	.	+	.	ID=YLR135W;Name=YLR135W;Alias=SLX4
-chrXII	SGD	CDS	415801	416658	.	-	.	ID=YLR136C;Name=YLR136C;Alias=TIS11
-chrXII	SGD	CDS	417006	418109	.	+	.	ID=YLR137W;Name=YLR137W;Alias=RKM5
-chrXII	SGD	CDS	418437	421394	.	+	.	ID=YLR138W;Name=YLR138W;Alias=NHA1
-chrXII	SGD	CDS	421542	423473	.	-	.	ID=YLR139C;Name=YLR139C;Alias=SLS1
-chrXII	SGD	CDS	423683	424774	.	+	.	ID=YLR141W;Name=YLR141W;Alias=RRN5
-chrXII	SGD	CDS	425186	426616	.	+	.	ID=YLR142W;Name=YLR142W;Alias=PUT1
-chrXII	SGD	CDS	427329	429386	.	+	.	ID=YLR143W;Name=YLR143W;Alias=DPH6
-chrXII	SGD	CDS	429677	432016	.	-	.	ID=YLR144C;Name=YLR144C;Alias=ACF2
-chrXII	SGD	CDS	432168	432773	.	+	.	ID=YLR145W;Name=YLR145W;Alias=RMP1
-chrXII	SGD	CDS	432823	433725	.	-	.	ID=YLR146C;Name=YLR146C;Alias=SPE4
-chrXII	SGD	CDS	433870	434058	.	+	.	ID=YLR146W-A;Name=YLR146W-A;Alias=
-chrXII	SGD	CDS	434158	434463	.	-	.	ID=YLR147C;Name=YLR147C;Alias=SMD3
-chrXII	SGD	CDS	434641	437397	.	+	.	ID=YLR148W;Name=YLR148W;Alias=PEP3
-chrXII	SGD	CDS	437631	439823	.	-	.	ID=YLR149C;Name=YLR149C;Alias=
-chrXII	SGD	CDS	440467	441288	.	+	.	ID=YLR150W;Name=YLR150W;Alias=STM1
-chrXII	SGD	CDS	441715	442737	.	-	.	ID=YLR151C;Name=YLR151C;Alias=PCD1
-chrXII	SGD	CDS	442958	444688	.	-	.	ID=YLR152C;Name=YLR152C;Alias=
-chrXII	SGD	CDS	445524	447575	.	-	.	ID=YLR153C;Name=YLR153C;Alias=ACS2
-chrXII	SGD	CDS	447982	448314	.	-	.	ID=YLR154C;Name=YLR154C;Alias=RNH203
-chrXII	SGD	CDS	454696	455070	.	+	.	ID=YLR154W-C;Name=YLR154W-C;Alias=TAR1
-chrXII	SGD	CDS	462522	462671	.	-	.	ID=YLR154C-G;Name=YLR154C-G;Alias=
-chrXII	SGD	CDS	468827	468958	.	-	.	ID=YLR154C-H;Name=YLR154C-H;Alias=
-chrXII	SGD	CDS	469317	470405	.	-	.	ID=YLR155C;Name=YLR155C;Alias=ASP3-1
-chrXII	SGD	CDS	472113	472457	.	+	.	ID=YLR156W;Name=YLR156W;Alias=
-chrXII	SGD	CDS	472479	472610	.	-	.	ID=YLR156C-A;Name=YLR156C-A;Alias=
-chrXII	SGD	CDS	472969	474057	.	-	.	ID=YLR157C;Name=YLR157C;Alias=ASP3-2
-chrXII	SGD	CDS	475764	475976	.	+	.	ID=YLR157W-D;Name=YLR157W-D;Alias=
-chrXII	SGD	CDS	481873	482037	.	+	.	ID=YLR157W-E;Name=YLR157W-E;Alias=
-chrXII	SGD	CDS	482059	482190	.	-	.	ID=YLR157C-C;Name=YLR157C-C;Alias=
-chrXII	SGD	CDS	482549	483637	.	-	.	ID=YLR158C;Name=YLR158C;Alias=ASP3-3
-chrXII	SGD	CDS	485345	485689	.	+	.	ID=YLR159W;Name=YLR159W;Alias=
-chrXII	SGD	CDS	485711	485842	.	-	.	ID=YLR159C-A;Name=YLR159C-A;Alias=
-chrXII	SGD	CDS	486201	487289	.	-	.	ID=YLR160C;Name=YLR160C;Alias=ASP3-4
-chrXII	SGD	CDS	488997	489341	.	+	.	ID=YLR161W;Name=YLR161W;Alias=
-chrXII	SGD	CDS	489573	489929	.	+	.	ID=YLR162W;Name=YLR162W;Alias=
-chrXII	SGD	CDS	490406	490594	.	+	.	ID=YLR162W-A;Name=YLR162W-A;Alias=RRT15
-chrXII	SGD	CDS	491866	493254	.	-	.	ID=YLR163C;Name=YLR163C;Alias=MAS1
-chrXII	SGD	CDS	493883	494389	.	+	.	ID=YLR164W;Name=YLR164W;Alias=SHH4
-chrXII	SGD	CDS	494494	495258	.	-	.	ID=YLR165C;Name=YLR165C;Alias=PUS5
-chrXII	SGD	CDS	495429	498044	.	-	.	ID=YLR166C;Name=YLR166C;Alias=SEC10
-chrXII	SGD	CDS	498947	499405	.	+	.	ID=YLR167W;Name=YLR167W;Alias=RPS31
-chrXII	SGD	CDS	499578	500270	.	-	.	ID=YLR168C;Name=YLR168C;Alias=UPS2
-chrXII	SGD	CDS	500579	501049	.	-	.	ID=YLR170C;Name=YLR170C;Alias=APS1
-chrXII	SGD	CDS	501260	502162	.	-	.	ID=YLR172C;Name=YLR172C;Alias=DPH5
-chrXII	SGD	CDS	502421	504247	.	+	.	ID=YLR173W;Name=YLR173W;Alias=
-chrXII	SGD	CDS	504591	505829	.	+	.	ID=YLR174W;Name=YLR174W;Alias=IDP2
-chrXII	SGD	CDS	506134	507585	.	+	.	ID=YLR175W;Name=YLR175W;Alias=CBF5
-chrXII	SGD	CDS	507797	510232	.	-	.	ID=YLR176C;Name=YLR176C;Alias=RFX1
-chrXII	SGD	CDS	511054	512940	.	+	.	ID=YLR177W;Name=YLR177W;Alias=
-chrXII	SGD	CDS	513162	513821	.	-	.	ID=YLR178C;Name=YLR178C;Alias=TFS1
-chrXII	SGD	CDS	514108	514713	.	-	.	ID=YLR179C;Name=YLR179C;Alias=
-chrXII	SGD	CDS	515262	516410	.	+	.	ID=YLR180W;Name=YLR180W;Alias=SAM1
-chrXII	SGD	CDS	516678	517670	.	-	.	ID=YLR181C;Name=YLR181C;Alias=VTA1
-chrXII	SGD	CDS	517940	520351	.	+	.	ID=YLR182W;Name=YLR182W;Alias=SWI6
-chrXII	SGD	CDS	520543	522012	.	-	.	ID=YLR183C;Name=YLR183C;Alias=TOS4
-chrXII	SGD	CDS	522663	523288	.	+	.	ID=YLR185W;Name=YLR185W;Alias=RPL37A
-chrXII	SGD	CDS	523632	524390	.	+	.	ID=YLR186W;Name=YLR186W;Alias=EMG1
-chrXII	SGD	CDS	524865	527945	.	+	.	ID=YLR187W;Name=YLR187W;Alias=SKG3
-chrXII	SGD	CDS	528300	530387	.	+	.	ID=YLR188W;Name=YLR188W;Alias=MDL1
-chrXII	SGD	CDS	530797	534393	.	-	.	ID=YLR189C;Name=YLR189C;Alias=ATG26
-chrXII	SGD	CDS	535214	536689	.	+	.	ID=YLR190W;Name=YLR190W;Alias=MMR1
-chrXII	SGD	CDS	537272	538432	.	+	.	ID=YLR191W;Name=YLR191W;Alias=PEX13
-chrXII	SGD	CDS	538792	539589	.	-	.	ID=YLR192C;Name=YLR192C;Alias=HCR1
-chrXII	SGD	CDS	540009	540536	.	-	.	ID=YLR193C;Name=YLR193C;Alias=UPS1
-chrXII	SGD	CDS	540809	541573	.	-	.	ID=YLR194C;Name=YLR194C;Alias=NCW2
-chrXII	SGD	CDS	541937	543304	.	-	.	ID=YLR195C;Name=YLR195C;Alias=NMT1
-chrXII	SGD	CDS	543968	545698	.	+	.	ID=YLR196W;Name=YLR196W;Alias=PWP1
-chrXII	SGD	CDS	546097	547611	.	+	.	ID=YLR197W;Name=YLR197W;Alias=NOP56
-chrXII	SGD	CDS	547853	548769	.	-	.	ID=YLR199C;Name=YLR199C;Alias=PBA1
-chrXII	SGD	CDS	549012	549356	.	+	.	ID=YLR200W;Name=YLR200W;Alias=YKE2
-chrXII	SGD	CDS	549511	550293	.	-	.	ID=YLR201C;Name=YLR201C;Alias=COQ9
-chrXII	SGD	CDS	550650	551960	.	-	.	ID=YLR203C;Name=YLR203C;Alias=MSS51
-chrXII	SGD	CDS	552270	552605	.	+	.	ID=YLR204W;Name=YLR204W;Alias=QRI5
-chrXII	SGD	CDS	552724	553677	.	-	.	ID=YLR205C;Name=YLR205C;Alias=HMX1
-chrXII	SGD	CDS	554578	556419	.	+	.	ID=YLR206W;Name=YLR206W;Alias=ENT2
-chrXII	SGD	CDS	556788	559289	.	+	.	ID=YLR207W;Name=YLR207W;Alias=HRD3
-chrXII	SGD	CDS	559551	560444	.	+	.	ID=YLR208W;Name=YLR208W;Alias=SEC13
-chrXII	SGD	CDS	560797	561732	.	-	.	ID=YLR209C;Name=YLR209C;Alias=PNP1
-chrXII	SGD	CDS	562008	563390	.	+	.	ID=YLR210W;Name=YLR210W;Alias=CLB4
-chrXII	SGD	CDS	563792	564531	.	-	.	ID=YLR211C;Name=YLR211C;Alias=ATG38
-chrXII	SGD	CDS	564860	566281	.	-	.	ID=YLR212C;Name=YLR212C;Alias=TUB4
-chrXII	SGD	CDS	566654	567922	.	-	.	ID=YLR213C;Name=YLR213C;Alias=CRR1
-chrXII	SGD	CDS	568567	570627	.	+	.	ID=YLR214W;Name=YLR214W;Alias=FRE1
-chrXII	SGD	CDS	570776	571858	.	-	.	ID=YLR215C;Name=YLR215C;Alias=CDC123
-chrXII	SGD	CDS	572096	573211	.	-	.	ID=YLR216C;Name=YLR216C;Alias=CPR6
-chrXII	SGD	CDS	573466	573918	.	-	.	ID=YLR218C;Name=YLR218C;Alias=COA4
-chrXII	SGD	CDS	574151	576337	.	+	.	ID=YLR219W;Name=YLR219W;Alias=MSC3
-chrXII	SGD	CDS	576825	577793	.	+	.	ID=YLR220W;Name=YLR220W;Alias=CCC1
-chrXII	SGD	CDS	578362	579024	.	-	.	ID=YLR221C;Name=YLR221C;Alias=RSA3
-chrXII	SGD	CDS	579318	581771	.	-	.	ID=YLR222C;Name=YLR222C;Alias=UTP13
-chrXII	SGD	CDS	582233	585490	.	-	.	ID=YLR223C;Name=YLR223C;Alias=IFH1
-chrXII	SGD	CDS	586464	587573	.	+	.	ID=YLR224W;Name=YLR224W;Alias=UCC1
-chrXII	SGD	CDS	587695	588918	.	-	.	ID=YLR225C;Name=YLR225C;Alias=
-chrXII	SGD	CDS	589354	590541	.	+	.	ID=YLR226W;Name=YLR226W;Alias=BUR2
-chrXII	SGD	CDS	590562	592043	.	-	.	ID=YLR227C;Name=YLR227C;Alias=ADY4
-chrXII	SGD	CDS	600019	602463	.	-	.	ID=YLR228C;Name=YLR228C;Alias=ECM22
-chrXII	SGD	CDS	604212	604787	.	-	.	ID=YLR229C;Name=YLR229C;Alias=CDC42
-chrXII	SGD	CDS	605758	607119	.	-	.	ID=YLR231C;Name=YLR231C;Alias=BNA5
-chrXII	SGD	CDS	607425	609524	.	-	.	ID=YLR233C;Name=YLR233C;Alias=EST1
-chrXII	SGD	CDS	609783	611753	.	+	.	ID=YLR234W;Name=YLR234W;Alias=TOP3
-chrXII	SGD	CDS	612367	614163	.	+	.	ID=YLR237W;Name=YLR237W;Alias=THI7
-chrXII	SGD	CDS	614755	616191	.	+	.	ID=YLR238W;Name=YLR238W;Alias=FAR10
-chrXII	SGD	CDS	616332	617318	.	-	.	ID=YLR239C;Name=YLR239C;Alias=LIP2
-chrXII	SGD	CDS	617533	620160	.	+	.	ID=YLR240W;Name=YLR240W;Alias=VPS34
-chrXII	SGD	CDS	620473	622821	.	+	.	ID=YLR241W;Name=YLR241W;Alias=CSC1
-chrXII	SGD	CDS	622918	623883	.	-	.	ID=YLR242C;Name=YLR242C;Alias=ARV1
-chrXII	SGD	CDS	624203	625021	.	+	.	ID=YLR243W;Name=YLR243W;Alias=GPN3
-chrXII	SGD	CDS	625168	626331	.	-	.	ID=YLR244C;Name=YLR244C;Alias=MAP1
-chrXII	SGD	CDS	626502	626930	.	-	.	ID=YLR245C;Name=YLR245C;Alias=CDD1
-chrXII	SGD	CDS	627118	628197	.	+	.	ID=YLR246W;Name=YLR246W;Alias=ERF2
-chrXII	SGD	CDS	628684	633354	.	-	.	ID=YLR247C;Name=YLR247C;Alias=IRC20
-chrXII	SGD	CDS	634252	636084	.	+	.	ID=YLR248W;Name=YLR248W;Alias=RCK2
-chrXII	SGD	CDS	636780	639914	.	+	.	ID=YLR249W;Name=YLR249W;Alias=YEF3
-chrXII	SGD	CDS	640317	641021	.	+	.	ID=YLR250W;Name=YLR250W;Alias=SSP120
-chrXII	SGD	CDS	641464	642057	.	+	.	ID=YLR251W;Name=YLR251W;Alias=SYM1
-chrXII	SGD	CDS	642627	644336	.	+	.	ID=YLR253W;Name=YLR253W;Alias=MCP2
-chrXII	SGD	CDS	644404	644973	.	-	.	ID=YLR254C;Name=YLR254C;Alias=NDL1
-chrXII	SGD	CDS	646415	650923	.	+	.	ID=YLR256W;Name=YLR256W;Alias=HAP1
-chrXII	SGD	CDS	658826	659791	.	+	.	ID=YLR257W;Name=YLR257W;Alias=
-chrXII	SGD	CDS	660716	662833	.	+	.	ID=YLR258W;Name=YLR258W;Alias=GSY2
-chrXII	SGD	CDS	663284	665002	.	-	.	ID=YLR259C;Name=YLR259C;Alias=HSP60
-chrXII	SGD	CDS	665844	667907	.	+	.	ID=YLR260W;Name=YLR260W;Alias=LCB5
-chrXII	SGD	CDS	668237	668563	.	-	.	ID=YLR261C;Name=YLR261C;Alias=VPS63
-chrXII	SGD	CDS	668244	668891	.	-	.	ID=YLR262C;Name=YLR262C;Alias=YPT6
-chrXII	SGD	CDS	669468	669662	.	-	.	ID=YLR262C-A;Name=YLR262C-A;Alias=TMA7
-chrXII	SGD	CDS	670340	672823	.	+	.	ID=YLR263W;Name=YLR263W;Alias=RED1
-chrXII	SGD	CDS	673131	673334	.	+	.	ID=YLR264W;Name=YLR264W;Alias=RPS28B
-chrXII	SGD	CDS	673828	673944	.	-	.	ID=YLR264C-A;Name=YLR264C-A;Alias=
-chrXII	SGD	CDS	674427	675455	.	-	.	ID=YLR265C;Name=YLR265C;Alias=NEJ1
-chrXII	SGD	CDS	675619	677724	.	-	.	ID=YLR266C;Name=YLR266C;Alias=PDR8
-chrXII	SGD	CDS	678212	679924	.	+	.	ID=YLR267W;Name=YLR267W;Alias=BOP2
-chrXII	SGD	CDS	680200	680844	.	+	.	ID=YLR268W;Name=YLR268W;Alias=SEC22
-chrXII	SGD	CDS	681186	682238	.	+	.	ID=YLR270W;Name=YLR270W;Alias=DCS1
-chrXII	SGD	CDS	682737	683561	.	+	.	ID=YLR271W;Name=YLR271W;Alias=CMG1
-chrXII	SGD	CDS	683672	687202	.	-	.	ID=YLR272C;Name=YLR272C;Alias=YCS4
-chrXII	SGD	CDS	689083	691029	.	-	.	ID=YLR273C;Name=YLR273C;Alias=PIG1
-chrXII	SGD	CDS	691555	693882	.	+	.	ID=YLR274W;Name=YLR274W;Alias=MCM5
-chrXII	SGD	CDS	694378	694800	.	+	.	ID=YLR275W;Name=YLR275W;Alias=SMD2
-chrXII	SGD	CDS	695046	696830	.	-	.	ID=YLR276C;Name=YLR276C;Alias=DBP9
-chrXII	SGD	CDS	697156	699495	.	-	.	ID=YLR277C;Name=YLR277C;Alias=YSH1
-chrXII	SGD	CDS	699999	704024	.	-	.	ID=YLR278C;Name=YLR278C;Alias=
-chrXII	SGD	CDS	704493	704960	.	-	.	ID=YLR281C;Name=YLR281C;Alias=
-chrXII	SGD	CDS	705186	706130	.	+	.	ID=YLR283W;Name=YLR283W;Alias=
-chrXII	SGD	CDS	706198	707040	.	-	.	ID=YLR284C;Name=YLR284C;Alias=ECI1
-chrXII	SGD	CDS	707360	708145	.	+	.	ID=YLR285W;Name=YLR285W;Alias=NNT1
-chrXII	SGD	CDS	708168	708338	.	-	.	ID=YLR285C-A;Name=YLR285C-A;Alias=
-chrXII	SGD	CDS	708448	710136	.	-	.	ID=YLR286C;Name=YLR286C;Alias=CTS1
-chrXII	SGD	CDS	710991	712058	.	-	.	ID=YLR287C;Name=YLR287C;Alias=
-chrXII	SGD	CDS	712537	713158	.	-	.	ID=YLR287C-A;Name=YLR287C-A;Alias=RPS30A
-chrXII	SGD	CDS	713480	714904	.	-	.	ID=YLR288C;Name=YLR288C;Alias=MEC3
-chrXII	SGD	CDS	715089	717026	.	+	.	ID=YLR289W;Name=YLR289W;Alias=GUF1
-chrXII	SGD	CDS	717145	717978	.	-	.	ID=YLR290C;Name=YLR290C;Alias=COQ11
-chrXII	SGD	CDS	718317	719462	.	-	.	ID=YLR291C;Name=YLR291C;Alias=GCD7
-chrXII	SGD	CDS	719789	720370	.	-	.	ID=YLR292C;Name=YLR292C;Alias=SEC72
-chrXII	SGD	CDS	720771	721430	.	-	.	ID=YLR293C;Name=YLR293C;Alias=GSP1
-chrXII	SGD	CDS	721999	722373	.	-	.	ID=YLR295C;Name=YLR295C;Alias=ATP14
-chrXII	SGD	CDS	724044	724433	.	+	.	ID=YLR297W;Name=YLR297W;Alias=
-chrXII	SGD	CDS	724721	725416	.	-	.	ID=YLR298C;Name=YLR298C;Alias=YHC1
-chrXII	SGD	CDS	726069	728051	.	+	.	ID=YLR299W;Name=YLR299W;Alias=ECM38
-chrXII	SGD	CDS	728955	730301	.	+	.	ID=YLR300W;Name=YLR300W;Alias=EXG1
-chrXII	SGD	CDS	730825	731559	.	+	.	ID=YLR301W;Name=YLR301W;Alias=HRI1
-chrXII	SGD	CDS	732542	733876	.	+	.	ID=YLR303W;Name=YLR303W;Alias=MET17
-chrXII	SGD	CDS	735212	737548	.	-	.	ID=YLR304C;Name=YLR304C;Alias=ACO1
-chrXII	SGD	CDS	738161	743863	.	-	.	ID=YLR305C;Name=YLR305C;Alias=STT4
-chrXII	SGD	CDS	744151	744851	.	+	.	ID=YLR306W;Name=YLR306W;Alias=UBC12
-chrXII	SGD	CDS	745620	746525	.	+	.	ID=YLR307W;Name=YLR307W;Alias=CDA1
-chrXII	SGD	CDS	746848	747111	.	-	.	ID=YLR307C-A;Name=YLR307C-A;Alias=
-chrXII	SGD	CDS	747937	748875	.	+	.	ID=YLR308W;Name=YLR308W;Alias=CDA2
-chrXII	SGD	CDS	749034	751769	.	-	.	ID=YLR309C;Name=YLR309C;Alias=IMH1
-chrXII	SGD	CDS	752224	756993	.	-	.	ID=YLR310C;Name=YLR310C;Alias=CDC25
-chrXII	SGD	CDS	757637	758833	.	-	.	ID=YLR312C;Name=YLR312C;Alias=ATG39
-chrXII	SGD	CDS	759480	760241	.	+	.	ID=YLR312W-A;Name=YLR312W-A;Alias=MRPL15
-chrXII	SGD	CDS	760750	762342	.	-	.	ID=YLR313C;Name=YLR313C;Alias=SPH1
-chrXII	SGD	CDS	762575	764137	.	-	.	ID=YLR314C;Name=YLR314C;Alias=CDC3
-chrXII	SGD	CDS	764808	765269	.	+	.	ID=YLR315W;Name=YLR315W;Alias=NKP2
-chrXII	SGD	CDS	765266	766358	.	-	.	ID=YLR316C;Name=YLR316C;Alias=TAD3
-chrXII	SGD	CDS	766542	769196	.	+	.	ID=YLR318W;Name=YLR318W;Alias=EST2
-chrXII	SGD	CDS	769318	771684	.	-	.	ID=YLR319C;Name=YLR319C;Alias=BUD6
-chrXII	SGD	CDS	771940	776304	.	+	.	ID=YLR320W;Name=YLR320W;Alias=MMS22
-chrXII	SGD	CDS	776584	777864	.	-	.	ID=YLR321C;Name=YLR321C;Alias=SFH1
-chrXII	SGD	CDS	778173	778952	.	-	.	ID=YLR323C;Name=YLR323C;Alias=CWC24
-chrXII	SGD	CDS	779215	780786	.	+	.	ID=YLR324W;Name=YLR324W;Alias=PEX30
-chrXII	SGD	CDS	781143	781379	.	-	.	ID=YLR325C;Name=YLR325C;Alias=RPL38
-chrXII	SGD	CDS	782174	782896	.	+	.	ID=YLR326W;Name=YLR326W;Alias=
-chrXII	SGD	CDS	783127	783387	.	-	.	ID=YLR327C;Name=YLR327C;Alias=TMA10
-chrXII	SGD	CDS	784913	786118	.	+	.	ID=YLR328W;Name=YLR328W;Alias=NMA1
-chrXII	SGD	CDS	786442	787333	.	+	.	ID=YLR329W;Name=YLR329W;Alias=REC102
-chrXII	SGD	CDS	787664	789679	.	+	.	ID=YLR330W;Name=YLR330W;Alias=CHS5
-chrXII	SGD	CDS	790676	791806	.	+	.	ID=YLR332W;Name=YLR332W;Alias=MID2
-chrXII	SGD	CDS	795573	796335	.	-	.	ID=YLR333C;Name=YLR333C;Alias=RPS25B
-chrXII	SGD	CDS	797430	799592	.	+	.	ID=YLR335W;Name=YLR335W;Alias=NUP2
-chrXII	SGD	CDS	799697	802396	.	-	.	ID=YLR336C;Name=YLR336C;Alias=SGD1
-chrXII	SGD	CDS	802653	805106	.	-	.	ID=YLR337C;Name=YLR337C;Alias=VRP1
-chrXII	SGD	CDS	805887	806825	.	+	.	ID=YLR340W;Name=YLR340W;Alias=RPP0
-chrXII	SGD	CDS	807385	808818	.	+	.	ID=YLR341W;Name=YLR341W;Alias=SPO77
-chrXII	SGD	CDS	809997	815627	.	+	.	ID=YLR342W;Name=YLR342W;Alias=FKS1
-chrXII	SGD	CDS	815810	815983	.	+	.	ID=YLR342W-A;Name=YLR342W-A;Alias=
-chrXII	SGD	CDS	816094	817761	.	+	.	ID=YLR343W;Name=YLR343W;Alias=GAS2
-chrXII	SGD	CDS	819312	820142	.	+	.	ID=YLR344W;Name=YLR344W;Alias=RPL26A
-chrXII	SGD	CDS	820511	822040	.	+	.	ID=YLR345W;Name=YLR345W;Alias=
-chrXII	SGD	CDS	822287	822592	.	-	.	ID=YLR346C;Name=YLR346C;Alias=CIS1
-chrXII	SGD	CDS	823828	826413	.	-	.	ID=YLR347C;Name=YLR347C;Alias=KAP95
-chrXII	SGD	CDS	826977	827873	.	-	.	ID=YLR348C;Name=YLR348C;Alias=DIC1
-chrXII	SGD	CDS	828730	829380	.	+	.	ID=YLR350W;Name=YLR350W;Alias=ORM2
-chrXII	SGD	CDS	829489	830364	.	-	.	ID=YLR351C;Name=YLR351C;Alias=NIT3
-chrXII	SGD	CDS	831116	833539	.	+	.	ID=YLR352W;Name=YLR352W;Alias=
-chrXII	SGD	CDS	834352	836163	.	+	.	ID=YLR353W;Name=YLR353W;Alias=BUD8
-chrXII	SGD	CDS	836350	837357	.	-	.	ID=YLR354C;Name=YLR354C;Alias=TAL1
-chrXII	SGD	CDS	838066	839253	.	-	.	ID=YLR355C;Name=YLR355C;Alias=ILV5
-chrXII	SGD	CDS	840321	840914	.	+	.	ID=YLR356W;Name=YLR356W;Alias=ATG33
-chrXII	SGD	CDS	841331	844000	.	+	.	ID=YLR357W;Name=YLR357W;Alias=RSC2
-chrXII	SGD	CDS	843487	844050	.	-	.	ID=YLR358C;Name=YLR358C;Alias=
-chrXII	SGD	CDS	844282	845730	.	+	.	ID=YLR359W;Name=YLR359W;Alias=ADE13
-chrXII	SGD	CDS	846103	847422	.	+	.	ID=YLR360W;Name=YLR360W;Alias=VPS38
-chrXII	SGD	CDS	847388	849124	.	-	.	ID=YLR361C;Name=YLR361C;Alias=DCR2
-chrXII	SGD	CDS	849383	849679	.	-	.	ID=YLR361C-A;Name=YLR361C-A;Alias=
-chrXII	SGD	CDS	849866	852019	.	+	.	ID=YLR362W;Name=YLR362W;Alias=STE11
-chrXII	SGD	CDS	852495	853151	.	-	.	ID=YLR363C;Name=YLR363C;Alias=NMD4
-chrXII	SGD	CDS	853461	853718	.	+	.	ID=YLR363W-A;Name=YLR363W-A;Alias=
-chrXII	SGD	CDS	854062	854391	.	+	.	ID=YLR364W;Name=YLR364W;Alias=GRX8
-chrXII	SGD	CDS	855878	857317	.	+	.	ID=YLR367W;Name=YLR367W;Alias=RPS22B
-chrXII	SGD	CDS	857540	859336	.	+	.	ID=YLR368W;Name=YLR368W;Alias=MDM30
-chrXII	SGD	CDS	859552	861525	.	+	.	ID=YLR369W;Name=YLR369W;Alias=SSQ1
-chrXII	SGD	CDS	861718	862254	.	-	.	ID=YLR370C;Name=YLR370C;Alias=ARC18
-chrXII	SGD	CDS	862714	866784	.	+	.	ID=YLR371W;Name=YLR371W;Alias=ROM2
-chrXII	SGD	CDS	867354	868391	.	+	.	ID=YLR372W;Name=YLR372W;Alias=ELO3
-chrXII	SGD	CDS	868662	871367	.	-	.	ID=YLR373C;Name=YLR373C;Alias=VID22
-chrXII	SGD	CDS	871697	872728	.	+	.	ID=YLR375W;Name=YLR375W;Alias=STP3
-chrXII	SGD	CDS	872826	873554	.	-	.	ID=YLR376C;Name=YLR376C;Alias=PSY3
-chrXII	SGD	CDS	873746	874792	.	-	.	ID=YLR377C;Name=YLR377C;Alias=FBP1
-chrXII	SGD	CDS	875736	877178	.	-	.	ID=YLR378C;Name=YLR378C;Alias=SEC61
-chrXII	SGD	CDS	878282	879508	.	+	.	ID=YLR380W;Name=YLR380W;Alias=CSR1
-chrXII	SGD	CDS	879723	881924	.	+	.	ID=YLR381W;Name=YLR381W;Alias=CTF3
-chrXII	SGD	CDS	882067	884751	.	-	.	ID=YLR382C;Name=YLR382C;Alias=NAM2
-chrXII	SGD	CDS	885288	888632	.	+	.	ID=YLR383W;Name=YLR383W;Alias=SMC6
-chrXII	SGD	CDS	888851	892900	.	-	.	ID=YLR384C;Name=YLR384C;Alias=IKI3
-chrXII	SGD	CDS	892992	893390	.	-	.	ID=YLR385C;Name=YLR385C;Alias=SWC7
-chrXII	SGD	CDS	893628	896270	.	+	.	ID=YLR386W;Name=YLR386W;Alias=VAC14
-chrXII	SGD	CDS	896374	897672	.	-	.	ID=YLR387C;Name=YLR387C;Alias=REH1
-chrXII	SGD	CDS	898158	898821	.	+	.	ID=YLR388W;Name=YLR388W;Alias=RPS29A
-chrXII	SGD	CDS	899577	902660	.	-	.	ID=YLR389C;Name=YLR389C;Alias=STE23
-chrXII	SGD	CDS	903066	903404	.	+	.	ID=YLR390W;Name=YLR390W;Alias=ECM19
-chrXII	SGD	CDS	903724	904440	.	+	.	ID=YLR390W-A;Name=YLR390W-A;Alias=CCW14
-chrXII	SGD	CDS	904749	906305	.	-	.	ID=YLR392C;Name=YLR392C;Alias=ART10
-chrXII	SGD	CDS	907079	907918	.	+	.	ID=YLR393W;Name=YLR393W;Alias=ATP10
-chrXII	SGD	CDS	907950	909398	.	+	.	ID=YLR394W;Name=YLR394W;Alias=CST9
-chrXII	SGD	CDS	909729	909965	.	-	.	ID=YLR395C;Name=YLR395C;Alias=COX8
-chrXII	SGD	CDS	910235	912310	.	-	.	ID=YLR396C;Name=YLR396C;Alias=VPS33
-chrXII	SGD	CDS	912550	914892	.	-	.	ID=YLR397C;Name=YLR397C;Alias=AFG2
-chrXII	SGD	CDS	915156	919019	.	-	.	ID=YLR398C;Name=YLR398C;Alias=SKI2
-chrXII	SGD	CDS	919536	921596	.	-	.	ID=YLR399C;Name=YLR399C;Alias=BDF1
-chrXII	SGD	CDS	922442	924448	.	-	.	ID=YLR401C;Name=YLR401C;Alias=DUS3
-chrXII	SGD	CDS	925568	927619	.	+	.	ID=YLR403W;Name=YLR403W;Alias=SFP1
-chrXII	SGD	CDS	928743	929600	.	+	.	ID=YLR404W;Name=YLR404W;Alias=SEI1
-chrXII	SGD	CDS	929789	930892	.	+	.	ID=YLR405W;Name=YLR405W;Alias=DUS4
-chrXII	SGD	CDS	931065	931755	.	-	.	ID=YLR406C;Name=YLR406C;Alias=RPL31B
-chrXII	SGD	CDS	932206	932355	.	-	.	ID=YLR406C-A;Name=YLR406C-A;Alias=
-chrXII	SGD	CDS	932967	933653	.	+	.	ID=YLR407W;Name=YLR407W;Alias=
-chrXII	SGD	CDS	933885	934253	.	-	.	ID=YLR408C;Name=YLR408C;Alias=BLS1
-chrXII	SGD	CDS	934414	937233	.	-	.	ID=YLR409C;Name=YLR409C;Alias=UTP21
-chrXII	SGD	CDS	937541	940981	.	+	.	ID=YLR410W;Name=YLR410W;Alias=VIP1
-chrXII	SGD	CDS	947253	947978	.	+	.	ID=YLR411W;Name=YLR411W;Alias=CTR3
-chrXII	SGD	CDS	948368	949192	.	+	.	ID=YLR412W;Name=YLR412W;Alias=BER1
-chrXII	SGD	CDS	950267	950473	.	-	.	ID=YLR412C-A;Name=YLR412C-A;Alias=
-chrXII	SGD	CDS	951156	953183	.	+	.	ID=YLR413W;Name=YLR413W;Alias=INA1
-chrXII	SGD	CDS	953353	954144	.	-	.	ID=YLR414C;Name=YLR414C;Alias=PUN1
-chrXII	SGD	CDS	954259	954597	.	-	.	ID=YLR415C;Name=YLR415C;Alias=
-chrXII	SGD	CDS	955010	956710	.	+	.	ID=YLR417W;Name=YLR417W;Alias=VPS36
-chrXII	SGD	CDS	956914	958095	.	-	.	ID=YLR418C;Name=YLR418C;Alias=CDC73
-chrXII	SGD	CDS	958428	962735	.	+	.	ID=YLR419W;Name=YLR419W;Alias=
-chrXII	SGD	CDS	963785	964879	.	+	.	ID=YLR420W;Name=YLR420W;Alias=URA4
-chrXII	SGD	CDS	965090	965560	.	-	.	ID=YLR421C;Name=YLR421C;Alias=RPN13
-chrXII	SGD	CDS	965897	971695	.	+	.	ID=YLR422W;Name=YLR422W;Alias=DCK1
-chrXII	SGD	CDS	971917	973170	.	-	.	ID=YLR423C;Name=YLR423C;Alias=ATG17
-chrXII	SGD	CDS	973395	975521	.	+	.	ID=YLR424W;Name=YLR424W;Alias=SPP382
-chrXII	SGD	CDS	982894	986817	.	+	.	ID=YLR425W;Name=YLR425W;Alias=TUS1
-chrXII	SGD	CDS	987062	988113	.	+	.	ID=YLR426W;Name=YLR426W;Alias=TDA5
-chrXII	SGD	CDS	988428	990440	.	+	.	ID=YLR427W;Name=YLR427W;Alias=MAG2
-chrXII	SGD	CDS	990777	992732	.	+	.	ID=YLR429W;Name=YLR429W;Alias=CRN1
-chrXII	SGD	CDS	993434	1000129	.	+	.	ID=YLR430W;Name=YLR430W;Alias=SEN1
-chrXII	SGD	CDS	1000342	1001703	.	-	.	ID=YLR431C;Name=YLR431C;Alias=ATG23
-chrXII	SGD	CDS	1002557	1004128	.	+	.	ID=YLR432W;Name=YLR432W;Alias=IMD3
-chrXII	SGD	CDS	1004347	1006008	.	-	.	ID=YLR433C;Name=YLR433C;Alias=CNA1
-chrXII	SGD	CDS	1006378	1006995	.	+	.	ID=YLR435W;Name=YLR435W;Alias=TSR2
-chrXII	SGD	CDS	1007421	1011245	.	-	.	ID=YLR436C;Name=YLR436C;Alias=ECM30
-chrXII	SGD	CDS	1011622	1012023	.	-	.	ID=YLR437C;Name=YLR437C;Alias=DIF1
-chrXII	SGD	CDS	1012501	1013775	.	+	.	ID=YLR438W;Name=YLR438W;Alias=CAR2
-chrXII	SGD	CDS	1013909	1014178	.	-	.	ID=YLR438C-A;Name=YLR438C-A;Alias=LSM3
-chrXII	SGD	CDS	1014491	1015450	.	+	.	ID=YLR439W;Name=YLR439W;Alias=MRPL4
-chrXII	SGD	CDS	1015568	1017697	.	-	.	ID=YLR440C;Name=YLR440C;Alias=SEC39
-chrXII	SGD	CDS	1018141	1018908	.	-	.	ID=YLR441C;Name=YLR441C;Alias=RPS1A
-chrXII	SGD	CDS	1019315	1022251	.	-	.	ID=YLR442C;Name=YLR442C;Alias=SIR3
-chrXII	SGD	CDS	1022625	1023971	.	+	.	ID=YLR443W;Name=YLR443W;Alias=ECM7
-chrXII	SGD	CDS	1024189	1024837	.	+	.	ID=YLR445W;Name=YLR445W;Alias=GMC2
-chrXII	SGD	CDS	1025214	1026515	.	+	.	ID=YLR446W;Name=YLR446W;Alias=
-chrXII	SGD	CDS	1026856	1027893	.	-	.	ID=YLR447C;Name=YLR447C;Alias=VMA6
-chrXII	SGD	CDS	1028854	1029768	.	+	.	ID=YLR448W;Name=YLR448W;Alias=RPL6B
-chrXII	SGD	CDS	1030834	1032012	.	+	.	ID=YLR449W;Name=YLR449W;Alias=FPR4
-chrXII	SGD	CDS	1032627	1035764	.	+	.	ID=YLR450W;Name=YLR450W;Alias=HMG2
-chrXII	SGD	CDS	1036093	1038753	.	+	.	ID=YLR451W;Name=YLR451W;Alias=LEU3
-chrXII	SGD	CDS	1039270	1041366	.	-	.	ID=YLR452C;Name=YLR452C;Alias=SST2
-chrXII	SGD	CDS	1041799	1042986	.	-	.	ID=YLR453C;Name=YLR453C;Alias=RIF2
-chrXII	SGD	CDS	1043998	1051884	.	+	.	ID=YLR454W;Name=YLR454W;Alias=FMP27
-chrXII	SGD	CDS	1053629	1054543	.	+	.	ID=YLR455W;Name=YLR455W;Alias=PDP3
-chrXII	SGD	CDS	1055070	1055684	.	+	.	ID=YLR456W;Name=YLR456W;Alias=
-chrXII	SGD	CDS	1055812	1056771	.	-	.	ID=YLR457C;Name=YLR457C;Alias=NBP1
-chrXII	SGD	CDS	1057334	1058518	.	+	.	ID=YLR459W;Name=YLR459W;Alias=GAB1
-chrXII	SGD	CDS	1059757	1060887	.	-	.	ID=YLR460C;Name=YLR460C;Alias=
-chrXII	SGD	CDS	1062919	1063281	.	+	.	ID=YLR461W;Name=YLR461W;Alias=PAU4
-chrXII	SGD	CDS	1065956	1066564	.	+	.	ID=YLR462W;Name=YLR462W;Alias=
-chrXII	SGD	CDS	1066572	1067501	.	+	.	ID=YLR464W;Name=YLR464W;Alias=
-chrXII	SGD	CDS	1067087	1071235	.	+	.	ID=YLR466W;Name=YLR466W;Alias=YRF1-4
-chrXII	SGD	CDS	1072508	1077898	.	+	.	ID=YLR467W;Name=YLR467W;Alias=YRF1-5
-chrXIII	SGD	CDS	461	4684	.	-	.	ID=YML133C;Name=YML133C;Alias=
-chrXIII	SGD	CDS	7244	8383	.	+	.	ID=YML132W;Name=YML132W;Alias=COS3
-chrXIII	SGD	CDS	10198	11295	.	+	.	ID=YML131W;Name=YML131W;Alias=
-chrXIII	SGD	CDS	11483	13174	.	-	.	ID=YML130C;Name=YML130C;Alias=ERO1
-chrXIII	SGD	CDS	14541	14753	.	-	.	ID=YML129C;Name=YML129C;Alias=COX14
-chrXIII	SGD	CDS	15135	16676	.	-	.	ID=YML128C;Name=YML128C;Alias=MSC1
-chrXIII	SGD	CDS	17064	18809	.	+	.	ID=YML127W;Name=YML127W;Alias=RSC9
-chrXIII	SGD	CDS	19060	20535	.	-	.	ID=YML126C;Name=YML126C;Alias=ERG13
-chrXIII	SGD	CDS	20761	21699	.	-	.	ID=YML125C;Name=YML125C;Alias=PGA3
-chrXIII	SGD	CDS	22048	23683	.	-	.	ID=YML124C;Name=YML124C;Alias=TUB3
-chrXIII	SGD	CDS	24037	25800	.	-	.	ID=YML123C;Name=YML123C;Alias=PHO84
-chrXIII	SGD	CDS	26930	27862	.	+	.	ID=YML121W;Name=YML121W;Alias=GTR1
-chrXIII	SGD	CDS	28266	29807	.	-	.	ID=YML120C;Name=YML120C;Alias=NDI1
-chrXIII	SGD	CDS	30611	31684	.	+	.	ID=YML119W;Name=YML119W;Alias=
-chrXIII	SGD	CDS	32334	33851	.	+	.	ID=YML118W;Name=YML118W;Alias=NGL3
-chrXIII	SGD	CDS	34243	37647	.	+	.	ID=YML117W;Name=YML117W;Alias=NAB6
-chrXIII	SGD	CDS	38196	39824	.	+	.	ID=YML116W;Name=YML116W;Alias=ATR1
-chrXIII	SGD	CDS	40187	41794	.	-	.	ID=YML115C;Name=YML115C;Alias=VAN1
-chrXIII	SGD	CDS	42043	43575	.	-	.	ID=YML114C;Name=YML114C;Alias=TAF8
-chrXIII	SGD	CDS	44045	44791	.	+	.	ID=YML113W;Name=YML113W;Alias=DAT1
-chrXIII	SGD	CDS	45063	45953	.	+	.	ID=YML112W;Name=YML112W;Alias=CTK3
-chrXIII	SGD	CDS	46942	49704	.	+	.	ID=YML111W;Name=YML111W;Alias=BUL2
-chrXIII	SGD	CDS	50031	50954	.	-	.	ID=YML110C;Name=YML110C;Alias=COQ5
-chrXIII	SGD	CDS	51640	54468	.	+	.	ID=YML109W;Name=YML109W;Alias=ZDS2
-chrXIII	SGD	CDS	54793	55110	.	+	.	ID=YML108W;Name=YML108W;Alias=
-chrXIII	SGD	CDS	55265	56269	.	-	.	ID=YML107C;Name=YML107C;Alias=PML39
-chrXIII	SGD	CDS	56773	57453	.	+	.	ID=YML106W;Name=YML106W;Alias=URA5
-chrXIII	SGD	CDS	57866	58687	.	-	.	ID=YML105C;Name=YML105C;Alias=SEC65
-chrXIII	SGD	CDS	58939	62322	.	-	.	ID=YML104C;Name=YML104C;Alias=MDM1
-chrXIII	SGD	CDS	62582	67549	.	-	.	ID=YML103C;Name=YML103C;Alias=NUP188
-chrXIII	SGD	CDS	68294	69700	.	+	.	ID=YML102W;Name=YML102W;Alias=CAC2
-chrXIII	SGD	CDS	69735	70088	.	-	.	ID=YML101C;Name=YML101C;Alias=CUE4
-chrXIII	SGD	CDS	70138	70311	.	+	.	ID=YML100W-A;Name=YML100W-A;Alias=
-chrXIII	SGD	CDS	70624	73920	.	+	.	ID=YML100W;Name=YML100W;Alias=TSL1
-chrXIII	SGD	CDS	74398	77040	.	-	.	ID=YML099C;Name=YML099C;Alias=ARG81
-chrXIII	SGD	CDS	77267	77770	.	+	.	ID=YML098W;Name=YML098W;Alias=TAF13
-chrXIII	SGD	CDS	78335	79690	.	-	.	ID=YML097C;Name=YML097C;Alias=VPS9
-chrXIII	SGD	CDS	79909	81486	.	+	.	ID=YML096W;Name=YML096W;Alias=
-chrXIII	SGD	CDS	81481	82113	.	-	.	ID=YML095C;Name=YML095C;Alias=RAD10
-chrXIII	SGD	CDS	82275	82849	.	+	.	ID=YML094W;Name=YML094W;Alias=GIM5
-chrXIII	SGD	CDS	83090	85789	.	+	.	ID=YML093W;Name=YML093W;Alias=UTP14
-chrXIII	SGD	CDS	85987	86739	.	-	.	ID=YML092C;Name=YML092C;Alias=PRE8
-chrXIII	SGD	CDS	87123	90731	.	-	.	ID=YML091C;Name=YML091C;Alias=RPM2
-chrXIII	SGD	CDS	92235	94241	.	+	.	ID=YML088W;Name=YML088W;Alias=UFO1
-chrXIII	SGD	CDS	94431	95369	.	-	.	ID=YML087C;Name=YML087C;Alias=AIM33
-chrXIII	SGD	CDS	95791	97371	.	-	.	ID=YML086C;Name=YML086C;Alias=ALO1
-chrXIII	SGD	CDS	97941	99400	.	-	.	ID=YML085C;Name=YML085C;Alias=TUB1
-chrXIII	SGD	CDS	99794	101050	.	-	.	ID=YML083C;Name=YML083C;Alias=
-chrXIII	SGD	CDS	101862	103811	.	+	.	ID=YML082W;Name=YML082W;Alias=
-chrXIII	SGD	CDS	103983	104162	.	-	.	ID=YML081C-A;Name=YML081C-A;Alias=ATP18
-chrXIII	SGD	CDS	104777	108532	.	+	.	ID=YML081W;Name=YML081W;Alias=TDA9
-chrXIII	SGD	CDS	108806	110077	.	+	.	ID=YML080W;Name=YML080W;Alias=DUS1
-chrXIII	SGD	CDS	110247	110852	.	+	.	ID=YML079W;Name=YML079W;Alias=
-chrXIII	SGD	CDS	111002	111550	.	+	.	ID=YML078W;Name=YML078W;Alias=CPR3
-chrXIII	SGD	CDS	111865	112344	.	+	.	ID=YML077W;Name=YML077W;Alias=BET5
-chrXIII	SGD	CDS	112513	115347	.	-	.	ID=YML076C;Name=YML076C;Alias=WAR1
-chrXIII	SGD	CDS	115734	118898	.	-	.	ID=YML075C;Name=YML075C;Alias=HMG1
-chrXIII	SGD	CDS	120089	121324	.	-	.	ID=YML074C;Name=YML074C;Alias=FPR3
-chrXIII	SGD	CDS	123227	124172	.	-	.	ID=YML073C;Name=YML073C;Alias=RPL6A
-chrXIII	SGD	CDS	124730	129367	.	-	.	ID=YML072C;Name=YML072C;Alias=TCB3
-chrXIII	SGD	CDS	129749	131572	.	-	.	ID=YML071C;Name=YML071C;Alias=COG8
-chrXIII	SGD	CDS	133475	135229	.	+	.	ID=YML070W;Name=YML070W;Alias=DAK1
-chrXIII	SGD	CDS	135500	137158	.	+	.	ID=YML069W;Name=YML069W;Alias=POB3
-chrXIII	SGD	CDS	137550	138944	.	+	.	ID=YML068W;Name=YML068W;Alias=ITT1
-chrXIII	SGD	CDS	139063	140214	.	-	.	ID=YML067C;Name=YML067C;Alias=ERV41
-chrXIII	SGD	CDS	140424	141533	.	-	.	ID=YML066C;Name=YML066C;Alias=SMA2
-chrXIII	SGD	CDS	142210	144954	.	+	.	ID=YML065W;Name=YML065W;Alias=ORC1
-chrXIII	SGD	CDS	145139	145876	.	-	.	ID=YML064C;Name=YML064C;Alias=TEM1
-chrXIII	SGD	CDS	146482	147249	.	+	.	ID=YML063W;Name=YML063W;Alias=RPS1B
-chrXIII	SGD	CDS	147505	148683	.	-	.	ID=YML062C;Name=YML062C;Alias=MFT1
-chrXIII	SGD	CDS	148953	151532	.	-	.	ID=YML061C;Name=YML061C;Alias=PIF1
-chrXIII	SGD	CDS	151871	153001	.	+	.	ID=YML060W;Name=YML060W;Alias=OGG1
-chrXIII	SGD	CDS	153219	158258	.	-	.	ID=YML059C;Name=YML059C;Alias=NTE1
-chrXIII	SGD	CDS	158760	158966	.	+	.	ID=YML058W-A;Name=YML058W-A;Alias=HUG1
-chrXIII	SGD	CDS	159383	159697	.	+	.	ID=YML058W;Name=YML058W;Alias=SML1
-chrXIII	SGD	CDS	160180	161994	.	+	.	ID=YML057W;Name=YML057W;Alias=CMP2
-chrXIII	SGD	CDS	162194	164176	.	-	.	ID=YML056C;Name=YML056C;Alias=IMD4
-chrXIII	SGD	CDS	164790	165326	.	+	.	ID=YML055W;Name=YML055W;Alias=SPC2
-chrXIII	SGD	CDS	165533	167308	.	-	.	ID=YML054C;Name=YML054C;Alias=CYB2
-chrXIII	SGD	CDS	167623	167781	.	-	.	ID=YML054C-A;Name=YML054C-A;Alias=
-chrXIII	SGD	CDS	169116	169754	.	-	.	ID=YML053C;Name=YML053C;Alias=
-chrXIII	SGD	CDS	170402	171310	.	+	.	ID=YML052W;Name=YML052W;Alias=SUR7
-chrXIII	SGD	CDS	171594	172901	.	+	.	ID=YML051W;Name=YML051W;Alias=GAL80
-chrXIII	SGD	CDS	173139	174074	.	+	.	ID=YML050W;Name=YML050W;Alias=AIM32
-chrXIII	SGD	CDS	174220	178305	.	-	.	ID=YML049C;Name=YML049C;Alias=RSE1
-chrXIII	SGD	CDS	178426	179637	.	+	.	ID=YML048W;Name=YML048W;Alias=GSF2
-chrXIII	SGD	CDS	180017	181075	.	-	.	ID=YML047C;Name=YML047C;Alias=PRM6
-chrXIII	SGD	CDS	181474	183363	.	+	.	ID=YML046W;Name=YML046W;Alias=PRP39
-chrXIII	SGD	CDS	190244	191767	.	-	.	ID=YML043C;Name=YML043C;Alias=RRN11
-chrXIII	SGD	CDS	192788	194800	.	+	.	ID=YML042W;Name=YML042W;Alias=CAT2
-chrXIII	SGD	CDS	194913	195755	.	-	.	ID=YML041C;Name=YML041C;Alias=VPS71
-chrXIII	SGD	CDS	202775	204103	.	-	.	ID=YML038C;Name=YML038C;Alias=YMD8
-chrXIII	SGD	CDS	204386	205408	.	-	.	ID=YML037C;Name=YML037C;Alias=
-chrXIII	SGD	CDS	205642	206293	.	+	.	ID=YML036W;Name=YML036W;Alias=CGI121
-chrXIII	SGD	CDS	206428	208860	.	-	.	ID=YML035C;Name=YML035C;Alias=AMD1
-chrXIII	SGD	CDS	209525	212155	.	+	.	ID=YML034W;Name=YML034W;Alias=SRC1
-chrXIII	SGD	CDS	212515	213930	.	-	.	ID=YML032C;Name=YML032C;Alias=RAD52
-chrXIII	SGD	CDS	214189	216156	.	+	.	ID=YML031W;Name=YML031W;Alias=NDC1
-chrXIII	SGD	CDS	216435	216914	.	+	.	ID=YML030W;Name=YML030W;Alias=RCF1
-chrXIII	SGD	CDS	217362	219878	.	+	.	ID=YML029W;Name=YML029W;Alias=USA1
-chrXIII	SGD	CDS	220138	220728	.	+	.	ID=YML028W;Name=YML028W;Alias=TSA1
-chrXIII	SGD	CDS	221406	222563	.	+	.	ID=YML027W;Name=YML027W;Alias=YOX1
-chrXIII	SGD	CDS	222987	223828	.	-	.	ID=YML026C;Name=YML026C;Alias=RPS18B
-chrXIII	SGD	CDS	224406	225365	.	-	.	ID=YML025C;Name=YML025C;Alias=YML6
-chrXIII	SGD	CDS	225889	226697	.	+	.	ID=YML024W;Name=YML024W;Alias=RPS17A
-chrXIII	SGD	CDS	226994	228664	.	-	.	ID=YML023C;Name=YML023C;Alias=NSE5
-chrXIII	SGD	CDS	228937	229500	.	+	.	ID=YML022W;Name=YML022W;Alias=APT1
-chrXIII	SGD	CDS	229734	230813	.	-	.	ID=YML021C;Name=YML021C;Alias=UNG1
-chrXIII	SGD	CDS	231149	233143	.	+	.	ID=YML020W;Name=YML020W;Alias=
-chrXIII	SGD	CDS	233457	234455	.	+	.	ID=YML019W;Name=YML019W;Alias=OST6
-chrXIII	SGD	CDS	234771	235952	.	-	.	ID=YML018C;Name=YML018C;Alias=
-chrXIII	SGD	CDS	236588	238731	.	+	.	ID=YML017W;Name=YML017W;Alias=PSP2
-chrXIII	SGD	CDS	239458	241536	.	-	.	ID=YML016C;Name=YML016C;Alias=PPZ1
-chrXIII	SGD	CDS	241989	243029	.	-	.	ID=YML015C;Name=YML015C;Alias=TAF11
-chrXIII	SGD	CDS	243225	244064	.	+	.	ID=YML014W;Name=YML014W;Alias=TRM9
-chrXIII	SGD	CDS	244149	245903	.	+	.	ID=YML013W;Name=YML013W;Alias=UBX2
-chrXIII	SGD	CDS	246116	246751	.	+	.	ID=YML012W;Name=YML012W;Alias=ERV25
-chrXIII	SGD	CDS	246895	247428	.	-	.	ID=YML011C;Name=YML011C;Alias=RAD33
-chrXIII	SGD	CDS	247677	250868	.	+	.	ID=YML010W;Name=YML010W;Alias=SPT5
-chrXIII	SGD	CDS	251304	251516	.	-	.	ID=YML009C;Name=YML009C;Alias=MRPL39
-chrXIII	SGD	CDS	251839	252990	.	-	.	ID=YML008C;Name=YML008C;Alias=ERG6
-chrXIII	SGD	CDS	253162	253272	.	-	.	ID=YML007C-A;Name=YML007C-A;Alias=
-chrXIII	SGD	CDS	253848	255800	.	+	.	ID=YML007W;Name=YML007W;Alias=YAP1
-chrXIII	SGD	CDS	256092	258416	.	-	.	ID=YML006C;Name=YML006C;Alias=GIS4
-chrXIII	SGD	CDS	260221	261609	.	+	.	ID=YML005W;Name=YML005W;Alias=TRM12
-chrXIII	SGD	CDS	261705	262685	.	-	.	ID=YML004C;Name=YML004C;Alias=GLO1
-chrXIII	SGD	CDS	263483	264355	.	+	.	ID=YML003W;Name=YML003W;Alias=
-chrXIII	SGD	CDS	264541	266754	.	+	.	ID=YML002W;Name=YML002W;Alias=
-chrXIII	SGD	CDS	267174	267800	.	+	.	ID=YML001W;Name=YML001W;Alias=YPT7
-chrXIII	SGD	CDS	269019	271136	.	-	.	ID=YMR001C;Name=YMR001C;Alias=CDC5
-chrXIII	SGD	CDS	271347	271577	.	-	.	ID=YMR001C-A;Name=YMR001C-A;Alias=
-chrXIII	SGD	CDS	272193	272663	.	+	.	ID=YMR002W;Name=YMR002W;Alias=MIX17
-chrXIII	SGD	CDS	273118	273714	.	+	.	ID=YMR003W;Name=YMR003W;Alias=AIM34
-chrXIII	SGD	CDS	274017	275552	.	+	.	ID=YMR004W;Name=YMR004W;Alias=MVP1
-chrXIII	SGD	CDS	276045	277211	.	+	.	ID=YMR005W;Name=YMR005W;Alias=TAF4
-chrXIII	SGD	CDS	277561	279681	.	-	.	ID=YMR006C;Name=YMR006C;Alias=PLB2
-chrXIII	SGD	CDS	280590	282584	.	-	.	ID=YMR008C;Name=YMR008C;Alias=PLB1
-chrXIII	SGD	CDS	284102	284641	.	+	.	ID=YMR009W;Name=YMR009W;Alias=ADI1
-chrXIII	SGD	CDS	285100	286317	.	+	.	ID=YMR010W;Name=YMR010W;Alias=ANY1
-chrXIII	SGD	CDS	288079	289704	.	+	.	ID=YMR011W;Name=YMR011W;Alias=HXT2
-chrXIII	SGD	CDS	291134	294967	.	+	.	ID=YMR012W;Name=YMR012W;Alias=CLU1
-chrXIII	SGD	CDS	295179	296738	.	-	.	ID=YMR013C;Name=YMR013C;Alias=SEC59
-chrXIII	SGD	CDS	298868	300427	.	+	.	ID=YMR014W;Name=YMR014W;Alias=BUD22
-chrXIII	SGD	CDS	300869	302485	.	-	.	ID=YMR015C;Name=YMR015C;Alias=ERG5
-chrXIII	SGD	CDS	303236	305593	.	-	.	ID=YMR016C;Name=YMR016C;Alias=SOK2
-chrXIII	SGD	CDS	307489	308682	.	+	.	ID=YMR017W;Name=YMR017W;Alias=SPO20
-chrXIII	SGD	CDS	310208	311752	.	+	.	ID=YMR018W;Name=YMR018W;Alias=PEX9
-chrXIII	SGD	CDS	312156	315005	.	+	.	ID=YMR019W;Name=YMR019W;Alias=STB4
-chrXIII	SGD	CDS	315377	316903	.	+	.	ID=YMR020W;Name=YMR020W;Alias=FMS1
-chrXIII	SGD	CDS	317165	318418	.	-	.	ID=YMR021C;Name=YMR021C;Alias=MAC1
-chrXIII	SGD	CDS	318680	319177	.	+	.	ID=YMR022W;Name=YMR022W;Alias=UBC7
-chrXIII	SGD	CDS	319437	321017	.	-	.	ID=YMR023C;Name=YMR023C;Alias=MSS1
-chrXIII	SGD	CDS	321875	323047	.	+	.	ID=YMR024W;Name=YMR024W;Alias=MRPL3
-chrXIII	SGD	CDS	323300	324187	.	+	.	ID=YMR025W;Name=YMR025W;Alias=CSI1
-chrXIII	SGD	CDS	324236	325435	.	-	.	ID=YMR026C;Name=YMR026C;Alias=PEX12
-chrXIII	SGD	CDS	325877	327289	.	+	.	ID=YMR027W;Name=YMR027W;Alias=
-chrXIII	SGD	CDS	327482	328582	.	+	.	ID=YMR028W;Name=YMR028W;Alias=TAP42
-chrXIII	SGD	CDS	328660	330231	.	-	.	ID=YMR029C;Name=YMR029C;Alias=FAR8
-chrXIII	SGD	CDS	330793	331923	.	+	.	ID=YMR030W;Name=YMR030W;Alias=RSF1
-chrXIII	SGD	CDS	332212	334743	.	-	.	ID=YMR031C;Name=YMR031C;Alias=EIS1
-chrXIII	SGD	CDS	335298	337307	.	+	.	ID=YMR032W;Name=YMR032W;Alias=HOF1
-chrXIII	SGD	CDS	337313	337603	.	+	.	ID=YMR030W-A;Name=YMR030W-A;Alias=
-chrXIII	SGD	CDS	337788	339277	.	+	.	ID=YMR033W;Name=YMR033W;Alias=ARP9
-chrXIII	SGD	CDS	339418	340722	.	-	.	ID=YMR034C;Name=YMR034C;Alias=RCH1
-chrXIII	SGD	CDS	341142	341675	.	+	.	ID=YMR035W;Name=YMR035W;Alias=IMP2
-chrXIII	SGD	CDS	341856	343520	.	-	.	ID=YMR036C;Name=YMR036C;Alias=MIH1
-chrXIII	SGD	CDS	344403	346517	.	-	.	ID=YMR037C;Name=YMR037C;Alias=MSN2
-chrXIII	SGD	CDS	347511	348260	.	-	.	ID=YMR038C;Name=YMR038C;Alias=CCS1
-chrXIII	SGD	CDS	348644	349522	.	-	.	ID=YMR039C;Name=YMR039C;Alias=SUB1
-chrXIII	SGD	CDS	350381	350863	.	+	.	ID=YMR040W;Name=YMR040W;Alias=YET2
-chrXIII	SGD	CDS	350966	351973	.	-	.	ID=YMR041C;Name=YMR041C;Alias=ARA2
-chrXIII	SGD	CDS	352603	353136	.	+	.	ID=YMR042W;Name=YMR042W;Alias=ARG80
-chrXIII	SGD	CDS	353871	354731	.	+	.	ID=YMR043W;Name=YMR043W;Alias=MCM1
-chrXIII	SGD	CDS	355384	356811	.	+	.	ID=YMR044W;Name=YMR044W;Alias=IOC4
-chrXIII	SGD	CDS	363364	366705	.	-	.	ID=YMR047C;Name=YMR047C;Alias=NUP116
-chrXIII	SGD	CDS	366981	367934	.	+	.	ID=YMR048W;Name=YMR048W;Alias=CSM3
-chrXIII	SGD	CDS	368094	370517	.	-	.	ID=YMR049C;Name=YMR049C;Alias=ERB1
-chrXIII	SGD	CDS	379586	380200	.	+	.	ID=YMR052W;Name=YMR052W;Alias=FAR3
-chrXIII	SGD	CDS	380346	382898	.	-	.	ID=YMR053C;Name=YMR053C;Alias=STB2
-chrXIII	SGD	CDS	383303	385975	.	+	.	ID=YMR054W;Name=YMR054W;Alias=STV1
-chrXIII	SGD	CDS	386101	387021	.	-	.	ID=YMR055C;Name=YMR055C;Alias=BUB2
-chrXIII	SGD	CDS	387315	388244	.	-	.	ID=YMR056C;Name=YMR056C;Alias=AAC1
-chrXIII	SGD	CDS	388822	390732	.	+	.	ID=YMR058W;Name=YMR058W;Alias=FET3
-chrXIII	SGD	CDS	391099	391485	.	+	.	ID=YMR059W;Name=YMR059W;Alias=SEN15
-chrXIII	SGD	CDS	391532	392515	.	-	.	ID=YMR060C;Name=YMR060C;Alias=SAM37
-chrXIII	SGD	CDS	392755	394788	.	+	.	ID=YMR061W;Name=YMR061W;Alias=RNA14
-chrXIII	SGD	CDS	395054	396379	.	-	.	ID=YMR062C;Name=YMR062C;Alias=ARG7
-chrXIII	SGD	CDS	397077	397796	.	+	.	ID=YMR063W;Name=YMR063W;Alias=RIM9
-chrXIII	SGD	CDS	397903	399459	.	+	.	ID=YMR064W;Name=YMR064W;Alias=AEP1
-chrXIII	SGD	CDS	399702	401216	.	+	.	ID=YMR065W;Name=YMR065W;Alias=KAR5
-chrXIII	SGD	CDS	401541	404237	.	+	.	ID=YMR066W;Name=YMR066W;Alias=SOV1
-chrXIII	SGD	CDS	404323	405573	.	-	.	ID=YMR067C;Name=YMR067C;Alias=UBX4
-chrXIII	SGD	CDS	406304	407584	.	+	.	ID=YMR068W;Name=YMR068W;Alias=AVO2
-chrXIII	SGD	CDS	407709	408566	.	+	.	ID=YMR069W;Name=YMR069W;Alias=NAT4
-chrXIII	SGD	CDS	409154	410626	.	+	.	ID=YMR070W;Name=YMR070W;Alias=MOT3
-chrXIII	SGD	CDS	410762	411265	.	-	.	ID=YMR071C;Name=YMR071C;Alias=TVP18
-chrXIII	SGD	CDS	411569	412120	.	+	.	ID=YMR072W;Name=YMR072W;Alias=ABF2
-chrXIII	SGD	CDS	412268	412873	.	-	.	ID=YMR073C;Name=YMR073C;Alias=IRC21
-chrXIII	SGD	CDS	413036	413473	.	-	.	ID=YMR074C;Name=YMR074C;Alias=SDD2
-chrXIII	SGD	CDS	413982	416036	.	+	.	ID=YMR075W;Name=YMR075W;Alias=RCO1
-chrXIII	SGD	CDS	416196	420029	.	-	.	ID=YMR076C;Name=YMR076C;Alias=PDS5
-chrXIII	SGD	CDS	421484	422149	.	-	.	ID=YMR077C;Name=YMR077C;Alias=VPS20
-chrXIII	SGD	CDS	422503	424728	.	-	.	ID=YMR078C;Name=YMR078C;Alias=CTF18
-chrXIII	SGD	CDS	424989	426059	.	+	.	ID=YMR079W;Name=YMR079W;Alias=SEC14
-chrXIII	SGD	CDS	426712	429627	.	-	.	ID=YMR080C;Name=YMR080C;Alias=NAM7
-chrXIII	SGD	CDS	430079	431095	.	-	.	ID=YMR081C;Name=YMR081C;Alias=ISF1
-chrXIII	SGD	CDS	434788	435915	.	+	.	ID=YMR083W;Name=YMR083W;Alias=ADH3
-chrXIII	SGD	CDS	436628	437416	.	+	.	ID=YMR084W;Name=YMR084W;Alias=
-chrXIII	SGD	CDS	437491	438789	.	+	.	ID=YMR085W;Name=YMR085W;Alias=
-chrXIII	SGD	CDS	439208	442090	.	+	.	ID=YMR086W;Name=YMR086W;Alias=SEG1
-chrXIII	SGD	CDS	442527	443381	.	+	.	ID=YMR087W;Name=YMR087W;Alias=
-chrXIII	SGD	CDS	443414	445102	.	-	.	ID=YMR088C;Name=YMR088C;Alias=VBA1
-chrXIII	SGD	CDS	445609	448086	.	-	.	ID=YMR089C;Name=YMR089C;Alias=YTA12
-chrXIII	SGD	CDS	449245	449928	.	+	.	ID=YMR090W;Name=YMR090W;Alias=
-chrXIII	SGD	CDS	450058	451365	.	-	.	ID=YMR091C;Name=YMR091C;Alias=NPL6
-chrXIII	SGD	CDS	451632	453479	.	-	.	ID=YMR092C;Name=YMR092C;Alias=AIP1
-chrXIII	SGD	CDS	454015	455556	.	+	.	ID=YMR093W;Name=YMR093W;Alias=UTP15
-chrXIII	SGD	CDS	455825	457261	.	+	.	ID=YMR094W;Name=YMR094W;Alias=CTF13
-chrXIII	SGD	CDS	457285	457959	.	-	.	ID=YMR095C;Name=YMR095C;Alias=SNO1
-chrXIII	SGD	CDS	458408	459301	.	+	.	ID=YMR096W;Name=YMR096W;Alias=SNZ1
-chrXIII	SGD	CDS	459424	460527	.	-	.	ID=YMR097C;Name=YMR097C;Alias=MTG1
-chrXIII	SGD	CDS	460771	462609	.	-	.	ID=YMR098C;Name=YMR098C;Alias=ATP25
-chrXIII	SGD	CDS	463934	464827	.	-	.	ID=YMR099C;Name=YMR099C;Alias=
-chrXIII	SGD	CDS	466300	468162	.	+	.	ID=YMR100W;Name=YMR100W;Alias=MUB1
-chrXIII	SGD	CDS	468445	469476	.	-	.	ID=YMR101C;Name=YMR101C;Alias=SRT1
-chrXIII	SGD	CDS	469848	472352	.	-	.	ID=YMR102C;Name=YMR102C;Alias=
-chrXIII	SGD	CDS	473420	475453	.	-	.	ID=YMR104C;Name=YMR104C;Alias=YPK2
-chrXIII	SGD	CDS	475897	477606	.	-	.	ID=YMR105C;Name=YMR105C;Alias=PGM2
-chrXIII	SGD	CDS	478064	478258	.	+	.	ID=YMR105W-A;Name=YMR105W-A;Alias=
-chrXIII	SGD	CDS	478301	480190	.	-	.	ID=YMR106C;Name=YMR106C;Alias=YKU80
-chrXIII	SGD	CDS	483014	483361	.	+	.	ID=YMR107W;Name=YMR107W;Alias=SPG4
-chrXIII	SGD	CDS	484084	486147	.	+	.	ID=YMR108W;Name=YMR108W;Alias=ILV2
-chrXIII	SGD	CDS	486587	490246	.	+	.	ID=YMR109W;Name=YMR109W;Alias=MYO5
-chrXIII	SGD	CDS	490394	491992	.	-	.	ID=YMR110C;Name=YMR110C;Alias=HFD1
-chrXIII	SGD	CDS	492404	493792	.	-	.	ID=YMR111C;Name=YMR111C;Alias=
-chrXIII	SGD	CDS	494100	494495	.	-	.	ID=YMR112C;Name=YMR112C;Alias=MED11
-chrXIII	SGD	CDS	494999	496282	.	+	.	ID=YMR113W;Name=YMR113W;Alias=FOL3
-chrXIII	SGD	CDS	496343	497449	.	-	.	ID=YMR114C;Name=YMR114C;Alias=
-chrXIII	SGD	CDS	497704	499209	.	+	.	ID=YMR115W;Name=YMR115W;Alias=MGR3
-chrXIII	SGD	CDS	499456	500688	.	-	.	ID=YMR116C;Name=YMR116C;Alias=ASC1
-chrXIII	SGD	CDS	501250	501891	.	-	.	ID=YMR117C;Name=YMR117C;Alias=SPC24
-chrXIII	SGD	CDS	502144	502734	.	-	.	ID=YMR118C;Name=YMR118C;Alias=SHH3
-chrXIII	SGD	CDS	505333	507207	.	+	.	ID=YMR119W;Name=YMR119W;Alias=ASI1
-chrXIII	SGD	CDS	507502	509280	.	-	.	ID=YMR120C;Name=YMR120C;Alias=ADE17
-chrXIII	SGD	CDS	509734	510348	.	-	.	ID=YMR121C;Name=YMR121C;Alias=RPL15B
-chrXIII	SGD	CDS	511315	511569	.	+	.	ID=YMR122W-A;Name=YMR122W-A;Alias=
-chrXIII	SGD	CDS	513593	513961	.	+	.	ID=YMR123W;Name=YMR123W;Alias=PKR1
-chrXIII	SGD	CDS	514456	517287	.	+	.	ID=YMR124W;Name=YMR124W;Alias=EPO1
-chrXIII	SGD	CDS	517539	520446	.	+	.	ID=YMR125W;Name=YMR125W;Alias=STO1
-chrXIII	SGD	CDS	520761	521789	.	-	.	ID=YMR126C;Name=YMR126C;Alias=DLT1
-chrXIII	SGD	CDS	522329	523345	.	-	.	ID=YMR127C;Name=YMR127C;Alias=SAS2
-chrXIII	SGD	CDS	523696	527499	.	+	.	ID=YMR128W;Name=YMR128W;Alias=ECM16
-chrXIII	SGD	CDS	527804	531817	.	+	.	ID=YMR129W;Name=YMR129W;Alias=POM152
-chrXIII	SGD	CDS	532119	533027	.	+	.	ID=YMR130W;Name=YMR130W;Alias=
-chrXIII	SGD	CDS	533163	534698	.	-	.	ID=YMR131C;Name=YMR131C;Alias=RRB1
-chrXIII	SGD	CDS	534944	535570	.	-	.	ID=YMR132C;Name=YMR132C;Alias=JLP2
-chrXIII	SGD	CDS	536207	537609	.	+	.	ID=YMR133W;Name=YMR133W;Alias=REC114
-chrXIII	SGD	CDS	537838	538551	.	+	.	ID=YMR134W;Name=YMR134W;Alias=ERG29
-chrXIII	SGD	CDS	538689	540056	.	-	.	ID=YMR135C;Name=YMR135C;Alias=GID8
-chrXIII	SGD	CDS	541199	542881	.	+	.	ID=YMR136W;Name=YMR136W;Alias=GAT2
-chrXIII	SGD	CDS	542978	544963	.	-	.	ID=YMR137C;Name=YMR137C;Alias=PSO2
-chrXIII	SGD	CDS	545155	545730	.	+	.	ID=YMR138W;Name=YMR138W;Alias=CIN4
-chrXIII	SGD	CDS	546125	547237	.	+	.	ID=YMR139W;Name=YMR139W;Alias=RIM11
-chrXIII	SGD	CDS	547714	549183	.	+	.	ID=YMR140W;Name=YMR140W;Alias=SIP5
-chrXIII	SGD	CDS	550206	551207	.	-	.	ID=YMR142C;Name=YMR142C;Alias=RPL13B
-chrXIII	SGD	CDS	551928	552903	.	+	.	ID=YMR143W;Name=YMR143W;Alias=RPS16A
-chrXIII	SGD	CDS	553362	554390	.	+	.	ID=YMR144W;Name=YMR144W;Alias=FDO1
-chrXIII	SGD	CDS	554793	556475	.	-	.	ID=YMR145C;Name=YMR145C;Alias=NDE1
-chrXIII	SGD	CDS	557481	558524	.	-	.	ID=YMR146C;Name=YMR146C;Alias=TIF34
-chrXIII	SGD	CDS	559199	559870	.	+	.	ID=YMR147W;Name=YMR147W;Alias=
-chrXIII	SGD	CDS	560366	560812	.	+	.	ID=YMR148W;Name=YMR148W;Alias=OSW5
-chrXIII	SGD	CDS	560996	561856	.	+	.	ID=YMR149W;Name=YMR149W;Alias=SWP1
-chrXIII	SGD	CDS	561956	562528	.	-	.	ID=YMR150C;Name=YMR150C;Alias=IMP1
-chrXIII	SGD	CDS	563096	564193	.	+	.	ID=YMR152W;Name=YMR152W;Alias=YIM1
-chrXIII	SGD	CDS	564435	565862	.	+	.	ID=YMR153W;Name=YMR153W;Alias=NUP53
-chrXIII	SGD	CDS	565999	568182	.	-	.	ID=YMR154C;Name=YMR154C;Alias=RIM13
-chrXIII	SGD	CDS	568551	570194	.	+	.	ID=YMR155W;Name=YMR155W;Alias=
-chrXIII	SGD	CDS	570300	571016	.	-	.	ID=YMR156C;Name=YMR156C;Alias=TPP1
-chrXIII	SGD	CDS	571277	572044	.	-	.	ID=YMR157C;Name=YMR157C;Alias=AIM36
-chrXIII	SGD	CDS	572248	572715	.	+	.	ID=YMR158W;Name=YMR158W;Alias=MRPS8
-chrXIII	SGD	CDS	573194	573331	.	-	.	ID=YMR158C-A;Name=YMR158C-A;Alias=
-chrXIII	SGD	CDS	574476	574928	.	-	.	ID=YMR159C;Name=YMR159C;Alias=ATG16
-chrXIII	SGD	CDS	575066	577516	.	+	.	ID=YMR160W;Name=YMR160W;Alias=
-chrXIII	SGD	CDS	577718	578392	.	+	.	ID=YMR161W;Name=YMR161W;Alias=HLJ1
-chrXIII	SGD	CDS	578951	583921	.	-	.	ID=YMR162C;Name=YMR162C;Alias=DNF3
-chrXIII	SGD	CDS	584271	586388	.	-	.	ID=YMR163C;Name=YMR163C;Alias=INP2
-chrXIII	SGD	CDS	587274	589550	.	-	.	ID=YMR164C;Name=YMR164C;Alias=MSS11
-chrXIII	SGD	CDS	590040	592628	.	-	.	ID=YMR165C;Name=YMR165C;Alias=PAH1
-chrXIII	SGD	CDS	593367	594473	.	-	.	ID=YMR166C;Name=YMR166C;Alias=MME1
-chrXIII	SGD	CDS	594886	597195	.	+	.	ID=YMR167W;Name=YMR167W;Alias=MLH1
-chrXIII	SGD	CDS	597332	599158	.	-	.	ID=YMR168C;Name=YMR168C;Alias=CEP3
-chrXIII	SGD	CDS	599352	600872	.	-	.	ID=YMR169C;Name=YMR169C;Alias=ALD3
-chrXIII	SGD	CDS	601562	603082	.	-	.	ID=YMR170C;Name=YMR170C;Alias=ALD2
-chrXIII	SGD	CDS	603868	605520	.	-	.	ID=YMR171C;Name=YMR171C;Alias=EAR1
-chrXIII	SGD	CDS	605981	608140	.	+	.	ID=YMR172W;Name=YMR172W;Alias=HOT1
-chrXIII	SGD	CDS	608689	609981	.	+	.	ID=YMR173W;Name=YMR173W;Alias=DDR48
-chrXIII	SGD	CDS	610159	610365	.	-	.	ID=YMR174C;Name=YMR174C;Alias=PAI3
-chrXIII	SGD	CDS	611016	611255	.	+	.	ID=YMR175W;Name=YMR175W;Alias=SIP18
-chrXIII	SGD	CDS	611314	611508	.	+	.	ID=YMR175W-A;Name=YMR175W-A;Alias=
-chrXIII	SGD	CDS	611740	615975	.	+	.	ID=YMR176W;Name=YMR176W;Alias=ECM5
-chrXIII	SGD	CDS	616566	618098	.	+	.	ID=YMR177W;Name=YMR177W;Alias=MMT1
-chrXIII	SGD	CDS	618479	619303	.	+	.	ID=YMR178W;Name=YMR178W;Alias=
-chrXIII	SGD	CDS	619858	622134	.	+	.	ID=YMR179W;Name=YMR179W;Alias=SPT21
-chrXIII	SGD	CDS	622251	623213	.	-	.	ID=YMR180C;Name=YMR180C;Alias=CTL1
-chrXIII	SGD	CDS	623616	624080	.	-	.	ID=YMR181C;Name=YMR181C;Alias=
-chrXIII	SGD	CDS	624532	625167	.	-	.	ID=YMR182C;Name=YMR182C;Alias=RGM1
-chrXIII	SGD	CDS	625811	625897	.	+	.	ID=YMR182W-A;Name=YMR182W-A;Alias=
-chrXIII	SGD	CDS	626921	627808	.	-	.	ID=YMR183C;Name=YMR183C;Alias=SSO2
-chrXIII	SGD	CDS	628189	628785	.	+	.	ID=YMR184W;Name=YMR184W;Alias=ADD37
-chrXIII	SGD	CDS	629025	631970	.	+	.	ID=YMR185W;Name=YMR185W;Alias=RTP1
-chrXIII	SGD	CDS	632355	634472	.	+	.	ID=YMR186W;Name=YMR186W;Alias=HSC82
-chrXIII	SGD	CDS	634689	635984	.	-	.	ID=YMR187C;Name=YMR187C;Alias=
-chrXIII	SGD	CDS	636291	637004	.	-	.	ID=YMR188C;Name=YMR188C;Alias=MRPS17
-chrXIII	SGD	CDS	637500	640604	.	+	.	ID=YMR189W;Name=YMR189W;Alias=GCV2
-chrXIII	SGD	CDS	640915	645258	.	-	.	ID=YMR190C;Name=YMR190C;Alias=SGS1
-chrXIII	SGD	CDS	645656	646777	.	+	.	ID=YMR191W;Name=YMR191W;Alias=SPG5
-chrXIII	SGD	CDS	647118	649280	.	+	.	ID=YMR192W;Name=YMR192W;Alias=GYL1
-chrXIII	SGD	CDS	650036	650812	.	+	.	ID=YMR193W;Name=YMR193W;Alias=MRPL24
-chrXIII	SGD	CDS	651145	651910	.	+	.	ID=YMR194W;Name=YMR194W;Alias=RPL36A
-chrXIII	SGD	CDS	652594	652887	.	-	.	ID=YMR194C-B;Name=YMR194C-B;Alias=CMC4
-chrXIII	SGD	CDS	654034	654417	.	+	.	ID=YMR195W;Name=YMR195W;Alias=ICY1
-chrXIII	SGD	CDS	655076	658342	.	+	.	ID=YMR196W;Name=YMR196W;Alias=
-chrXIII	SGD	CDS	658545	659198	.	-	.	ID=YMR197C;Name=YMR197C;Alias=VTI1
-chrXIII	SGD	CDS	659745	661529	.	+	.	ID=YMR198W;Name=YMR198W;Alias=CIK1
-chrXIII	SGD	CDS	662644	664284	.	+	.	ID=YMR199W;Name=YMR199W;Alias=CLN1
-chrXIII	SGD	CDS	664752	665522	.	+	.	ID=YMR200W;Name=YMR200W;Alias=ROT1
-chrXIII	SGD	CDS	665845	667044	.	-	.	ID=YMR201C;Name=YMR201C;Alias=RAD14
-chrXIII	SGD	CDS	667537	668205	.	+	.	ID=YMR202W;Name=YMR202W;Alias=ERG2
-chrXIII	SGD	CDS	668492	669655	.	+	.	ID=YMR203W;Name=YMR203W;Alias=TOM40
-chrXIII	SGD	CDS	670063	671325	.	-	.	ID=YMR204C;Name=YMR204C;Alias=INP1
-chrXIII	SGD	CDS	671887	674766	.	-	.	ID=YMR205C;Name=YMR205C;Alias=PFK2
-chrXIII	SGD	CDS	675896	676837	.	+	.	ID=YMR206W;Name=YMR206W;Alias=
-chrXIII	SGD	CDS	677193	683564	.	-	.	ID=YMR207C;Name=YMR207C;Alias=HFA1
-chrXIII	SGD	CDS	684467	685798	.	+	.	ID=YMR208W;Name=YMR208W;Alias=ERG12
-chrXIII	SGD	CDS	685911	687284	.	-	.	ID=YMR209C;Name=YMR209C;Alias=
-chrXIII	SGD	CDS	687516	688865	.	+	.	ID=YMR210W;Name=YMR210W;Alias=MGL2
-chrXIII	SGD	CDS	689083	690510	.	+	.	ID=YMR211W;Name=YMR211W;Alias=DML1
-chrXIII	SGD	CDS	690695	693043	.	-	.	ID=YMR212C;Name=YMR212C;Alias=EFR3
-chrXIII	SGD	CDS	693381	695153	.	+	.	ID=YMR213W;Name=YMR213W;Alias=CEF1
-chrXIII	SGD	CDS	695350	696483	.	+	.	ID=YMR214W;Name=YMR214W;Alias=SCJ1
-chrXIII	SGD	CDS	696796	698370	.	+	.	ID=YMR215W;Name=YMR215W;Alias=GAS3
-chrXIII	SGD	CDS	698811	701039	.	-	.	ID=YMR216C;Name=YMR216C;Alias=SKY1
-chrXIII	SGD	CDS	701790	703367	.	+	.	ID=YMR217W;Name=YMR217W;Alias=GUA1
-chrXIII	SGD	CDS	703579	706887	.	-	.	ID=YMR218C;Name=YMR218C;Alias=TRS130
-chrXIII	SGD	CDS	707133	712109	.	+	.	ID=YMR219W;Name=YMR219W;Alias=ESC1
-chrXIII	SGD	CDS	712316	713671	.	+	.	ID=YMR220W;Name=YMR220W;Alias=ERG8
-chrXIII	SGD	CDS	713931	715445	.	-	.	ID=YMR221C;Name=YMR221C;Alias=FMP42
-chrXIII	SGD	CDS	715638	716309	.	-	.	ID=YMR222C;Name=YMR222C;Alias=FSH2
-chrXIII	SGD	CDS	716715	718130	.	+	.	ID=YMR223W;Name=YMR223W;Alias=UBP8
-chrXIII	SGD	CDS	718575	720653	.	-	.	ID=YMR224C;Name=YMR224C;Alias=MRE11
-chrXIII	SGD	CDS	720960	721403	.	-	.	ID=YMR225C;Name=YMR225C;Alias=MRPL44
-chrXIII	SGD	CDS	721593	722396	.	-	.	ID=YMR226C;Name=YMR226C;Alias=
-chrXIII	SGD	CDS	722613	724385	.	-	.	ID=YMR227C;Name=YMR227C;Alias=TAF7
-chrXIII	SGD	CDS	724626	725651	.	+	.	ID=YMR228W;Name=YMR228W;Alias=MTF1
-chrXIII	SGD	CDS	725934	731123	.	-	.	ID=YMR229C;Name=YMR229C;Alias=RRP5
-chrXIII	SGD	CDS	732414	733141	.	+	.	ID=YMR230W;Name=YMR230W;Alias=RPS10B
-chrXIII	SGD	CDS	733268	733456	.	+	.	ID=YMR230W-A;Name=YMR230W-A;Alias=
-chrXIII	SGD	CDS	733545	736634	.	+	.	ID=YMR231W;Name=YMR231W;Alias=PEP5
-chrXIII	SGD	CDS	736926	738959	.	+	.	ID=YMR232W;Name=YMR232W;Alias=FUS2
-chrXIII	SGD	CDS	739185	739865	.	+	.	ID=YMR233W;Name=YMR233W;Alias=TRI1
-chrXIII	SGD	CDS	740266	741312	.	+	.	ID=YMR234W;Name=YMR234W;Alias=RNH1
-chrXIII	SGD	CDS	741512	742735	.	-	.	ID=YMR235C;Name=YMR235C;Alias=RNA1
-chrXIII	SGD	CDS	742971	743444	.	+	.	ID=YMR236W;Name=YMR236W;Alias=TAF9
-chrXIII	SGD	CDS	743749	745923	.	+	.	ID=YMR237W;Name=YMR237W;Alias=BCH1
-chrXIII	SGD	CDS	746353	747729	.	+	.	ID=YMR238W;Name=YMR238W;Alias=DFG5
-chrXIII	SGD	CDS	748262	749677	.	-	.	ID=YMR239C;Name=YMR239C;Alias=RNT1
-chrXIII	SGD	CDS	749930	751240	.	-	.	ID=YMR240C;Name=YMR240C;Alias=CUS1
-chrXIII	SGD	CDS	751961	752905	.	+	.	ID=YMR241W;Name=YMR241W;Alias=YHM2
-chrXIII	SGD	CDS	753225	754220	.	-	.	ID=YMR242C;Name=YMR242C;Alias=RPL20A
-chrXIII	SGD	CDS	754297	754386	.	+	.	ID=YMR242W-A;Name=YMR242W-A;Alias=
-chrXIII	SGD	CDS	754838	756166	.	-	.	ID=YMR243C;Name=YMR243C;Alias=ZRC1
-chrXIII	SGD	CDS	757250	758317	.	+	.	ID=YMR244W;Name=YMR244W;Alias=
-chrXIII	SGD	CDS	758517	758831	.	-	.	ID=YMR244C-A;Name=YMR244C-A;Alias=COA6
-chrXIII	SGD	CDS	759807	761891	.	+	.	ID=YMR246W;Name=YMR246W;Alias=FAA4
-chrXIII	SGD	CDS	763351	768039	.	-	.	ID=YMR247C;Name=YMR247C;Alias=RKR1
-chrXIII	SGD	CDS	769283	769426	.	+	.	ID=YMR247W-A;Name=YMR247W-A;Alias=
-chrXIII	SGD	CDS	770801	772558	.	+	.	ID=YMR250W;Name=YMR250W;Alias=GAD1
-chrXIII	SGD	CDS	772915	774015	.	+	.	ID=YMR251W;Name=YMR251W;Alias=GTO3
-chrXIII	SGD	CDS	774752	774931	.	+	.	ID=YMR251W-A;Name=YMR251W-A;Alias=HOR7
-chrXIII	SGD	CDS	775315	775719	.	-	.	ID=YMR252C;Name=YMR252C;Alias=
-chrXIII	SGD	CDS	775946	777190	.	-	.	ID=YMR253C;Name=YMR253C;Alias=
-chrXIII	SGD	CDS	778001	778567	.	+	.	ID=YMR255W;Name=YMR255W;Alias=GFD1
-chrXIII	SGD	CDS	778945	779127	.	-	.	ID=YMR256C;Name=YMR256C;Alias=COX7
-chrXIII	SGD	CDS	779629	782031	.	-	.	ID=YMR257C;Name=YMR257C;Alias=PET111
-chrXIII	SGD	CDS	782620	784281	.	-	.	ID=YMR258C;Name=YMR258C;Alias=ROY1
-chrXIII	SGD	CDS	784621	788883	.	-	.	ID=YMR259C;Name=YMR259C;Alias=TRM732
-chrXIII	SGD	CDS	789378	789839	.	-	.	ID=YMR260C;Name=YMR260C;Alias=TIF11
-chrXIII	SGD	CDS	790205	793369	.	-	.	ID=YMR261C;Name=YMR261C;Alias=TPS3
-chrXIII	SGD	CDS	793726	794667	.	+	.	ID=YMR262W;Name=YMR262W;Alias=
-chrXIII	SGD	CDS	794919	795524	.	+	.	ID=YMR263W;Name=YMR263W;Alias=SAP30
-chrXIII	SGD	CDS	795805	796416	.	+	.	ID=YMR264W;Name=YMR264W;Alias=CUE1
-chrXIII	SGD	CDS	796540	797925	.	-	.	ID=YMR265C;Name=YMR265C;Alias=
-chrXIII	SGD	CDS	798518	801379	.	+	.	ID=YMR266W;Name=YMR266W;Alias=RSN1
-chrXIII	SGD	CDS	801772	802704	.	+	.	ID=YMR267W;Name=YMR267W;Alias=PPA2
-chrXIII	SGD	CDS	802888	804222	.	-	.	ID=YMR268C;Name=YMR268C;Alias=PRP24
-chrXIII	SGD	CDS	804456	805091	.	+	.	ID=YMR269W;Name=YMR269W;Alias=TMA23
-chrXIII	SGD	CDS	805326	806423	.	-	.	ID=YMR270C;Name=YMR270C;Alias=RRN9
-chrXIII	SGD	CDS	806865	807548	.	-	.	ID=YMR271C;Name=YMR271C;Alias=URA10
-chrXIII	SGD	CDS	809623	810777	.	-	.	ID=YMR272C;Name=YMR272C;Alias=SCS7
-chrXIII	SGD	CDS	811089	811196	.	+	.	ID=YMR272W-B;Name=YMR272W-B;Alias=
-chrXIII	SGD	CDS	811233	813980	.	-	.	ID=YMR273C;Name=YMR273C;Alias=ZDS1
-chrXIII	SGD	CDS	814364	815311	.	-	.	ID=YMR274C;Name=YMR274C;Alias=RCE1
-chrXIII	SGD	CDS	815651	818581	.	-	.	ID=YMR275C;Name=YMR275C;Alias=BUL1
-chrXIII	SGD	CDS	818827	819948	.	+	.	ID=YMR276W;Name=YMR276W;Alias=DSK2
-chrXIII	SGD	CDS	820256	822454	.	+	.	ID=YMR277W;Name=YMR277W;Alias=FCP1
-chrXIII	SGD	CDS	822763	824631	.	+	.	ID=YMR278W;Name=YMR278W;Alias=PRM15
-chrXIII	SGD	CDS	824729	826351	.	-	.	ID=YMR279C;Name=YMR279C;Alias=
-chrXIII	SGD	CDS	827028	831329	.	-	.	ID=YMR280C;Name=YMR280C;Alias=CAT8
-chrXIII	SGD	CDS	832339	833253	.	+	.	ID=YMR281W;Name=YMR281W;Alias=GPI12
-chrXIII	SGD	CDS	833356	835098	.	-	.	ID=YMR282C;Name=YMR282C;Alias=AEP2
-chrXIII	SGD	CDS	835326	836867	.	-	.	ID=YMR283C;Name=YMR283C;Alias=RIT1
-chrXIII	SGD	CDS	838187	839995	.	+	.	ID=YMR284W;Name=YMR284W;Alias=YKU70
-chrXIII	SGD	CDS	840144	841691	.	-	.	ID=YMR285C;Name=YMR285C;Alias=NGL2
-chrXIII	SGD	CDS	841942	842202	.	+	.	ID=YMR286W;Name=YMR286W;Alias=MRPL33
-chrXIII	SGD	CDS	842436	845345	.	-	.	ID=YMR287C;Name=YMR287C;Alias=DSS1
-chrXIII	SGD	CDS	845571	848486	.	+	.	ID=YMR288W;Name=YMR288W;Alias=HSH155
-chrXIII	SGD	CDS	848685	849809	.	+	.	ID=YMR289W;Name=YMR289W;Alias=ABZ2
-chrXIII	SGD	CDS	850074	851591	.	-	.	ID=YMR290C;Name=YMR290C;Alias=HAS1
-chrXIII	SGD	CDS	852630	854390	.	+	.	ID=YMR291W;Name=YMR291W;Alias=TDA1
-chrXIII	SGD	CDS	854795	855293	.	+	.	ID=YMR292W;Name=YMR292W;Alias=GOT1
-chrXIII	SGD	CDS	855399	856793	.	-	.	ID=YMR293C;Name=YMR293C;Alias=HER2
-chrXIII	SGD	CDS	856966	858087	.	+	.	ID=YMR294W;Name=YMR294W;Alias=JNM1
-chrXIII	SGD	CDS	858297	858890	.	-	.	ID=YMR295C;Name=YMR295C;Alias=
-chrXIII	SGD	CDS	859215	860891	.	-	.	ID=YMR296C;Name=YMR296C;Alias=LCB1
-chrXIII	SGD	CDS	861922	863520	.	+	.	ID=YMR297W;Name=YMR297W;Alias=PRC1
-chrXIII	SGD	CDS	863819	864271	.	+	.	ID=YMR298W;Name=YMR298W;Alias=LIP1
-chrXIII	SGD	CDS	864412	865350	.	-	.	ID=YMR299C;Name=YMR299C;Alias=DYN3
-chrXIII	SGD	CDS	865559	867091	.	-	.	ID=YMR300C;Name=YMR300C;Alias=ADE4
-chrXIII	SGD	CDS	867555	869627	.	-	.	ID=YMR301C;Name=YMR301C;Alias=ATM1
-chrXIII	SGD	CDS	870073	872625	.	-	.	ID=YMR302C;Name=YMR302C;Alias=YME2
-chrXIII	SGD	CDS	873291	874337	.	-	.	ID=YMR303C;Name=YMR303C;Alias=ADH2
-chrXIII	SGD	CDS	874987	878679	.	+	.	ID=YMR304W;Name=YMR304W;Alias=UBP15
-chrXIII	SGD	CDS	879063	880232	.	-	.	ID=YMR305C;Name=YMR305C;Alias=SCW10
-chrXIII	SGD	CDS	881159	886516	.	+	.	ID=YMR306W;Name=YMR306W;Alias=FKS3
-chrXIII	SGD	CDS	887003	888682	.	+	.	ID=YMR307W;Name=YMR307W;Alias=GAS1
-chrXIII	SGD	CDS	888952	892221	.	-	.	ID=YMR308C;Name=YMR308C;Alias=PSE1
-chrXIII	SGD	CDS	892988	895426	.	-	.	ID=YMR309C;Name=YMR309C;Alias=NIP1
-chrXIII	SGD	CDS	895716	896669	.	-	.	ID=YMR310C;Name=YMR310C;Alias=
-chrXIII	SGD	CDS	896914	897603	.	-	.	ID=YMR311C;Name=YMR311C;Alias=GLC8
-chrXIII	SGD	CDS	898405	899226	.	+	.	ID=YMR312W;Name=YMR312W;Alias=ELP6
-chrXIII	SGD	CDS	899379	901307	.	-	.	ID=YMR313C;Name=YMR313C;Alias=TGL3
-chrXIII	SGD	CDS	901709	902413	.	+	.	ID=YMR314W;Name=YMR314W;Alias=PRE5
-chrXIII	SGD	CDS	902800	903849	.	+	.	ID=YMR315W;Name=YMR315W;Alias=
-chrXIII	SGD	CDS	904286	904393	.	+	.	ID=YMR315W-A;Name=YMR315W-A;Alias=
-chrXIII	SGD	CDS	904825	905835	.	+	.	ID=YMR316W;Name=YMR316W;Alias=DIA1
-chrXIII	SGD	CDS	905662	905973	.	-	.	ID=YMR316C-A;Name=YMR316C-A;Alias=
-chrXIII	SGD	CDS	907364	910786	.	+	.	ID=YMR317W;Name=YMR317W;Alias=
-chrXIII	SGD	CDS	911061	912143	.	-	.	ID=YMR318C;Name=YMR318C;Alias=ADH6
-chrXIII	SGD	CDS	912880	914538	.	-	.	ID=YMR319C;Name=YMR319C;Alias=FET4
-chrXIII	SGD	CDS	917579	917896	.	-	.	ID=YMR321C;Name=YMR321C;Alias=
-chrXIII	SGD	CDS	918366	919079	.	-	.	ID=YMR322C;Name=YMR322C;Alias=SNO4
-chrXIII	SGD	CDS	920088	921401	.	+	.	ID=YMR323W;Name=YMR323W;Alias=ERR3
-chrXIII	SGD	CDS	922641	923015	.	+	.	ID=YMR325W;Name=YMR325W;Alias=PAU19
-chrXIV	SGD	CDS	371	6098	.	-	.	ID=YNL339C;Name=YNL339C;Alias=YRF1-6
-chrXIV	SGD	CDS	8330	9475	.	+	.	ID=YNL336W;Name=YNL336W;Alias=COS1
-chrXIV	SGD	CDS	11452	12129	.	+	.	ID=YNL335W;Name=YNL335W;Alias=DDI3
-chrXIV	SGD	CDS	12208	12876	.	-	.	ID=YNL334C;Name=YNL334C;Alias=SNO2
-chrXIV	SGD	CDS	13267	14163	.	+	.	ID=YNL333W;Name=YNL333W;Alias=SNZ2
-chrXIV	SGD	CDS	14832	15854	.	+	.	ID=YNL332W;Name=YNL332W;Alias=THI12
-chrXIV	SGD	CDS	16118	17248	.	-	.	ID=YNL331C;Name=YNL331C;Alias=AAD14
-chrXIV	SGD	CDS	18001	19302	.	-	.	ID=YNL330C;Name=YNL330C;Alias=RPD3
-chrXIV	SGD	CDS	19541	22633	.	-	.	ID=YNL329C;Name=YNL329C;Alias=PEX6
-chrXIV	SGD	CDS	22834	23274	.	-	.	ID=YNL328C;Name=YNL328C;Alias=MDJ2
-chrXIV	SGD	CDS	24048	27173	.	+	.	ID=YNL327W;Name=YNL327W;Alias=EGT2
-chrXIV	SGD	CDS	27337	28347	.	-	.	ID=YNL326C;Name=YNL326C;Alias=PFA3
-chrXIV	SGD	CDS	28739	31378	.	-	.	ID=YNL325C;Name=YNL325C;Alias=FIG4
-chrXIV	SGD	CDS	31944	33188	.	+	.	ID=YNL323W;Name=YNL323W;Alias=LEM3
-chrXIV	SGD	CDS	33294	34235	.	-	.	ID=YNL322C;Name=YNL322C;Alias=KRE1
-chrXIV	SGD	CDS	34696	37422	.	+	.	ID=YNL321W;Name=YNL321W;Alias=VNX1
-chrXIV	SGD	CDS	37700	38554	.	+	.	ID=YNL320W;Name=YNL320W;Alias=
-chrXIV	SGD	CDS	38707	40329	.	-	.	ID=YNL318C;Name=YNL318C;Alias=HXT14
-chrXIV	SGD	CDS	40619	42016	.	+	.	ID=YNL317W;Name=YNL317W;Alias=PFS2
-chrXIV	SGD	CDS	42071	43075	.	-	.	ID=YNL316C;Name=YNL316C;Alias=PHA2
-chrXIV	SGD	CDS	43324	44280	.	-	.	ID=YNL315C;Name=YNL315C;Alias=ATP11
-chrXIV	SGD	CDS	44447	45214	.	+	.	ID=YNL314W;Name=YNL314W;Alias=DAL82
-chrXIV	SGD	CDS	45308	48022	.	-	.	ID=YNL313C;Name=YNL313C;Alias=EMW1
-chrXIV	SGD	CDS	48287	49216	.	+	.	ID=YNL312W;Name=YNL312W;Alias=RFA2
-chrXIV	SGD	CDS	49397	51688	.	-	.	ID=YNL311C;Name=YNL311C;Alias=SKP2
-chrXIV	SGD	CDS	51907	52431	.	-	.	ID=YNL310C;Name=YNL310C;Alias=ZIM17
-chrXIV	SGD	CDS	52662	53924	.	+	.	ID=YNL309W;Name=YNL309W;Alias=STB1
-chrXIV	SGD	CDS	54122	55897	.	-	.	ID=YNL308C;Name=YNL308C;Alias=KRI1
-chrXIV	SGD	CDS	56446	57573	.	-	.	ID=YNL307C;Name=YNL307C;Alias=MCK1
-chrXIV	SGD	CDS	58155	58808	.	+	.	ID=YNL306W;Name=YNL306W;Alias=MRPS18
-chrXIV	SGD	CDS	58898	59791	.	-	.	ID=YNL305C;Name=YNL305C;Alias=BXI1
-chrXIV	SGD	CDS	60297	61550	.	+	.	ID=YNL304W;Name=YNL304W;Alias=YPT11
-chrXIV	SGD	CDS	61958	62943	.	-	.	ID=YNL302C;Name=YNL302C;Alias=RPS19B
-chrXIV	SGD	CDS	63570	64562	.	-	.	ID=YNL301C;Name=YNL301C;Alias=RPL18B
-chrXIV	SGD	CDS	65744	66052	.	+	.	ID=YNL300W;Name=YNL300W;Alias=TOS6
-chrXIV	SGD	CDS	66517	68445	.	+	.	ID=YNL299W;Name=YNL299W;Alias=TRF5
-chrXIV	SGD	CDS	68915	71443	.	+	.	ID=YNL298W;Name=YNL298W;Alias=CLA4
-chrXIV	SGD	CDS	71673	76583	.	-	.	ID=YNL297C;Name=YNL297C;Alias=MON2
-chrXIV	SGD	CDS	76946	78520	.	+	.	ID=YNL295W;Name=YNL295W;Alias=MRX6
-chrXIV	SGD	CDS	78659	80260	.	-	.	ID=YNL294C;Name=YNL294C;Alias=RIM21
-chrXIV	SGD	CDS	80640	82541	.	+	.	ID=YNL293W;Name=YNL293W;Alias=MSB3
-chrXIV	SGD	CDS	82806	84017	.	+	.	ID=YNL292W;Name=YNL292W;Alias=PUS4
-chrXIV	SGD	CDS	84169	85815	.	-	.	ID=YNL291C;Name=YNL291C;Alias=MID1
-chrXIV	SGD	CDS	86218	87240	.	+	.	ID=YNL290W;Name=YNL290W;Alias=RFC3
-chrXIV	SGD	CDS	87897	88736	.	+	.	ID=YNL289W;Name=YNL289W;Alias=PCL1
-chrXIV	SGD	CDS	90303	91424	.	+	.	ID=YNL288W;Name=YNL288W;Alias=CAF40
-chrXIV	SGD	CDS	91994	94801	.	+	.	ID=YNL287W;Name=YNL287W;Alias=SEC21
-chrXIV	SGD	CDS	95223	96080	.	+	.	ID=YNL286W;Name=YNL286W;Alias=CUS2
-chrXIV	SGD	CDS	103134	104102	.	-	.	ID=YNL284C;Name=YNL284C;Alias=MRPL10
-chrXIV	SGD	CDS	105184	106695	.	-	.	ID=YNL283C;Name=YNL283C;Alias=WSC2
-chrXIV	SGD	CDS	107687	108274	.	+	.	ID=YNL282W;Name=YNL282W;Alias=POP3
-chrXIV	SGD	CDS	108467	108928	.	+	.	ID=YNL281W;Name=YNL281W;Alias=HCH1
-chrXIV	SGD	CDS	109095	110411	.	-	.	ID=YNL280C;Name=YNL280C;Alias=ERG24
-chrXIV	SGD	CDS	110917	112902	.	+	.	ID=YNL279W;Name=YNL279W;Alias=PRM1
-chrXIV	SGD	CDS	113271	116453	.	+	.	ID=YNL278W;Name=YNL278W;Alias=CAF120
-chrXIV	SGD	CDS	116679	116867	.	+	.	ID=YNL277W-A;Name=YNL277W-A;Alias=
-chrXIV	SGD	CDS	117349	118809	.	+	.	ID=YNL277W;Name=YNL277W;Alias=MET2
-chrXIV	SGD	CDS	119268	120998	.	+	.	ID=YNL275W;Name=YNL275W;Alias=BOR1
-chrXIV	SGD	CDS	121118	122170	.	-	.	ID=YNL274C;Name=YNL274C;Alias=GOR1
-chrXIV	SGD	CDS	122883	126599	.	+	.	ID=YNL273W;Name=YNL273W;Alias=TOF1
-chrXIV	SGD	CDS	126805	129084	.	-	.	ID=YNL272C;Name=YNL272C;Alias=SEC2
-chrXIV	SGD	CDS	129522	135383	.	-	.	ID=YNL271C;Name=YNL271C;Alias=BNI1
-chrXIV	SGD	CDS	135940	137661	.	-	.	ID=YNL270C;Name=YNL270C;Alias=ALP1
-chrXIV	SGD	CDS	137699	138094	.	+	.	ID=YNL269W;Name=YNL269W;Alias=BSC4
-chrXIV	SGD	CDS	138550	140385	.	+	.	ID=YNL268W;Name=YNL268W;Alias=LYP1
-chrXIV	SGD	CDS	140878	144078	.	+	.	ID=YNL267W;Name=YNL267W;Alias=PIK1
-chrXIV	SGD	CDS	144280	145281	.	-	.	ID=YNL265C;Name=YNL265C;Alias=IST1
-chrXIV	SGD	CDS	145563	146615	.	-	.	ID=YNL264C;Name=YNL264C;Alias=PDR17
-chrXIV	SGD	CDS	146896	147840	.	-	.	ID=YNL263C;Name=YNL263C;Alias=YIF1
-chrXIV	SGD	CDS	148212	154880	.	+	.	ID=YNL262W;Name=YNL262W;Alias=POL2
-chrXIV	SGD	CDS	155100	156539	.	+	.	ID=YNL261W;Name=YNL261W;Alias=ORC5
-chrXIV	SGD	CDS	156859	157455	.	-	.	ID=YNL260C;Name=YNL260C;Alias=LTO1
-chrXIV	SGD	CDS	157644	157865	.	-	.	ID=YNL259C;Name=YNL259C;Alias=ATX1
-chrXIV	SGD	CDS	158109	160373	.	-	.	ID=YNL258C;Name=YNL258C;Alias=DSL1
-chrXIV	SGD	CDS	160631	164320	.	-	.	ID=YNL257C;Name=YNL257C;Alias=SIP3
-chrXIV	SGD	CDS	164623	167097	.	+	.	ID=YNL256W;Name=YNL256W;Alias=FOL1
-chrXIV	SGD	CDS	167329	167790	.	-	.	ID=YNL255C;Name=YNL255C;Alias=GIS2
-chrXIV	SGD	CDS	168043	169248	.	-	.	ID=YNL254C;Name=YNL254C;Alias=RTC4
-chrXIV	SGD	CDS	170018	171286	.	+	.	ID=YNL253W;Name=YNL253W;Alias=TEX1
-chrXIV	SGD	CDS	171441	172286	.	-	.	ID=YNL252C;Name=YNL252C;Alias=MRPL17
-chrXIV	SGD	CDS	172588	174315	.	-	.	ID=YNL251C;Name=YNL251C;Alias=NRD1
-chrXIV	SGD	CDS	175410	179348	.	+	.	ID=YNL250W;Name=YNL250W;Alias=RAD50
-chrXIV	SGD	CDS	179394	181022	.	-	.	ID=YNL249C;Name=YNL249C;Alias=MPA43
-chrXIV	SGD	CDS	181361	182608	.	-	.	ID=YNL248C;Name=YNL248C;Alias=RPA49
-chrXIV	SGD	CDS	182875	185178	.	+	.	ID=YNL247W;Name=YNL247W;Alias=
-chrXIV	SGD	CDS	185460	186349	.	+	.	ID=YNL246W;Name=YNL246W;Alias=VPS75
-chrXIV	SGD	CDS	186346	186885	.	-	.	ID=YNL245C;Name=YNL245C;Alias=CWC25
-chrXIV	SGD	CDS	187170	187496	.	-	.	ID=YNL244C;Name=YNL244C;Alias=SUI1
-chrXIV	SGD	CDS	188051	190957	.	+	.	ID=YNL243W;Name=YNL243W;Alias=SLA2
-chrXIV	SGD	CDS	191324	196102	.	+	.	ID=YNL242W;Name=YNL242W;Alias=ATG2
-chrXIV	SGD	CDS	196426	197943	.	-	.	ID=YNL241C;Name=YNL241C;Alias=ZWF1
-chrXIV	SGD	CDS	198502	199977	.	-	.	ID=YNL240C;Name=YNL240C;Alias=NAR1
-chrXIV	SGD	CDS	200569	201933	.	+	.	ID=YNL239W;Name=YNL239W;Alias=LAP3
-chrXIV	SGD	CDS	202428	204872	.	+	.	ID=YNL238W;Name=YNL238W;Alias=KEX2
-chrXIV	SGD	CDS	205188	206567	.	+	.	ID=YNL237W;Name=YNL237W;Alias=YTP1
-chrXIV	SGD	CDS	206930	209854	.	+	.	ID=YNL236W;Name=YNL236W;Alias=SIN4
-chrXIV	SGD	CDS	210233	211513	.	+	.	ID=YNL234W;Name=YNL234W;Alias=
-chrXIV	SGD	CDS	211922	214600	.	+	.	ID=YNL233W;Name=YNL233W;Alias=BNI4
-chrXIV	SGD	CDS	214923	215801	.	+	.	ID=YNL232W;Name=YNL232W;Alias=CSL4
-chrXIV	SGD	CDS	215987	217042	.	-	.	ID=YNL231C;Name=YNL231C;Alias=PDR16
-chrXIV	SGD	CDS	217523	218662	.	-	.	ID=YNL230C;Name=YNL230C;Alias=ELA1
-chrXIV	SGD	CDS	219137	220201	.	-	.	ID=YNL229C;Name=YNL229C;Alias=URE2
-chrXIV	SGD	CDS	220659	222431	.	-	.	ID=YNL227C;Name=YNL227C;Alias=JJJ1
-chrXIV	SGD	CDS	222724	224469	.	-	.	ID=YNL225C;Name=YNL225C;Alias=CNM67
-chrXIV	SGD	CDS	224796	227099	.	-	.	ID=YNL224C;Name=YNL224C;Alias=SQS1
-chrXIV	SGD	CDS	227370	228854	.	+	.	ID=YNL223W;Name=YNL223W;Alias=ATG4
-chrXIV	SGD	CDS	229094	229714	.	+	.	ID=YNL222W;Name=YNL222W;Alias=SSU72
-chrXIV	SGD	CDS	231068	233695	.	-	.	ID=YNL221C;Name=YNL221C;Alias=POP1
-chrXIV	SGD	CDS	234413	235714	.	+	.	ID=YNL220W;Name=YNL220W;Alias=ADE12
-chrXIV	SGD	CDS	235996	237663	.	-	.	ID=YNL219C;Name=YNL219C;Alias=ALG9
-chrXIV	SGD	CDS	238238	240001	.	+	.	ID=YNL218W;Name=YNL218W;Alias=MGS1
-chrXIV	SGD	CDS	240331	241311	.	+	.	ID=YNL217W;Name=YNL217W;Alias=
-chrXIV	SGD	CDS	241689	244172	.	+	.	ID=YNL216W;Name=YNL216W;Alias=RAP1
-chrXIV	SGD	CDS	244468	245430	.	+	.	ID=YNL215W;Name=YNL215W;Alias=IES2
-chrXIV	SGD	CDS	245617	246216	.	+	.	ID=YNL214W;Name=YNL214W;Alias=PEX17
-chrXIV	SGD	CDS	246460	247104	.	-	.	ID=YNL213C;Name=YNL213C;Alias=RRG9
-chrXIV	SGD	CDS	247461	249809	.	+	.	ID=YNL212W;Name=YNL212W;Alias=VID27
-chrXIV	SGD	CDS	250055	250315	.	-	.	ID=YNL211C;Name=YNL211C;Alias=MRX7
-chrXIV	SGD	CDS	250931	251743	.	+	.	ID=YNL210W;Name=YNL210W;Alias=MER1
-chrXIV	SGD	CDS	252059	253900	.	+	.	ID=YNL209W;Name=YNL209W;Alias=SSB2
-chrXIV	SGD	CDS	254418	255017	.	+	.	ID=YNL208W;Name=YNL208W;Alias=
-chrXIV	SGD	CDS	255353	256630	.	+	.	ID=YNL207W;Name=YNL207W;Alias=RIO2
-chrXIV	SGD	CDS	256788	258155	.	-	.	ID=YNL206C;Name=YNL206C;Alias=RTT106
-chrXIV	SGD	CDS	258375	259277	.	-	.	ID=YNL204C;Name=YNL204C;Alias=SPS18
-chrXIV	SGD	CDS	259578	260456	.	+	.	ID=YNL202W;Name=YNL202W;Alias=SPS19
-chrXIV	SGD	CDS	260627	263203	.	-	.	ID=YNL201C;Name=YNL201C;Alias=PSY2
-chrXIV	SGD	CDS	263713	264453	.	-	.	ID=YNL200C;Name=YNL200C;Alias=NNR1
-chrXIV	SGD	CDS	264926	266530	.	-	.	ID=YNL199C;Name=YNL199C;Alias=GCR2
-chrXIV	SGD	CDS	267608	269593	.	-	.	ID=YNL197C;Name=YNL197C;Alias=WHI3
-chrXIV	SGD	CDS	270275	271171	.	-	.	ID=YNL196C;Name=YNL196C;Alias=SLZ1
-chrXIV	SGD	CDS	271523	272308	.	-	.	ID=YNL195C;Name=YNL195C;Alias=
-chrXIV	SGD	CDS	272710	273615	.	-	.	ID=YNL194C;Name=YNL194C;Alias=
-chrXIV	SGD	CDS	274368	276044	.	+	.	ID=YNL193W;Name=YNL193W;Alias=
-chrXIV	SGD	CDS	276502	279897	.	+	.	ID=YNL192W;Name=YNL192W;Alias=CHS1
-chrXIV	SGD	CDS	280432	281505	.	+	.	ID=YNL191W;Name=YNL191W;Alias=DUG3
-chrXIV	SGD	CDS	282395	283009	.	+	.	ID=YNL190W;Name=YNL190W;Alias=
-chrXIV	SGD	CDS	284260	285888	.	+	.	ID=YNL189W;Name=YNL189W;Alias=SRP1
-chrXIV	SGD	CDS	286308	287609	.	+	.	ID=YNL188W;Name=YNL188W;Alias=KAR1
-chrXIV	SGD	CDS	287994	289067	.	+	.	ID=YNL187W;Name=YNL187W;Alias=SWT21
-chrXIV	SGD	CDS	289498	291876	.	+	.	ID=YNL186W;Name=YNL186W;Alias=UBP10
-chrXIV	SGD	CDS	292193	292669	.	-	.	ID=YNL185C;Name=YNL185C;Alias=MRPL19
-chrXIV	SGD	CDS	292557	292883	.	-	.	ID=YNL184C;Name=YNL184C;Alias=
-chrXIV	SGD	CDS	293137	295509	.	-	.	ID=YNL183C;Name=YNL183C;Alias=NPR1
-chrXIV	SGD	CDS	295960	297627	.	-	.	ID=YNL182C;Name=YNL182C;Alias=IPI3
-chrXIV	SGD	CDS	298335	299558	.	+	.	ID=YNL181W;Name=YNL181W;Alias=PBR1
-chrXIV	SGD	CDS	299654	300649	.	-	.	ID=YNL180C;Name=YNL180C;Alias=RHO5
-chrXIV	SGD	CDS	302680	303402	.	+	.	ID=YNL178W;Name=YNL178W;Alias=RPS3
-chrXIV	SGD	CDS	303686	304615	.	-	.	ID=YNL177C;Name=YNL177C;Alias=MRPL22
-chrXIV	SGD	CDS	305070	306980	.	-	.	ID=YNL176C;Name=YNL176C;Alias=TDA7
-chrXIV	SGD	CDS	307401	308612	.	-	.	ID=YNL175C;Name=YNL175C;Alias=NOP13
-chrXIV	SGD	CDS	308957	310057	.	-	.	ID=YNL173C;Name=YNL173C;Alias=MDG1
-chrXIV	SGD	CDS	310636	315882	.	+	.	ID=YNL172W;Name=YNL172W;Alias=APC1
-chrXIV	SGD	CDS	316169	317671	.	-	.	ID=YNL169C;Name=YNL169C;Alias=PSD1
-chrXIV	SGD	CDS	318030	318809	.	-	.	ID=YNL168C;Name=YNL168C;Alias=FMP41
-chrXIV	SGD	CDS	319416	321359	.	-	.	ID=YNL167C;Name=YNL167C;Alias=SKO1
-chrXIV	SGD	CDS	322219	323565	.	-	.	ID=YNL166C;Name=YNL166C;Alias=BNI5
-chrXIV	SGD	CDS	323832	325052	.	+	.	ID=YNL165W;Name=YNL165W;Alias=
-chrXIV	SGD	CDS	325265	326320	.	-	.	ID=YNL164C;Name=YNL164C;Alias=IBD2
-chrXIV	SGD	CDS	326741	330073	.	-	.	ID=YNL163C;Name=YNL163C;Alias=RIA1
-chrXIV	SGD	CDS	330329	330547	.	+	.	ID=YNL162W-A;Name=YNL162W-A;Alias=
-chrXIV	SGD	CDS	331322	332154	.	+	.	ID=YNL162W;Name=YNL162W;Alias=RPL42A
-chrXIV	SGD	CDS	332597	334867	.	+	.	ID=YNL161W;Name=YNL161W;Alias=CBK1
-chrXIV	SGD	CDS	336545	337609	.	+	.	ID=YNL160W;Name=YNL160W;Alias=YGP1
-chrXIV	SGD	CDS	338478	339347	.	-	.	ID=YNL159C;Name=YNL159C;Alias=ASI2
-chrXIV	SGD	CDS	339612	340208	.	+	.	ID=YNL158W;Name=YNL158W;Alias=PGA1
-chrXIV	SGD	CDS	340352	340858	.	+	.	ID=YNL157W;Name=YNL157W;Alias=IGO1
-chrXIV	SGD	CDS	341069	341968	.	-	.	ID=YNL156C;Name=YNL156C;Alias=NSG2
-chrXIV	SGD	CDS	342516	343340	.	+	.	ID=YNL155W;Name=YNL155W;Alias=CUZ1
-chrXIV	SGD	CDS	343636	345276	.	-	.	ID=YNL154C;Name=YNL154C;Alias=YCK2
-chrXIV	SGD	CDS	345669	346058	.	-	.	ID=YNL153C;Name=YNL153C;Alias=GIM3
-chrXIV	SGD	CDS	346313	347542	.	+	.	ID=YNL152W;Name=YNL152W;Alias=INN1
-chrXIV	SGD	CDS	347766	348521	.	-	.	ID=YNL151C;Name=YNL151C;Alias=RPC31
-chrXIV	SGD	CDS	349367	349756	.	-	.	ID=YNL149C;Name=YNL149C;Alias=PGA2
-chrXIV	SGD	CDS	349907	350671	.	-	.	ID=YNL148C;Name=YNL148C;Alias=ALF1
-chrXIV	SGD	CDS	350940	351383	.	+	.	ID=YNL147W;Name=YNL147W;Alias=LSM7
-chrXIV	SGD	CDS	351386	351580	.	-	.	ID=YNL146C-A;Name=YNL146C-A;Alias=
-chrXIV	SGD	CDS	351715	352017	.	+	.	ID=YNL146W;Name=YNL146W;Alias=
-chrXIV	SGD	CDS	352414	352530	.	+	.	ID=YNL145W;Name=YNL145W;Alias=MFA2
-chrXIV	SGD	CDS	352820	355042	.	-	.	ID=YNL144C;Name=YNL144C;Alias=
-chrXIV	SGD	CDS	356794	357186	.	-	.	ID=YNL143C;Name=YNL143C;Alias=
-chrXIV	SGD	CDS	357453	358952	.	+	.	ID=YNL142W;Name=YNL142W;Alias=MEP2
-chrXIV	SGD	CDS	359596	360639	.	+	.	ID=YNL141W;Name=YNL141W;Alias=AAH1
-chrXIV	SGD	CDS	360917	361486	.	-	.	ID=YNL140C;Name=YNL140C;Alias=
-chrXIV	SGD	CDS	360924	365717	.	-	.	ID=YNL139C;Name=YNL139C;Alias=THO2
-chrXIV	SGD	CDS	366033	366412	.	+	.	ID=YNL138W-A;Name=YNL138W-A;Alias=YSF3
-chrXIV	SGD	CDS	366741	368321	.	+	.	ID=YNL138W;Name=YNL138W;Alias=SRV2
-chrXIV	SGD	CDS	368595	370055	.	-	.	ID=YNL137C;Name=YNL137C;Alias=NAM9
-chrXIV	SGD	CDS	370368	371645	.	+	.	ID=YNL136W;Name=YNL136W;Alias=EAF7
-chrXIV	SGD	CDS	371882	372226	.	-	.	ID=YNL135C;Name=YNL135C;Alias=FPR1
-chrXIV	SGD	CDS	372451	373581	.	-	.	ID=YNL134C;Name=YNL134C;Alias=
-chrXIV	SGD	CDS	374171	374692	.	-	.	ID=YNL133C;Name=YNL133C;Alias=FYV6
-chrXIV	SGD	CDS	375321	378491	.	+	.	ID=YNL132W;Name=YNL132W;Alias=KRE33
-chrXIV	SGD	CDS	378767	379225	.	+	.	ID=YNL131W;Name=YNL131W;Alias=TOM22
-chrXIV	SGD	CDS	379558	380831	.	-	.	ID=YNL130C;Name=YNL130C;Alias=CPT1
-chrXIV	SGD	CDS	381245	381391	.	-	.	ID=YNL130C-A;Name=YNL130C-A;Alias=DGR1
-chrXIV	SGD	CDS	381480	382202	.	+	.	ID=YNL129W;Name=YNL129W;Alias=NRK1
-chrXIV	SGD	CDS	382359	383663	.	+	.	ID=YNL128W;Name=YNL128W;Alias=TEP1
-chrXIV	SGD	CDS	383987	386848	.	+	.	ID=YNL127W;Name=YNL127W;Alias=FAR11
-chrXIV	SGD	CDS	387227	389767	.	+	.	ID=YNL126W;Name=YNL126W;Alias=SPC98
-chrXIV	SGD	CDS	390146	392167	.	-	.	ID=YNL125C;Name=YNL125C;Alias=ESBP6
-chrXIV	SGD	CDS	392892	394370	.	+	.	ID=YNL124W;Name=YNL124W;Alias=NAF1
-chrXIV	SGD	CDS	394685	397678	.	+	.	ID=YNL123W;Name=YNL123W;Alias=NMA111
-chrXIV	SGD	CDS	398023	398370	.	-	.	ID=YNL122C;Name=YNL122C;Alias=
-chrXIV	SGD	CDS	398684	400537	.	-	.	ID=YNL121C;Name=YNL121C;Alias=TOM70
-chrXIV	SGD	CDS	401040	402521	.	+	.	ID=YNL119W;Name=YNL119W;Alias=NCS2
-chrXIV	SGD	CDS	402652	405564	.	-	.	ID=YNL118C;Name=YNL118C;Alias=DCP2
-chrXIV	SGD	CDS	406358	408022	.	+	.	ID=YNL117W;Name=YNL117W;Alias=MLS1
-chrXIV	SGD	CDS	408341	409909	.	+	.	ID=YNL116W;Name=YNL116W;Alias=DMA2
-chrXIV	SGD	CDS	410119	412053	.	-	.	ID=YNL115C;Name=YNL115C;Alias=
-chrXIV	SGD	CDS	412771	413199	.	+	.	ID=YNL113W;Name=YNL113W;Alias=RPC19
-chrXIV	SGD	CDS	413639	416281	.	+	.	ID=YNL112W;Name=YNL112W;Alias=DBP2
-chrXIV	SGD	CDS	416940	417302	.	-	.	ID=YNL111C;Name=YNL111C;Alias=CYB5
-chrXIV	SGD	CDS	417826	418488	.	-	.	ID=YNL110C;Name=YNL110C;Alias=NOP15
-chrXIV	SGD	CDS	419014	419826	.	-	.	ID=YNL108C;Name=YNL108C;Alias=
-chrXIV	SGD	CDS	420098	420778	.	+	.	ID=YNL107W;Name=YNL107W;Alias=YAF9
-chrXIV	SGD	CDS	420944	424495	.	-	.	ID=YNL106C;Name=YNL106C;Alias=INP52
-chrXIV	SGD	CDS	424895	426754	.	-	.	ID=YNL104C;Name=YNL104C;Alias=LEU4
-chrXIV	SGD	CDS	427735	429753	.	+	.	ID=YNL103W;Name=YNL103W;Alias=MET4
-chrXIV	SGD	CDS	430087	434493	.	+	.	ID=YNL102W;Name=YNL102W;Alias=POL1
-chrXIV	SGD	CDS	434999	437140	.	+	.	ID=YNL101W;Name=YNL101W;Alias=AVT4
-chrXIV	SGD	CDS	437613	438317	.	+	.	ID=YNL100W;Name=YNL100W;Alias=MIC27
-chrXIV	SGD	CDS	438567	439283	.	-	.	ID=YNL099C;Name=YNL099C;Alias=OCA1
-chrXIV	SGD	CDS	439602	440570	.	-	.	ID=YNL098C;Name=YNL098C;Alias=RAS2
-chrXIV	SGD	CDS	440797	440919	.	-	.	ID=YNL097C-B;Name=YNL097C-B;Alias=
-chrXIV	SGD	CDS	441366	442358	.	-	.	ID=YNL097C;Name=YNL097C;Alias=PHO23
-chrXIV	SGD	CDS	443398	444315	.	-	.	ID=YNL096C;Name=YNL096C;Alias=RPS7B
-chrXIV	SGD	CDS	444912	446840	.	-	.	ID=YNL095C;Name=YNL095C;Alias=
-chrXIV	SGD	CDS	447611	449374	.	+	.	ID=YNL094W;Name=YNL094W;Alias=APP1
-chrXIV	SGD	CDS	449868	450530	.	+	.	ID=YNL093W;Name=YNL093W;Alias=YPT53
-chrXIV	SGD	CDS	450871	452073	.	+	.	ID=YNL092W;Name=YNL092W;Alias=
-chrXIV	SGD	CDS	452408	456130	.	+	.	ID=YNL091W;Name=YNL091W;Alias=NST1
-chrXIV	SGD	CDS	456565	457143	.	+	.	ID=YNL090W;Name=YNL090W;Alias=RHO2
-chrXIV	SGD	CDS	457704	461990	.	+	.	ID=YNL088W;Name=YNL088W;Alias=TOP2
-chrXIV	SGD	CDS	462411	465947	.	+	.	ID=YNL087W;Name=YNL087W;Alias=TCB2
-chrXIV	SGD	CDS	466334	466642	.	+	.	ID=YNL086W;Name=YNL086W;Alias=SNN1
-chrXIV	SGD	CDS	467131	469623	.	+	.	ID=YNL085W;Name=YNL085W;Alias=MKT1
-chrXIV	SGD	CDS	470053	471102	.	-	.	ID=YNL084C;Name=YNL084C;Alias=END3
-chrXIV	SGD	CDS	471377	472861	.	+	.	ID=YNL083W;Name=YNL083W;Alias=SAL1
-chrXIV	SGD	CDS	473391	476012	.	+	.	ID=YNL082W;Name=YNL082W;Alias=PMS1
-chrXIV	SGD	CDS	476188	476619	.	-	.	ID=YNL081C;Name=YNL081C;Alias=SWS2
-chrXIV	SGD	CDS	476932	478032	.	-	.	ID=YNL080C;Name=YNL080C;Alias=EOS1
-chrXIV	SGD	CDS	478566	479165	.	-	.	ID=YNL079C;Name=YNL079C;Alias=TPM1
-chrXIV	SGD	CDS	479768	480991	.	+	.	ID=YNL078W;Name=YNL078W;Alias=NIS1
-chrXIV	SGD	CDS	481391	482977	.	+	.	ID=YNL077W;Name=YNL077W;Alias=APJ1
-chrXIV	SGD	CDS	483556	485310	.	+	.	ID=YNL076W;Name=YNL076W;Alias=MKS1
-chrXIV	SGD	CDS	485607	486479	.	+	.	ID=YNL075W;Name=YNL075W;Alias=IMP4
-chrXIV	SGD	CDS	486766	488124	.	-	.	ID=YNL074C;Name=YNL074C;Alias=MLF3
-chrXIV	SGD	CDS	488386	490116	.	+	.	ID=YNL073W;Name=YNL073W;Alias=MSK1
-chrXIV	SGD	CDS	490317	491240	.	+	.	ID=YNL072W;Name=YNL072W;Alias=RNH201
-chrXIV	SGD	CDS	491523	492971	.	+	.	ID=YNL071W;Name=YNL071W;Alias=LAT1
-chrXIV	SGD	CDS	493366	493548	.	+	.	ID=YNL070W;Name=YNL070W;Alias=TOM7
-chrXIV	SGD	CDS	493956	495001	.	-	.	ID=YNL069C;Name=YNL069C;Alias=RPL16B
-chrXIV	SGD	CDS	495701	498289	.	-	.	ID=YNL068C;Name=YNL068C;Alias=FKH2
-chrXIV	SGD	CDS	499417	499557	.	+	.	ID=YNL067W-B;Name=YNL067W-B;Alias=
-chrXIV	SGD	CDS	499681	500256	.	+	.	ID=YNL067W;Name=YNL067W;Alias=RPL9B
-chrXIV	SGD	CDS	501157	502777	.	+	.	ID=YNL066W;Name=YNL066W;Alias=SUN4
-chrXIV	SGD	CDS	503724	505484	.	+	.	ID=YNL065W;Name=YNL065W;Alias=AQR1
-chrXIV	SGD	CDS	505868	507097	.	-	.	ID=YNL064C;Name=YNL064C;Alias=YDJ1
-chrXIV	SGD	CDS	507758	508702	.	+	.	ID=YNL063W;Name=YNL063W;Alias=MTQ1
-chrXIV	SGD	CDS	508776	510212	.	-	.	ID=YNL062C;Name=YNL062C;Alias=GCD10
-chrXIV	SGD	CDS	510540	512396	.	+	.	ID=YNL061W;Name=YNL061W;Alias=NOP2
-chrXIV	SGD	CDS	512668	514935	.	-	.	ID=YNL059C;Name=YNL059C;Alias=ARP5
-chrXIV	SGD	CDS	515763	516713	.	-	.	ID=YNL058C;Name=YNL058C;Alias=
-chrXIV	SGD	CDS	517249	517842	.	+	.	ID=YNL056W;Name=YNL056W;Alias=OCA2
-chrXIV	SGD	CDS	517994	518845	.	-	.	ID=YNL055C;Name=YNL055C;Alias=POR1
-chrXIV	SGD	CDS	526086	529583	.	+	.	ID=YNL054W;Name=YNL054W;Alias=VAC7
-chrXIV	SGD	CDS	529942	531411	.	+	.	ID=YNL053W;Name=YNL053W;Alias=MSG5
-chrXIV	SGD	CDS	531725	532186	.	+	.	ID=YNL052W;Name=YNL052W;Alias=COX5A
-chrXIV	SGD	CDS	532659	533870	.	+	.	ID=YNL051W;Name=YNL051W;Alias=COG5
-chrXIV	SGD	CDS	534079	534982	.	-	.	ID=YNL050C;Name=YNL050C;Alias=
-chrXIV	SGD	CDS	535281	537911	.	-	.	ID=YNL049C;Name=YNL049C;Alias=SFB2
-chrXIV	SGD	CDS	538173	539819	.	+	.	ID=YNL048W;Name=YNL048W;Alias=ALG11
-chrXIV	SGD	CDS	539911	541881	.	-	.	ID=YNL047C;Name=YNL047C;Alias=SLM2
-chrXIV	SGD	CDS	542304	542822	.	+	.	ID=YNL046W;Name=YNL046W;Alias=
-chrXIV	SGD	CDS	542963	544978	.	+	.	ID=YNL045W;Name=YNL045W;Alias=LAP2
-chrXIV	SGD	CDS	545268	545877	.	+	.	ID=YNL044W;Name=YNL044W;Alias=YIP3
-chrXIV	SGD	CDS	547113	547370	.	+	.	ID=YNL042W-B;Name=YNL042W-B;Alias=
-chrXIV	SGD	CDS	548100	549290	.	+	.	ID=YNL042W;Name=YNL042W;Alias=BOP3
-chrXIV	SGD	CDS	549468	551987	.	-	.	ID=YNL041C;Name=YNL041C;Alias=COG6
-chrXIV	SGD	CDS	553380	554750	.	+	.	ID=YNL040W;Name=YNL040W;Alias=
-chrXIV	SGD	CDS	555048	556832	.	+	.	ID=YNL039W;Name=YNL039W;Alias=BDP1
-chrXIV	SGD	CDS	557020	557783	.	+	.	ID=YNL038W;Name=YNL038W;Alias=GPI15
-chrXIV	SGD	CDS	557920	559002	.	-	.	ID=YNL037C;Name=YNL037C;Alias=IDH1
-chrXIV	SGD	CDS	559814	560479	.	+	.	ID=YNL036W;Name=YNL036W;Alias=NCE103
-chrXIV	SGD	CDS	568522	569691	.	-	.	ID=YNL035C;Name=YNL035C;Alias=
-chrXIV	SGD	CDS	570477	572315	.	+	.	ID=YNL034W;Name=YNL034W;Alias=
-chrXIV	SGD	CDS	572999	573853	.	+	.	ID=YNL033W;Name=YNL033W;Alias=
-chrXIV	SGD	CDS	574506	575351	.	+	.	ID=YNL032W;Name=YNL032W;Alias=SIW14
-chrXIV	SGD	CDS	575640	576050	.	-	.	ID=YNL031C;Name=YNL031C;Alias=HHT2
-chrXIV	SGD	CDS	576727	577038	.	+	.	ID=YNL030W;Name=YNL030W;Alias=HHF2
-chrXIV	SGD	CDS	577205	578773	.	-	.	ID=YNL029C;Name=YNL029C;Alias=KTR5
-chrXIV	SGD	CDS	579580	581616	.	+	.	ID=YNL027W;Name=YNL027W;Alias=CRZ1
-chrXIV	SGD	CDS	581920	583374	.	+	.	ID=YNL026W;Name=YNL026W;Alias=SAM50
-chrXIV	SGD	CDS	584320	585291	.	-	.	ID=YNL025C;Name=YNL025C;Alias=SSN8
-chrXIV	SGD	CDS	586602	586820	.	-	.	ID=YNL024C-A;Name=YNL024C-A;Alias=KSH1
-chrXIV	SGD	CDS	587107	587847	.	-	.	ID=YNL024C;Name=YNL024C;Alias=EFM6
-chrXIV	SGD	CDS	588263	591160	.	-	.	ID=YNL023C;Name=YNL023C;Alias=FAP1
-chrXIV	SGD	CDS	591427	592899	.	-	.	ID=YNL022C;Name=YNL022C;Alias=RCM1
-chrXIV	SGD	CDS	593227	595347	.	+	.	ID=YNL021W;Name=YNL021W;Alias=HDA1
-chrXIV	SGD	CDS	595623	597539	.	-	.	ID=YNL020C;Name=YNL020C;Alias=ARK1
-chrXIV	SGD	CDS	598376	599230	.	-	.	ID=YNL019C;Name=YNL019C;Alias=
-chrXIV	SGD	CDS	599936	601774	.	-	.	ID=YNL018C;Name=YNL018C;Alias=
-chrXIV	SGD	CDS	602907	604268	.	+	.	ID=YNL016W;Name=YNL016W;Alias=PUB1
-chrXIV	SGD	CDS	605384	605611	.	+	.	ID=YNL015W;Name=YNL015W;Alias=PBI2
-chrXIV	SGD	CDS	606319	609453	.	+	.	ID=YNL014W;Name=YNL014W;Alias=HEF3
-chrXIV	SGD	CDS	609686	611665	.	+	.	ID=YNL012W;Name=YNL012W;Alias=SPO1
-chrXIV	SGD	CDS	611836	613170	.	-	.	ID=YNL011C;Name=YNL011C;Alias=
-chrXIV	SGD	CDS	613635	614360	.	+	.	ID=YNL010W;Name=YNL010W;Alias=
-chrXIV	SGD	CDS	614821	616083	.	+	.	ID=YNL009W;Name=YNL009W;Alias=IDP3
-chrXIV	SGD	CDS	616211	618241	.	-	.	ID=YNL008C;Name=YNL008C;Alias=ASI3
-chrXIV	SGD	CDS	618507	619565	.	-	.	ID=YNL007C;Name=YNL007C;Alias=SIS1
-chrXIV	SGD	CDS	620067	620978	.	+	.	ID=YNL006W;Name=YNL006W;Alias=LST8
-chrXIV	SGD	CDS	621313	622428	.	-	.	ID=YNL005C;Name=YNL005C;Alias=MRP7
-chrXIV	SGD	CDS	622915	624621	.	+	.	ID=YNL004W;Name=YNL004W;Alias=HRB1
-chrXIV	SGD	CDS	624975	625829	.	-	.	ID=YNL003C;Name=YNL003C;Alias=PET8
-chrXIV	SGD	CDS	626174	627142	.	-	.	ID=YNL002C;Name=YNL002C;Alias=RLP7
-chrXIV	SGD	CDS	627456	628616	.	+	.	ID=YNL001W;Name=YNL001W;Alias=DOM34
-chrXIV	SGD	CDS	629622	631061	.	-	.	ID=YNR001C;Name=YNR001C;Alias=CIT1
-chrXIV	SGD	CDS	633008	633856	.	-	.	ID=YNR002C;Name=YNR002C;Alias=ATO2
-chrXIV	SGD	CDS	634344	635297	.	-	.	ID=YNR003C;Name=YNR003C;Alias=RPC34
-chrXIV	SGD	CDS	635943	636383	.	+	.	ID=YNR004W;Name=YNR004W;Alias=SWM2
-chrXIV	SGD	CDS	636986	638854	.	+	.	ID=YNR006W;Name=YNR006W;Alias=VPS27
-chrXIV	SGD	CDS	639182	640114	.	-	.	ID=YNR007C;Name=YNR007C;Alias=ATG3
-chrXIV	SGD	CDS	640396	642381	.	+	.	ID=YNR008W;Name=YNR008W;Alias=LRO1
-chrXIV	SGD	CDS	642690	643439	.	+	.	ID=YNR009W;Name=YNR009W;Alias=NRM1
-chrXIV	SGD	CDS	643744	644193	.	+	.	ID=YNR010W;Name=YNR010W;Alias=CSE2
-chrXIV	SGD	CDS	644320	646950	.	-	.	ID=YNR011C;Name=YNR011C;Alias=PRP2
-chrXIV	SGD	CDS	647432	648937	.	+	.	ID=YNR012W;Name=YNR012W;Alias=URK1
-chrXIV	SGD	CDS	649028	651712	.	-	.	ID=YNR013C;Name=YNR013C;Alias=PHO91
-chrXIV	SGD	CDS	652465	653103	.	+	.	ID=YNR014W;Name=YNR014W;Alias=
-chrXIV	SGD	CDS	653387	654541	.	+	.	ID=YNR015W;Name=YNR015W;Alias=SMM1
-chrXIV	SGD	CDS	654673	661374	.	-	.	ID=YNR016C;Name=YNR016C;Alias=ACC1
-chrXIV	SGD	CDS	662913	663581	.	+	.	ID=YNR017W;Name=YNR017W;Alias=TIM23
-chrXIV	SGD	CDS	664270	664944	.	+	.	ID=YNR018W;Name=YNR018W;Alias=RCF2
-chrXIV	SGD	CDS	665339	667267	.	+	.	ID=YNR019W;Name=YNR019W;Alias=ARE2
-chrXIV	SGD	CDS	667410	668222	.	-	.	ID=YNR020C;Name=YNR020C;Alias=ATP23
-chrXIV	SGD	CDS	668377	669591	.	+	.	ID=YNR021W;Name=YNR021W;Alias=
-chrXIV	SGD	CDS	669774	670193	.	-	.	ID=YNR022C;Name=YNR022C;Alias=MRPL50
-chrXIV	SGD	CDS	670418	672118	.	+	.	ID=YNR023W;Name=YNR023W;Alias=SNF12
-chrXIV	SGD	CDS	672409	672969	.	+	.	ID=YNR024W;Name=YNR024W;Alias=MPP6
-chrXIV	SGD	CDS	673274	674689	.	-	.	ID=YNR026C;Name=YNR026C;Alias=SEC12
-chrXIV	SGD	CDS	674923	675876	.	+	.	ID=YNR027W;Name=YNR027W;Alias=BUD17
-chrXIV	SGD	CDS	676177	677103	.	+	.	ID=YNR028W;Name=YNR028W;Alias=CPR8
-chrXIV	SGD	CDS	677199	678488	.	-	.	ID=YNR029C;Name=YNR029C;Alias=
-chrXIV	SGD	CDS	678799	680454	.	+	.	ID=YNR030W;Name=YNR030W;Alias=ALG12
-chrXIV	SGD	CDS	680694	685433	.	-	.	ID=YNR031C;Name=YNR031C;Alias=SSK2
-chrXIV	SGD	CDS	686010	687116	.	+	.	ID=YNR032W;Name=YNR032W;Alias=PPG1
-chrXIV	SGD	CDS	687243	687464	.	-	.	ID=YNR032C-A;Name=YNR032C-A;Alias=HUB1
-chrXIV	SGD	CDS	687635	689998	.	+	.	ID=YNR033W;Name=YNR033W;Alias=ABZ1
-chrXIV	SGD	CDS	690321	691286	.	+	.	ID=YNR034W;Name=YNR034W;Alias=SOL1
-chrXIV	SGD	CDS	692561	692857	.	+	.	ID=YNR034W-A;Name=YNR034W-A;Alias=EGO4
-chrXIV	SGD	CDS	693019	694047	.	-	.	ID=YNR035C;Name=YNR035C;Alias=ARC35
-chrXIV	SGD	CDS	694361	694822	.	-	.	ID=YNR036C;Name=YNR036C;Alias=MRPS12
-chrXIV	SGD	CDS	695052	695327	.	-	.	ID=YNR037C;Name=YNR037C;Alias=RSM19
-chrXIV	SGD	CDS	695595	697484	.	+	.	ID=YNR038W;Name=YNR038W;Alias=DBP6
-chrXIV	SGD	CDS	697614	699431	.	-	.	ID=YNR039C;Name=YNR039C;Alias=ZRG17
-chrXIV	SGD	CDS	699690	700460	.	+	.	ID=YNR040W;Name=YNR040W;Alias=
-chrXIV	SGD	CDS	700541	701659	.	-	.	ID=YNR041C;Name=YNR041C;Alias=COQ2
-chrXIV	SGD	CDS	701895	703085	.	+	.	ID=YNR043W;Name=YNR043W;Alias=MVD1
-chrXIV	SGD	CDS	703699	705876	.	+	.	ID=YNR044W;Name=YNR044W;Alias=AGA1
-chrXIV	SGD	CDS	706139	707608	.	+	.	ID=YNR045W;Name=YNR045W;Alias=PET494
-chrXIV	SGD	CDS	707788	708195	.	+	.	ID=YNR046W;Name=YNR046W;Alias=TRM112
-chrXIV	SGD	CDS	708523	711204	.	+	.	ID=YNR047W;Name=YNR047W;Alias=FPK1
-chrXIV	SGD	CDS	711630	712811	.	+	.	ID=YNR048W;Name=YNR048W;Alias=
-chrXIV	SGD	CDS	713023	713655	.	-	.	ID=YNR049C;Name=YNR049C;Alias=MSO1
-chrXIV	SGD	CDS	714048	715388	.	-	.	ID=YNR050C;Name=YNR050C;Alias=LYS9
-chrXIV	SGD	CDS	716780	718327	.	-	.	ID=YNR051C;Name=YNR051C;Alias=BRE5
-chrXIV	SGD	CDS	719346	720647	.	-	.	ID=YNR052C;Name=YNR052C;Alias=POP2
-chrXIV	SGD	CDS	721120	723112	.	-	.	ID=YNR053C;Name=YNR053C;Alias=NOG2
-chrXIV	SGD	CDS	723356	724306	.	-	.	ID=YNR054C;Name=YNR054C;Alias=ESF2
-chrXIV	SGD	CDS	728426	730186	.	-	.	ID=YNR055C;Name=YNR055C;Alias=HOL1
-chrXIV	SGD	CDS	731618	733303	.	-	.	ID=YNR056C;Name=YNR056C;Alias=BIO5
-chrXIV	SGD	CDS	733356	734069	.	-	.	ID=YNR057C;Name=YNR057C;Alias=BIO4
-chrXIV	SGD	CDS	734291	735733	.	+	.	ID=YNR058W;Name=YNR058W;Alias=BIO3
-chrXIV	SGD	CDS	736803	738545	.	+	.	ID=YNR059W;Name=YNR059W;Alias=MNT4
-chrXIV	SGD	CDS	739951	742110	.	+	.	ID=YNR060W;Name=YNR060W;Alias=FRE4
-chrXIV	SGD	CDS	742881	743540	.	-	.	ID=YNR061C;Name=YNR061C;Alias=
-chrXIV	SGD	CDS	744360	745343	.	-	.	ID=YNR062C;Name=YNR062C;Alias=
-chrXIV	SGD	CDS	746943	748766	.	+	.	ID=YNR063W;Name=YNR063W;Alias=
-chrXIV	SGD	CDS	749136	750008	.	-	.	ID=YNR064C;Name=YNR064C;Alias=
-chrXIV	SGD	CDS	750350	753700	.	-	.	ID=YNR065C;Name=YNR065C;Alias=
-chrXIV	SGD	CDS	753725	755035	.	-	.	ID=YNR066C;Name=YNR066C;Alias=
-chrXIV	SGD	CDS	755746	759099	.	-	.	ID=YNR067C;Name=YNR067C;Alias=DSE4
-chrXIV	SGD	CDS	760067	760885	.	-	.	ID=YNR068C;Name=YNR068C;Alias=
-chrXIV	SGD	CDS	761123	762592	.	-	.	ID=YNR069C;Name=YNR069C;Alias=BSC5
-chrXIV	SGD	CDS	765375	769376	.	+	.	ID=YNR070W;Name=YNR070W;Alias=PDR18
-chrXIV	SGD	CDS	770440	771468	.	-	.	ID=YNR071C;Name=YNR071C;Alias=
-chrXIV	SGD	CDS	772657	774351	.	+	.	ID=YNR072W;Name=YNR072W;Alias=HXT17
-chrXIV	SGD	CDS	774792	776300	.	-	.	ID=YNR073C;Name=YNR073C;Alias=MAN2
-chrXIV	SGD	CDS	777602	778738	.	-	.	ID=YNR074C;Name=YNR074C;Alias=AIF1
-chrXIV	SGD	CDS	779916	781040	.	+	.	ID=YNR075W;Name=YNR075W;Alias=COS10
-chrXIV	SGD	CDS	781511	781603	.	-	.	ID=YNR075C-A;Name=YNR075C-A;Alias=
-chrXIV	SGD	CDS	781918	782280	.	+	.	ID=YNR076W;Name=YNR076W;Alias=PAU6
-chrXIV	SGD	CDS	783287	783541	.	-	.	ID=YNR077C;Name=YNR077C;Alias=
-chrXV	SGD	CDS	585	740	.	+	.	ID=YOL166W-A;Name=YOL166W-A;Alias=
-chrXV	SGD	CDS	1647	2078	.	-	.	ID=YOL165C;Name=YOL165C;Alias=AAD15
-chrXV	SGD	CDS	4130	4312	.	+	.	ID=YOL164W-A;Name=YOL164W-A;Alias=
-chrXV	SGD	CDS	6175	8115	.	+	.	ID=YOL164W;Name=YOL164W;Alias=BDS1
-chrXV	SGD	CDS	9597	10106	.	+	.	ID=YOL163W;Name=YOL163W;Alias=
-chrXV	SGD	CDS	10119	10766	.	+	.	ID=YOL162W;Name=YOL162W;Alias=
-chrXV	SGD	CDS	11549	11911	.	-	.	ID=YOL161C;Name=YOL161C;Alias=PAU20
-chrXV	SGD	CDS	15233	15505	.	-	.	ID=YOL159C-A;Name=YOL159C-A;Alias=
-chrXV	SGD	CDS	17281	17796	.	-	.	ID=YOL159C;Name=YOL159C;Alias=CSS3
-chrXV	SGD	CDS	19491	21311	.	-	.	ID=YOL158C;Name=YOL158C;Alias=ENB1
-chrXV	SGD	CDS	22525	24294	.	-	.	ID=YOL157C;Name=YOL157C;Alias=IMA2
-chrXV	SGD	CDS	25273	26976	.	+	.	ID=YOL156W;Name=YOL156W;Alias=HXT11
-chrXV	SGD	CDS	27084	27218	.	+	.	ID=YOL155W-A;Name=YOL155W-A;Alias=
-chrXV	SGD	CDS	28703	31606	.	-	.	ID=YOL155C;Name=YOL155C;Alias=HPF1
-chrXV	SGD	CDS	34658	35407	.	+	.	ID=YOL154W;Name=YOL154W;Alias=ZPS1
-chrXV	SGD	CDS	40748	42610	.	+	.	ID=YOL152W;Name=YOL152W;Alias=FRE7
-chrXV	SGD	CDS	43694	44722	.	+	.	ID=YOL151W;Name=YOL151W;Alias=GRE2
-chrXV	SGD	CDS	44938	45633	.	+	.	ID=YOL149W;Name=YOL149W;Alias=DCP1
-chrXV	SGD	CDS	45760	47574	.	-	.	ID=YOL148C;Name=YOL148C;Alias=SPT20
-chrXV	SGD	CDS	47933	48643	.	-	.	ID=YOL147C;Name=YOL147C;Alias=PEX11
-chrXV	SGD	CDS	48864	49448	.	+	.	ID=YOL146W;Name=YOL146W;Alias=PSF3
-chrXV	SGD	CDS	49555	52788	.	-	.	ID=YOL145C;Name=YOL145C;Alias=CTR9
-chrXV	SGD	CDS	53098	54552	.	+	.	ID=YOL144W;Name=YOL144W;Alias=NOP8
-chrXV	SGD	CDS	54595	55104	.	-	.	ID=YOL143C;Name=YOL143C;Alias=RIB4
-chrXV	SGD	CDS	55558	56280	.	+	.	ID=YOL142W;Name=YOL142W;Alias=RRP40
-chrXV	SGD	CDS	56452	58539	.	+	.	ID=YOL141W;Name=YOL141W;Alias=PPM2
-chrXV	SGD	CDS	58759	60030	.	+	.	ID=YOL140W;Name=YOL140W;Alias=ARG8
-chrXV	SGD	CDS	60383	61024	.	-	.	ID=YOL139C;Name=YOL139C;Alias=CDC33
-chrXV	SGD	CDS	61325	65350	.	-	.	ID=YOL138C;Name=YOL138C;Alias=RTC1
-chrXV	SGD	CDS	65621	67114	.	+	.	ID=YOL137W;Name=YOL137W;Alias=BSC6
-chrXV	SGD	CDS	67561	68754	.	-	.	ID=YOL136C;Name=YOL136C;Alias=PFK27
-chrXV	SGD	CDS	69376	70044	.	-	.	ID=YOL135C;Name=YOL135C;Alias=MED7
-chrXV	SGD	CDS	70325	70690	.	+	.	ID=YOL133W;Name=YOL133W;Alias=HRT1
-chrXV	SGD	CDS	71300	72715	.	+	.	ID=YOL132W;Name=YOL132W;Alias=GAS4
-chrXV	SGD	CDS	73031	73357	.	+	.	ID=YOL131W;Name=YOL131W;Alias=
-chrXV	SGD	CDS	74400	76979	.	+	.	ID=YOL130W;Name=YOL130W;Alias=ALR1
-chrXV	SGD	CDS	77560	78114	.	+	.	ID=YOL129W;Name=YOL129W;Alias=VPS68
-chrXV	SGD	CDS	78352	79479	.	-	.	ID=YOL128C;Name=YOL128C;Alias=YGK3
-chrXV	SGD	CDS	80348	81190	.	+	.	ID=YOL127W;Name=YOL127W;Alias=RPL25
-chrXV	SGD	CDS	81787	82920	.	-	.	ID=YOL126C;Name=YOL126C;Alias=MDH2
-chrXV	SGD	CDS	83834	85264	.	+	.	ID=YOL125W;Name=YOL125W;Alias=TRM13
-chrXV	SGD	CDS	85456	86757	.	-	.	ID=YOL124C;Name=YOL124C;Alias=TRM11
-chrXV	SGD	CDS	87844	89448	.	+	.	ID=YOL123W;Name=YOL123W;Alias=HRP1
-chrXV	SGD	CDS	89692	91419	.	-	.	ID=YOL122C;Name=YOL122C;Alias=SMF1
-chrXV	SGD	CDS	92026	92850	.	-	.	ID=YOL121C;Name=YOL121C;Alias=RPS19A
-chrXV	SGD	CDS	93395	94402	.	-	.	ID=YOL120C;Name=YOL120C;Alias=RPL18A
-chrXV	SGD	CDS	94856	96361	.	-	.	ID=YOL119C;Name=YOL119C;Alias=MCH4
-chrXV	SGD	CDS	97551	99488	.	+	.	ID=YOL117W;Name=YOL117W;Alias=RRI2
-chrXV	SGD	CDS	99809	100957	.	+	.	ID=YOL116W;Name=YOL116W;Alias=MSN1
-chrXV	SGD	CDS	101475	103229	.	+	.	ID=YOL115W;Name=YOL115W;Alias=PAP2
-chrXV	SGD	CDS	103317	103925	.	-	.	ID=YOL114C;Name=YOL114C;Alias=PTH4
-chrXV	SGD	CDS	104326	106293	.	+	.	ID=YOL113W;Name=YOL113W;Alias=SKM1
-chrXV	SGD	CDS	106710	108188	.	+	.	ID=YOL112W;Name=YOL112W;Alias=MSB4
-chrXV	SGD	CDS	108258	108896	.	-	.	ID=YOL111C;Name=YOL111C;Alias=MDY2
-chrXV	SGD	CDS	109176	109889	.	+	.	ID=YOL110W;Name=YOL110W;Alias=SHR5
-chrXV	SGD	CDS	110297	110638	.	+	.	ID=YOL109W;Name=YOL109W;Alias=ZEO1
-chrXV	SGD	CDS	111431	111886	.	-	.	ID=YOL108C;Name=YOL108C;Alias=INO4
-chrXV	SGD	CDS	112102	113130	.	+	.	ID=YOL107W;Name=YOL107W;Alias=
-chrXV	SGD	CDS	114138	115808	.	-	.	ID=YOL105C;Name=YOL105C;Alias=WSC3
-chrXV	SGD	CDS	116396	117454	.	-	.	ID=YOL104C;Name=YOL104C;Alias=NDJ1
-chrXV	SGD	CDS	124001	125830	.	+	.	ID=YOL103W;Name=YOL103W;Alias=ITR2
-chrXV	SGD	CDS	125997	126689	.	-	.	ID=YOL102C;Name=YOL102C;Alias=TPT1
-chrXV	SGD	CDS	126982	127920	.	-	.	ID=YOL101C;Name=YOL101C;Alias=IZH4
-chrXV	SGD	CDS	129237	132482	.	+	.	ID=YOL100W;Name=YOL100W;Alias=PKH2
-chrXV	SGD	CDS	132725	135838	.	-	.	ID=YOL098C;Name=YOL098C;Alias=SDD3
-chrXV	SGD	CDS	136220	136405	.	+	.	ID=YOL097W-A;Name=YOL097W-A;Alias=
-chrXV	SGD	CDS	136527	137825	.	-	.	ID=YOL097C;Name=YOL097C;Alias=WRS1
-chrXV	SGD	CDS	138107	139045	.	-	.	ID=YOL096C;Name=YOL096C;Alias=COQ3
-chrXV	SGD	CDS	139227	141347	.	-	.	ID=YOL095C;Name=YOL095C;Alias=HMI1
-chrXV	SGD	CDS	141584	142555	.	-	.	ID=YOL094C;Name=YOL094C;Alias=RFC4
-chrXV	SGD	CDS	142815	143696	.	+	.	ID=YOL093W;Name=YOL093W;Alias=TRM10
-chrXV	SGD	CDS	144204	145130	.	+	.	ID=YOL092W;Name=YOL092W;Alias=YPQ1
-chrXV	SGD	CDS	145334	147163	.	+	.	ID=YOL091W;Name=YOL091W;Alias=SPO21
-chrXV	SGD	CDS	147382	150276	.	+	.	ID=YOL090W;Name=YOL090W;Alias=MSH2
-chrXV	SGD	CDS	150398	153490	.	-	.	ID=YOL089C;Name=YOL089C;Alias=HAL9
-chrXV	SGD	CDS	153912	154745	.	-	.	ID=YOL088C;Name=YOL088C;Alias=MPD2
-chrXV	SGD	CDS	155287	158637	.	-	.	ID=YOL087C;Name=YOL087C;Alias=DUF1
-chrXV	SGD	CDS	159173	159445	.	+	.	ID=YOL086W-A;Name=YOL086W-A;Alias=MHF1
-chrXV	SGD	CDS	159548	160594	.	-	.	ID=YOL086C;Name=YOL086C;Alias=ADH1
-chrXV	SGD	CDS	162356	165331	.	+	.	ID=YOL084W;Name=YOL084W;Alias=PHM7
-chrXV	SGD	CDS	165714	166952	.	+	.	ID=YOL083W;Name=YOL083W;Alias=ATG34
-chrXV	SGD	CDS	168727	169974	.	+	.	ID=YOL082W;Name=YOL082W;Alias=ATG19
-chrXV	SGD	CDS	171070	180309	.	+	.	ID=YOL081W;Name=YOL081W;Alias=IRA2
-chrXV	SGD	CDS	180558	181427	.	-	.	ID=YOL080C;Name=YOL080C;Alias=REX4
-chrXV	SGD	CDS	181682	185212	.	+	.	ID=YOL078W;Name=YOL078W;Alias=AVO1
-chrXV	SGD	CDS	185438	185644	.	+	.	ID=YOL077W-A;Name=YOL077W-A;Alias=ATP19
-chrXV	SGD	CDS	185848	186723	.	-	.	ID=YOL077C;Name=YOL077C;Alias=BRX1
-chrXV	SGD	CDS	187024	189414	.	+	.	ID=YOL076W;Name=YOL076W;Alias=MDM20
-chrXV	SGD	CDS	189658	193542	.	-	.	ID=YOL075C;Name=YOL075C;Alias=
-chrXV	SGD	CDS	193832	194800	.	-	.	ID=YOL073C;Name=YOL073C;Alias=DSC2
-chrXV	SGD	CDS	194970	196337	.	+	.	ID=YOL072W;Name=YOL072W;Alias=THP1
-chrXV	SGD	CDS	196507	196995	.	+	.	ID=YOL071W;Name=YOL071W;Alias=SDH5
-chrXV	SGD	CDS	197220	198725	.	-	.	ID=YOL070C;Name=YOL070C;Alias=NBA1
-chrXV	SGD	CDS	198942	200297	.	+	.	ID=YOL069W;Name=YOL069W;Alias=NUF2
-chrXV	SGD	CDS	200368	201879	.	-	.	ID=YOL068C;Name=YOL068C;Alias=HST1
-chrXV	SGD	CDS	201985	202518	.	-	.	ID=YOL067C;Name=YOL067C;Alias=RTG1
-chrXV	SGD	CDS	202696	204471	.	-	.	ID=YOL066C;Name=YOL066C;Alias=RIB2
-chrXV	SGD	CDS	204731	205885	.	-	.	ID=YOL065C;Name=YOL065C;Alias=INP54
-chrXV	SGD	CDS	206103	207176	.	-	.	ID=YOL064C;Name=YOL064C;Alias=MET22
-chrXV	SGD	CDS	207392	210265	.	-	.	ID=YOL063C;Name=YOL063C;Alias=CRT10
-chrXV	SGD	CDS	210520	211995	.	-	.	ID=YOL062C;Name=YOL062C;Alias=APM4
-chrXV	SGD	CDS	212244	213734	.	+	.	ID=YOL061W;Name=YOL061W;Alias=PRS5
-chrXV	SGD	CDS	214017	216137	.	-	.	ID=YOL060C;Name=YOL060C;Alias=MAM3
-chrXV	SGD	CDS	217126	218448	.	+	.	ID=YOL059W;Name=YOL059W;Alias=GPD2
-chrXV	SGD	CDS	219211	220473	.	+	.	ID=YOL058W;Name=YOL058W;Alias=ARG1
-chrXV	SGD	CDS	220767	222902	.	+	.	ID=YOL057W;Name=YOL057W;Alias=
-chrXV	SGD	CDS	223268	224179	.	+	.	ID=YOL056W;Name=YOL056W;Alias=GPM3
-chrXV	SGD	CDS	224420	226075	.	-	.	ID=YOL055C;Name=YOL055C;Alias=THI20
-chrXV	SGD	CDS	228614	229834	.	+	.	ID=YOL054W;Name=YOL054W;Alias=PSH1
-chrXV	SGD	CDS	230085	231272	.	+	.	ID=YOL053W;Name=YOL053W;Alias=AIM39
-chrXV	SGD	CDS	231570	231755	.	-	.	ID=YOL052C-A;Name=YOL052C-A;Alias=DDR2
-chrXV	SGD	CDS	232446	233636	.	-	.	ID=YOL052C;Name=YOL052C;Alias=SPE2
-chrXV	SGD	CDS	234940	238185	.	+	.	ID=YOL051W;Name=YOL051W;Alias=GAL11
-chrXV	SGD	CDS	238619	240094	.	+	.	ID=YOL049W;Name=YOL049W;Alias=GSH2
-chrXV	SGD	CDS	240204	241310	.	-	.	ID=YOL048C;Name=YOL048C;Alias=RRT8
-chrXV	SGD	CDS	241614	242747	.	-	.	ID=YOL047C;Name=YOL047C;Alias=LDS2
-chrXV	SGD	CDS	243497	246802	.	+	.	ID=YOL045W;Name=YOL045W;Alias=PSK2
-chrXV	SGD	CDS	247150	248301	.	+	.	ID=YOL044W;Name=YOL044W;Alias=PEX15
-chrXV	SGD	CDS	248392	249534	.	-	.	ID=YOL043C;Name=YOL043C;Alias=NTG2
-chrXV	SGD	CDS	249825	250916	.	+	.	ID=YOL042W;Name=YOL042W;Alias=NGL1
-chrXV	SGD	CDS	251267	252646	.	-	.	ID=YOL041C;Name=YOL041C;Alias=NOP12
-chrXV	SGD	CDS	253149	253577	.	-	.	ID=YOL040C;Name=YOL040C;Alias=RPS15
-chrXV	SGD	CDS	254297	254617	.	+	.	ID=YOL039W;Name=YOL039W;Alias=RPP2A
-chrXV	SGD	CDS	254926	255021	.	-	.	ID=YOL038C-A;Name=YOL038C-A;Alias=
-chrXV	SGD	CDS	255337	256101	.	+	.	ID=YOL038W;Name=YOL038W;Alias=PRE6
-chrXV	SGD	CDS	256745	259030	.	+	.	ID=YOL036W;Name=YOL036W;Alias=
-chrXV	SGD	CDS	259923	263204	.	+	.	ID=YOL034W;Name=YOL034W;Alias=SMC5
-chrXV	SGD	CDS	263475	265085	.	+	.	ID=YOL033W;Name=YOL033W;Alias=MSE1
-chrXV	SGD	CDS	265429	266169	.	+	.	ID=YOL032W;Name=YOL032W;Alias=OPI10
-chrXV	SGD	CDS	266264	267529	.	-	.	ID=YOL031C;Name=YOL031C;Alias=SIL1
-chrXV	SGD	CDS	268187	269641	.	+	.	ID=YOL030W;Name=YOL030W;Alias=GAS5
-chrXV	SGD	CDS	269815	270420	.	-	.	ID=YOL029C;Name=YOL029C;Alias=
-chrXV	SGD	CDS	270633	271370	.	-	.	ID=YOL028C;Name=YOL028C;Alias=YAP7
-chrXV	SGD	CDS	272003	273724	.	-	.	ID=YOL027C;Name=YOL027C;Alias=MDM38
-chrXV	SGD	CDS	274012	274353	.	-	.	ID=YOL026C;Name=YOL026C;Alias=MIM1
-chrXV	SGD	CDS	274957	276939	.	+	.	ID=YOL025W;Name=YOL025W;Alias=LAG2
-chrXV	SGD	CDS	277086	277604	.	+	.	ID=YOL024W;Name=YOL024W;Alias=
-chrXV	SGD	CDS	278056	280086	.	+	.	ID=YOL023W;Name=YOL023W;Alias=IFM1
-chrXV	SGD	CDS	280272	281498	.	-	.	ID=YOL022C;Name=YOL022C;Alias=TSR4
-chrXV	SGD	CDS	282421	285426	.	-	.	ID=YOL021C;Name=YOL021C;Alias=DIS3
-chrXV	SGD	CDS	286172	287950	.	+	.	ID=YOL020W;Name=YOL020W;Alias=TAT2
-chrXV	SGD	CDS	288420	288572	.	+	.	ID=YOL019W-A;Name=YOL019W-A;Alias=
-chrXV	SGD	CDS	288898	290553	.	+	.	ID=YOL019W;Name=YOL019W;Alias=
-chrXV	SGD	CDS	290881	292074	.	-	.	ID=YOL018C;Name=YOL018C;Alias=TLG2
-chrXV	SGD	CDS	292529	294673	.	+	.	ID=YOL017W;Name=YOL017W;Alias=ESC8
-chrXV	SGD	CDS	294777	296120	.	-	.	ID=YOL016C;Name=YOL016C;Alias=CMK2
-chrXV	SGD	CDS	297078	298838	.	+	.	ID=YOL015W;Name=YOL015W;Alias=IRC10
-chrXV	SGD	CDS	299693	300067	.	+	.	ID=YOL014W;Name=YOL014W;Alias=
-chrXV	SGD	CDS	301047	301238	.	+	.	ID=YOL013W-A;Name=YOL013W-A;Alias=
-chrXV	SGD	CDS	301380	303035	.	-	.	ID=YOL013C;Name=YOL013C;Alias=HRD1
-chrXV	SGD	CDS	303579	303983	.	-	.	ID=YOL012C;Name=YOL012C;Alias=HTZ1
-chrXV	SGD	CDS	305349	307409	.	+	.	ID=YOL011W;Name=YOL011W;Alias=PLB3
-chrXV	SGD	CDS	307938	309041	.	+	.	ID=YOL010W;Name=YOL010W;Alias=RCL1
-chrXV	SGD	CDS	309324	310139	.	-	.	ID=YOL009C;Name=YOL009C;Alias=MDM12
-chrXV	SGD	CDS	310312	310935	.	+	.	ID=YOL008W;Name=YOL008W;Alias=COQ10
-chrXV	SGD	CDS	311342	312367	.	-	.	ID=YOL007C;Name=YOL007C;Alias=CSI2
-chrXV	SGD	CDS	313078	315387	.	-	.	ID=YOL006C;Name=YOL006C;Alias=TOP1
-chrXV	SGD	CDS	315813	316175	.	-	.	ID=YOL005C;Name=YOL005C;Alias=RPB11
-chrXV	SGD	CDS	316938	321548	.	+	.	ID=YOL004W;Name=YOL004W;Alias=SIN3
-chrXV	SGD	CDS	321858	322994	.	-	.	ID=YOL003C;Name=YOL003C;Alias=PFA4
-chrXV	SGD	CDS	323411	324364	.	-	.	ID=YOL002C;Name=YOL002C;Alias=IZH2
-chrXV	SGD	CDS	325249	326130	.	+	.	ID=YOL001W;Name=YOL001W;Alias=PHO80
-chrXV	SGD	CDS	326832	329033	.	+	.	ID=YOR001W;Name=YOR001W;Alias=RRP6
-chrXV	SGD	CDS	329417	331051	.	+	.	ID=YOR002W;Name=YOR002W;Alias=ALG6
-chrXV	SGD	CDS	331455	332891	.	+	.	ID=YOR003W;Name=YOR003W;Alias=YSP3
-chrXV	SGD	CDS	333592	334356	.	+	.	ID=YOR004W;Name=YOR004W;Alias=UTP23
-chrXV	SGD	CDS	334509	337343	.	-	.	ID=YOR005C;Name=YOR005C;Alias=DNL4
-chrXV	SGD	CDS	337680	338621	.	-	.	ID=YOR006C;Name=YOR006C;Alias=TSR3
-chrXV	SGD	CDS	338938	339978	.	-	.	ID=YOR007C;Name=YOR007C;Alias=SGT2
-chrXV	SGD	CDS	341278	342414	.	-	.	ID=YOR008C;Name=YOR008C;Alias=SLG1
-chrXV	SGD	CDS	342857	343081	.	-	.	ID=YOR008C-A;Name=YOR008C-A;Alias=
-chrXV	SGD	CDS	344335	345798	.	+	.	ID=YOR009W;Name=YOR009W;Alias=TIR4
-chrXV	SGD	CDS	346195	346950	.	-	.	ID=YOR010C;Name=YOR010C;Alias=TIR2
-chrXV	SGD	CDS	349679	353863	.	+	.	ID=YOR011W;Name=YOR011W;Alias=AUS1
-chrXV	SGD	CDS	355652	355858	.	+	.	ID=YOR011W-A;Name=YOR011W-A;Alias=
-chrXV	SGD	CDS	356543	356956	.	+	.	ID=YOR012W;Name=YOR012W;Alias=
-chrXV	SGD	CDS	357674	359947	.	+	.	ID=YOR014W;Name=YOR014W;Alias=RTS1
-chrXV	SGD	CDS	360461	361084	.	-	.	ID=YOR016C;Name=YOR016C;Alias=ERP4
-chrXV	SGD	CDS	361412	363814	.	+	.	ID=YOR017W;Name=YOR017W;Alias=PET127
-chrXV	SGD	CDS	364369	366882	.	+	.	ID=YOR018W;Name=YOR018W;Alias=ROD1
-chrXV	SGD	CDS	368127	370319	.	+	.	ID=YOR019W;Name=YOR019W;Alias=
-chrXV	SGD	CDS	370524	370844	.	-	.	ID=YOR020C;Name=YOR020C;Alias=HSP10
-chrXV	SGD	CDS	371685	371957	.	+	.	ID=YOR020W-A;Name=YOR020W-A;Alias=
-chrXV	SGD	CDS	372798	373439	.	-	.	ID=YOR021C;Name=YOR021C;Alias=SFM1
-chrXV	SGD	CDS	373710	375857	.	-	.	ID=YOR022C;Name=YOR022C;Alias=DDL1
-chrXV	SGD	CDS	376012	377712	.	-	.	ID=YOR023C;Name=YOR023C;Alias=AHC1
-chrXV	SGD	CDS	378219	379562	.	+	.	ID=YOR025W;Name=YOR025W;Alias=HST3
-chrXV	SGD	CDS	379781	380806	.	+	.	ID=YOR026W;Name=YOR026W;Alias=BUB3
-chrXV	SGD	CDS	381053	382822	.	+	.	ID=YOR027W;Name=YOR027W;Alias=STI1
-chrXV	SGD	CDS	383533	384420	.	-	.	ID=YOR028C;Name=YOR028C;Alias=CIN5
-chrXV	SGD	CDS	386825	388684	.	+	.	ID=YOR030W;Name=YOR030W;Alias=DFG16
-chrXV	SGD	CDS	389771	391075	.	-	.	ID=YOR032C;Name=YOR032C;Alias=HMS1
-chrXV	SGD	CDS	392176	392376	.	+	.	ID=YOR032W-A;Name=YOR032W-A;Alias=
-chrXV	SGD	CDS	392416	394524	.	-	.	ID=YOR033C;Name=YOR033C;Alias=EXO1
-chrXV	SGD	CDS	394837	397086	.	-	.	ID=YOR034C;Name=YOR034C;Alias=AKR2
-chrXV	SGD	CDS	397426	397668	.	-	.	ID=YOR034C-A;Name=YOR034C-A;Alias=
-chrXV	SGD	CDS	397735	400104	.	-	.	ID=YOR035C;Name=YOR035C;Alias=SHE4
-chrXV	SGD	CDS	400348	401214	.	+	.	ID=YOR036W;Name=YOR036W;Alias=PEP12
-chrXV	SGD	CDS	401555	402655	.	+	.	ID=YOR037W;Name=YOR037W;Alias=CYC2
-chrXV	SGD	CDS	402761	405388	.	-	.	ID=YOR038C;Name=YOR038C;Alias=HIR2
-chrXV	SGD	CDS	405768	406544	.	+	.	ID=YOR039W;Name=YOR039W;Alias=CKB2
-chrXV	SGD	CDS	407064	407921	.	+	.	ID=YOR040W;Name=YOR040W;Alias=GLO4
-chrXV	SGD	CDS	408425	409660	.	+	.	ID=YOR042W;Name=YOR042W;Alias=CUE5
-chrXV	SGD	CDS	410870	412330	.	+	.	ID=YOR043W;Name=YOR043W;Alias=WHI2
-chrXV	SGD	CDS	413007	413480	.	+	.	ID=YOR044W;Name=YOR044W;Alias=IRC23
-chrXV	SGD	CDS	413852	414037	.	+	.	ID=YOR045W;Name=YOR045W;Alias=TOM6
-chrXV	SGD	CDS	414459	415907	.	-	.	ID=YOR046C;Name=YOR046C;Alias=DBP5
-chrXV	SGD	CDS	416347	417681	.	-	.	ID=YOR047C;Name=YOR047C;Alias=STD1
-chrXV	SGD	CDS	418630	421650	.	-	.	ID=YOR048C;Name=YOR048C;Alias=RAT1
-chrXV	SGD	CDS	422668	423732	.	-	.	ID=YOR049C;Name=YOR049C;Alias=RSB1
-chrXV	SGD	CDS	424846	426084	.	-	.	ID=YOR051C;Name=YOR051C;Alias=ETT1
-chrXV	SGD	CDS	426772	427224	.	-	.	ID=YOR052C;Name=YOR052C;Alias=TMC1
-chrXV	SGD	CDS	427833	429857	.	-	.	ID=YOR054C;Name=YOR054C;Alias=VHS3
-chrXV	SGD	CDS	430247	431626	.	-	.	ID=YOR056C;Name=YOR056C;Alias=NOB1
-chrXV	SGD	CDS	432186	433373	.	+	.	ID=YOR057W;Name=YOR057W;Alias=SGT1
-chrXV	SGD	CDS	433688	436345	.	-	.	ID=YOR058C;Name=YOR058C;Alias=ASE1
-chrXV	SGD	CDS	438906	440258	.	-	.	ID=YOR059C;Name=YOR059C;Alias=LPL1
-chrXV	SGD	CDS	440390	441163	.	-	.	ID=YOR060C;Name=YOR060C;Alias=SLD7
-chrXV	SGD	CDS	441534	442553	.	+	.	ID=YOR061W;Name=YOR061W;Alias=CKA2
-chrXV	SGD	CDS	442725	443531	.	-	.	ID=YOR062C;Name=YOR062C;Alias=
-chrXV	SGD	CDS	444686	445849	.	+	.	ID=YOR063W;Name=YOR063W;Alias=RPL3
-chrXV	SGD	CDS	446079	446738	.	-	.	ID=YOR064C;Name=YOR064C;Alias=YNG1
-chrXV	SGD	CDS	447439	448368	.	+	.	ID=YOR065W;Name=YOR065W;Alias=CYT1
-chrXV	SGD	CDS	449436	451325	.	+	.	ID=YOR066W;Name=YOR066W;Alias=MSA1
-chrXV	SGD	CDS	451729	453462	.	-	.	ID=YOR067C;Name=YOR067C;Alias=ALG8
-chrXV	SGD	CDS	453768	455795	.	+	.	ID=YOR069W;Name=YOR069W;Alias=VPS5
-chrXV	SGD	CDS	453869	454213	.	-	.	ID=YOR068C;Name=YOR068C;Alias=VAM10
-chrXV	SGD	CDS	455907	457820	.	-	.	ID=YOR070C;Name=YOR070C;Alias=GYP1
-chrXV	SGD	CDS	459480	461276	.	-	.	ID=YOR071C;Name=YOR071C;Alias=NRT1
-chrXV	SGD	CDS	464469	464630	.	+	.	ID=YOR072W-B;Name=YOR072W-B;Alias=
-chrXV	SGD	CDS	464771	466543	.	+	.	ID=YOR073W;Name=YOR073W;Alias=SGO1
-chrXV	SGD	CDS	466675	467589	.	-	.	ID=YOR074C;Name=YOR074C;Alias=CDC21
-chrXV	SGD	CDS	468212	469252	.	+	.	ID=YOR075W;Name=YOR075W;Alias=UFE1
-chrXV	SGD	CDS	469377	471620	.	-	.	ID=YOR076C;Name=YOR076C;Alias=SKI7
-chrXV	SGD	CDS	471899	472597	.	+	.	ID=YOR077W;Name=YOR077W;Alias=RTS2
-chrXV	SGD	CDS	472725	473369	.	+	.	ID=YOR078W;Name=YOR078W;Alias=BUD21
-chrXV	SGD	CDS	473475	474416	.	-	.	ID=YOR079C;Name=YOR079C;Alias=ATX2
-chrXV	SGD	CDS	474594	476792	.	+	.	ID=YOR080W;Name=YOR080W;Alias=DIA2
-chrXV	SGD	CDS	476939	479188	.	-	.	ID=YOR081C;Name=YOR081C;Alias=TGL5
-chrXV	SGD	CDS	479533	480420	.	+	.	ID=YOR083W;Name=YOR083W;Alias=WHI5
-chrXV	SGD	CDS	480587	481750	.	+	.	ID=YOR084W;Name=YOR084W;Alias=LPX1
-chrXV	SGD	CDS	482033	483085	.	+	.	ID=YOR085W;Name=YOR085W;Alias=OST3
-chrXV	SGD	CDS	483219	486779	.	-	.	ID=YOR086C;Name=YOR086C;Alias=TCB1
-chrXV	SGD	CDS	487707	489734	.	+	.	ID=YOR087W;Name=YOR087W;Alias=YVC1
-chrXV	SGD	CDS	490196	490828	.	-	.	ID=YOR089C;Name=YOR089C;Alias=VPS21
-chrXV	SGD	CDS	491123	492841	.	-	.	ID=YOR090C;Name=YOR090C;Alias=PTC5
-chrXV	SGD	CDS	493433	494470	.	+	.	ID=YOR091W;Name=YOR091W;Alias=TMA46
-chrXV	SGD	CDS	495127	496968	.	+	.	ID=YOR092W;Name=YOR092W;Alias=ECM3
-chrXV	SGD	CDS	497506	502452	.	-	.	ID=YOR093C;Name=YOR093C;Alias=CMR2
-chrXV	SGD	CDS	502795	503346	.	+	.	ID=YOR094W;Name=YOR094W;Alias=ARF3
-chrXV	SGD	CDS	503552	504328	.	-	.	ID=YOR095C;Name=YOR095C;Alias=RKI1
-chrXV	SGD	CDS	505794	506767	.	+	.	ID=YOR096W;Name=YOR096W;Alias=RPS7A
-chrXV	SGD	CDS	506978	507505	.	-	.	ID=YOR097C;Name=YOR097C;Alias=
-chrXV	SGD	CDS	507948	511178	.	-	.	ID=YOR098C;Name=YOR098C;Alias=NUP1
-chrXV	SGD	CDS	511825	513006	.	+	.	ID=YOR099W;Name=YOR099W;Alias=KTR1
-chrXV	SGD	CDS	513295	514278	.	-	.	ID=YOR100C;Name=YOR100C;Alias=CRC1
-chrXV	SGD	CDS	515244	516173	.	+	.	ID=YOR101W;Name=YOR101W;Alias=RAS1
-chrXV	SGD	CDS	516449	516841	.	-	.	ID=YOR103C;Name=YOR103C;Alias=OST2
-chrXV	SGD	CDS	517642	518490	.	+	.	ID=YOR104W;Name=YOR104W;Alias=PIN2
-chrXV	SGD	CDS	518195	518521	.	+	.	ID=YOR105W;Name=YOR105W;Alias=
-chrXV	SGD	CDS	519121	519972	.	+	.	ID=YOR106W;Name=YOR106W;Alias=VAM3
-chrXV	SGD	CDS	521353	522282	.	+	.	ID=YOR107W;Name=YOR107W;Alias=RGS2
-chrXV	SGD	CDS	523027	524841	.	+	.	ID=YOR108W;Name=YOR108W;Alias=LEU9
-chrXV	SGD	CDS	525278	528601	.	+	.	ID=YOR109W;Name=YOR109W;Alias=INP53
-chrXV	SGD	CDS	528941	530248	.	+	.	ID=YOR110W;Name=YOR110W;Alias=TFC7
-chrXV	SGD	CDS	530429	531127	.	+	.	ID=YOR111W;Name=YOR111W;Alias=
-chrXV	SGD	CDS	531508	533793	.	+	.	ID=YOR112W;Name=YOR112W;Alias=CEX1
-chrXV	SGD	CDS	534075	536819	.	+	.	ID=YOR113W;Name=YOR113W;Alias=AZF1
-chrXV	SGD	CDS	537570	538454	.	+	.	ID=YOR114W;Name=YOR114W;Alias=
-chrXV	SGD	CDS	538659	539465	.	-	.	ID=YOR115C;Name=YOR115C;Alias=TRS33
-chrXV	SGD	CDS	539763	544145	.	-	.	ID=YOR116C;Name=YOR116C;Alias=RPO31
-chrXV	SGD	CDS	545029	546333	.	+	.	ID=YOR117W;Name=YOR117W;Alias=RPT5
-chrXV	SGD	CDS	546857	548560	.	+	.	ID=YOR118W;Name=YOR118W;Alias=RTC5
-chrXV	SGD	CDS	548792	550246	.	-	.	ID=YOR119C;Name=YOR119C;Alias=RIO1
-chrXV	SGD	CDS	551114	552052	.	+	.	ID=YOR120W;Name=YOR120W;Alias=GCY1
-chrXV	SGD	CDS	552298	552887	.	-	.	ID=YOR122C;Name=YOR122C;Alias=PFY1
-chrXV	SGD	CDS	553176	554570	.	-	.	ID=YOR123C;Name=YOR123C;Alias=LEO1
-chrXV	SGD	CDS	554824	558642	.	-	.	ID=YOR124C;Name=YOR124C;Alias=UBP2
-chrXV	SGD	CDS	559030	559731	.	-	.	ID=YOR125C;Name=YOR125C;Alias=CAT5
-chrXV	SGD	CDS	559961	560677	.	-	.	ID=YOR126C;Name=YOR126C;Alias=IAH1
-chrXV	SGD	CDS	561170	564193	.	+	.	ID=YOR127W;Name=YOR127W;Alias=RGA1
-chrXV	SGD	CDS	564476	566191	.	-	.	ID=YOR128C;Name=YOR128C;Alias=ADE2
-chrXV	SGD	CDS	566877	569558	.	-	.	ID=YOR129C;Name=YOR129C;Alias=AFI1
-chrXV	SGD	CDS	569929	570807	.	-	.	ID=YOR130C;Name=YOR130C;Alias=ORT1
-chrXV	SGD	CDS	572182	572838	.	-	.	ID=YOR131C;Name=YOR131C;Alias=
-chrXV	SGD	CDS	573175	574830	.	+	.	ID=YOR132W;Name=YOR132W;Alias=VPS17
-chrXV	SGD	CDS	575098	577626	.	+	.	ID=YOR133W;Name=YOR133W;Alias=EFT1
-chrXV	SGD	CDS	578564	579793	.	+	.	ID=YOR134W;Name=YOR134W;Alias=BAG7
-chrXV	SGD	CDS	580250	581359	.	+	.	ID=YOR136W;Name=YOR136W;Alias=IDH2
-chrXV	SGD	CDS	581813	583681	.	-	.	ID=YOR137C;Name=YOR137C;Alias=SIA1
-chrXV	SGD	CDS	584309	586324	.	-	.	ID=YOR138C;Name=YOR138C;Alias=RUP1
-chrXV	SGD	CDS	586981	589281	.	+	.	ID=YOR140W;Name=YOR140W;Alias=SFL1
-chrXV	SGD	CDS	589942	592587	.	-	.	ID=YOR141C;Name=YOR141C;Alias=ARP8
-chrXV	SGD	CDS	593057	594046	.	+	.	ID=YOR142W;Name=YOR142W;Alias=LSC1
-chrXV	SGD	CDS	601383	602342	.	-	.	ID=YOR143C;Name=YOR143C;Alias=THI80
-chrXV	SGD	CDS	602717	605092	.	-	.	ID=YOR144C;Name=YOR144C;Alias=ELG1
-chrXV	SGD	CDS	605347	606171	.	-	.	ID=YOR145C;Name=YOR145C;Alias=PNO1
-chrXV	SGD	CDS	606607	608475	.	+	.	ID=YOR147W;Name=YOR147W;Alias=MDM32
-chrXV	SGD	CDS	608640	609197	.	-	.	ID=YOR148C;Name=YOR148C;Alias=SPP2
-chrXV	SGD	CDS	609838	611388	.	-	.	ID=YOR149C;Name=YOR149C;Alias=SMP3
-chrXV	SGD	CDS	611999	612490	.	+	.	ID=YOR150W;Name=YOR150W;Alias=MRPL23
-chrXV	SGD	CDS	612997	616671	.	-	.	ID=YOR151C;Name=YOR151C;Alias=RPB2
-chrXV	SGD	CDS	617518	618288	.	-	.	ID=YOR152C;Name=YOR152C;Alias=ATG40
-chrXV	SGD	CDS	619840	624375	.	+	.	ID=YOR153W;Name=YOR153W;Alias=PDR5
-chrXV	SGD	CDS	624729	626492	.	+	.	ID=YOR154W;Name=YOR154W;Alias=SLP1
-chrXV	SGD	CDS	626628	627980	.	-	.	ID=YOR155C;Name=YOR155C;Alias=ISN1
-chrXV	SGD	CDS	628360	630540	.	-	.	ID=YOR156C;Name=YOR156C;Alias=NFI1
-chrXV	SGD	CDS	630966	631751	.	-	.	ID=YOR157C;Name=YOR157C;Alias=PUP1
-chrXV	SGD	CDS	632164	633120	.	+	.	ID=YOR158W;Name=YOR158W;Alias=PET123
-chrXV	SGD	CDS	633282	633566	.	-	.	ID=YOR159C;Name=YOR159C;Alias=SME1
-chrXV	SGD	CDS	633839	636757	.	+	.	ID=YOR160W;Name=YOR160W;Alias=MTR10
-chrXV	SGD	CDS	636939	638558	.	-	.	ID=YOR161C;Name=YOR161C;Alias=PNS1
-chrXV	SGD	CDS	639121	639267	.	-	.	ID=YOR161C-C;Name=YOR161C-C;Alias=
-chrXV	SGD	CDS	639560	641992	.	-	.	ID=YOR162C;Name=YOR162C;Alias=YRR1
-chrXV	SGD	CDS	642741	643307	.	+	.	ID=YOR163W;Name=YOR163W;Alias=DDP1
-chrXV	SGD	CDS	643394	644332	.	-	.	ID=YOR164C;Name=YOR164C;Alias=GET4
-chrXV	SGD	CDS	644566	646896	.	+	.	ID=YOR165W;Name=YOR165W;Alias=SEY1
-chrXV	SGD	CDS	647126	648502	.	-	.	ID=YOR166C;Name=YOR166C;Alias=SWT1
-chrXV	SGD	CDS	648804	649007	.	-	.	ID=YOR167C;Name=YOR167C;Alias=RPS28A
-chrXV	SGD	CDS	649303	651732	.	+	.	ID=YOR168W;Name=YOR168W;Alias=GLN4
-chrXV	SGD	CDS	652010	653884	.	-	.	ID=YOR171C;Name=YOR171C;Alias=LCB4
-chrXV	SGD	CDS	654210	656570	.	+	.	ID=YOR172W;Name=YOR172W;Alias=YRM1
-chrXV	SGD	CDS	657264	658325	.	+	.	ID=YOR173W;Name=YOR173W;Alias=DCS2
-chrXV	SGD	CDS	658747	659601	.	+	.	ID=YOR174W;Name=YOR174W;Alias=MED4
-chrXV	SGD	CDS	659815	661674	.	-	.	ID=YOR175C;Name=YOR175C;Alias=ALE1
-chrXV	SGD	CDS	662401	663582	.	+	.	ID=YOR176W;Name=YOR176W;Alias=HEM15
-chrXV	SGD	CDS	665785	667179	.	-	.	ID=YOR177C;Name=YOR177C;Alias=MPC54
-chrXV	SGD	CDS	667860	670241	.	-	.	ID=YOR178C;Name=YOR178C;Alias=GAC1
-chrXV	SGD	CDS	671845	672411	.	-	.	ID=YOR179C;Name=YOR179C;Alias=SYC1
-chrXV	SGD	CDS	674352	675167	.	-	.	ID=YOR180C;Name=YOR180C;Alias=DCI1
-chrXV	SGD	CDS	675939	677840	.	+	.	ID=YOR181W;Name=YOR181W;Alias=LAS17
-chrXV	SGD	CDS	678191	678793	.	-	.	ID=YOR182C;Name=YOR182C;Alias=RPS30B
-chrXV	SGD	CDS	678872	679261	.	+	.	ID=YOR183W;Name=YOR183W;Alias=FYV12
-chrXV	SGD	CDS	679357	680544	.	+	.	ID=YOR184W;Name=YOR184W;Alias=SER1
-chrXV	SGD	CDS	681444	682106	.	-	.	ID=YOR185C;Name=YOR185C;Alias=GSP2
-chrXV	SGD	CDS	683111	683545	.	+	.	ID=YOR186W;Name=YOR186W;Alias=
-chrXV	SGD	CDS	684030	685343	.	+	.	ID=YOR187W;Name=YOR187W;Alias=TUF1
-chrXV	SGD	CDS	685767	689180	.	+	.	ID=YOR188W;Name=YOR188W;Alias=MSB1
-chrXV	SGD	CDS	689624	689974	.	+	.	ID=YOR189W;Name=YOR189W;Alias=IES4
-chrXV	SGD	CDS	690695	692032	.	+	.	ID=YOR190W;Name=YOR190W;Alias=SPR1
-chrXV	SGD	CDS	692475	697334	.	+	.	ID=YOR191W;Name=YOR191W;Alias=ULS1
-chrXV	SGD	CDS	698768	700567	.	-	.	ID=YOR192C;Name=YOR192C;Alias=THI72
-chrXV	SGD	CDS	703988	704224	.	-	.	ID=YOR192C-C;Name=YOR192C-C;Alias=
-chrXV	SGD	CDS	710446	711576	.	+	.	ID=YOR193W;Name=YOR193W;Alias=PEX27
-chrXV	SGD	CDS	711683	712543	.	-	.	ID=YOR194C;Name=YOR194C;Alias=TOA1
-chrXV	SGD	CDS	712866	715331	.	+	.	ID=YOR195W;Name=YOR195W;Alias=SLK19
-chrXV	SGD	CDS	715593	716837	.	-	.	ID=YOR196C;Name=YOR196C;Alias=LIP5
-chrXV	SGD	CDS	717086	718384	.	+	.	ID=YOR197W;Name=YOR197W;Alias=MCA1
-chrXV	SGD	CDS	718653	720065	.	-	.	ID=YOR198C;Name=YOR198C;Alias=BFR1
-chrXV	SGD	CDS	720470	721708	.	-	.	ID=YOR201C;Name=YOR201C;Alias=MRM1
-chrXV	SGD	CDS	721946	722608	.	+	.	ID=YOR202W;Name=YOR202W;Alias=HIS3
-chrXV	SGD	CDS	722911	724725	.	+	.	ID=YOR204W;Name=YOR204W;Alias=DED1
-chrXV	SGD	CDS	725564	727234	.	-	.	ID=YOR205C;Name=YOR205C;Alias=GEP3
-chrXV	SGD	CDS	727512	729644	.	+	.	ID=YOR206W;Name=YOR206W;Alias=NOC2
-chrXV	SGD	CDS	730008	733457	.	-	.	ID=YOR207C;Name=YOR207C;Alias=RET1
-chrXV	SGD	CDS	733925	736177	.	+	.	ID=YOR208W;Name=YOR208W;Alias=PTP2
-chrXV	SGD	CDS	736437	737726	.	-	.	ID=YOR209C;Name=YOR209C;Alias=NPT1
-chrXV	SGD	CDS	738320	738532	.	+	.	ID=YOR210W;Name=YOR210W;Alias=RPB10
-chrXV	SGD	CDS	738924	741569	.	-	.	ID=YOR211C;Name=YOR211C;Alias=MGM1
-chrXV	SGD	CDS	742910	744181	.	+	.	ID=YOR212W;Name=YOR212W;Alias=STE4
-chrXV	SGD	CDS	744535	745281	.	-	.	ID=YOR213C;Name=YOR213C;Alias=SAS5
-chrXV	SGD	CDS	745593	746303	.	-	.	ID=YOR214C;Name=YOR214C;Alias=SPR2
-chrXV	SGD	CDS	746725	747282	.	-	.	ID=YOR215C;Name=YOR215C;Alias=AIM41
-chrXV	SGD	CDS	747525	748979	.	-	.	ID=YOR216C;Name=YOR216C;Alias=RUD3
-chrXV	SGD	CDS	749301	751886	.	+	.	ID=YOR217W;Name=YOR217W;Alias=RFC1
-chrXV	SGD	CDS	752214	755009	.	-	.	ID=YOR219C;Name=YOR219C;Alias=STE13
-chrXV	SGD	CDS	755328	756125	.	+	.	ID=YOR220W;Name=YOR220W;Alias=RCN2
-chrXV	SGD	CDS	756476	757558	.	-	.	ID=YOR221C;Name=YOR221C;Alias=MCT1
-chrXV	SGD	CDS	758330	759253	.	+	.	ID=YOR222W;Name=YOR222W;Alias=ODC2
-chrXV	SGD	CDS	759782	760660	.	+	.	ID=YOR223W;Name=YOR223W;Alias=DSC3
-chrXV	SGD	CDS	760825	761265	.	-	.	ID=YOR224C;Name=YOR224C;Alias=RPB8
-chrXV	SGD	CDS	761614	762084	.	-	.	ID=YOR226C;Name=YOR226C;Alias=ISU2
-chrXV	SGD	CDS	762825	766565	.	+	.	ID=YOR227W;Name=YOR227W;Alias=HER1
-chrXV	SGD	CDS	766869	767777	.	-	.	ID=YOR228C;Name=YOR228C;Alias=MCP1
-chrXV	SGD	CDS	768409	769812	.	+	.	ID=YOR229W;Name=YOR229W;Alias=WTM2
-chrXV	SGD	CDS	770800	772113	.	+	.	ID=YOR230W;Name=YOR230W;Alias=WTM1
-chrXV	SGD	CDS	772601	774127	.	+	.	ID=YOR231W;Name=YOR231W;Alias=MKK1
-chrXV	SGD	CDS	774573	775259	.	+	.	ID=YOR232W;Name=YOR232W;Alias=MGE1
-chrXV	SGD	CDS	775846	778248	.	+	.	ID=YOR233W;Name=YOR233W;Alias=KIN4
-chrXV	SGD	CDS	778555	779405	.	-	.	ID=YOR234C;Name=YOR234C;Alias=RPL33B
-chrXV	SGD	CDS	780906	781541	.	+	.	ID=YOR236W;Name=YOR236W;Alias=DFR1
-chrXV	SGD	CDS	781994	783298	.	+	.	ID=YOR237W;Name=YOR237W;Alias=HES1
-chrXV	SGD	CDS	783677	784588	.	+	.	ID=YOR238W;Name=YOR238W;Alias=
-chrXV	SGD	CDS	784857	786744	.	+	.	ID=YOR239W;Name=YOR239W;Alias=ABP140
-chrXV	SGD	CDS	786995	788641	.	+	.	ID=YOR241W;Name=YOR241W;Alias=MET7
-chrXV	SGD	CDS	788742	789857	.	-	.	ID=YOR242C;Name=YOR242C;Alias=SSP2
-chrXV	SGD	CDS	790211	792241	.	-	.	ID=YOR243C;Name=YOR243C;Alias=PUS7
-chrXV	SGD	CDS	792531	793868	.	+	.	ID=YOR244W;Name=YOR244W;Alias=ESA1
-chrXV	SGD	CDS	794076	795332	.	-	.	ID=YOR245C;Name=YOR245C;Alias=DGA1
-chrXV	SGD	CDS	795801	796793	.	-	.	ID=YOR246C;Name=YOR246C;Alias=ENV9
-chrXV	SGD	CDS	797676	798308	.	+	.	ID=YOR247W;Name=YOR247W;Alias=SRL1
-chrXV	SGD	CDS	798674	800731	.	-	.	ID=YOR249C;Name=YOR249C;Alias=APC5
-chrXV	SGD	CDS	800970	802307	.	-	.	ID=YOR250C;Name=YOR250C;Alias=CLP1
-chrXV	SGD	CDS	802550	803464	.	-	.	ID=YOR251C;Name=YOR251C;Alias=TUM1
-chrXV	SGD	CDS	803667	804203	.	+	.	ID=YOR252W;Name=YOR252W;Alias=TMA16
-chrXV	SGD	CDS	804377	804907	.	+	.	ID=YOR253W;Name=YOR253W;Alias=NAT5
-chrXV	SGD	CDS	805032	807023	.	-	.	ID=YOR254C;Name=YOR254C;Alias=SEC63
-chrXV	SGD	CDS	807271	808107	.	+	.	ID=YOR255W;Name=YOR255W;Alias=OSW1
-chrXV	SGD	CDS	808254	810683	.	-	.	ID=YOR256C;Name=YOR256C;Alias=TRE2
-chrXV	SGD	CDS	811008	811493	.	+	.	ID=YOR257W;Name=YOR257W;Alias=CDC31
-chrXV	SGD	CDS	811671	812324	.	+	.	ID=YOR258W;Name=YOR258W;Alias=HNT3
-chrXV	SGD	CDS	812395	813708	.	-	.	ID=YOR259C;Name=YOR259C;Alias=RPT4
-chrXV	SGD	CDS	813984	815720	.	+	.	ID=YOR260W;Name=YOR260W;Alias=GCD1
-chrXV	SGD	CDS	815915	816931	.	-	.	ID=YOR261C;Name=YOR261C;Alias=RPN8
-chrXV	SGD	CDS	817292	818335	.	+	.	ID=YOR262W;Name=YOR262W;Alias=GPN2
-chrXV	SGD	CDS	818866	820158	.	+	.	ID=YOR264W;Name=YOR264W;Alias=DSE3
-chrXV	SGD	CDS	820454	820774	.	+	.	ID=YOR265W;Name=YOR265W;Alias=RBL2
-chrXV	SGD	CDS	821023	822294	.	+	.	ID=YOR266W;Name=YOR266W;Alias=PNT1
-chrXV	SGD	CDS	822588	824867	.	-	.	ID=YOR267C;Name=YOR267C;Alias=HRK1
-chrXV	SGD	CDS	825534	825932	.	-	.	ID=YOR268C;Name=YOR268C;Alias=
-chrXV	SGD	CDS	826385	827869	.	+	.	ID=YOR269W;Name=YOR269W;Alias=PAC1
-chrXV	SGD	CDS	828052	830574	.	-	.	ID=YOR270C;Name=YOR270C;Alias=VPH1
-chrXV	SGD	CDS	831059	832042	.	-	.	ID=YOR271C;Name=YOR271C;Alias=FSF1
-chrXV	SGD	CDS	832813	834195	.	+	.	ID=YOR272W;Name=YOR272W;Alias=YTM1
-chrXV	SGD	CDS	834452	836431	.	-	.	ID=YOR273C;Name=YOR273C;Alias=TPO4
-chrXV	SGD	CDS	837674	838960	.	+	.	ID=YOR274W;Name=YOR274W;Alias=MOD5
-chrXV	SGD	CDS	839084	841069	.	-	.	ID=YOR275C;Name=YOR275C;Alias=RIM20
-chrXV	SGD	CDS	841333	841818	.	+	.	ID=YOR276W;Name=YOR276W;Alias=CAF20
-chrXV	SGD	CDS	842817	843644	.	+	.	ID=YOR278W;Name=YOR278W;Alias=HEM4
-chrXV	SGD	CDS	843698	844630	.	-	.	ID=YOR279C;Name=YOR279C;Alias=RFM1
-chrXV	SGD	CDS	844992	845792	.	-	.	ID=YOR280C;Name=YOR280C;Alias=FSH3
-chrXV	SGD	CDS	846269	847129	.	-	.	ID=YOR281C;Name=YOR281C;Alias=PLP2
-chrXV	SGD	CDS	847453	848145	.	+	.	ID=YOR283W;Name=YOR283W;Alias=
-chrXV	SGD	CDS	848478	849209	.	+	.	ID=YOR284W;Name=YOR284W;Alias=HUA2
-chrXV	SGD	CDS	849635	850054	.	+	.	ID=YOR285W;Name=YOR285W;Alias=RDL1
-chrXV	SGD	CDS	850280	850729	.	+	.	ID=YOR286W;Name=YOR286W;Alias=RDL2
-chrXV	SGD	CDS	850937	851839	.	-	.	ID=YOR287C;Name=YOR287C;Alias=RRP36
-chrXV	SGD	CDS	852121	853077	.	-	.	ID=YOR288C;Name=YOR288C;Alias=MPD1
-chrXV	SGD	CDS	853357	854112	.	+	.	ID=YOR289W;Name=YOR289W;Alias=
-chrXV	SGD	CDS	855147	860258	.	-	.	ID=YOR290C;Name=YOR290C;Alias=SNF2
-chrXV	SGD	CDS	861175	865593	.	+	.	ID=YOR291W;Name=YOR291W;Alias=YPK9
-chrXV	SGD	CDS	865653	866582	.	-	.	ID=YOR292C;Name=YOR292C;Alias=
-chrXV	SGD	CDS	867098	867852	.	+	.	ID=YOR293W;Name=YOR293W;Alias=RPS10A
-chrXV	SGD	CDS	867998	868147	.	-	.	ID=YOR293C-A;Name=YOR293C-A;Alias=
-chrXV	SGD	CDS	868340	868951	.	+	.	ID=YOR294W;Name=YOR294W;Alias=RRS1
-chrXV	SGD	CDS	869208	869894	.	+	.	ID=YOR295W;Name=YOR295W;Alias=UAF30
-chrXV	SGD	CDS	870202	874071	.	+	.	ID=YOR296W;Name=YOR296W;Alias=
-chrXV	SGD	CDS	874743	875321	.	-	.	ID=YOR297C;Name=YOR297C;Alias=TIM18
-chrXV	SGD	CDS	875599	877038	.	+	.	ID=YOR298W;Name=YOR298W;Alias=MUM3
-chrXV	SGD	CDS	877230	877685	.	-	.	ID=YOR298C-A;Name=YOR298C-A;Alias=MBF1
-chrXV	SGD	CDS	878435	880675	.	+	.	ID=YOR299W;Name=YOR299W;Alias=BUD7
-chrXV	SGD	CDS	880965	882272	.	+	.	ID=YOR301W;Name=YOR301W;Alias=RAX1
-chrXV	SGD	CDS	882765	882842	.	+	.	ID=YOR302W;Name=YOR302W;Alias=
-chrXV	SGD	CDS	882899	884134	.	+	.	ID=YOR303W;Name=YOR303W;Alias=CPA1
-chrXV	SGD	CDS	884514	887876	.	+	.	ID=YOR304W;Name=YOR304W;Alias=ISW2
-chrXV	SGD	CDS	888520	888750	.	-	.	ID=YOR304C-A;Name=YOR304C-A;Alias=BIL1
-chrXV	SGD	CDS	889022	889750	.	+	.	ID=YOR305W;Name=YOR305W;Alias=RRG7
-chrXV	SGD	CDS	889867	891432	.	-	.	ID=YOR306C;Name=YOR306C;Alias=MCH5
-chrXV	SGD	CDS	892731	894092	.	-	.	ID=YOR307C;Name=YOR307C;Alias=SLY41
-chrXV	SGD	CDS	894624	896387	.	-	.	ID=YOR308C;Name=YOR308C;Alias=SNU66
-chrXV	SGD	CDS	896825	898360	.	-	.	ID=YOR310C;Name=YOR310C;Alias=NOP58
-chrXV	SGD	CDS	899056	899928	.	-	.	ID=YOR311C;Name=YOR311C;Alias=DGK1
-chrXV	SGD	CDS	900250	901194	.	-	.	ID=YOR312C;Name=YOR312C;Alias=RPL20B
-chrXV	SGD	CDS	901858	902874	.	-	.	ID=YOR313C;Name=YOR313C;Alias=SPS4
-chrXV	SGD	CDS	904760	905800	.	+	.	ID=YOR315W;Name=YOR315W;Alias=SFG1
-chrXV	SGD	CDS	906236	907555	.	-	.	ID=YOR316C;Name=YOR316C;Alias=COT1
-chrXV	SGD	CDS	907726	907935	.	-	.	ID=YOR316C-A;Name=YOR316C-A;Alias=
-chrXV	SGD	CDS	909343	911445	.	+	.	ID=YOR317W;Name=YOR317W;Alias=FAA1
-chrXV	SGD	CDS	912822	913463	.	+	.	ID=YOR319W;Name=YOR319W;Alias=HSH49
-chrXV	SGD	CDS	913619	915094	.	-	.	ID=YOR320C;Name=YOR320C;Alias=GNT1
-chrXV	SGD	CDS	916030	918291	.	+	.	ID=YOR321W;Name=YOR321W;Alias=PMT3
-chrXV	SGD	CDS	918606	921062	.	-	.	ID=YOR322C;Name=YOR322C;Alias=LDB19
-chrXV	SGD	CDS	921535	922905	.	-	.	ID=YOR323C;Name=YOR323C;Alias=PRO2
-chrXV	SGD	CDS	923232	925040	.	-	.	ID=YOR324C;Name=YOR324C;Alias=FRT1
-chrXV	SGD	CDS	925721	930445	.	+	.	ID=YOR326W;Name=YOR326W;Alias=MYO2
-chrXV	SGD	CDS	930734	931081	.	-	.	ID=YOR327C;Name=YOR327C;Alias=SNC2
-chrXV	SGD	CDS	931803	936497	.	+	.	ID=YOR328W;Name=YOR328W;Alias=PDR10
-chrXV	SGD	CDS	936731	939349	.	-	.	ID=YOR329C;Name=YOR329C;Alias=SCD5
-chrXV	SGD	CDS	939621	943385	.	-	.	ID=YOR330C;Name=YOR330C;Alias=MIP1
-chrXV	SGD	CDS	943656	944357	.	+	.	ID=YOR332W;Name=YOR332W;Alias=VMA4
-chrXV	SGD	CDS	944596	946008	.	+	.	ID=YOR334W;Name=YOR334W;Alias=MRS2
-chrXV	SGD	CDS	946233	949109	.	-	.	ID=YOR335C;Name=YOR335C;Alias=ALA1
-chrXV	SGD	CDS	949773	953870	.	+	.	ID=YOR336W;Name=YOR336W;Alias=KRE5
-chrXV	SGD	CDS	954344	956623	.	+	.	ID=YOR337W;Name=YOR337W;Alias=TEA1
-chrXV	SGD	CDS	956898	957989	.	+	.	ID=YOR338W;Name=YOR338W;Alias=
-chrXV	SGD	CDS	958362	958832	.	-	.	ID=YOR339C;Name=YOR339C;Alias=UBC11
-chrXV	SGD	CDS	959202	960182	.	-	.	ID=YOR340C;Name=YOR340C;Alias=RPA43
-chrXV	SGD	CDS	960987	965981	.	+	.	ID=YOR341W;Name=YOR341W;Alias=RPA190
-chrXV	SGD	CDS	966666	967625	.	-	.	ID=YOR342C;Name=YOR342C;Alias=
-chrXV	SGD	CDS	977194	978069	.	-	.	ID=YOR344C;Name=YOR344C;Alias=TYE7
-chrXV	SGD	CDS	981828	984785	.	+	.	ID=YOR346W;Name=YOR346W;Alias=REV1
-chrXV	SGD	CDS	984942	986462	.	-	.	ID=YOR347C;Name=YOR347C;Alias=PYK2
-chrXV	SGD	CDS	986899	988782	.	-	.	ID=YOR348C;Name=YOR348C;Alias=PUT4
-chrXV	SGD	CDS	989789	992833	.	+	.	ID=YOR349W;Name=YOR349W;Alias=CIN1
-chrXV	SGD	CDS	992864	994855	.	-	.	ID=YOR350C;Name=YOR350C;Alias=MNE1
-chrXV	SGD	CDS	995018	996511	.	-	.	ID=YOR351C;Name=YOR351C;Alias=MEK1
-chrXV	SGD	CDS	997213	998244	.	+	.	ID=YOR352W;Name=YOR352W;Alias=TFB6
-chrXV	SGD	CDS	998453	1000828	.	-	.	ID=YOR353C;Name=YOR353C;Alias=SOG2
-chrXV	SGD	CDS	1001147	1003225	.	-	.	ID=YOR354C;Name=YOR354C;Alias=MSC6
-chrXV	SGD	CDS	1005137	1006705	.	+	.	ID=YOR355W;Name=YOR355W;Alias=GDS1
-chrXV	SGD	CDS	1007221	1009116	.	+	.	ID=YOR356W;Name=YOR356W;Alias=CIR2
-chrXV	SGD	CDS	1009224	1009712	.	-	.	ID=YOR357C;Name=YOR357C;Alias=SNX3
-chrXV	SGD	CDS	1010161	1010889	.	+	.	ID=YOR358W;Name=YOR358W;Alias=HAP5
-chrXV	SGD	CDS	1011189	1012760	.	+	.	ID=YOR359W;Name=YOR359W;Alias=VTS1
-chrXV	SGD	CDS	1013241	1014821	.	-	.	ID=YOR360C;Name=YOR360C;Alias=PDE2
-chrXV	SGD	CDS	1015361	1017652	.	-	.	ID=YOR361C;Name=YOR361C;Alias=PRT1
-chrXV	SGD	CDS	1017880	1018746	.	-	.	ID=YOR362C;Name=YOR362C;Alias=PRE10
-chrXV	SGD	CDS	1020222	1023212	.	-	.	ID=YOR363C;Name=YOR363C;Alias=PIP2
-chrXV	SGD	CDS	1023461	1025572	.	-	.	ID=YOR365C;Name=YOR365C;Alias=
-chrXV	SGD	CDS	1026007	1026609	.	+	.	ID=YOR367W;Name=YOR367W;Alias=SCP1
-chrXV	SGD	CDS	1026843	1028048	.	+	.	ID=YOR368W;Name=YOR368W;Alias=RAD17
-chrXV	SGD	CDS	1028194	1028625	.	-	.	ID=YOR369C;Name=YOR369C;Alias=RPS12
-chrXV	SGD	CDS	1029183	1030994	.	-	.	ID=YOR370C;Name=YOR370C;Alias=MRS6
-chrXV	SGD	CDS	1031489	1034182	.	-	.	ID=YOR371C;Name=YOR371C;Alias=GPB1
-chrXV	SGD	CDS	1034807	1036471	.	-	.	ID=YOR372C;Name=YOR372C;Alias=NDD1
-chrXV	SGD	CDS	1036834	1039389	.	+	.	ID=YOR373W;Name=YOR373W;Alias=NUD1
-chrXV	SGD	CDS	1039840	1041399	.	+	.	ID=YOR374W;Name=YOR374W;Alias=ALD4
-chrXV	SGD	CDS	1041678	1043042	.	-	.	ID=YOR375C;Name=YOR375C;Alias=GDH1
-chrXV	SGD	CDS	1045196	1045351	.	+	.	ID=YOR376W-A;Name=YOR376W-A;Alias=
-chrXV	SGD	CDS	1046226	1047803	.	+	.	ID=YOR377W;Name=YOR377W;Alias=ATF1
-chrXV	SGD	CDS	1049511	1051058	.	+	.	ID=YOR378W;Name=YOR378W;Alias=AMF1
-chrXV	SGD	CDS	1051290	1052930	.	+	.	ID=YOR380W;Name=YOR380W;Alias=RDR1
-chrXV	SGD	CDS	1055545	1057680	.	+	.	ID=YOR381W;Name=YOR381W;Alias=FRE3
-chrXV	SGD	CDS	1058423	1058590	.	+	.	ID=YOR381W-A;Name=YOR381W-A;Alias=
-chrXV	SGD	CDS	1059531	1059992	.	+	.	ID=YOR382W;Name=YOR382W;Alias=FIT2
-chrXV	SGD	CDS	1060441	1061055	.	-	.	ID=YOR383C;Name=YOR383C;Alias=FIT3
-chrXV	SGD	CDS	1061564	1063648	.	+	.	ID=YOR384W;Name=YOR384W;Alias=FRE5
-chrXV	SGD	CDS	1065043	1065915	.	+	.	ID=YOR385W;Name=YOR385W;Alias=
-chrXV	SGD	CDS	1066839	1068536	.	+	.	ID=YOR386W;Name=YOR386W;Alias=PHR1
-chrXV	SGD	CDS	1069621	1070241	.	-	.	ID=YOR387C;Name=YOR387C;Alias=
-chrXV	SGD	CDS	1071793	1072923	.	-	.	ID=YOR388C;Name=YOR388C;Alias=FDH1
-chrXV	SGD	CDS	1074213	1076087	.	+	.	ID=YOR389W;Name=YOR389W;Alias=
-chrXV	SGD	CDS	1076784	1077911	.	+	.	ID=YOR390W;Name=YOR390W;Alias=FEX1
-chrXV	SGD	CDS	1078545	1079258	.	-	.	ID=YOR391C;Name=YOR391C;Alias=HSP33
-chrXV	SGD	CDS	1080276	1081589	.	+	.	ID=YOR393W;Name=YOR393W;Alias=ERR1
-chrXV	SGD	CDS	1082718	1083212	.	+	.	ID=YOR394W;Name=YOR394W;Alias=PAU21
-chrXV	SGD	CDS	1084202	1084369	.	-	.	ID=YOR394C-A;Name=YOR394C-A;Alias=
-chrXV	SGD	CDS	1085473	1090863	.	+	.	ID=YOR396W;Name=YOR396W;Alias=YRF1-8
-chrXVI	SGD	CDS	280	6007	.	-	.	ID=YPL283C;Name=YPL283C;Alias=YRF1-7
-chrXVI	SGD	CDS	7933	8427	.	-	.	ID=YPL282C;Name=YPL282C;Alias=PAU22
-chrXVI	SGD	CDS	9557	10870	.	-	.	ID=YPL281C;Name=YPL281C;Alias=ERR2
-chrXVI	SGD	CDS	11887	12600	.	+	.	ID=YPL280W;Name=YPL280W;Alias=HSP32
-chrXVI	SGD	CDS	13228	14355	.	-	.	ID=YPL279C;Name=YPL279C;Alias=FEX2
-chrXVI	SGD	CDS	15053	15355	.	-	.	ID=YPL278C;Name=YPL278C;Alias=
-chrXVI	SGD	CDS	15405	16868	.	-	.	ID=YPL277C;Name=YPL277C;Alias=
-chrXVI	SGD	CDS	22938	24701	.	+	.	ID=YPL274W;Name=YPL274W;Alias=SAM3
-chrXVI	SGD	CDS	25087	26064	.	+	.	ID=YPL273W;Name=YPL273W;Alias=SAM4
-chrXVI	SGD	CDS	26611	28164	.	-	.	ID=YPL272C;Name=YPL272C;Alias=PBI1
-chrXVI	SGD	CDS	30079	30267	.	+	.	ID=YPL271W;Name=YPL271W;Alias=ATP15
-chrXVI	SGD	CDS	30482	32803	.	+	.	ID=YPL270W;Name=YPL270W;Alias=MDL2
-chrXVI	SGD	CDS	33013	34947	.	+	.	ID=YPL269W;Name=YPL269W;Alias=KAR9
-chrXVI	SGD	CDS	35236	37845	.	+	.	ID=YPL268W;Name=YPL268W;Alias=PLC1
-chrXVI	SGD	CDS	38169	38798	.	+	.	ID=YPL267W;Name=YPL267W;Alias=ACM1
-chrXVI	SGD	CDS	39121	40077	.	+	.	ID=YPL266W;Name=YPL266W;Alias=DIM1
-chrXVI	SGD	CDS	41043	42869	.	+	.	ID=YPL265W;Name=YPL265W;Alias=DIP5
-chrXVI	SGD	CDS	43283	44344	.	-	.	ID=YPL264C;Name=YPL264C;Alias=
-chrXVI	SGD	CDS	44551	46506	.	-	.	ID=YPL263C;Name=YPL263C;Alias=KEL3
-chrXVI	SGD	CDS	47336	48802	.	+	.	ID=YPL262W;Name=YPL262W;Alias=FUM1
-chrXVI	SGD	CDS	49303	50958	.	+	.	ID=YPL260W;Name=YPL260W;Alias=CUB1
-chrXVI	SGD	CDS	51244	52671	.	-	.	ID=YPL259C;Name=YPL259C;Alias=APM1
-chrXVI	SGD	CDS	53498	55153	.	-	.	ID=YPL258C;Name=YPL258C;Alias=THI21
-chrXVI	SGD	CDS	63279	63860	.	+	.	ID=YPL257W;Name=YPL257W;Alias=
-chrXVI	SGD	CDS	64977	66614	.	-	.	ID=YPL256C;Name=YPL256C;Alias=CLN2
-chrXVI	SGD	CDS	67725	68882	.	+	.	ID=YPL255W;Name=YPL255W;Alias=BBP1
-chrXVI	SGD	CDS	69485	70951	.	+	.	ID=YPL254W;Name=YPL254W;Alias=HFI1
-chrXVI	SGD	CDS	71063	73006	.	-	.	ID=YPL253C;Name=YPL253C;Alias=VIK1
-chrXVI	SGD	CDS	73363	73881	.	-	.	ID=YPL252C;Name=YPL252C;Alias=YAH1
-chrXVI	SGD	CDS	74309	74719	.	-	.	ID=YPL250C;Name=YPL250C;Alias=ATG41
-chrXVI	SGD	CDS	75699	76239	.	-	.	ID=YPL249C-A;Name=YPL249C-A;Alias=RPL36B
-chrXVI	SGD	CDS	76669	79353	.	-	.	ID=YPL249C;Name=YPL249C;Alias=GYP5
-chrXVI	SGD	CDS	79711	82356	.	-	.	ID=YPL248C;Name=YPL248C;Alias=GAL4
-chrXVI	SGD	CDS	82625	84196	.	-	.	ID=YPL247C;Name=YPL247C;Alias=
-chrXVI	SGD	CDS	84509	85297	.	-	.	ID=YPL246C;Name=YPL246C;Alias=RBD2
-chrXVI	SGD	CDS	85586	86950	.	+	.	ID=YPL245W;Name=YPL245W;Alias=
-chrXVI	SGD	CDS	87014	88033	.	-	.	ID=YPL244C;Name=YPL244C;Alias=HUT1
-chrXVI	SGD	CDS	88517	90316	.	+	.	ID=YPL243W;Name=YPL243W;Alias=SRP68
-chrXVI	SGD	CDS	90622	95109	.	-	.	ID=YPL242C;Name=YPL242C;Alias=IQG1
-chrXVI	SGD	CDS	95372	96258	.	-	.	ID=YPL241C;Name=YPL241C;Alias=CIN2
-chrXVI	SGD	CDS	96496	98625	.	-	.	ID=YPL240C;Name=YPL240C;Alias=HSP82
-chrXVI	SGD	CDS	99484	100086	.	+	.	ID=YPL239W;Name=YPL239W;Alias=YAR1
-chrXVI	SGD	CDS	100496	101353	.	+	.	ID=YPL237W;Name=YPL237W;Alias=SUI3
-chrXVI	SGD	CDS	101608	102702	.	-	.	ID=YPL236C;Name=YPL236C;Alias=ENV7
-chrXVI	SGD	CDS	103232	104647	.	+	.	ID=YPL235W;Name=YPL235W;Alias=RVB2
-chrXVI	SGD	CDS	104946	105440	.	-	.	ID=YPL234C;Name=YPL234C;Alias=VMA11
-chrXVI	SGD	CDS	106172	106822	.	+	.	ID=YPL233W;Name=YPL233W;Alias=NSL1
-chrXVI	SGD	CDS	107275	108147	.	+	.	ID=YPL232W;Name=YPL232W;Alias=SSO1
-chrXVI	SGD	CDS	108652	114315	.	+	.	ID=YPL231W;Name=YPL231W;Alias=FAS2
-chrXVI	SGD	CDS	115219	116487	.	+	.	ID=YPL230W;Name=YPL230W;Alias=USV1
-chrXVI	SGD	CDS	117067	117687	.	+	.	ID=YPL229W;Name=YPL229W;Alias=
-chrXVI	SGD	CDS	118382	120031	.	+	.	ID=YPL228W;Name=YPL228W;Alias=CET1
-chrXVI	SGD	CDS	120163	121167	.	-	.	ID=YPL227C;Name=YPL227C;Alias=ALG5
-chrXVI	SGD	CDS	121767	125357	.	+	.	ID=YPL226W;Name=YPL226W;Alias=NEW1
-chrXVI	SGD	CDS	126006	126446	.	+	.	ID=YPL225W;Name=YPL225W;Alias=
-chrXVI	SGD	CDS	126634	128088	.	-	.	ID=YPL224C;Name=YPL224C;Alias=MMT2
-chrXVI	SGD	CDS	128632	129138	.	-	.	ID=YPL223C;Name=YPL223C;Alias=GRE1
-chrXVI	SGD	CDS	130162	132228	.	+	.	ID=YPL222W;Name=YPL222W;Alias=FMP40
-chrXVI	SGD	CDS	133043	135424	.	+	.	ID=YPL221W;Name=YPL221W;Alias=FLC1
-chrXVI	SGD	CDS	135790	136443	.	+	.	ID=YPL220W;Name=YPL220W;Alias=RPL1A
-chrXVI	SGD	CDS	136750	138228	.	+	.	ID=YPL219W;Name=YPL219W;Alias=PCL8
-chrXVI	SGD	CDS	138698	139409	.	+	.	ID=YPL218W;Name=YPL218W;Alias=SAR1
-chrXVI	SGD	CDS	139620	143171	.	-	.	ID=YPL217C;Name=YPL217C;Alias=BMS1
-chrXVI	SGD	CDS	143821	147129	.	+	.	ID=YPL216W;Name=YPL216W;Alias=
-chrXVI	SGD	CDS	147416	148423	.	+	.	ID=YPL215W;Name=YPL215W;Alias=CBP3
-chrXVI	SGD	CDS	148569	150191	.	-	.	ID=YPL214C;Name=YPL214C;Alias=THI6
-chrXVI	SGD	CDS	150614	151330	.	+	.	ID=YPL213W;Name=YPL213W;Alias=LEA1
-chrXVI	SGD	CDS	151515	153149	.	-	.	ID=YPL212C;Name=YPL212C;Alias=PUS1
-chrXVI	SGD	CDS	153495	154040	.	+	.	ID=YPL211W;Name=YPL211W;Alias=NIP7
-chrXVI	SGD	CDS	154290	156212	.	-	.	ID=YPL210C;Name=YPL210C;Alias=SRP72
-chrXVI	SGD	CDS	156490	157593	.	-	.	ID=YPL209C;Name=YPL209C;Alias=IPL1
-chrXVI	SGD	CDS	157842	159593	.	+	.	ID=YPL208W;Name=YPL208W;Alias=RKM1
-chrXVI	SGD	CDS	159909	162341	.	+	.	ID=YPL207W;Name=YPL207W;Alias=TYW1
-chrXVI	SGD	CDS	162632	163597	.	-	.	ID=YPL206C;Name=YPL206C;Alias=PGC1
-chrXVI	SGD	CDS	164276	165760	.	+	.	ID=YPL204W;Name=YPL204W;Alias=HRR25
-chrXVI	SGD	CDS	166256	167398	.	+	.	ID=YPL203W;Name=YPL203W;Alias=TPK2
-chrXVI	SGD	CDS	168088	169338	.	-	.	ID=YPL202C;Name=YPL202C;Alias=AFT2
-chrXVI	SGD	CDS	169770	171155	.	-	.	ID=YPL201C;Name=YPL201C;Alias=YIG1
-chrXVI	SGD	CDS	171484	171954	.	+	.	ID=YPL200W;Name=YPL200W;Alias=CSM4
-chrXVI	SGD	CDS	172033	172755	.	-	.	ID=YPL199C;Name=YPL199C;Alias=
-chrXVI	SGD	CDS	173152	174702	.	+	.	ID=YPL198W;Name=YPL198W;Alias=RPL7B
-chrXVI	SGD	CDS	175043	175864	.	+	.	ID=YPL196W;Name=YPL196W;Alias=OXR1
-chrXVI	SGD	CDS	176223	179021	.	+	.	ID=YPL195W;Name=YPL195W;Alias=APL5
-chrXVI	SGD	CDS	179277	181115	.	+	.	ID=YPL194W;Name=YPL194W;Alias=DDC1
-chrXVI	SGD	CDS	181403	182548	.	+	.	ID=YPL193W;Name=YPL193W;Alias=RSA1
-chrXVI	SGD	CDS	182655	183056	.	-	.	ID=YPL192C;Name=YPL192C;Alias=PRM3
-chrXVI	SGD	CDS	183597	184679	.	-	.	ID=YPL191C;Name=YPL191C;Alias=
-chrXVI	SGD	CDS	185317	187725	.	-	.	ID=YPL190C;Name=YPL190C;Alias=NAB3
-chrXVI	SGD	CDS	188307	188513	.	-	.	ID=YPL189C-A;Name=YPL189C-A;Alias=COA2
-chrXVI	SGD	CDS	189154	190983	.	+	.	ID=YPL189W;Name=YPL189W;Alias=GUP2
-chrXVI	SGD	CDS	191406	192650	.	+	.	ID=YPL188W;Name=YPL188W;Alias=POS5
-chrXVI	SGD	CDS	193648	194145	.	+	.	ID=YPL187W;Name=YPL187W;Alias=MF%28ALPHA%291
-chrXVI	SGD	CDS	194512	195426	.	-	.	ID=YPL186C;Name=YPL186C;Alias=UIP4
-chrXVI	SGD	CDS	195950	197788	.	-	.	ID=YPL184C;Name=YPL184C;Alias=MRN1
-chrXVI	SGD	CDS	199095	199376	.	+	.	ID=YPL183W-A;Name=YPL183W-A;Alias=RTC6
-chrXVI	SGD	CDS	199495	202536	.	-	.	ID=YPL183C;Name=YPL183C;Alias=RTT10
-chrXVI	SGD	CDS	203421	204941	.	+	.	ID=YPL181W;Name=YPL181W;Alias=CTI6
-chrXVI	SGD	CDS	205248	207647	.	+	.	ID=YPL180W;Name=YPL180W;Alias=TCO89
-chrXVI	SGD	CDS	208157	209806	.	+	.	ID=YPL179W;Name=YPL179W;Alias=PPQ1
-chrXVI	SGD	CDS	212158	212784	.	+	.	ID=YPL178W;Name=YPL178W;Alias=CBC2
-chrXVI	SGD	CDS	213042	213962	.	-	.	ID=YPL177C;Name=YPL177C;Alias=CUP9
-chrXVI	SGD	CDS	216012	218363	.	-	.	ID=YPL176C;Name=YPL176C;Alias=TRE1
-chrXVI	SGD	CDS	218630	220088	.	+	.	ID=YPL175W;Name=YPL175W;Alias=SPT14
-chrXVI	SGD	CDS	220167	222773	.	-	.	ID=YPL174C;Name=YPL174C;Alias=NIP100
-chrXVI	SGD	CDS	223143	224036	.	+	.	ID=YPL173W;Name=YPL173W;Alias=MRPL40
-chrXVI	SGD	CDS	224353	225741	.	-	.	ID=YPL172C;Name=YPL172C;Alias=COX10
-chrXVI	SGD	CDS	226169	227371	.	-	.	ID=YPL171C;Name=YPL171C;Alias=OYE3
-chrXVI	SGD	CDS	228314	228772	.	+	.	ID=YPL170W;Name=YPL170W;Alias=DAP1
-chrXVI	SGD	CDS	229039	230838	.	-	.	ID=YPL169C;Name=YPL169C;Alias=MEX67
-chrXVI	SGD	CDS	231217	232509	.	+	.	ID=YPL168W;Name=YPL168W;Alias=MRX4
-chrXVI	SGD	CDS	232593	237107	.	-	.	ID=YPL167C;Name=YPL167C;Alias=REV3
-chrXVI	SGD	CDS	237338	237979	.	+	.	ID=YPL166W;Name=YPL166W;Alias=ATG29
-chrXVI	SGD	CDS	237956	239077	.	-	.	ID=YPL165C;Name=YPL165C;Alias=SET6
-chrXVI	SGD	CDS	239350	241497	.	-	.	ID=YPL164C;Name=YPL164C;Alias=MLH3
-chrXVI	SGD	CDS	241918	242700	.	-	.	ID=YPL163C;Name=YPL163C;Alias=SVS1
-chrXVI	SGD	CDS	243206	244027	.	-	.	ID=YPL162C;Name=YPL162C;Alias=
-chrXVI	SGD	CDS	244319	246220	.	-	.	ID=YPL161C;Name=YPL161C;Alias=BEM4
-chrXVI	SGD	CDS	246990	250262	.	+	.	ID=YPL160W;Name=YPL160W;Alias=CDC60
-chrXVI	SGD	CDS	250907	251668	.	-	.	ID=YPL159C;Name=YPL159C;Alias=PET20
-chrXVI	SGD	CDS	252034	254310	.	-	.	ID=YPL158C;Name=YPL158C;Alias=AIM44
-chrXVI	SGD	CDS	254814	255761	.	+	.	ID=YPL157W;Name=YPL157W;Alias=TGS1
-chrXVI	SGD	CDS	255913	256767	.	-	.	ID=YPL156C;Name=YPL156C;Alias=PRM4
-chrXVI	SGD	CDS	257216	259336	.	-	.	ID=YPL155C;Name=YPL155C;Alias=KIP2
-chrXVI	SGD	CDS	259714	260931	.	-	.	ID=YPL154C;Name=YPL154C;Alias=PEP4
-chrXVI	SGD	CDS	261727	264192	.	-	.	ID=YPL153C;Name=YPL153C;Alias=RAD53
-chrXVI	SGD	CDS	264602	264700	.	+	.	ID=YPL152W-A;Name=YPL152W-A;Alias=
-chrXVI	SGD	CDS	265028	266104	.	+	.	ID=YPL152W;Name=YPL152W;Alias=RRD2
-chrXVI	SGD	CDS	266180	267535	.	-	.	ID=YPL151C;Name=YPL151C;Alias=PRP46
-chrXVI	SGD	CDS	268188	270893	.	+	.	ID=YPL150W;Name=YPL150W;Alias=
-chrXVI	SGD	CDS	271310	272194	.	+	.	ID=YPL149W;Name=YPL149W;Alias=ATG5
-chrXVI	SGD	CDS	272294	272815	.	-	.	ID=YPL148C;Name=YPL148C;Alias=PPT2
-chrXVI	SGD	CDS	273255	275867	.	+	.	ID=YPL147W;Name=YPL147W;Alias=PXA1
-chrXVI	SGD	CDS	276162	277529	.	-	.	ID=YPL146C;Name=YPL146C;Alias=NOP53
-chrXVI	SGD	CDS	278395	279699	.	-	.	ID=YPL145C;Name=YPL145C;Alias=KES1
-chrXVI	SGD	CDS	280480	280926	.	+	.	ID=YPL144W;Name=YPL144W;Alias=POC4
-chrXVI	SGD	CDS	282122	282970	.	+	.	ID=YPL143W;Name=YPL143W;Alias=RPL33A
-chrXVI	SGD	CDS	283464	286061	.	-	.	ID=YPL141C;Name=YPL141C;Alias=FRK1
-chrXVI	SGD	CDS	287514	289034	.	-	.	ID=YPL140C;Name=YPL140C;Alias=MKK2
-chrXVI	SGD	CDS	289669	291051	.	-	.	ID=YPL139C;Name=YPL139C;Alias=UME1
-chrXVI	SGD	CDS	291366	292427	.	-	.	ID=YPL138C;Name=YPL138C;Alias=SPP1
-chrXVI	SGD	CDS	292817	296647	.	-	.	ID=YPL137C;Name=YPL137C;Alias=GIP3
-chrXVI	SGD	CDS	297553	298050	.	+	.	ID=YPL135W;Name=YPL135W;Alias=ISU1
-chrXVI	SGD	CDS	298571	299503	.	-	.	ID=YPL134C;Name=YPL134C;Alias=ODC1
-chrXVI	SGD	CDS	299888	301228	.	-	.	ID=YPL133C;Name=YPL133C;Alias=RDS2
-chrXVI	SGD	CDS	301716	302618	.	+	.	ID=YPL132W;Name=YPL132W;Alias=COX11
-chrXVI	SGD	CDS	303121	304014	.	+	.	ID=YPL131W;Name=YPL131W;Alias=RPL5
-chrXVI	SGD	CDS	304387	305058	.	+	.	ID=YPL130W;Name=YPL130W;Alias=SPO19
-chrXVI	SGD	CDS	305298	306137	.	+	.	ID=YPL129W;Name=YPL129W;Alias=TAF14
-chrXVI	SGD	CDS	306533	308221	.	-	.	ID=YPL128C;Name=YPL128C;Alias=TBF1
-chrXVI	SGD	CDS	308828	309604	.	-	.	ID=YPL127C;Name=YPL127C;Alias=HHO1
-chrXVI	SGD	CDS	310210	312900	.	+	.	ID=YPL126W;Name=YPL126W;Alias=NAN1
-chrXVI	SGD	CDS	313388	316486	.	+	.	ID=YPL125W;Name=YPL125W;Alias=KAP120
-chrXVI	SGD	CDS	316755	317516	.	+	.	ID=YPL124W;Name=YPL124W;Alias=SPC29
-chrXVI	SGD	CDS	317641	318945	.	-	.	ID=YPL123C;Name=YPL123C;Alias=RNY1
-chrXVI	SGD	CDS	319226	320767	.	-	.	ID=YPL122C;Name=YPL122C;Alias=TFB2
-chrXVI	SGD	CDS	320962	321630	.	-	.	ID=YPL121C;Name=YPL121C;Alias=MEI5
-chrXVI	SGD	CDS	322071	323744	.	+	.	ID=YPL120W;Name=YPL120W;Alias=VPS30
-chrXVI	SGD	CDS	324024	324287	.	-	.	ID=YPL119C-A;Name=YPL119C-A;Alias=
-chrXVI	SGD	CDS	324411	326264	.	-	.	ID=YPL119C;Name=YPL119C;Alias=DBP1
-chrXVI	SGD	CDS	326628	327662	.	+	.	ID=YPL118W;Name=YPL118W;Alias=MRP51
-chrXVI	SGD	CDS	327864	328730	.	-	.	ID=YPL117C;Name=YPL117C;Alias=IDI1
-chrXVI	SGD	CDS	329606	331699	.	+	.	ID=YPL116W;Name=YPL116W;Alias=HOS3
-chrXVI	SGD	CDS	332100	335486	.	-	.	ID=YPL115C;Name=YPL115C;Alias=BEM3
-chrXVI	SGD	CDS	335953	337143	.	-	.	ID=YPL113C;Name=YPL113C;Alias=
-chrXVI	SGD	CDS	337436	338620	.	-	.	ID=YPL112C;Name=YPL112C;Alias=PEX25
-chrXVI	SGD	CDS	339944	340945	.	+	.	ID=YPL111W;Name=YPL111W;Alias=CAR1
-chrXVI	SGD	CDS	341068	344739	.	-	.	ID=YPL110C;Name=YPL110C;Alias=GDE1
-chrXVI	SGD	CDS	345264	347389	.	-	.	ID=YPL109C;Name=YPL109C;Alias=
-chrXVI	SGD	CDS	348446	348952	.	+	.	ID=YPL108W;Name=YPL108W;Alias=
-chrXVI	SGD	CDS	349119	349865	.	+	.	ID=YPL107W;Name=YPL107W;Alias=
-chrXVI	SGD	CDS	350194	352275	.	-	.	ID=YPL106C;Name=YPL106C;Alias=SSE1
-chrXVI	SGD	CDS	352863	355412	.	-	.	ID=YPL105C;Name=YPL105C;Alias=SYH1
-chrXVI	SGD	CDS	355700	357676	.	+	.	ID=YPL104W;Name=YPL104W;Alias=MSD1
-chrXVI	SGD	CDS	358000	359406	.	-	.	ID=YPL103C;Name=YPL103C;Alias=FMP30
-chrXVI	SGD	CDS	360209	361579	.	+	.	ID=YPL101W;Name=YPL101W;Alias=ELP4
-chrXVI	SGD	CDS	361872	363362	.	+	.	ID=YPL100W;Name=YPL100W;Alias=ATG21
-chrXVI	SGD	CDS	363520	364068	.	-	.	ID=YPL099C;Name=YPL099C;Alias=INA17
-chrXVI	SGD	CDS	364386	364727	.	-	.	ID=YPL098C;Name=YPL098C;Alias=MGR2
-chrXVI	SGD	CDS	364952	366430	.	+	.	ID=YPL097W;Name=YPL097W;Alias=MSY1
-chrXVI	SGD	CDS	366529	366735	.	-	.	ID=YPL096C-A;Name=YPL096C-A;Alias=ERI1
-chrXVI	SGD	CDS	366927	368018	.	+	.	ID=YPL096W;Name=YPL096W;Alias=PNG1
-chrXVI	SGD	CDS	368071	369441	.	-	.	ID=YPL095C;Name=YPL095C;Alias=EEB1
-chrXVI	SGD	CDS	369839	370663	.	-	.	ID=YPL094C;Name=YPL094C;Alias=SEC62
-chrXVI	SGD	CDS	370978	372921	.	+	.	ID=YPL093W;Name=YPL093W;Alias=NOG1
-chrXVI	SGD	CDS	373793	375169	.	+	.	ID=YPL092W;Name=YPL092W;Alias=SSU1
-chrXVI	SGD	CDS	375502	376953	.	+	.	ID=YPL091W;Name=YPL091W;Alias=GLR1
-chrXVI	SGD	CDS	377291	378395	.	-	.	ID=YPL090C;Name=YPL090C;Alias=RPS6A
-chrXVI	SGD	CDS	379120	381150	.	-	.	ID=YPL089C;Name=YPL089C;Alias=RLM1
-chrXVI	SGD	CDS	381965	382993	.	+	.	ID=YPL088W;Name=YPL088W;Alias=
-chrXVI	SGD	CDS	383455	384408	.	+	.	ID=YPL087W;Name=YPL087W;Alias=YDC1
-chrXVI	SGD	CDS	384773	386446	.	-	.	ID=YPL086C;Name=YPL086C;Alias=ELP3
-chrXVI	SGD	CDS	387067	393654	.	+	.	ID=YPL085W;Name=YPL085W;Alias=SEC16
-chrXVI	SGD	CDS	394038	396572	.	+	.	ID=YPL084W;Name=YPL084W;Alias=BRO1
-chrXVI	SGD	CDS	396702	398105	.	-	.	ID=YPL083C;Name=YPL083C;Alias=SEN54
-chrXVI	SGD	CDS	398480	404083	.	-	.	ID=YPL082C;Name=YPL082C;Alias=MOT1
-chrXVI	SGD	CDS	404950	406044	.	+	.	ID=YPL081W;Name=YPL081W;Alias=RPS9A
-chrXVI	SGD	CDS	406636	407539	.	+	.	ID=YPL079W;Name=YPL079W;Alias=RPL21B
-chrXVI	SGD	CDS	408010	408744	.	-	.	ID=YPL078C;Name=YPL078C;Alias=ATP4
-chrXVI	SGD	CDS	409368	410090	.	-	.	ID=YPL077C;Name=YPL077C;Alias=
-chrXVI	SGD	CDS	410443	411285	.	+	.	ID=YPL076W;Name=YPL076W;Alias=GPI2
-chrXVI	SGD	CDS	412254	415362	.	+	.	ID=YPL075W;Name=YPL075W;Alias=GCR1
-chrXVI	SGD	CDS	415763	418027	.	+	.	ID=YPL074W;Name=YPL074W;Alias=YTA6
-chrXVI	SGD	CDS	418512	420011	.	+	.	ID=YPL072W;Name=YPL072W;Alias=UBP16
-chrXVI	SGD	CDS	420048	420518	.	-	.	ID=YPL071C;Name=YPL071C;Alias=
-chrXVI	SGD	CDS	420948	422786	.	+	.	ID=YPL070W;Name=YPL070W;Alias=MUK1
-chrXVI	SGD	CDS	422885	423892	.	-	.	ID=YPL069C;Name=YPL069C;Alias=BTS1
-chrXVI	SGD	CDS	424215	425096	.	-	.	ID=YPL068C;Name=YPL068C;Alias=
-chrXVI	SGD	CDS	425251	425847	.	-	.	ID=YPL067C;Name=YPL067C;Alias=
-chrXVI	SGD	CDS	426233	427672	.	+	.	ID=YPL066W;Name=YPL066W;Alias=RGL1
-chrXVI	SGD	CDS	427927	428655	.	+	.	ID=YPL065W;Name=YPL065W;Alias=VPS28
-chrXVI	SGD	CDS	428711	429616	.	-	.	ID=YPL064C;Name=YPL064C;Alias=CWC27
-chrXVI	SGD	CDS	429939	431369	.	+	.	ID=YPL063W;Name=YPL063W;Alias=TIM50
-chrXVI	SGD	CDS	432588	434090	.	+	.	ID=YPL061W;Name=YPL061W;Alias=ALD6
-chrXVI	SGD	CDS	434523	435764	.	+	.	ID=YPL060W;Name=YPL060W;Alias=MFM1
-chrXVI	SGD	CDS	444579	445031	.	+	.	ID=YPL059W;Name=YPL059W;Alias=GRX5
-chrXVI	SGD	CDS	445842	450377	.	-	.	ID=YPL058C;Name=YPL058C;Alias=PDR12
-chrXVI	SGD	CDS	451909	453057	.	-	.	ID=YPL057C;Name=YPL057C;Alias=SUR1
-chrXVI	SGD	CDS	453430	453735	.	-	.	ID=YPL056C;Name=YPL056C;Alias=LCL1
-chrXVI	SGD	CDS	453992	454990	.	-	.	ID=YPL055C;Name=YPL055C;Alias=LGE1
-chrXVI	SGD	CDS	455759	456664	.	+	.	ID=YPL054W;Name=YPL054W;Alias=LEE1
-chrXVI	SGD	CDS	457118	458458	.	-	.	ID=YPL053C;Name=YPL053C;Alias=KTR6
-chrXVI	SGD	CDS	458799	459678	.	+	.	ID=YPL052W;Name=YPL052W;Alias=OAZ1
-chrXVI	SGD	CDS	459963	460559	.	+	.	ID=YPL051W;Name=YPL051W;Alias=ARL3
-chrXVI	SGD	CDS	460779	461966	.	-	.	ID=YPL050C;Name=YPL050C;Alias=MNN9
-chrXVI	SGD	CDS	462481	463839	.	-	.	ID=YPL049C;Name=YPL049C;Alias=DIG1
-chrXVI	SGD	CDS	464401	465648	.	+	.	ID=YPL048W;Name=YPL048W;Alias=CAM1
-chrXVI	SGD	CDS	465962	466261	.	+	.	ID=YPL047W;Name=YPL047W;Alias=SGF11
-chrXVI	SGD	CDS	466644	466943	.	-	.	ID=YPL046C;Name=YPL046C;Alias=ELC1
-chrXVI	SGD	CDS	467260	469656	.	+	.	ID=YPL045W;Name=YPL045W;Alias=VPS16
-chrXVI	SGD	CDS	469939	471996	.	+	.	ID=YPL043W;Name=YPL043W;Alias=NOP4
-chrXVI	SGD	CDS	473040	474707	.	-	.	ID=YPL042C;Name=YPL042C;Alias=SSN3
-chrXVI	SGD	CDS	475118	475741	.	-	.	ID=YPL041C;Name=YPL041C;Alias=MRX11
-chrXVI	SGD	CDS	475993	479001	.	-	.	ID=YPL040C;Name=YPL040C;Alias=ISM1
-chrXVI	SGD	CDS	479225	480175	.	+	.	ID=YPL039W;Name=YPL039W;Alias=
-chrXVI	SGD	CDS	480182	480373	.	+	.	ID=YPL038W-A;Name=YPL038W-A;Alias=
-chrXVI	SGD	CDS	480535	481068	.	+	.	ID=YPL038W;Name=YPL038W;Alias=MET31
-chrXVI	SGD	CDS	481428	481901	.	-	.	ID=YPL037C;Name=YPL037C;Alias=EGD1
-chrXVI	SGD	CDS	482843	485686	.	+	.	ID=YPL036W;Name=YPL036W;Alias=PMA2
-chrXVI	SGD	CDS	486712	487209	.	+	.	ID=YPL034W;Name=YPL034W;Alias=
-chrXVI	SGD	CDS	487362	488207	.	-	.	ID=YPL033C;Name=YPL033C;Alias=SRL4
-chrXVI	SGD	CDS	488887	491364	.	-	.	ID=YPL032C;Name=YPL032C;Alias=SVL3
-chrXVI	SGD	CDS	492018	493037	.	-	.	ID=YPL031C;Name=YPL031C;Alias=PHO85
-chrXVI	SGD	CDS	493543	495246	.	+	.	ID=YPL030W;Name=YPL030W;Alias=TRM44
-chrXVI	SGD	CDS	495506	497719	.	+	.	ID=YPL029W;Name=YPL029W;Alias=SUV3
-chrXVI	SGD	CDS	498096	499292	.	+	.	ID=YPL028W;Name=YPL028W;Alias=ERG10
-chrXVI	SGD	CDS	499665	500402	.	+	.	ID=YPL027W;Name=YPL027W;Alias=SMA1
-chrXVI	SGD	CDS	500675	502183	.	-	.	ID=YPL026C;Name=YPL026C;Alias=SKS1
-chrXVI	SGD	CDS	503517	504242	.	+	.	ID=YPL024W;Name=YPL024W;Alias=RMI1
-chrXVI	SGD	CDS	504339	506312	.	-	.	ID=YPL023C;Name=YPL023C;Alias=MET12
-chrXVI	SGD	CDS	506697	509999	.	+	.	ID=YPL022W;Name=YPL022W;Alias=RAD1
-chrXVI	SGD	CDS	511101	511664	.	+	.	ID=YPL021W;Name=YPL021W;Alias=ECM23
-chrXVI	SGD	CDS	512313	514178	.	-	.	ID=YPL020C;Name=YPL020C;Alias=ULP1
-chrXVI	SGD	CDS	514511	517018	.	-	.	ID=YPL019C;Name=YPL019C;Alias=VTC3
-chrXVI	SGD	CDS	517651	518760	.	+	.	ID=YPL018W;Name=YPL018W;Alias=CTF19
-chrXVI	SGD	CDS	518734	520233	.	-	.	ID=YPL017C;Name=YPL017C;Alias=IRC15
-chrXVI	SGD	CDS	521014	524958	.	+	.	ID=YPL016W;Name=YPL016W;Alias=SWI1
-chrXVI	SGD	CDS	525810	526883	.	-	.	ID=YPL015C;Name=YPL015C;Alias=HST2
-chrXVI	SGD	CDS	527547	528692	.	+	.	ID=YPL014W;Name=YPL014W;Alias=CIP1
-chrXVI	SGD	CDS	528985	529350	.	-	.	ID=YPL013C;Name=YPL013C;Alias=MRPS16
-chrXVI	SGD	CDS	529723	533409	.	+	.	ID=YPL012W;Name=YPL012W;Alias=RRP12
-chrXVI	SGD	CDS	533642	534703	.	-	.	ID=YPL011C;Name=YPL011C;Alias=TAF3
-chrXVI	SGD	CDS	535018	535587	.	+	.	ID=YPL010W;Name=YPL010W;Alias=RET3
-chrXVI	SGD	CDS	535820	538936	.	-	.	ID=YPL009C;Name=YPL009C;Alias=RQC2
-chrXVI	SGD	CDS	539385	541970	.	+	.	ID=YPL008W;Name=YPL008W;Alias=CHL1
-chrXVI	SGD	CDS	542082	543848	.	-	.	ID=YPL007C;Name=YPL007C;Alias=TFC8
-chrXVI	SGD	CDS	544631	548143	.	+	.	ID=YPL006W;Name=YPL006W;Alias=NCR1
-chrXVI	SGD	CDS	548486	550306	.	+	.	ID=YPL005W;Name=YPL005W;Alias=AEP3
-chrXVI	SGD	CDS	550632	551657	.	-	.	ID=YPL004C;Name=YPL004C;Alias=LSP1
-chrXVI	SGD	CDS	552020	553408	.	+	.	ID=YPL003W;Name=YPL003W;Alias=ULA1
-chrXVI	SGD	CDS	553627	554328	.	-	.	ID=YPL002C;Name=YPL002C;Alias=SNF8
-chrXVI	SGD	CDS	554605	555729	.	+	.	ID=YPL001W;Name=YPL001W;Alias=HAT1
-chrXVI	SGD	CDS	556377	557837	.	+	.	ID=YPR001W;Name=YPR001W;Alias=CIT3
-chrXVI	SGD	CDS	558385	559935	.	+	.	ID=YPR002W;Name=YPR002W;Alias=PDH1
-chrXVI	SGD	CDS	561504	563768	.	-	.	ID=YPR003C;Name=YPR003C;Alias=
-chrXVI	SGD	CDS	564007	565041	.	-	.	ID=YPR004C;Name=YPR004C;Alias=AIM45
-chrXVI	SGD	CDS	565787	566671	.	-	.	ID=YPR005C;Name=YPR005C;Alias=HAL1
-chrXVI	SGD	CDS	567269	568996	.	-	.	ID=YPR006C;Name=YPR006C;Alias=ICL2
-chrXVI	SGD	CDS	569336	571378	.	-	.	ID=YPR007C;Name=YPR007C;Alias=REC8
-chrXVI	SGD	CDS	573018	575102	.	+	.	ID=YPR008W;Name=YPR008W;Alias=HAA1
-chrXVI	SGD	CDS	576552	577358	.	+	.	ID=YPR009W;Name=YPR009W;Alias=SUT2
-chrXVI	SGD	CDS	577585	581196	.	-	.	ID=YPR010C;Name=YPR010C;Alias=RPA135
-chrXVI	SGD	CDS	582373	582734	.	-	.	ID=YPR010C-A;Name=YPR010C-A;Alias=
-chrXVI	SGD	CDS	583062	584042	.	-	.	ID=YPR011C;Name=YPR011C;Alias=
-chrXVI	SGD	CDS	584632	585585	.	-	.	ID=YPR013C;Name=YPR013C;Alias=CMR3
-chrXVI	SGD	CDS	590283	591026	.	-	.	ID=YPR015C;Name=YPR015C;Alias=
-chrXVI	SGD	CDS	592332	593069	.	-	.	ID=YPR016C;Name=YPR016C;Alias=TIF6
-chrXVI	SGD	CDS	593486	593917	.	-	.	ID=YPR017C;Name=YPR017C;Alias=DSS4
-chrXVI	SGD	CDS	594476	596296	.	+	.	ID=YPR018W;Name=YPR018W;Alias=RLF2
-chrXVI	SGD	CDS	596750	599551	.	+	.	ID=YPR019W;Name=YPR019W;Alias=MCM4
-chrXVI	SGD	CDS	599870	600217	.	+	.	ID=YPR020W;Name=YPR020W;Alias=ATP20
-chrXVI	SGD	CDS	600649	603357	.	-	.	ID=YPR021C;Name=YPR021C;Alias=AGC1
-chrXVI	SGD	CDS	603911	607312	.	-	.	ID=YPR022C;Name=YPR022C;Alias=SDD4
-chrXVI	SGD	CDS	608826	610031	.	-	.	ID=YPR023C;Name=YPR023C;Alias=EAF3
-chrXVI	SGD	CDS	610481	612724	.	+	.	ID=YPR024W;Name=YPR024W;Alias=YME1
-chrXVI	SGD	CDS	613377	614558	.	-	.	ID=YPR025C;Name=YPR025C;Alias=CCL1
-chrXVI	SGD	CDS	615379	619014	.	+	.	ID=YPR026W;Name=YPR026W;Alias=ATH1
-chrXVI	SGD	CDS	620425	621258	.	-	.	ID=YPR027C;Name=YPR027C;Alias=
-chrXVI	SGD	CDS	623527	624202	.	+	.	ID=YPR028W;Name=YPR028W;Alias=YOP1
-chrXVI	SGD	CDS	624469	626967	.	-	.	ID=YPR029C;Name=YPR029C;Alias=APL4
-chrXVI	SGD	CDS	627880	631245	.	+	.	ID=YPR030W;Name=YPR030W;Alias=CSR2
-chrXVI	SGD	CDS	631515	633761	.	+	.	ID=YPR031W;Name=YPR031W;Alias=NTO1
-chrXVI	SGD	CDS	634123	637224	.	+	.	ID=YPR032W;Name=YPR032W;Alias=SRO7
-chrXVI	SGD	CDS	637379	639019	.	-	.	ID=YPR033C;Name=YPR033C;Alias=HTS1
-chrXVI	SGD	CDS	639525	640958	.	+	.	ID=YPR034W;Name=YPR034W;Alias=ARP7
-chrXVI	SGD	CDS	642208	643320	.	+	.	ID=YPR035W;Name=YPR035W;Alias=GLN1
-chrXVI	SGD	CDS	643836	645272	.	+	.	ID=YPR036W;Name=YPR036W;Alias=VMA13
-chrXVI	SGD	CDS	645950	646153	.	+	.	ID=YPR036W-A;Name=YPR036W-A;Alias=SPO24
-chrXVI	SGD	CDS	646448	647038	.	-	.	ID=YPR037C;Name=YPR037C;Alias=ERV2
-chrXVI	SGD	CDS	647305	648375	.	+	.	ID=YPR040W;Name=YPR040W;Alias=TIP41
-chrXVI	SGD	CDS	648704	649921	.	+	.	ID=YPR041W;Name=YPR041W;Alias=TIF5
-chrXVI	SGD	CDS	650435	653662	.	-	.	ID=YPR042C;Name=YPR042C;Alias=PUF2
-chrXVI	SGD	CDS	654166	654847	.	+	.	ID=YPR043W;Name=YPR043W;Alias=RPL43A
-chrXVI	SGD	CDS	655140	656552	.	-	.	ID=YPR045C;Name=YPR045C;Alias=THP3
-chrXVI	SGD	CDS	656799	657344	.	+	.	ID=YPR046W;Name=YPR046W;Alias=MCM16
-chrXVI	SGD	CDS	657529	658938	.	+	.	ID=YPR047W;Name=YPR047W;Alias=MSF1
-chrXVI	SGD	CDS	659182	661053	.	+	.	ID=YPR048W;Name=YPR048W;Alias=TAH18
-chrXVI	SGD	CDS	661137	664673	.	-	.	ID=YPR049C;Name=YPR049C;Alias=ATG11
-chrXVI	SGD	CDS	664960	665490	.	+	.	ID=YPR051W;Name=YPR051W;Alias=MAK3
-chrXVI	SGD	CDS	665693	665974	.	-	.	ID=YPR052C;Name=YPR052C;Alias=NHP6A
-chrXVI	SGD	CDS	666280	667446	.	+	.	ID=YPR054W;Name=YPR054W;Alias=SMK1
-chrXVI	SGD	CDS	667676	670873	.	+	.	ID=YPR055W;Name=YPR055W;Alias=SEC8
-chrXVI	SGD	CDS	671126	672142	.	+	.	ID=YPR056W;Name=YPR056W;Alias=TFB4
-chrXVI	SGD	CDS	672471	673496	.	+	.	ID=YPR057W;Name=YPR057W;Alias=BRR1
-chrXVI	SGD	CDS	673751	674674	.	+	.	ID=YPR058W;Name=YPR058W;Alias=YMC1
-chrXVI	SGD	CDS	674861	675631	.	-	.	ID=YPR060C;Name=YPR060C;Alias=ARO7
-chrXVI	SGD	CDS	675977	676882	.	-	.	ID=YPR061C;Name=YPR061C;Alias=JID1
-chrXVI	SGD	CDS	677165	677641	.	+	.	ID=YPR062W;Name=YPR062W;Alias=FCY1
-chrXVI	SGD	CDS	677812	678320	.	-	.	ID=YPR063C;Name=YPR063C;Alias=
-chrXVI	SGD	CDS	679693	680799	.	+	.	ID=YPR065W;Name=YPR065W;Alias=ROX1
-chrXVI	SGD	CDS	681213	682112	.	+	.	ID=YPR066W;Name=YPR066W;Alias=UBA3
-chrXVI	SGD	CDS	682220	682777	.	+	.	ID=YPR067W;Name=YPR067W;Alias=ISA2
-chrXVI	SGD	CDS	682941	684353	.	-	.	ID=YPR068C;Name=YPR068C;Alias=HOS1
-chrXVI	SGD	CDS	684556	685437	.	-	.	ID=YPR069C;Name=YPR069C;Alias=SPE3
-chrXVI	SGD	CDS	685898	687598	.	+	.	ID=YPR070W;Name=YPR070W;Alias=MED1
-chrXVI	SGD	CDS	688172	688807	.	+	.	ID=YPR071W;Name=YPR071W;Alias=
-chrXVI	SGD	CDS	690107	691789	.	+	.	ID=YPR072W;Name=YPR072W;Alias=NOT5
-chrXVI	SGD	CDS	691933	692418	.	-	.	ID=YPR073C;Name=YPR073C;Alias=LTP1
-chrXVI	SGD	CDS	692796	694838	.	-	.	ID=YPR074C;Name=YPR074C;Alias=TKL1
-chrXVI	SGD	CDS	695737	696819	.	-	.	ID=YPR075C;Name=YPR075C;Alias=OPY2
-chrXVI	SGD	CDS	697147	698265	.	-	.	ID=YPR078C;Name=YPR078C;Alias=
-chrXVI	SGD	CDS	698869	700014	.	+	.	ID=YPR079W;Name=YPR079W;Alias=MRL1
-chrXVI	SGD	CDS	700594	701970	.	+	.	ID=YPR080W;Name=YPR080W;Alias=TEF1
-chrXVI	SGD	CDS	702114	703970	.	-	.	ID=YPR081C;Name=YPR081C;Alias=GRS2
-chrXVI	SGD	CDS	704225	704656	.	-	.	ID=YPR082C;Name=YPR082C;Alias=DIB1
-chrXVI	SGD	CDS	704854	706593	.	+	.	ID=YPR083W;Name=YPR083W;Alias=MDM36
-chrXVI	SGD	CDS	706972	708342	.	+	.	ID=YPR084W;Name=YPR084W;Alias=
-chrXVI	SGD	CDS	708497	709828	.	-	.	ID=YPR085C;Name=YPR085C;Alias=ASA1
-chrXVI	SGD	CDS	710101	711138	.	+	.	ID=YPR086W;Name=YPR086W;Alias=SUA7
-chrXVI	SGD	CDS	711403	713028	.	-	.	ID=YPR088C;Name=YPR088C;Alias=SRP54
-chrXVI	SGD	CDS	713275	715941	.	+	.	ID=YPR089W;Name=YPR089W;Alias=
-chrXVI	SGD	CDS	716156	718468	.	-	.	ID=YPR091C;Name=YPR091C;Alias=NVJ2
-chrXVI	SGD	CDS	719558	720424	.	-	.	ID=YPR093C;Name=YPR093C;Alias=ASR1
-chrXVI	SGD	CDS	720637	720960	.	+	.	ID=YPR094W;Name=YPR094W;Alias=RDS3
-chrXVI	SGD	CDS	721037	724717	.	-	.	ID=YPR095C;Name=YPR095C;Alias=SYT1
-chrXVI	SGD	CDS	724842	725144	.	-	.	ID=YPR096C;Name=YPR096C;Alias=
-chrXVI	SGD	CDS	725394	728615	.	+	.	ID=YPR097W;Name=YPR097W;Alias=
-chrXVI	SGD	CDS	728947	729528	.	-	.	ID=YPR098C;Name=YPR098C;Alias=
-chrXVI	SGD	CDS	729791	730213	.	+	.	ID=YPR100W;Name=YPR100W;Alias=MRPL51
-chrXVI	SGD	CDS	730492	731019	.	+	.	ID=YPR101W;Name=YPR101W;Alias=SNT309
-chrXVI	SGD	CDS	731224	731748	.	-	.	ID=YPR102C;Name=YPR102C;Alias=RPL11A
-chrXVI	SGD	CDS	732349	733212	.	+	.	ID=YPR103W;Name=YPR103W;Alias=PRE2
-chrXVI	SGD	CDS	733623	736433	.	-	.	ID=YPR104C;Name=YPR104C;Alias=FHL1
-chrXVI	SGD	CDS	736984	739569	.	-	.	ID=YPR105C;Name=YPR105C;Alias=COG4
-chrXVI	SGD	CDS	740061	741392	.	+	.	ID=YPR106W;Name=YPR106W;Alias=ISR1
-chrXVI	SGD	CDS	741438	742064	.	-	.	ID=YPR107C;Name=YPR107C;Alias=YTH1
-chrXVI	SGD	CDS	742454	743743	.	+	.	ID=YPR108W;Name=YPR108W;Alias=RPN7
-chrXVI	SGD	CDS	744175	744387	.	+	.	ID=YPR108W-A;Name=YPR108W-A;Alias=
-chrXVI	SGD	CDS	744689	745573	.	+	.	ID=YPR109W;Name=YPR109W;Alias=
-chrXVI	SGD	CDS	745828	746835	.	-	.	ID=YPR110C;Name=YPR110C;Alias=RPC40
-chrXVI	SGD	CDS	747306	749000	.	+	.	ID=YPR111W;Name=YPR111W;Alias=DBF20
-chrXVI	SGD	CDS	749256	751919	.	-	.	ID=YPR112C;Name=YPR112C;Alias=MRD1
-chrXVI	SGD	CDS	752257	752919	.	+	.	ID=YPR113W;Name=YPR113W;Alias=PIS1
-chrXVI	SGD	CDS	753301	754248	.	+	.	ID=YPR114W;Name=YPR114W;Alias=
-chrXVI	SGD	CDS	754877	758128	.	+	.	ID=YPR115W;Name=YPR115W;Alias=RGC1
-chrXVI	SGD	CDS	758648	759481	.	+	.	ID=YPR116W;Name=YPR116W;Alias=RRG8
-chrXVI	SGD	CDS	760025	767494	.	+	.	ID=YPR117W;Name=YPR117W;Alias=
-chrXVI	SGD	CDS	767752	768987	.	+	.	ID=YPR118W;Name=YPR118W;Alias=MRI1
-chrXVI	SGD	CDS	771653	773128	.	+	.	ID=YPR119W;Name=YPR119W;Alias=CLB2
-chrXVI	SGD	CDS	773875	775182	.	-	.	ID=YPR120C;Name=YPR120C;Alias=CLB5
-chrXVI	SGD	CDS	778583	780301	.	+	.	ID=YPR121W;Name=YPR121W;Alias=THI22
-chrXVI	SGD	CDS	782045	785671	.	+	.	ID=YPR122W;Name=YPR122W;Alias=AXL1
-chrXVI	SGD	CDS	786208	787428	.	+	.	ID=YPR124W;Name=YPR124W;Alias=CTR1
-chrXVI	SGD	CDS	787961	789325	.	+	.	ID=YPR125W;Name=YPR125W;Alias=YLH47
-chrXVI	SGD	CDS	790083	791120	.	+	.	ID=YPR127W;Name=YPR127W;Alias=
-chrXVI	SGD	CDS	791218	792204	.	-	.	ID=YPR128C;Name=YPR128C;Alias=ANT1
-chrXVI	SGD	CDS	792687	793736	.	+	.	ID=YPR129W;Name=YPR129W;Alias=SCD6
-chrXVI	SGD	CDS	793911	794498	.	-	.	ID=YPR131C;Name=YPR131C;Alias=NAT3
-chrXVI	SGD	CDS	794965	795767	.	+	.	ID=YPR132W;Name=YPR132W;Alias=RPS23B
-chrXVI	SGD	CDS	795978	797210	.	-	.	ID=YPR133C;Name=YPR133C;Alias=SPN1
-chrXVI	SGD	CDS	797557	797709	.	+	.	ID=YPR133W-A;Name=YPR133W-A;Alias=TOM5
-chrXVI	SGD	CDS	798051	798857	.	+	.	ID=YPR134W;Name=YPR134W;Alias=MSS18
-chrXVI	SGD	CDS	799234	802017	.	+	.	ID=YPR135W;Name=YPR135W;Alias=CTF4
-chrXVI	SGD	CDS	802359	804080	.	+	.	ID=YPR137W;Name=YPR137W;Alias=RRP9
-chrXVI	SGD	CDS	810984	812453	.	-	.	ID=YPR138C;Name=YPR138C;Alias=MEP3
-chrXVI	SGD	CDS	813156	814058	.	-	.	ID=YPR139C;Name=YPR139C;Alias=LOA1
-chrXVI	SGD	CDS	814391	815536	.	+	.	ID=YPR140W;Name=YPR140W;Alias=TAZ1
-chrXVI	SGD	CDS	815734	817923	.	-	.	ID=YPR141C;Name=YPR141C;Alias=KAR3
-chrXVI	SGD	CDS	818323	819075	.	+	.	ID=YPR143W;Name=YPR143W;Alias=RRP15
-chrXVI	SGD	CDS	819765	821423	.	-	.	ID=YPR144C;Name=YPR144C;Alias=NOC4
-chrXVI	SGD	CDS	822620	824338	.	+	.	ID=YPR145W;Name=YPR145W;Alias=ASN1
-chrXVI	SGD	CDS	824690	824926	.	-	.	ID=YPR145C-A;Name=YPR145C-A;Alias=
-chrXVI	SGD	CDS	825645	826559	.	-	.	ID=YPR147C;Name=YPR147C;Alias=
-chrXVI	SGD	CDS	826833	828140	.	-	.	ID=YPR148C;Name=YPR148C;Alias=
-chrXVI	SGD	CDS	829918	830439	.	+	.	ID=YPR149W;Name=YPR149W;Alias=NCE102
-chrXVI	SGD	CDS	831055	831675	.	-	.	ID=YPR151C;Name=YPR151C;Alias=SUE1
-chrXVI	SGD	CDS	832061	833458	.	-	.	ID=YPR152C;Name=YPR152C;Alias=URN1
-chrXVI	SGD	CDS	833689	834245	.	+	.	ID=YPR153W;Name=YPR153W;Alias=MAY24
-chrXVI	SGD	CDS	834565	835212	.	+	.	ID=YPR154W;Name=YPR154W;Alias=PIN3
-chrXVI	SGD	CDS	835563	837413	.	-	.	ID=YPR155C;Name=YPR155C;Alias=NCA2
-chrXVI	SGD	CDS	837909	839777	.	-	.	ID=YPR156C;Name=YPR156C;Alias=TPO3
-chrXVI	SGD	CDS	841266	842669	.	+	.	ID=YPR157W;Name=YPR157W;Alias=TDA6
-chrXVI	SGD	CDS	843262	844020	.	+	.	ID=YPR158W;Name=YPR158W;Alias=CUR1
-chrXVI	SGD	CDS	857583	859745	.	+	.	ID=YPR159W;Name=YPR159W;Alias=KRE6
-chrXVI	SGD	CDS	860314	860415	.	-	.	ID=YPR159C-A;Name=YPR159C-A;Alias=
-chrXVI	SGD	CDS	861306	864014	.	+	.	ID=YPR160W;Name=YPR160W;Alias=GPH1
-chrXVI	SGD	CDS	864449	866422	.	-	.	ID=YPR161C;Name=YPR161C;Alias=SGV1
-chrXVI	SGD	CDS	866715	868304	.	-	.	ID=YPR162C;Name=YPR162C;Alias=ORC4
-chrXVI	SGD	CDS	868645	869955	.	-	.	ID=YPR163C;Name=YPR163C;Alias=TIF3
-chrXVI	SGD	CDS	870703	874926	.	+	.	ID=YPR164W;Name=YPR164W;Alias=MMS1
-chrXVI	SGD	CDS	875368	875997	.	+	.	ID=YPR165W;Name=YPR165W;Alias=RHO1
-chrXVI	SGD	CDS	876282	876629	.	-	.	ID=YPR166C;Name=YPR166C;Alias=MRP2
-chrXVI	SGD	CDS	876847	877632	.	-	.	ID=YPR167C;Name=YPR167C;Alias=MET16
-chrXVI	SGD	CDS	878076	878549	.	+	.	ID=YPR168W;Name=YPR168W;Alias=NUT2
-chrXVI	SGD	CDS	878690	880168	.	+	.	ID=YPR169W;Name=YPR169W;Alias=JIP5
-chrXVI	SGD	CDS	883239	883595	.	+	.	ID=YPR170W-B;Name=YPR170W-B;Alias=
-chrXVI	SGD	CDS	883828	885558	.	+	.	ID=YPR171W;Name=YPR171W;Alias=BSP1
-chrXVI	SGD	CDS	885796	886398	.	+	.	ID=YPR172W;Name=YPR172W;Alias=
-chrXVI	SGD	CDS	886524	887837	.	-	.	ID=YPR173C;Name=YPR173C;Alias=VPS4
-chrXVI	SGD	CDS	888043	888708	.	-	.	ID=YPR174C;Name=YPR174C;Alias=
-chrXVI	SGD	CDS	888974	891043	.	+	.	ID=YPR175W;Name=YPR175W;Alias=DPB2
-chrXVI	SGD	CDS	891101	892078	.	-	.	ID=YPR176C;Name=YPR176C;Alias=BET2
-chrXVI	SGD	CDS	892332	893729	.	+	.	ID=YPR178W;Name=YPR178W;Alias=PRP4
-chrXVI	SGD	CDS	893797	895764	.	-	.	ID=YPR179C;Name=YPR179C;Alias=HDA3
-chrXVI	SGD	CDS	895961	897004	.	+	.	ID=YPR180W;Name=YPR180W;Alias=AOS1
-chrXVI	SGD	CDS	897361	899667	.	-	.	ID=YPR181C;Name=YPR181C;Alias=SEC23
-chrXVI	SGD	CDS	900194	900454	.	+	.	ID=YPR182W;Name=YPR182W;Alias=SMX3
-chrXVI	SGD	CDS	900755	901558	.	+	.	ID=YPR183W;Name=YPR183W;Alias=DPM1
-chrXVI	SGD	CDS	902044	906654	.	+	.	ID=YPR184W;Name=YPR184W;Alias=GDB1
-chrXVI	SGD	CDS	907218	909434	.	+	.	ID=YPR185W;Name=YPR185W;Alias=ATG13
-chrXVI	SGD	CDS	909733	911022	.	-	.	ID=YPR186C;Name=YPR186C;Alias=PZF1
-chrXVI	SGD	CDS	911257	911800	.	+	.	ID=YPR187W;Name=YPR187W;Alias=RPO26
-chrXVI	SGD	CDS	911988	912479	.	-	.	ID=YPR188C;Name=YPR188C;Alias=MLC2
-chrXVI	SGD	CDS	912664	916962	.	+	.	ID=YPR189W;Name=YPR189W;Alias=SKI3
-chrXVI	SGD	CDS	917077	919041	.	-	.	ID=YPR190C;Name=YPR190C;Alias=RPC82
-chrXVI	SGD	CDS	919381	920487	.	+	.	ID=YPR191W;Name=YPR191W;Alias=QCR2
-chrXVI	SGD	CDS	921860	922777	.	+	.	ID=YPR192W;Name=YPR192W;Alias=AQY1
-chrXVI	SGD	CDS	922909	923379	.	-	.	ID=YPR193C;Name=YPR193C;Alias=HPA2
-chrXVI	SGD	CDS	924304	926937	.	-	.	ID=YPR194C;Name=YPR194C;Alias=OPT2
-chrXVI	SGD	CDS	931376	932788	.	+	.	ID=YPR196W;Name=YPR196W;Alias=
-chrXVI	SGD	CDS	934034	935665	.	+	.	ID=YPR198W;Name=YPR198W;Alias=SGE1
-chrXVI	SGD	CDS	938148	939032	.	-	.	ID=YPR199C;Name=YPR199C;Alias=ARR1
-chrXVI	SGD	CDS	939279	939671	.	-	.	ID=YPR200C;Name=YPR200C;Alias=ARR2
-chrXVI	SGD	CDS	939922	941136	.	+	.	ID=YPR201W;Name=YPR201W;Alias=ARR3
-chrXVI	SGD	CDS	943032	943896	.	+	.	ID=YPR202W;Name=YPR202W;Alias=
-chrXVI	SGD	CDS	943880	944188	.	+	.	ID=YPR203W;Name=YPR203W;Alias=
-chrXVI	SGD	CDS	944603	947701	.	+	.	ID=YPR204W;Name=YPR204W;Alias=
-chrmt	SGD	CDS	13818	16322	.	+	.	ID=Q0050;Name=Q0050;Alias=AI1
-chrmt	SGD	CDS	13818	18830	.	+	.	ID=Q0055;Name=Q0055;Alias=AI2
-chrmt	SGD	CDS	13818	19996	.	+	.	ID=Q0060;Name=Q0060;Alias=AI3
-chrmt	SGD	CDS	13818	21935	.	+	.	ID=Q0065;Name=Q0065;Alias=AI4
-chrmt	SGD	CDS	13818	23167	.	+	.	ID=Q0070;Name=Q0070;Alias=AI5_ALPHA
-chrmt	SGD	CDS	13818	26701	.	+	.	ID=Q0045;Name=Q0045;Alias=COX1
-chrmt	SGD	CDS	24156	25255	.	+	.	ID=Q0075;Name=Q0075;Alias=AI5_BETA
-chrmt	SGD	CDS	27666	27812	.	+	.	ID=Q0080;Name=Q0080;Alias=ATP8
-chrmt	SGD	CDS	28487	29266	.	+	.	ID=Q0085;Name=Q0085;Alias=ATP6
-chrmt	SGD	CDS	36540	38579	.	+	.	ID=Q0110;Name=Q0110;Alias=BI2
-chrmt	SGD	CDS	36540	40265	.	+	.	ID=Q0115;Name=Q0115;Alias=BI3
-chrmt	SGD	CDS	36540	42251	.	+	.	ID=Q0120;Name=Q0120;Alias=BI4
-chrmt	SGD	CDS	36540	43647	.	+	.	ID=Q0105;Name=Q0105;Alias=COB
-chrmt	SGD	CDS	46723	46953	.	+	.	ID=Q0130;Name=Q0130;Alias=OLI1
-chrmt	SGD	CDS	48901	50097	.	+	.	ID=Q0140;Name=Q0140;Alias=VAR1
-chrmt	SGD	CDS	61022	61729	.	+	.	ID=Q0160;Name=Q0160;Alias=SCEI
-chrmt	SGD	CDS	73758	74513	.	+	.	ID=Q0250;Name=Q0250;Alias=COX2
-chrmt	SGD	CDS	74495	75984	.	+	.	ID=Q0255;Name=Q0255;Alias=
-chrmt	SGD	CDS	79213	80022	.	+	.	ID=Q0275;Name=Q0275;Alias=COX3
diff --git a/data/SGDref.PoFF.gff.gz b/data/SGDref.PoFF.gff.gz
new file mode 100644
index 0000000..0b7373e
Binary files /dev/null and b/data/SGDref.PoFF.gff.gz differ
diff --git a/data/TE_lib.LTRonly.tidy.fa b/data/TE_lib.LTRonly.tidy.fa
new file mode 100644
index 0000000..a7b6c29
--- /dev/null
+++ b/data/TE_lib.LTRonly.tidy.fa
@@ -0,0 +1,76 @@
+>TY1/TY2-LTR#LTR/Copia/TY1
+TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAATATATTATC
+ATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAG
+CTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT
+GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATAT
+CCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAACAATG
+GAATCCCAACAATTATCTCAACATTCACATATTTCTCA
+>TY1/TY2-LTR#LTR/Copia/TY1p
+TGTTGGAATGAAATTCTAATATCATCTATTTAATAGTATATTATAATATGCGGTGCAAGA
+GGATGACATAAAGATTGAGAAACAGTCATCCAATCTAATGGAAGCTGAAATGCAAGGATT
+GATAATGTAATAGGATAATGAATAACAACATATAAAAAGAAAGAAGATAAAATAATAACA
+CTATGTAGAACTATCGATTCCCTTTTGTGGATTCCTATATCCTCGAGGAGAACTTCTAGT
+ATATTCTATATACCTAATATTATAGCCTTTAGTAACAATGGAATCCCAACAATTATCTAA
+TTACCCACACAATTCTCA
+>TY1/TY2-LTR#LTR/Copia/TY2
+TGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATC
+ATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGC
+TGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAATGATGAT
+AATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATGGATTCCTAAATCCTC
+GAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAAATGGAATCC
+CAACAATTACATCAAAATCCACATTCTCTTCA
+>TY3-LTR#LTR/Gypsy/TY3
+TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCACCCTGAACGTTCATAAA
+ACACATATGAAACAACCTTATAACAAAACGAACAACATGAGACAAAACCCGACCTTCCCT
+AGCTGAACTACCCAAAGTATAAATGCCTGAACAATTAGTTTAGATCCGAGATTCCGCGCT
+TCCACCACTTAGTATGATTCATATTTTATATAATATATAAGATAAGTAACATTCCGTGAA
+TTAATCTGATAAACTGTTTTGACAACTGGTTACTTCCCTAAGACTGTTTATATTAGGATT
+GTCAAGACACTCCGGTATTACTCGAGCCCGTAATACAACA
+>TY3-LTR#LTR/Gypsy/TY3p
+TGTTGTATCTCAAGATGAGATACCTCAGCATTACTAGATTTACCAACCTAGACATAAAAC
+ATGTATGAAACACGTACGAAACAATAGACAAGATTGAGTATACTAGGCAACCTACTTGCC
+TAAGATGAACCAAACTAACCAAACGTATAAATACCTGAACAATTAGTTTAGATCCGAGAT
+TCCGCGCTTCCACCCTTTAGTTAGATTCAGATCTTATATAGATTATATAGGATAAGTAAC
+ATTCTGTGAATCACGATAATAATAAGTCTGACAACAAGTTACTCTCCTAAACGACTTTAG
+GATTGTCAAGACATCCGGTATTACTCGAGCCCGTAATACAACA
+>TY4-LTR#LTR/Copia/TY4
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATGGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACAACTCGTATACGTTTAAGTGTGATTGCGCCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGTGTTAAAGACCTATTAGTTGAACAT
+GTTATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTCACTTCTTCATTAATACTAATTTTTAACCTCT
+AATTATCAACA
+>TY4-LTR#LTR/Copia/TY4p
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATAGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACACCTCGTATACGTTTAAGTGTGATTGCACCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGAGTTAAAAATCTATTAGTTGAACAT
+GATATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTTATTTCTTCATTAGTACTATATTTTAACCTCT
+AATTATCAACA
+>TY5-LTR#LTR/Copia/TY5
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTACATA
+ACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCA
+CTACGTCAACA
+>TY5-LTR#LTR/Copia/TY5p
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTTACAT
+AACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTC
+ACTACGTCAACA
+>TSU4-LTR#LTR/Copia/TSU4p
+TGTTGGAATATGTGACTTCGGACATTCCTTAGCGTGAGTCAAAAGTTAATGAAGAGGGCA
+AATTCTAATTATAGAATTTTCCGGACAATAAAGATCTATTAATTGATCAGAACTCAGTAT
+ATAAGAGAATGAGTTACACCTGTTAACTTATTATTAATGTTCTGAGTTATGTCTAAACCA
+TTGGGTTTCATATAACCAATCAGCGTGTGTTTTTATACCTCTCTTATATAATAATAAGAA
+AGAACTGCTTATTCTTAATTATTACAACTTACTAAACCAACTAATTATCAACA
+>TSU4-LTR#LTR/Copia/TSU4b
+TGTTGGAATAAAGTGATCTTGGACATAACATTCTTATGTCAAAACAGGCGATCTCAACAT
+TCCTAATATGATATTAATTATGTTGTTCTGAAACAAACATACTTAATGAAGACGAGTTTA
+AAGACCTATTAATTGATCAAGAATTAGTATATAAGAAGATGATTTATACCTGAGAACCTA
+TTATCAATGTTCTGAATTATACTTGAACCATTGGGTTTCATATAACCAATCAGCGTGCGT
+TTTATATACCTCTCTTATATAATAAGAAAGAACTGCTTATTCTTAATTATTACTACCTAC
+TAAACTTACTAATTATCAACA
diff --git a/data/TE_lib.tidy.fa b/data/TE_lib.tidy.fa
new file mode 100644
index 0000000..2fc55ea
--- /dev/null
+++ b/data/TE_lib.tidy.fa
@@ -0,0 +1,1039 @@
+>TY1-I#LTR/Copia
+TGGTAGCGCCTGTGCTTCGGTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGA
+CGTTTCAGCTTCCAAAACAGAAGAATGTGAGAAGGCTTCCACTAAGGCTAACTCTCAACA
+GACAACAACACCTGCTTCATCAGCTGTTCCAGAGAACCCCCATCATGCCTCTCCTCAAAC
+TGCTCAGTCACATTCACCACAGAATGGGCCGTACCCACAGCAGTGCATGATGACCCAAAA
+CCAAGCCAATCCATCTGGTTGGTCATTTTACGGACACCCATCTATGATTCCGTATACACC
+TTATCAAATGTCGCCTATGTACTTTCCACCTGGGCCACAATCACAGTTTCCGCAGTATCC
+ATCATCAGTTGGAACGCCTCTGAGCACTCCATCACCTGAGTCAGGTAATACATTTACTGA
+TTCATCCTCAGCGGACTCTGATATGACATCCACTAAAAAATATGTCAGACCACCACCAAT
+GTTAACCTCACCTAATGACTTTCCAAATTGGGTTAAAACATACATCAAATTTTTACAAAA
+CTCGAATCTCGGTGGTATTATTCCGACAGTAAACGGAAAACCCGTACGTCAGATCACTGA
+TGATGAACTCACCTTCTTGTATAACACTTTTCAAATATTTGCTCCCTCTCAATTCCTACC
+TACCTGGGTCAAAGACATCCTATCCGTTGATTATACGGATATCATGAAAATTCTTTCCAA
+AAGTATTGAAAAAATGCAATCTGATACCCAAGAGGCAAACGACATTGTGACCCTGGCAAA
+TTTGCAATATAATGGCAGTACACCTGCAGATGCATTTGAAACAAAAGTCACAAACATTAT
+CGACAGACTGAACAATAATGGCATTCATATCAATAACAAGGTCGCATGCCAATTAATTAT
+GAGAGGTCTATCTGGCGAATATAAATTTTTACGCTACACACGTCATCGACATCTAAATAT
+GACAGTCGCTGAACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAG
+AAACAGCAAACCTAATTACAGGAGAAATCTGAGTGATGAGAAGAATGATTCTCGCAGCTA
+TACGAATACAACCAAACCCAAAGTTATAGCTCGGAATCCTCAAAAAACAAATAATTCGAA
+ATCGAAAACAGCCAGGGCTCACAATGTATCCACATCTAATAACTCTCCCAGCACGGACAA
+CGATTCCATCAGTAAATCAACTACTGAACCGATTCAATTGAACAATAAGCACGACCTTCA
+CCTAGGCCAGGAACTTACTGAATCTACGGTAAATCACACTAATCATTCTGATGATGAACT
+CCCTGGACACCTCCTTCTCGATTCAGGAGCATCACGAACCCTTATAAGATCTGCTCATCA
+CATACACTCAGCATCATCTAATCCTGACATAAACGTAGTTGATGCTCAAAAAAGAAATAT
+ACCAATTAACGCTATTGGTGACCTACAATTTCACTTCCAGGACAACACCAAAACATCAAT
+AAAGGTATTGCACACTCCTAACATAGCCTATGACTTACTCAGTTTGAATGAATTGGCTGC
+AGTAGATATCACAGCATGCTTTACCAAAAACGTCTTAGAACGATCTGACGGCACTGTACT
+TGCACCTATCGTACAATATGGAGACTTTTACTGGGTATCTAAAAGGTACTTGCTTCCATC
+AAATATCTCCGTACCCACCATCAATAATGTCCATACAAGTGAAAGTACACGCAAATATCC
+TTATCCTTTCATTCATCGAATGCTTGCGCATGCCAATGCACAGACAATTCGATACTCACT
+TAAAAATAACACCATCACGTATTTTAACGAATCAGATGTCGACTGGTCTAGTGCTATTGA
+CTATCAATGTCCTGATTGTTTAATCGGCAAAAGCACCAAACACAGACATATCAAAGGTTC
+ACGACTAAAATACCAAAATTCATACGAACCCTTTCAATACCTACATACTGACATATTTGG
+TCCAGTTCACAACCTACCAAAAAGTGCACCATCCTATTTCATCTCATTTACTGATGAGAC
+AACAAAATTCCGTTGGGTTTATCCATTGCACGACCGTCGCGAGGACTCTATCCTCGATGT
+ATTTACCACGATACTAGCTTTCATTAAAAACCAATTTCAGGCCAGTGTCTTGGTTATACA
+AATGGACCGTGGTTCTGAGTATACTAACAGAACTCTCCATAAATTCCTTGAAAAAAATGG
+TATAACTCCATGCTATACAACCACAGCGGATTCCCGAGCACATGGAGTCGCTGAACGGCT
+AAACCGTACCTTATTAGATGACTGCCGTACTCAACTGCAATGTAGTGGTTTACCGAACCA
+TTTATGGTTCTCTGCAATCGAATTTTCTACTATTGTGAGAAATTCACTAGCTTCACCTAA
+AAGCAAAAAATCTGCAAGACAACATGCTGGCTTGGCAGGACTTGATATCAGTACTTTGTT
+ACCTTTCGGTCAACCTGTTATCGTCAATGATCACAACCCTAACTCCAAAATACATCCTCG
+TGGCATCCCAGGCTACGCTCTACATCCGTCTCGAAACTCTTATGGATATATCATCTATCT
+TCCATCCTTAAAGAAGACAGTAGATACAACTAACTATGTTATTCTTCAGGGCAAGGAATC
+CAGATTAGATCAATTCAATTACGACGCACTCACTTTCGATGAAGACTTAAACCGTTTAAC
+TGCTTCATATCATTCGTTCATTGCGTCAAATGAGATCCAAGAATCCAATGATCTTAACAT
+AGAATCTGACCATGACTTCCAATCCGACATTGAACTACATCCTGAGCAACCGAGAAATGT
+CCTTTCAAAAGCTGTGAGTCCAACCGATTCCACACCTCCGTCAACTCATACTGAAGATTC
+GAAACGTGTTTCTAAAACCAATATTCGCGCACCCAGAGAAGTTGACCCCAACATATCTGA
+ATCTAATATTCTTCCATCAAAGAAGAGATCTAGCACCCCCCAAATTTCCAATATCGAGAG
+TACCGGTTCGGGTGGTATGCATAAATTAAATGTTCCTTTACTTGCTCCCATGTCCCAATC
+TAACACACATGAGTCGTCGCACGCCAGTAAATCTAAAGATTTCAGACACTCAGACTCGTA
+CAGTGAAAATGAGACTAATCATACAAACGTACCAATATCCAGTACGGGTGGTACCAACAA
+CAAAACTGTTCCGCAGATAAGTGACCAAGAGACTGAGAAAAGGATTATACACCGTTCACC
+TTCAATCGATGCTTCTCCACCGGAAAATAATTCATCGCACAATATTGTTCCTATCAAAAC
+GCCAACTACTGTTTCTGAACAGAATACCGAGGAATCTATCATCGCTGATCTCCCACTCCC
+TGATCTACCTCCAGAATCTCCTACCGAATTCCCTGACCCATTTAAAGAACTCCCACCGAT
+CAATTCTCGTCAAACTAATTCCAGTTTGGGTGGTATTGGTGACTCTAATGCCTATACTAC
+TATCAACAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTAAGGTATCACGAGA
+CACATGGAATACTAAGAATATGCGTAGTTTAGAACCTCCGAGATCGAAGAAACGAATTCA
+CCTGATTGCAGCTGTAAAAGCAGTAAAATCAATCAAACCAATACGGACAACCTTACGATA
+CGATGAGGCAATCACCTATAATAAAGATATTAAAGAAAAAGAAAAATATATCGAGGCATA
+CCACAAAGAAGTCAATCAACTGTTGAAGATGAAAACTTGGGACACTGACGAATATTATGA
+CAGAAAAGAAATAGACCCTAAAAGAGTAATAAACTCAATGTTTATCTTCAACAAGAAACG
+TGACGGTACTCATAAAGCTAGATTTGTTGCAAGAGGTGATATTCAGCATCCTGACACTTA
+CGACTCAGGCATGCAATCCAATACCGTACATCACTATGCATTAATGACATCCCTGTCACT
+TGCATTAGACAATAACTACTATATTACACAATTAGACATATCTTCGGCATATTTGTATGC
+AGACATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGAATGAATGATAAGTT
+GATACGTTTGAAGAAATCACTTTATGGATTGAAACAAAGTGGAGCGAACTGGTACGAAAC
+TATCAAATCATACCTGATACAACAATGTGGTATGGAAGAAGTTCGTGGATGGTCATGCGT
+ATTTAAAAACAGTCAAGTGACAATTTGTTTATTCGTAGATGATATGGTATTGTTTAGCAA
+AAATCTAAATTCAAACAAAAGAATTATAGACAAGCTTAAGATGCAATACGACACCAAGAT
+TATAAATCTAGGCGAAAGTGATGAGGAAATTCAATATGACATTCTTGGCTTGGAAATCAA
+ATACCAAAGAGGTAAATACATGAAATTGGGTATGGAAAACTCATTAACTGAAAAAATACC
+CAAACTAAACGTACCTTTGAACCCAAAAGGAAGGAAACTTAGCGCTCCAGGTCAACCAGG
+TCTATATATAGACCAGCAAGAACTAGAGCTAGAAGAAGATGATTACAAAATGAAGGTACA
+TGAAATGCAAAAGCTGATAGGTCTAGCATCATATGTTGGATATAAATTTAGATTTGACCT
+ATTATACTACATCAACACACTTGCACAACATATACTATTTCCGTCCAAGCAAGTGTTAGA
+TATGACATATGAATTGATACAGTTCATATGGAATACGAGAGATAAGCAATTAATATGGCA
+CAAAAGCAAACCTGTTAAGCCAACAAATAAATTAGTTGTTATAAGCGATGCCTCGTATGG
+CAACCAACCGTATTATAAATCACAAATTGGCAACATATATTTACTTAATGGAAAGGTAAT
+TGGAGGAAAGTCCACCAAGGCTTCATTAACATGTACTTCAACTACGGAAGCAGAAATACA
+CGCGATAAGTGAATCTGTCCCATTATTAAATAATCTAAGTTACCTGATACAAGAACTTGA
+CAAGAAACCAATTACCAAAGGATTACTAACCGACAGTAAATCTACAATCAGTATAATTAT
+ATCCAATAATGAAGAGAAATTTAGGAACAGATTTTTTGGTACTAAAGCAATGAGATTGAG
+AGATGAAGTATCAGGAAATCATCTGCACGTATGCTATATCGAAACCAAAAAGAATATTGC
+AGACGTAATGACCAAACCTCTTCCGATAAAAACATTCAAACTATTAACAAACAAATGGAT
+TCATTAGATCTATTACATTATGGGTGGTA
+>TY1-LTR#LTR/Copia
+TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAATATATTATC
+ATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAG
+CTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT
+GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATAT
+CCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAACAATG
+GAATCCCAACAATTATCTCAACATTCACATATTTCTCA
+>TY1p-I#LTR/Copia
+TGGTAGCGCCTGTGCTTCGGTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGA
+CGTTTCAGCTTCCAAAATTCAAGAATATGATAAGGCTTCCACTAAGGCTAACTCTCAACA
+GACAACAACACCTGCTTCATCAGCTGTTCCAGAGAACCCCCATCATGCCTCTCCTCAAAC
+TGCTCAGTCACATTCACCACAGAATGGGCCGTACCCACAGCAGTGCATGATGACCCAAAA
+CCAAGCCAATCCATCTGGTTGGTCATTTTACGGACACCCATCTATGATTCCGTATACACC
+TTATCAAATGTCGCCTATGTACTTTCCACCTGGGCCACAATCACAGTTTCCGCAGTATCC
+ACCATCAGTTGGAACGCCTCTGAGCACCCCATCACCTGAGTCAGGTAATACATTTACTGA
+TTCATCCTCAGCGGACTCTGATATGACATCCACTAAAAAATATGTCAGACCACCACCAAT
+GTTAACCTCACCTAATGACTTTCTAAATTGGGTTAAAACATACATCAAATTTTTACAAAA
+CTCGAATCTCGGTGATATTATTCCGACAGTATACGGAAAACCCGTACGTCAGATCACTGA
+TGATGAACTCACCTTCTTGTATAACACTTTTCAAATATTTGCTCCCTCTCAATTCCTACC
+TACCTGGGTCAAAGACATCCTATCTGTTGATTATACGGATATCATGAAAATTCTTTCCAA
+AAGTATTGAAAAAACGCAATCTGATACCCAAGAGGCAAATGACATTGTGACCCTGGCAAA
+TTTGCAATATAATGGCAGTACACCTGCAGATGCATTTGAAACAAAAGTCACAAACATTAT
+CGACAGACTAAATAATAATGGCATTCATATCAATAACAAGGTCGCATGCCAATTAATTAT
+GAGAGGTCTATCTGGCGAATATAAATTTTTACGCTACACACGTCATCGACATCTAAATAT
+GACAGTCGCTGAACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAG
+AAACAGTAAACCCAATTACAGGAGAAATCCGAGTGATGAGAAGAATGATTCTCGCAGCTA
+TACGAATACAACCAAACCCAAAGTTATAGCTCGGAATCCTCAAAAAACAAATAATTCGAA
+ATCGAAAACAGCCAGGGCTCATAATGTATCCACATCTAATAACTCTCCCAGCACTGACAA
+CGATTCCATCAGTAAATCAACTACTGAACCGATTCAATTGAACAATAAGCACGACCTTCA
+TCTTAGGCCAGAAACTTACTGAATCTACAGTAAATCATACGAATCATTCCGATGATGAAC
+TTCCTGGACACCTTCTTCTTGATTCAGGAGCATCACGAACTCTTATAAGATCTGCCCATC
+ACATACACTCAGCGATATCTAATCCCGACATAAGCGTAGTTGATGTTCAAAAAAACAATA
+TACCAATTAACGCTGTTGGTGATCTTCAATTTCACTTCCAGGACGACACCAAAACAACAA
+TAAAGGTATTGCACACACCTAACATAGCCTATGACTTACTCAGTTTGAATGAACTGGCTG
+CACTAAATATTACAGCGTGCTTTACCAAAAACGTCTTAGAACGACCTGACGGCACCGTAC
+TTGCACCTATCGTAAAACATGGAGACTTTTACTGGGTGTCTAAAAGGTACTTGCTTCCGT
+CGAATATCTCAGTACCCACAATTAATAACGTTCACACAAGTGAAAACACACGTAAGTATC
+CTTATCCTTTCATTCATCGGATGCTTGCGCATGCCAATGCCCAGACAATTAGATATTCAC
+TTAAAAAGAACACTATTACGTATTTCAATGAATCAGATGTTGACTGGTCTAACGCTACTG
+ATTATCAATGTCCCGATTGTTTAATCGGCAAAAGCACCAAACATAGACATATCATAGGAT
+CACGGCTAAAATACCAAAGTTCATATGAACCTTTTCAATACTTACATACTGACATATTTG
+GGCCTGTTCACAACCTACCAAAGAGTGCACCATCCTATTTCATCTCATTCACTGATGAGA
+AAACAAAATTCCGTTGGGTTTATCCATTACACGACCGTCGCGAGGACTCTATTCTCGATA
+TCTTTACTAAGATACTAGCTTTCATTAAAAACCAGTTTCAGTCCAATGTTTTGGTTATTC
+AAATGGACCGTGGTTCTGAGTACACTAACAAAACTCTCCATAAATTCCTTGAAAAATATG
+GCATAACCCCATGTTATACAACCACAGCGGATTCCCGAGCACATGGTGTCGCTGAACGGC
+TGAACCGTACCTTATTAGATGACTGTCGTACTCAACTGCAATGTAGTGGTCTACCGAATC
+ATCTATGGTTCTCGGCAGTCGAATTTTCTACTATCGTACGGAACTCACTAGCTTCACCTA
+AAAGCAAAAAATCCGCAAGACAACTCGCTGGGTTGGCAGGACTCGACATCAGTACTTTAT
+TACCTTTCGGTCAACCCGTTATAGTCAATAATCATAACCCTGACTCCAAAATTCATCCTC
+GTGGCATTCCTGGCTACGCTCTACATCCATCTCGAAACTCTTATGGATATATCATCTATG
+TCCCGTCTTTGAAGAAGACAGTAGATACAACTAATTACGTTATTCTTCAGGGCAAGGAAT
+CCAGATTAGACCAATTCAATTACGACGCACTCACCTTCGATGAAGACGTGAATCGTATAA
+CTGCTTCATATCAATCGTTCATTGCTTCAAATGAGATCCAACAATCTAACGATCTTAACA
+TAGAATCTGACCATGATTTTCAATCTGACGTAGAACTGAACCCTGACCACCAGAGAAATG
+TCCCTTCAAACGTTCCGATTCCAACTGACTCTCCACCTCCATCAACTCATACTGAAGATT
+CAAAACCTATATCTGAAATCAATCTTCGTGCACCCAAAGAAGTTGATCCTAACATATCTG
+AATCTAATATTCTTCCATCTAAGAAGAGATCTAACATCCCCCAAATTTCTGCTACCGACA
+GTGCCGGTTCGGGTGGTATAAATAAATCAGATGTTCCTTTACTTACTCCTTTGTCCAAAT
+CTGACACACAAAATTCATACCAAGCCAGTGAATCTGATGATTTCAGTGACTCAGACTCAC
+ACAGCGACATCGATACTGACTCTACAAACGTGACAATACCCAGTTTGGGTGGTATCAACA
+ACAAAACTGTTCCGCAGACAAGTGACCAAGAGACTGAGAAAAGGATTATACATCGTTCAC
+CTTCAATCGATGCTTCTCCACCGGAAAATAATTCATCGCACAATATTGTTCCTATCAAAA
+CGCCAACTAATGTTTCTGAACAGAATACCGAGGAATCTATTATCGCTGATCTCCCACTCC
+CTGATCTATCTCCAGAATCTCCTACCGAATTCCCTGACCCATTTAAAGAACTCCCACCGA
+TAAATTCTCATCAAACTAATTCCAGTTTGGGTGGTATGGATGACTCTAATATCTCTGCTA
+CTATCACTAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTGAGGTATCACGAG
+ACACATGGAATAGTAAGAATATGCGTAGCTTAGAACCTCCAAGGTCAAAGAAACGAATAC
+ATCTAATCGCGGCTGTAAAAGCAGTAAAATCAATCAAACCAATACGAACAACCTTAAGAT
+ACGATGAGGCAATCACCTATAATAAAGATATTAAAGAAAAGGAAAAATATATCGAAGCAT
+ACCACAAAGAAGTCAACCAACTGTTGAAAATGAATACTTGGGACACTGACAAATATTATG
+ACAGAAAAGAAATAGACCCTAAAAGAGTAATAAACTCAATGTTTATCTTCAACAAGAAAC
+GTGACGGAACTCATAAAGCTAGATTTGTTGCAAGAGGTGACATTCAGCATCCTGATACGT
+ACGATACAGGTATGCAATCCAACACTGTACATCATTATGCGTTGATGACATCCCTATCAC
+TTGCATTAGACGATGACTCCTTCATTACACAATTAGACATATCTTCGGCGTACTTGTATG
+CAGACATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGAATGAACAACAAGT
+TAATACGGTTGAGGAAATCACTTTATGGTTTGAAACAAAGTGGTGCAAACTGGTATGAAA
+CGATCAAATCATATCTGATTGAACAATGTGATATGGAAGAAGTTCGCGGATGGTCATGCG
+TATTTAAGAACAATCAAGTAACAATCTGCTTATTCGTTGATGATATGATATTGTTCAGCA
+AAGACTTAAATTCAAATAAAAGAATTATAGCAAAACTCAAGATGCAATACGATACCAAGA
+TTATAAATCTAGGTGAAAGCGATGATGAAATTCAATACGACATCCTTGGCTTAGAAATCA
+AATATCAAAGAGGTAAATACATGAAATTAGGTATGGAAAACTCACTAACTGAGAAAATAC
+CCAAATTAAACGTACCTTTGAATCCAAAAGGAAGAAAACTTGGTGCTCCAGGTCAACCAG
+GTCTCTATATAAACCAGAAGGAGCTAGAGCTAGAAGAAGACGACTACAACATGAAGGTGC
+ATGAAATGCAAAAGTTGATAGGTCTAGCGTCATATGTTGGATATAAATTCAGATTTGACC
+TATTATACTATATCAACACACTTGCACAACATATACTATTTCCGTCCAAACAAGTGTTAA
+ACATGACATATGAATTGATACAATTCTTATGGGACACTAGAGACAAACAATTAATATGGC
+ACAAAAGCAAATCTGCAAAACCAGAAAATAAATTAGTTGTAATAAGCGATGCCTCTTATG
+GCAACCAACCATATTACAAATCTCAGATTGGTAATATCTATTTACTAAATGGAAAGGTGA
+TCGGAGGAAAATCAACAAAAGCTTCATTAACATGTACTTCAACCACAGAAGCAGAAATAC
+ACGCAATCAGTGAAGCCATTCCATTATTAAATAACTTGAGTCACCTTATACAAGAACTAA
+ATGGGAAATCAATCATTAAAGGCTTACTTACTGACAGCAGATCTACAATCAGTATAGTTA
+TGTCCAAAAATGAAGAGAAACTTAGAAACAGATTTTTCGGTACCAAAGCAATGAGACTTC
+GGGACGAAGTATCAAATAATAACCTCCACGTATGCTACGTGGATACCAAAAGGAACATTG
+CTGACGTGATGACAAAACCCCTCCCAATAAAAACATTTAAACTATTAACAAACAAGTGGA
+TTCATTAGATCTATTACATTATGGGTGGTA
+>TY1p-LTR#LTR/Copia
+TGTTGGAATGAAATTCTAATATCATCTATTTAATAGTATATTATAATATGCGGTGCAAGA
+GGATGACATAAAGATTGAGAAACAGTCATCCAATCTAATGGAAGCTGAAATGCAAGGATT
+GATAATGTAATAGGATAATGAATAACAACATATAAAAAGAAAGAAGATAAAATAATAACA
+CTATGTAGAACTATCGATTCCCTTTTGTGGATTCCTATATCCTCGAGGAGAACTTCTAGT
+ATATTCTATATACCTAATATTATAGCCTTTAGTAACAATGGAATCCCAACAATTATCTAA
+TTACCCACACAATTCTCA
+>TY2-I#LTR/Copia
+TGGTAGCGCCTATGCTTCGGTTACTTCTAAGGAAGTCCCATCAAATCAAGATCCGTTAGC
+CGTTTCAGCTTCCAATTTACCGGAATTTGATAGAGATTCCACTAAGGTTAATTCTCAACA
+AGAGACAACACCTGGGACATCAGCTGTTCCAGAGAACCATCATCATGTCTCTCCTCAACC
+TGCTTCAGTACCACCTCCACAGAATGGACAGTACCAACAGCACGGCATGATGACCCCAAA
+CAAAGCTATGGCCTCTAACTGGGCACATTACCAACAACCATCTATGATGACGTGTTCACA
+TTATCAAACGTCACCTGCGTATTATCAACCGGACCCACACTATCCGTTGCCACAGTATAT
+CCCACCACTGAGTACTTCCTCACCTGATCCAATCGATTTAAAAAATCAACACTCTGAAAT
+ACCTCAAGCTAAGACAAAGGTGGGAAATAACGTCTTACCACCACACACTTTAACATCAGA
+AGAAAACTTTTCTACATGGGTTAAATTTTACATCAGATTTTTGAAGAACTCTAATCTCGG
+TGACATCATTCCAAATGACCAGGGTGAAATCAAAAGACAAATGACTTATGAAGAACATGC
+GTATATATACAATACCTTCCAAGCATTTGCCCCATTTCATTTATTGCCAACATGGGTAAA
+ACAAATTTTAGAAATTAATTATGCTGACATCCTTACAGTCCTTTGTAAAAGTGTGTCCAA
+AATGCAAACTAACAATCAAGAATTAAAGGATTGGATAGCTCTTGCCAACCTTGAGTACGA
+CGGAAGTACATCTGCTGATACATTTGAAATTACAGTCAGTACGATCATTCAGAGGCTAAA
+AGAAAACAATATCAATGTTAGCGACAGATTGGCCTGTCAACTAATACTTAAAGGTCTATC
+CGGTGACTTCAAATACCTACGTAATCAATATCGTACCAAAACGAACATGAAACTTTCCCA
+ATTATTCGCTGAAATTCAATTAATATATGACGAAAATAAAATCATGAATCTAAATAAACC
+GTCCCAATACAAACAACACAGCGAATACAAAAATGTTTCTCGCACATCTCCAAACACGAC
+TAACACAAAGGTTACAACTCGTAATTATCATAGAACAAATAGTTCAAAACCAAGAGCAGC
+AAAAGCTCACAATATTGCTACATCTAGTAAATTCTCAAGGGTGAACAATGATCACATTAA
+TGAATCAACCGTTTCATCACAATACTTAAGCGATGACAACGAACTTAGTCTTAGGCCAGC
+AACAGAAAGAATCTAAGCCAACACACACAATAGACTCGAATGACGAACTACCTGATCACC
+TTCTTATTGATTCAGGAGCTTCGCAAACGCTTGTCAGATCAGCCCATTATTTACACCATG
+CAACACCCAATTCTGAAATAAACATAGTCGATGCTCAAAAACAAGACATTCCTATAAATG
+CCATTGGTAATCTTCACTTCAACTTTCAGAACGGCACCAAAACATCAATAAAAGCACTAC
+ACACACCAAACATAGCCTATGATCTATTAAGTTTGAGTGAGCTGGCTAACCAAAATATTA
+CTGCCTGCTTTACCAGAAACACTTTAGAAAGATCGGATGGTACAGTACTAGCTCCCATAG
+TCAAACATGGAGACTTTTACTGGTTATCTAAAAAATACCTAATTCCTTCGCACATTTCAA
+AGCTAACAATAAACAACGTCAACAAAAGCAAAAGCGTAAATAAATATCCATATCCGTTAA
+TACATCGAATGCTTGGACATGCTAACTTCCGAAGTATTCAGAAGTCTCTTAAGAAGAATG
+CAGTTACATATTTGAAGGAATCGGATATTGAATGGTCTAACGCTAGCACATATCAATGTC
+CTGACTGTCTAATCGGCAAAAGCACGAAACATAGACATGTCAAAGGATCACGACTAAAGT
+ACCAAGAATCATATGAGCCTTTTCAGTACTTGCATACCGATATATTTGGTCCTGTACATC
+ACTTACCGAAAAGTGCACCTTCTTACTTTATATCGTTTACAGATGAGAAAACCAGATTCC
+AATGGGTGTACCCATTACACGACCGTCGTGAAGAATCTATCCTCAATGTTTTTACATCGA
+TATTAGCATTTATTAAGAACCAATTCAATGCTCGCGTTCTAGTTATCCAGATGGATCGTG
+GCTCCGAGTACACTAACAAAACTCTTCATAAGTTCTTTACGAACAGAGGTATTACTGCAT
+GCTATACAACCACGGCAGATTCTAGAGCACACGGTGTCGCTGAACGATTAAATCGTACTT
+TATTAAACGATTGTCGCACACTGCTTCATTGCAGTGGTCTACCAAATCATCTATGGTTCT
+CAGCAGTCGAATTTTCTACTATAATCAGAAATTCATTAGTCTCACCAAAAAACGATAAAT
+CTGCAAGACAACATGCAGGTTTAGCTGGACTGGACATTACTACTATACTACCTTTCGGTC
+AACCGGTTATAGTTAACAACCATAATCCCGACTCGAAAATACATCCTCGTGGCATTCCAG
+GTTACGCCTTACATCCGTCACGAAACTCTTATGGCTATATTATCTATCTTCCATCATTAA
+AAAAGACAGTAGATACTACCAATTACGTTATATTACAAGACAACCAATCCAAATTGGACC
+AATTCAATTATGATACACTCACCTTTGATGATGATCTCAATCGTTTAACAGCCCATAACC
+AATCTTTTATTGAACAAAATGAAACAGAGCAGTCATATGATCAAAATACAGAATCTGATC
+ATGACTATCAATCGGAGATTGAAATAAACTCTGATCCTCTAGTGAACGACTTCTCGTCCC
+AATCAATGAACCCCTTACAATTAGACCACGAACCAGTCCAAAAAGTACGTGCACCAAAAG
+AAGTTGATGCCGACATATCTGAATACAATATTCTTCCATCTCCTGTACGATCTCGTACAC
+CCCATATCATTAATAAAGAGAGTACCGAAATGGGTGGTACCATTGAATCAGATACTACTT
+CACCTAGACACTCGTCTACCTTCACTGCACGAAACCAAAAGCGACCTGGTAGTCCCAATG
+ATATGATTGATTTGACCTCACAGGATAGAGTTAATTATGGACTTGAAAACATCAAAACTA
+CACGTTTGGGTGGTACGGAGGAACCATATATTCAACGAAATAGTGATACAAATATCAAAT
+ACAGGACTACAAATAGTACGCCCTCAATAGATGACCGTTCGTCCAACAGTGAATCCACTA
+CTCCCATCATCTCCATAGAAACAAAGGCTGTATGTGATAATACACCCTCCATTGATACGG
+ATCCGCCAGAATATCGATCTTCTGACCATGCGACTCCTAATATAATGCCTGACAAATCCT
+CAAAAAATGTTACGGCTGATTCTATTCTTGACGACCTCCCACTTCCTGACTTAACCCATA
+AATCTCCTACGGACACTTCTGATGTTTCAAAAGATATTCCACACATACACTCTCGTCAGA
+CTAATTCCAGTTTGGGTGGTATGGATGATTCTAATGTTCTGACTACTACCAAAAGTAAGA
+AAAGATCATTAGAAGATAATGAAACTGAAATTGAGGTATCCCGAGACACATGGAATAATA
+AGAATATGAGAAGTCTGGAACCACCAAGATCGAAGAAACGCATAAATTTAATTGCAGCAA
+TAAAAGGAGTGAAATCGATCAAACCAGTTCGAACGACCTTAAGATATGATGAAGCAATTA
+CATATAATAAAGACAACAAAGAAAAAGACAGATATGTTGAAGCTTATCATAAAGAAATTA
+GCCAACTATTGAAAATGAACACTTGGGATACAAACAAATATTATGATAGAAATGACATAG
+ATCCTAAAAAAGTAATAAACTCAATGTTTATATTTAACAAGAAACGTGATGGTACACACA
+AAGCTAGATTTGTTGCAAGAGGCGACATTCAACACCCCGATACATATGATTCTGATATGC
+AATCCAATACCGTACATCACTATGCACTGATGACGTCACTGTCAATCGCATTAGACAACG
+ACTATTATATCACACAGCTGGACATATCCTCTGCTTACTTATATGCTGATATCAAAGAAG
+AATTATACATAAGACCTCCACCACATTTAGGTTTGAATGATAAATTACTACGTTTGAGAA
+AATCACTCTATGGTTTGAAACAAAGTGGTGCAAACTGGTATGAAACCATTAAATCATATT
+TAATAAATTGTTGCGACATGCAAGAAGTTCGCGGATGGTCATGCGTATTTAAGAATAGTC
+AAGTAACAATTTGCTTATTCGTTGATGATATGATATTATTCAGCAAAGACTTAAATGCAA
+ATAAGAAAATCATAACAACACTCAAGAAACAATACGATACAAAGATAATAAATCTGGGTG
+AAAGAGATAACGAAATTCAGTACGACATACTTGGATTAGAGATCAAATATCAAAGAAGCA
+AGTACATGAAATTAGGTATGGAAAAATCCTTGACAGAAAAATTACCCAAACTAAACGTAC
+CTTTGAACCCAAAAGGAAAGAAACTTAGAGCTCCAGGTCAACCAGGTCATTATATAGACC
+AGGATGAACTAGAAATAGATGAAGATGAATACAAAGAGAAGGTACATGAAATGCAAAAGT
+TGATTGGTCTAGCTTCATATGTTGGATATAAATTTAGATTTGACTTACTATACTACATCA
+ACACACTTGCTCAACATATACTATTCCCCTCTAGACAAGTTTTAGACATGACATATGAGT
+TAATACAATTCATGTGGGACACTAGAGATAAACAATTAATATGGCACAAAAACAAACCTA
+CCAAGCCAGATAATAAACTAGTCGCAATAAGCGATGCTTCATATGGTAACCAACCATATT
+ACAAGTCACAAATTGGTAACATTTTCCTACTCAACGGAAAAGTGATTGGAGGAAAGTCGA
+CAAAGGCTTCGTTAACATGCACTTCAACTACAGAAGCAGAAATACACGCAGTCAGTGAAG
+CTATACCGCTATTGAATAACCTCAGTCACCTTGTGCAAGAACTTAACAAGAAACCAATTA
+TTAAAGGCTTACTTACTGATAGTAGATCAACGATCAGTATAATTAAGTCTACAAATGAAG
+AGAAATTTAGAAACAGATTTTTTGGCACAAAGGCAATGAGACTTAGAGATGAAGTATCAG
+GTAATAATTTATACGTATACTACATCGAGACCAAGAAGAACATTGCTGATGTGATGACAA
+AACCTCTTCCGATAAAAACATTTAAACTATTAACAAACAAATGGATTCATTAGATCTATT
+ACATTATGGGTGGTA
+>TY2-LTR#LTR/Copia
+TGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATC
+ATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGC
+TGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAATGATGAT
+AATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATGGATTCCTAAATCCTC
+GAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAAATGGAATCC
+CAACAATTACATCAAAATCCACATTCTCTTCA
+>TY3-I#LTR/Gypsy
+CCTGGTAGCGTTAAAGGTTACTAATTGTTCAAACGAACCATCGAAAAGCCGAACCTAGCT
+ACACCACACCCCAGTATGAGCTTTATGGATCAAATCCCAGGAGGAGGAAATTATCCAAAA
+CTCCCAGTAGAATGCCTTCCTAACTTCCCGATCCAACCATCTTTGACCTTCAGAGGTAGA
+AATGACTCGCATAAACTGAAAAACTTTATCTCCGAAATAATGTTAAACATGTCTATGATA
+TCTTGGCCGAATGATGCCAGTCGTATTGTGTACTGCAGAAGACATTTATTAAACCCCGCT
+GCTCAGTGGGCTAATGACTTTGTACAAGAACAAGGTATACTTGAAATAACATTCGACACA
+TTCATACAAGGATTATATCAGCATTTCTATAAGCCACCAGATATCAATAAAATCTTTAAT
+GCAATCACGCAACTTTCCGAAGCTAAACTTGGTATTGAGCGTCTCAACCAACGATTCAGA
+AAGATTTGGGACAGAATGCCACCAGACTTCATGACCGAAAAAGCTGCCATAATGACATAT
+ACTAGGCTATTGACAAAGGAAACCTATAATATTGTCAGAATGCACAAACCAGAGACATTA
+AAAGACGCCATGGAAGAGGCTTACCAGACAACTGCACTAACTGAAAGATTCTTCCCAGGA
+TTCGAACTTGATGCTGATGGAGACACTATCATCGGTGCCACAACCCACTTACAAGAAGAA
+TACGACTCTGACTATGATTCAGAAGATAATCTGACCCAGAATGGATACGTCCATACCGTA
+AGGACAAGAAGATCTTACAATAAACCAATGTCAAATCATCGAAACAGGAGAAATAACAAC
+CCATCTAGAGAAGAATGTATAAAAAATCGGCTATGCTTCTATTGTAAGAAAGAGGGACAT
+CGCCTGAACGAATGTAGAGCACGTAAGGCGAGTTCTAACCGATCTTGAACTCGAATCAAA
+AGACCAACAAACTCCTTTTATCAAAACCTTACCAATTGTACACTATATCGCCATCCCCGA
+GATGGACAATACCGCCGAAAAAACCATAAAAATACAAAACACGAAAGTAAAAACCCTGTT
+TGACAGTGGATCACCCACGTCATTTATCCGAAGAGATATTGTAGAACTTCTCAAATACGA
+AATCTACGAGACCCCTCCACTCCGTTTTAGAGGATTCGTAGCCACCAAATCCGCCGTTAC
+ATCCGAAGCAGTCACCATTGACCTCAAAATCAATGACCTGCATATAACTTTAGCCGCGTA
+CATACTGGATAACATGGACTACCAATTGTTAATTGGAAATCCAATCTTACGCCGCTACCC
+GAAAATCCTGCACACAGTACTGAATACCAGAGAGAGCCCCGACTCCTTAAAGCCCAAGAC
+TTATCGCTCCGAAACCGTTAATAACGTTAGAACCTACTCCGCTGGTAATCGTGGTAACCC
+CAGAAACATAAAACTGTCTTTTGCCCCCACCATTCTCGAAGCAACTGACCCGAAATCCGC
+TGGTAATCGTGGTGACTCCAGAACCAAAACCCTGTCTCTTGCAACCACTACTCCTGCAGC
+AATTGACCCGCTTACGACCCTTGATAACCCAGGTAGTACTCAAAGTACATTTGCGCAATT
+CCCGATACCTGAAGAAGCGAGCATCCTAGAAGAGGATGGAAAATACTCCAACGTTGTCTC
+AACCATTCAGAGTGTAGAACCTAATGCTACTGATCACAGCAATAAGGACACCTTTTGCAC
+TTTGCCAGTTTGGTTACAACAGAAGTATAGAGAGATCATACGTAATGATCTCCCACCAAG
+ACCTGCCGACATTAATAACATCCCCGTAAAACATGATATTGAAATTAAACCTGGCGCAAG
+ACTACCTCGACTACAGCCATACCATGTTACAGAAAAGAACGAACAAGAAATCAACAAAAT
+AGTTCAAAAACTGCTCGATAACAAGTTCATTGTTCCCTCAAAGTCGCCTTGCAGCTCCCC
+TGTAGTCCTCGTCCCGAAGAAAGACGGTACCTTCCGACTCTGCGTCGATTACCGCACCCT
+GAACAAAGCTACCATCTCCGACCCATTCCCATTACCCAGAATCGACAACCTATTGAGCCG
+TATTGGAAATGCCCAGATATTTACCACGCTAGATTTGCATAGTGGTTACCACCAGATCCC
+GATGGAACCCAAAGACCGCTACAAAACCGCCTTTGTCACACCATCCGGTAAGTATGAATA
+TACCGTCATGCCATTTGGCTTAGTCAATGCACCTAGTACATTCGCAAGATACATGGCTGA
+TACATTTAGAGACCTGAGATTCGTCAATGTTTACCTTGATGATATATTAATATTCTCCGA
+ATCTCCAGAAGAACATTGGAAACATTTAGACACGGTACTAGAAAGATTAAAGAACGAGAA
+CCTCATTGTTAAGAAGAAAAAATGTAAATTTGCATCTGAAGAAACTGAGTTTTTAGGCTA
+TAGTATTGGAATCCAGAAAATAGCTCCACTACAGCACAAATGTGCAGCAATCCGAGACTT
+TCCGACGCCTAAAACAGTAAAACAAGCACAGAGATTTTTAGGAATGATTAATTACTACAG
+ACGATTCATTCCAAATTGCTCCAAGATTGCACAGCCAATCCAACTGTTTATTTGTGACAA
+AAGTCAATGGACAGAAAAACAAGACAAGGCAATTGATAAACTAAAAGACGCCTTGTGTAA
+CTCCCCCGTCCTAGTACCATTCAACAACAAAGCAAACTACCGACTTACAACAGACGCCTC
+AAAAGACGGCATTGGTGCTGTTCTAGAAGAAGTCGACAACAAGAACAAACTTGTTGGTGT
+CGTCGGTTACTTCTCTAAATCCTTAGAGAGTGCCCAGAAAAACTATCCTGCTGGCGAATT
+AGAACTACTTGGAATTATCAAAGCACTCCACCACTTCCGATATATGCTTCACGGAAAGCA
+TTTCACGTTAAGAACAGACCACATTAGTTTGTTATCATTACAAAACAAGAACGAACCCGC
+ACGACGCGTGCAACGCTGGTTAGATGACCTAGCCACATATGACTTCACCTTAGAATACCT
+AGCTGGACCCAAGAACGTTGTCGCAGATGCCATATCCCGTGCCGTATATACTATAACCCC
+CGAAACATCCCGACCTATCGACACAGAAAGCTGGAAATCTTACTACAAATCAGACCCATT
+ATGTAGTGCTGTCTTAATTCATATGAAAGAATTGACACAACACAACGTCACACCTGAAGA
+TATGTCAGCCTTCCGTAGTTACCAGAAGAAACTCGAACTATCAGAGACCTTCCGAAAGAA
+TTATTCCCTAGAAGACGAAATGATCTATTACCAAGACCGACTAGTAGTACCAATAAAACA
+ACAGAACGCAGTTATGAGACTATATCATGACCATACCTTATTTGGAGGACATTTTGGTGT
+AACAGTGACCCTTGCGAAAATCAGCCCAATTTACTATTGGCCAAAATTACAACATTCGAT
+CATACAATACATCAGGACCTGCGTACAATGTCAACTAATAAAATCACACCGACCACGCTT
+ACATGGACTATTACAACCACTCCCTATAGCAGAAGGAAGATGGCTTGATATATCAATGGA
+TTTTGTGACAGGATTACCCCCGACATCAAATAACTTGAATATGATCCTCGTCGTAGTTGA
+TCGTTTTTCGAAACGCGCTCACTTCATAGCTACAAGGAAAACCTTAGACGCAACACAACT
+AATAGATCTACTCTTTCGATACATTTTTTCATATCATGGTTTTCCCAGGACAATAACCAG
+TGATAGAGATGTCCGTATGACCGCCGACAAATATCAAGAACTCACGAAAAGACTAGGAAT
+AAAATCGACAATGTCTTCCGCGAACCACCCCCAAACAGATGGACAATCCGAACGAACGAT
+ACAGACATTAAACAGGTTACTAAGAGCCTATGCTTCAACCAATATTCAGAATTGGCATGT
+ATATTTACCACAAATCGAATTTGTTTACAATTCTACACCTACTAGAACACTTGGAAAATC
+ACCATTTGAAATTGATTTAGGATATTTACCGAATACCCCTGCTATTAAGTCAGATGACGA
+AGTCAACGCAAGAAGTTTTACTGCCGTAGAACTTGCCAAACACCTCAAAGCCCTTACCAT
+CCAAACGAAGGAACAGCTAGAACACGCTCAAATCGAAATGGAAACTAATAACAATCAAAG
+ACGTAAACCCTTATTGTTAAACATAGGAGATCACGTATTAGTGCATAGAGATGCATACTT
+CAAGAAAGGTGCTTATATGAAAGTACAACAAATATACGTCGGACCATTTCGAGTTGTCAA
+GAAAATAAACGATAACGCCTACGAACTAGATTTAAACTCTCACAAGAAAAAGCACAGAGT
+TATTAATGTACAATTCCTGAAAAAGTTTGTATACCGTCCAGACGCGTACCCAAAGAATAA
+ACCAATCAGCTCCACTGAAAGAATTAAGAGAGCACACGAAGTTACTGCACTCATAGGAAT
+AGATACTACACACAAAACTTACTTATGTCACATGCAAGATGTAGACCCAACACTTTCAGT
+AGAATACTCAGAAGCTGAATTTTGCCAAATTCCCGAAAGAACACGAAGATCAATATTAGC
+CAACTTTAGACAACTCTACGAAACACAAGACAACCCTGAGAGAGAGGAAGA
+>TY3-LTR#LTR/Gypsy
+TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCACCCTGAACGTTCATAAA
+ACACATATGAAACAACCTTATAACAAAACGAACAACATGAGACAAAACCCGACCTTCCCT
+AGCTGAACTACCCAAAGTATAAATGCCTGAACAATTAGTTTAGATCCGAGATTCCGCGCT
+TCCACCACTTAGTATGATTCATATTTTATATAATATATAAGATAAGTAACATTCCGTGAA
+TTAATCTGATAAACTGTTTTGACAACTGGTTACTTCCCTAAGACTGTTTATATTAGGATT
+GTCAAGACACTCCGGTATTACTCGAGCCCGTAATACAACA
+>TY3p-I#LTR/Gypsy
+TCTGGTAGCGTTAAAGGTTACTAATTGTTCAAGCAAACCAACGAATCCCTGAACCTAGCT
+ACACCAACATCTGTCATGAGCTTTATGGATCAAATCCCAGGAGGAGGAAGTTACCCAAAG
+CTTCCGGTGGAATGTCTTCCCAATTTCCCGATCCAACCAGCACTAACCTTCAGAGGTAGA
+AATGACTCGCACAAGTTGAAAAACTTCATCTCTGAAATAATGTTAAACATGTCTATGATT
+CCTTGGCCCAACGAAGCCAGTCGTATTGTCTATTGTAGAAAACACTTACTGAACCCTGCT
+GCTCAATGGGCTAATGATTTTGTCCAAGAGCAAGGCATACTGGAAATAACATTCGACACC
+TTCATACAAGGACTCTATCAGCATTTCTATAAGCCACCAGACATCAACAAAATCTTCAAT
+ACGATCAATCAACTATCTGAAGCAAAACTGGGTATTGAACGTCTCAACAAACAATTCAAA
+ATGATTTGGGACAGAATGCCACCAGACTTTATGACCGAAAAAGCCGCTATTATGACATAT
+ACCCGCTTACTGACAAAGGAAACCTACAATATAGTTAGATTGCATAAACCAAAAACGTTG
+AGAGGAGCCATGGAGGAGGCTTACCAAACAACAGCACTAACTCAGAGATTCTTCCCAGAA
+TTTGAGCTAGACGCCGATGGAGATACTATAATCGCAGCCGCAACTCGTTTACACGAACAG
+TACGACTACGACAGTGACCCACAAGAAAACTTTTTGGTCCAGAAGAGACACGTCCACGCA
+GTTCGGACAAGAAGATCATACAATAAACCGACCGCGACTTATCACAACAGGAGAAGCAAT
+AATCCATCTAGAGAAGAGTGTGTAAAGAACCGTCTCTGTTTTTATTGTAAGAAAGAAGGA
+CACCGTCTGAACGAGTGTAGAGCTCGTAATGCGAGTTCTAGCCGATCCTGAACTTAAGTC
+GAAAGACCACACGAAACTTTCTATCACATCCCGACCTATTGTACATTATATCGCCATACC
+TGAAATGGACAAAACTGCCGAAAAACACATAAAAATAAAAAACACGAAAATAAAAACCCT
+GTTTGATAGTGGATCGCCCACATCATTTATCCGAAGAGATACCGTAAATCTCCTGAATCT
+GCCAACCCATGATACTCCACCGCTCCGCTTTAGAGGATTCATATCCACCGAATCCGCCAC
+CACTTCAGAAGCAGTTACGCTCGACCTTACAGTCGACAATCTGCAAATCAATGTAGCCGC
+GTATGTACTCGATAAAATGGACTACCAACTTCTAATCGGAAATCCAATTCTACGCCGCTA
+CCCAAAACTCCTGTACACAATCCTGAACACTAAGCAGTGTACCTCCGCCCAGAAGCCCAA
+GGCTTACCATCCCGAAAACATTAACTATGTGAAAGCAAAATCCGCTGGTAATCGTGGTAA
+CTCCAGAAACAAAACACTGTCCTTTGCCCCCACTATTCCTGAAGCAACTGACCAGAAATC
+CGCTGGTAATCGTAGTAACTCCAGAACAAATACTATGTCTTTTGCAACTACCAATCCAGA
+AACAACTGACCCGCTTACGACCCTCGACAATCCAGGTAGTACTCAAAGTACATTTGCGCA
+ATTCCCGATACCTGAAGAAGCGACCATCCTAGAAGAGGATGGAAAATACTCCAACGTTGT
+TTCAACCATACAGAACGTAGAACCTAAAGCTACTGATCACAGCAACAAGGACACATTTTC
+AACGTTGCCTGTTTGGTTACAACAGAAGTATATAGAGATTATACGTAATGATCTCCCGCC
+AAGACCGGCCAATATCCACAACATGCCCGTAAAACACGACATTGAAATTAAACTTGACAC
+AAGACTACCTCGACTACAGCCATATCATGTTACAGAAAGGAACGAACAAGAAATTAACAA
+GATCGTTCAAGAACTGCTCGACAACAAGTTCATTGTCCCCTCTAAATCTCCGTGCAGTTC
+CCCTGTAGTCCTTGTCCCGAAGAAAGATGGTACGTTTAGACTTTGCGTTGACTACCGTGC
+CCTGAACAAGGTTACCATCTCCGACCCATTCCCATTACCCAGAATCGACAACCTATTAAG
+CCGTATTGGGAATGCCCAAATATTCACCACGCTAGATTTGCACAGTGGTTATCACCAGAT
+TCCAATGGAACCAAAAGACCGCTACAAAACCGCTTTTGTCACCCCGTCCGGTAAATATGA
+ATACACTGTCATGCCATTTGGTCTAGTGAATGCACCTAGCACCTTTGCAAGATACATGGC
+CGACATTTTCAGAGACTTGAGATTTGTCAATGTCTACCTTGATGATATACTAATCTTCTC
+TGAATCCCAAGAAGAACACTGGAAACATTTAGACACAGTTCTTGGAAGACTTAAGAAGGA
+AAACCTTATTGTCAAAAAGAAAAAATGCAAGTTTGCATCAGAACAAATTGAATTTCTAGG
+TTATAATATTGGAATTCAGAAAATAACCCCATTACAACACAAATGTGCTGCCATTCGAGA
+TTTTCCGAAACCCAGAACAGTAAAGCAAGCACAACGATTTTTAGGAATGATTAATTACTA
+TAGACGATTCATTCCAAATTGCTCTAAGATTGCACAACCAATCCAGCTCTTTATATGCGA
+CAAGAGTCAATGGACAGAAGAGCAGGACAAGGCAATCGAGAAATTAAAATCCGCCCTATG
+TAATTCCCCTGTTCTAGTACCATTTAACAACAAAGCAATTTACCGATTAACTACAGACGC
+ATCAAAAGATGGCATCGGTGCCGTTCTAGAAGAAGTCAATGCCAAAAACGCACTTGTCGG
+TGTCGTCGGTTATTTCTCTAAATCCTTAGAAAGTGCTCAAAAGAACTACCCCGCCGGTGA
+ACTAGAACTACTTGGAATTATTAAGGCACTTCACCACTTCCGTTATATGCTCCATGGAAA
+ACATTTTACATTGAGAACGGATCACATTAGCTTACTGTCACTGCAGAATAAGAATGAACC
+TGCACGAAGAGTTCAAAGATGGTTGGATGACCTAGCCACTTATAACTTCACCCTAGAATA
+CTTAGCTGGACCCAAAAACGTCGTCGCAGATGCTATATCCCGTGCCGTGTACACTATAAT
+CCCAGAAATACCCCAACCTATCGACCCAGAAAATTGGAAAACTCATTACAAATCAGACCC
+ATTATGCAGTGCCACCTTGATTTACATGGAAGAATTGACACAACACAATGTCATGCCTGA
+GGATATGTCCGCATTCCGTAGCTATCACAAGAAATTTCAGTTATCAGAGACCTTCCGAAA
+GAACTACTCCCTAGAAAATGGAATAATCTACTATCGAGACCGATTAGTAGTCCCGGTAAA
+ACAACAGAACGAAGTCATAAAACTGTATCACGATCATACTTTATTCGGAGGCCATTTTGG
+TGTAACTGTAACATTTGGAAAGATTGCTCCAATTTTTTACTGGCCGAAATTGCAACATTC
+GATTACACAATACATCCGTACCTGCGTACAATGTCAACTCACAAAATCACATCGACCACG
+TTCACAAGGACTATTGCAACCGCTTCCCGTAGCAGAAGGAAGATGGCTTAATATATCAAT
+GGATTTCGTGACTGGACTACCCGTAACAACAAACGATTTGAATATGATCCTCGTTGTTGT
+TGACCGCTTCTCGAAACGCGCTCACTTCATAGCTACAAGGAAAACAGCAGACGCATCACA
+GCTAATAAATACGCTATTCCGCTATATCTTTTCATATCATGGTTTCCCGAAAACAATAAC
+CAGTGATAGAGACATCCGTATAACCGCAGAAAAATATCAAGAACTTACAAAAAGATTAGG
+GATAAAATCGACAATGTCTTCTGCAAACCACCCCCAAACAGATGGACAATCCGAAAGAAC
+GATTCAAACATTGAACCGATTGATAAGAGCTTATGCCTCCACCAATACCCGGAACTGGCA
+CACCTACTTACCACAAATTGAATTTGTCTATAACTCCACACCGACCAGAACACTTGGAAA
+GTCACCATTCGAAATTGATTTAGGATATACTCCCAATGCACCTACCATTAAAACGGATTG
+CGAAATCAATGCAAGAAGTTTTACCGCCGTAGAACTGGCCCGACACCTCAAAGCTATTAC
+GATCCAAACAAAAGAACGACTAGAGTCTGCTCAGATTGAAATGGAAACTAATAACAACCA
+AAGACGTAAAACTTTGTTACTGAACATAGGAGATCACGTACTAGTGCATAGAGATGCATA
+CTTCAAGAAAGGAACGTATATGAAGGTACAACCTATATACGTTGGACCATTTCGAGTTGT
+CAAGAAAATAAATGATAACGCTTACGAACTCGACCTGGATTCACACAAGAGAAAACATAG
+AGTTATTAACGTACAATACCTAAAGAAATTTGTATACCGACCCGACGCATATCCAAAGAA
+TAAACCAATCAGTTCCGTTGAAAGAATCAACAGAGCCAATGAAGTCATTGCAGTTATAGG
+GATAGATACCACACACAAAACATACTTATGTCGTATGCAGGATGTGGACCCGACAATCTC
+AGTAGAATATTCAGAAGCTGAATTCTACCAAATCCCAGAGGAAATACGAAAGTCAATATT
+AGCCAATTTTAGACAACTGTACGAAACTCAAGACAACTCCGAGAGAGAGGAAGAT
+>TY3p-LTR#LTR/Gypsy
+TGTTGTATCTCAAGATGAGATACCTCAGCATTACTAGATTTACCAACCTAGACATAAAAC
+ATGTATGAAACACGTACGAAACAATAGACAAGATTGAGTATACTAGGCAACCTACTTGCC
+TAAGATGAACCAAACTAACCAAACGTATAAATACCTGAACAATTAGTTTAGATCCGAGAT
+TCCGCGCTTCCACCCTTTAGTTAGATTCAGATCTTATATAGATTATATAGGATAAGTAAC
+ATTCTGTGAATCACGATAATAATAAGTCTGACAACAAGTTACTCTCCTAAACGACTTTAG
+GATTGTCAAGACATCCGGTATTACTCGAGCCCGTAATACAACA
+>TY4-I#LTR/Copia
+TGGCGACCCCAGTGAGGGGTGAAACAAGAAATGTTATTGACGACAACATTTCTGCGCGGA
+TTCAATCGAAAGTCAAAACAAATGATACTGTCAGACAGACGCCATCATCATTAAGAAAAG
+TTTCTATTAAAGATGAACAGGTGAGACAATATCAAAGAAACTTAAATAGGTTTAAAACCA
+TACTAAATGGTTTAAAGGCAGAAGAGGAAAAACTTTCTGAGGCTGATGATATTCAGATGC
+TAGCTGAAAAATTATTAAAACTCGGAGAAACCATTGACAAGGTTGAGAATAGGATTGTGG
+ATCTAGTTGAAAAGATACAATTATTGGAAACAAACGAGAACAATAATATATTACATGAAC
+ATATAGATGCTACAGGGACTTACTATTTATTCGATACGTTAACTTCAACCAACAAAAGAT
+TCTACCCTAAGGATTGTGTTTTTGATTATAGGACTAATAATGTCGAGAACATTCCTATTC
+TCTTAAACAATTTTAAAAAATTCATCAAGAAATATCAATTTGATGATGTCTTTGAAAATG
+ATATCATAGAAATCGATCCTCGTGAAAATGAAATCTTGTGCAAGATAATCAAAGAAGGAC
+TCGGTGAAAGTTTAGATATCATGAACACAAATACAACTGACATTTTTAGGATAATCGATG
+GTTTAAAAAAACAAAATATAGAAGTTTGCATGGTAGAGATGTCAGAATTAGAGCCTGGGG
+AAAAGGTTTTGGTTGATACAACATGTAGAAATTCCGCATTGTTAATGAATAAACTTCAAA
+AGTTGGTACTAATGGAAAAATGGATTTTTTCTAAATGCTGCCAAGATTGTCCTAATCTAA
+AGGATTACCTACAAGAAGCTATCATGGGAACCTTACATGAATCCTTAAGAAATTCTGTGA
+AACAACGTTTGTACAACATTCCACATGACGTAGGAATTGATCACGAAGAATTTCTAATCA
+ATACTGTTATTGAAACAGTAATTGATTTGAGCCCAATTGCAGACGATCAAATAGAAAATA
+GCTGCATGTATTGCAAATCTGTTTTCCATTGCTCAATTAACTGCAAAAAGAAACCAAATA
+GGGAACTTAGGCCTGACTCGACCAATTTCTCAAAAACCTATTATCTACAAGGTGCACAGA
+GACAACAACCACTTAAGTCCAGTGCAAAACGAACAAAAGTCTTGGAACAAGACACAAAAA
+AGGTCGAACAAAGTGTACAACAGCAAAAAACTGGTAATTATTGATACCGGTTCCGGAGTA
+AACATTACCAATGACAAAACCTTACTGCATAATTACGAAGACAGTAATCGCAGTACACGA
+TTTTTTGGTATTGGGAAAAACAGTTCAGTGTCTCTTAAAGGGTATGGCTATATAAAAATC
+AAGAATGGTCACAACAATACTGACAATAAGTGTCTATTAACTTACTATGTACCGGAAGAA
+GAATCCACTATAATCAGCTGTTATGACTTAGCCAAGAAAACCAAAATGGTTTTAAGTCGA
+AAATATACCAGATTGGGAAACAAAATCATAAAAATTAAAACCAAGATAGTTAATGGTGTC
+ATTCACGTAAAAATGAACGAGTTAATTGAACGTCCTTCCGATGATTCAAAAATAAATGCA
+ATAAAACCTACTTCTTCTCCTGGATTTAAACTAAATAAAAGGTCTATTACCTTGGAAGAT
+GCTCATAAAAGAATGGGCCATACAGGAATTCAACAAATTGAAAATTCCATAAAACATAAT
+CATTATGAAGAATCCCTTGACTTAATCAAAGAACCAAATGAATTTTGGTGTCAAACCTGT
+AAAATCTCTAAAGCCACGAAAAGAAATCATTATACCGGGTCTATGAATAATCATAGTACT
+GATCATGAACCAGGCTCATCATGGTGCATGGATATATTTGGCCCTGTATCAAGTTCAAAC
+GCGGACACTAAAAGGTACATGCTTATTATGGTGGATAACAACACGAGATATTGCATGACC
+TCCACACACTTCAATAAGAATGCTGAAACTATTTTAGCTCAAGTTAGAAAGAATATTCAG
+TACGTGGAAGCACAATTTGACAGGAAAGTCAGAGAAATTAATTCAGACAGAGGTACTGAA
+TTCACAAATGATCAGATAGAAGAATATTTTATTTCAAAAGGAATACATCACATACTTACT
+TCTACACAAGATCATGCTGCTAACGGAAGAGCAGAAAGATACATAAGAACAATAATAACT
+GATGCAACAACACTCCTAAGACAAAGTAACTTAAGAGTAAAATTTTGGGAATACGCAGTA
+ACTTCTGCTACCAATATAAGAAATTACCTGGAACACAAAAGTACAGGTAAACTACCATTG
+AAGGCAATCTCACGTCAACCTGTGACAGTGAGATTAATGTCATTCTTACCATTTGGCGAA
+AAAGGAATAATTTGGAATCATAATCACAAAAAATTGAAACCATCTGGACTTCCTTCTATA
+ATTCTATGCAAAGATCCAAATAGTTATGGATACAAATTCTTTATACCATCCAAAAATAAA
+ATTGTCACATCTGATAATTATACAATTCCCAACTATACAATGGACGGTAGAGTAAGAAAT
+ACTCAGAATATTAACAAGAGTCATCAATTCAGTTCAGATAATGATGATGAAGAAGATCAA
+ATCGAAACGGTCACAAACTTATGTGAAGCTTTGGAAAACTACGAAGATGATAATAAACCA
+ATTACTCGCCTGGAAGATTTGTTCACAGAGGAAGAGTTATCTCAAATAGACTCAAACTCA
+AAATACCCATCTCCTAGTAATAACCTAGAAGGGGACTTGGATTACGTATTTTCTGATGTT
+GAGGAATCTGGAGATTATGACGTTGAATCTGAACTTTCAACGACAAATAATTCAATCTCA
+ACTGATAAAAACAAAATTTTGTCAAACAAGGATTTTAATTCAGAACTTGCATCGACTGAA
+ATATCCATCAGTGGAATCGATAAGAAAGGATTAATAAATACAAGTCATATTGATGAAGAT
+AAGTATGATGAAAAAGTCCACAGAATTCCATCGATTATACAAGAGAAACTGGTAGGAAGG
+AAAAATACTATTAAAATCAATGACGAAAACAAAATCTCCGACAGAATTCGTAGTAAAAAC
+ATTGGGAGTATTTTAAACACTGGACTCAGTAGATGTGTAGATATCACCGATGAATCTATT
+ACTAACAAAGATGAGTCAATGCACAACGCAAAACCCGAACTAATTCAGGAGCAGTTAAAA
+AAAACAAATCATGAAACTTCGTTTCCTAAAGAAGGGAGCATTGGAACAAATGTAAAATTC
+CGAAATACAAACAATGAGATTTCTTTAAAAACAGGCGATACGAGTTTACCAATAAAAACT
+TTAGAAAGCATTAACAATCACCATAGTAATGATTATTCCACAAACAAAGTTGAAAAGTTT
+GAGAAGGAAAATCATCATCCGCCCCCGATTGAGGACATTGTGGATATGAGTGATCAAACT
+GATATGGAATCAAACTGTCAGGATGGTAATAACTTAAAAGAATTAAAAGTCACCGATAAA
+AATGTACCAACTGACAATGGAACAAATGTGTCACCAAGGTTGGAACAAAATATTGAAGCA
+TCTGGATCACCAGTACAAACAGTTAATAAAAGTGCCTTCTTAAACAAAGAATTCAGTTCT
+TTGAACATGAAAAGAAAACGGAAAAGACACGATAAAAACAATAGTCTAACAAGCTATGAA
+TTAGAAAGAGATAAGAAGCGTTCAAAAAAGAATCGAGTGAAATTAATTCCAGATAATATG
+GAAACAGTTTCAGCACCAAAAATTCGAGCCATATATTATAATGAAGCTATTTCAAAAAAT
+CCTGACCTCAAAGAAAAACATGAATACAAACAGGCATATCATAAAGAATTACAGAATTTA
+AAAGATATGAAGGTATTTGATGTCGATGTGAAGTACAGTAGATCAGAAATCCCTGATAAT
+TTAATAGTACCCACCAACACGATATTCACAAAGAAAAGAAATGGGATTTATAAGGCTAGG
+ATAGTCTGCAGAGGTGATACTCAGTCACCAGACACTTACAGTGTAATAACTACAGAATCT
+TTAAATCACAATCATATTAAGATATTCTTAATGATTGCAAACAACAGAAATATGTTTATG
+AAGACCCTGGATATCAATCATGCATTCCTATATGCTAAATTGGAAGAAGAAATATACATC
+CCACATCCGCATGATAGGAGATGTGTAGTCAAGCTAAATAAGGCGTTATATGGTCTAAAA
+CAGAGTCCTAAAGAATGGAATGATCATCTAAGACAATACTTGAATGGAATTGGACTGAAA
+GATAACTCTTATACTCCGGGATTATACCAAACCGAGGATAAAAATCTAATGATTGCAGTC
+TATGTTGATGACTGCGTAATTGCGGCAAGCAATGAACAGAGATTGGATGAATTCATAAAC
+AAATTGAAAAGTAATTTTGAACTGAAAATTACAGGAACATTAATAGACGATGTACTCGAT
+ACAGATATATTAGGAATGGATCTAGTATACAACAAAAGACTTGGTACTATCGATTTAACA
+TTAAAATCATTCATAAATAGAATGGATAAAAAATACAACGAGGAATTGAAAAAGATTAGA
+AAAAGTTCAATTCCGCATATGTCAACTTATAAAATAGATCCTAAGAAAGACGTACTGCAA
+ATGTCAGAAGAAGAGTTTAGACAAGGTGTTCTAAAGCTACAACAATTACTAGGTGAACTA
+AACTATGTCAGACACAAATGCAGATACGACATTGAATTTGCTGTTAAGAAAGTGGCTAGA
+CTAGTAAATTACCCACATGAAAGAGTCTTTTATATGATTTACAAAATAATCCAGTACTTG
+GTTAGGTATAAAGATATTGGAATACACTATGACCGAGACTGTAATAAAGACAAAAAGGTT
+ATTGCTATAACTGATGCATCAGTTGGATCAGAATATGATGCTCAATCAAGGATTGGAGTT
+ATATTATGGTACGGTATGAATATTTTTAATGTTTATTCTAACAAGAGCACAAACAGATGT
+GTATCATCAACAGAAGCAGAGCTTCATGCCATTTATGAAGGCTATGCAGACTCAGAAACG
+TTGAAGGTAACATTAAAGGAGCTAGGAGAAGGAGACAATAATGACATTGTCATGATCACT
+GACTCAAAGCCAGCCATTCAAGGATTAAATCGCAGCTATCAACAACCAAAAGAGAAATTC
+ACTTGGATAAAAACTGAAATAATAAAAGAAAAAATTAAAGAGAAGAGTATAAAACTGTTA
+AAAATTACCGGCAAAGGTAATATTGCTGATTTACTAACAAAACCAGTATCAGCATCTGAT
+TTTAAAAGATTTATACAAGTATTAAAAAATAAAATAACATCACAGGATATTTTGGCCTCA
+ACAGACTATTGATAATTAATTAATGAAGTTCTAAACACACAATGAATATCTGTTGAAGTA
+CAATAATATATCTTTAAGGGAGCA
+>TY4-LTR#LTR/Copia
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATGGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACAACTCGTATACGTTTAAGTGTGATTGCGCCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGTGTTAAAGACCTATTAGTTGAACAT
+GTTATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTCACTTCTTCATTAATACTAATTTTTAACCTCT
+AATTATCAACA
+>TY4p-I#LTR/Copia
+TGGCGACCCCAGTGAGGGATGGAACAAGAAATGTTATTGACGACAACATTTCTGCGCGGA
+TTCAATCGAAAGTCAAAACAAATGATACTGTCAGACAGACGCCATCATCATTAAGAAAAG
+TTTCTATTAAAGATGAACAGGTACGGCAATATCAAAGAAACTTAAATAGGTTTAAAACCA
+TACTAAATGGTTTAAAGGCAGAAGAGGAAAAACTTTCTGAGGCTGATGATATTCAGATGC
+TAGCCGAAAAATTATTAAAACTCGGAGAAACCATTGACAAGGTTGAGAATAGGATTCTGG
+ATTTAGTTGAAAAGATACAATTATTGGAAACAAATGAGAACAATAATATTTTACATGAAC
+ATACAGATGCTACAGGGACTTACTATTTATTCGATACGTTAACTTCAACCAACAAAAGAT
+TCTACCCTAAAGATTGTGTTTTTGATTATAGGACTAACAATGTTGAGAACATTCCTATTC
+TTTTAAACAATTTTAAAAAATTTATCAAGAAATATCAATTTGATGATGTCTTTGAAAATG
+ATATCATAGAAATCGATCCTCGTGAAAATGAAATCTTGTGCAAAATAATCAAAGAAGGAC
+TCGGTGAAAGTTTAGATATCATGAACACAAATACAACTGACATTTTTAGGATAATCGATG
+GTTTAAAAAACAAATATAGAAGTCTGCACGGTAGAGATGTCAGAATTAGAGCCTGGGAAA
+AGGTTTTGGTTGATACAACATGTAGAAATTCCGCATTATTAATGAATAAACTTCAAAAAT
+TGGTACTAATGGAAAAATGGATTTTTTCCAAATGCTGCCAAGATTGTCCCAATCTAAAAG
+ATTACCTACAAGAAGCTATCATGGGAACCTTACATGAATCCTTAAGAAATTCTGTGAAAC
+AACGTTTGTACAATATTCCACATAACGTAGGAATTAATCACGAAGAATTTCTAATCAATA
+CTGTTATTGAAACAGTAATTGATTTGAGCCCAATGGGTGACGATCAAATAGAAAATAGCT
+GCATGTATTGCAAATCTGTTTTCCATTGCTCAATTAACTGCAAAAAGAAACCAAATAGAG
+AACTTAGGCCTGACACGGCAAATTTCTCAAAAACCTATTATACGCAAGGTGCACAGAGAC
+AACAACAACTTAAGTCCAGTACAAAACGAACAAAAGTCTTGGAACAAGACACAAAAAAGG
+TCGAACAAAGTGTACAACAGCAAAAAACTGGTAATTATTGATACCGGTTCCGGTGTAAAC
+ATTACCAATGACAAAACCTTACTGCATAATTACGAAGACAATACTCGCAGTACACGATTT
+TTTGGTATCGGGAAAAACAGCTCAGTGTCTGTTAAAGGGTATGGCTATATAAAAATCAAG
+AATGGTCACGACAATACTGACAATAAGTGCTTATTGACTTACTATGTACCGGAAGAAGAA
+TCCACTATAATCAGCTGTTATGACTTAGCCAAGAAAACCAAATTGGTTTTAAGTCGAAAA
+TATACCAACTTGGGAAACAAAATCATAAAAATAAAAACCAAGATAATAAATGGTGTCATT
+CACGTAAAAATGAATGAGTTAATTGAACGTCCTTCCGATGATTCAAAAATAAATGCAATA
+AAACCTACTTCTTCTACTGGATTTAAACCAAATAAAATGTCTATTACCTTGGAAGATGCT
+CATAAAAGAATGGGCCATACAGGAATTCAACAAATTGAAAATTCCATAAAACATAATCAT
+TATGAAGAATACCTTGACTTAATCAAAGAACCAAATGAATTTTGGTGTCAAACCTGTAAA
+ATCTCTAAAGCCACGAAAAGAAATCATTATACCGGGTCTATGAATAATCATAGTACTGAT
+CATGAACCAGGCTCATCATGGTGCATGGATATATTTGGTCCTGTTTCAAGTTCAAACGCG
+GACACTAAAAGGTACATGCTTATTATGGTGGATAACAACACGAGATATTGCATGACCTCC
+ACACACTTCAATAAGAATGCTGAAACTATATTAACACAAATCAGAAAGAATATTCAGTAC
+GTGGAAACACAATTTGACAGAAAAGTCAGAGAAATTAATTCAGACAGAGGTACTGAATTC
+ACAAATGATCAGATAGAAGAATATTTTATTTCAAAAGGAATACATCATATACTTACTTCT
+ACACAAGATCATGCTGCTAATGGAAGAGCAGAAAGATACATCAGAACAATAATAACTGAT
+GCAACAACACTCCTAAGACAAAGTAACTTAAGAGTAAAATTTTGGGAATACGCAGTAACT
+TCTGCTACCAATATAAGAAATTGCCTGGAACACAAACGTACAGGTAAACTACCATTGAAG
+GCAATCTCACGTCAACCTGTTACAGTGAGATTAATGTCATTCTTACCATTTGGCGAAAAA
+GGAATAATTTGGAACCATAATCACAAAAAATTGAAACCATCGGGACATCCTTCTATAATT
+TTATGCAAAGATCCAAATAGTTATGGATACAAATTCTTTATACCATCCATAAATAAAATT
+GTCACATCTGATAATTATACAATTCCCAACTATACTATGGACGGTAGAGTAAGAAATACT
+CAGAATATTTACAAAAGTCATCAAATCAGTTCACATAATGCTGATGAAGAAGATCAAATC
+GATACGGTCACAAACTTATGTGAAGCTTTGGAAAACTACGAAGATGATAATAGACCAATT
+ACTCGCCTGGAAGATTTTTTCACAGAGGAAGAGTTATCTCAAATAGACTCAAACGCAAAA
+TACCCATCTCCTAGTAATAACCTAGAAGGGGACTTGGATTACGTATTTTCTGATGTTGAA
+GAATCTGGAGATTATGACCTTGAATCTGAACTTTCAGCGACAAATACCTCAATCTCAACT
+GATAAAAACAAAATTTTGTCAAACAAGGATTCTAATTCAGAACTTGCATCGACTGAAATA
+TCCATCAGTGGAATCGATAAAAAAGGATTAATAAATACAACTCATATTGATGAAGATAAT
+TGTGATGAAAAAGTCCACAGAATTCCATCGATTATACAAGAAAACCTCGTAGGAAGTAAA
+AATACTATTAAAATCAATGACGAAAACAAAATCTCCAACAGAATTCGTAGTAAAAACATT
+GGGAGTACATTAAACTCTGGACTCAGTAGATGTGTAGATATTACCGATGAATCTATTACT
+AACAAAGATGAGTCAATACACAACCCAAAACCAGAACTAATACAGGAGCAGTTTAATAAA
+ACAAACCATGAAACTTCGTTTCCTAAAGAAGGGAGCATTGGAAGAAATGTAAAATTCCGA
+AATCCAAACAATGAGATTTCTTTAAAAACAAGCGAAACGAGTTTACCAATAAAAACTTTA
+GAAAGTATTAACAATCACCACAGTAATGATTATTCCACAAACAAAGTTGAAAAGTTTGAG
+AAGGAAAATCATCATCCGCCCCCGATTGAGGACGTTGTGGATATGAGTGATCAAACAGAT
+ATGGAATCAAACTGTCAGGATGATAATAACATAAAAAAATTAGAAGACACCGACGAAAAT
+GTACCAACTGAGAATGGAACCAATGTGTCACCAAGGTTGGAACGAAGTAGTAAAAAAAAT
+GAGATCAACACTACAACCAATTAAAACGACAACTGAAGCATCTGGATCGTCAGTACAAAC
+AGTTAATAAAAGTGCCTTTTTAAACAAAGAATTTAATTCTTTGAATATGAAAAGAAAACG
+GAAAAGACACGATAAAAACAATAGCTTAACAAGCTACGAATTAGAAAGAGATAAGAAGCG
+TTCAAAGAAGAATCGAGTGAAATTAATTCCAGATAATATGGAAACAAGTTCAGCACCGAA
+AATTAGAGCCATATATTATAATGAAGCTATTTCAAAAAATCCTGACCTCAAAGAAAAACA
+TGAATACAAACAGGCATATCATAAAGAATTACAAAATCTAAAAGATATGAAGGTATTTGA
+TGTCGATGTGAAGTACAGTAGATCAGAAATCCCTGATAATTTAATAGTACCCACCAACAC
+AATATTCACAAAGAAGAGAAATGGGATTTATAAGGCTAGGATAGTCTGCAGAGGCGATAC
+TCAGTCACCGGACACTTACAATGTAATAACTACAGAATCTTTAAATCACAATCATATTAA
+GATATTCTTAATGATTGCAAACAACAGAAATATGTTTATGAAGACTCTGGATATCAATCA
+TGCATTCCTATATGCTAAATTGGAAGAAGAAATATACATCCCACATCCGCATGATCGGAG
+ATGTGTAGTCAAACTAAATAAGGCGTTATATGGTCTAAAACAGAGTCCTAAAGAATGGAA
+TGATCATCTAAGACAATACTTGAATGGTATTGGATTGAAAGATAACTCTTATACTCCGGG
+ATTATACCAAACCGAGGATAAAAATCTAATGATTGCAGTTTATGTTGATGACTGCGTAAT
+TGCGGCAAACAATGAACAGAGATTGGATGAATTCATAAACAAATTGAAAAGTAATTTTGA
+ACTGAAAATTACAGGAACATTAATAGATGATGTACTCGATACAGATATATTAGGAATGGA
+CTTAGTATACAACAAAAGACTTGGTACTATCGATTTAACATTGAAATCATTCATAAATAA
+AATGGATAAAAAATACAAAGAGGAATTGAAAAAGATTAGAAAAAGTTCAATTCCGCATAC
+GTCAACTTATAAAATAGATCCTAAGAAAGACGGACTGCAAATGTCAGAAGAAGAGTTTAG
+ACAAGGTGTTCTGAAATTACAGCAATTACTAGGTGAACTAAACTATGTCAGATACAAATG
+CAGATACGACATTGAATTTGCTGTTAAGAAAGTGGCTAGACTAGTAAATTACCCACATGA
+AAACGTCTTCTATATGATTTACAAAATAATCCAGTACTTGGTTCGGTATAAAGATATTGG
+AATACACTATGACCGAGACTGTAATAAAGATAAGAAGGTTATTGCTATTACTGATGCATC
+AGTTGGATCAGAATATGATGCTCAATCAAGGATTGGAGTTATATTATGGTACGGGATGAA
+TATTTTTAATGTTTATTCTAACAAGAGCACAAACAGATGTGTATCATCAACAGAAGCAGA
+GCTTCATGCCATTTATGAGGGCTATGCAGACTCAGAAACGTTGAAGGAAACATTAAAAGA
+GCTAGGAGAAGGAGAAAATAATGACATTGTCATGATCACTGACTCAAAGCCAGCCATTCA
+AGGATTAAATCGTAGCTATCAACAACCAAAAGAAAAATTCACTTGGATAAAAACTGAAAT
+AATAAAAGAAAAAATTAAAGAGAAGAGTATAAAACTGTTAAAAATTACCGGCAAAGGTAA
+TATTGCTGATTTACTAACAAAACCAGTATCAGCATCTGATTTTGAAAGATTTATACAAGT
+ATTAAAAAATAAAATAACATCACAGGATATTTTGGCCTCAACAGACTATTGATAATTAAT
+TAATGAAGTTCTAAACACACAAGGAATATCTGTTGAAGTACAATAATATATCTTTAAGGG
+AGCA
+>TY4p-LTR#LTR/Copia
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATAGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACACCTCGTATACGTTTAAGTGTGATTGCACCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGAGTTAAAAATCTATTAGTTGAACAT
+GATATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTTATTTCTTCATTAGTACTATATTTTAACCTCT
+AATTATCAACA
+>TY5-I#LTR/Copia
+GGTTATGAGCCCTGAGAGCAATGCTTCAGAGACCATAATTAATCTATCTAATCCCAACAA
+TTATAAACAGTGGCTGTACGGTATCGAGACCGCTGCTGAATATGCTAACGAATATATGAA
+CGAATTCGTTCATACCGGAGATATCCAATCAATGAAAAGGGATTACAATCTCAGCGCGAA
+TGATGAAAGCTTTGTCAAAACCGTATTTAACAGTTTCCTGGTAAAGCTCTACAAGAAAAC
+TATCGTGGGTGAAGCTGCATGTGAAATGAACTGGATATGTGATGATTCACTTGGAAGGGT
+CTCTGCTTATGATATTTTCTCGCACTTCGAAGAAAACTATAATGAAGTCACTATTGGATC
+CAGGCTTACTCTTATAGAGGACTTACCAAATATATCCTCCAAGCCTGTAGATGAAATCGC
+TTCCTTTTTGAAAACCCTATTCACAATGCTTGAAGACAATAGCGAAGAACAGGACAAAAA
+GAAAAGACGCGATACCAATATCGCGTTGCTATTAATGACCTTCTTACCCGAGTTAAAGGA
+ATCATTCCACGAGAAATTCGGTGACTCTAAAGCTCTTCAGCTGTCACAAGTCATTAGATT
+CTGTAAATTAAAGGCGTCATCGAATTCATTATCTTCAGTCTCAGATACATTGGTTGCACA
+AGACAGAAGAAGCTATCAAAAGAAAGGAAATAAGGGATGTATGATTTGTGGGGCTGATCA
+TCGCTTAAGCAACTGTTCTCTGCTTAAAAGAAGAATACCAGAAGCCAGAATCTTTAAATT
+ATATCCTAATGACAAGACGAATAGATCTTCATCTGCTAGTGTTGCGATTCCTGACTATGA
+AACGCAAGGCCAAACAGCAGGACAGATAACACCAAAGTCCTGGCTCTGTATGTTATCTTC
+GACCGTCCCAGCTACCAAATCCTCAGATTGGATTTGTGACACAGGATGTACTTCACACAT
+GTGCCACGACCGTTCTATGTTCTCATCATTTACTAGATCCTCTAAGAAAGACTTTGTCAG
+AGGAGTCGGCGGTTCCATACCCATCATGGGCTCCGGGACTGTAAACATCGGCACTGTTCA
+ATTAAATGACGTATCCTACGTCCCTGATTTACCAGTCAACCTAATATCCATTTGGAAACT
+ATGTGCTAAATCCAACTCTTCTGTTACGTTCACAAAAGAGGGTGTCACTGTGAAATCACC
+TGATGACGTGATTTCTACGGCTGGGAAGTTAAACAATTATCTGTACATTTTCGATGATCT
+TACGCCCGTAACTACCTTCTCTTCGCAAAATTACTTCTGCTCTAAAACATTGGATTCATC
+TAAAATGATAACTTCCGCAGCGTTTCATACCGTTGCAGATAAAATGTTGTCGCAACACAT
+TTCTCCCACTGCTCTCCCGGTAAAATGGCATGCTCGTATGGGCCATCCCGGAGCAGATAT
+TTACAATTCCTTGGCTAGAACTCTGCGTTTTCCAAAATTTAAGACGGCTGAATACACTAT
+TTGTCCTACCTGCTCACTAGCAAAAGGAATCATCAAAAAGGGTAAAGTCTCGCTCAAAAA
+ATATACCCAACCTCTTCAAATGGTACAGGCTGATCTCTGTGGTGGGTTTCGCTACCAAGA
+GTTTCAGTCAAATAAATATTTTCTTACTATCCGTGATGCCTATAGTCGCTACTACTCTGT
+AATACATTTAAAATCCAAAGCAGACGCTCCGATAAAATTCATGGAATGGATCAACGAAAC
+CGAACAATACTTTAGCTCCCGGGGTGGATTCAAAGTCGGATCTGTTCGTACAGACAATGG
+TACAGAATTCGTAAATAAAAATCTTCATGCGTTTTTTAAATCTAAAGGAATAGAGCATCA
+GTTAACTATTCCATATCATAGTTATCAAAATGGTGCTGTTGAACGTGCACATCGTACCAT
+CGAAGAACGCACTCGTTGTCTCCTTATCGGGGGGCGTGTTCCTCCGTCCTTGTGGTCTGA
+AGCTGTTTCTTGCGCAGTCTATTTAATCAATAGGTCCCCTGTAGTGTCCAAAAATAACAG
+TATCCCATACTGCCGGTGGTTCAACATCCCCGCAAAAGATTTCGGTATCGCACATCTTCG
+AATTTTTGGATGTACAGCATACGCAACCTTACAACCTAGTCTTCGAGACGGCAAACTTGC
+CCCAACTGTCATATCTGGTGTTATGGTTGGCTATGACTCTAACCATCGAGGATACAGGAT
+TTATCATCCCGAAACTGGCCGCATCTTTGTGAGCAGTCAAGTTCGATTTGACGAACACAT
+GTTTCCTCTTGCTGATACAGAGGCAGTTCACGTCTCTCACGACTTTGCCACTTCCGCTAT
+TGGGGGGGTGTCCAAATATCCTGAAACAGGGTCAACCGTCTCTGCTCCAAAGAACGACGG
+ATCTGACTTGGCAAATTTGCCAATAACTGTTCCCAAAAATGTAAATCAACCAGCACATAA
+ACCTAATACCAGTAACATCTCTTCCTCTGATGATGATGAGGATATTTCAATGGAAATCGA
+AATGGAAAAACCTATCCCTGAGTGTAACCAAGACAACTTACCAAACTCCGGATGTCCACC
+AACAAGGATACAACATTCTAACTTTGAATCCTTACCAACCGTGTCTACCGAAGACGAAAC
+TAATTCTTCTATGGAGAAAACTCCTGAAAGAGTTCCAGCGGCACTAACTTATCGAGAAAT
+TCCAAAATCATCCGATTCAGAATATATTCCGACATGCCGAAATAGAACTAGACGTGTTAA
+AAGAACTAATAAGAAACCAACGCGATCCCGCGAAATAGAAATATATGATATATCACGTCC
+AAACGTAATATCGAGTGACAACTTACCTGAAGTTAGAAGTGCCAAGCAAAGAAAGACGGT
+GTCCAATACAAATGATACTGTAGCAAGGACAAATAGACTTCCAACCGTGCTACGAACTCT
+AGACTCAAACAACATTGACACGCTGCATGTTGCCAGTACTGGTGAAGAAGTGTCCATCGA
+AAGACTTTCAAGCATGGCTCTTCAGGAAGCGAAGAACAATTCCGCCAGAACTAATCAAGC
+TAATTCTCTTACTGATTGGTTTCCAGTAGGCGCAATGCCGATACCTGACCAGAGGTATCT
+ATCCGTTCACGATGGAACATATATCAGCGACTCACAAGATGTGGGTGATACTGACCTCAC
+TCCTGCTGTAACCAGGCTAGTTACTGAAGAGAATTCAATCGAATCTCCTCCATCGTTGGA
+TTCATCGCCTCCAAATACCTCATTTAACGCGGCTCTAACTGCTATTATCCATAGCACAAA
+AAAAGGAAACCCGAAAACCTATGCCCAAGCAATGGGAAGGCCTGACTTTCAAGAATGGCA
+CAACGCATGCCTCAAGGAACTTTCCGCGTTCAAAGATCACAATACGTACAAATTGGTGTC
+TCTTCCAAAGCAAAGAAGAGCTCTTGGATCGCGCTGGGTATTCACAATAAAAGACTCCGG
+GACGTACAAAGCTCGCCTTGTCGCCCAAGGACATACTCAAAAGGCTGGTATTGACTATCA
+AGAAACTTTTGCACCAGTCATTCGATATGACTCTGTTAGATTATTTCTGGCCCTTGCTAG
+CTGCCTCAAACTAATAGTATATCAGATGGACGTTGACACCGCGTTTCTAAACTCAAAAAT
+GAATGAGCCGGTATACGTAAAACAACCACCCGGATTTATTAATGAAAGTAATCCCGACTA
+TGTATGGGAACTATACGGCGGTATGTATGGACTCAAGCAAGCCCCATTACTATGGAACGA
+ACATATCAACAATACTCTTCAAAAGATTGGTTTTCGTCGACATGAAGGCGAACATGGCTT
+ATACTTTCGTTCCACATCTGATGGTCCCATCTACATTGCCCTATACGTAGACGACTTACT
+TGTTGCTGCTCCCTCTCCGAAAATATATGACAGGGTTAAGCAGAAACTAACGAAGTTATA
+CTCAATGAAGGATCTAGGTAAAGTTGACAAATTCCTCGGTCTTAACATTAATCAATTTTC
+AAATGGAGACATCACTCTCTCACTTCAAGACTATATTGCTAAAGCTGCATCTGAAAGCGA
+AATAAACATATGTAAGCCTACACAGACTCCGCTCTGTGACTCAAAGCCTCTTTTCGAAAC
+AACTTCCCCGCACCTAAAGGACATCACTCCTTATCAGAGCATAGTTGGACAGCTTCTCTT
+TTGTGCAAATACTGGTCGTCCTGACATATCTTATCCGGTCTCACTACTCTCCAGGTTTCT
+TCGCGAACCTCGCGCAATCCATTTGGAGTCTGCTCGACGAGTTCTACGGTACCTATATAC
+CACCAGAAGTATGTGTCTCAAGTATCGTTCTGGATCTCTGTTGGCACTAACTGTATATTG
+TGATGCATCTCATGGAGCAATTCACGATCTCCCACACTCTACTGGGGGGTACGTGACTCT
+ACTTGCTGGTGCTCCAGTTACGTGGTCATCAAAGAAACTCAAGGGTGTGATTCCTGTATC
+ATCTACTGAGGCAGAATACATTACTGCAAGTGAAACTGTCATGGAGATAGAATGGATTCA
+AAACTTGTTTGAACACTTAGGCCAGCCACTTATCTCATCAACATTATACGTAGATAATGA
+ACCTGCTATAAAACTATCTAAACATCCTGTATTTCACACGAGAACAAAACACATTGCCTT
+GAGATATCACAAGCTAAGAAGTGCAGTGGCAGCAGGCATAATTACCATAGAGCATGTTAT
+TACAAAGAGACAAGTTGCTGACATATTTACAAAAATCCTTCCAGCAGAATCATTCAAAGC
+ACATAGGGCTGTCATGGTGAGGGAACCAGAAACTGCAAAATAACCACTCTCATGCGTATT
+CAGTTATGGGGGGA
+>TY5-LTR#LTR/Copia
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTACATA
+ACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCA
+CTACGTCAACA
+>TY5p-I#LTR/Copia
+GGTTATGAGCCCTGAGAGCAATGCTTCAGAGACCATAATTAATCTATCTAATCCCAACAA
+TTATAAACAGTGGCTGTACGGTATCGAGACCGCTGCTGAATATGCTAACGAATATATGAA
+CGAATTCGTTCATACCGGAGATATCCAATCAATGAAAAGGGATTACAATCTCAGCGCGAA
+TGATGAAAGCTTTGTCAAAACCGTATTTAACAGTTTCCTGGTAAAGCTCTACAAGAAAAC
+TATCGTGGGTGAAGCTGCATGTGAAATGAACTGGATATGTGATGATTCACTTGGAAGGGT
+CTCTGCTTATGATATTTTCTCGCACTTCGAAGAAAACTATAATGAAGTCACTATTGGATC
+CAGGCTTACTCTTATAGAGGACTTACCAAATATATCCTCCAAGCCTGTAGATGAAATCGC
+TTCCTTTTTTGAAAACCCTATTCACAATGCTTGAAGACAATAGCGAAGAACAGGACAAAA
+AGAAAAGACGCGATACCAATATCGCGTTGCTATTAATGACCTTCTTACCCGAGTTAAAGG
+AATCATTCCACGAGAAATTCGGTGACTCTAAAGCTCTTCAGCTGTCACAAGTCATTAGAT
+TCTGTAAATTAAAGGCGTCATCGAATTCATTATCTTCAGTCTCAGATGCATTGGTTGCAC
+AAGACAGAAGAAGCTATCAAAAGAAAGGAAATAAGGGATGTATGATTTGTGGGGCTGATC
+ATCGCTTAAGCAACTGTTCTCTGCTTAAAAGAAGAATACCAGAAGCCAGAATCTTTAAAT
+TATATCCTAATGACAAGACGAATAGATCTTCATCTGCTAGTGTTGCGATTCCTGACTATG
+AAACGCAAGGCCAAACAGCAGGACAGATAACACCAAAGTCCTGGCTCTGTATGTTATCTT
+CGACCGTCCCAGCTACCAAATCCTCAGATTGGATTTTTGACACAGGATGTACTTCACACA
+TGTGCCACGACCGTTCTATGTTCTCATCATTTACTAGATCCTCTAAGAAAGACTTTGTCA
+GAGGAGTCGGCGGTTCCATACCCATCATGGGCTCCGGGACTGTAAACATCGGCACTGTTC
+AATTAAATGACGTATCCTACGTCCCTGATTTACCAGTCAACCTAATATCCATTTGGAAAC
+TATGTGCTAAATCCAACTCTTCTGTTACGTTCACAAAAGAGGGTGTCACTGTGAAATCAC
+CTGATGACGTGATTTCTACGGCTGGGAAGTTAAACAATTATCTGTACATTTTCGATGATC
+TTACGCCCGTAACTACCTTCTCTTCGCAAAATTACTTCTGCTCTAAAACATTGGATTCAT
+CTAAAATGATAACTTCCGCAGCGTTTCATACCGTTGCAGATAAAATGTTGTCGCAACACA
+TTTCTCCCACTGCTCTCCCGGTAAAATGGCATGCTCGTATGGGCCATCCCGGAGCAGATA
+TTTACAATTCCTTGGCTAGAACTCTGCGTTTTCCAAAATTTTAAGACGGCTGAATACACT
+ATTTGTCCTACCTGCTCACTAGCAAAAGGAATCATCAAAAAGGGTAAAGTCTCGCTCAAA
+AAATATACCCAACCTCTTCAAATGGTACAGGCTGATCTCTGTGGTGGGTTTCGCTACCAA
+GAGTTTCAGTCAAATAAATATTTTCTTACTATCCGTGATGCCTATAGTCGCTACTACTCT
+GTAATACATTTAAAATCCAAAGCAGACGCTCCGATAAAATTCATGGAATGGATCAACGAA
+ACCGAACAATACTTTAGCTCCCGGGGTGGATTCAAAGTCGGATCTGTTCGTACAGACAAT
+GGTACAGAATTCGTAAATAAAAATCTTCATGCGTTTTTTAAATCTAAAGGAATAGAGCAT
+CAGTTAACTATTCCATATCATAGTTATCAAAATGGTGCTGTTGAACGTGCACATCGTACC
+ATCGAAGAACGCACTCGTTGTCTCCTTATCGGGGGCGTGTTCCTCCGTCCTTGTGGTCTG
+AAGCTGTTTCTTGCGCAGTCTATTTAATCAATAGGTCCCCTGTAGTGTCCAAAAATAACA
+GTATCCCATACTGCCGGTGGTTCAACATCCCCGCAAAAGATTTCGGTATCGCACATCTTC
+GAATTTTTGGATGTACAGCATACGCAACCTTACAACCTAGTCTTCGAGACGGCAAACTTG
+CCCCAACTGTCATATCTGGTGTTTATGGTTGGCTATGACTCTAACCATCGAGGATACAGG
+ATTTATCATCCCGAAACTGGCCGCATCTTTGTGAGCAGTCAAGTTCGATTTGACGAACAC
+ATGTTTCCTCTTGCTGATACAGAGGCAGTTCACGTCTCTCACGACTTTGCCACTTCCGCT
+ATTGGGGGGGTGTCCAAATATCCTGAAACAGGGTCAACCGTCTCTGCTCCAAAGAACGAC
+GGATCTGACTTGGCAAATTTGCCAATAACTGTTCCCAAAAATGTAAATCAACCAGCACAT
+AAACCTAATACCAGTAACATCTCTTCCTCTGATGATGATGAGGATATTTCAATGGAAATC
+GAAATGGAAAAACCTATCCCTGAGTGTAACCAAGACAACTTACCAAACTCCGGATGTCCA
+CCAACAAGGATACAACATTCTAACTTTGAATCCTTACCAACCGTGTCTACCGAAGACGAA
+ACTAATTCTTCTATGGAGAAAACTCCTGAAAGAGTTCCAGCGGCACTAACTTATCGAGAA
+ATTCCAAAATCATCCGATTCAGAATATATTCCGACATGCCGAAATAGAACTAGACGTGTT
+AAAAGAACTAATAAGAAACCAACGCGATCCCGCGAAATAGAAATATATGATATATCACGT
+CCAAACGTAATATCGAGTGACAACTTACCTGAAGTTAGAAGTGCCAAGCAAAGAAAGACG
+GTGTCCAATACAAATGATACTGTAGCAAGGACAAATAGACTTCCAACCGTGCTACGAACT
+CTAGACTCAAACAACATTGACACGCTGCATGTTGCCAGTACTGGTGAAGAAGTGTCCATC
+GAAAGACTTTCAAGCATGGCTCTTCAGGAAGCGAAGAACAATTCCGCCAGAACTAATCAA
+GCTAATTCTCTTACTGATTGGTTTCCAGTAGGCGCAATGCCGATACCTGACCAGAGGTAT
+CTATCCGTTCACGATGGAACATATATCAGCGACTCACAAGATGTGGGTGATACTGACCTC
+ACTCCTGCTGTAACCAGGCTAGTTACTGAAGAGAATTCAATCGAATCTCCTCCATCGTTG
+GATTCATCGCCTCCAAATACCTCATTTAACGCGGCTCTAACTGCTATTATCCATAGCACA
+AAAAAAAGGAAACCCGAAAACCTATGCCCAAGCAATGGGAAGGCCTGACTTTCAAGAATG
+GCACAACGCATGCCTCAAGGAACTTTCCGCGTTCAAAGATCACAATACGTACAAATTGGT
+GTCTCTTCCAAAGCAAAGAAGAGCTCTTGGATCGCGCTGGGTATTCACAATAAAAGACTC
+CGGGACGTACAAAGCTCGCCTTGTCGCCCAAGGACATACTCAAAAGGCTGGTATTGACTA
+TCAAGAAACTTTTGCACCAGTCATTCGATATGACTCTGTTAGATTATTTCTGGCCCTTGC
+TAGCTGCCTCAAACTAATAGTATATCAGATGGACGTTGACACCGCGTTTCTAAACTCAAA
+AATGAATGAGCCGGTATACGTAAAACAACCACCCGGATTTATTAATGAAAGTAATCCCGA
+CTATGTATGGAACTATACGGCGGTATGTATGGACTCAAGCAAGCCCCATTACTATGGAAC
+GAACATATCAACAATACTCTTCAAAAGATTGGTTTTCGTCGACATGAAGGCGAACATGGC
+TTATACTTTCGTTCCACATCTGATGGTCCCATCTACATTGCCCTATACGTAGACGACTTA
+CTTGTTGCTGCTCCCTCTCCGAAAATATATGACAGGGTTAAGCAGAAACTAACGAAGTTA
+TACTCAATGAAGGATCTAGGTAAAGTTGACAAATTCCTCGGTCTTAACATTAATCAATTT
+TCAAATGGAGACATCACTCTCTCACTTCAAGACTATATTGCTAAAGCTGCATCTGAAAGC
+GAAATAAACATATGTAAGCCTACACAGACTCCGCTCTGTGACTCAAAGCCTCTTTTCGAA
+ACAACTTCCCCGCACCTAAAGGACATCACTCCTTATCAGAGCATAGTTGGACAGCTTCTC
+TTTTGTGCAAATACTGGTCGTCCTGACATATCTTATCCGGTCTCACTACTCTCCAGGTTT
+CTTCGCGAACCTCGCGCAATCCATTTGGAGTCTGCTCGACGAGTTCTACGGTACCTATAT
+ACCACCAGAAGTATGTGTCTCAAGTATCGTTTCTGGATCTCTGTTGGCACTAACTGTATA
+TTGTGATGCATCTCATGGAGCAATTCACGATCTCCCACACTCTACTGGGGGTACGTGACT
+CTACTTGCTGGTGCTCCAGTTACGTGGTCATCAAAGAAACTCAAGGGTGTGATTCCTGTA
+TCATCTACTGAGGCAGAATACATTACTGCAAGTGAAACTGTCATGGAGATAGAATGGATT
+CAAAACTTGTTTGAACACTTAGGCCAGCCACTTATCTCATCAACATTATACGTAGATAAT
+GAACCTGCTATAAAAACTATCTAAACATCCTGTATTTCACACGAGAACAAAACACATTGC
+CTTGAGATATCACAAGCTAAGAAGTGCAGTGGCAGCAGGCATAATTACCATAGAGCATGT
+TATTACAAAGAGACAAGTTGCTGACATATTTACAAAAATCCTTCCAGCAGAATCATTCAA
+AGCACATAGGGCTGTCATGGTGAGGGAACCAGAAACTGCAAAATAACCACTCTCATGCGT
+ATTCAGTTATGGGGGGA
+>TY5p-LTR#LTR/Copia
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTTACAT
+AACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTC
+ACTACGTCAACA
+>TSU4b-I#LTR/Copia
+TGGCGACCCCAGTGAGGGATGAGACAAGATATGTTATTGACGACAACATATCTACGCAGG
+TTCAATCAAAAGTCAAATTTCAAAACTTAAGTTTTGATACTTCCGTTAAAAACAAACAAA
+GGATTCAAACTCAAATTGATTTAAAAATGTATGAAAGATTCTTAAACAAATTAACCACTA
+AAAAGAATAAAATTGCAAATGAGGCTGAAGAGGATGATGATATTTCAAATCTCGACCAGT
+TAATTGAAGTCGATGAAAAAATTGAAAAAACTAATAATATAATTCTTAGGTTACAAGAAA
+AGTTAGAATTGATTGAATTCAATAAAGATGTTAAGAAGTTACATAAAAGAAATGATTCCA
+CTGGAACATATTACTTATTCGACACAATTACCTCAAAAAATAATAAATATTATCCTAAGG
+ATTGGATATTCAAGTATAAGATGAATAAAATTGGAGATATTCCTGTTTTTTTGAACAACT
+TTCACCAATTCATTGAAAAATATGAATTCGATAATGTTTTTGATCAACAAATACAAAACA
+TCGATCCCCGTGAAAACGAAATCTTATGTAAGATTATCAAAGAAGGTTTTGATGAAAGTC
+CTGATATAATGAACATTAATACAGTTGACATCTTTAGAATCATTAGTGAATTAAAGAAAA
+AATACACTCGTTTTTTTGGCAGAGATAGAAGGTTAAAGGCTTGGGAAAAAGTGTTGGTGG
+ATACAACTTGTAAGAATACTGAATTATTGATAAATGAACTTCAAAAGTTAATATTAATGG
+AAAAATGGATTCTTTCAAAGTGTTGTCAAGATTGTCCAAATCTTACACACATTTTAGAAG
+AGGCTATTCTTGGAACCTTACATGAATCTGTGAGAAATCCGGTTAAACAACGTTTACACA
+TGTACTCAATTAGTGAAAATGAAAAAACTGAAGAAATTCTGATTAACATCGTAATTGAAA
+CAGTAATGGACTTGAGTCCACCTGACTCTCATTATACAGAAAGAAATTGTAAGTACTGTA
+AATCGGAATTACACAGCTCTGTGAACTGTAGAAAGAAAGTAAACAGAGAACTTAGGCCTA
+CTACATCCAGCTACTCAAAAGGTAATTATTCACAAGGCTCAAACCAAAAAGAATACACAA
+AGACTGGCACAAAACCATTCAGAACTTTTGAAAAGACAAAAGAAGAAGAACAAAAAGGGT
+TCAAACAAAACTCTAGTAATTATTGATACCGGTTCAGGCGTCAATATTACGAATAATAAG
+AATTTATTACACGAGTACGAGGACAACAAAGAAAAAGTAAAATTCTTCGGTATTGGGAAA
+GATAACTCAGTTCCTGTTAAAGGATCAGGATACATTAAAATAAAAAGTAACACAAATGAT
+GATTACTTATTAACTCATTATGTTCCTGAAGAAAAAACTACCATTATCAGTGGATATGAT
+TTAGCCAAAGAAACCGATCTCGTATTAAACCAAAACTACTCCACCTTGGAAAACAAGGAC
+ATGAACATTAAAACTCATGTAAAAGATGGAATTATTCACGTAAGAATGGATGACTTAATA
+GATCATCCTGCATATGATTATAAAATCAATGCGATACAACCTACTTCTTCTAAAAAAATT
+AGACTGAAGCCCAAAATTATAAGCTTAAAAGATGCTCATAAACGAATGGGACATACAGGA
+GTTCAACAAATTGAAAACTCTATTAAACATAGTCATTACGAAGAAAGTATTGATTTAATT
+AAAGAACCAAATGAATTTTGGTGTGAAACTTGTAAAGTTTCAAAAGCCACGAGAAGGAAC
+CATTATGCTGGATCCATGAATGAACACAGTATCGATCATGAACCTGGTTCATCGTGGTGC
+ATGGATATCTTTGGTCCAGTATCAAATTCGAACTTGGATACAAAAAGATACATGCTTATT
+ATGGTTGATAACAATACAAGATATTGTATCACCTCCACACATTTTAATAAAAATGCTGAA
+ACTATCTTGGCACAGATCAAGAAGAATATTCAGTATGTGGAAACTCAATTCGACAGAAAA
+GTCAGAGAAATCAATTCAGATCAAGGAACTGAATTTACAAATGATCAAATCGCAAAATAT
+TTTGTTTCAAAAGGAATTCATCATATATTTTCCGCTACACAAGATCATGCTGCCAACGGA
+AGAGCAGAAAGGTACATCAGAACCATCGTTACTGATGCAACAACTTTGTTAAAACATAGT
+AACTTACGTATTAAATTTTGGGAATACGCAGTAATATCTGCTACCAATGTACGCAATTGT
+TTAGAAAACAAAACCACAGGTCAACTACCGCTAAAGGCGATATCTAGTCAACCTGTTAAA
+GTGAGATTCATGTCCTTCTTACCATTTGGAGAACAAGGAATAATTTGGAATCATAATCAC
+AATAAACTAAAACCATCAGGACTTAGTGCTATAATATTATGCAAAGATCCTAATAGTCAC
+GGATACAAATTTTTTGTACCATCTATTAAAAAAATTGTCACTTCCGATAATTACACAATT
+CCAGACTATGCTGTGGATCCAATATTAAGGAACACACAGAACATATACCTAGATGATCAA
+AGCAGATCAGATACTTTCAATGAAGCAGAAAACATAGATGCTGTTTCAAGGTTGTATGAT
+TCACTGGAAGATTACGAAGATGATCATAAACAAGTTACACTACTTACAGACTTGTTCACC
+ACAGAAGAACTAGCCCAAATCGAAGCTAATTCTAAATATCCATCTCCTAGTGATAATCTA
+GAAGGTAATTTAGACTACGTTTTCTCTAACATAGAAGAATCTGACGAAGATGAATACGAT
+CATGTAACAAACATGGATGTAGATTCAGAACTTCAATCGAAAGAAAATATCACTACTGAA
+AGTGAAACAAACGAAATAAATAAACCAAGTAATACTGATGAGGATGTTTACGAAGAAAAT
+GTTTATAGAATTCCTACGGCAATACAAGAAAACCTTGTTGGAAGCCAGAAAACTATAAAC
+ATCAATAATGAGGATAATATTGCTAGCAGAATGCAAAAGAATATCAGTGGAAATGAAATA
+AACTACAAAGAATTATCAGATGACGACAGTGATTGTAGCCTTCATGATTCTACAAATGAC
+TCAGTTACGATTACAAGCAAAAAGGATAATTTAACAGATGATAAAGATTTACAATCACAG
+CAAGAATTATTCGAAAAAGTTAGTGATCCAGAAGTATTACCTGAACACATGAAAATTGAA
+AAAGATGTGGAGTCTCAAAATTCAGATAATGAAACCTCACAAGGCGTACAGTTTCAACCT
+GAATCAATTGTCACATCATCAAGTGACAATGATACTCAAAATGATGACTATTCAACTGAC
+AAAGAAAGTCATCACCTGCCCCTGGTTGTAAACGTTATGGACAATACTGACCAAACATAT
+GATAAACCAAACAAGGAAAAAAGTAAAAACAACTCTGATATAAGTATCTCACCGAAAGGT
+AATAATGAAGAGTTAGTACAATTGGTAGATAGTAACAAAGCCGAAAAACAGGATGCTACA
+CTAGAATCATCAGCGATAACAGATGAACCAATTGAAATAGAAAACCCAGCAGCAAACAAA
+GCTGGATTCTTAAATAAAGCGTTCAATTCTCTTAATAAGAAAAGGAAGAGACCTATTGAA
+AACAAGACTTCCTTTAATGACACAGCTAAAAGAGACAATAAACGTCAAAGAAAAAACATA
+ATCAAACTACTTCCGGATAACACAGAAACAAGTTCTGCACCGAGAATAAAAACCATCTAC
+TACAATGAAGCTATTTCAAGAAATGCTGATCTCAAAGAAAAACATGCTTATAAAGAGGCA
+TACAGGAAAGAATTACAAAATCTCAAGGATATGAATGTATTCGACGTAGATGTCAAATAC
+AACAGATCTGATGTTCCTAGTAATTTAATAATTCCGACAAATACAATATTCTCAAAGAAG
+AGAAATGGTATTTATAAAGCAAGAATTGTTTGTAGAGGTGATATCCAGACACCAGACACG
+TATAATGTTATTGGAACAGAATCACTGAACCATAATCACATTAAAATATTTCTGATGATT
+GCAAACAATAGAAACATGTTCATGAAAACATTAGATATTAATCATGCGTTCCTATATGCG
+AAATTAGAAGAAGACATATACATTCCACACCCACATGACAGGAGATGTGTTGTTAAACTA
+AATAAAGCACTATATGGGCTTAAGCAGAGTCCTAAAGAATGGAACGACCATCTTAGACGA
+TATTTAAACAGTATTGGATTAAAAGATAACACTTATACTCCAGGACTATACCAATCCAAG
+GATAAAAAACTCATGATCGCAGTTTATGTTGATGACTGTGTGATTGCAGCAAGTGATGAA
+CAAAGATTAGATGATTTCATAAACAATTTAGAAAATACCTTTGAGCTAAAAATCACCGGT
+ACTCTAATAGATGATATATTGGACACAGACATCTTAGGGATGGACTTGATCTATAACAAA
+AAACTTGGTACGGTGGATTTAACGTTAAAATCATTCATAGAAAAAATGGGTGAGAAGTAT
+AAAAAGGAATTGGATAAGGTTAGAAAAAGTTCAATTCCACATACATCAGTATACAAGATT
+GATCCCAAAAAGGGAGAATTAAAGATGACCGAAAAAGAATATAAAAACGGTGTGTTGAAA
+TTACAACAACTACTAGGAGAACTTAACTATGTTAGGTACAAGTGTAGATACGATGTTGAA
+TTTGCGGTCAAGAAAGTAGCTAGATTAGTAAACTTTCCTCATGAACAGGTATTTTACATG
+ATTTACAAAATCATACAATATTTAGTACAACATACGAATATCGGAATACACTATGATAGA
+GACCTCAACAAAGATAAGAAAATCACTACTATCACTGATGCATCAGTTGGAACAGAATAC
+GATGCGCAATCAAGAATTGGAGTTATAATTTGGTATGGAAAGAACATTTTCAATGTATAC
+TCAAATAAAAGCACCAACAAGTGCGTATCCTCAACCGAAGCGGAACTTCATGCTATCTAT
+GAAGGTTATGCAGACTCAGAAACCCTGAAAGCAACCTTAACAGAACTCGGAGAAGGTAAA
+GATAAAGAAATTACAATGATTACGGATTCAAAACCAGCTATTGAAGGCTTAAATCGTAGT
+TACCTACAACCGAAACAGAAGTTCACATGGATAAAAACCGAAATAATTAAAGAGAAGCTA
+AAAGAGAAGATTATAAAACTAATAAAAATCAATGGTAAAGACAATATAGCAGATTTACTC
+ACAAAACCAGTATCAATTTCTGACTTTGATAGATTTATTAAAGTATTGAATAATCAGATA
+ACACCACAGGATATTTTGGCCTCAACGGACTATTGATAATTACATTACTTAATTAAGAAC
+CAAACGCACAACAGATATCTGTTGGAGTACAATAATATATCTTTAAGGGGGC
+>TSU4b-LTR#LTR/Copia
+TGTTGGAATAAAGTGATCTTGGACATAACATTCTTATGTCAAAACAGGCGATCTCAACAT
+TCCTAATATGATATTAATTATGTTGTTCTGAAACAAACATACTTAATGAAGACGAGTTTA
+AAGACCTATTAATTGATCAAGAATTAGTATATAAGAAGATGATTTATACCTGAGAACCTA
+TTATCAATGTTCTGAATTATACTTGAACCATTGGGTTTCATATAACCAATCAGCGTGCGT
+TTTATATACCTCTCTTATATAATAAGAAAGAACTGCTTATTCTTAATTATTACTACCTAC
+TAAACTTACTAATTATCAACA
+>TSU4p-I#LTR/Copia
+TGGCGACCCCAGTGAGGGATGACACAAGATATGTTACTGACTACAACATTTCTAACCTGG
+TTCAATCAAAAGTCAAACTCCAAAAATCAAGTATTGATATTTCCGTTAAAAACAAACTAA
+GGAATCAAACTCAAATCGATTTGAAAACGTATGAAAGATTCTTACACAGATTAACCACTA
+AAAAGAATAAAATTACAAATGAGGCTGAAGAGGATGACGATATTTCAAATCTCGACCTTT
+TAATTGAAGTAGATGAAAAAATCGAAAAAACTAATAATATAATTCTTAGGTTACAAGAAA
+AGTTAGAATCGATTGAATTAGATAAAGATGCTAAGAAGTTACACGAAAGAAATGATTCCA
+CTGGAACATATTACTTATTCGATACTCTTACCTTAAAAAACAGGAAATATTATCCTAAGG
+ATTGGATTTTCAAGCATAAAATGAATAAAATTGGAGATATTCCTGTGTTTTTGAACAGCT
+TTCAACAATTCATTGAAAAGCATGAATTCGATAATATTTTTGAACAACAAATACAAAACA
+TCGATCCTCGTGAAAACGAAATCTTGTGTAAGATTATCAAAGAAGGTTTCGATGAAAGTC
+CTGATATAATGAACATTAACACAGTTGACATCTTTAGAATCATTCGTGATTTAAAGAAAA
+AATACACAAGCCTTTTTGGCAGAGATGTAAGACTAAAGGCTTGGGAAAAAGTGTTGGTGG
+ATACAACTTGTAAGAATACTGACTTATTGATGAATGAACTTCAAAAGTTAGTATTAATGG
+AAAAATGGATCCTTTCAAAATGTTGTCAAGACTGTCCAAATCTCACACACATTTTAGTAG
+AAGCAATTCTTGGAACCTTACATGAATCGTTGAGAAATCCGGTTAAGCAACGTTTACACA
+TCTGCTCAATTGATGAAAATGAGAGAGTCGAAGAAGTTCTAATCAATATCGTAATTGAAA
+CAGTAATGGACTTGAGTACAACAGATTTGTATTATCCAGAAAGAAATTGCAAGTACTGTA
+AATCGGAATTCCACAGCTCGGTAAATTGTAGAAAGAAACTAACCAGAGAACTTAGGCCTA
+CCACGCCCAGTTACTCAAAAGGTTATTATTCGCAAGGTTCAACCCAAAAAGAATACACTA
+AAACTGGCACAAACCCAGACAGAGCCGTTAAAAAGGCTAAAGAAGAAGAACAGAAAGGGT
+TCAAACAGAAACCTAGTCATTATTGATACTGGGTCAGGCGTCAACATTACGAATAACAAG
+AGATTATTACATGAGTATGAAGACAACAAAGAAAAGATAAGATTCTTTGGTATTGGAAAA
+AACAATTCAGTTCCCGTTAAAGGATCAGGATACATTAAAATAAAAAGTAACACAAATGAT
+GATTACTTATTAACTCATTATGTTCCTGAGGAGGAAACTACCATTATCAGTGGCTATGAG
+TTAGCTAAAGAAACCGATCTTGTCTTGAACAAAAACTACTCCACGTTGGAAAACAAGGAC
+ATGAACATTAAGACTCATGTAAAAGATGGGATTATTCATGTAAAAATGGACGATTTAATT
+GATCATCCTGCATATGATTTTAAAATCAATGCAATACAACCTACTTCTTCTAAAAAAATT
+AGACTGAAGCCAAAAATTATAAGCTTAAAAGATGCTCATAAACGAATGGGACATACAGGA
+GTTCAACAAATTGAAAACTCCATTAAACATAGCCATTACGAAGAAAGTATTGACTTAATT
+AAAGAACCAAATGAATTTTGGTGCGAAACTTGTAAAGTTTCAAAAACCACGAGAAGGAAC
+CATTATGCTGGATCTATGAACGAACACAGTATCGGTCATGAACCTGGTTCATCGTGGTGC
+ATGGATATCTTTGGTCCAGTATCGAACTCGAACTCGGATACGAAAAGATACATGTTTATT
+ATGGTTGATAACAATACAAGATATTGTATCACCTCCACACATTTTAACAAAAATGCTGAA
+ACTATCTTAGCACAGATCAAGAAGAATATTCAGTATGTGGAAACTCAATTTGACAGAAAA
+GTCAGAAAAATCAATTCAGATCAAGGAACTGAATTCACAAATGATCAGATAGCAGAATAT
+TTTGTTTCAAAAGGAATTCATCATATTTTTTCCGCTACACAAGATCATGCTGCCAATGGA
+AGAGCAGAAAGACACATCAGAACCATCGTTACTGATGCAACAACCTTGTTAAAACATAGT
+AACTTGCGTATTAAATTTTGGGAGTATGCAGTAACATCTGCCACCAATGTACGCAATTGT
+TTAGAAAACAAAGCCACAGGTCAACTGCCGCTAAAGGCGATCTCTAGTCAACCTGTTAAA
+GTGAGATTCATGTCCTTCTTACCATTCGGAGAACAAGGAATAATTTGGAATCATAATCAC
+AACAAACTAAGACCTTCAGGACTTCGTGCTATTATATTATGCAAAGACCCTAATAGTCAC
+GGATACAAATTTTTTGTACCATCTCTTAAAAAAATTGTCACTTCTGATAATTACACAATT
+CCAGACTATGCAGTGGACCCAATATTAAGGAACACCCAGAACATATACCTAGATGATCGA
+AGTAGATCAGATACCTTCAATAAGACAGAAAACTCAGATGCAGTTTCAAGGTTATATGAT
+GCATTGGAAAATTACGAAGATGATCATAAACAAGTTACACTATTTACAGACTTGTTTACC
+ACAGAAGAATTAGCTCAAATCGAAACTAATGCTAAATATCCGTCTCCTAGTGATAATCTA
+GAAGGAAATTTAGACTACGTCTTCTCCAACACAGAAGAATCTGAAGAAGATGAATCTGAT
+CATGTGACAAACATGGATGTAGATTCAGAACTTAAACCAAATGAAAAGATCACTACAGAA
+AGTGAACGAAACGAATTAAATAAATCAAGTAATACTGATGAGGATTTTTACGATGAAAAA
+GCTTATAGAATTCCCACGGCAATACAAGAAAACCTTGTTGGAAGCCAGAAGACTATAAAC
+ATTAATAATGAGGATAATATTGCTAGCAGAATGCAAAGGAAGATTAGTGGAAATGAAATA
+AACTACAATGAATTGTCGGATGACGAGAGCGATTACAGATCTCATGACCTCACAGATGAT
+AATATCTCGAAATCCCAGCAAGAAATATTCAAGAAAACTATCGATTCAGAAGTACTACCT
+GAACAGATAAACATTGAAAAACATGTTACATTGCAAGATTCGGATAATGATACGTCACAA
+TGCGTAGAGGCTCAGCCTGAGTCAATTGTCACATCATCGAAAGAAGATGATGTTCAAAAT
+GATGACTATTCTTCTGACAAAGAAAGTCATCACCTGCCCCTGGGTGTAAATGTTATGGAC
+AATTCGATCCAAACATGTGTTGAACCAAACAAGGCAGAAAGCAAACACAACTCTGATACA
+ATTGCCTCACCGAAAGGTAATAATGAAGAGTTAGTACAATTGGTAGGAAGTAGCGGAGCA
+GAAAAACCGGATGCTACACCAGAATCATCAATGACAACAGATGAACCAATTGACCCAGGA
+AACCCAGCAGTAAACAAAGCTGGATTCCTAAACAAAACGTTCAATTCTCTCAATAAGAAA
+AGAAAGAGACCTGTTGAAAACAAGACTCCCTTCAATGACACAGTTGAAAGAGATTATAAA
+CGTCAAAGAAAAAAAATAATCAAACTACTTCCGGATAACACAGAAACAAGTTCTGCACCG
+AGAATCAAAACCATCTACTATAATGAAGCTATTTCAAGAAATGTTGATTTCAAAGAAAAA
+CATGCTTATAAAGAAGCATACAGGAAGGAATTACAAAATCTCAAGGACATGAAGGTATTC
+GACGTTGATGTCAAATACAACAGATCTGATGTTCCCAGTAATTTAATAATCCCGACGAAT
+ACAATATTCTCAAAGAAGAGAAATGGCATTTATAAAGCAAGAATTGTTTGTAGAGGTGAT
+ATCCAGACACCGGACACGTATAATGTTATTGGAACAGAATCCCTGAACCATAACCACATT
+AAAATATTTCTGATGATTGCAAACAATAGGAATATGTTCATGAAAACATTGGATATTAAC
+CATGCGTTCCTATATGCTAAATTAGAAGAAGACATATACATTCCACACCCACATGACAGG
+AGATGCGTTGTTAAACTAGACAAAGCGTTATATGGTCTCAAGCAGAGTCCTAAAGAATGG
+AACGACCATCTTAGACGATATTTAAATAGTGTTGGACTAAAAGATAACACATATACTCCA
+GGACTATACCAATCCAAGGATAAAAAACTCATGATCGCAGTTTATGTTGATGACTGTGTG
+ATTGCAGCAAGTGATGAACAAAGATTAGATGATTTCATAAGCAATTTAGAAAACACCTTT
+GAGCTAAAAATTACTGGTACTCTAATAGATGATATATTGGATACAGACATCTTGGGGATG
+GATTTGATCTATAACAAGAAACGTGGCACGGTGGATTTAACGTTAAAATCATTCATAGAA
+AAAATGGGTGAGAAGTATAAAAAGGAATTGGATAAGGTTAGAAAAAGTTCAATTCCACAT
+ACATCAATATACAGGATTGATCCCAAAAAGGGAGAACTAAAAATGACCGAAAAAGAATAT
+AAAGACGGTGTGTTGAAATTACAACAACTACTAGGAGAACTTAATTATTTTAGGTACAAG
+TGTAGATACGATGTTGAATTTGCGGTTAAGAAAGTAGCTAGATTAGTTAACTTCCCTCAT
+GAACAGGTATTCTACATGATTTACAAAATCATACAATATCTAGTACAACATGCGAATATT
+GGAATACACTATGATAGAGACCTTAACAAAGATAAGCAAATCACTACTATTACAGATGCA
+TCAGTTGGAACAGAATACGATGCACAATCAAGAATTGGAGTTATAATTTGGTATGGAAAG
+AACATTTTCAATGTATACTCAAATAAAAGCACCAACAAGTGTGTATCCTCAACCGAAGCG
+GAACTTCATGCTATCTATGAAGGTTATGCAGACTCAGAAACCCTGAAAGCAACCTTAACA
+GAACTTGGAGAAGGAAAAAATAAAGAACTTACAATGATTACTGATTCAAAACCAGCTATC
+GAAGGCTTAAAACGGAGCTACCTACAACCCAAACAGAAGTTCACATGGATAAAAACCGAA
+ATAATTAAAGAGAAACTAAAAGAGAAGACTATAAAACTAATAAAAATCAATGGTAAAGAA
+AATATAGCAGATTTACTTACAAAACCAGTATCAATTTCTGACTTTGATAGATTTATTAAG
+GTATTGAAGAATAAGATAACACCACAGGATATTTTGGCCTCAACGGACTATTGATAATTA
+AATTACTTAATTAAGAACCGAACACACAGCAGATATCTGTTGGAGTACAATAATATATCT
+TTAAGGGGGCA
+>TSU4p-LTR#LTR/Copia
+TGTTGGAATATGTGACTTCGGACATTCCTTAGCGTGAGTCAAAAGTTAATGAAGAGGGCA
+AATTCTAATTATAGAATTTTCCGGACAATAAAGATCTATTAATTGATCAGAACTCAGTAT
+ATAAGAGAATGAGTTACACCTGTTAACTTATTATTAATGTTCTGAGTTATGTCTAAACCA
+TTGGGTTTCATATAACCAATCAGCGTGTGTTTTTATACCTCTCTTATATAATAATAAGAA
+AGAACTGCTTATTCTTAATTATTACAACTTACTAAACCAACTAATTATCAACA
diff --git a/data/TE_lib.v20221221.LTRonly.tidy.fa b/data/TE_lib.v20221221.LTRonly.tidy.fa
new file mode 100644
index 0000000..900797b
--- /dev/null
+++ b/data/TE_lib.v20221221.LTRonly.tidy.fa
@@ -0,0 +1,70 @@
+>TY1/TY2-LTR#LTR/Copia/TY1
+TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAATATATTATC
+ATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAG
+CTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT
+GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATAT
+CCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAACAATG
+GAATCCCAACAATTATCTCAACATTCACATATTTCTCA
+>TY1/TY2-LTR#LTR/Copia/TY1p
+TGTTGGAATGAAATTCTAATATCATCTATTTAATAGTATATTATAATATGCGGTGCAAGA
+GGATGACATAAAGATTGAGAAACAGTCATCCAATCTAATGGAAGCTGAAATGCAAGGATT
+GATAATGTAATAGGATAATGAATAACAACATATAAAAAGAAAGAAGATAAAATAATAACA
+CTATGTAGAACTATCGATTCCCTTTTGTGGATTCCTATATCCTCGAGGAGAACTTCTAGT
+ATATTCTATATACCTAATATTATAGCCTTTAGTAACAATGGAATCCCAACAATTATCTAA
+TTACCCACACAATTCTCA
+>TY1/TY2-LTR#LTR/Copia/TY2
+TGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATC
+ATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGC
+TGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAATGATGAT
+AATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATGGATTCCTAAATCCTC
+GAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAAATGGAATCC
+CAACAATTACATCAAAATCCACATTCTCTTCA
+>TY3-LTR#LTR/Gypsy/TY3
+TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCACCCTGAACGTTCATAAA
+ACACATATGAAACAACCTTATAACAAAACGAACAACATGAGACAAAACCCGACCTTCCCT
+AGCTGAACTACCCAAAGTATAAATGCCTGAACAATTAGTTTAGATCCGAGATTCCGCGCT
+TCCACCACTTAGTATGATTCATATTTTATATAATATATAAGATAAGTAACATTCCGTGAA
+TTAATCTGATAAACTGTTTTGACAACTGGTTACTTCCCTAAGACTGTTTATATTAGGATT
+GTCAAGACACTCCGGTATTACTCGAGCCCGTAATACAACA
+>TY3-LTR#LTR/Gypsy/TY3p
+TGTTGTATCTCAAGATGAGATACCTCAGCATTACTAGATTTACCAACCTAGACATAAAAC
+ATGTATGAAACACGTACGAAACAATAGACAAGATTGAGTATACTAGGCAACCTACTTGCC
+TAAGATGAACCAAACTAACCAAACGTATAAATACCTGAACAATTAGTTTAGATCCGAGAT
+TCCGCGCTTCCACCCTTTAGTTAGATTCAGATCTTATATAGATTATATAGGATAAGTAAC
+ATTCTGTGAATCACGATAATAATAAGTCTGACAACAAGTTACTCTCCTAAACGACTTTAG
+GATTGTCAAGACATCCGGTATTACTCGAGCCCGTAATACAACA
+>TY4-LTR#LTR/Copia/TY4
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATGGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACAACTCGTATACGTTTAAGTGTGATTGCGCCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGTGTTAAAGACCTATTAGTTGAACAT
+GTTATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTCACTTCTTCATTAATACTAATTTTTAACCTCT
+AATTATCAACA
+>TY4-LTR#LTR/Copia/TY4p
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATAGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACACCTCGTATACGTTTAAGTGTGATTGCACCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGAGTTAAAAATCTATTAGTTGAACAT
+GATATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTTATTTCTTCATTAGTACTATATTTTAACCTCT
+AATTATCAACA
+>TY5-LTR#LTR/Copia/TY5
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTACATA
+ACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCA
+CTACGTCAACA
+>TY5-LTR#LTR/Copia/TY5p
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTTACAT
+AACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTC
+ACTACGTCAACA
+>TSU4-LTR#LTR/Copia/TSU4b
+TGTTGGAATAAAGTGATCTTGGACATAACATTCTTATGTCAAAACAGGCGATCTCAACAT
+TCCTAATATGATATTAATTATGTTGTTCTGAAACAAACATACTTAATGAAGACGAGTTTA
+AAGACCTATTAATTGATCAAGAATTAGTATATAAGAAGATGATTTATACCTGAGAACCTA
+TTATCAATGTTCTGAATTATACTTGAACCATTGGGTTTCATATAACCAATCAGCGTGCGT
+TTTATATACCTCTCTTATATAATAAGAAAGAACTGCTTATTCTTAATTATTACTACCTAC
+TAAACTTACTAATTATCAACA
diff --git a/data/TE_lib.v20221221.tidy.fa b/data/TE_lib.v20221221.tidy.fa
new file mode 100644
index 0000000..a66764e
--- /dev/null
+++ b/data/TE_lib.v20221221.tidy.fa
@@ -0,0 +1,1033 @@
+>TY1-I#LTR/Copia
+TGGTAGCGCCTGTGCTTCGGTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGA
+CGTTTCAGCTTCCAAAACAGAAGAATGTGAGAAGGCTTCCACTAAGGCTAACTCTCAACA
+GACAACAACACCTGCTTCATCAGCTGTTCCAGAGAACCCCCATCATGCCTCTCCTCAAAC
+TGCTCAGTCACATTCACCACAGAATGGGCCGTACCCACAGCAGTGCATGATGACCCAAAA
+CCAAGCCAATCCATCTGGTTGGTCATTTTACGGACACCCATCTATGATTCCGTATACACC
+TTATCAAATGTCGCCTATGTACTTTCCACCTGGGCCACAATCACAGTTTCCGCAGTATCC
+ATCATCAGTTGGAACGCCTCTGAGCACTCCATCACCTGAGTCAGGTAATACATTTACTGA
+TTCATCCTCAGCGGACTCTGATATGACATCCACTAAAAAATATGTCAGACCACCACCAAT
+GTTAACCTCACCTAATGACTTTCCAAATTGGGTTAAAACATACATCAAATTTTTACAAAA
+CTCGAATCTCGGTGGTATTATTCCGACAGTAAACGGAAAACCCGTACGTCAGATCACTGA
+TGATGAACTCACCTTCTTGTATAACACTTTTCAAATATTTGCTCCCTCTCAATTCCTACC
+TACCTGGGTCAAAGACATCCTATCCGTTGATTATACGGATATCATGAAAATTCTTTCCAA
+AAGTATTGAAAAAATGCAATCTGATACCCAAGAGGCAAACGACATTGTGACCCTGGCAAA
+TTTGCAATATAATGGCAGTACACCTGCAGATGCATTTGAAACAAAAGTCACAAACATTAT
+CGACAGACTGAACAATAATGGCATTCATATCAATAACAAGGTCGCATGCCAATTAATTAT
+GAGAGGTCTATCTGGCGAATATAAATTTTTACGCTACACACGTCATCGACATCTAAATAT
+GACAGTCGCTGAACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAG
+AAACAGCAAACCTAATTACAGGAGAAATCTGAGTGATGAGAAGAATGATTCTCGCAGCTA
+TACGAATACAACCAAACCCAAAGTTATAGCTCGGAATCCTCAAAAAACAAATAATTCGAA
+ATCGAAAACAGCCAGGGCTCACAATGTATCCACATCTAATAACTCTCCCAGCACGGACAA
+CGATTCCATCAGTAAATCAACTACTGAACCGATTCAATTGAACAATAAGCACGACCTTCA
+CCTAGGCCAGGAACTTACTGAATCTACGGTAAATCACACTAATCATTCTGATGATGAACT
+CCCTGGACACCTCCTTCTCGATTCAGGAGCATCACGAACCCTTATAAGATCTGCTCATCA
+CATACACTCAGCATCATCTAATCCTGACATAAACGTAGTTGATGCTCAAAAAAGAAATAT
+ACCAATTAACGCTATTGGTGACCTACAATTTCACTTCCAGGACAACACCAAAACATCAAT
+AAAGGTATTGCACACTCCTAACATAGCCTATGACTTACTCAGTTTGAATGAATTGGCTGC
+AGTAGATATCACAGCATGCTTTACCAAAAACGTCTTAGAACGATCTGACGGCACTGTACT
+TGCACCTATCGTACAATATGGAGACTTTTACTGGGTATCTAAAAGGTACTTGCTTCCATC
+AAATATCTCCGTACCCACCATCAATAATGTCCATACAAGTGAAAGTACACGCAAATATCC
+TTATCCTTTCATTCATCGAATGCTTGCGCATGCCAATGCACAGACAATTCGATACTCACT
+TAAAAATAACACCATCACGTATTTTAACGAATCAGATGTCGACTGGTCTAGTGCTATTGA
+CTATCAATGTCCTGATTGTTTAATCGGCAAAAGCACCAAACACAGACATATCAAAGGTTC
+ACGACTAAAATACCAAAATTCATACGAACCCTTTCAATACCTACATACTGACATATTTGG
+TCCAGTTCACAACCTACCAAAAAGTGCACCATCCTATTTCATCTCATTTACTGATGAGAC
+AACAAAATTCCGTTGGGTTTATCCATTGCACGACCGTCGCGAGGACTCTATCCTCGATGT
+ATTTACCACGATACTAGCTTTCATTAAAAACCAATTTCAGGCCAGTGTCTTGGTTATACA
+AATGGACCGTGGTTCTGAGTATACTAACAGAACTCTCCATAAATTCCTTGAAAAAAATGG
+TATAACTCCATGCTATACAACCACAGCGGATTCCCGAGCACATGGAGTCGCTGAACGGCT
+AAACCGTACCTTATTAGATGACTGCCGTACTCAACTGCAATGTAGTGGTTTACCGAACCA
+TTTATGGTTCTCTGCAATCGAATTTTCTACTATTGTGAGAAATTCACTAGCTTCACCTAA
+AAGCAAAAAATCTGCAAGACAACATGCTGGCTTGGCAGGACTTGATATCAGTACTTTGTT
+ACCTTTCGGTCAACCTGTTATCGTCAATGATCACAACCCTAACTCCAAAATACATCCTCG
+TGGCATCCCAGGCTACGCTCTACATCCGTCTCGAAACTCTTATGGATATATCATCTATCT
+TCCATCCTTAAAGAAGACAGTAGATACAACTAACTATGTTATTCTTCAGGGCAAGGAATC
+CAGATTAGATCAATTCAATTACGACGCACTCACTTTCGATGAAGACTTAAACCGTTTAAC
+TGCTTCATATCATTCGTTCATTGCGTCAAATGAGATCCAAGAATCCAATGATCTTAACAT
+AGAATCTGACCATGACTTCCAATCCGACATTGAACTACATCCTGAGCAACCGAGAAATGT
+CCTTTCAAAAGCTGTGAGTCCAACCGATTCCACACCTCCGTCAACTCATACTGAAGATTC
+GAAACGTGTTTCTAAAACCAATATTCGCGCACCCAGAGAAGTTGACCCCAACATATCTGA
+ATCTAATATTCTTCCATCAAAGAAGAGATCTAGCACCCCCCAAATTTCCAATATCGAGAG
+TACCGGTTCGGGTGGTATGCATAAATTAAATGTTCCTTTACTTGCTCCCATGTCCCAATC
+TAACACACATGAGTCGTCGCACGCCAGTAAATCTAAAGATTTCAGACACTCAGACTCGTA
+CAGTGAAAATGAGACTAATCATACAAACGTACCAATATCCAGTACGGGTGGTACCAACAA
+CAAAACTGTTCCGCAGATAAGTGACCAAGAGACTGAGAAAAGGATTATACACCGTTCACC
+TTCAATCGATGCTTCTCCACCGGAAAATAATTCATCGCACAATATTGTTCCTATCAAAAC
+GCCAACTACTGTTTCTGAACAGAATACCGAGGAATCTATCATCGCTGATCTCCCACTCCC
+TGATCTACCTCCAGAATCTCCTACCGAATTCCCTGACCCATTTAAAGAACTCCCACCGAT
+CAATTCTCGTCAAACTAATTCCAGTTTGGGTGGTATTGGTGACTCTAATGCCTATACTAC
+TATCAACAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTAAGGTATCACGAGA
+CACATGGAATACTAAGAATATGCGTAGTTTAGAACCTCCGAGATCGAAGAAACGAATTCA
+CCTGATTGCAGCTGTAAAAGCAGTAAAATCAATCAAACCAATACGGACAACCTTACGATA
+CGATGAGGCAATCACCTATAATAAAGATATTAAAGAAAAAGAAAAATATATCGAGGCATA
+CCACAAAGAAGTCAATCAACTGTTGAAGATGAAAACTTGGGACACTGACGAATATTATGA
+CAGAAAAGAAATAGACCCTAAAAGAGTAATAAACTCAATGTTTATCTTCAACAAGAAACG
+TGACGGTACTCATAAAGCTAGATTTGTTGCAAGAGGTGATATTCAGCATCCTGACACTTA
+CGACTCAGGCATGCAATCCAATACCGTACATCACTATGCATTAATGACATCCCTGTCACT
+TGCATTAGACAATAACTACTATATTACACAATTAGACATATCTTCGGCATATTTGTATGC
+AGACATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGAATGAATGATAAGTT
+GATACGTTTGAAGAAATCACTTTATGGATTGAAACAAAGTGGAGCGAACTGGTACGAAAC
+TATCAAATCATACCTGATACAACAATGTGGTATGGAAGAAGTTCGTGGATGGTCATGCGT
+ATTTAAAAACAGTCAAGTGACAATTTGTTTATTCGTAGATGATATGGTATTGTTTAGCAA
+AAATCTAAATTCAAACAAAAGAATTATAGACAAGCTTAAGATGCAATACGACACCAAGAT
+TATAAATCTAGGCGAAAGTGATGAGGAAATTCAATATGACATTCTTGGCTTGGAAATCAA
+ATACCAAAGAGGTAAATACATGAAATTGGGTATGGAAAACTCATTAACTGAAAAAATACC
+CAAACTAAACGTACCTTTGAACCCAAAAGGAAGGAAACTTAGCGCTCCAGGTCAACCAGG
+TCTATATATAGACCAGCAAGAACTAGAGCTAGAAGAAGATGATTACAAAATGAAGGTACA
+TGAAATGCAAAAGCTGATAGGTCTAGCATCATATGTTGGATATAAATTTAGATTTGACCT
+ATTATACTACATCAACACACTTGCACAACATATACTATTTCCGTCCAAGCAAGTGTTAGA
+TATGACATATGAATTGATACAGTTCATATGGAATACGAGAGATAAGCAATTAATATGGCA
+CAAAAGCAAACCTGTTAAGCCAACAAATAAATTAGTTGTTATAAGCGATGCCTCGTATGG
+CAACCAACCGTATTATAAATCACAAATTGGCAACATATATTTACTTAATGGAAAGGTAAT
+TGGAGGAAAGTCCACCAAGGCTTCATTAACATGTACTTCAACTACGGAAGCAGAAATACA
+CGCGATAAGTGAATCTGTCCCATTATTAAATAATCTAAGTTACCTGATACAAGAACTTGA
+CAAGAAACCAATTACCAAAGGATTACTAACCGACAGTAAATCTACAATCAGTATAATTAT
+ATCCAATAATGAAGAGAAATTTAGGAACAGATTTTTTGGTACTAAAGCAATGAGATTGAG
+AGATGAAGTATCAGGAAATCATCTGCACGTATGCTATATCGAAACCAAAAAGAATATTGC
+AGACGTAATGACCAAACCTCTTCCGATAAAAACATTCAAACTATTAACAAACAAATGGAT
+TCATTAGATCTATTACATTATGGGTGGTA
+>TY1-LTR#LTR/Copia
+TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAATATATTATC
+ATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAG
+CTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAAT
+GAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATAT
+CCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAACAATG
+GAATCCCAACAATTATCTCAACATTCACATATTTCTCA
+>TY1p-I#LTR/Copia
+TGGTAGCGCCTGTGCTTCGGTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGA
+CGTTTCAGCTTCCAAAATTCAAGAATATGATAAGGCTTCCACTAAGGCTAACTCTCAACA
+GACAACAACACCTGCTTCATCAGCTGTTCCAGAGAACCCCCATCATGCCTCTCCTCAAAC
+TGCTCAGTCACATTCACCACAGAATGGGCCGTACCCACAGCAGTGCATGATGACCCAAAA
+CCAAGCCAATCCATCTGGTTGGTCATTTTACGGACACCCATCTATGATTCCGTATACACC
+TTATCAAATGTCGCCTATGTACTTTCCACCTGGGCCACAATCACAGTTTCCGCAGTATCC
+ACCATCAGTTGGAACGCCTCTGAGCACCCCATCACCTGAGTCAGGTAATACATTTACTGA
+TTCATCCTCAGCGGACTCTGATATGACATCCACTAAAAAATATGTCAGACCACCACCAAT
+GTTAACCTCACCTAATGACTTTCTAAATTGGGTTAAAACATACATCAAATTTTTACAAAA
+CTCGAATCTCGGTGATATTATTCCGACAGTATACGGAAAACCCGTACGTCAGATCACTGA
+TGATGAACTCACCTTCTTGTATAACACTTTTCAAATATTTGCTCCCTCTCAATTCCTACC
+TACCTGGGTCAAAGACATCCTATCTGTTGATTATACGGATATCATGAAAATTCTTTCCAA
+AAGTATTGAAAAAACGCAATCTGATACCCAAGAGGCAAATGACATTGTGACCCTGGCAAA
+TTTGCAATATAATGGCAGTACACCTGCAGATGCATTTGAAACAAAAGTCACAAACATTAT
+CGACAGACTAAATAATAATGGCATTCATATCAATAACAAGGTCGCATGCCAATTAATTAT
+GAGAGGTCTATCTGGCGAATATAAATTTTTACGCTACACACGTCATCGACATCTAAATAT
+GACAGTCGCTGAACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAG
+AAACAGTAAACCCAATTACAGGAGAAATCCGAGTGATGAGAAGAATGATTCTCGCAGCTA
+TACGAATACAACCAAACCCAAAGTTATAGCTCGGAATCCTCAAAAAACAAATAATTCGAA
+ATCGAAAACAGCCAGGGCTCATAATGTATCCACATCTAATAACTCTCCCAGCACTGACAA
+CGATTCCATCAGTAAATCAACTACTGAACCGATTCAATTGAACAATAAGCACGACCTTCA
+TCTTAGGCCAGAAACTTACTGAATCTACAGTAAATCATACGAATCATTCCGATGATGAAC
+TTCCTGGACACCTTCTTCTTGATTCAGGAGCATCACGAACTCTTATAAGATCTGCCCATC
+ACATACACTCAGCGATATCTAATCCCGACATAAGCGTAGTTGATGTTCAAAAAAACAATA
+TACCAATTAACGCTGTTGGTGATCTTCAATTTCACTTCCAGGACGACACCAAAACAACAA
+TAAAGGTATTGCACACACCTAACATAGCCTATGACTTACTCAGTTTGAATGAACTGGCTG
+CACTAAATATTACAGCGTGCTTTACCAAAAACGTCTTAGAACGACCTGACGGCACCGTAC
+TTGCACCTATCGTAAAACATGGAGACTTTTACTGGGTGTCTAAAAGGTACTTGCTTCCGT
+CGAATATCTCAGTACCCACAATTAATAACGTTCACACAAGTGAAAACACACGTAAGTATC
+CTTATCCTTTCATTCATCGGATGCTTGCGCATGCCAATGCCCAGACAATTAGATATTCAC
+TTAAAAAGAACACTATTACGTATTTCAATGAATCAGATGTTGACTGGTCTAACGCTACTG
+ATTATCAATGTCCCGATTGTTTAATCGGCAAAAGCACCAAACATAGACATATCATAGGAT
+CACGGCTAAAATACCAAAGTTCATATGAACCTTTTCAATACTTACATACTGACATATTTG
+GGCCTGTTCACAACCTACCAAAGAGTGCACCATCCTATTTCATCTCATTCACTGATGAGA
+AAACAAAATTCCGTTGGGTTTATCCATTACACGACCGTCGCGAGGACTCTATTCTCGATA
+TCTTTACTAAGATACTAGCTTTCATTAAAAACCAGTTTCAGTCCAATGTTTTGGTTATTC
+AAATGGACCGTGGTTCTGAGTACACTAACAAAACTCTCCATAAATTCCTTGAAAAATATG
+GCATAACCCCATGTTATACAACCACAGCGGATTCCCGAGCACATGGTGTCGCTGAACGGC
+TGAACCGTACCTTATTAGATGACTGTCGTACTCAACTGCAATGTAGTGGTCTACCGAATC
+ATCTATGGTTCTCGGCAGTCGAATTTTCTACTATCGTACGGAACTCACTAGCTTCACCTA
+AAAGCAAAAAATCCGCAAGACAACTCGCTGGGTTGGCAGGACTCGACATCAGTACTTTAT
+TACCTTTCGGTCAACCCGTTATAGTCAATAATCATAACCCTGACTCCAAAATTCATCCTC
+GTGGCATTCCTGGCTACGCTCTACATCCATCTCGAAACTCTTATGGATATATCATCTATG
+TCCCGTCTTTGAAGAAGACAGTAGATACAACTAATTACGTTATTCTTCAGGGCAAGGAAT
+CCAGATTAGACCAATTCAATTACGACGCACTCACCTTCGATGAAGACGTGAATCGTATAA
+CTGCTTCATATCAATCGTTCATTGCTTCAAATGAGATCCAACAATCTAACGATCTTAACA
+TAGAATCTGACCATGATTTTCAATCTGACGTAGAACTGAACCCTGACCACCAGAGAAATG
+TCCCTTCAAACGTTCCGATTCCAACTGACTCTCCACCTCCATCAACTCATACTGAAGATT
+CAAAACCTATATCTGAAATCAATCTTCGTGCACCCAAAGAAGTTGATCCTAACATATCTG
+AATCTAATATTCTTCCATCTAAGAAGAGATCTAACATCCCCCAAATTTCTGCTACCGACA
+GTGCCGGTTCGGGTGGTATAAATAAATCAGATGTTCCTTTACTTACTCCTTTGTCCAAAT
+CTGACACACAAAATTCATACCAAGCCAGTGAATCTGATGATTTCAGTGACTCAGACTCAC
+ACAGCGACATCGATACTGACTCTACAAACGTGACAATACCCAGTTTGGGTGGTATCAACA
+ACAAAACTGTTCCGCAGACAAGTGACCAAGAGACTGAGAAAAGGATTATACATCGTTCAC
+CTTCAATCGATGCTTCTCCACCGGAAAATAATTCATCGCACAATATTGTTCCTATCAAAA
+CGCCAACTAATGTTTCTGAACAGAATACCGAGGAATCTATTATCGCTGATCTCCCACTCC
+CTGATCTATCTCCAGAATCTCCTACCGAATTCCCTGACCCATTTAAAGAACTCCCACCGA
+TAAATTCTCATCAAACTAATTCCAGTTTGGGTGGTATGGATGACTCTAATATCTCTGCTA
+CTATCACTAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTGAGGTATCACGAG
+ACACATGGAATAGTAAGAATATGCGTAGCTTAGAACCTCCAAGGTCAAAGAAACGAATAC
+ATCTAATCGCGGCTGTAAAAGCAGTAAAATCAATCAAACCAATACGAACAACCTTAAGAT
+ACGATGAGGCAATCACCTATAATAAAGATATTAAAGAAAAGGAAAAATATATCGAAGCAT
+ACCACAAAGAAGTCAACCAACTGTTGAAAATGAATACTTGGGACACTGACAAATATTATG
+ACAGAAAAGAAATAGACCCTAAAAGAGTAATAAACTCAATGTTTATCTTCAACAAGAAAC
+GTGACGGAACTCATAAAGCTAGATTTGTTGCAAGAGGTGACATTCAGCATCCTGATACGT
+ACGATACAGGTATGCAATCCAACACTGTACATCATTATGCGTTGATGACATCCCTATCAC
+TTGCATTAGACGATGACTCCTTCATTACACAATTAGACATATCTTCGGCGTACTTGTATG
+CAGACATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGAATGAACAACAAGT
+TAATACGGTTGAGGAAATCACTTTATGGTTTGAAACAAAGTGGTGCAAACTGGTATGAAA
+CGATCAAATCATATCTGATTGAACAATGTGATATGGAAGAAGTTCGCGGATGGTCATGCG
+TATTTAAGAACAATCAAGTAACAATCTGCTTATTCGTTGATGATATGATATTGTTCAGCA
+AAGACTTAAATTCAAATAAAAGAATTATAGCAAAACTCAAGATGCAATACGATACCAAGA
+TTATAAATCTAGGTGAAAGCGATGATGAAATTCAATACGACATCCTTGGCTTAGAAATCA
+AATATCAAAGAGGTAAATACATGAAATTAGGTATGGAAAACTCACTAACTGAGAAAATAC
+CCAAATTAAACGTACCTTTGAATCCAAAAGGAAGAAAACTTGGTGCTCCAGGTCAACCAG
+GTCTCTATATAAACCAGAAGGAGCTAGAGCTAGAAGAAGACGACTACAACATGAAGGTGC
+ATGAAATGCAAAAGTTGATAGGTCTAGCGTCATATGTTGGATATAAATTCAGATTTGACC
+TATTATACTATATCAACACACTTGCACAACATATACTATTTCCGTCCAAACAAGTGTTAA
+ACATGACATATGAATTGATACAATTCTTATGGGACACTAGAGACAAACAATTAATATGGC
+ACAAAAGCAAATCTGCAAAACCAGAAAATAAATTAGTTGTAATAAGCGATGCCTCTTATG
+GCAACCAACCATATTACAAATCTCAGATTGGTAATATCTATTTACTAAATGGAAAGGTGA
+TCGGAGGAAAATCAACAAAAGCTTCATTAACATGTACTTCAACCACAGAAGCAGAAATAC
+ACGCAATCAGTGAAGCCATTCCATTATTAAATAACTTGAGTCACCTTATACAAGAACTAA
+ATGGGAAATCAATCATTAAAGGCTTACTTACTGACAGCAGATCTACAATCAGTATAGTTA
+TGTCCAAAAATGAAGAGAAACTTAGAAACAGATTTTTCGGTACCAAAGCAATGAGACTTC
+GGGACGAAGTATCAAATAATAACCTCCACGTATGCTACGTGGATACCAAAAGGAACATTG
+CTGACGTGATGACAAAACCCCTCCCAATAAAAACATTTAAACTATTAACAAACAAGTGGA
+TTCATTAGATCTATTACATTATGGGTGGTA
+>TY1p-LTR#LTR/Copia
+TGTTGGAATGAAATTCTAATATCATCTATTTAATAGTATATTATAATATGCGGTGCAAGA
+GGATGACATAAAGATTGAGAAACAGTCATCCAATCTAATGGAAGCTGAAATGCAAGGATT
+GATAATGTAATAGGATAATGAATAACAACATATAAAAAGAAAGAAGATAAAATAATAACA
+CTATGTAGAACTATCGATTCCCTTTTGTGGATTCCTATATCCTCGAGGAGAACTTCTAGT
+ATATTCTATATACCTAATATTATAGCCTTTAGTAACAATGGAATCCCAACAATTATCTAA
+TTACCCACACAATTCTCA
+>TY2-I#LTR/Copia
+TGGTAGCGCCTATGCTTCGGTTACTTCTAAGGAAGTCCCATCAAATCAAGATCCGTTAGC
+CGTTTCAGCTTCCAATTTACCGGAATTTGATAGAGATTCCACTAAGGTTAATTCTCAACA
+AGAGACAACACCTGGGACATCAGCTGTTCCAGAGAACCATCATCATGTCTCTCCTCAACC
+TGCTTCAGTACCACCTCCACAGAATGGACAGTACCAACAGCACGGCATGATGACCCCAAA
+CAAAGCTATGGCCTCTAACTGGGCACATTACCAACAACCATCTATGATGACGTGTTCACA
+TTATCAAACGTCACCTGCGTATTATCAACCGGACCCACACTATCCGTTGCCACAGTATAT
+CCCACCACTGAGTACTTCCTCACCTGATCCAATCGATTTAAAAAATCAACACTCTGAAAT
+ACCTCAAGCTAAGACAAAGGTGGGAAATAACGTCTTACCACCACACACTTTAACATCAGA
+AGAAAACTTTTCTACATGGGTTAAATTTTACATCAGATTTTTGAAGAACTCTAATCTCGG
+TGACATCATTCCAAATGACCAGGGTGAAATCAAAAGACAAATGACTTATGAAGAACATGC
+GTATATATACAATACCTTCCAAGCATTTGCCCCATTTCATTTATTGCCAACATGGGTAAA
+ACAAATTTTAGAAATTAATTATGCTGACATCCTTACAGTCCTTTGTAAAAGTGTGTCCAA
+AATGCAAACTAACAATCAAGAATTAAAGGATTGGATAGCTCTTGCCAACCTTGAGTACGA
+CGGAAGTACATCTGCTGATACATTTGAAATTACAGTCAGTACGATCATTCAGAGGCTAAA
+AGAAAACAATATCAATGTTAGCGACAGATTGGCCTGTCAACTAATACTTAAAGGTCTATC
+CGGTGACTTCAAATACCTACGTAATCAATATCGTACCAAAACGAACATGAAACTTTCCCA
+ATTATTCGCTGAAATTCAATTAATATATGACGAAAATAAAATCATGAATCTAAATAAACC
+GTCCCAATACAAACAACACAGCGAATACAAAAATGTTTCTCGCACATCTCCAAACACGAC
+TAACACAAAGGTTACAACTCGTAATTATCATAGAACAAATAGTTCAAAACCAAGAGCAGC
+AAAAGCTCACAATATTGCTACATCTAGTAAATTCTCAAGGGTGAACAATGATCACATTAA
+TGAATCAACCGTTTCATCACAATACTTAAGCGATGACAACGAACTTAGTCTTAGGCCAGC
+AACAGAAAGAATCTAAGCCAACACACACAATAGACTCGAATGACGAACTACCTGATCACC
+TTCTTATTGATTCAGGAGCTTCGCAAACGCTTGTCAGATCAGCCCATTATTTACACCATG
+CAACACCCAATTCTGAAATAAACATAGTCGATGCTCAAAAACAAGACATTCCTATAAATG
+CCATTGGTAATCTTCACTTCAACTTTCAGAACGGCACCAAAACATCAATAAAAGCACTAC
+ACACACCAAACATAGCCTATGATCTATTAAGTTTGAGTGAGCTGGCTAACCAAAATATTA
+CTGCCTGCTTTACCAGAAACACTTTAGAAAGATCGGATGGTACAGTACTAGCTCCCATAG
+TCAAACATGGAGACTTTTACTGGTTATCTAAAAAATACCTAATTCCTTCGCACATTTCAA
+AGCTAACAATAAACAACGTCAACAAAAGCAAAAGCGTAAATAAATATCCATATCCGTTAA
+TACATCGAATGCTTGGACATGCTAACTTCCGAAGTATTCAGAAGTCTCTTAAGAAGAATG
+CAGTTACATATTTGAAGGAATCGGATATTGAATGGTCTAACGCTAGCACATATCAATGTC
+CTGACTGTCTAATCGGCAAAAGCACGAAACATAGACATGTCAAAGGATCACGACTAAAGT
+ACCAAGAATCATATGAGCCTTTTCAGTACTTGCATACCGATATATTTGGTCCTGTACATC
+ACTTACCGAAAAGTGCACCTTCTTACTTTATATCGTTTACAGATGAGAAAACCAGATTCC
+AATGGGTGTACCCATTACACGACCGTCGTGAAGAATCTATCCTCAATGTTTTTACATCGA
+TATTAGCATTTATTAAGAACCAATTCAATGCTCGCGTTCTAGTTATCCAGATGGATCGTG
+GCTCCGAGTACACTAACAAAACTCTTCATAAGTTCTTTACGAACAGAGGTATTACTGCAT
+GCTATACAACCACGGCAGATTCTAGAGCACACGGTGTCGCTGAACGATTAAATCGTACTT
+TATTAAACGATTGTCGCACACTGCTTCATTGCAGTGGTCTACCAAATCATCTATGGTTCT
+CAGCAGTCGAATTTTCTACTATAATCAGAAATTCATTAGTCTCACCAAAAAACGATAAAT
+CTGCAAGACAACATGCAGGTTTAGCTGGACTGGACATTACTACTATACTACCTTTCGGTC
+AACCGGTTATAGTTAACAACCATAATCCCGACTCGAAAATACATCCTCGTGGCATTCCAG
+GTTACGCCTTACATCCGTCACGAAACTCTTATGGCTATATTATCTATCTTCCATCATTAA
+AAAAGACAGTAGATACTACCAATTACGTTATATTACAAGACAACCAATCCAAATTGGACC
+AATTCAATTATGATACACTCACCTTTGATGATGATCTCAATCGTTTAACAGCCCATAACC
+AATCTTTTATTGAACAAAATGAAACAGAGCAGTCATATGATCAAAATACAGAATCTGATC
+ATGACTATCAATCGGAGATTGAAATAAACTCTGATCCTCTAGTGAACGACTTCTCGTCCC
+AATCAATGAACCCCTTACAATTAGACCACGAACCAGTCCAAAAAGTACGTGCACCAAAAG
+AAGTTGATGCCGACATATCTGAATACAATATTCTTCCATCTCCTGTACGATCTCGTACAC
+CCCATATCATTAATAAAGAGAGTACCGAAATGGGTGGTACCATTGAATCAGATACTACTT
+CACCTAGACACTCGTCTACCTTCACTGCACGAAACCAAAAGCGACCTGGTAGTCCCAATG
+ATATGATTGATTTGACCTCACAGGATAGAGTTAATTATGGACTTGAAAACATCAAAACTA
+CACGTTTGGGTGGTACGGAGGAACCATATATTCAACGAAATAGTGATACAAATATCAAAT
+ACAGGACTACAAATAGTACGCCCTCAATAGATGACCGTTCGTCCAACAGTGAATCCACTA
+CTCCCATCATCTCCATAGAAACAAAGGCTGTATGTGATAATACACCCTCCATTGATACGG
+ATCCGCCAGAATATCGATCTTCTGACCATGCGACTCCTAATATAATGCCTGACAAATCCT
+CAAAAAATGTTACGGCTGATTCTATTCTTGACGACCTCCCACTTCCTGACTTAACCCATA
+AATCTCCTACGGACACTTCTGATGTTTCAAAAGATATTCCACACATACACTCTCGTCAGA
+CTAATTCCAGTTTGGGTGGTATGGATGATTCTAATGTTCTGACTACTACCAAAAGTAAGA
+AAAGATCATTAGAAGATAATGAAACTGAAATTGAGGTATCCCGAGACACATGGAATAATA
+AGAATATGAGAAGTCTGGAACCACCAAGATCGAAGAAACGCATAAATTTAATTGCAGCAA
+TAAAAGGAGTGAAATCGATCAAACCAGTTCGAACGACCTTAAGATATGATGAAGCAATTA
+CATATAATAAAGACAACAAAGAAAAAGACAGATATGTTGAAGCTTATCATAAAGAAATTA
+GCCAACTATTGAAAATGAACACTTGGGATACAAACAAATATTATGATAGAAATGACATAG
+ATCCTAAAAAAGTAATAAACTCAATGTTTATATTTAACAAGAAACGTGATGGTACACACA
+AAGCTAGATTTGTTGCAAGAGGCGACATTCAACACCCCGATACATATGATTCTGATATGC
+AATCCAATACCGTACATCACTATGCACTGATGACGTCACTGTCAATCGCATTAGACAACG
+ACTATTATATCACACAGCTGGACATATCCTCTGCTTACTTATATGCTGATATCAAAGAAG
+AATTATACATAAGACCTCCACCACATTTAGGTTTGAATGATAAATTACTACGTTTGAGAA
+AATCACTCTATGGTTTGAAACAAAGTGGTGCAAACTGGTATGAAACCATTAAATCATATT
+TAATAAATTGTTGCGACATGCAAGAAGTTCGCGGATGGTCATGCGTATTTAAGAATAGTC
+AAGTAACAATTTGCTTATTCGTTGATGATATGATATTATTCAGCAAAGACTTAAATGCAA
+ATAAGAAAATCATAACAACACTCAAGAAACAATACGATACAAAGATAATAAATCTGGGTG
+AAAGAGATAACGAAATTCAGTACGACATACTTGGATTAGAGATCAAATATCAAAGAAGCA
+AGTACATGAAATTAGGTATGGAAAAATCCTTGACAGAAAAATTACCCAAACTAAACGTAC
+CTTTGAACCCAAAAGGAAAGAAACTTAGAGCTCCAGGTCAACCAGGTCATTATATAGACC
+AGGATGAACTAGAAATAGATGAAGATGAATACAAAGAGAAGGTACATGAAATGCAAAAGT
+TGATTGGTCTAGCTTCATATGTTGGATATAAATTTAGATTTGACTTACTATACTACATCA
+ACACACTTGCTCAACATATACTATTCCCCTCTAGACAAGTTTTAGACATGACATATGAGT
+TAATACAATTCATGTGGGACACTAGAGATAAACAATTAATATGGCACAAAAACAAACCTA
+CCAAGCCAGATAATAAACTAGTCGCAATAAGCGATGCTTCATATGGTAACCAACCATATT
+ACAAGTCACAAATTGGTAACATTTTCCTACTCAACGGAAAAGTGATTGGAGGAAAGTCGA
+CAAAGGCTTCGTTAACATGCACTTCAACTACAGAAGCAGAAATACACGCAGTCAGTGAAG
+CTATACCGCTATTGAATAACCTCAGTCACCTTGTGCAAGAACTTAACAAGAAACCAATTA
+TTAAAGGCTTACTTACTGATAGTAGATCAACGATCAGTATAATTAAGTCTACAAATGAAG
+AGAAATTTAGAAACAGATTTTTTGGCACAAAGGCAATGAGACTTAGAGATGAAGTATCAG
+GTAATAATTTATACGTATACTACATCGAGACCAAGAAGAACATTGCTGATGTGATGACAA
+AACCTCTTCCGATAAAAACATTTAAACTATTAACAAACAAATGGATTCATTAGATCTATT
+ACATTATGGGTGGTA
+>TY2-LTR#LTR/Copia
+TGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATC
+ATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGC
+TGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAATGATGAT
+AATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATGGATTCCTAAATCCTC
+GAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAAATGGAATCC
+CAACAATTACATCAAAATCCACATTCTCTTCA
+>TY3-I#LTR/Gypsy
+CCTGGTAGCGTTAAAGGTTACTAATTGTTCAAACGAACCATCGAAAAGCCGAACCTAGCT
+ACACCACACCCCAGTATGAGCTTTATGGATCAAATCCCAGGAGGAGGAAATTATCCAAAA
+CTCCCAGTAGAATGCCTTCCTAACTTCCCGATCCAACCATCTTTGACCTTCAGAGGTAGA
+AATGACTCGCATAAACTGAAAAACTTTATCTCCGAAATAATGTTAAACATGTCTATGATA
+TCTTGGCCGAATGATGCCAGTCGTATTGTGTACTGCAGAAGACATTTATTAAACCCCGCT
+GCTCAGTGGGCTAATGACTTTGTACAAGAACAAGGTATACTTGAAATAACATTCGACACA
+TTCATACAAGGATTATATCAGCATTTCTATAAGCCACCAGATATCAATAAAATCTTTAAT
+GCAATCACGCAACTTTCCGAAGCTAAACTTGGTATTGAGCGTCTCAACCAACGATTCAGA
+AAGATTTGGGACAGAATGCCACCAGACTTCATGACCGAAAAAGCTGCCATAATGACATAT
+ACTAGGCTATTGACAAAGGAAACCTATAATATTGTCAGAATGCACAAACCAGAGACATTA
+AAAGACGCCATGGAAGAGGCTTACCAGACAACTGCACTAACTGAAAGATTCTTCCCAGGA
+TTCGAACTTGATGCTGATGGAGACACTATCATCGGTGCCACAACCCACTTACAAGAAGAA
+TACGACTCTGACTATGATTCAGAAGATAATCTGACCCAGAATGGATACGTCCATACCGTA
+AGGACAAGAAGATCTTACAATAAACCAATGTCAAATCATCGAAACAGGAGAAATAACAAC
+CCATCTAGAGAAGAATGTATAAAAAATCGGCTATGCTTCTATTGTAAGAAAGAGGGACAT
+CGCCTGAACGAATGTAGAGCACGTAAGGCGAGTTCTAACCGATCTTGAACTCGAATCAAA
+AGACCAACAAACTCCTTTTATCAAAACCTTACCAATTGTACACTATATCGCCATCCCCGA
+GATGGACAATACCGCCGAAAAAACCATAAAAATACAAAACACGAAAGTAAAAACCCTGTT
+TGACAGTGGATCACCCACGTCATTTATCCGAAGAGATATTGTAGAACTTCTCAAATACGA
+AATCTACGAGACCCCTCCACTCCGTTTTAGAGGATTCGTAGCCACCAAATCCGCCGTTAC
+ATCCGAAGCAGTCACCATTGACCTCAAAATCAATGACCTGCATATAACTTTAGCCGCGTA
+CATACTGGATAACATGGACTACCAATTGTTAATTGGAAATCCAATCTTACGCCGCTACCC
+GAAAATCCTGCACACAGTACTGAATACCAGAGAGAGCCCCGACTCCTTAAAGCCCAAGAC
+TTATCGCTCCGAAACCGTTAATAACGTTAGAACCTACTCCGCTGGTAATCGTGGTAACCC
+CAGAAACATAAAACTGTCTTTTGCCCCCACCATTCTCGAAGCAACTGACCCGAAATCCGC
+TGGTAATCGTGGTGACTCCAGAACCAAAACCCTGTCTCTTGCAACCACTACTCCTGCAGC
+AATTGACCCGCTTACGACCCTTGATAACCCAGGTAGTACTCAAAGTACATTTGCGCAATT
+CCCGATACCTGAAGAAGCGAGCATCCTAGAAGAGGATGGAAAATACTCCAACGTTGTCTC
+AACCATTCAGAGTGTAGAACCTAATGCTACTGATCACAGCAATAAGGACACCTTTTGCAC
+TTTGCCAGTTTGGTTACAACAGAAGTATAGAGAGATCATACGTAATGATCTCCCACCAAG
+ACCTGCCGACATTAATAACATCCCCGTAAAACATGATATTGAAATTAAACCTGGCGCAAG
+ACTACCTCGACTACAGCCATACCATGTTACAGAAAAGAACGAACAAGAAATCAACAAAAT
+AGTTCAAAAACTGCTCGATAACAAGTTCATTGTTCCCTCAAAGTCGCCTTGCAGCTCCCC
+TGTAGTCCTCGTCCCGAAGAAAGACGGTACCTTCCGACTCTGCGTCGATTACCGCACCCT
+GAACAAAGCTACCATCTCCGACCCATTCCCATTACCCAGAATCGACAACCTATTGAGCCG
+TATTGGAAATGCCCAGATATTTACCACGCTAGATTTGCATAGTGGTTACCACCAGATCCC
+GATGGAACCCAAAGACCGCTACAAAACCGCCTTTGTCACACCATCCGGTAAGTATGAATA
+TACCGTCATGCCATTTGGCTTAGTCAATGCACCTAGTACATTCGCAAGATACATGGCTGA
+TACATTTAGAGACCTGAGATTCGTCAATGTTTACCTTGATGATATATTAATATTCTCCGA
+ATCTCCAGAAGAACATTGGAAACATTTAGACACGGTACTAGAAAGATTAAAGAACGAGAA
+CCTCATTGTTAAGAAGAAAAAATGTAAATTTGCATCTGAAGAAACTGAGTTTTTAGGCTA
+TAGTATTGGAATCCAGAAAATAGCTCCACTACAGCACAAATGTGCAGCAATCCGAGACTT
+TCCGACGCCTAAAACAGTAAAACAAGCACAGAGATTTTTAGGAATGATTAATTACTACAG
+ACGATTCATTCCAAATTGCTCCAAGATTGCACAGCCAATCCAACTGTTTATTTGTGACAA
+AAGTCAATGGACAGAAAAACAAGACAAGGCAATTGATAAACTAAAAGACGCCTTGTGTAA
+CTCCCCCGTCCTAGTACCATTCAACAACAAAGCAAACTACCGACTTACAACAGACGCCTC
+AAAAGACGGCATTGGTGCTGTTCTAGAAGAAGTCGACAACAAGAACAAACTTGTTGGTGT
+CGTCGGTTACTTCTCTAAATCCTTAGAGAGTGCCCAGAAAAACTATCCTGCTGGCGAATT
+AGAACTACTTGGAATTATCAAAGCACTCCACCACTTCCGATATATGCTTCACGGAAAGCA
+TTTCACGTTAAGAACAGACCACATTAGTTTGTTATCATTACAAAACAAGAACGAACCCGC
+ACGACGCGTGCAACGCTGGTTAGATGACCTAGCCACATATGACTTCACCTTAGAATACCT
+AGCTGGACCCAAGAACGTTGTCGCAGATGCCATATCCCGTGCCGTATATACTATAACCCC
+CGAAACATCCCGACCTATCGACACAGAAAGCTGGAAATCTTACTACAAATCAGACCCATT
+ATGTAGTGCTGTCTTAATTCATATGAAAGAATTGACACAACACAACGTCACACCTGAAGA
+TATGTCAGCCTTCCGTAGTTACCAGAAGAAACTCGAACTATCAGAGACCTTCCGAAAGAA
+TTATTCCCTAGAAGACGAAATGATCTATTACCAAGACCGACTAGTAGTACCAATAAAACA
+ACAGAACGCAGTTATGAGACTATATCATGACCATACCTTATTTGGAGGACATTTTGGTGT
+AACAGTGACCCTTGCGAAAATCAGCCCAATTTACTATTGGCCAAAATTACAACATTCGAT
+CATACAATACATCAGGACCTGCGTACAATGTCAACTAATAAAATCACACCGACCACGCTT
+ACATGGACTATTACAACCACTCCCTATAGCAGAAGGAAGATGGCTTGATATATCAATGGA
+TTTTGTGACAGGATTACCCCCGACATCAAATAACTTGAATATGATCCTCGTCGTAGTTGA
+TCGTTTTTCGAAACGCGCTCACTTCATAGCTACAAGGAAAACCTTAGACGCAACACAACT
+AATAGATCTACTCTTTCGATACATTTTTTCATATCATGGTTTTCCCAGGACAATAACCAG
+TGATAGAGATGTCCGTATGACCGCCGACAAATATCAAGAACTCACGAAAAGACTAGGAAT
+AAAATCGACAATGTCTTCCGCGAACCACCCCCAAACAGATGGACAATCCGAACGAACGAT
+ACAGACATTAAACAGGTTACTAAGAGCCTATGCTTCAACCAATATTCAGAATTGGCATGT
+ATATTTACCACAAATCGAATTTGTTTACAATTCTACACCTACTAGAACACTTGGAAAATC
+ACCATTTGAAATTGATTTAGGATATTTACCGAATACCCCTGCTATTAAGTCAGATGACGA
+AGTCAACGCAAGAAGTTTTACTGCCGTAGAACTTGCCAAACACCTCAAAGCCCTTACCAT
+CCAAACGAAGGAACAGCTAGAACACGCTCAAATCGAAATGGAAACTAATAACAATCAAAG
+ACGTAAACCCTTATTGTTAAACATAGGAGATCACGTATTAGTGCATAGAGATGCATACTT
+CAAGAAAGGTGCTTATATGAAAGTACAACAAATATACGTCGGACCATTTCGAGTTGTCAA
+GAAAATAAACGATAACGCCTACGAACTAGATTTAAACTCTCACAAGAAAAAGCACAGAGT
+TATTAATGTACAATTCCTGAAAAAGTTTGTATACCGTCCAGACGCGTACCCAAAGAATAA
+ACCAATCAGCTCCACTGAAAGAATTAAGAGAGCACACGAAGTTACTGCACTCATAGGAAT
+AGATACTACACACAAAACTTACTTATGTCACATGCAAGATGTAGACCCAACACTTTCAGT
+AGAATACTCAGAAGCTGAATTTTGCCAAATTCCCGAAAGAACACGAAGATCAATATTAGC
+CAACTTTAGACAACTCTACGAAACACAAGACAACCCTGAGAGAGAGGAAGA
+>TY3-LTR#LTR/Gypsy
+TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCACCCTGAACGTTCATAAA
+ACACATATGAAACAACCTTATAACAAAACGAACAACATGAGACAAAACCCGACCTTCCCT
+AGCTGAACTACCCAAAGTATAAATGCCTGAACAATTAGTTTAGATCCGAGATTCCGCGCT
+TCCACCACTTAGTATGATTCATATTTTATATAATATATAAGATAAGTAACATTCCGTGAA
+TTAATCTGATAAACTGTTTTGACAACTGGTTACTTCCCTAAGACTGTTTATATTAGGATT
+GTCAAGACACTCCGGTATTACTCGAGCCCGTAATACAACA
+>TY3p-I#LTR/Gypsy
+TCTGGTAGCGTTAAAGGTTACTAATTGTTCAAGCAAACCAACGAATCCCTGAACCTAGCT
+ACACCAACATCTGTCATGAGCTTTATGGATCAAATCCCAGGAGGAGGAAGTTACCCAAAG
+CTTCCGGTGGAATGTCTTCCCAATTTCCCGATCCAACCAGCACTAACCTTCAGAGGTAGA
+AATGACTCGCACAAGTTGAAAAACTTCATCTCTGAAATAATGTTAAACATGTCTATGATT
+CCTTGGCCCAACGAAGCCAGTCGTATTGTCTATTGTAGAAAACACTTACTGAACCCTGCT
+GCTCAATGGGCTAATGATTTTGTCCAAGAGCAAGGCATACTGGAAATAACATTCGACACC
+TTCATACAAGGACTCTATCAGCATTTCTATAAGCCACCAGACATCAACAAAATCTTCAAT
+ACGATCAATCAACTATCTGAAGCAAAACTGGGTATTGAACGTCTCAACAAACAATTCAAA
+ATGATTTGGGACAGAATGCCACCAGACTTTATGACCGAAAAAGCCGCTATTATGACATAT
+ACCCGCTTACTGACAAAGGAAACCTACAATATAGTTAGATTGCATAAACCAAAAACGTTG
+AGAGGAGCCATGGAGGAGGCTTACCAAACAACAGCACTAACTCAGAGATTCTTCCCAGAA
+TTTGAGCTAGACGCCGATGGAGATACTATAATCGCAGCCGCAACTCGTTTACACGAACAG
+TACGACTACGACAGTGACCCACAAGAAAACTTTTTGGTCCAGAAGAGACACGTCCACGCA
+GTTCGGACAAGAAGATCATACAATAAACCGACCGCGACTTATCACAACAGGAGAAGCAAT
+AATCCATCTAGAGAAGAGTGTGTAAAGAACCGTCTCTGTTTTTATTGTAAGAAAGAAGGA
+CACCGTCTGAACGAGTGTAGAGCTCGTAATGCGAGTTCTAGCCGATCCTGAACTTAAGTC
+GAAAGACCACACGAAACTTTCTATCACATCCCGACCTATTGTACATTATATCGCCATACC
+TGAAATGGACAAAACTGCCGAAAAACACATAAAAATAAAAAACACGAAAATAAAAACCCT
+GTTTGATAGTGGATCGCCCACATCATTTATCCGAAGAGATACCGTAAATCTCCTGAATCT
+GCCAACCCATGATACTCCACCGCTCCGCTTTAGAGGATTCATATCCACCGAATCCGCCAC
+CACTTCAGAAGCAGTTACGCTCGACCTTACAGTCGACAATCTGCAAATCAATGTAGCCGC
+GTATGTACTCGATAAAATGGACTACCAACTTCTAATCGGAAATCCAATTCTACGCCGCTA
+CCCAAAACTCCTGTACACAATCCTGAACACTAAGCAGTGTACCTCCGCCCAGAAGCCCAA
+GGCTTACCATCCCGAAAACATTAACTATGTGAAAGCAAAATCCGCTGGTAATCGTGGTAA
+CTCCAGAAACAAAACACTGTCCTTTGCCCCCACTATTCCTGAAGCAACTGACCAGAAATC
+CGCTGGTAATCGTAGTAACTCCAGAACAAATACTATGTCTTTTGCAACTACCAATCCAGA
+AACAACTGACCCGCTTACGACCCTCGACAATCCAGGTAGTACTCAAAGTACATTTGCGCA
+ATTCCCGATACCTGAAGAAGCGACCATCCTAGAAGAGGATGGAAAATACTCCAACGTTGT
+TTCAACCATACAGAACGTAGAACCTAAAGCTACTGATCACAGCAACAAGGACACATTTTC
+AACGTTGCCTGTTTGGTTACAACAGAAGTATATAGAGATTATACGTAATGATCTCCCGCC
+AAGACCGGCCAATATCCACAACATGCCCGTAAAACACGACATTGAAATTAAACTTGACAC
+AAGACTACCTCGACTACAGCCATATCATGTTACAGAAAGGAACGAACAAGAAATTAACAA
+GATCGTTCAAGAACTGCTCGACAACAAGTTCATTGTCCCCTCTAAATCTCCGTGCAGTTC
+CCCTGTAGTCCTTGTCCCGAAGAAAGATGGTACGTTTAGACTTTGCGTTGACTACCGTGC
+CCTGAACAAGGTTACCATCTCCGACCCATTCCCATTACCCAGAATCGACAACCTATTAAG
+CCGTATTGGGAATGCCCAAATATTCACCACGCTAGATTTGCACAGTGGTTATCACCAGAT
+TCCAATGGAACCAAAAGACCGCTACAAAACCGCTTTTGTCACCCCGTCCGGTAAATATGA
+ATACACTGTCATGCCATTTGGTCTAGTGAATGCACCTAGCACCTTTGCAAGATACATGGC
+CGACATTTTCAGAGACTTGAGATTTGTCAATGTCTACCTTGATGATATACTAATCTTCTC
+TGAATCCCAAGAAGAACACTGGAAACATTTAGACACAGTTCTTGGAAGACTTAAGAAGGA
+AAACCTTATTGTCAAAAAGAAAAAATGCAAGTTTGCATCAGAACAAATTGAATTTCTAGG
+TTATAATATTGGAATTCAGAAAATAACCCCATTACAACACAAATGTGCTGCCATTCGAGA
+TTTTCCGAAACCCAGAACAGTAAAGCAAGCACAACGATTTTTAGGAATGATTAATTACTA
+TAGACGATTCATTCCAAATTGCTCTAAGATTGCACAACCAATCCAGCTCTTTATATGCGA
+CAAGAGTCAATGGACAGAAGAGCAGGACAAGGCAATCGAGAAATTAAAATCCGCCCTATG
+TAATTCCCCTGTTCTAGTACCATTTAACAACAAAGCAATTTACCGATTAACTACAGACGC
+ATCAAAAGATGGCATCGGTGCCGTTCTAGAAGAAGTCAATGCCAAAAACGCACTTGTCGG
+TGTCGTCGGTTATTTCTCTAAATCCTTAGAAAGTGCTCAAAAGAACTACCCCGCCGGTGA
+ACTAGAACTACTTGGAATTATTAAGGCACTTCACCACTTCCGTTATATGCTCCATGGAAA
+ACATTTTACATTGAGAACGGATCACATTAGCTTACTGTCACTGCAGAATAAGAATGAACC
+TGCACGAAGAGTTCAAAGATGGTTGGATGACCTAGCCACTTATAACTTCACCCTAGAATA
+CTTAGCTGGACCCAAAAACGTCGTCGCAGATGCTATATCCCGTGCCGTGTACACTATAAT
+CCCAGAAATACCCCAACCTATCGACCCAGAAAATTGGAAAACTCATTACAAATCAGACCC
+ATTATGCAGTGCCACCTTGATTTACATGGAAGAATTGACACAACACAATGTCATGCCTGA
+GGATATGTCCGCATTCCGTAGCTATCACAAGAAATTTCAGTTATCAGAGACCTTCCGAAA
+GAACTACTCCCTAGAAAATGGAATAATCTACTATCGAGACCGATTAGTAGTCCCGGTAAA
+ACAACAGAACGAAGTCATAAAACTGTATCACGATCATACTTTATTCGGAGGCCATTTTGG
+TGTAACTGTAACATTTGGAAAGATTGCTCCAATTTTTTACTGGCCGAAATTGCAACATTC
+GATTACACAATACATCCGTACCTGCGTACAATGTCAACTCACAAAATCACATCGACCACG
+TTCACAAGGACTATTGCAACCGCTTCCCGTAGCAGAAGGAAGATGGCTTAATATATCAAT
+GGATTTCGTGACTGGACTACCCGTAACAACAAACGATTTGAATATGATCCTCGTTGTTGT
+TGACCGCTTCTCGAAACGCGCTCACTTCATAGCTACAAGGAAAACAGCAGACGCATCACA
+GCTAATAAATACGCTATTCCGCTATATCTTTTCATATCATGGTTTCCCGAAAACAATAAC
+CAGTGATAGAGACATCCGTATAACCGCAGAAAAATATCAAGAACTTACAAAAAGATTAGG
+GATAAAATCGACAATGTCTTCTGCAAACCACCCCCAAACAGATGGACAATCCGAAAGAAC
+GATTCAAACATTGAACCGATTGATAAGAGCTTATGCCTCCACCAATACCCGGAACTGGCA
+CACCTACTTACCACAAATTGAATTTGTCTATAACTCCACACCGACCAGAACACTTGGAAA
+GTCACCATTCGAAATTGATTTAGGATATACTCCCAATGCACCTACCATTAAAACGGATTG
+CGAAATCAATGCAAGAAGTTTTACCGCCGTAGAACTGGCCCGACACCTCAAAGCTATTAC
+GATCCAAACAAAAGAACGACTAGAGTCTGCTCAGATTGAAATGGAAACTAATAACAACCA
+AAGACGTAAAACTTTGTTACTGAACATAGGAGATCACGTACTAGTGCATAGAGATGCATA
+CTTCAAGAAAGGAACGTATATGAAGGTACAACCTATATACGTTGGACCATTTCGAGTTGT
+CAAGAAAATAAATGATAACGCTTACGAACTCGACCTGGATTCACACAAGAGAAAACATAG
+AGTTATTAACGTACAATACCTAAAGAAATTTGTATACCGACCCGACGCATATCCAAAGAA
+TAAACCAATCAGTTCCGTTGAAAGAATCAACAGAGCCAATGAAGTCATTGCAGTTATAGG
+GATAGATACCACACACAAAACATACTTATGTCGTATGCAGGATGTGGACCCGACAATCTC
+AGTAGAATATTCAGAAGCTGAATTCTACCAAATCCCAGAGGAAATACGAAAGTCAATATT
+AGCCAATTTTAGACAACTGTACGAAACTCAAGACAACTCCGAGAGAGAGGAAGAT
+>TY3p-LTR#LTR/Gypsy
+TGTTGTATCTCAAGATGAGATACCTCAGCATTACTAGATTTACCAACCTAGACATAAAAC
+ATGTATGAAACACGTACGAAACAATAGACAAGATTGAGTATACTAGGCAACCTACTTGCC
+TAAGATGAACCAAACTAACCAAACGTATAAATACCTGAACAATTAGTTTAGATCCGAGAT
+TCCGCGCTTCCACCCTTTAGTTAGATTCAGATCTTATATAGATTATATAGGATAAGTAAC
+ATTCTGTGAATCACGATAATAATAAGTCTGACAACAAGTTACTCTCCTAAACGACTTTAG
+GATTGTCAAGACATCCGGTATTACTCGAGCCCGTAATACAACA
+>TY4-I#LTR/Copia
+TGGCGACCCCAGTGAGGGGTGAAACAAGAAATGTTATTGACGACAACATTTCTGCGCGGA
+TTCAATCGAAAGTCAAAACAAATGATACTGTCAGACAGACGCCATCATCATTAAGAAAAG
+TTTCTATTAAAGATGAACAGGTGAGACAATATCAAAGAAACTTAAATAGGTTTAAAACCA
+TACTAAATGGTTTAAAGGCAGAAGAGGAAAAACTTTCTGAGGCTGATGATATTCAGATGC
+TAGCTGAAAAATTATTAAAACTCGGAGAAACCATTGACAAGGTTGAGAATAGGATTGTGG
+ATCTAGTTGAAAAGATACAATTATTGGAAACAAACGAGAACAATAATATATTACATGAAC
+ATATAGATGCTACAGGGACTTACTATTTATTCGATACGTTAACTTCAACCAACAAAAGAT
+TCTACCCTAAGGATTGTGTTTTTGATTATAGGACTAATAATGTCGAGAACATTCCTATTC
+TCTTAAACAATTTTAAAAAATTCATCAAGAAATATCAATTTGATGATGTCTTTGAAAATG
+ATATCATAGAAATCGATCCTCGTGAAAATGAAATCTTGTGCAAGATAATCAAAGAAGGAC
+TCGGTGAAAGTTTAGATATCATGAACACAAATACAACTGACATTTTTAGGATAATCGATG
+GTTTAAAAAAACAAAATATAGAAGTTTGCATGGTAGAGATGTCAGAATTAGAGCCTGGGG
+AAAAGGTTTTGGTTGATACAACATGTAGAAATTCCGCATTGTTAATGAATAAACTTCAAA
+AGTTGGTACTAATGGAAAAATGGATTTTTTCTAAATGCTGCCAAGATTGTCCTAATCTAA
+AGGATTACCTACAAGAAGCTATCATGGGAACCTTACATGAATCCTTAAGAAATTCTGTGA
+AACAACGTTTGTACAACATTCCACATGACGTAGGAATTGATCACGAAGAATTTCTAATCA
+ATACTGTTATTGAAACAGTAATTGATTTGAGCCCAATTGCAGACGATCAAATAGAAAATA
+GCTGCATGTATTGCAAATCTGTTTTCCATTGCTCAATTAACTGCAAAAAGAAACCAAATA
+GGGAACTTAGGCCTGACTCGACCAATTTCTCAAAAACCTATTATCTACAAGGTGCACAGA
+GACAACAACCACTTAAGTCCAGTGCAAAACGAACAAAAGTCTTGGAACAAGACACAAAAA
+AGGTCGAACAAAGTGTACAACAGCAAAAAACTGGTAATTATTGATACCGGTTCCGGAGTA
+AACATTACCAATGACAAAACCTTACTGCATAATTACGAAGACAGTAATCGCAGTACACGA
+TTTTTTGGTATTGGGAAAAACAGTTCAGTGTCTCTTAAAGGGTATGGCTATATAAAAATC
+AAGAATGGTCACAACAATACTGACAATAAGTGTCTATTAACTTACTATGTACCGGAAGAA
+GAATCCACTATAATCAGCTGTTATGACTTAGCCAAGAAAACCAAAATGGTTTTAAGTCGA
+AAATATACCAGATTGGGAAACAAAATCATAAAAATTAAAACCAAGATAGTTAATGGTGTC
+ATTCACGTAAAAATGAACGAGTTAATTGAACGTCCTTCCGATGATTCAAAAATAAATGCA
+ATAAAACCTACTTCTTCTCCTGGATTTAAACTAAATAAAAGGTCTATTACCTTGGAAGAT
+GCTCATAAAAGAATGGGCCATACAGGAATTCAACAAATTGAAAATTCCATAAAACATAAT
+CATTATGAAGAATCCCTTGACTTAATCAAAGAACCAAATGAATTTTGGTGTCAAACCTGT
+AAAATCTCTAAAGCCACGAAAAGAAATCATTATACCGGGTCTATGAATAATCATAGTACT
+GATCATGAACCAGGCTCATCATGGTGCATGGATATATTTGGCCCTGTATCAAGTTCAAAC
+GCGGACACTAAAAGGTACATGCTTATTATGGTGGATAACAACACGAGATATTGCATGACC
+TCCACACACTTCAATAAGAATGCTGAAACTATTTTAGCTCAAGTTAGAAAGAATATTCAG
+TACGTGGAAGCACAATTTGACAGGAAAGTCAGAGAAATTAATTCAGACAGAGGTACTGAA
+TTCACAAATGATCAGATAGAAGAATATTTTATTTCAAAAGGAATACATCACATACTTACT
+TCTACACAAGATCATGCTGCTAACGGAAGAGCAGAAAGATACATAAGAACAATAATAACT
+GATGCAACAACACTCCTAAGACAAAGTAACTTAAGAGTAAAATTTTGGGAATACGCAGTA
+ACTTCTGCTACCAATATAAGAAATTACCTGGAACACAAAAGTACAGGTAAACTACCATTG
+AAGGCAATCTCACGTCAACCTGTGACAGTGAGATTAATGTCATTCTTACCATTTGGCGAA
+AAAGGAATAATTTGGAATCATAATCACAAAAAATTGAAACCATCTGGACTTCCTTCTATA
+ATTCTATGCAAAGATCCAAATAGTTATGGATACAAATTCTTTATACCATCCAAAAATAAA
+ATTGTCACATCTGATAATTATACAATTCCCAACTATACAATGGACGGTAGAGTAAGAAAT
+ACTCAGAATATTAACAAGAGTCATCAATTCAGTTCAGATAATGATGATGAAGAAGATCAA
+ATCGAAACGGTCACAAACTTATGTGAAGCTTTGGAAAACTACGAAGATGATAATAAACCA
+ATTACTCGCCTGGAAGATTTGTTCACAGAGGAAGAGTTATCTCAAATAGACTCAAACTCA
+AAATACCCATCTCCTAGTAATAACCTAGAAGGGGACTTGGATTACGTATTTTCTGATGTT
+GAGGAATCTGGAGATTATGACGTTGAATCTGAACTTTCAACGACAAATAATTCAATCTCA
+ACTGATAAAAACAAAATTTTGTCAAACAAGGATTTTAATTCAGAACTTGCATCGACTGAA
+ATATCCATCAGTGGAATCGATAAGAAAGGATTAATAAATACAAGTCATATTGATGAAGAT
+AAGTATGATGAAAAAGTCCACAGAATTCCATCGATTATACAAGAGAAACTGGTAGGAAGG
+AAAAATACTATTAAAATCAATGACGAAAACAAAATCTCCGACAGAATTCGTAGTAAAAAC
+ATTGGGAGTATTTTAAACACTGGACTCAGTAGATGTGTAGATATCACCGATGAATCTATT
+ACTAACAAAGATGAGTCAATGCACAACGCAAAACCCGAACTAATTCAGGAGCAGTTAAAA
+AAAACAAATCATGAAACTTCGTTTCCTAAAGAAGGGAGCATTGGAACAAATGTAAAATTC
+CGAAATACAAACAATGAGATTTCTTTAAAAACAGGCGATACGAGTTTACCAATAAAAACT
+TTAGAAAGCATTAACAATCACCATAGTAATGATTATTCCACAAACAAAGTTGAAAAGTTT
+GAGAAGGAAAATCATCATCCGCCCCCGATTGAGGACATTGTGGATATGAGTGATCAAACT
+GATATGGAATCAAACTGTCAGGATGGTAATAACTTAAAAGAATTAAAAGTCACCGATAAA
+AATGTACCAACTGACAATGGAACAAATGTGTCACCAAGGTTGGAACAAAATATTGAAGCA
+TCTGGATCACCAGTACAAACAGTTAATAAAAGTGCCTTCTTAAACAAAGAATTCAGTTCT
+TTGAACATGAAAAGAAAACGGAAAAGACACGATAAAAACAATAGTCTAACAAGCTATGAA
+TTAGAAAGAGATAAGAAGCGTTCAAAAAAGAATCGAGTGAAATTAATTCCAGATAATATG
+GAAACAGTTTCAGCACCAAAAATTCGAGCCATATATTATAATGAAGCTATTTCAAAAAAT
+CCTGACCTCAAAGAAAAACATGAATACAAACAGGCATATCATAAAGAATTACAGAATTTA
+AAAGATATGAAGGTATTTGATGTCGATGTGAAGTACAGTAGATCAGAAATCCCTGATAAT
+TTAATAGTACCCACCAACACGATATTCACAAAGAAAAGAAATGGGATTTATAAGGCTAGG
+ATAGTCTGCAGAGGTGATACTCAGTCACCAGACACTTACAGTGTAATAACTACAGAATCT
+TTAAATCACAATCATATTAAGATATTCTTAATGATTGCAAACAACAGAAATATGTTTATG
+AAGACCCTGGATATCAATCATGCATTCCTATATGCTAAATTGGAAGAAGAAATATACATC
+CCACATCCGCATGATAGGAGATGTGTAGTCAAGCTAAATAAGGCGTTATATGGTCTAAAA
+CAGAGTCCTAAAGAATGGAATGATCATCTAAGACAATACTTGAATGGAATTGGACTGAAA
+GATAACTCTTATACTCCGGGATTATACCAAACCGAGGATAAAAATCTAATGATTGCAGTC
+TATGTTGATGACTGCGTAATTGCGGCAAGCAATGAACAGAGATTGGATGAATTCATAAAC
+AAATTGAAAAGTAATTTTGAACTGAAAATTACAGGAACATTAATAGACGATGTACTCGAT
+ACAGATATATTAGGAATGGATCTAGTATACAACAAAAGACTTGGTACTATCGATTTAACA
+TTAAAATCATTCATAAATAGAATGGATAAAAAATACAACGAGGAATTGAAAAAGATTAGA
+AAAAGTTCAATTCCGCATATGTCAACTTATAAAATAGATCCTAAGAAAGACGTACTGCAA
+ATGTCAGAAGAAGAGTTTAGACAAGGTGTTCTAAAGCTACAACAATTACTAGGTGAACTA
+AACTATGTCAGACACAAATGCAGATACGACATTGAATTTGCTGTTAAGAAAGTGGCTAGA
+CTAGTAAATTACCCACATGAAAGAGTCTTTTATATGATTTACAAAATAATCCAGTACTTG
+GTTAGGTATAAAGATATTGGAATACACTATGACCGAGACTGTAATAAAGACAAAAAGGTT
+ATTGCTATAACTGATGCATCAGTTGGATCAGAATATGATGCTCAATCAAGGATTGGAGTT
+ATATTATGGTACGGTATGAATATTTTTAATGTTTATTCTAACAAGAGCACAAACAGATGT
+GTATCATCAACAGAAGCAGAGCTTCATGCCATTTATGAAGGCTATGCAGACTCAGAAACG
+TTGAAGGTAACATTAAAGGAGCTAGGAGAAGGAGACAATAATGACATTGTCATGATCACT
+GACTCAAAGCCAGCCATTCAAGGATTAAATCGCAGCTATCAACAACCAAAAGAGAAATTC
+ACTTGGATAAAAACTGAAATAATAAAAGAAAAAATTAAAGAGAAGAGTATAAAACTGTTA
+AAAATTACCGGCAAAGGTAATATTGCTGATTTACTAACAAAACCAGTATCAGCATCTGAT
+TTTAAAAGATTTATACAAGTATTAAAAAATAAAATAACATCACAGGATATTTTGGCCTCA
+ACAGACTATTGATAATTAATTAATGAAGTTCTAAACACACAATGAATATCTGTTGAAGTA
+CAATAATATATCTTTAAGGGAGCA
+>TY4-LTR#LTR/Copia
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATGGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACAACTCGTATACGTTTAAGTGTGATTGCGCCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGTGTTAAAGACCTATTAGTTGAACAT
+GTTATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTCACTTCTTCATTAATACTAATTTTTAACCTCT
+AATTATCAACA
+>TY4p-I#LTR/Copia
+TGGCGACCCCAGTGAGGGATGGAACAAGAAATGTTATTGACGACAACATTTCTGCGCGGA
+TTCAATCGAAAGTCAAAACAAATGATACTGTCAGACAGACGCCATCATCATTAAGAAAAG
+TTTCTATTAAAGATGAACAGGTACGGCAATATCAAAGAAACTTAAATAGGTTTAAAACCA
+TACTAAATGGTTTAAAGGCAGAAGAGGAAAAACTTTCTGAGGCTGATGATATTCAGATGC
+TAGCCGAAAAATTATTAAAACTCGGAGAAACCATTGACAAGGTTGAGAATAGGATTCTGG
+ATTTAGTTGAAAAGATACAATTATTGGAAACAAATGAGAACAATAATATTTTACATGAAC
+ATACAGATGCTACAGGGACTTACTATTTATTCGATACGTTAACTTCAACCAACAAAAGAT
+TCTACCCTAAAGATTGTGTTTTTGATTATAGGACTAACAATGTTGAGAACATTCCTATTC
+TTTTAAACAATTTTAAAAAATTTATCAAGAAATATCAATTTGATGATGTCTTTGAAAATG
+ATATCATAGAAATCGATCCTCGTGAAAATGAAATCTTGTGCAAAATAATCAAAGAAGGAC
+TCGGTGAAAGTTTAGATATCATGAACACAAATACAACTGACATTTTTAGGATAATCGATG
+GTTTAAAAAACAAATATAGAAGTCTGCACGGTAGAGATGTCAGAATTAGAGCCTGGGAAA
+AGGTTTTGGTTGATACAACATGTAGAAATTCCGCATTATTAATGAATAAACTTCAAAAAT
+TGGTACTAATGGAAAAATGGATTTTTTCCAAATGCTGCCAAGATTGTCCCAATCTAAAAG
+ATTACCTACAAGAAGCTATCATGGGAACCTTACATGAATCCTTAAGAAATTCTGTGAAAC
+AACGTTTGTACAATATTCCACATAACGTAGGAATTAATCACGAAGAATTTCTAATCAATA
+CTGTTATTGAAACAGTAATTGATTTGAGCCCAATGGGTGACGATCAAATAGAAAATAGCT
+GCATGTATTGCAAATCTGTTTTCCATTGCTCAATTAACTGCAAAAAGAAACCAAATAGAG
+AACTTAGGCCTGACACGGCAAATTTCTCAAAAACCTATTATACGCAAGGTGCACAGAGAC
+AACAACAACTTAAGTCCAGTACAAAACGAACAAAAGTCTTGGAACAAGACACAAAAAAGG
+TCGAACAAAGTGTACAACAGCAAAAAACTGGTAATTATTGATACCGGTTCCGGTGTAAAC
+ATTACCAATGACAAAACCTTACTGCATAATTACGAAGACAATACTCGCAGTACACGATTT
+TTTGGTATCGGGAAAAACAGCTCAGTGTCTGTTAAAGGGTATGGCTATATAAAAATCAAG
+AATGGTCACGACAATACTGACAATAAGTGCTTATTGACTTACTATGTACCGGAAGAAGAA
+TCCACTATAATCAGCTGTTATGACTTAGCCAAGAAAACCAAATTGGTTTTAAGTCGAAAA
+TATACCAACTTGGGAAACAAAATCATAAAAATAAAAACCAAGATAATAAATGGTGTCATT
+CACGTAAAAATGAATGAGTTAATTGAACGTCCTTCCGATGATTCAAAAATAAATGCAATA
+AAACCTACTTCTTCTACTGGATTTAAACCAAATAAAATGTCTATTACCTTGGAAGATGCT
+CATAAAAGAATGGGCCATACAGGAATTCAACAAATTGAAAATTCCATAAAACATAATCAT
+TATGAAGAATACCTTGACTTAATCAAAGAACCAAATGAATTTTGGTGTCAAACCTGTAAA
+ATCTCTAAAGCCACGAAAAGAAATCATTATACCGGGTCTATGAATAATCATAGTACTGAT
+CATGAACCAGGCTCATCATGGTGCATGGATATATTTGGTCCTGTTTCAAGTTCAAACGCG
+GACACTAAAAGGTACATGCTTATTATGGTGGATAACAACACGAGATATTGCATGACCTCC
+ACACACTTCAATAAGAATGCTGAAACTATATTAACACAAATCAGAAAGAATATTCAGTAC
+GTGGAAACACAATTTGACAGAAAAGTCAGAGAAATTAATTCAGACAGAGGTACTGAATTC
+ACAAATGATCAGATAGAAGAATATTTTATTTCAAAAGGAATACATCATATACTTACTTCT
+ACACAAGATCATGCTGCTAATGGAAGAGCAGAAAGATACATCAGAACAATAATAACTGAT
+GCAACAACACTCCTAAGACAAAGTAACTTAAGAGTAAAATTTTGGGAATACGCAGTAACT
+TCTGCTACCAATATAAGAAATTGCCTGGAACACAAACGTACAGGTAAACTACCATTGAAG
+GCAATCTCACGTCAACCTGTTACAGTGAGATTAATGTCATTCTTACCATTTGGCGAAAAA
+GGAATAATTTGGAACCATAATCACAAAAAATTGAAACCATCGGGACATCCTTCTATAATT
+TTATGCAAAGATCCAAATAGTTATGGATACAAATTCTTTATACCATCCATAAATAAAATT
+GTCACATCTGATAATTATACAATTCCCAACTATACTATGGACGGTAGAGTAAGAAATACT
+CAGAATATTTACAAAAGTCATCAAATCAGTTCACATAATGCTGATGAAGAAGATCAAATC
+GATACGGTCACAAACTTATGTGAAGCTTTGGAAAACTACGAAGATGATAATAGACCAATT
+ACTCGCCTGGAAGATTTTTTCACAGAGGAAGAGTTATCTCAAATAGACTCAAACGCAAAA
+TACCCATCTCCTAGTAATAACCTAGAAGGGGACTTGGATTACGTATTTTCTGATGTTGAA
+GAATCTGGAGATTATGACCTTGAATCTGAACTTTCAGCGACAAATACCTCAATCTCAACT
+GATAAAAACAAAATTTTGTCAAACAAGGATTCTAATTCAGAACTTGCATCGACTGAAATA
+TCCATCAGTGGAATCGATAAAAAAGGATTAATAAATACAACTCATATTGATGAAGATAAT
+TGTGATGAAAAAGTCCACAGAATTCCATCGATTATACAAGAAAACCTCGTAGGAAGTAAA
+AATACTATTAAAATCAATGACGAAAACAAAATCTCCAACAGAATTCGTAGTAAAAACATT
+GGGAGTACATTAAACTCTGGACTCAGTAGATGTGTAGATATTACCGATGAATCTATTACT
+AACAAAGATGAGTCAATACACAACCCAAAACCAGAACTAATACAGGAGCAGTTTAATAAA
+ACAAACCATGAAACTTCGTTTCCTAAAGAAGGGAGCATTGGAAGAAATGTAAAATTCCGA
+AATCCAAACAATGAGATTTCTTTAAAAACAAGCGAAACGAGTTTACCAATAAAAACTTTA
+GAAAGTATTAACAATCACCACAGTAATGATTATTCCACAAACAAAGTTGAAAAGTTTGAG
+AAGGAAAATCATCATCCGCCCCCGATTGAGGACGTTGTGGATATGAGTGATCAAACAGAT
+ATGGAATCAAACTGTCAGGATGATAATAACATAAAAAAATTAGAAGACACCGACGAAAAT
+GTACCAACTGAGAATGGAACCAATGTGTCACCAAGGTTGGAACGAAGTAGTAAAAAAAAT
+GAGATCAACACTACAACCAATTAAAACGACAACTGAAGCATCTGGATCGTCAGTACAAAC
+AGTTAATAAAAGTGCCTTTTTAAACAAAGAATTTAATTCTTTGAATATGAAAAGAAAACG
+GAAAAGACACGATAAAAACAATAGCTTAACAAGCTACGAATTAGAAAGAGATAAGAAGCG
+TTCAAAGAAGAATCGAGTGAAATTAATTCCAGATAATATGGAAACAAGTTCAGCACCGAA
+AATTAGAGCCATATATTATAATGAAGCTATTTCAAAAAATCCTGACCTCAAAGAAAAACA
+TGAATACAAACAGGCATATCATAAAGAATTACAAAATCTAAAAGATATGAAGGTATTTGA
+TGTCGATGTGAAGTACAGTAGATCAGAAATCCCTGATAATTTAATAGTACCCACCAACAC
+AATATTCACAAAGAAGAGAAATGGGATTTATAAGGCTAGGATAGTCTGCAGAGGCGATAC
+TCAGTCACCGGACACTTACAATGTAATAACTACAGAATCTTTAAATCACAATCATATTAA
+GATATTCTTAATGATTGCAAACAACAGAAATATGTTTATGAAGACTCTGGATATCAATCA
+TGCATTCCTATATGCTAAATTGGAAGAAGAAATATACATCCCACATCCGCATGATCGGAG
+ATGTGTAGTCAAACTAAATAAGGCGTTATATGGTCTAAAACAGAGTCCTAAAGAATGGAA
+TGATCATCTAAGACAATACTTGAATGGTATTGGATTGAAAGATAACTCTTATACTCCGGG
+ATTATACCAAACCGAGGATAAAAATCTAATGATTGCAGTTTATGTTGATGACTGCGTAAT
+TGCGGCAAACAATGAACAGAGATTGGATGAATTCATAAACAAATTGAAAAGTAATTTTGA
+ACTGAAAATTACAGGAACATTAATAGATGATGTACTCGATACAGATATATTAGGAATGGA
+CTTAGTATACAACAAAAGACTTGGTACTATCGATTTAACATTGAAATCATTCATAAATAA
+AATGGATAAAAAATACAAAGAGGAATTGAAAAAGATTAGAAAAAGTTCAATTCCGCATAC
+GTCAACTTATAAAATAGATCCTAAGAAAGACGGACTGCAAATGTCAGAAGAAGAGTTTAG
+ACAAGGTGTTCTGAAATTACAGCAATTACTAGGTGAACTAAACTATGTCAGATACAAATG
+CAGATACGACATTGAATTTGCTGTTAAGAAAGTGGCTAGACTAGTAAATTACCCACATGA
+AAACGTCTTCTATATGATTTACAAAATAATCCAGTACTTGGTTCGGTATAAAGATATTGG
+AATACACTATGACCGAGACTGTAATAAAGATAAGAAGGTTATTGCTATTACTGATGCATC
+AGTTGGATCAGAATATGATGCTCAATCAAGGATTGGAGTTATATTATGGTACGGGATGAA
+TATTTTTAATGTTTATTCTAACAAGAGCACAAACAGATGTGTATCATCAACAGAAGCAGA
+GCTTCATGCCATTTATGAGGGCTATGCAGACTCAGAAACGTTGAAGGAAACATTAAAAGA
+GCTAGGAGAAGGAGAAAATAATGACATTGTCATGATCACTGACTCAAAGCCAGCCATTCA
+AGGATTAAATCGTAGCTATCAACAACCAAAAGAAAAATTCACTTGGATAAAAACTGAAAT
+AATAAAAGAAAAAATTAAAGAGAAGAGTATAAAACTGTTAAAAATTACCGGCAAAGGTAA
+TATTGCTGATTTACTAACAAAACCAGTATCAGCATCTGATTTTGAAAGATTTATACAAGT
+ATTAAAAAATAAAATAACATCACAGGATATTTTGGCCTCAACAGACTATTGATAATTAAT
+TAATGAAGTTCTAAACACACAAGGAATATCTGTTGAAGTACAATAATATATCTTTAAGGG
+AGCA
+>TY4p-LTR#LTR/Copia
+TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATAGTAACAATCTAATGCTTAC
+ATCGTATATTAATGTACACCTCGTATACGTTTAAGTGTGATTGCACCTATTGCAGAAGGA
+ATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGAGTTAAAAATCTATTAGTTGAACAT
+GATATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCG
+GAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTC
+TCTTATTTAGTATAAGAAGATCAGTACTTATTTCTTCATTAGTACTATATTTTAACCTCT
+AATTATCAACA
+>TY5-I#LTR/Copia
+GGTTATGAGCCCTGAGAGCAATGCTTCAGAGACCATAATTAATCTATCTAATCCCAACAA
+TTATAAACAGTGGCTGTACGGTATCGAGACCGCTGCTGAATATGCTAACGAATATATGAA
+CGAATTCGTTCATACCGGAGATATCCAATCAATGAAAAGGGATTACAATCTCAGCGCGAA
+TGATGAAAGCTTTGTCAAAACCGTATTTAACAGTTTCCTGGTAAAGCTCTACAAGAAAAC
+TATCGTGGGTGAAGCTGCATGTGAAATGAACTGGATATGTGATGATTCACTTGGAAGGGT
+CTCTGCTTATGATATTTTCTCGCACTTCGAAGAAAACTATAATGAAGTCACTATTGGATC
+CAGGCTTACTCTTATAGAGGACTTACCAAATATATCCTCCAAGCCTGTAGATGAAATCGC
+TTCCTTTTTGAAAACCCTATTCACAATGCTTGAAGACAATAGCGAAGAACAGGACAAAAA
+GAAAAGACGCGATACCAATATCGCGTTGCTATTAATGACCTTCTTACCCGAGTTAAAGGA
+ATCATTCCACGAGAAATTCGGTGACTCTAAAGCTCTTCAGCTGTCACAAGTCATTAGATT
+CTGTAAATTAAAGGCGTCATCGAATTCATTATCTTCAGTCTCAGATACATTGGTTGCACA
+AGACAGAAGAAGCTATCAAAAGAAAGGAAATAAGGGATGTATGATTTGTGGGGCTGATCA
+TCGCTTAAGCAACTGTTCTCTGCTTAAAAGAAGAATACCAGAAGCCAGAATCTTTAAATT
+ATATCCTAATGACAAGACGAATAGATCTTCATCTGCTAGTGTTGCGATTCCTGACTATGA
+AACGCAAGGCCAAACAGCAGGACAGATAACACCAAAGTCCTGGCTCTGTATGTTATCTTC
+GACCGTCCCAGCTACCAAATCCTCAGATTGGATTTGTGACACAGGATGTACTTCACACAT
+GTGCCACGACCGTTCTATGTTCTCATCATTTACTAGATCCTCTAAGAAAGACTTTGTCAG
+AGGAGTCGGCGGTTCCATACCCATCATGGGCTCCGGGACTGTAAACATCGGCACTGTTCA
+ATTAAATGACGTATCCTACGTCCCTGATTTACCAGTCAACCTAATATCCATTTGGAAACT
+ATGTGCTAAATCCAACTCTTCTGTTACGTTCACAAAAGAGGGTGTCACTGTGAAATCACC
+TGATGACGTGATTTCTACGGCTGGGAAGTTAAACAATTATCTGTACATTTTCGATGATCT
+TACGCCCGTAACTACCTTCTCTTCGCAAAATTACTTCTGCTCTAAAACATTGGATTCATC
+TAAAATGATAACTTCCGCAGCGTTTCATACCGTTGCAGATAAAATGTTGTCGCAACACAT
+TTCTCCCACTGCTCTCCCGGTAAAATGGCATGCTCGTATGGGCCATCCCGGAGCAGATAT
+TTACAATTCCTTGGCTAGAACTCTGCGTTTTCCAAAATTTAAGACGGCTGAATACACTAT
+TTGTCCTACCTGCTCACTAGCAAAAGGAATCATCAAAAAGGGTAAAGTCTCGCTCAAAAA
+ATATACCCAACCTCTTCAAATGGTACAGGCTGATCTCTGTGGTGGGTTTCGCTACCAAGA
+GTTTCAGTCAAATAAATATTTTCTTACTATCCGTGATGCCTATAGTCGCTACTACTCTGT
+AATACATTTAAAATCCAAAGCAGACGCTCCGATAAAATTCATGGAATGGATCAACGAAAC
+CGAACAATACTTTAGCTCCCGGGGTGGATTCAAAGTCGGATCTGTTCGTACAGACAATGG
+TACAGAATTCGTAAATAAAAATCTTCATGCGTTTTTTAAATCTAAAGGAATAGAGCATCA
+GTTAACTATTCCATATCATAGTTATCAAAATGGTGCTGTTGAACGTGCACATCGTACCAT
+CGAAGAACGCACTCGTTGTCTCCTTATCGGGGGGCGTGTTCCTCCGTCCTTGTGGTCTGA
+AGCTGTTTCTTGCGCAGTCTATTTAATCAATAGGTCCCCTGTAGTGTCCAAAAATAACAG
+TATCCCATACTGCCGGTGGTTCAACATCCCCGCAAAAGATTTCGGTATCGCACATCTTCG
+AATTTTTGGATGTACAGCATACGCAACCTTACAACCTAGTCTTCGAGACGGCAAACTTGC
+CCCAACTGTCATATCTGGTGTTATGGTTGGCTATGACTCTAACCATCGAGGATACAGGAT
+TTATCATCCCGAAACTGGCCGCATCTTTGTGAGCAGTCAAGTTCGATTTGACGAACACAT
+GTTTCCTCTTGCTGATACAGAGGCAGTTCACGTCTCTCACGACTTTGCCACTTCCGCTAT
+TGGGGGGGTGTCCAAATATCCTGAAACAGGGTCAACCGTCTCTGCTCCAAAGAACGACGG
+ATCTGACTTGGCAAATTTGCCAATAACTGTTCCCAAAAATGTAAATCAACCAGCACATAA
+ACCTAATACCAGTAACATCTCTTCCTCTGATGATGATGAGGATATTTCAATGGAAATCGA
+AATGGAAAAACCTATCCCTGAGTGTAACCAAGACAACTTACCAAACTCCGGATGTCCACC
+AACAAGGATACAACATTCTAACTTTGAATCCTTACCAACCGTGTCTACCGAAGACGAAAC
+TAATTCTTCTATGGAGAAAACTCCTGAAAGAGTTCCAGCGGCACTAACTTATCGAGAAAT
+TCCAAAATCATCCGATTCAGAATATATTCCGACATGCCGAAATAGAACTAGACGTGTTAA
+AAGAACTAATAAGAAACCAACGCGATCCCGCGAAATAGAAATATATGATATATCACGTCC
+AAACGTAATATCGAGTGACAACTTACCTGAAGTTAGAAGTGCCAAGCAAAGAAAGACGGT
+GTCCAATACAAATGATACTGTAGCAAGGACAAATAGACTTCCAACCGTGCTACGAACTCT
+AGACTCAAACAACATTGACACGCTGCATGTTGCCAGTACTGGTGAAGAAGTGTCCATCGA
+AAGACTTTCAAGCATGGCTCTTCAGGAAGCGAAGAACAATTCCGCCAGAACTAATCAAGC
+TAATTCTCTTACTGATTGGTTTCCAGTAGGCGCAATGCCGATACCTGACCAGAGGTATCT
+ATCCGTTCACGATGGAACATATATCAGCGACTCACAAGATGTGGGTGATACTGACCTCAC
+TCCTGCTGTAACCAGGCTAGTTACTGAAGAGAATTCAATCGAATCTCCTCCATCGTTGGA
+TTCATCGCCTCCAAATACCTCATTTAACGCGGCTCTAACTGCTATTATCCATAGCACAAA
+AAAAGGAAACCCGAAAACCTATGCCCAAGCAATGGGAAGGCCTGACTTTCAAGAATGGCA
+CAACGCATGCCTCAAGGAACTTTCCGCGTTCAAAGATCACAATACGTACAAATTGGTGTC
+TCTTCCAAAGCAAAGAAGAGCTCTTGGATCGCGCTGGGTATTCACAATAAAAGACTCCGG
+GACGTACAAAGCTCGCCTTGTCGCCCAAGGACATACTCAAAAGGCTGGTATTGACTATCA
+AGAAACTTTTGCACCAGTCATTCGATATGACTCTGTTAGATTATTTCTGGCCCTTGCTAG
+CTGCCTCAAACTAATAGTATATCAGATGGACGTTGACACCGCGTTTCTAAACTCAAAAAT
+GAATGAGCCGGTATACGTAAAACAACCACCCGGATTTATTAATGAAAGTAATCCCGACTA
+TGTATGGGAACTATACGGCGGTATGTATGGACTCAAGCAAGCCCCATTACTATGGAACGA
+ACATATCAACAATACTCTTCAAAAGATTGGTTTTCGTCGACATGAAGGCGAACATGGCTT
+ATACTTTCGTTCCACATCTGATGGTCCCATCTACATTGCCCTATACGTAGACGACTTACT
+TGTTGCTGCTCCCTCTCCGAAAATATATGACAGGGTTAAGCAGAAACTAACGAAGTTATA
+CTCAATGAAGGATCTAGGTAAAGTTGACAAATTCCTCGGTCTTAACATTAATCAATTTTC
+AAATGGAGACATCACTCTCTCACTTCAAGACTATATTGCTAAAGCTGCATCTGAAAGCGA
+AATAAACATATGTAAGCCTACACAGACTCCGCTCTGTGACTCAAAGCCTCTTTTCGAAAC
+AACTTCCCCGCACCTAAAGGACATCACTCCTTATCAGAGCATAGTTGGACAGCTTCTCTT
+TTGTGCAAATACTGGTCGTCCTGACATATCTTATCCGGTCTCACTACTCTCCAGGTTTCT
+TCGCGAACCTCGCGCAATCCATTTGGAGTCTGCTCGACGAGTTCTACGGTACCTATATAC
+CACCAGAAGTATGTGTCTCAAGTATCGTTCTGGATCTCTGTTGGCACTAACTGTATATTG
+TGATGCATCTCATGGAGCAATTCACGATCTCCCACACTCTACTGGGGGGTACGTGACTCT
+ACTTGCTGGTGCTCCAGTTACGTGGTCATCAAAGAAACTCAAGGGTGTGATTCCTGTATC
+ATCTACTGAGGCAGAATACATTACTGCAAGTGAAACTGTCATGGAGATAGAATGGATTCA
+AAACTTGTTTGAACACTTAGGCCAGCCACTTATCTCATCAACATTATACGTAGATAATGA
+ACCTGCTATAAAACTATCTAAACATCCTGTATTTCACACGAGAACAAAACACATTGCCTT
+GAGATATCACAAGCTAAGAAGTGCAGTGGCAGCAGGCATAATTACCATAGAGCATGTTAT
+TACAAAGAGACAAGTTGCTGACATATTTACAAAAATCCTTCCAGCAGAATCATTCAAAGC
+ACATAGGGCTGTCATGGTGAGGGAACCAGAAACTGCAAAATAACCACTCTCATGCGTATT
+CAGTTATGGGGGGA
+>TY5-LTR#LTR/Copia
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTACATA
+ACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCA
+CTACGTCAACA
+>TY5p-I#LTR/Copia
+GGTTATGAGCCCTGAGAGCAATGCTTCAGAGACCATAATTAATCTATCTAATCCCAACAA
+TTATAAACAGTGGCTGTACGGTATCGAGACCGCTGCTGAATATGCTAACGAATATATGAA
+CGAATTCGTTCATACCGGAGATATCCAATCAATGAAAAGGGATTACAATCTCAGCGCGAA
+TGATGAAAGCTTTGTCAAAACCGTATTTAACAGTTTCCTGGTAAAGCTCTACAAGAAAAC
+TATCGTGGGTGAAGCTGCATGTGAAATGAACTGGATATGTGATGATTCACTTGGAAGGGT
+CTCTGCTTATGATATTTTCTCGCACTTCGAAGAAAACTATAATGAAGTCACTATTGGATC
+CAGGCTTACTCTTATAGAGGACTTACCAAATATATCCTCCAAGCCTGTAGATGAAATCGC
+TTCCTTTTTTGAAAACCCTATTCACAATGCTTGAAGACAATAGCGAAGAACAGGACAAAA
+AGAAAAGACGCGATACCAATATCGCGTTGCTATTAATGACCTTCTTACCCGAGTTAAAGG
+AATCATTCCACGAGAAATTCGGTGACTCTAAAGCTCTTCAGCTGTCACAAGTCATTAGAT
+TCTGTAAATTAAAGGCGTCATCGAATTCATTATCTTCAGTCTCAGATGCATTGGTTGCAC
+AAGACAGAAGAAGCTATCAAAAGAAAGGAAATAAGGGATGTATGATTTGTGGGGCTGATC
+ATCGCTTAAGCAACTGTTCTCTGCTTAAAAGAAGAATACCAGAAGCCAGAATCTTTAAAT
+TATATCCTAATGACAAGACGAATAGATCTTCATCTGCTAGTGTTGCGATTCCTGACTATG
+AAACGCAAGGCCAAACAGCAGGACAGATAACACCAAAGTCCTGGCTCTGTATGTTATCTT
+CGACCGTCCCAGCTACCAAATCCTCAGATTGGATTTTTGACACAGGATGTACTTCACACA
+TGTGCCACGACCGTTCTATGTTCTCATCATTTACTAGATCCTCTAAGAAAGACTTTGTCA
+GAGGAGTCGGCGGTTCCATACCCATCATGGGCTCCGGGACTGTAAACATCGGCACTGTTC
+AATTAAATGACGTATCCTACGTCCCTGATTTACCAGTCAACCTAATATCCATTTGGAAAC
+TATGTGCTAAATCCAACTCTTCTGTTACGTTCACAAAAGAGGGTGTCACTGTGAAATCAC
+CTGATGACGTGATTTCTACGGCTGGGAAGTTAAACAATTATCTGTACATTTTCGATGATC
+TTACGCCCGTAACTACCTTCTCTTCGCAAAATTACTTCTGCTCTAAAACATTGGATTCAT
+CTAAAATGATAACTTCCGCAGCGTTTCATACCGTTGCAGATAAAATGTTGTCGCAACACA
+TTTCTCCCACTGCTCTCCCGGTAAAATGGCATGCTCGTATGGGCCATCCCGGAGCAGATA
+TTTACAATTCCTTGGCTAGAACTCTGCGTTTTCCAAAATTTTAAGACGGCTGAATACACT
+ATTTGTCCTACCTGCTCACTAGCAAAAGGAATCATCAAAAAGGGTAAAGTCTCGCTCAAA
+AAATATACCCAACCTCTTCAAATGGTACAGGCTGATCTCTGTGGTGGGTTTCGCTACCAA
+GAGTTTCAGTCAAATAAATATTTTCTTACTATCCGTGATGCCTATAGTCGCTACTACTCT
+GTAATACATTTAAAATCCAAAGCAGACGCTCCGATAAAATTCATGGAATGGATCAACGAA
+ACCGAACAATACTTTAGCTCCCGGGGTGGATTCAAAGTCGGATCTGTTCGTACAGACAAT
+GGTACAGAATTCGTAAATAAAAATCTTCATGCGTTTTTTAAATCTAAAGGAATAGAGCAT
+CAGTTAACTATTCCATATCATAGTTATCAAAATGGTGCTGTTGAACGTGCACATCGTACC
+ATCGAAGAACGCACTCGTTGTCTCCTTATCGGGGGCGTGTTCCTCCGTCCTTGTGGTCTG
+AAGCTGTTTCTTGCGCAGTCTATTTAATCAATAGGTCCCCTGTAGTGTCCAAAAATAACA
+GTATCCCATACTGCCGGTGGTTCAACATCCCCGCAAAAGATTTCGGTATCGCACATCTTC
+GAATTTTTGGATGTACAGCATACGCAACCTTACAACCTAGTCTTCGAGACGGCAAACTTG
+CCCCAACTGTCATATCTGGTGTTTATGGTTGGCTATGACTCTAACCATCGAGGATACAGG
+ATTTATCATCCCGAAACTGGCCGCATCTTTGTGAGCAGTCAAGTTCGATTTGACGAACAC
+ATGTTTCCTCTTGCTGATACAGAGGCAGTTCACGTCTCTCACGACTTTGCCACTTCCGCT
+ATTGGGGGGGTGTCCAAATATCCTGAAACAGGGTCAACCGTCTCTGCTCCAAAGAACGAC
+GGATCTGACTTGGCAAATTTGCCAATAACTGTTCCCAAAAATGTAAATCAACCAGCACAT
+AAACCTAATACCAGTAACATCTCTTCCTCTGATGATGATGAGGATATTTCAATGGAAATC
+GAAATGGAAAAACCTATCCCTGAGTGTAACCAAGACAACTTACCAAACTCCGGATGTCCA
+CCAACAAGGATACAACATTCTAACTTTGAATCCTTACCAACCGTGTCTACCGAAGACGAA
+ACTAATTCTTCTATGGAGAAAACTCCTGAAAGAGTTCCAGCGGCACTAACTTATCGAGAA
+ATTCCAAAATCATCCGATTCAGAATATATTCCGACATGCCGAAATAGAACTAGACGTGTT
+AAAAGAACTAATAAGAAACCAACGCGATCCCGCGAAATAGAAATATATGATATATCACGT
+CCAAACGTAATATCGAGTGACAACTTACCTGAAGTTAGAAGTGCCAAGCAAAGAAAGACG
+GTGTCCAATACAAATGATACTGTAGCAAGGACAAATAGACTTCCAACCGTGCTACGAACT
+CTAGACTCAAACAACATTGACACGCTGCATGTTGCCAGTACTGGTGAAGAAGTGTCCATC
+GAAAGACTTTCAAGCATGGCTCTTCAGGAAGCGAAGAACAATTCCGCCAGAACTAATCAA
+GCTAATTCTCTTACTGATTGGTTTCCAGTAGGCGCAATGCCGATACCTGACCAGAGGTAT
+CTATCCGTTCACGATGGAACATATATCAGCGACTCACAAGATGTGGGTGATACTGACCTC
+ACTCCTGCTGTAACCAGGCTAGTTACTGAAGAGAATTCAATCGAATCTCCTCCATCGTTG
+GATTCATCGCCTCCAAATACCTCATTTAACGCGGCTCTAACTGCTATTATCCATAGCACA
+AAAAAAAGGAAACCCGAAAACCTATGCCCAAGCAATGGGAAGGCCTGACTTTCAAGAATG
+GCACAACGCATGCCTCAAGGAACTTTCCGCGTTCAAAGATCACAATACGTACAAATTGGT
+GTCTCTTCCAAAGCAAAGAAGAGCTCTTGGATCGCGCTGGGTATTCACAATAAAAGACTC
+CGGGACGTACAAAGCTCGCCTTGTCGCCCAAGGACATACTCAAAAGGCTGGTATTGACTA
+TCAAGAAACTTTTGCACCAGTCATTCGATATGACTCTGTTAGATTATTTCTGGCCCTTGC
+TAGCTGCCTCAAACTAATAGTATATCAGATGGACGTTGACACCGCGTTTCTAAACTCAAA
+AATGAATGAGCCGGTATACGTAAAACAACCACCCGGATTTATTAATGAAAGTAATCCCGA
+CTATGTATGGAACTATACGGCGGTATGTATGGACTCAAGCAAGCCCCATTACTATGGAAC
+GAACATATCAACAATACTCTTCAAAAGATTGGTTTTCGTCGACATGAAGGCGAACATGGC
+TTATACTTTCGTTCCACATCTGATGGTCCCATCTACATTGCCCTATACGTAGACGACTTA
+CTTGTTGCTGCTCCCTCTCCGAAAATATATGACAGGGTTAAGCAGAAACTAACGAAGTTA
+TACTCAATGAAGGATCTAGGTAAAGTTGACAAATTCCTCGGTCTTAACATTAATCAATTT
+TCAAATGGAGACATCACTCTCTCACTTCAAGACTATATTGCTAAAGCTGCATCTGAAAGC
+GAAATAAACATATGTAAGCCTACACAGACTCCGCTCTGTGACTCAAAGCCTCTTTTCGAA
+ACAACTTCCCCGCACCTAAAGGACATCACTCCTTATCAGAGCATAGTTGGACAGCTTCTC
+TTTTGTGCAAATACTGGTCGTCCTGACATATCTTATCCGGTCTCACTACTCTCCAGGTTT
+CTTCGCGAACCTCGCGCAATCCATTTGGAGTCTGCTCGACGAGTTCTACGGTACCTATAT
+ACCACCAGAAGTATGTGTCTCAAGTATCGTTTCTGGATCTCTGTTGGCACTAACTGTATA
+TTGTGATGCATCTCATGGAGCAATTCACGATCTCCCACACTCTACTGGGGGTACGTGACT
+CTACTTGCTGGTGCTCCAGTTACGTGGTCATCAAAGAAACTCAAGGGTGTGATTCCTGTA
+TCATCTACTGAGGCAGAATACATTACTGCAAGTGAAACTGTCATGGAGATAGAATGGATT
+CAAAACTTGTTTGAACACTTAGGCCAGCCACTTATCTCATCAACATTATACGTAGATAAT
+GAACCTGCTATAAAAACTATCTAAACATCCTGTATTTCACACGAGAACAAAACACATTGC
+CTTGAGATATCACAAGCTAAGAAGTGCAGTGGCAGCAGGCATAATTACCATAGAGCATGT
+TATTACAAAGAGACAAGTTGCTGACATATTTACAAAAATCCTTCCAGCAGAATCATTCAA
+AGCACATAGGGCTGTCATGGTGAGGGAACCAGAAACTGCAAAATAACCACTCTCATGCGT
+ATTCAGTTATGGGGGGA
+>TY5p-LTR#LTR/Copia
+TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATT
+GTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTAC
+TTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTTACAT
+AACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTC
+ACTACGTCAACA
+>TSU4b-I#LTR/Copia
+TGGCGACCCCAGTGAGGGATGAGACAAGATATGTTATTGACGACAACATATCTACGCAGG
+TTCAATCAAAAGTCAAATTTCAAAACTTAAGTTTTGATACTTCCGTTAAAAACAAACAAA
+GGATTCAAACTCAAATTGATTTAAAAATGTATGAAAGATTCTTAAACAAATTAACCACTA
+AAAAGAATAAAATTGCAAATGAGGCTGAAGAGGATGATGATATTTCAAATCTCGACCAGT
+TAATTGAAGTCGATGAAAAAATTGAAAAAACTAATAATATAATTCTTAGGTTACAAGAAA
+AGTTAGAATTGATTGAATTCAATAAAGATGTTAAGAAGTTACATAAAAGAAATGATTCCA
+CTGGAACATATTACTTATTCGACACAATTACCTCAAAAAATAATAAATATTATCCTAAGG
+ATTGGATATTCAAGTATAAGATGAATAAAATTGGAGATATTCCTGTTTTTTTGAACAACT
+TTCACCAATTCATTGAAAAATATGAATTCGATAATGTTTTTGATCAACAAATACAAAACA
+TCGATCCCCGTGAAAACGAAATCTTATGTAAGATTATCAAAGAAGGTTTTGATGAAAGTC
+CTGATATAATGAACATTAATACAGTTGACATCTTTAGAATCATTAGTGAATTAAAGAAAA
+AATACACTCGTTTTTTTGGCAGAGATAGAAGGTTAAAGGCTTGGGAAAAAGTGTTGGTGG
+ATACAACTTGTAAGAATACTGAATTATTGATAAATGAACTTCAAAAGTTAATATTAATGG
+AAAAATGGATTCTTTCAAAGTGTTGTCAAGATTGTCCAAATCTTACACACATTTTAGAAG
+AGGCTATTCTTGGAACCTTACATGAATCTGTGAGAAATCCGGTTAAACAACGTTTACACA
+TGTACTCAATTAGTGAAAATGAAAAAACTGAAGAAATTCTGATTAACATCGTAATTGAAA
+CAGTAATGGACTTGAGTCCACCTGACTCTCATTATACAGAAAGAAATTGTAAGTACTGTA
+AATCGGAATTACACAGCTCTGTGAACTGTAGAAAGAAAGTAAACAGAGAACTTAGGCCTA
+CTACATCCAGCTACTCAAAAGGTAATTATTCACAAGGCTCAAACCAAAAAGAATACACAA
+AGACTGGCACAAAACCATTCAGAACTTTTGAAAAGACAAAAGAAGAAGAACAAAAAGGGT
+TCAAACAAAACTCTAGTAATTATTGATACCGGTTCAGGCGTCAATATTACGAATAATAAG
+AATTTATTACACGAGTACGAGGACAACAAAGAAAAAGTAAAATTCTTCGGTATTGGGAAA
+GATAACTCAGTTCCTGTTAAAGGATCAGGATACATTAAAATAAAAAGTAACACAAATGAT
+GATTACTTATTAACTCATTATGTTCCTGAAGAAAAAACTACCATTATCAGTGGATATGAT
+TTAGCCAAAGAAACCGATCTCGTATTAAACCAAAACTACTCCACCTTGGAAAACAAGGAC
+ATGAACATTAAAACTCATGTAAAAGATGGAATTATTCACGTAAGAATGGATGACTTAATA
+GATCATCCTGCATATGATTATAAAATCAATGCGATACAACCTACTTCTTCTAAAAAAATT
+AGACTGAAGCCCAAAATTATAAGCTTAAAAGATGCTCATAAACGAATGGGACATACAGGA
+GTTCAACAAATTGAAAACTCTATTAAACATAGTCATTACGAAGAAAGTATTGATTTAATT
+AAAGAACCAAATGAATTTTGGTGTGAAACTTGTAAAGTTTCAAAAGCCACGAGAAGGAAC
+CATTATGCTGGATCCATGAATGAACACAGTATCGATCATGAACCTGGTTCATCGTGGTGC
+ATGGATATCTTTGGTCCAGTATCAAATTCGAACTTGGATACAAAAAGATACATGCTTATT
+ATGGTTGATAACAATACAAGATATTGTATCACCTCCACACATTTTAATAAAAATGCTGAA
+ACTATCTTGGCACAGATCAAGAAGAATATTCAGTATGTGGAAACTCAATTCGACAGAAAA
+GTCAGAGAAATCAATTCAGATCAAGGAACTGAATTTACAAATGATCAAATCGCAAAATAT
+TTTGTTTCAAAAGGAATTCATCATATATTTTCCGCTACACAAGATCATGCTGCCAACGGA
+AGAGCAGAAAGGTACATCAGAACCATCGTTACTGATGCAACAACTTTGTTAAAACATAGT
+AACTTACGTATTAAATTTTGGGAATACGCAGTAATATCTGCTACCAATGTACGCAATTGT
+TTAGAAAACAAAACCACAGGTCAACTACCGCTAAAGGCGATATCTAGTCAACCTGTTAAA
+GTGAGATTCATGTCCTTCTTACCATTTGGAGAACAAGGAATAATTTGGAATCATAATCAC
+AATAAACTAAAACCATCAGGACTTAGTGCTATAATATTATGCAAAGATCCTAATAGTCAC
+GGATACAAATTTTTTGTACCATCTATTAAAAAAATTGTCACTTCCGATAATTACACAATT
+CCAGACTATGCTGTGGATCCAATATTAAGGAACACACAGAACATATACCTAGATGATCAA
+AGCAGATCAGATACTTTCAATGAAGCAGAAAACATAGATGCTGTTTCAAGGTTGTATGAT
+TCACTGGAAGATTACGAAGATGATCATAAACAAGTTACACTACTTACAGACTTGTTCACC
+ACAGAAGAACTAGCCCAAATCGAAGCTAATTCTAAATATCCATCTCCTAGTGATAATCTA
+GAAGGTAATTTAGACTACGTTTTCTCTAACATAGAAGAATCTGACGAAGATGAATACGAT
+CATGTAACAAACATGGATGTAGATTCAGAACTTCAATCGAAAGAAAATATCACTACTGAA
+AGTGAAACAAACGAAATAAATAAACCAAGTAATACTGATGAGGATGTTTACGAAGAAAAT
+GTTTATAGAATTCCTACGGCAATACAAGAAAACCTTGTTGGAAGCCAGAAAACTATAAAC
+ATCAATAATGAGGATAATATTGCTAGCAGAATGCAAAAGAATATCAGTGGAAATGAAATA
+AACTACAAAGAATTATCAGATGACGACAGTGATTGTAGCCTTCATGATTCTACAAATGAC
+TCAGTTACGATTACAAGCAAAAAGGATAATTTAACAGATGATAAAGATTTACAATCACAG
+CAAGAATTATTCGAAAAAGTTAGTGATCCAGAAGTATTACCTGAACACATGAAAATTGAA
+AAAGATGTGGAGTCTCAAAATTCAGATAATGAAACCTCACAAGGCGTACAGTTTCAACCT
+GAATCAATTGTCACATCATCAAGTGACAATGATACTCAAAATGATGACTATTCAACTGAC
+AAAGAAAGTCATCACCTGCCCCTGGTTGTAAACGTTATGGACAATACTGACCAAACATAT
+GATAAACCAAACAAGGAAAAAAGTAAAAACAACTCTGATATAAGTATCTCACCGAAAGGT
+AATAATGAAGAGTTAGTACAATTGGTAGATAGTAACAAAGCCGAAAAACAGGATGCTACA
+CTAGAATCATCAGCGATAACAGATGAACCAATTGAAATAGAAAACCCAGCAGCAAACAAA
+GCTGGATTCTTAAATAAAGCGTTCAATTCTCTTAATAAGAAAAGGAAGAGACCTATTGAA
+AACAAGACTTCCTTTAATGACACAGCTAAAAGAGACAATAAACGTCAAAGAAAAAACATA
+ATCAAACTACTTCCGGATAACACAGAAACAAGTTCTGCACCGAGAATAAAAACCATCTAC
+TACAATGAAGCTATTTCAAGAAATGCTGATCTCAAAGAAAAACATGCTTATAAAGAGGCA
+TACAGGAAAGAATTACAAAATCTCAAGGATATGAATGTATTCGACGTAGATGTCAAATAC
+AACAGATCTGATGTTCCTAGTAATTTAATAATTCCGACAAATACAATATTCTCAAAGAAG
+AGAAATGGTATTTATAAAGCAAGAATTGTTTGTAGAGGTGATATCCAGACACCAGACACG
+TATAATGTTATTGGAACAGAATCACTGAACCATAATCACATTAAAATATTTCTGATGATT
+GCAAACAATAGAAACATGTTCATGAAAACATTAGATATTAATCATGCGTTCCTATATGCG
+AAATTAGAAGAAGACATATACATTCCACACCCACATGACAGGAGATGTGTTGTTAAACTA
+AATAAAGCACTATATGGGCTTAAGCAGAGTCCTAAAGAATGGAACGACCATCTTAGACGA
+TATTTAAACAGTATTGGATTAAAAGATAACACTTATACTCCAGGACTATACCAATCCAAG
+GATAAAAAACTCATGATCGCAGTTTATGTTGATGACTGTGTGATTGCAGCAAGTGATGAA
+CAAAGATTAGATGATTTCATAAACAATTTAGAAAATACCTTTGAGCTAAAAATCACCGGT
+ACTCTAATAGATGATATATTGGACACAGACATCTTAGGGATGGACTTGATCTATAACAAA
+AAACTTGGTACGGTGGATTTAACGTTAAAATCATTCATAGAAAAAATGGGTGAGAAGTAT
+AAAAAGGAATTGGATAAGGTTAGAAAAAGTTCAATTCCACATACATCAGTATACAAGATT
+GATCCCAAAAAGGGAGAATTAAAGATGACCGAAAAAGAATATAAAAACGGTGTGTTGAAA
+TTACAACAACTACTAGGAGAACTTAACTATGTTAGGTACAAGTGTAGATACGATGTTGAA
+TTTGCGGTCAAGAAAGTAGCTAGATTAGTAAACTTTCCTCATGAACAGGTATTTTACATG
+ATTTACAAAATCATACAATATTTAGTACAACATACGAATATCGGAATACACTATGATAGA
+GACCTCAACAAAGATAAGAAAATCACTACTATCACTGATGCATCAGTTGGAACAGAATAC
+GATGCGCAATCAAGAATTGGAGTTATAATTTGGTATGGAAAGAACATTTTCAATGTATAC
+TCAAATAAAAGCACCAACAAGTGCGTATCCTCAACCGAAGCGGAACTTCATGCTATCTAT
+GAAGGTTATGCAGACTCAGAAACCCTGAAAGCAACCTTAACAGAACTCGGAGAAGGTAAA
+GATAAAGAAATTACAATGATTACGGATTCAAAACCAGCTATTGAAGGCTTAAATCGTAGT
+TACCTACAACCGAAACAGAAGTTCACATGGATAAAAACCGAAATAATTAAAGAGAAGCTA
+AAAGAGAAGATTATAAAACTAATAAAAATCAATGGTAAAGACAATATAGCAGATTTACTC
+ACAAAACCAGTATCAATTTCTGACTTTGATAGATTTATTAAAGTATTGAATAATCAGATA
+ACACCACAGGATATTTTGGCCTCAACGGACTATTGATAATTACATTACTTAATTAAGAAC
+CAAACGCACAACAGATATCTGTTGGAGTACAATAATATATCTTTAAGGGGGC
+>TSU4b-LTR#LTR/Copia
+TGTTGGAATAAAGTGATCTTGGACATAACATTCTTATGTCAAAACAGGCGATCTCAACAT
+TCCTAATATGATATTAATTATGTTGTTCTGAAACAAACATACTTAATGAAGACGAGTTTA
+AAGACCTATTAATTGATCAAGAATTAGTATATAAGAAGATGATTTATACCTGAGAACCTA
+TTATCAATGTTCTGAATTATACTTGAACCATTGGGTTTCATATAACCAATCAGCGTGCGT
+TTTATATACCTCTCTTATATAATAAGAAAGAACTGCTTATTCTTAATTATTACTACCTAC
+TAAACTTACTAATTATCAACA
+>TSU4p-I#LTR/Copia
+TGGCGACCCCAGTGAGGGATGACACAAGATATGTTACTGACTACAACATTTCTAACCTGG
+TTCAATCAAAAGTCAAACTCCAAAAATCAAGTATTGATATTTCCGTTAAAAACAAACTAA
+GGAATCAAACTCAAATCGATTTGAAAACGTATGAAAGATTCTTACACAGATTAACCACTA
+AAAAGAATAAAATTACAAATGAGGCTGAAGAGGATGACGATATTTCAAATCTCGACCTTT
+TAATTGAAGTAGATGAAAAAATCGAAAAAACTAATAATATAATTCTTAGGTTACAAGAAA
+AGTTAGAATCGATTGAATTAGATAAAGATGCTAAGAAGTTACACGAAAGAAATGATTCCA
+CTGGAACATATTACTTATTCGATACTCTTACCTTAAAAAACAGGAAATATTATCCTAAGG
+ATTGGATTTTCAAGCATAAAATGAATAAAATTGGAGATATTCCTGTGTTTTTGAACAGCT
+TTCAACAATTCATTGAAAAGCATGAATTCGATAATATTTTTGAACAACAAATACAAAACA
+TCGATCCTCGTGAAAACGAAATCTTGTGTAAGATTATCAAAGAAGGTTTCGATGAAAGTC
+CTGATATAATGAACATTAACACAGTTGACATCTTTAGAATCATTCGTGATTTAAAGAAAA
+AATACACAAGCCTTTTTGGCAGAGATGTAAGACTAAAGGCTTGGGAAAAAGTGTTGGTGG
+ATACAACTTGTAAGAATACTGACTTATTGATGAATGAACTTCAAAAGTTAGTATTAATGG
+AAAAATGGATCCTTTCAAAATGTTGTCAAGACTGTCCAAATCTCACACACATTTTAGTAG
+AAGCAATTCTTGGAACCTTACATGAATCGTTGAGAAATCCGGTTAAGCAACGTTTACACA
+TCTGCTCAATTGATGAAAATGAGAGAGTCGAAGAAGTTCTAATCAATATCGTAATTGAAA
+CAGTAATGGACTTGAGTACAACAGATTTGTATTATCCAGAAAGAAATTGCAAGTACTGTA
+AATCGGAATTCCACAGCTCGGTAAATTGTAGAAAGAAACTAACCAGAGAACTTAGGCCTA
+CCACGCCCAGTTACTCAAAAGGTTATTATTCGCAAGGTTCAACCCAAAAAGAATACACTA
+AAACTGGCACAAACCCAGACAGAGCCGTTAAAAAGGCTAAAGAAGAAGAACAGAAAGGGT
+TCAAACAGAAACCTAGTCATTATTGATACTGGGTCAGGCGTCAACATTACGAATAACAAG
+AGATTATTACATGAGTATGAAGACAACAAAGAAAAGATAAGATTCTTTGGTATTGGAAAA
+AACAATTCAGTTCCCGTTAAAGGATCAGGATACATTAAAATAAAAAGTAACACAAATGAT
+GATTACTTATTAACTCATTATGTTCCTGAGGAGGAAACTACCATTATCAGTGGCTATGAG
+TTAGCTAAAGAAACCGATCTTGTCTTGAACAAAAACTACTCCACGTTGGAAAACAAGGAC
+ATGAACATTAAGACTCATGTAAAAGATGGGATTATTCATGTAAAAATGGACGATTTAATT
+GATCATCCTGCATATGATTTTAAAATCAATGCAATACAACCTACTTCTTCTAAAAAAATT
+AGACTGAAGCCAAAAATTATAAGCTTAAAAGATGCTCATAAACGAATGGGACATACAGGA
+GTTCAACAAATTGAAAACTCCATTAAACATAGCCATTACGAAGAAAGTATTGACTTAATT
+AAAGAACCAAATGAATTTTGGTGCGAAACTTGTAAAGTTTCAAAAACCACGAGAAGGAAC
+CATTATGCTGGATCTATGAACGAACACAGTATCGGTCATGAACCTGGTTCATCGTGGTGC
+ATGGATATCTTTGGTCCAGTATCGAACTCGAACTCGGATACGAAAAGATACATGTTTATT
+ATGGTTGATAACAATACAAGATATTGTATCACCTCCACACATTTTAACAAAAATGCTGAA
+ACTATCTTAGCACAGATCAAGAAGAATATTCAGTATGTGGAAACTCAATTTGACAGAAAA
+GTCAGAAAAATCAATTCAGATCAAGGAACTGAATTCACAAATGATCAGATAGCAGAATAT
+TTTGTTTCAAAAGGAATTCATCATATTTTTTCCGCTACACAAGATCATGCTGCCAATGGA
+AGAGCAGAAAGACACATCAGAACCATCGTTACTGATGCAACAACCTTGTTAAAACATAGT
+AACTTGCGTATTAAATTTTGGGAGTATGCAGTAACATCTGCCACCAATGTACGCAATTGT
+TTAGAAAACAAAGCCACAGGTCAACTGCCGCTAAAGGCGATCTCTAGTCAACCTGTTAAA
+GTGAGATTCATGTCCTTCTTACCATTCGGAGAACAAGGAATAATTTGGAATCATAATCAC
+AACAAACTAAGACCTTCAGGACTTCGTGCTATTATATTATGCAAAGACCCTAATAGTCAC
+GGATACAAATTTTTTGTACCATCTCTTAAAAAAATTGTCACTTCTGATAATTACACAATT
+CCAGACTATGCAGTGGACCCAATATTAAGGAACACCCAGAACATATACCTAGATGATCGA
+AGTAGATCAGATACCTTCAATAAGACAGAAAACTCAGATGCAGTTTCAAGGTTATATGAT
+GCATTGGAAAATTACGAAGATGATCATAAACAAGTTACACTATTTACAGACTTGTTTACC
+ACAGAAGAATTAGCTCAAATCGAAACTAATGCTAAATATCCGTCTCCTAGTGATAATCTA
+GAAGGAAATTTAGACTACGTCTTCTCCAACACAGAAGAATCTGAAGAAGATGAATCTGAT
+CATGTGACAAACATGGATGTAGATTCAGAACTTAAACCAAATGAAAAGATCACTACAGAA
+AGTGAACGAAACGAATTAAATAAATCAAGTAATACTGATGAGGATTTTTACGATGAAAAA
+GCTTATAGAATTCCCACGGCAATACAAGAAAACCTTGTTGGAAGCCAGAAGACTATAAAC
+ATTAATAATGAGGATAATATTGCTAGCAGAATGCAAAGGAAGATTAGTGGAAATGAAATA
+AACTACAATGAATTGTCGGATGACGAGAGCGATTACAGATCTCATGACCTCACAGATGAT
+AATATCTCGAAATCCCAGCAAGAAATATTCAAGAAAACTATCGATTCAGAAGTACTACCT
+GAACAGATAAACATTGAAAAACATGTTACATTGCAAGATTCGGATAATGATACGTCACAA
+TGCGTAGAGGCTCAGCCTGAGTCAATTGTCACATCATCGAAAGAAGATGATGTTCAAAAT
+GATGACTATTCTTCTGACAAAGAAAGTCATCACCTGCCCCTGGGTGTAAATGTTATGGAC
+AATTCGATCCAAACATGTGTTGAACCAAACAAGGCAGAAAGCAAACACAACTCTGATACA
+ATTGCCTCACCGAAAGGTAATAATGAAGAGTTAGTACAATTGGTAGGAAGTAGCGGAGCA
+GAAAAACCGGATGCTACACCAGAATCATCAATGACAACAGATGAACCAATTGACCCAGGA
+AACCCAGCAGTAAACAAAGCTGGATTCCTAAACAAAACGTTCAATTCTCTCAATAAGAAA
+AGAAAGAGACCTGTTGAAAACAAGACTCCCTTCAATGACACAGTTGAAAGAGATTATAAA
+CGTCAAAGAAAAAAAATAATCAAACTACTTCCGGATAACACAGAAACAAGTTCTGCACCG
+AGAATCAAAACCATCTACTATAATGAAGCTATTTCAAGAAATGTTGATTTCAAAGAAAAA
+CATGCTTATAAAGAAGCATACAGGAAGGAATTACAAAATCTCAAGGACATGAAGGTATTC
+GACGTTGATGTCAAATACAACAGATCTGATGTTCCCAGTAATTTAATAATCCCGACGAAT
+ACAATATTCTCAAAGAAGAGAAATGGCATTTATAAAGCAAGAATTGTTTGTAGAGGTGAT
+ATCCAGACACCGGACACGTATAATGTTATTGGAACAGAATCCCTGAACCATAACCACATT
+AAAATATTTCTGATGATTGCAAACAATAGGAATATGTTCATGAAAACATTGGATATTAAC
+CATGCGTTCCTATATGCTAAATTAGAAGAAGACATATACATTCCACACCCACATGACAGG
+AGATGCGTTGTTAAACTAGACAAAGCGTTATATGGTCTCAAGCAGAGTCCTAAAGAATGG
+AACGACCATCTTAGACGATATTTAAATAGTGTTGGACTAAAAGATAACACATATACTCCA
+GGACTATACCAATCCAAGGATAAAAAACTCATGATCGCAGTTTATGTTGATGACTGTGTG
+ATTGCAGCAAGTGATGAACAAAGATTAGATGATTTCATAAGCAATTTAGAAAACACCTTT
+GAGCTAAAAATTACTGGTACTCTAATAGATGATATATTGGATACAGACATCTTGGGGATG
+GATTTGATCTATAACAAGAAACGTGGCACGGTGGATTTAACGTTAAAATCATTCATAGAA
+AAAATGGGTGAGAAGTATAAAAAGGAATTGGATAAGGTTAGAAAAAGTTCAATTCCACAT
+ACATCAATATACAGGATTGATCCCAAAAAGGGAGAACTAAAAATGACCGAAAAAGAATAT
+AAAGACGGTGTGTTGAAATTACAACAACTACTAGGAGAACTTAATTATTTTAGGTACAAG
+TGTAGATACGATGTTGAATTTGCGGTTAAGAAAGTAGCTAGATTAGTTAACTTCCCTCAT
+GAACAGGTATTCTACATGATTTACAAAATCATACAATATCTAGTACAACATGCGAATATT
+GGAATACACTATGATAGAGACCTTAACAAAGATAAGCAAATCACTACTATTACAGATGCA
+TCAGTTGGAACAGAATACGATGCACAATCAAGAATTGGAGTTATAATTTGGTATGGAAAG
+AACATTTTCAATGTATACTCAAATAAAAGCACCAACAAGTGTGTATCCTCAACCGAAGCG
+GAACTTCATGCTATCTATGAAGGTTATGCAGACTCAGAAACCCTGAAAGCAACCTTAACA
+GAACTTGGAGAAGGAAAAAATAAAGAACTTACAATGATTACTGATTCAAAACCAGCTATC
+GAAGGCTTAAAACGGAGCTACCTACAACCCAAACAGAAGTTCACATGGATAAAAACCGAA
+ATAATTAAAGAGAAACTAAAAGAGAAGACTATAAAACTAATAAAAATCAATGGTAAAGAA
+AATATAGCAGATTTACTTACAAAACCAGTATCAATTTCTGACTTTGATAGATTTATTAAG
+GTATTGAAGAATAAGATAACACCACAGGATATTTTGGCCTCAACGGACTATTGATAATTA
+AATTACTTAATTAAGAACCGAACACACAGCAGATATCTGTTGGAGTACAATAATATATCT
+TTAAGGGGGCA
diff --git a/data/TY_lib.Yue_et_al_2017_NG.LTRonly.fa b/data/TY_lib.Yue_et_al_2017_NG.LTRonly.fa
deleted file mode 100644
index 4fe75b5..0000000
--- a/data/TY_lib.Yue_et_al_2017_NG.LTRonly.fa
+++ /dev/null
@@ -1,18 +0,0 @@
->TY1/TY2-LTR#LTR/Copia/TY1
-TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACATATTTCTCA
->TY1/TY2-LTR#LTR/Copia/TY1p
-TGTTGGAATGAAATTCTAATATCATCTATTTAATAGTATATTATAATATGCGGTGCAAGAGGATGACATAAAGATTGAGAAACAGTCATCCAATCTAATGGAAGCTGAAATGCAAGGATTGATAATGTAATAGGATAATGAATAACAACATATAAAAAGAAAGAAGATAAAATAATAACACTATGTAGAACTATCGATTCCCTTTTGTGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTATATACCTAATATTATAGCCTTTAGTAACAATGGAATCCCAACAATTATCTAATTACCCACACAATTCTCA
->TY1/TY2-LTR#LTR/Copia/TY2
-TGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAATGATGATAATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATGGATTCCTAAATCCTCGAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAAATGGAATCCCAACAATTACATCAAAATCCACATTCTCTTCA
->TY3-LTR#LTR/Gypsy/TY3
-TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCACCCTGAACGTTCATAAAACACATATGAAACAACCTTATAACAAAACGAACAACATGAGACAAAACCCGACCTTCCCTAGCTGAACTACCCAAAGTATAAATGCCTGAACAATTAGTTTAGATCCGAGATTCCGCGCTTCCACCACTTAGTATGATTCATATTTTATATAATATATAAGATAAGTAACATTCCGTGAATTAATCTGATAAACTGTTTTGACAACTGGTTACTTCCCTAAGACTGTTTATATTAGGATTGTCAAGACACTCCGGTATTACTCGAGCCCGTAATACAACA
->TY3-LTR#LTR/Gypsy/TY3p
-TGTTGTATCTCAAGATGAGATACCTCAGCATTACTAGATTTACCAACCTAGACATAAAACATGTATGAAACACGTACGAAACAATAGACAAGATTGAGTATACTAGGCAACCTACTTGCCTAAGATGAACCAAACTAACCAAACGTATAAATACCTGAACAATTAGTTTAGATCCGAGATTCCGCGCTTCCACCCTTTAGTTAGATTCAGATCTTATATAGATTATATAGGATAAGTAACATTCTGTGAATCACGATAATAATAAGTCTGACAACAAGTTACTCTCCTAAACGACTTTAGGATTGTCAAGACATCCGGTATTACTCGAGCCCGTAATACAACA
->TY4-LTR#LTR/Copia/TY4
-TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATGGTAACAATCTAATGCTTACATCGTATATTAATGTACAACTCGTATACGTTTAAGTGTGATTGCGCCTATTGCAGAAGGAATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGTGTTAAAGACCTATTAGTTGAACATGTTATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCGGAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTCTCTTATTTAGTATAAGAAGATCAGTACTCACTTCTTCATTAATACTAATTTTTAACCTCTAATTATCAACA
->TY4-LTR#LTR/Copia/TY4p
-TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATAGTAACAATCTAATGCTTACATCGTATATTAATGTACACCTCGTATACGTTTAAGTGTGATTGCACCTATTGCAGAAGGAATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGAGTTAAAAATCTATTAGTTGAACATGATATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCGGAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTCTCTTATTTAGTATAAGAAGATCAGTACTTATTTCTTCATTAGTACTATATTTTAACCTCTAATTATCAACA
->TY5-LTR#LTR/Copia/TY5
-TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATTGTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTACTTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTACATAACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCACTACGTCAACA
->TY5-LTR#LTR/Copia/TY5p
-TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATTGTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTACTTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTTACATAACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCACTACGTCAACA
diff --git a/data/TY_lib.Yue_et_al_2017_NG.fa b/data/TY_lib.Yue_et_al_2017_NG.fa
deleted file mode 100644
index cb04beb..0000000
--- a/data/TY_lib.Yue_et_al_2017_NG.fa
+++ /dev/null
@@ -1,36 +0,0 @@
->TY1-I#LTR/Copia
-TGGTAGCGCCTGTGCTTCGGTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGACGTTTCAGCTTCCAAAACAGAAGAATGTGAGAAGGCTTCCACTAAGGCTAACTCTCAACAGACAACAACACCTGCTTCATCAGCTGTTCCAGAGAACCCCCATCATGCCTCTCCTCAAACTGCTCAGTCACATTCACCACAGAATGGGCCGTACCCACAGCAGTGCATGATGACCCAAAACCAAGCCAATCCATCTGGTTGGTCATTTTACGGACACCCATCTATGATTCCGTATACACCTTATCAAATGTCGCCTATGTACTTTCCACCTGGGCCACAATCACAGTTTCCGCAGTATCCATCATCAGTTGGAACGCCTCTGAGCACTCCATCACCTGAGTCAGGTAATACATTTACTGATTCATCCTCAGCGGACTCTGATATGACATCCACTAAAAAATATGTCAGACCACCACCAATGTTAACCTCACCTAATGACTTTCCAAATTGGGTTAAAACATACATCAAATTTTTACAAAACTCGAATCTCGGTGGTATTATTCCGACAGTAAACGGAAAACCCGTACGTCAGATCACTGATGATGAACTCACCTTCTTGTATAACACTTTTCAAATATTTGCTCCCTCTCAATTCCTACCTACCTGGGTCAAAGACATCCTATCCGTTGATTATACGGATATCATGAAAATTCTTTCCAAAAGTATTGAAAAAATGCAATCTGATACCCAAGAGGCAAACGACATTGTGACCCTGGCAAATTTGCAATATAATGGCAGTACACCTGCAGATGCATTTGAAACAAAAGTCACAAACATTATCGACAGACTGAACAATAATGGCATTCATATCAATAACAAGGTCGCATGCCAATTAATTATGAGAGGTCTATCTGGCGAATATAAATTTTTACGCTACACACGTCATCGACATCTAAATATGACAGTCGCTGAACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAGAAACAGCAAACCTAATTACAGGAGAAATCTGAGTGATGAGAAGAATGATTCTCGCAGCTATACGAATACAACCAAACCCAAAGTTATAGCTCGGAATCCTCAAAAAACAAATAATTCGAAATCGAAAACAGCCAGGGCTCACAATGTATCCACATCTAATAACTCTCCCAGCACGGACAACGATTCCATCAGTAAATCAACTACTGAACCGATTCAATTGAACAATAAGCACGACCTTCACCTAGGCCAGGAACTTACTGAATCTACGGTAAATCACACTAATCATTCTGATGATGAACTCCCTGGACACCTCCTTCTCGATTCAGGAGCATCACGAACCCTTATAAGATCTGCTCATCACATACACTCAGCATCATCTAATCCTGACATAAACGTAGTTGATGCTCAAAAAAGAAATATACCAATTAACGCTATTGGTGACCTACAATTTCACTTCCAGGACAACACCAAAACATCAATAAAGGTATTGCACACTCCTAACATAGCCTATGACTTACTCAGTTTGAATGAATTGGCTGCAGTAGATATCACAGCATGCTTTACCAAAAACGTCTTAGAACGATCTGACGGCACTGTACTTGCACCTATCGTACAATATGGAGACTTTTACTGGGTATCTAAAAGGTACTTGCTTCCATCAAATATCTCCGTACCCACCATCAATAATGTCCATACAAGTGAAAGTACACGCAAATATCCTTATCCTTTCATTCATCGAATGCTTGCGCATGCCAATGCACAGACAATTCGATACTCACTTAAAAATAACACCATCACGTATTTTAACGAATCAGATGTCGACTGGTCTAGTGCTATTGACTATCAATGTCCTGATTGTTTAATCGGCAAAAGCACCAAACACAGACATATCAAAGGTTCACGACTAAAATACCAAAATTCATACGAACCCTTTCAATACCTACATACTGACATATTTGGTCCAGTTCACAACCTACCAAAAAGTGCACCATCCTATTTCATCTCATTTACTGATGAGACAACAAAATTCCGTTGGGTTTATCCATTGCACGACCGTCGCGAGGACTCTATCCTCGATGTATTTACCACGATACTAGCTTTCATTAAAAACCAATTTCAGGCCAGTGTCTTGGTTATACAAATGGACCGTGGTTCTGAGTATACTAACAGAACTCTCCATAAATTCCTTGAAAAAAATGGTATAACTCCATGCTATACAACCACAGCGGATTCCCGAGCACATGGAGTCGCTGAACGGCTAAACCGTACCTTATTAGATGACTGCCGTACTCAACTGCAATGTAGTGGTTTACCGAACCATTTATGGTTCTCTGCAATCGAATTTTCTACTATTGTGAGAAATTCACTAGCTTCACCTAAAAGCAAAAAATCTGCAAGACAACATGCTGGCTTGGCAGGACTTGATATCAGTACTTTGTTACCTTTCGGTCAACCTGTTATCGTCAATGATCACAACCCTAACTCCAAAATACATCCTCGTGGCATCCCAGGCTACGCTCTACATCCGTCTCGAAACTCTTATGGATATATCATCTATCTTCCATCCTTAAAGAAGACAGTAGATACAACTAACTATGTTATTCTTCAGGGCAAGGAATCCAGATTAGATCAATTCAATTACGACGCACTCACTTTCGATGAAGACTTAAACCGTTTAACTGCTTCATATCATTCGTTCATTGCGTCAAATGAGATCCAAGAATCCAATGATCTTAACATAGAATCTGACCATGACTTCCAATCCGACATTGAACTACATCCTGAGCAACCGAGAAATGTCCTTTCAAAAGCTGTGAGTCCAACCGATTCCACACCTCCGTCAACTCATACTGAAGATTCGAAACGTGTTTCTAAAACCAATATTCGCGCACCCAGAGAAGTTGACCCCAACATATCTGAATCTAATATTCTTCCATCAAAGAAGAGATCTAGCACCCCCCAAATTTCCAATATCGAGAGTACCGGTTCGGGTGGTATGCATAAATTAAATGTTCCTTTACTTGCTCCCATGTCCCAATCTAACACACATGAGTCGTCGCACGCCAGTAAATCTAAAGATTTCAGACACTCAGACTCGTACAGTGAAAATGAGACTAATCATACAAACGTACCAATATCCAGTACGGGTGGTACCAACAACAAAACTGTTCCGCAGATAAGTGACCAAGAGACTGAGAAAAGGATTATACACCGTTCACCTTCAATCGATGCTTCTCCACCGGAAAATAATTCATCGCACAATATTGTTCCTATCAAAACGCCAACTACTGTTTCTGAACAGAATACCGAGGAATCTATCATCGCTGATCTCCCACTCCCTGATCTACCTCCAGAATCTCCTACCGAATTCCCTGACCCATTTAAAGAACTCCCACCGATCAATTCTCGTCAAACTAATTCCAGTTTGGGTGGTATTGGTGACTCTAATGCCTATACTACTATCAACAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTAAGGTATCACGAGACACATGGAATACTAAGAATATGCGTAGTTTAGAACCTCCGAGATCGAAGAAACGAATTCACCTGATTGCAGCTGTAAAAGCAGTAAAATCAATCAAACCAATACGGACAACCTTACGATACGATGAGGCAATCACCTATAATAAAGATATTAAAGAAAAAGAAAAATATATCGAGGCATACCACAAAGAAGTCAATCAACTGTTGAAGATGAAAACTTGGGACACTGACGAATATTATGACAGAAAAGAAATAGACCCTAAAAGAGTAATAAACTCAATGTTTATCTTCAACAAGAAACGTGACGGTACTCATAAAGCTAGATTTGTTGCAAGAGGTGATATTCAGCATCCTGACACTTACGACTCAGGCATGCAATCCAATACCGTACATCACTATGCATTAATGACATCCCTGTCACTTGCATTAGACAATAACTACTATATTACACAATTAGACATATCTTCGGCATATTTGTATGCAGACATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGAATGAATGATAAGTTGATACGTTTGAAGAAATCACTTTATGGATTGAAACAAAGTGGAGCGAACTGGTACGAAACTATCAAATCATACCTGATACAACAATGTGGTATGGAAGAAGTTCGTGGATGGTCATGCGTATTTAAAAACAGTCAAGTGACAATTTGTTTATTCGTAGATGATATGGTATTGTTTAGCAAAAATCTAAATTCAAACAAAAGAATTATAGACAAGCTTAAGATGCAATACGACACCAAGATTATAAATCTAGGCGAAAGTGATGAGGAAATTCAATATGACATTCTTGGCTTGGAAATCAAATACCAAAGAGGTAAATACATGAAATTGGGTATGGAAAACTCATTAACTGAAAAAATACCCAAACTAAACGTACCTTTGAACCCAAAAGGAAGGAAACTTAGCGCTCCAGGTCAACCAGGTCTATATATAGACCAGCAAGAACTAGAGCTAGAAGAAGATGATTACAAAATGAAGGTACATGAAATGCAAAAGCTGATAGGTCTAGCATCATATGTTGGATATAAATTTAGATTTGACCTATTATACTACATCAACACACTTGCACAACATATACTATTTCCGTCCAAGCAAGTGTTAGATATGACATATGAATTGATACAGTTCATATGGAATACGAGAGATAAGCAATTAATATGGCACAAAAGCAAACCTGTTAAGCCAACAAATAAATTAGTTGTTATAAGCGATGCCTCGTATGGCAACCAACCGTATTATAAATCACAAATTGGCAACATATATTTACTTAATGGAAAGGTAATTGGAGGAAAGTCCACCAAGGCTTCATTAACATGTACTTCAACTACGGAAGCAGAAATACACGCGATAAGTGAATCTGTCCCATTATTAAATAATCTAAGTTACCTGATACAAGAACTTGACAAGAAACCAATTACCAAAGGATTACTAACCGACAGTAAATCTACAATCAGTATAATTATATCCAATAATGAAGAGAAATTTAGGAACAGATTTTTTGGTACTAAAGCAATGAGATTGAGAGATGAAGTATCAGGAAATCATCTGCACGTATGCTATATCGAAACCAAAAAGAATATTGCAGACGTAATGACCAAACCTCTTCCGATAAAAACATTCAAACTATTAACAAACAAATGGATTCATTAGATCTATTACATTATGGGTGGTA
->TY1-LTR#LTR/Copia
-TGTTGGAATAAAAATCCACTATCGTCTATCAACTAATAGTTATATTATCAATATATTATCATATACGGTGTTAAGATGATGACATAAGTTATGAGAAGCTGTCATCGAAGTTAGAGGAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATAAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAATATAGATTCCATTTTGAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTAATATTATAGCCTTTATCAACAATGGAATCCCAACAATTATCTCAACATTCACATATTTCTCA
->TY1p-I#LTR/Copia
-TGGTAGCGCCTGTGCTTCGGTTACTTCTAAGGAAGTCCACACAAATCAAGATCCGTTAGACGTTTCAGCTTCCAAAATTCAAGAATATGATAAGGCTTCCACTAAGGCTAACTCTCAACAGACAACAACACCTGCTTCATCAGCTGTTCCAGAGAACCCCCATCATGCCTCTCCTCAAACTGCTCAGTCACATTCACCACAGAATGGGCCGTACCCACAGCAGTGCATGATGACCCAAAACCAAGCCAATCCATCTGGTTGGTCATTTTACGGACACCCATCTATGATTCCGTATACACCTTATCAAATGTCGCCTATGTACTTTCCACCTGGGCCACAATCACAGTTTCCGCAGTATCCACCATCAGTTGGAACGCCTCTGAGCACCCCATCACCTGAGTCAGGTAATACATTTACTGATTCATCCTCAGCGGACTCTGATATGACATCCACTAAAAAATATGTCAGACCACCACCAATGTTAACCTCACCTAATGACTTTCTAAATTGGGTTAAAACATACATCAAATTTTTACAAAACTCGAATCTCGGTGATATTATTCCGACAGTATACGGAAAACCCGTACGTCAGATCACTGATGATGAACTCACCTTCTTGTATAACACTTTTCAAATATTTGCTCCCTCTCAATTCCTACCTACCTGGGTCAAAGACATCCTATCTGTTGATTATACGGATATCATGAAAATTCTTTCCAAAAGTATTGAAAAAACGCAATCTGATACCCAAGAGGCAAATGACATTGTGACCCTGGCAAATTTGCAATATAATGGCAGTACACCTGCAGATGCATTTGAAACAAAAGTCACAAACATTATCGACAGACTAAATAATAATGGCATTCATATCAATAACAAGGTCGCATGCCAATTAATTATGAGAGGTCTATCTGGCGAATATAAATTTTTACGCTACACACGTCATCGACATCTAAATATGACAGTCGCTGAACTGTTCTTAGATATCCATGCTATTTATGAAGAACAACAGGGATCGAGAAACAGTAAACCCAATTACAGGAGAAATCCGAGTGATGAGAAGAATGATTCTCGCAGCTATACGAATACAACCAAACCCAAAGTTATAGCTCGGAATCCTCAAAAAACAAATAATTCGAAATCGAAAACAGCCAGGGCTCATAATGTATCCACATCTAATAACTCTCCCAGCACTGACAACGATTCCATCAGTAAATCAACTACTGAACCGATTCAATTGAACAATAAGCACGACCTTCATCTTAGGCCAGAAACTTACTGAATCTACAGTAAATCATACGAATCATTCCGATGATGAACTTCCTGGACACCTTCTTCTTGATTCAGGAGCATCACGAACTCTTATAAGATCTGCCCATCACATACACTCAGCGATATCTAATCCCGACATAAGCGTAGTTGATGTTCAAAAAAACAATATACCAATTAACGCTGTTGGTGATCTTCAATTTCACTTCCAGGACGACACCAAAACAACAATAAAGGTATTGCACACACCTAACATAGCCTATGACTTACTCAGTTTGAATGAACTGGCTGCACTAAATATTACAGCGTGCTTTACCAAAAACGTCTTAGAACGACCTGACGGCACCGTACTTGCACCTATCGTAAAACATGGAGACTTTTACTGGGTGTCTAAAAGGTACTTGCTTCCGTCGAATATCTCAGTACCCACAATTAATAACGTTCACACAAGTGAAAACACACGTAAGTATCCTTATCCTTTCATTCATCGGATGCTTGCGCATGCCAATGCCCAGACAATTAGATATTCACTTAAAAAGAACACTATTACGTATTTCAATGAATCAGATGTTGACTGGTCTAACGCTACTGATTATCAATGTCCCGATTGTTTAATCGGCAAAAGCACCAAACATAGACATATCATAGGATCACGGCTAAAATACCAAAGTTCATATGAACCTTTTCAATACTTACATACTGACATATTTGGGCCTGTTCACAACCTACCAAAGAGTGCACCATCCTATTTCATCTCATTCACTGATGAGAAAACAAAATTCCGTTGGGTTTATCCATTACACGACCGTCGCGAGGACTCTATTCTCGATATCTTTACTAAGATACTAGCTTTCATTAAAAACCAGTTTCAGTCCAATGTTTTGGTTATTCAAATGGACCGTGGTTCTGAGTACACTAACAAAACTCTCCATAAATTCCTTGAAAAATATGGCATAACCCCATGTTATACAACCACAGCGGATTCCCGAGCACATGGTGTCGCTGAACGGCTGAACCGTACCTTATTAGATGACTGTCGTACTCAACTGCAATGTAGTGGTCTACCGAATCATCTATGGTTCTCGGCAGTCGAATTTTCTACTATCGTACGGAACTCACTAGCTTCACCTAAAAGCAAAAAATCCGCAAGACAACTCGCTGGGTTGGCAGGACTCGACATCAGTACTTTATTACCTTTCGGTCAACCCGTTATAGTCAATAATCATAACCCTGACTCCAAAATTCATCCTCGTGGCATTCCTGGCTACGCTCTACATCCATCTCGAAACTCTTATGGATATATCATCTATGTCCCGTCTTTGAAGAAGACAGTAGATACAACTAATTACGTTATTCTTCAGGGCAAGGAATCCAGATTAGACCAATTCAATTACGACGCACTCACCTTCGATGAAGACGTGAATCGTATAACTGCTTCATATCAATCGTTCATTGCTTCAAATGAGATCCAACAATCTAACGATCTTAACATAGAATCTGACCATGATTTTCAATCTGACGTAGAACTGAACCCTGACCACCAGAGAAATGTCCCTTCAAACGTTCCGATTCCAACTGACTCTCCACCTCCATCAACTCATACTGAAGATTCAAAACCTATATCTGAAATCAATCTTCGTGCACCCAAAGAAGTTGATCCTAACATATCTGAATCTAATATTCTTCCATCTAAGAAGAGATCTAACATCCCCCAAATTTCTGCTACCGACAGTGCCGGTTCGGGTGGTATAAATAAATCAGATGTTCCTTTACTTACTCCTTTGTCCAAATCTGACACACAAAATTCATACCAAGCCAGTGAATCTGATGATTTCAGTGACTCAGACTCACACAGCGACATCGATACTGACTCTACAAACGTGACAATACCCAGTTTGGGTGGTATCAACAACAAAACTGTTCCGCAGACAAGTGACCAAGAGACTGAGAAAAGGATTATACATCGTTCACCTTCAATCGATGCTTCTCCACCGGAAAATAATTCATCGCACAATATTGTTCCTATCAAAACGCCAACTAATGTTTCTGAACAGAATACCGAGGAATCTATTATCGCTGATCTCCCACTCCCTGATCTATCTCCAGAATCTCCTACCGAATTCCCTGACCCATTTAAAGAACTCCCACCGATAAATTCTCATCAAACTAATTCCAGTTTGGGTGGTATGGATGACTCTAATATCTCTGCTACTATCACTAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTGAGGTATCACGAGACACATGGAATAGTAAGAATATGCGTAGCTTAGAACCTCCAAGGTCAAAGAAACGAATACATCTAATCGCGGCTGTAAAAGCAGTAAAATCAATCAAACCAATACGAACAACCTTAAGATACGATGAGGCAATCACCTATAATAAAGATATTAAAGAAAAGGAAAAATATATCGAAGCATACCACAAAGAAGTCAACCAACTGTTGAAAATGAATACTTGGGACACTGACAAATATTATGACAGAAAAGAAATAGACCCTAAAAGAGTAATAAACTCAATGTTTATCTTCAACAAGAAACGTGACGGAACTCATAAAGCTAGATTTGTTGCAAGAGGTGACATTCAGCATCCTGATACGTACGATACAGGTATGCAATCCAACACTGTACATCATTATGCGTTGATGACATCCCTATCACTTGCATTAGACGATGACTCCTTCATTACACAATTAGACATATCTTCGGCGTACTTGTATGCAGACATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGAATGAACAACAAGTTAATACGGTTGAGGAAATCACTTTATGGTTTGAAACAAAGTGGTGCAAACTGGTATGAAACGATCAAATCATATCTGATTGAACAATGTGATATGGAAGAAGTTCGCGGATGGTCATGCGTATTTAAGAACAATCAAGTAACAATCTGCTTATTCGTTGATGATATGATATTGTTCAGCAAAGACTTAAATTCAAATAAAAGAATTATAGCAAAACTCAAGATGCAATACGATACCAAGATTATAAATCTAGGTGAAAGCGATGATGAAATTCAATACGACATCCTTGGCTTAGAAATCAAATATCAAAGAGGTAAATACATGAAATTAGGTATGGAAAACTCACTAACTGAGAAAATACCCAAATTAAACGTACCTTTGAATCCAAAAGGAAGAAAACTTGGTGCTCCAGGTCAACCAGGTCTCTATATAAACCAGAAGGAGCTAGAGCTAGAAGAAGACGACTACAACATGAAGGTGCATGAAATGCAAAAGTTGATAGGTCTAGCGTCATATGTTGGATATAAATTCAGATTTGACCTATTATACTATATCAACACACTTGCACAACATATACTATTTCCGTCCAAACAAGTGTTAAACATGACATATGAATTGATACAATTCTTATGGGACACTAGAGACAAACAATTAATATGGCACAAAAGCAAATCTGCAAAACCAGAAAATAAATTAGTTGTAATAAGCGATGCCTCTTATGGCAACCAACCATATTACAAATCTCAGATTGGTAATATCTATTTACTAAATGGAAAGGTGATCGGAGGAAAATCAACAAAAGCTTCATTAACATGTACTTCAACCACAGAAGCAGAAATACACGCAATCAGTGAAGCCATTCCATTATTAAATAACTTGAGTCACCTTATACAAGAACTAAATGGGAAATCAATCATTAAAGGCTTACTTACTGACAGCAGATCTACAATCAGTATAGTTATGTCCAAAAATGAAGAGAAACTTAGAAACAGATTTTTCGGTACCAAAGCAATGAGACTTCGGGACGAAGTATCAAATAATAACCTCCACGTATGCTACGTGGATACCAAAAGGAACATTGCTGACGTGATGACAAAACCCCTCCCAATAAAAACATTTAAACTATTAACAAACAAGTGGATTCATTAGATCTATTACATTATGGGTGGTA
->TY1p-LTR#LTR/Copia
-TGTTGGAATGAAATTCTAATATCATCTATTTAATAGTATATTATAATATGCGGTGCAAGAGGATGACATAAAGATTGAGAAACAGTCATCCAATCTAATGGAAGCTGAAATGCAAGGATTGATAATGTAATAGGATAATGAATAACAACATATAAAAAGAAAGAAGATAAAATAATAACACTATGTAGAACTATCGATTCCCTTTTGTGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTATATACCTAATATTATAGCCTTTAGTAACAATGGAATCCCAACAATTATCTAATTACCCACACAATTCTCA
->TY2-I#LTR/Copia
-TGGTAGCGCCTATGCTTCGGTTACTTCTAAGGAAGTCCCATCAAATCAAGATCCGTTAGCCGTTTCAGCTTCCAATTTACCGGAATTTGATAGAGATTCCACTAAGGTTAATTCTCAACAAGAGACAACACCTGGGACATCAGCTGTTCCAGAGAACCATCATCATGTCTCTCCTCAACCTGCTTCAGTACCACCTCCACAGAATGGACAGTACCAACAGCACGGCATGATGACCCCAAACAAAGCTATGGCCTCTAACTGGGCACATTACCAACAACCATCTATGATGACGTGTTCACATTATCAAACGTCACCTGCGTATTATCAACCGGACCCACACTATCCGTTGCCACAGTATATCCCACCACTGAGTACTTCCTCACCTGATCCAATCGATTTAAAAAATCAACACTCTGAAATACCTCAAGCTAAGACAAAGGTGGGAAATAACGTCTTACCACCACACACTTTAACATCAGAAGAAAACTTTTCTACATGGGTTAAATTTTACATCAGATTTTTGAAGAACTCTAATCTCGGTGACATCATTCCAAATGACCAGGGTGAAATCAAAAGACAAATGACTTATGAAGAACATGCGTATATATACAATACCTTCCAAGCATTTGCCCCATTTCATTTATTGCCAACATGGGTAAAACAAATTTTAGAAATTAATTATGCTGACATCCTTACAGTCCTTTGTAAAAGTGTGTCCAAAATGCAAACTAACAATCAAGAATTAAAGGATTGGATAGCTCTTGCCAACCTTGAGTACGACGGAAGTACATCTGCTGATACATTTGAAATTACAGTCAGTACGATCATTCAGAGGCTAAAAGAAAACAATATCAATGTTAGCGACAGATTGGCCTGTCAACTAATACTTAAAGGTCTATCCGGTGACTTCAAATACCTACGTAATCAATATCGTACCAAAACGAACATGAAACTTTCCCAATTATTCGCTGAAATTCAATTAATATATGACGAAAATAAAATCATGAATCTAAATAAACCGTCCCAATACAAACAACACAGCGAATACAAAAATGTTTCTCGCACATCTCCAAACACGACTAACACAAAGGTTACAACTCGTAATTATCATAGAACAAATAGTTCAAAACCAAGAGCAGCAAAAGCTCACAATATTGCTACATCTAGTAAATTCTCAAGGGTGAACAATGATCACATTAATGAATCAACCGTTTCATCACAATACTTAAGCGATGACAACGAACTTAGTCTTAGGCCAGCAACAGAAAGAATCTAAGCCAACACACACAATAGACTCGAATGACGAACTACCTGATCACCTTCTTATTGATTCAGGAGCTTCGCAAACGCTTGTCAGATCAGCCCATTATTTACACCATGCAACACCCAATTCTGAAATAAACATAGTCGATGCTCAAAAACAAGACATTCCTATAAATGCCATTGGTAATCTTCACTTCAACTTTCAGAACGGCACCAAAACATCAATAAAAGCACTACACACACCAAACATAGCCTATGATCTATTAAGTTTGAGTGAGCTGGCTAACCAAAATATTACTGCCTGCTTTACCAGAAACACTTTAGAAAGATCGGATGGTACAGTACTAGCTCCCATAGTCAAACATGGAGACTTTTACTGGTTATCTAAAAAATACCTAATTCCTTCGCACATTTCAAAGCTAACAATAAACAACGTCAACAAAAGCAAAAGCGTAAATAAATATCCATATCCGTTAATACATCGAATGCTTGGACATGCTAACTTCCGAAGTATTCAGAAGTCTCTTAAGAAGAATGCAGTTACATATTTGAAGGAATCGGATATTGAATGGTCTAACGCTAGCACATATCAATGTCCTGACTGTCTAATCGGCAAAAGCACGAAACATAGACATGTCAAAGGATCACGACTAAAGTACCAAGAATCATATGAGCCTTTTCAGTACTTGCATACCGATATATTTGGTCCTGTACATCACTTACCGAAAAGTGCACCTTCTTACTTTATATCGTTTACAGATGAGAAAACCAGATTCCAATGGGTGTACCCATTACACGACCGTCGTGAAGAATCTATCCTCAATGTTTTTACATCGATATTAGCATTTATTAAGAACCAATTCAATGCTCGCGTTCTAGTTATCCAGATGGATCGTGGCTCCGAGTACACTAACAAAACTCTTCATAAGTTCTTTACGAACAGAGGTATTACTGCATGCTATACAACCACGGCAGATTCTAGAGCACACGGTGTCGCTGAACGATTAAATCGTACTTTATTAAACGATTGTCGCACACTGCTTCATTGCAGTGGTCTACCAAATCATCTATGGTTCTCAGCAGTCGAATTTTCTACTATAATCAGAAATTCATTAGTCTCACCAAAAAACGATAAATCTGCAAGACAACATGCAGGTTTAGCTGGACTGGACATTACTACTATACTACCTTTCGGTCAACCGGTTATAGTTAACAACCATAATCCCGACTCGAAAATACATCCTCGTGGCATTCCAGGTTACGCCTTACATCCGTCACGAAACTCTTATGGCTATATTATCTATCTTCCATCATTAAAAAAGACAGTAGATACTACCAATTACGTTATATTACAAGACAACCAATCCAAATTGGACCAATTCAATTATGATACACTCACCTTTGATGATGATCTCAATCGTTTAACAGCCCATAACCAATCTTTTATTGAACAAAATGAAACAGAGCAGTCATATGATCAAAATACAGAATCTGATCATGACTATCAATCGGAGATTGAAATAAACTCTGATCCTCTAGTGAACGACTTCTCGTCCCAATCAATGAACCCCTTACAATTAGACCACGAACCAGTCCAAAAAGTACGTGCACCAAAAGAAGTTGATGCCGACATATCTGAATACAATATTCTTCCATCTCCTGTACGATCTCGTACACCCCATATCATTAATAAAGAGAGTACCGAAATGGGTGGTACCATTGAATCAGATACTACTTCACCTAGACACTCGTCTACCTTCACTGCACGAAACCAAAAGCGACCTGGTAGTCCCAATGATATGATTGATTTGACCTCACAGGATAGAGTTAATTATGGACTTGAAAACATCAAAACTACACGTTTGGGTGGTACGGAGGAACCATATATTCAACGAAATAGTGATACAAATATCAAATACAGGACTACAAATAGTACGCCCTCAATAGATGACCGTTCGTCCAACAGTGAATCCACTACTCCCATCATCTCCATAGAAACAAAGGCTGTATGTGATAATACACCCTCCATTGATACGGATCCGCCAGAATATCGATCTTCTGACCATGCGACTCCTAATATAATGCCTGACAAATCCTCAAAAAATGTTACGGCTGATTCTATTCTTGACGACCTCCCACTTCCTGACTTAACCCATAAATCTCCTACGGACACTTCTGATGTTTCAAAAGATATTCCACACATACACTCTCGTCAGACTAATTCCAGTTTGGGTGGTATGGATGATTCTAATGTTCTGACTACTACCAAAAGTAAGAAAAGATCATTAGAAGATAATGAAACTGAAATTGAGGTATCCCGAGACACATGGAATAATAAGAATATGAGAAGTCTGGAACCACCAAGATCGAAGAAACGCATAAATTTAATTGCAGCAATAAAAGGAGTGAAATCGATCAAACCAGTTCGAACGACCTTAAGATATGATGAAGCAATTACATATAATAAAGACAACAAAGAAAAAGACAGATATGTTGAAGCTTATCATAAAGAAATTAGCCAACTATTGAAAATGAACACTTGGGATACAAACAAATATTATGATAGAAATGACATAGATCCTAAAAAAGTAATAAACTCAATGTTTATATTTAACAAGAAACGTGATGGTACACACAAAGCTAGATTTGTTGCAAGAGGCGACATTCAACACCCCGATACATATGATTCTGATATGCAATCCAATACCGTACATCACTATGCACTGATGACGTCACTGTCAATCGCATTAGACAACGACTATTATATCACACAGCTGGACATATCCTCTGCTTACTTATATGCTGATATCAAAGAAGAATTATACATAAGACCTCCACCACATTTAGGTTTGAATGATAAATTACTACGTTTGAGAAAATCACTCTATGGTTTGAAACAAAGTGGTGCAAACTGGTATGAAACCATTAAATCATATTTAATAAATTGTTGCGACATGCAAGAAGTTCGCGGATGGTCATGCGTATTTAAGAATAGTCAAGTAACAATTTGCTTATTCGTTGATGATATGATATTATTCAGCAAAGACTTAAATGCAAATAAGAAAATCATAACAACACTCAAGAAACAATACGATACAAAGATAATAAATCTGGGTGAAAGAGATAACGAAATTCAGTACGACATACTTGGATTAGAGATCAAATATCAAAGAAGCAAGTACATGAAATTAGGTATGGAAAAATCCTTGACAGAAAAATTACCCAAACTAAACGTACCTTTGAACCCAAAAGGAAAGAAACTTAGAGCTCCAGGTCAACCAGGTCATTATATAGACCAGGATGAACTAGAAATAGATGAAGATGAATACAAAGAGAAGGTACATGAAATGCAAAAGTTGATTGGTCTAGCTTCATATGTTGGATATAAATTTAGATTTGACTTACTATACTACATCAACACACTTGCTCAACATATACTATTCCCCTCTAGACAAGTTTTAGACATGACATATGAGTTAATACAATTCATGTGGGACACTAGAGATAAACAATTAATATGGCACAAAAACAAACCTACCAAGCCAGATAATAAACTAGTCGCAATAAGCGATGCTTCATATGGTAACCAACCATATTACAAGTCACAAATTGGTAACATTTTCCTACTCAACGGAAAAGTGATTGGAGGAAAGTCGACAAAGGCTTCGTTAACATGCACTTCAACTACAGAAGCAGAAATACACGCAGTCAGTGAAGCTATACCGCTATTGAATAACCTCAGTCACCTTGTGCAAGAACTTAACAAGAAACCAATTATTAAAGGCTTACTTACTGATAGTAGATCAACGATCAGTATAATTAAGTCTACAAATGAAGAGAAATTTAGAAACAGATTTTTTGGCACAAAGGCAATGAGACTTAGAGATGAAGTATCAGGTAATAATTTATACGTATACTACATCGAGACCAAGAAGAACATTGCTGATGTGATGACAAAACCTCTTCCGATAAAAACATTTAAACTATTAACAAACAAATGGATTCATTAGATCTATTACATTATGGGTGGTA
->TY2-LTR#LTR/Copia
-TGTTGGAATAAAAATCAACTATCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAAAATGATGATAATAATATTTATAGAATTGTGTAGAATTGCAGATTCCCTTTTATGGATTCCTAAATCCTCGAGGAGAACTTCTAGTATATCTACATACCTAATATTATTGCCTTATTAAAAATGGAATCCCAACAATTACATCAAAATCCACATTCTCTTCA
->TY3-I#LTR/Gypsy
-CCTGGTAGCGTTAAAGGTTACTAATTGTTCAAACGAACCATCGAAAAGCCGAACCTAGCTACACCACACCCCAGTATGAGCTTTATGGATCAAATCCCAGGAGGAGGAAATTATCCAAAACTCCCAGTAGAATGCCTTCCTAACTTCCCGATCCAACCATCTTTGACCTTCAGAGGTAGAAATGACTCGCATAAACTGAAAAACTTTATCTCCGAAATAATGTTAAACATGTCTATGATATCTTGGCCGAATGATGCCAGTCGTATTGTGTACTGCAGAAGACATTTATTAAACCCCGCTGCTCAGTGGGCTAATGACTTTGTACAAGAACAAGGTATACTTGAAATAACATTCGACACATTCATACAAGGATTATATCAGCATTTCTATAAGCCACCAGATATCAATAAAATCTTTAATGCAATCACGCAACTTTCCGAAGCTAAACTTGGTATTGAGCGTCTCAACCAACGATTCAGAAAGATTTGGGACAGAATGCCACCAGACTTCATGACCGAAAAAGCTGCCATAATGACATATACTAGGCTATTGACAAAGGAAACCTATAATATTGTCAGAATGCACAAACCAGAGACATTAAAAGACGCCATGGAAGAGGCTTACCAGACAACTGCACTAACTGAAAGATTCTTCCCAGGATTCGAACTTGATGCTGATGGAGACACTATCATCGGTGCCACAACCCACTTACAAGAAGAATACGACTCTGACTATGATTCAGAAGATAATCTGACCCAGAATGGATACGTCCATACCGTAAGGACAAGAAGATCTTACAATAAACCAATGTCAAATCATCGAAACAGGAGAAATAACAACCCATCTAGAGAAGAATGTATAAAAAATCGGCTATGCTTCTATTGTAAGAAAGAGGGACATCGCCTGAACGAATGTAGAGCACGTAAGGCGAGTTCTAACCGATCTTGAACTCGAATCAAAAGACCAACAAACTCCTTTTATCAAAACCTTACCAATTGTACACTATATCGCCATCCCCGAGATGGACAATACCGCCGAAAAAACCATAAAAATACAAAACACGAAAGTAAAAACCCTGTTTGACAGTGGATCACCCACGTCATTTATCCGAAGAGATATTGTAGAACTTCTCAAATACGAAATCTACGAGACCCCTCCACTCCGTTTTAGAGGATTCGTAGCCACCAAATCCGCCGTTACATCCGAAGCAGTCACCATTGACCTCAAAATCAATGACCTGCATATAACTTTAGCCGCGTACATACTGGATAACATGGACTACCAATTGTTAATTGGAAATCCAATCTTACGCCGCTACCCGAAAATCCTGCACACAGTACTGAATACCAGAGAGAGCCCCGACTCCTTAAAGCCCAAGACTTATCGCTCCGAAACCGTTAATAACGTTAGAACCTACTCCGCTGGTAATCGTGGTAACCCCAGAAACATAAAACTGTCTTTTGCCCCCACCATTCTCGAAGCAACTGACCCGAAATCCGCTGGTAATCGTGGTGACTCCAGAACCAAAACCCTGTCTCTTGCAACCACTACTCCTGCAGCAATTGACCCGCTTACGACCCTTGATAACCCAGGTAGTACTCAAAGTACATTTGCGCAATTCCCGATACCTGAAGAAGCGAGCATCCTAGAAGAGGATGGAAAATACTCCAACGTTGTCTCAACCATTCAGAGTGTAGAACCTAATGCTACTGATCACAGCAATAAGGACACCTTTTGCACTTTGCCAGTTTGGTTACAACAGAAGTATAGAGAGATCATACGTAATGATCTCCCACCAAGACCTGCCGACATTAATAACATCCCCGTAAAACATGATATTGAAATTAAACCTGGCGCAAGACTACCTCGACTACAGCCATACCATGTTACAGAAAAGAACGAACAAGAAATCAACAAAATAGTTCAAAAACTGCTCGATAACAAGTTCATTGTTCCCTCAAAGTCGCCTTGCAGCTCCCCTGTAGTCCTCGTCCCGAAGAAAGACGGTACCTTCCGACTCTGCGTCGATTACCGCACCCTGAACAAAGCTACCATCTCCGACCCATTCCCATTACCCAGAATCGACAACCTATTGAGCCGTATTGGAAATGCCCAGATATTTACCACGCTAGATTTGCATAGTGGTTACCACCAGATCCCGATGGAACCCAAAGACCGCTACAAAACCGCCTTTGTCACACCATCCGGTAAGTATGAATATACCGTCATGCCATTTGGCTTAGTCAATGCACCTAGTACATTCGCAAGATACATGGCTGATACATTTAGAGACCTGAGATTCGTCAATGTTTACCTTGATGATATATTAATATTCTCCGAATCTCCAGAAGAACATTGGAAACATTTAGACACGGTACTAGAAAGATTAAAGAACGAGAACCTCATTGTTAAGAAGAAAAAATGTAAATTTGCATCTGAAGAAACTGAGTTTTTAGGCTATAGTATTGGAATCCAGAAAATAGCTCCACTACAGCACAAATGTGCAGCAATCCGAGACTTTCCGACGCCTAAAACAGTAAAACAAGCACAGAGATTTTTAGGAATGATTAATTACTACAGACGATTCATTCCAAATTGCTCCAAGATTGCACAGCCAATCCAACTGTTTATTTGTGACAAAAGTCAATGGACAGAAAAACAAGACAAGGCAATTGATAAACTAAAAGACGCCTTGTGTAACTCCCCCGTCCTAGTACCATTCAACAACAAAGCAAACTACCGACTTACAACAGACGCCTCAAAAGACGGCATTGGTGCTGTTCTAGAAGAAGTCGACAACAAGAACAAACTTGTTGGTGTCGTCGGTTACTTCTCTAAATCCTTAGAGAGTGCCCAGAAAAACTATCCTGCTGGCGAATTAGAACTACTTGGAATTATCAAAGCACTCCACCACTTCCGATATATGCTTCACGGAAAGCATTTCACGTTAAGAACAGACCACATTAGTTTGTTATCATTACAAAACAAGAACGAACCCGCACGACGCGTGCAACGCTGGTTAGATGACCTAGCCACATATGACTTCACCTTAGAATACCTAGCTGGACCCAAGAACGTTGTCGCAGATGCCATATCCCGTGCCGTATATACTATAACCCCCGAAACATCCCGACCTATCGACACAGAAAGCTGGAAATCTTACTACAAATCAGACCCATTATGTAGTGCTGTCTTAATTCATATGAAAGAATTGACACAACACAACGTCACACCTGAAGATATGTCAGCCTTCCGTAGTTACCAGAAGAAACTCGAACTATCAGAGACCTTCCGAAAGAATTATTCCCTAGAAGACGAAATGATCTATTACCAAGACCGACTAGTAGTACCAATAAAACAACAGAACGCAGTTATGAGACTATATCATGACCATACCTTATTTGGAGGACATTTTGGTGTAACAGTGACCCTTGCGAAAATCAGCCCAATTTACTATTGGCCAAAATTACAACATTCGATCATACAATACATCAGGACCTGCGTACAATGTCAACTAATAAAATCACACCGACCACGCTTACATGGACTATTACAACCACTCCCTATAGCAGAAGGAAGATGGCTTGATATATCAATGGATTTTGTGACAGGATTACCCCCGACATCAAATAACTTGAATATGATCCTCGTCGTAGTTGATCGTTTTTCGAAACGCGCTCACTTCATAGCTACAAGGAAAACCTTAGACGCAACACAACTAATAGATCTACTCTTTCGATACATTTTTTCATATCATGGTTTTCCCAGGACAATAACCAGTGATAGAGATGTCCGTATGACCGCCGACAAATATCAAGAACTCACGAAAAGACTAGGAATAAAATCGACAATGTCTTCCGCGAACCACCCCCAAACAGATGGACAATCCGAACGAACGATACAGACATTAAACAGGTTACTAAGAGCCTATGCTTCAACCAATATTCAGAATTGGCATGTATATTTACCACAAATCGAATTTGTTTACAATTCTACACCTACTAGAACACTTGGAAAATCACCATTTGAAATTGATTTAGGATATTTACCGAATACCCCTGCTATTAAGTCAGATGACGAAGTCAACGCAAGAAGTTTTACTGCCGTAGAACTTGCCAAACACCTCAAAGCCCTTACCATCCAAACGAAGGAACAGCTAGAACACGCTCAAATCGAAATGGAAACTAATAACAATCAAAGACGTAAACCCTTATTGTTAAACATAGGAGATCACGTATTAGTGCATAGAGATGCATACTTCAAGAAAGGTGCTTATATGAAAGTACAACAAATATACGTCGGACCATTTCGAGTTGTCAAGAAAATAAACGATAACGCCTACGAACTAGATTTAAACTCTCACAAGAAAAAGCACAGAGTTATTAATGTACAATTCCTGAAAAAGTTTGTATACCGTCCAGACGCGTACCCAAAGAATAAACCAATCAGCTCCACTGAAAGAATTAAGAGAGCACACGAAGTTACTGCACTCATAGGAATAGATACTACACACAAAACTTACTTATGTCACATGCAAGATGTAGACCCAACACTTTCAGTAGAATACTCAGAAGCTGAATTTTGCCAAATTCCCGAAAGAACACGAAGATCAATATTAGCCAACTTTAGACAACTCTACGAAACACAAGACAACCCTGAGAGAGAGGAAGA
->TY3-LTR#LTR/Gypsy
-TGTTGTATCTCAAAATGAGATATGTCAGTATGACAATACGTCACCCTGAACGTTCATAAAACACATATGAAACAACCTTATAACAAAACGAACAACATGAGACAAAACCCGACCTTCCCTAGCTGAACTACCCAAAGTATAAATGCCTGAACAATTAGTTTAGATCCGAGATTCCGCGCTTCCACCACTTAGTATGATTCATATTTTATATAATATATAAGATAAGTAACATTCCGTGAATTAATCTGATAAACTGTTTTGACAACTGGTTACTTCCCTAAGACTGTTTATATTAGGATTGTCAAGACACTCCGGTATTACTCGAGCCCGTAATACAACA
->TY3p-I#LTR/Gypsy
-TCTGGTAGCGTTAAAGGTTACTAATTGTTCAAGCAAACCAACGAATCCCTGAACCTAGCTACACCAACATCTGTCATGAGCTTTATGGATCAAATCCCAGGAGGAGGAAGTTACCCAAAGCTTCCGGTGGAATGTCTTCCCAATTTCCCGATCCAACCAGCACTAACCTTCAGAGGTAGAAATGACTCGCACAAGTTGAAAAACTTCATCTCTGAAATAATGTTAAACATGTCTATGATTCCTTGGCCCAACGAAGCCAGTCGTATTGTCTATTGTAGAAAACACTTACTGAACCCTGCTGCTCAATGGGCTAATGATTTTGTCCAAGAGCAAGGCATACTGGAAATAACATTCGACACCTTCATACAAGGACTCTATCAGCATTTCTATAAGCCACCAGACATCAACAAAATCTTCAATACGATCAATCAACTATCTGAAGCAAAACTGGGTATTGAACGTCTCAACAAACAATTCAAAATGATTTGGGACAGAATGCCACCAGACTTTATGACCGAAAAAGCCGCTATTATGACATATACCCGCTTACTGACAAAGGAAACCTACAATATAGTTAGATTGCATAAACCAAAAACGTTGAGAGGAGCCATGGAGGAGGCTTACCAAACAACAGCACTAACTCAGAGATTCTTCCCAGAATTTGAGCTAGACGCCGATGGAGATACTATAATCGCAGCCGCAACTCGTTTACACGAACAGTACGACTACGACAGTGACCCACAAGAAAACTTTTTGGTCCAGAAGAGACACGTCCACGCAGTTCGGACAAGAAGATCATACAATAAACCGACCGCGACTTATCACAACAGGAGAAGCAATAATCCATCTAGAGAAGAGTGTGTAAAGAACCGTCTCTGTTTTTATTGTAAGAAAGAAGGACACCGTCTGAACGAGTGTAGAGCTCGTAATGCGAGTTCTAGCCGATCCTGAACTTAAGTCGAAAGACCACACGAAACTTTCTATCACATCCCGACCTATTGTACATTATATCGCCATACCTGAAATGGACAAAACTGCCGAAAAACACATAAAAATAAAAAACACGAAAATAAAAACCCTGTTTGATAGTGGATCGCCCACATCATTTATCCGAAGAGATACCGTAAATCTCCTGAATCTGCCAACCCATGATACTCCACCGCTCCGCTTTAGAGGATTCATATCCACCGAATCCGCCACCACTTCAGAAGCAGTTACGCTCGACCTTACAGTCGACAATCTGCAAATCAATGTAGCCGCGTATGTACTCGATAAAATGGACTACCAACTTCTAATCGGAAATCCAATTCTACGCCGCTACCCAAAACTCCTGTACACAATCCTGAACACTAAGCAGTGTACCTCCGCCCAGAAGCCCAAGGCTTACCATCCCGAAAACATTAACTATGTGAAAGCAAAATCCGCTGGTAATCGTGGTAACTCCAGAAACAAAACACTGTCCTTTGCCCCCACTATTCCTGAAGCAACTGACCAGAAATCCGCTGGTAATCGTAGTAACTCCAGAACAAATACTATGTCTTTTGCAACTACCAATCCAGAAACAACTGACCCGCTTACGACCCTCGACAATCCAGGTAGTACTCAAAGTACATTTGCGCAATTCCCGATACCTGAAGAAGCGACCATCCTAGAAGAGGATGGAAAATACTCCAACGTTGTTTCAACCATACAGAACGTAGAACCTAAAGCTACTGATCACAGCAACAAGGACACATTTTCAACGTTGCCTGTTTGGTTACAACAGAAGTATATAGAGATTATACGTAATGATCTCCCGCCAAGACCGGCCAATATCCACAACATGCCCGTAAAACACGACATTGAAATTAAACTTGACACAAGACTACCTCGACTACAGCCATATCATGTTACAGAAAGGAACGAACAAGAAATTAACAAGATCGTTCAAGAACTGCTCGACAACAAGTTCATTGTCCCCTCTAAATCTCCGTGCAGTTCCCCTGTAGTCCTTGTCCCGAAGAAAGATGGTACGTTTAGACTTTGCGTTGACTACCGTGCCCTGAACAAGGTTACCATCTCCGACCCATTCCCATTACCCAGAATCGACAACCTATTAAGCCGTATTGGGAATGCCCAAATATTCACCACGCTAGATTTGCACAGTGGTTATCACCAGATTCCAATGGAACCAAAAGACCGCTACAAAACCGCTTTTGTCACCCCGTCCGGTAAATATGAATACACTGTCATGCCATTTGGTCTAGTGAATGCACCTAGCACCTTTGCAAGATACATGGCCGACATTTTCAGAGACTTGAGATTTGTCAATGTCTACCTTGATGATATACTAATCTTCTCTGAATCCCAAGAAGAACACTGGAAACATTTAGACACAGTTCTTGGAAGACTTAAGAAGGAAAACCTTATTGTCAAAAAGAAAAAATGCAAGTTTGCATCAGAACAAATTGAATTTCTAGGTTATAATATTGGAATTCAGAAAATAACCCCATTACAACACAAATGTGCTGCCATTCGAGATTTTCCGAAACCCAGAACAGTAAAGCAAGCACAACGATTTTTAGGAATGATTAATTACTATAGACGATTCATTCCAAATTGCTCTAAGATTGCACAACCAATCCAGCTCTTTATATGCGACAAGAGTCAATGGACAGAAGAGCAGGACAAGGCAATCGAGAAATTAAAATCCGCCCTATGTAATTCCCCTGTTCTAGTACCATTTAACAACAAAGCAATTTACCGATTAACTACAGACGCATCAAAAGATGGCATCGGTGCCGTTCTAGAAGAAGTCAATGCCAAAAACGCACTTGTCGGTGTCGTCGGTTATTTCTCTAAATCCTTAGAAAGTGCTCAAAAGAACTACCCCGCCGGTGAACTAGAACTACTTGGAATTATTAAGGCACTTCACCACTTCCGTTATATGCTCCATGGAAAACATTTTACATTGAGAACGGATCACATTAGCTTACTGTCACTGCAGAATAAGAATGAACCTGCACGAAGAGTTCAAAGATGGTTGGATGACCTAGCCACTTATAACTTCACCCTAGAATACTTAGCTGGACCCAAAAACGTCGTCGCAGATGCTATATCCCGTGCCGTGTACACTATAATCCCAGAAATACCCCAACCTATCGACCCAGAAAATTGGAAAACTCATTACAAATCAGACCCATTATGCAGTGCCACCTTGATTTACATGGAAGAATTGACACAACACAATGTCATGCCTGAGGATATGTCCGCATTCCGTAGCTATCACAAGAAATTTCAGTTATCAGAGACCTTCCGAAAGAACTACTCCCTAGAAAATGGAATAATCTACTATCGAGACCGATTAGTAGTCCCGGTAAAACAACAGAACGAAGTCATAAAACTGTATCACGATCATACTTTATTCGGAGGCCATTTTGGTGTAACTGTAACATTTGGAAAGATTGCTCCAATTTTTTACTGGCCGAAATTGCAACATTCGATTACACAATACATCCGTACCTGCGTACAATGTCAACTCACAAAATCACATCGACCACGTTCACAAGGACTATTGCAACCGCTTCCCGTAGCAGAAGGAAGATGGCTTAATATATCAATGGATTTCGTGACTGGACTACCCGTAACAACAAACGATTTGAATATGATCCTCGTTGTTGTTGACCGCTTCTCGAAACGCGCTCACTTCATAGCTACAAGGAAAACAGCAGACGCATCACAGCTAATAAATACGCTATTCCGCTATATCTTTTCATATCATGGTTTCCCGAAAACAATAACCAGTGATAGAGACATCCGTATAACCGCAGAAAAATATCAAGAACTTACAAAAAGATTAGGGATAAAATCGACAATGTCTTCTGCAAACCACCCCCAAACAGATGGACAATCCGAAAGAACGATTCAAACATTGAACCGATTGATAAGAGCTTATGCCTCCACCAATACCCGGAACTGGCACACCTACTTACCACAAATTGAATTTGTCTATAACTCCACACCGACCAGAACACTTGGAAAGTCACCATTCGAAATTGATTTAGGATATACTCCCAATGCACCTACCATTAAAACGGATTGCGAAATCAATGCAAGAAGTTTTACCGCCGTAGAACTGGCCCGACACCTCAAAGCTATTACGATCCAAACAAAAGAACGACTAGAGTCTGCTCAGATTGAAATGGAAACTAATAACAACCAAAGACGTAAAACTTTGTTACTGAACATAGGAGATCACGTACTAGTGCATAGAGATGCATACTTCAAGAAAGGAACGTATATGAAGGTACAACCTATATACGTTGGACCATTTCGAGTTGTCAAGAAAATAAATGATAACGCTTACGAACTCGACCTGGATTCACACAAGAGAAAACATAGAGTTATTAACGTACAATACCTAAAGAAATTTGTATACCGACCCGACGCATATCCAAAGAATAAACCAATCAGTTCCGTTGAAAGAATCAACAGAGCCAATGAAGTCATTGCAGTTATAGGGATAGATACCACACACAAAACATACTTATGTCGTATGCAGGATGTGGACCCGACAATCTCAGTAGAATATTCAGAAGCTGAATTCTACCAAATCCCAGAGGAAATACGAAAGTCAATATTAGCCAATTTTAGACAACTGTACGAAACTCAAGACAACTCCGAGAGAGAGGAAGAT
->TY3p-LTR#LTR/Gypsy
-TGTTGTATCTCAAGATGAGATACCTCAGCATTACTAGATTTACCAACCTAGACATAAAACATGTATGAAACACGTACGAAACAATAGACAAGATTGAGTATACTAGGCAACCTACTTGCCTAAGATGAACCAAACTAACCAAACGTATAAATACCTGAACAATTAGTTTAGATCCGAGATTCCGCGCTTCCACCCTTTAGTTAGATTCAGATCTTATATAGATTATATAGGATAAGTAACATTCTGTGAATCACGATAATAATAAGTCTGACAACAAGTTACTCTCCTAAACGACTTTAGGATTGTCAAGACATCCGGTATTACTCGAGCCCGTAATACAACA
->TY4-I#LTR/Copia
-TGGCGACCCCAGTGAGGGGTGAAACAAGAAATGTTATTGACGACAACATTTCTGCGCGGATTCAATCGAAAGTCAAAACAAATGATACTGTCAGACAGACGCCATCATCATTAAGAAAAGTTTCTATTAAAGATGAACAGGTGAGACAATATCAAAGAAACTTAAATAGGTTTAAAACCATACTAAATGGTTTAAAGGCAGAAGAGGAAAAACTTTCTGAGGCTGATGATATTCAGATGCTAGCTGAAAAATTATTAAAACTCGGAGAAACCATTGACAAGGTTGAGAATAGGATTGTGGATCTAGTTGAAAAGATACAATTATTGGAAACAAACGAGAACAATAATATATTACATGAACATATAGATGCTACAGGGACTTACTATTTATTCGATACGTTAACTTCAACCAACAAAAGATTCTACCCTAAGGATTGTGTTTTTGATTATAGGACTAATAATGTCGAGAACATTCCTATTCTCTTAAACAATTTTAAAAAATTCATCAAGAAATATCAATTTGATGATGTCTTTGAAAATGATATCATAGAAATCGATCCTCGTGAAAATGAAATCTTGTGCAAGATAATCAAAGAAGGACTCGGTGAAAGTTTAGATATCATGAACACAAATACAACTGACATTTTTAGGATAATCGATGGTTTAAAAAAACAAAATATAGAAGTTTGCATGGTAGAGATGTCAGAATTAGAGCCTGGGGAAAAGGTTTTGGTTGATACAACATGTAGAAATTCCGCATTGTTAATGAATAAACTTCAAAAGTTGGTACTAATGGAAAAATGGATTTTTTCTAAATGCTGCCAAGATTGTCCTAATCTAAAGGATTACCTACAAGAAGCTATCATGGGAACCTTACATGAATCCTTAAGAAATTCTGTGAAACAACGTTTGTACAACATTCCACATGACGTAGGAATTGATCACGAAGAATTTCTAATCAATACTGTTATTGAAACAGTAATTGATTTGAGCCCAATTGCAGACGATCAAATAGAAAATAGCTGCATGTATTGCAAATCTGTTTTCCATTGCTCAATTAACTGCAAAAAGAAACCAAATAGGGAACTTAGGCCTGACTCGACCAATTTCTCAAAAACCTATTATCTACAAGGTGCACAGAGACAACAACCACTTAAGTCCAGTGCAAAACGAACAAAAGTCTTGGAACAAGACACAAAAAAGGTCGAACAAAGTGTACAACAGCAAAAAACTGGTAATTATTGATACCGGTTCCGGAGTAAACATTACCAATGACAAAACCTTACTGCATAATTACGAAGACAGTAATCGCAGTACACGATTTTTTGGTATTGGGAAAAACAGTTCAGTGTCTCTTAAAGGGTATGGCTATATAAAAATCAAGAATGGTCACAACAATACTGACAATAAGTGTCTATTAACTTACTATGTACCGGAAGAAGAATCCACTATAATCAGCTGTTATGACTTAGCCAAGAAAACCAAAATGGTTTTAAGTCGAAAATATACCAGATTGGGAAACAAAATCATAAAAATTAAAACCAAGATAGTTAATGGTGTCATTCACGTAAAAATGAACGAGTTAATTGAACGTCCTTCCGATGATTCAAAAATAAATGCAATAAAACCTACTTCTTCTCCTGGATTTAAACTAAATAAAAGGTCTATTACCTTGGAAGATGCTCATAAAAGAATGGGCCATACAGGAATTCAACAAATTGAAAATTCCATAAAACATAATCATTATGAAGAATCCCTTGACTTAATCAAAGAACCAAATGAATTTTGGTGTCAAACCTGTAAAATCTCTAAAGCCACGAAAAGAAATCATTATACCGGGTCTATGAATAATCATAGTACTGATCATGAACCAGGCTCATCATGGTGCATGGATATATTTGGCCCTGTATCAAGTTCAAACGCGGACACTAAAAGGTACATGCTTATTATGGTGGATAACAACACGAGATATTGCATGACCTCCACACACTTCAATAAGAATGCTGAAACTATTTTAGCTCAAGTTAGAAAGAATATTCAGTACGTGGAAGCACAATTTGACAGGAAAGTCAGAGAAATTAATTCAGACAGAGGTACTGAATTCACAAATGATCAGATAGAAGAATATTTTATTTCAAAAGGAATACATCACATACTTACTTCTACACAAGATCATGCTGCTAACGGAAGAGCAGAAAGATACATAAGAACAATAATAACTGATGCAACAACACTCCTAAGACAAAGTAACTTAAGAGTAAAATTTTGGGAATACGCAGTAACTTCTGCTACCAATATAAGAAATTACCTGGAACACAAAAGTACAGGTAAACTACCATTGAAGGCAATCTCACGTCAACCTGTGACAGTGAGATTAATGTCATTCTTACCATTTGGCGAAAAAGGAATAATTTGGAATCATAATCACAAAAAATTGAAACCATCTGGACTTCCTTCTATAATTCTATGCAAAGATCCAAATAGTTATGGATACAAATTCTTTATACCATCCAAAAATAAAATTGTCACATCTGATAATTATACAATTCCCAACTATACAATGGACGGTAGAGTAAGAAATACTCAGAATATTAACAAGAGTCATCAATTCAGTTCAGATAATGATGATGAAGAAGATCAAATCGAAACGGTCACAAACTTATGTGAAGCTTTGGAAAACTACGAAGATGATAATAAACCAATTACTCGCCTGGAAGATTTGTTCACAGAGGAAGAGTTATCTCAAATAGACTCAAACTCAAAATACCCATCTCCTAGTAATAACCTAGAAGGGGACTTGGATTACGTATTTTCTGATGTTGAGGAATCTGGAGATTATGACGTTGAATCTGAACTTTCAACGACAAATAATTCAATCTCAACTGATAAAAACAAAATTTTGTCAAACAAGGATTTTAATTCAGAACTTGCATCGACTGAAATATCCATCAGTGGAATCGATAAGAAAGGATTAATAAATACAAGTCATATTGATGAAGATAAGTATGATGAAAAAGTCCACAGAATTCCATCGATTATACAAGAGAAACTGGTAGGAAGGAAAAATACTATTAAAATCAATGACGAAAACAAAATCTCCGACAGAATTCGTAGTAAAAACATTGGGAGTATTTTAAACACTGGACTCAGTAGATGTGTAGATATCACCGATGAATCTATTACTAACAAAGATGAGTCAATGCACAACGCAAAACCCGAACTAATTCAGGAGCAGTTAAAAAAAACAAATCATGAAACTTCGTTTCCTAAAGAAGGGAGCATTGGAACAAATGTAAAATTCCGAAATACAAACAATGAGATTTCTTTAAAAACAGGCGATACGAGTTTACCAATAAAAACTTTAGAAAGCATTAACAATCACCATAGTAATGATTATTCCACAAACAAAGTTGAAAAGTTTGAGAAGGAAAATCATCATCCGCCCCCGATTGAGGACATTGTGGATATGAGTGATCAAACTGATATGGAATCAAACTGTCAGGATGGTAATAACTTAAAAGAATTAAAAGTCACCGATAAAAATGTACCAACTGACAATGGAACAAATGTGTCACCAAGGTTGGAACAAAATATTGAAGCATCTGGATCACCAGTACAAACAGTTAATAAAAGTGCCTTCTTAAACAAAGAATTCAGTTCTTTGAACATGAAAAGAAAACGGAAAAGACACGATAAAAACAATAGTCTAACAAGCTATGAATTAGAAAGAGATAAGAAGCGTTCAAAAAAGAATCGAGTGAAATTAATTCCAGATAATATGGAAACAGTTTCAGCACCAAAAATTCGAGCCATATATTATAATGAAGCTATTTCAAAAAATCCTGACCTCAAAGAAAAACATGAATACAAACAGGCATATCATAAAGAATTACAGAATTTAAAAGATATGAAGGTATTTGATGTCGATGTGAAGTACAGTAGATCAGAAATCCCTGATAATTTAATAGTACCCACCAACACGATATTCACAAAGAAAAGAAATGGGATTTATAAGGCTAGGATAGTCTGCAGAGGTGATACTCAGTCACCAGACACTTACAGTGTAATAACTACAGAATCTTTAAATCACAATCATATTAAGATATTCTTAATGATTGCAAACAACAGAAATATGTTTATGAAGACCCTGGATATCAATCATGCATTCCTATATGCTAAATTGGAAGAAGAAATATACATCCCACATCCGCATGATAGGAGATGTGTAGTCAAGCTAAATAAGGCGTTATATGGTCTAAAACAGAGTCCTAAAGAATGGAATGATCATCTAAGACAATACTTGAATGGAATTGGACTGAAAGATAACTCTTATACTCCGGGATTATACCAAACCGAGGATAAAAATCTAATGATTGCAGTCTATGTTGATGACTGCGTAATTGCGGCAAGCAATGAACAGAGATTGGATGAATTCATAAACAAATTGAAAAGTAATTTTGAACTGAAAATTACAGGAACATTAATAGACGATGTACTCGATACAGATATATTAGGAATGGATCTAGTATACAACAAAAGACTTGGTACTATCGATTTAACATTAAAATCATTCATAAATAGAATGGATAAAAAATACAACGAGGAATTGAAAAAGATTAGAAAAAGTTCAATTCCGCATATGTCAACTTATAAAATAGATCCTAAGAAAGACGTACTGCAAATGTCAGAAGAAGAGTTTAGACAAGGTGTTCTAAAGCTACAACAATTACTAGGTGAACTAAACTATGTCAGACACAAATGCAGATACGACATTGAATTTGCTGTTAAGAAAGTGGCTAGACTAGTAAATTACCCACATGAAAGAGTCTTTTATATGATTTACAAAATAATCCAGTACTTGGTTAGGTATAAAGATATTGGAATACACTATGACCGAGACTGTAATAAAGACAAAAAGGTTATTGCTATAACTGATGCATCAGTTGGATCAGAATATGATGCTCAATCAAGGATTGGAGTTATATTATGGTACGGTATGAATATTTTTAATGTTTATTCTAACAAGAGCACAAACAGATGTGTATCATCAACAGAAGCAGAGCTTCATGCCATTTATGAAGGCTATGCAGACTCAGAAACGTTGAAGGTAACATTAAAGGAGCTAGGAGAAGGAGACAATAATGACATTGTCATGATCACTGACTCAAAGCCAGCCATTCAAGGATTAAATCGCAGCTATCAACAACCAAAAGAGAAATTCACTTGGATAAAAACTGAAATAATAAAAGAAAAAATTAAAGAGAAGAGTATAAAACTGTTAAAAATTACCGGCAAAGGTAATATTGCTGATTTACTAACAAAACCAGTATCAGCATCTGATTTTAAAAGATTTATACAAGTATTAAAAAATAAAATAACATCACAGGATATTTTGGCCTCAACAGACTATTGATAATTAATTAATGAAGTTCTAAACACACAATGAATATCTGTTGAAGTACAATAATATATCTTTAAGGGAGCA
->TY4-LTR#LTR/Copia
-TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATGGTAACAATCTAATGCTTACATCGTATATTAATGTACAACTCGTATACGTTTAAGTGTGATTGCGCCTATTGCAGAAGGAATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGTGTTAAAGACCTATTAGTTGAACATGTTATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCGGAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTCTCTTATTTAGTATAAGAAGATCAGTACTCACTTCTTCATTAATACTAATTTTTAACCTCTAATTATCAACA
->TY4p-I#LTR/Copia
-TGGCGACCCCAGTGAGGGATGGAACAAGAAATGTTATTGACGACAACATTTCTGCGCGGATTCAATCGAAAGTCAAAACAAATGATACTGTCAGACAGACGCCATCATCATTAAGAAAAGTTTCTATTAAAGATGAACAGGTACGGCAATATCAAAGAAACTTAAATAGGTTTAAAACCATACTAAATGGTTTAAAGGCAGAAGAGGAAAAACTTTCTGAGGCTGATGATATTCAGATGCTAGCCGAAAAATTATTAAAACTCGGAGAAACCATTGACAAGGTTGAGAATAGGATTCTGGATTTAGTTGAAAAGATACAATTATTGGAAACAAATGAGAACAATAATATTTTACATGAACATACAGATGCTACAGGGACTTACTATTTATTCGATACGTTAACTTCAACCAACAAAAGATTCTACCCTAAAGATTGTGTTTTTGATTATAGGACTAACAATGTTGAGAACATTCCTATTCTTTTAAACAATTTTAAAAAATTTATCAAGAAATATCAATTTGATGATGTCTTTGAAAATGATATCATAGAAATCGATCCTCGTGAAAATGAAATCTTGTGCAAAATAATCAAAGAAGGACTCGGTGAAAGTTTAGATATCATGAACACAAATACAACTGACATTTTTAGGATAATCGATGGTTTAAAAAACAAATATAGAAGTCTGCACGGTAGAGATGTCAGAATTAGAGCCTGGGAAAAGGTTTTGGTTGATACAACATGTAGAAATTCCGCATTATTAATGAATAAACTTCAAAAATTGGTACTAATGGAAAAATGGATTTTTTCCAAATGCTGCCAAGATTGTCCCAATCTAAAAGATTACCTACAAGAAGCTATCATGGGAACCTTACATGAATCCTTAAGAAATTCTGTGAAACAACGTTTGTACAATATTCCACATAACGTAGGAATTAATCACGAAGAATTTCTAATCAATACTGTTATTGAAACAGTAATTGATTTGAGCCCAATGGGTGACGATCAAATAGAAAATAGCTGCATGTATTGCAAATCTGTTTTCCATTGCTCAATTAACTGCAAAAAGAAACCAAATAGAGAACTTAGGCCTGACACGGCAAATTTCTCAAAAACCTATTATACGCAAGGTGCACAGAGACAACAACAACTTAAGTCCAGTACAAAACGAACAAAAGTCTTGGAACAAGACACAAAAAAGGTCGAACAAAGTGTACAACAGCAAAAAACTGGTAATTATTGATACCGGTTCCGGTGTAAACATTACCAATGACAAAACCTTACTGCATAATTACGAAGACAATACTCGCAGTACACGATTTTTTGGTATCGGGAAAAACAGCTCAGTGTCTGTTAAAGGGTATGGCTATATAAAAATCAAGAATGGTCACGACAATACTGACAATAAGTGCTTATTGACTTACTATGTACCGGAAGAAGAATCCACTATAATCAGCTGTTATGACTTAGCCAAGAAAACCAAATTGGTTTTAAGTCGAAAATATACCAACTTGGGAAACAAAATCATAAAAATAAAAACCAAGATAATAAATGGTGTCATTCACGTAAAAATGAATGAGTTAATTGAACGTCCTTCCGATGATTCAAAAATAAATGCAATAAAACCTACTTCTTCTACTGGATTTAAACCAAATAAAATGTCTATTACCTTGGAAGATGCTCATAAAAGAATGGGCCATACAGGAATTCAACAAATTGAAAATTCCATAAAACATAATCATTATGAAGAATACCTTGACTTAATCAAAGAACCAAATGAATTTTGGTGTCAAACCTGTAAAATCTCTAAAGCCACGAAAAGAAATCATTATACCGGGTCTATGAATAATCATAGTACTGATCATGAACCAGGCTCATCATGGTGCATGGATATATTTGGTCCTGTTTCAAGTTCAAACGCGGACACTAAAAGGTACATGCTTATTATGGTGGATAACAACACGAGATATTGCATGACCTCCACACACTTCAATAAGAATGCTGAAACTATATTAACACAAATCAGAAAGAATATTCAGTACGTGGAAACACAATTTGACAGAAAAGTCAGAGAAATTAATTCAGACAGAGGTACTGAATTCACAAATGATCAGATAGAAGAATATTTTATTTCAAAAGGAATACATCATATACTTACTTCTACACAAGATCATGCTGCTAATGGAAGAGCAGAAAGATACATCAGAACAATAATAACTGATGCAACAACACTCCTAAGACAAAGTAACTTAAGAGTAAAATTTTGGGAATACGCAGTAACTTCTGCTACCAATATAAGAAATTGCCTGGAACACAAACGTACAGGTAAACTACCATTGAAGGCAATCTCACGTCAACCTGTTACAGTGAGATTAATGTCATTCTTACCATTTGGCGAAAAAGGAATAATTTGGAACCATAATCACAAAAAATTGAAACCATCGGGACATCCTTCTATAATTTTATGCAAAGATCCAAATAGTTATGGATACAAATTCTTTATACCATCCATAAATAAAATTGTCACATCTGATAATTATACAATTCCCAACTATACTATGGACGGTAGAGTAAGAAATACTCAGAATATTTACAAAAGTCATCAAATCAGTTCACATAATGCTGATGAAGAAGATCAAATCGATACGGTCACAAACTTATGTGAAGCTTTGGAAAACTACGAAGATGATAATAGACCAATTACTCGCCTGGAAGATTTTTTCACAGAGGAAGAGTTATCTCAAATAGACTCAAACGCAAAATACCCATCTCCTAGTAATAACCTAGAAGGGGACTTGGATTACGTATTTTCTGATGTTGAAGAATCTGGAGATTATGACCTTGAATCTGAACTTTCAGCGACAAATACCTCAATCTCAACTGATAAAAACAAAATTTTGTCAAACAAGGATTCTAATTCAGAACTTGCATCGACTGAAATATCCATCAGTGGAATCGATAAAAAAGGATTAATAAATACAACTCATATTGATGAAGATAATTGTGATGAAAAAGTCCACAGAATTCCATCGATTATACAAGAAAACCTCGTAGGAAGTAAAAATACTATTAAAATCAATGACGAAAACAAAATCTCCAACAGAATTCGTAGTAAAAACATTGGGAGTACATTAAACTCTGGACTCAGTAGATGTGTAGATATTACCGATGAATCTATTACTAACAAAGATGAGTCAATACACAACCCAAAACCAGAACTAATACAGGAGCAGTTTAATAAAACAAACCATGAAACTTCGTTTCCTAAAGAAGGGAGCATTGGAAGAAATGTAAAATTCCGAAATCCAAACAATGAGATTTCTTTAAAAACAAGCGAAACGAGTTTACCAATAAAAACTTTAGAAAGTATTAACAATCACCACAGTAATGATTATTCCACAAACAAAGTTGAAAAGTTTGAGAAGGAAAATCATCATCCGCCCCCGATTGAGGACGTTGTGGATATGAGTGATCAAACAGATATGGAATCAAACTGTCAGGATGATAATAACATAAAAAAATTAGAAGACACCGACGAAAATGTACCAACTGAGAATGGAACCAATGTGTCACCAAGGTTGGAACGAAGTAGTAAAAAAAATGAGATCAACACTACAACCAATTAAAACGACAACTGAAGCATCTGGATCGTCAGTACAAACAGTTAATAAAAGTGCCTTTTTAAACAAAGAATTTAATTCTTTGAATATGAAAAGAAAACGGAAAAGACACGATAAAAACAATAGCTTAACAAGCTACGAATTAGAAAGAGATAAGAAGCGTTCAAAGAAGAATCGAGTGAAATTAATTCCAGATAATATGGAAACAAGTTCAGCACCGAAAATTAGAGCCATATATTATAATGAAGCTATTTCAAAAAATCCTGACCTCAAAGAAAAACATGAATACAAACAGGCATATCATAAAGAATTACAAAATCTAAAAGATATGAAGGTATTTGATGTCGATGTGAAGTACAGTAGATCAGAAATCCCTGATAATTTAATAGTACCCACCAACACAATATTCACAAAGAAGAGAAATGGGATTTATAAGGCTAGGATAGTCTGCAGAGGCGATACTCAGTCACCGGACACTTACAATGTAATAACTACAGAATCTTTAAATCACAATCATATTAAGATATTCTTAATGATTGCAAACAACAGAAATATGTTTATGAAGACTCTGGATATCAATCATGCATTCCTATATGCTAAATTGGAAGAAGAAATATACATCCCACATCCGCATGATCGGAGATGTGTAGTCAAACTAAATAAGGCGTTATATGGTCTAAAACAGAGTCCTAAAGAATGGAATGATCATCTAAGACAATACTTGAATGGTATTGGATTGAAAGATAACTCTTATACTCCGGGATTATACCAAACCGAGGATAAAAATCTAATGATTGCAGTTTATGTTGATGACTGCGTAATTGCGGCAAACAATGAACAGAGATTGGATGAATTCATAAACAAATTGAAAAGTAATTTTGAACTGAAAATTACAGGAACATTAATAGATGATGTACTCGATACAGATATATTAGGAATGGACTTAGTATACAACAAAAGACTTGGTACTATCGATTTAACATTGAAATCATTCATAAATAAAATGGATAAAAAATACAAAGAGGAATTGAAAAAGATTAGAAAAAGTTCAATTCCGCATACGTCAACTTATAAAATAGATCCTAAGAAAGACGGACTGCAAATGTCAGAAGAAGAGTTTAGACAAGGTGTTCTGAAATTACAGCAATTACTAGGTGAACTAAACTATGTCAGATACAAATGCAGATACGACATTGAATTTGCTGTTAAGAAAGTGGCTAGACTAGTAAATTACCCACATGAAAACGTCTTCTATATGATTTACAAAATAATCCAGTACTTGGTTCGGTATAAAGATATTGGAATACACTATGACCGAGACTGTAATAAAGATAAGAAGGTTATTGCTATTACTGATGCATCAGTTGGATCAGAATATGATGCTCAATCAAGGATTGGAGTTATATTATGGTACGGGATGAATATTTTTAATGTTTATTCTAACAAGAGCACAAACAGATGTGTATCATCAACAGAAGCAGAGCTTCATGCCATTTATGAGGGCTATGCAGACTCAGAAACGTTGAAGGAAACATTAAAAGAGCTAGGAGAAGGAGAAAATAATGACATTGTCATGATCACTGACTCAAAGCCAGCCATTCAAGGATTAAATCGTAGCTATCAACAACCAAAAGAAAAATTCACTTGGATAAAAACTGAAATAATAAAAGAAAAAATTAAAGAGAAGAGTATAAAACTGTTAAAAATTACCGGCAAAGGTAATATTGCTGATTTACTAACAAAACCAGTATCAGCATCTGATTTTGAAAGATTTATACAAGTATTAAAAAATAAAATAACATCACAGGATATTTTGGCCTCAACAGACTATTGATAATTAATTAATGAAGTTCTAAACACACAAGGAATATCTGTTGAAGTACAATAATATATCTTTAAGGGAGCA
->TY4p-LTR#LTR/Copia
-TGTTGGAACGAGAGTAATTAATAGTGACATGAGTTGCTATAGTAACAATCTAATGCTTACATCGTATATTAATGTACACCTCGTATACGTTTAAGTGTGATTGCACCTATTGCAGAAGGAATGTTAAACGAGAAGCTCAGACAATACTGAAGCTGAGTTAAAAATCTATTAGTTGAACATGATATGGTAGGTACATATATGAGGAATATGAGTCGTCACATCAATGTATAGTAACTACCGGAATCACTATTATATTGGTCATAATTAATATGACCAATCGGCGTGTGTTTTATATACCTCTCTTATTTAGTATAAGAAGATCAGTACTTATTTCTTCATTAGTACTATATTTTAACCTCTAATTATCAACA
->TY5-I#LTR/Copia
-GGTTATGAGCCCTGAGAGCAATGCTTCAGAGACCATAATTAATCTATCTAATCCCAACAATTATAAACAGTGGCTGTACGGTATCGAGACCGCTGCTGAATATGCTAACGAATATATGAACGAATTCGTTCATACCGGAGATATCCAATCAATGAAAAGGGATTACAATCTCAGCGCGAATGATGAAAGCTTTGTCAAAACCGTATTTAACAGTTTCCTGGTAAAGCTCTACAAGAAAACTATCGTGGGTGAAGCTGCATGTGAAATGAACTGGATATGTGATGATTCACTTGGAAGGGTCTCTGCTTATGATATTTTCTCGCACTTCGAAGAAAACTATAATGAAGTCACTATTGGATCCAGGCTTACTCTTATAGAGGACTTACCAAATATATCCTCCAAGCCTGTAGATGAAATCGCTTCCTTTTTGAAAACCCTATTCACAATGCTTGAAGACAATAGCGAAGAACAGGACAAAAAGAAAAGACGCGATACCAATATCGCGTTGCTATTAATGACCTTCTTACCCGAGTTAAAGGAATCATTCCACGAGAAATTCGGTGACTCTAAAGCTCTTCAGCTGTCACAAGTCATTAGATTCTGTAAATTAAAGGCGTCATCGAATTCATTATCTTCAGTCTCAGATACATTGGTTGCACAAGACAGAAGAAGCTATCAAAAGAAAGGAAATAAGGGATGTATGATTTGTGGGGCTGATCATCGCTTAAGCAACTGTTCTCTGCTTAAAAGAAGAATACCAGAAGCCAGAATCTTTAAATTATATCCTAATGACAAGACGAATAGATCTTCATCTGCTAGTGTTGCGATTCCTGACTATGAAACGCAAGGCCAAACAGCAGGACAGATAACACCAAAGTCCTGGCTCTGTATGTTATCTTCGACCGTCCCAGCTACCAAATCCTCAGATTGGATTTGTGACACAGGATGTACTTCACACATGTGCCACGACCGTTCTATGTTCTCATCATTTACTAGATCCTCTAAGAAAGACTTTGTCAGAGGAGTCGGCGGTTCCATACCCATCATGGGCTCCGGGACTGTAAACATCGGCACTGTTCAATTAAATGACGTATCCTACGTCCCTGATTTACCAGTCAACCTAATATCCATTTGGAAACTATGTGCTAAATCCAACTCTTCTGTTACGTTCACAAAAGAGGGTGTCACTGTGAAATCACCTGATGACGTGATTTCTACGGCTGGGAAGTTAAACAATTATCTGTACATTTTCGATGATCTTACGCCCGTAACTACCTTCTCTTCGCAAAATTACTTCTGCTCTAAAACATTGGATTCATCTAAAATGATAACTTCCGCAGCGTTTCATACCGTTGCAGATAAAATGTTGTCGCAACACATTTCTCCCACTGCTCTCCCGGTAAAATGGCATGCTCGTATGGGCCATCCCGGAGCAGATATTTACAATTCCTTGGCTAGAACTCTGCGTTTTCCAAAATTTAAGACGGCTGAATACACTATTTGTCCTACCTGCTCACTAGCAAAAGGAATCATCAAAAAGGGTAAAGTCTCGCTCAAAAAATATACCCAACCTCTTCAAATGGTACAGGCTGATCTCTGTGGTGGGTTTCGCTACCAAGAGTTTCAGTCAAATAAATATTTTCTTACTATCCGTGATGCCTATAGTCGCTACTACTCTGTAATACATTTAAAATCCAAAGCAGACGCTCCGATAAAATTCATGGAATGGATCAACGAAACCGAACAATACTTTAGCTCCCGGGGTGGATTCAAAGTCGGATCTGTTCGTACAGACAATGGTACAGAATTCGTAAATAAAAATCTTCATGCGTTTTTTAAATCTAAAGGAATAGAGCATCAGTTAACTATTCCATATCATAGTTATCAAAATGGTGCTGTTGAACGTGCACATCGTACCATCGAAGAACGCACTCGTTGTCTCCTTATCGGGGGGCGTGTTCCTCCGTCCTTGTGGTCTGAAGCTGTTTCTTGCGCAGTCTATTTAATCAATAGGTCCCCTGTAGTGTCCAAAAATAACAGTATCCCATACTGCCGGTGGTTCAACATCCCCGCAAAAGATTTCGGTATCGCACATCTTCGAATTTTTGGATGTACAGCATACGCAACCTTACAACCTAGTCTTCGAGACGGCAAACTTGCCCCAACTGTCATATCTGGTGTTATGGTTGGCTATGACTCTAACCATCGAGGATACAGGATTTATCATCCCGAAACTGGCCGCATCTTTGTGAGCAGTCAAGTTCGATTTGACGAACACATGTTTCCTCTTGCTGATACAGAGGCAGTTCACGTCTCTCACGACTTTGCCACTTCCGCTATTGGGGGGGTGTCCAAATATCCTGAAACAGGGTCAACCGTCTCTGCTCCAAAGAACGACGGATCTGACTTGGCAAATTTGCCAATAACTGTTCCCAAAAATGTAAATCAACCAGCACATAAACCTAATACCAGTAACATCTCTTCCTCTGATGATGATGAGGATATTTCAATGGAAATCGAAATGGAAAAACCTATCCCTGAGTGTAACCAAGACAACTTACCAAACTCCGGATGTCCACCAACAAGGATACAACATTCTAACTTTGAATCCTTACCAACCGTGTCTACCGAAGACGAAACTAATTCTTCTATGGAGAAAACTCCTGAAAGAGTTCCAGCGGCACTAACTTATCGAGAAATTCCAAAATCATCCGATTCAGAATATATTCCGACATGCCGAAATAGAACTAGACGTGTTAAAAGAACTAATAAGAAACCAACGCGATCCCGCGAAATAGAAATATATGATATATCACGTCCAAACGTAATATCGAGTGACAACTTACCTGAAGTTAGAAGTGCCAAGCAAAGAAAGACGGTGTCCAATACAAATGATACTGTAGCAAGGACAAATAGACTTCCAACCGTGCTACGAACTCTAGACTCAAACAACATTGACACGCTGCATGTTGCCAGTACTGGTGAAGAAGTGTCCATCGAAAGACTTTCAAGCATGGCTCTTCAGGAAGCGAAGAACAATTCCGCCAGAACTAATCAAGCTAATTCTCTTACTGATTGGTTTCCAGTAGGCGCAATGCCGATACCTGACCAGAGGTATCTATCCGTTCACGATGGAACATATATCAGCGACTCACAAGATGTGGGTGATACTGACCTCACTCCTGCTGTAACCAGGCTAGTTACTGAAGAGAATTCAATCGAATCTCCTCCATCGTTGGATTCATCGCCTCCAAATACCTCATTTAACGCGGCTCTAACTGCTATTATCCATAGCACAAAAAAAGGAAACCCGAAAACCTATGCCCAAGCAATGGGAAGGCCTGACTTTCAAGAATGGCACAACGCATGCCTCAAGGAACTTTCCGCGTTCAAAGATCACAATACGTACAAATTGGTGTCTCTTCCAAAGCAAAGAAGAGCTCTTGGATCGCGCTGGGTATTCACAATAAAAGACTCCGGGACGTACAAAGCTCGCCTTGTCGCCCAAGGACATACTCAAAAGGCTGGTATTGACTATCAAGAAACTTTTGCACCAGTCATTCGATATGACTCTGTTAGATTATTTCTGGCCCTTGCTAGCTGCCTCAAACTAATAGTATATCAGATGGACGTTGACACCGCGTTTCTAAACTCAAAAATGAATGAGCCGGTATACGTAAAACAACCACCCGGATTTATTAATGAAAGTAATCCCGACTATGTATGGGAACTATACGGCGGTATGTATGGACTCAAGCAAGCCCCATTACTATGGAACGAACATATCAACAATACTCTTCAAAAGATTGGTTTTCGTCGACATGAAGGCGAACATGGCTTATACTTTCGTTCCACATCTGATGGTCCCATCTACATTGCCCTATACGTAGACGACTTACTTGTTGCTGCTCCCTCTCCGAAAATATATGACAGGGTTAAGCAGAAACTAACGAAGTTATACTCAATGAAGGATCTAGGTAAAGTTGACAAATTCCTCGGTCTTAACATTAATCAATTTTCAAATGGAGACATCACTCTCTCACTTCAAGACTATATTGCTAAAGCTGCATCTGAAAGCGAAATAAACATATGTAAGCCTACACAGACTCCGCTCTGTGACTCAAAGCCTCTTTTCGAAACAACTTCCCCGCACCTAAAGGACATCACTCCTTATCAGAGCATAGTTGGACAGCTTCTCTTTTGTGCAAATACTGGTCGTCCTGACATATCTTATCCGGTCTCACTACTCTCCAGGTTTCTTCGCGAACCTCGCGCAATCCATTTGGAGTCTGCTCGACGAGTTCTACGGTACCTATATACCACCAGAAGTATGTGTCTCAAGTATCGTTCTGGATCTCTGTTGGCACTAACTGTATATTGTGATGCATCTCATGGAGCAATTCACGATCTCCCACACTCTACTGGGGGGTACGTGACTCTACTTGCTGGTGCTCCAGTTACGTGGTCATCAAAGAAACTCAAGGGTGTGATTCCTGTATCATCTACTGAGGCAGAATACATTACTGCAAGTGAAACTGTCATGGAGATAGAATGGATTCAAAACTTGTTTGAACACTTAGGCCAGCCACTTATCTCATCAACATTATACGTAGATAATGAACCTGCTATAAAACTATCTAAACATCCTGTATTTCACACGAGAACAAAACACATTGCCTTGAGATATCACAAGCTAAGAAGTGCAGTGGCAGCAGGCATAATTACCATAGAGCATGTTATTACAAAGAGACAAGTTGCTGACATATTTACAAAAATCCTTCCAGCAGAATCATTCAAAGCACATAGGGCTGTCATGGTGAGGGAACCAGAAACTGCAAAATAACCACTCTCATGCGTATTCAGTTATGGGGGGA
->TY5-LTR#LTR/Copia
-TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATTGTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTACTTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTACATAACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCACTACGTCAACA
->TY5p-I#LTR/Copia
-GGTTATGAGCCCTGAGAGCAATGCTTCAGAGACCATAATTAATCTATCTAATCCCAACAATTATAAACAGTGGCTGTACGGTATCGAGACCGCTGCTGAATATGCTAACGAATATATGAACGAATTCGTTCATACCGGAGATATCCAATCAATGAAAAGGGATTACAATCTCAGCGCGAATGATGAAAGCTTTGTCAAAACCGTATTTAACAGTTTCCTGGTAAAGCTCTACAAGAAAACTATCGTGGGTGAAGCTGCATGTGAAATGAACTGGATATGTGATGATTCACTTGGAAGGGTCTCTGCTTATGATATTTTCTCGCACTTCGAAGAAAACTATAATGAAGTCACTATTGGATCCAGGCTTACTCTTATAGAGGACTTACCAAATATATCCTCCAAGCCTGTAGATGAAATCGCTTCCTTTTTTGAAAACCCTATTCACAATGCTTGAAGACAATAGCGAAGAACAGGACAAAAAGAAAAGACGCGATACCAATATCGCGTTGCTATTAATGACCTTCTTACCCGAGTTAAAGGAATCATTCCACGAGAAATTCGGTGACTCTAAAGCTCTTCAGCTGTCACAAGTCATTAGATTCTGTAAATTAAAGGCGTCATCGAATTCATTATCTTCAGTCTCAGATGCATTGGTTGCACAAGACAGAAGAAGCTATCAAAAGAAAGGAAATAAGGGATGTATGATTTGTGGGGCTGATCATCGCTTAAGCAACTGTTCTCTGCTTAAAAGAAGAATACCAGAAGCCAGAATCTTTAAATTATATCCTAATGACAAGACGAATAGATCTTCATCTGCTAGTGTTGCGATTCCTGACTATGAAACGCAAGGCCAAACAGCAGGACAGATAACACCAAAGTCCTGGCTCTGTATGTTATCTTCGACCGTCCCAGCTACCAAATCCTCAGATTGGATTTTTGACACAGGATGTACTTCACACATGTGCCACGACCGTTCTATGTTCTCATCATTTACTAGATCCTCTAAGAAAGACTTTGTCAGAGGAGTCGGCGGTTCCATACCCATCATGGGCTCCGGGACTGTAAACATCGGCACTGTTCAATTAAATGACGTATCCTACGTCCCTGATTTACCAGTCAACCTAATATCCATTTGGAAACTATGTGCTAAATCCAACTCTTCTGTTACGTTCACAAAAGAGGGTGTCACTGTGAAATCACCTGATGACGTGATTTCTACGGCTGGGAAGTTAAACAATTATCTGTACATTTTCGATGATCTTACGCCCGTAACTACCTTCTCTTCGCAAAATTACTTCTGCTCTAAAACATTGGATTCATCTAAAATGATAACTTCCGCAGCGTTTCATACCGTTGCAGATAAAATGTTGTCGCAACACATTTCTCCCACTGCTCTCCCGGTAAAATGGCATGCTCGTATGGGCCATCCCGGAGCAGATATTTACAATTCCTTGGCTAGAACTCTGCGTTTTCCAAAATTTTAAGACGGCTGAATACACTATTTGTCCTACCTGCTCACTAGCAAAAGGAATCATCAAAAAGGGTAAAGTCTCGCTCAAAAAATATACCCAACCTCTTCAAATGGTACAGGCTGATCTCTGTGGTGGGTTTCGCTACCAAGAGTTTCAGTCAAATAAATATTTTCTTACTATCCGTGATGCCTATAGTCGCTACTACTCTGTAATACATTTAAAATCCAAAGCAGACGCTCCGATAAAATTCATGGAATGGATCAACGAAACCGAACAATACTTTAGCTCCCGGGGTGGATTCAAAGTCGGATCTGTTCGTACAGACAATGGTACAGAATTCGTAAATAAAAATCTTCATGCGTTTTTTAAATCTAAAGGAATAGAGCATCAGTTAACTATTCCATATCATAGTTATCAAAATGGTGCTGTTGAACGTGCACATCGTACCATCGAAGAACGCACTCGTTGTCTCCTTATCGGGGGCGTGTTCCTCCGTCCTTGTGGTCTGAAGCTGTTTCTTGCGCAGTCTATTTAATCAATAGGTCCCCTGTAGTGTCCAAAAATAACAGTATCCCATACTGCCGGTGGTTCAACATCCCCGCAAAAGATTTCGGTATCGCACATCTTCGAATTTTTGGATGTACAGCATACGCAACCTTACAACCTAGTCTTCGAGACGGCAAACTTGCCCCAACTGTCATATCTGGTGTTTATGGTTGGCTATGACTCTAACCATCGAGGATACAGGATTTATCATCCCGAAACTGGCCGCATCTTTGTGAGCAGTCAAGTTCGATTTGACGAACACATGTTTCCTCTTGCTGATACAGAGGCAGTTCACGTCTCTCACGACTTTGCCACTTCCGCTATTGGGGGGGTGTCCAAATATCCTGAAACAGGGTCAACCGTCTCTGCTCCAAAGAACGACGGATCTGACTTGGCAAATTTGCCAATAACTGTTCCCAAAAATGTAAATCAACCAGCACATAAACCTAATACCAGTAACATCTCTTCCTCTGATGATGATGAGGATATTTCAATGGAAATCGAAATGGAAAAACCTATCCCTGAGTGTAACCAAGACAACTTACCAAACTCCGGATGTCCACCAACAAGGATACAACATTCTAACTTTGAATCCTTACCAACCGTGTCTACCGAAGACGAAACTAATTCTTCTATGGAGAAAACTCCTGAAAGAGTTCCAGCGGCACTAACTTATCGAGAAATTCCAAAATCATCCGATTCAGAATATATTCCGACATGCCGAAATAGAACTAGACGTGTTAAAAGAACTAATAAGAAACCAACGCGATCCCGCGAAATAGAAATATATGATATATCACGTCCAAACGTAATATCGAGTGACAACTTACCTGAAGTTAGAAGTGCCAAGCAAAGAAAGACGGTGTCCAATACAAATGATACTGTAGCAAGGACAAATAGACTTCCAACCGTGCTACGAACTCTAGACTCAAACAACATTGACACGCTGCATGTTGCCAGTACTGGTGAAGAAGTGTCCATCGAAAGACTTTCAAGCATGGCTCTTCAGGAAGCGAAGAACAATTCCGCCAGAACTAATCAAGCTAATTCTCTTACTGATTGGTTTCCAGTAGGCGCAATGCCGATACCTGACCAGAGGTATCTATCCGTTCACGATGGAACATATATCAGCGACTCACAAGATGTGGGTGATACTGACCTCACTCCTGCTGTAACCAGGCTAGTTACTGAAGAGAATTCAATCGAATCTCCTCCATCGTTGGATTCATCGCCTCCAAATACCTCATTTAACGCGGCTCTAACTGCTATTATCCATAGCACAAAAAAAAGGAAACCCGAAAACCTATGCCCAAGCAATGGGAAGGCCTGACTTTCAAGAATGGCACAACGCATGCCTCAAGGAACTTTCCGCGTTCAAAGATCACAATACGTACAAATTGGTGTCTCTTCCAAAGCAAAGAAGAGCTCTTGGATCGCGCTGGGTATTCACAATAAAAGACTCCGGGACGTACAAAGCTCGCCTTGTCGCCCAAGGACATACTCAAAAGGCTGGTATTGACTATCAAGAAACTTTTGCACCAGTCATTCGATATGACTCTGTTAGATTATTTCTGGCCCTTGCTAGCTGCCTCAAACTAATAGTATATCAGATGGACGTTGACACCGCGTTTCTAAACTCAAAAATGAATGAGCCGGTATACGTAAAACAACCACCCGGATTTATTAATGAAAGTAATCCCGACTATGTATGGAACTATACGGCGGTATGTATGGACTCAAGCAAGCCCCATTACTATGGAACGAACATATCAACAATACTCTTCAAAAGATTGGTTTTCGTCGACATGAAGGCGAACATGGCTTATACTTTCGTTCCACATCTGATGGTCCCATCTACATTGCCCTATACGTAGACGACTTACTTGTTGCTGCTCCCTCTCCGAAAATATATGACAGGGTTAAGCAGAAACTAACGAAGTTATACTCAATGAAGGATCTAGGTAAAGTTGACAAATTCCTCGGTCTTAACATTAATCAATTTTCAAATGGAGACATCACTCTCTCACTTCAAGACTATATTGCTAAAGCTGCATCTGAAAGCGAAATAAACATATGTAAGCCTACACAGACTCCGCTCTGTGACTCAAAGCCTCTTTTCGAAACAACTTCCCCGCACCTAAAGGACATCACTCCTTATCAGAGCATAGTTGGACAGCTTCTCTTTTGTGCAAATACTGGTCGTCCTGACATATCTTATCCGGTCTCACTACTCTCCAGGTTTCTTCGCGAACCTCGCGCAATCCATTTGGAGTCTGCTCGACGAGTTCTACGGTACCTATATACCACCAGAAGTATGTGTCTCAAGTATCGTTTCTGGATCTCTGTTGGCACTAACTGTATATTGTGATGCATCTCATGGAGCAATTCACGATCTCCCACACTCTACTGGGGGTACGTGACTCTACTTGCTGGTGCTCCAGTTACGTGGTCATCAAAGAAACTCAAGGGTGTGATTCCTGTATCATCTACTGAGGCAGAATACATTACTGCAAGTGAAACTGTCATGGAGATAGAATGGATTCAAAACTTGTTTGAACACTTAGGCCAGCCACTTATCTCATCAACATTATACGTAGATAATGAACCTGCTATAAAAACTATCTAAACATCCTGTATTTCACACGAGAACAAAACACATTGCCTTGAGATATCACAAGCTAAGAAGTGCAGTGGCAGCAGGCATAATTACCATAGAGCATGTTATTACAAAGAGACAAGTTGCTGACATATTTACAAAAATCCTTCCAGCAGAATCATTCAAAGCACATAGGGCTGTCATGGTGAGGGAACCAGAAACTGCAAAATAACCACTCTCATGCGTATTCAGTTATGGGGGGA
->TY5p-LTR#LTR/Copia
-TGTTGAATGTGATAACCCAAAAGCATGATATGGGTAATGTTTCAGTACTGTTTCAGAATTGTTTCAGTAATGTTTTAGACAAGGAAAACATAGAGCAGCAAACCTCCGATCCGACAGTACTTAAGAAACCATAGTTTCTGTGTACAAGAGTAGTACCTATGTAATTCTTACATTTTACATAACATATAGAAAGGTCCAATAAACTTACAACATTATGACATATAAGCTAGATCGTAATTCACTACGTCAACA
diff --git a/data/YPS138.centromere.fa b/data/YPS138.centromere.fa
new file mode 100644
index 0000000..1cd1f9b
--- /dev/null
+++ b/data/YPS138.centromere.fa
@@ -0,0 +1,32 @@
+>CEN1
+ATCACATGTTACTTTTGTAAAATAATTATATTAATATTTAAATATTTCAAAGATATTATTTATTTTATAAATACTTTTACTTAATAAAATTCATGTTTTTGAATTCCGAAATGTTTAA
+>CEN10
+AAGTCACGTGCCATATAATTAAACTAAAAATATATTTTCTTATTAGTATAAAATATTATTTTATTTTTTTTAATTAAAATGTTTATATAATATATTGTATATGATTTCCGAAAGCAAA
+>CEN11
+GTCACATGACTATATTATTAATTTCAAAATAAATATTATAACATTTTAAAAAAATATAATTAATTTAATTTTCAAAAAAATATAAAATATTATTTGTTCGCGGTGTCCGAACATAAAA
+>CEN12
+GTCACGTGTAAATTAATATAATTTATAATTATATTAAATTATTATACTAAATATATAAATTTATTTTATTTAATTTTATTTTTATATAAATTAATGTATTTGATATCCGAAAAGAAAAA
+>CEN13
+AATATCACATGACATAAATTGAAAATGTTTCATTTTTTTTATTTTTTTTGTAAATAATTTTACAAGTTAGTAAAAAATATATAGATATATTTTAATGTATATGCTTTCCGAACTTTTAAT
+>CEN14
+GTCACGTGTAGCTTTTATACTATATTTTAATTATTTTTAAATATTTCATTTTATATAACTTTTTTTCATTTATATTTCTATTTATTATTTGTATTGTATTTGACGTCCGAAGGTAAAA
+>CEN15
+TCACGTGCTATTCTTTCAAAAATATTTTAAAACCTAAAAATGCTTTATTGTAAATTAGATTATTGTTTTCAAAATTTTTATTAAGAGATTCGTTGTATATGACTTCCGAGTACAAAAT
+>CEN16
+GTCACCTGACTAATTTAAAACTTTTATTTTATTCTTTTTTTAATTTCTAAATTTCTAAATATAAATTAAATAAAAATAAACACAATTTCTTTTGTTTTTCATTTCCGAAAGTAAAAA
+>CEN2
+GTCACATGATAAAACTAACAGTAGAATATTAAATAAAATAATATTATATATATAATAATTATTAAAAAATATAATTATTATAAAATTTAAAGTTGGTTTTGTTTTCCGAACATAAAAA
+>CEN3
+ATCACATGACTATTTAAATTAAAAAATATATTTAAAAATTTTATTCTATATCTATTTTATGTTTATCAATAATAAAACATTAAAATATCAAATGTATATGTTTTCCGAAAAATAAAAA
+>CEN4
+TGATCACATGATATACTTTAAATTATTTTATTATTATATTATTTATATAAAACAATAGTAATAAAATGTTTTTAAAAAAAGGCAAGATATTCTTAGTATCTGATTTCCGAACAGGAAAA
+>CEN5
+GTCACGTGATTAAAAAAGAATTCTAAAAATTTATTGTTTTTTATTTAATATTGTTTATTATTTAAAAAATAAAAATATAAAATGTATTTGAGTTGTTTTAGAATTCCGAAACAAAAAA
+>CEN6
+GTCACGTGTACATAATTTATATATTTTTTAAAATATTTAATAAATTTATAAAAAAATGCTTTAAAAATTAAAAATGAGAAAAAATATACACAGGTGTTTGATTTCCGAAGTTATAAA
+>CEN7
+GCACGTGTATGTTTTTAATATTTTCTATTTTATAAATAAATATTATTAAAGATATTAAATTAATAAATAAGTATAATATTTTTTAAATACCATTGGTTTTGCTTTCCGAACAATTAAA
+>CEN8
+GTCACATGACCTCTATTAAATAATTTTTAAAATAAGTTATTTTTCTATAAATAATATATTTGATTTCAAAATTTCATTGTTAAATATTTTCCGGGTTTTGTTTTCCGAAGCAAAAAT
+>CEN9
+ATCACGTGAGTACTAAATAATATTTTTAAATTACTTTTAAAATTTATTTATATATTTAATATATTTATATTTTTTTCTTAAAATATTTATTGATGTTCTTGTTTTCCGAAATCTTTTT
diff --git a/data/fuzzy_defragmentation.txt b/data/fuzzy_defragmentation.txt
index 507527a..388928c 100644
--- a/data/fuzzy_defragmentation.txt
+++ b/data/fuzzy_defragmentation.txt
@@ -1,5 +1,6 @@
 TY1TY2 TY1-LTR TY2-LTR TY1p-LTR TY2p-LTR TY1-I TY1p-I TY2-I TY2p-I 
 TY3 TY3-I TY3p-I TY3-LTR TY3p-LTR
-TY4 TY4-I TY4p-I TY4-LTR TY4p-LTR
+TY4 TY4-I TY4p-I TY4-LTR TY4p-LTR 
 TY5 TY5-I TY5p-I TY5-LTR TY5p-LTR
+TSU4 TSU4-I TSU4b-I TSU4p-I TSU4-LTR TSU4b-LTR TSU4p-LTR
 
diff --git a/data/te_proteins.fasta.gz b/data/te_proteins.fasta.gz
index 1941590..2aadafc 100644
Binary files a/data/te_proteins.fasta.gz and b/data/te_proteins.fasta.gz differ
diff --git a/install_dependencies.sh b/install_dependencies.sh
index 85ebabf..ee06505 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -1,13 +1,72 @@
 #!/bin/bash
-# last update: 2020/09/10
+# last update: 2022/12/21
 set -e -o pipefail
 
 LRSDAY_HOME=$(pwd)
 BUILD="build"
+lite_installation="no";
 mainland_china_installation="no";
 #########################                                                                                                       
 
-while getopts ":hc" opt
+timestamp () {
+  date +"%F %T"
+}
+
+clean () {
+    dir=$1
+    if [ -d $dir ] 
+    then
+	echo "remove previously failed installation in $BUILD/$dir"
+	rm -rf $dir
+    fi
+}
+
+download () {
+  url=$1
+  download_location=$2
+  echo "Downloading $url to $download_location"
+  wget -c --no-check-certificate $url -O $download_location
+}
+
+clone () {
+  url=$1
+  dir=$(basename $url)
+  echo "run clone for \"git clone $url\""
+  git clone $url --depth 1
+  cd $dir
+  git fetch --unshallow
+}
+
+tidy_version () { 
+    echo "$1" | awk -F. '{ printf("%d%03d%03d%03d\n", $1,$2,$3,$4); }';
+}
+
+check_installed () {
+    if [ -e "$1/installed" ]; then
+        echo "installed"
+    else
+        echo ""
+    fi
+}
+
+note_installed () {
+    touch "$1/installed"
+}
+
+echo ""
+echo ""
+echo "##################################################################"
+echo "###                                                            ###"
+echo "###                  Welcome to LRSDAY                         ###"
+echo "###                                                            ###"
+echo "##################################################################"
+echo ""
+echo ""
+echo "[$(timestamp)] Installation starts ..."
+echo ""
+
+
+while getopts ":hlc" opt
 do
     case "${opt}" in
         h)
@@ -15,6 +74,10 @@ do
             echo "bash install_dependencies.sh"
             echo "When installing within mainland China, please run this script with the '-c' option >"
             echo "bash install_dependencies.sh -c";;
+        l)
+	    echo "Detected the '-l' option >"
+	    echo "Set installation mode as 'lite' by skipping the installation of a few non-essential dependencies"
+	    lite_installation="yes";;
         c)
 	    echo "Detected the '-c' option >"
 	    echo "Set installation location as 'mainland_china'"
@@ -27,7 +90,7 @@ echo "";
 
 if [ -z "$MAKE_JOBS" ]
 then
-    echo "Defaulting to 2 concurrent jobs when executing make. Override with MAKE_JOBS=<NUM>"
+    echo "[$(timestamp)] Defaulting to 2 concurrent jobs when executing make. Override with MAKE_JOBS=<NUM>"
     MAKE_JOBS=2
 fi
 
@@ -38,100 +101,117 @@ if [ ! -z "$INSTALL_DEPS" ]; then
     xargs -a debiandeps sudo apt-get install -y
 fi
 
+MINICONDA2_VERSION="py27_4.8.3" # released on 2020.06.06
+if [[ "$mainland_china_installation" == "no" ]]
+then
+    MINICONDA2_DOWNLOAD_URL="https://repo.anaconda.com/miniconda/Miniconda2-${MINICONDA2_VERSION}-Linux-x86_64.sh"
+else
+    MINICONDA2_DOWNLOAD_URL="https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda2-${MINICONDA2_VERSION}-Linux-x86_64.sh"
+fi
 
-MINICONDA3_VERSION="py37_4.8.2" # released on 2020.03.11
+MINICONDA3_VERSION="py37_4.9.2" # released on 2020.11.23                                                                                                                
 if [[ "$mainland_china_installation" == "yes" ]]
 then
-    MINICONDA3_DOWNLOAD_URL="https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
-else
     MINICONDA3_DOWNLOAD_URL="https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
+else
+    MINICONDA3_DOWNLOAD_URL="https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
 fi
-echo "MINICONDA3_DOWNLOAD_URL=$MINICONDA3_DOWNLOAD_URL"
 
 # for reads preparation and preprocessing
-SRA_VERSION="2.9.6" # released on 2019.03.18
-SRA_DOWNLOAD_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz"
-
-GUPPY_VERSION="4.0.15" # released on 2020.08.30
-GUPPY_DOWNLOAD_URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_${GUPPY_VERSION}_linux64.tar.gz"
+GUPPY_VERSION="6.2.1" # released on 2022.06.07
+GUPPY_GPU_DOWNLOAD_URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_${GUPPY_VERSION}_linux64.tar.gz"
+GUPPY_CPU_DOWNLOAD_URL="https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_${GUPPY_VERSION}_linux64.tar.gz"
 
 PORECHOP_VERSION="0.2.4" # 
 PORECHOP_GITHUB_COMMIT_VERSION="109e437" # committed on 2018.10.19
 PORECHOP_DOWNLOAD_URL="https://github.com/rrwick/Porechop.git"
 
-FILTLONG_VERSION="0.2.0" #
-FILTLONG_GITHUB_COMMIT_VERSION="13504b7" # committed on 2019.05.15
+FILTLONG_VERSION="0.2.1" #
+FILTLONG_GITHUB_COMMIT_VERSION="c56f02b" # committed on 2021.07.01
 FILTLONG_DOWNLOAD_URL="https://github.com/rrwick/Filtlong.git"
 
-NANOPLOT_VERSION="1.29.1" # released on 2020.05.05
-NUMPY_VERSION="1.16.3"
-SCIPY_VERSION="1.2.1"
-NANOPLOT_DOWNLOAD_URL="https://github.com/wdecoster/NanoPlot.git"
+NANOPLOT_VERSION="1.40.0" # released on 2022.04.08
 
 # for genome assembly
-MINIMAP2_VERSION="2.17" # released on 2019.05.05
+MINIMAP2_VERSION="2.22" # released on 2021.08.07
 MINIMAP2_DOWNLOAD_URL="https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2"
 
-CANU_VERSION="2.1.1" # released on 2020.10.19
+CANU_VERSION="2.2" # released on 2021.08.27
 CANU_DOWNLOAD_URL="https://github.com/marbl/canu/releases/download/v${CANU_VERSION}/canu-${CANU_VERSION}.Linux-amd64.tar.xz"
 
-FLYE_VERSION="2.8.2" # released on 2020.12.10
+# WHATSHAP_VERSION="1.1"
+
+FLYE_VERSION="2.9.1" # released on 2021.08.22
 FLYE_DOWNLOAD_URL="https://github.com/fenderglass/Flye/archive/${FLYE_VERSION}.tar.gz"
 
 WTDBG2_VERSION="2.5" # 
-WTDBG2_GITHUB_COMMIT_VERSION="b77c565" # committed on 2019.12.11
+WTDBG2_GITHUB_COMMIT_VERSION="b77c565" # committed on 2020.12.11
 WTDBG2_DOWNLOAD_URL="https://github.com/ruanjue/wtdbg2.git"
 
+
 SMARTDENOVO_VERSION="" # 
-SMARTDENOVO_GITHUB_COMMIT_VERSION="5cc1356" # committed on 2018.02.19
+SMARTDENOVO_GITHUB_COMMIT_VERSION="8488de9" # committed on 2021.02.24
 SMARTDENOVO_DOWNLOAD_URL="https://github.com/ruanjue/smartdenovo"
 
-RAVEN_VERSION="1.3.0" # released on 2020.12.17
-RAVEN_DOWNLOAD_URL="https://github.com/lbcb-sci/raven/releases/download/${RAVEN_VERSION}/raven-v${RAVEN_VERSION}.tar.gz"
+RAVEN_VERSION="1.8.1" # released on 2022.08.04
+RAVEN_GITHUB_COMMIT_VERSION="0ea10b3"
+#RAVEN_DOWNLOAD_URL="https://github.com/lbcb-sci/raven/releases/download/${RAVEN_VERSION}/raven-v${RAVEN_VERSION}.tar.gz"
 
-SHASTA_VERSION="0.7.0" # 
-SHASTA_GITHUB_COMMIT_VERSION="f22692f" # committed on 2021.01.10
-SHASTA_DOWNLOAD_URL="https://github.com/chanzuckerberg/shasta/releases/download/${SHASTA_VERSION}/shasta-Linux-${SHASTA_VERSION}"
+SHASTA_VERSION="0.11.1" # 
+SHASTA_GITHUB_COMMIT_VERSION="b739b1e"
+SHASTA_DOWNLOAD_URL="https://github.com/paoloshasta/shasta/releases/download/${SHASTA_VERSION}/shasta-Linux-${SHASTA_VERSION}"
 
 # for assembly polishing
 
 PB_ASSEMBLY_VERSION="0.0.8" #
-BAX2BAM_VERSION="0.0.9" #
-PBMM2_VERSION="1.3.0" #
+BAX2BAM_VERSION="0.0.11" #
+PBMM2_VERSION="1.9.0" #
 
-NANOPOLISH_VERSION="0.13.2" #
-NANOPOLISH_GITHUB_COMMIT_VERSION="c7b5a75" # commited on 2019.03.27 
-NANOPOLISH_DOWNLOAD_URL="https://github.com/jts/nanopolish.git"
+NANOPOLISH_VERSION="0.14.0" # released on 2021.04.06
 
 PARALLEL_VERSION="20180722" # released on 2018.07.22
 PARALLEL_DOWNLOAD_URL="http://ftp.gnu.org/gnu/parallel/parallel-${PARALLEL_VERSION}.tar.bz2"
 
-RACON_VERSION="1.4.13" # released on 2020.03.25
-RACON_DOWNLOAD_URL="https://github.com/lbcb-sci/racon/releases/download/${RACON_VERSION}/racon-v${RACON_VERSION}.tar.gz"
+RACON_VERSION="1.5.0" # released on 2021.03.26
+#RACON_GITHUB_COMMIT_VERSION="9119181"
+#RACON_DOWNLOAD_URL="https://github.com/lbcb-sci/racon/releases/download/${RACON_VERSION}/racon-v${RACON_VERSION}.tar.gz"
+#RACON_DOWNLOAD_URL="https://github.com/lbcb-sci/racon.git"
 
-MEDAKA_VERSION="1.2.0" # released on 2020.11.07
+MEDAKA_VERSION="1.7.2" # released on 2022.09.21
 MEDAKA_DOWNLOAD_URL="https://github.com/nanoporetech/medaka/archive/v${MEDAKA_VERSION}.tar.gz"
 
-MARGINPOLISH_VERSION="1.3.0" # released on 2020.03.04
-MARGINPOLISH_GITHUB_COMMIT_VERSION="5492204" # commited on 2020.03.25 
-MARGINPOLISH_DOWNLOAD_URL="https://github.com/UCSC-nanopore-cgl/marginPolish.git"
+# MARGINPOLISH_VERSION="1.3.0" # released on 2020.03.04
+# MARGINPOLISH_GITHUB_COMMIT_VERSION="5492204" # commited on 2020.03.25 
+# # MARGINPOLISH_DOWNLOAD_URL="https://github.com/UCSC-nanopore-cgl/marginPolish.git"
+# MARGINPOLISH_DOWNLOAD_URL="https://github.com/UCSC-nanopore-cgl/MarginPolish/archive/refs/tags/v${MARGINPOLISH_VERSION}.tar.gz"
 
-PEPPER_VERSION="0.1" # released on 2020.12.10
-PEPPER_GITHUB_COMMIT_VERSION="e938ca7" # commited on 2020.11.24 
-PEPPER_DOWNLOAD_URL="https://github.com/kishwarshafin/pepper.git"
+# HELEN_VERSION="0.0.1" # released on 2020.12.10
+# HELEN_GITHUB_COMMIT_VERSION="a075e9f" # commited on 2020.10.28 
+# HELEN_DOWNLOAD_URL="https://github.com/kishwarshafin/helen.git"
+
+# HOMOPOLISH_VERSION="0.2.1" # released on 2020.12.10
+# HOMOPOLISH_DOWNLOAD_URL="https://github.com/ythuang0522/homopolish"
+
+# MARGIN_VERSION="2.3.1" # released on 2022.03.25
+# MARGIN_DOWNLOAD_URL="https://github.com/UCSC-nanopore-cgl/margin"
+# MARGIN_GITHUB_COMMIT_VERSION="9bf845f" # commited on 2022.03.25 
+
+# PEPPER_VERSION="0.4" # released on 2020.12.10
+# PEPPER_GITHUB_COMMIT_VERSION="734d226" # commited on 2021.03.08 
+# PEPPER_DOWNLOAD_URL="https://github.com/kishwarshafin/pepper.git"
 
 # for assembly scaffolding
 RAGOUT_VERSION="2.3" # released on 2020.03.18
-RAGOUT_DOWNLOAD_URL="https://github.com/fenderglass/Ragout/archive/${RAGOUT_VERSION}.tar.gz"
+RAGOUT_GITHUB_COMMIT_VERSION="7b92fe7" # commited on 2020.12.09"
+RAGOUT_DOWNLOAD_URL="https://github.com/fenderglass/Ragout.git"
 
-RAGOO_VERSION="1.11" # released on 2019.09.03
-RAGOO_DOWNLOAD_URL="https://github.com/malonge/RaGOO/archive/v${RAGOO_VERSION}.tar.gz"
+RAGTAG_VERSION="2.1.0" # released on 2021.11.01
 
-QUAST_VERSION="5.0.2" # one of its dependency needs "csh" to be pre-installed
+# QUAST_VERSION="5.0.2" # one of its dependency needs "csh" to be pre-installed
 
 HDF_VERSION="1.10.6" # 
-# HDF_VERSION_prefix=${HDF_VERSION%.*}
-# HDF_DOWNLOAD_URL="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF_VERSION_prefix}/hdf5-${HDF_VERSION}/src/hdf5-${HDF_VERSION}.tar.gz"
+HDF_VERSION_prefix=${HDF_VERSION%.*}
+HDF_DOWNLOAD_URL="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF_VERSION_prefix}/hdf5-${HDF_VERSION}/src/hdf5-${HDF_VERSION}.tar.gz"
 
 # SONLIB_VERSION="" # 
 # SONLIB_GITHUB_COMMIT_VERSION="1afbd97" # committed on 2017.08.09
@@ -141,13 +221,13 @@ HDF_VERSION="1.10.6" #
 # HAL_GITHUB_COMMIT_VERSION="a2ad656" # committed on 2017.09.09
 # HAL_DOWNLOAD_URL="https://github.com/glennhickey/hal.git"
 
-MUMMER4_VERSION="4.0.0beta2" # released on 2017.10.14
+MUMMER4_VERSION="4.0.0rc1" # released on 2020.10.03
 MUMMER4_DOWNLOAD_URL="https://github.com/gmarcais/mummer/releases/download/v${MUMMER4_VERSION}/mummer-${MUMMER4_VERSION}.tar.gz"
 
-GNUPLOT_VERSION="5.4.0" # released on 2020.07.01
+GNUPLOT_VERSION="4.6.6" # released on 2015.02.18
 GNUPLOT_DOWNLOAD_URL="https://sourceforge.net/projects/gnuplot/files/gnuplot/${GNUPLOT_VERSION}/gnuplot-${GNUPLOT_VERSION}.tar.gz"
 
-BEDTOOLS_VERSION="2.29.2" # released on 2019.12.18
+BEDTOOLS_VERSION="2.30.0" # released on 2021.01.24
 BEDTOOLS_DOWNLOAD_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/bedtools-${BEDTOOLS_VERSION}.tar.gz"
 
 SPADES_VERSION="3.14.1" # released on 2020.05.02
@@ -156,28 +236,31 @@ SPADES_DOWNLOAD_URL="http://cab.spbu.ru/files/release${SPADES_VERSION}/SPAdes-${
 PRODIGAL_VERSION="2.6.3" # released on 2016.02.12
 PRODIGAL_DOWNLOAD_URL="https://github.com/hyattpd/Prodigal/archive/v${PRODIGAL_VERSION}.tar.gz"
 
-CAP_VERSION="" # see http://seq.cs.iastate.edu/cap3.html
-CAP_DOWNLOAD_URL="http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar"
+CAP3_VERSION="" # see http://seq.cs.iastate.edu/cap3.html
+CAP3_DOWNLOAD_URL="https://github.com/yjx1217/CAP3.git" # "http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar"
 
 BWA_VERSION="0.7.17" # released on 2017.10.23
 BWA_DOWNLOAD_URL="http://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2"
 
-SAMTOOLS_VERSION="1.11" # released on 2020.09.22
+SAMTOOLS_VERSION="1.16.1" # released on 2022.09.02
+HTSLIB_VERSION="1.16" # released on 2022.09.02
 SAMTOOLS_DOWNLOAD_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2"
 
-CIRCLATOR_VERSION="1.5.5" # released on 2018.01.31
+CIRCLATOR_VERSION="1.5.5" # released on 2020.10.29
 CIRCLATOR_DOWNLOAD_URL="https://github.com/sanger-pathogens/circlator/archive/v${CIRCLATOR_VERSION}.tar.gz"
 
 TRIMMOMATIC_VERSION="0.38" # 
 TRIMMOMATIC_DOWNLOAD_URL="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${TRIMMOMATIC_VERSION}.zip"
 
 GATK3_VERSION="3.6-6" #
-GATK3_DOWNLOAD_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${SRA_VERSION}/GenomeAnalysisTK.jar"
+GATK3_DOWNLOAD_URL="https://github.com/yjx1217/GATK3_Archive/raw/main/gatk3.jar.gz"
 
 PICARD_VERSION="2.23.4" # released on 2020.09.03
 PICARD_DOWNLOAD_URL="https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar"
 
-PILON_VERSION="1.23" # released on 2018.11.27
+# HAPOG_VERSION="1.2" # released on 2021.10.01
+ 
+PILON_VERSION="1.24" # released on 2021.01.29
 PILON_DOWNLOAD_URL="https://github.com/broadinstitute/pilon/releases/download/v${PILON_VERSION}/pilon-${PILON_VERSION}.jar"
 
 EXONERATE_VERSION="2.2.0" # 
@@ -185,12 +268,13 @@ EXONERATE_DOWNLOAD_URL="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exo
 
 BLAST_VERSION="2.2.31" # 
 RMBLAST_VERSION="2.2.28" # 
-BLAST_DOWNLOAD_URL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
-RMBLAST_DOWNLOAD_URL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/${RMBLAST_VERSION}/ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
+BLAST_DOWNLOAD_URL="http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
+RMBLAST_DOWNLOAD_URL="http://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/${RMBLAST_VERSION}/ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
 
 SNAP_VERSION="" # 
 SNAP_GITHUB_COMMIT_VERSION="a89d68e" # committed on 2017.05.18
-SNAP_DOWNLOAD_URL="https://github.com/KorfLab/SNAP"
+# SNAP_GITHUB_COMMIT_VERSION="bbf2050" # commited on 2022.04.12 
+SNAP_DOWNLOAD_URL="https://github.com/KorfLab/SNAP.git"
 
 RAPSEARCH_VERSION="2.24" #
 RAPSEARCH_DOWNLOAD_URL="https://sourceforge.net/projects/rapsearch2/files/RAPSearch${RAPSEARCH_VERSION}_64bits.tar.gz"
@@ -202,13 +286,18 @@ SNOSCAN_VERSION="0.9.1" #
 SNOSCAN_DOWNLOAD_URL="http://eddylab.org/software/snoscan/snoscan.tar.gz"
 
 REPEATMASKER_VERSION="open-4-0-7" #
+# REPEATMASKER_VERSION="4.1.0" #
 REPEATMASKER_DOWNLOAD_URL="http://www.repeatmasker.org/RepeatMasker-${REPEATMASKER_VERSION}.tar.gz"
 
-TRF_VERSION="409" #
-TRF_DOWNLOAD_URL="http://tandem.bu.edu/trf/downloads/trf${TRF_VERSION}.linux64"
+#REPBASE_VERSION="20181026"
+REPBASE_VERSION="20170127"
+REPBASE_DOWNLOAD_URL="https://github.com/yjx1217/RMRB.git"
 
+TRF_VERSION="409" #
+TRF_DOWNLOAD_URL="https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64"
 REANNOTATE_VERSION="17.03.2015-LongQueryName"
-REANNOTATE_DOWNLOAD_URL="https://github.com/yjx1217/REannotate_LongQueryName/archive/version_${REANNOTATE_VERSION}.tar.gz"
+REANNOTATE_GITHUB_COMMIT_VERSION="7fdb339"
+REANNOTATE_DOWNLOAD_URL="https://github.com/yjx1217/REannotate_LongQueryName"
 
 CLUSTALW_VERSION="2.1" #
 CLUSTALW_DOWNLOAD_URL="http://www.clustal.org/download/${CLUSTALW_VERSION}/clustalw-${CLUSTALW_VERSION}.tar.gz"
@@ -217,7 +306,6 @@ MUSCLE_VERSION="3.8.31" #
 MUSCLE_DOWNLOAD_URL="http://www.drive5.com/muscle/downloads${MUSCLE_VERSION}/muscle${MUSCLE_VERSION}_i86linux64.tar.gz"
 
 HMMER_VERSION="3.2.1" # released on 2018.06.13
-#HMMER_DOWNLOAD_URL="http://eddylab.org/software/hmmer3/${HMMER_VERSION}/hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz"
 HMMER_DOWNLOAD_URL="http://eddylab.org/software/hmmer/hmmer-${HMMER_VERSION}.tar.gz"
 
 BAMTOOLS_VERSION="2.4.2" # released on 2017.11.02
@@ -231,12 +319,12 @@ AUGUSTUS_DOWNLOAD_URL="http://bioinf.uni-greifswald.de/augustus/binaries/old/aug
 EVM_VERSION="1.1.1" # released on 2015.07.03
 EVM_DOWNLOAD_URL="https://github.com/EVidenceModeler/EVidenceModeler/archive/v${EVM_VERSION}.tar.gz"
 
-PROTEINORTHO_VERSION="6.0.25" # released on 
-# PROTEINORTHO_DOWNLOAD_URL="https://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v${PROTEINORTHO_VERSION}.tar.gz"
+PROTEINORTHO_VERSION="6.0.35" # released on 2022.09.15
 DIAMOND_VERSION="2.0.6"
 
+#MAKER_VERSION="3.01.03" #
 MAKER_VERSION="3.00.0-beta" #
-MAKER_DOWNLOAD_URL="http://topaz.genetics.utah.edu/maker_downloads/static/maker-${MAKER_VERSION}.tgz"
+MAKER_DOWNLOAD_URL="https://github.com/yjx1217/Maker3beta_archive.git"
 
 # for MFannot
 EMBOSS_VERSION="6.5.7" # released on 2012.07.25
@@ -275,13 +363,13 @@ GRAB_FASTA_DOWNLOAD_URL="https://github.com/BFL-lab/grab-fasta.git"
 # for MFannot
 MFANNOT_DATA_GITHUB_COMMIT_VERSION="b039ac5" # committed on 2016.12.07
 MFANNOT_VERSION="1.35" #
-MFANNOT_GITHUB_COMMIT_VERSION="6472b97" # committed on 2018.10.31
+MFANNOT_GITHUB_COMMIT_VERSION="6472b97" # committed on 2018.10.31 # "104e1c5" # committed on 2021.02.10
 MFANNOT_DATA_DOWNLOAD_URL="https://github.com/BFL-lab/MFannot_data.git"
 MFANNOT_DOWNLOAD_URL="https://github.com/BFL-lab/MFannot.git"
 
-# downloading URLs for dependencies
-# QUAST_DOWNLOAD_URL="https://downloads.sourceforge.net/project/quast/quast-${QUAST_VERSION}.tar.gz"
-
+# # GFF3
+# GFF3TOOLKIT_VERSION="2.1.0" # released on 2021.12.09
+# GFF3TOOLKIT_DOWNLOAD_URL="https://github.com/NAL-i5K/GFF3toolkit"
 
 # UCSC Utilities
 BLAT_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat"
@@ -290,141 +378,228 @@ PSLSORT_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslS
 PSLSCORE_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslScore"
 PSLCDNAFILTER_DOWNLOAD_URL="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/pslCDnaFilter"
 
+
 # Create the $BUILD directory for dependency installation
-echo ""
-echo "Create $BUILD directory if it does not already exist"
-mkdir -p $BUILD
+
+if [ -d $BUILD ]
+then
+    echo ""
+    echo "[$(timestamp)] Detected previously generated $BUILD directory."
+else
+    echo "[$(timestamp)] Create the new $BUILD directory."
+    mkdir $BUILD
+    echo ""
+fi
+
 cd $BUILD
 build_dir=$(pwd)
 
 echo ""
-echo "Download and install all the dependencies"
+echo "[$(timestamp)] Download and install all the dependencies"
 echo ""
 
 # Downloading all the dependencies
-download () {
-  url=$1
-  download_location=$2
-  echo "Downloading $url to $download_location"
-  wget --no-check-certificate $url -O $download_location
-}
-
-download_and_extract() {
-    url=$1
-    download_location=$2
-    echo "Downloading $url to $download_location"
-    wget --no-check-certificate $url -O $download_location
-    if [[ $download_location =~ \.bz2$ ]]; then
-        extract_command="tar -xjf"
-    elif [[ $download_location =~ \.xz$ || $download_location =~ \.tar$ ]]; then
-        extract_command="tar -xf"
-    else
-        extract_command="tar -zxf"
-    fi
-    $($extract_command $download_location)
-    rm $download_location
-
-}
-
-check_installed() {
-    if [ -e "$1/installed" ]; then
-        echo "installed"
-    else
-        echo ""
-    fi
-}
-
-note_installed() {
-    touch "$1/installed"
-}
 
 # ---------- set Perl & Python environment variables -------------
 PYTHONPATH="$build_dir"
 PERL5LIB="$build_dir:$PERL5LIB"
 PERL5LIB="$build_dir/cpanm/perlmods/lib/perl5:$PERL5LIB"
-cpanm_dir=$build_dir/cpanm
 
-if [ ! -e "$build_dir/cpanm" ]; then
-    mkdir -p  $build_dir/cpanm
+echo ""
+echo "[$(timestamp)] Installing Perl modules ..."
+cpanm_dir=$build_dir/cpanm
+if [ -z $(check_installed $cpanm_dir) ]; then
+    clean "$build_dir/cpanm"
+    mkdir -p  $cpanm_dir
     cd $cpanm_dir
-    wget --no-check-certificate -O - https://cpanmin.us/ > cpanm
+    # wget -c --no-check-certificate -O - https://cpanmin.us/ > cpanm
+    # work around for the unstable downloading issue
+    cp $LRSDAY_HOME/misc/cpanm .
+
     chmod +x cpanm
     mkdir -p perlmods
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Test::More@1.302086
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Text::Soundex@3.05
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Env@1.04
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed File::Which@1.21
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Term::ReadKey@2.37
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Carp@1.38
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Perl::Unsafe::Signals@0.03
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Carp::Clan@6.06 
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Bit::Vector@7.4
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Inline@0.80
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Inline::C@0.78
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed List::MoreUtils@0.419
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Acme::Damn@0.08
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Sys::SigAction@0.23
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed forks@0.36
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed forks::shared@0.36
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Want@0.29
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed IO::All@0.86
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed IO::Prompt@0.997004
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed DBI@1.636
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Proc::ProcessTable@0.53
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed threads@2.16
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed PerlIO::gzip@0.20
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed ExtUtils::CBuilder@0.280224 
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed LWP::Simple@6.26
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed LWP::UserAgent
+    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed Bio::Perl@1.007001
+    if [ ! -z "$USE_POSTGRES" ]; then
+	# need $POSTGRES_HOME pre-defined
+	$cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed DBD::Pg
+    else
+	$cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed DBD::SQLite@1.54
+    fi
+    note_installed $cpanm_dir
 fi
 
-# Testing the packages when they are getting installed slows them down. Is this absolutely required?
-xargs -a "$LRSDAY_HOME/perldeps" $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed || (echo "Could not install some Perl modules. See logs for failures" && exit 1)
-if [ ! -z "$USE_POSTGRES" ]; then
-    # need $POSTGRES_HOME pre-defined
-    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed DBD::Pg
-else
-    $cpanm_dir/cpanm -l $cpanm_dir/perlmods --notest --skip-installed DBD::SQLite@1.54
+# ------------- Miniconda2 --------------------
+if [[ $lite_installation == "no" ]]
+then
+    echo ""
+    echo "[$(timestamp)] Installing miniconda2 ..."
+    miniconda2_dir="$build_dir/miniconda2/bin"
+    if [ -z $(check_installed $miniconda2_dir) ]; then
+	cd $build_dir
+	clean "$build_dir/miniconda2"
+	download $MINICONDA2_DOWNLOAD_URL "Miniconda2-${MINICONDA2_VERSION}-Linux-x86_64.sh"
+	bash Miniconda2-${MINICONDA2_VERSION}-Linux-x86_64.sh -b -p $build_dir/miniconda2
+	if [[ "$mainland_china_installation" == "yes" ]]
+	then
+	    $miniconda2_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
+            $miniconda2_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free
+            $miniconda2_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/pro
+            $miniconda2_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
+            $miniconda2_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
+            $miniconda2_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
+	    
+            $miniconda2_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/main
+            $miniconda2_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/free
+            $miniconda2_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/pro
+            $miniconda2_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/msys2
+            $miniconda2_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/cloud/bioconda
+            $miniconda2_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/cloud/conda-forge
+	    
+	    # $miniconda2_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
+	    # $miniconda2_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
+	    # $miniconda2_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
+	    # $miniconda2_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
+	    # $miniconda2_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
+	else 
+	    $miniconda2_dir/conda config --add channels defaults
+	    $miniconda2_dir/conda config --add channels bioconda
+	    $miniconda2_dir/conda config --add channels conda-forge
+	fi
+	$miniconda2_dir/conda config --set show_channel_urls yes
+	$miniconda2_dir/conda config --set ssl_verify no
+	$miniconda2_dir/conda config --set channel_priority flexible
+	$miniconda2_dir/pip install --timeout 1000 cython==0.29.14 numpy==1.13.1
+	rm Miniconda2-${MINICONDA2_VERSION}-Linux-x86_64.sh 
+	note_installed $miniconda2_dir
+    fi
 fi
 
 # ------------- Miniconda3 --------------------
+echo ""
+echo "[$(timestamp)] Installing miniconda3 ..."
 miniconda3_dir="$build_dir/miniconda3/bin"
 if [ -z $(check_installed $miniconda3_dir) ]; then
     cd $build_dir
+    clean "$build_dir/miniconda3"
     download $MINICONDA3_DOWNLOAD_URL "Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh"
     bash Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh -b -p $build_dir/miniconda3
     if [[ "$mainland_china_installation" == "yes" ]]
     then
-	$miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
-	$miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
-	$miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
-	$miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
-	$miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
+	$miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
+        $miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free
+        $miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/pro
+        $miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
+        $miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
+        $miniconda3_dir/conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
+
+        $miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/main
+        $miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/free
+        $miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/pro
+        $miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/pkgs/msys2
+        $miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/cloud/bioconda
+        $miniconda3_dir/conda config --add channels https://anaconda.mirrors.sjtug.sjtu.edu.cn/cloud/conda-forge
+
+	# $miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
+	# $miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
+	# $miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
+	# $miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
+	# $miniconda3_dir/conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
     else 
 	$miniconda3_dir/conda config --add channels defaults
 	$miniconda3_dir/conda config --add channels bioconda
 	$miniconda3_dir/conda config --add channels conda-forge
     fi
+    $miniconda3_dir/conda config --set show_channel_urls yes
+    $miniconda3_dir/conda config --set ssl_verify no
+    $miniconda3_dir/conda config --set channel_priority flexible
+    cd $build_dir
+    rm Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh 
+    note_installed $miniconda3_dir
 fi
-$miniconda3_dir/conda config --set show_channel_urls yes
-note_installed $miniconda3_dir
-rm Miniconda3-${MINICONDA3_VERSION}-Linux-x86_64.sh 
+
 
 # ----------------- PB-ASSEMBLY ----------------------
-pacbio_dir=$build_dir/conda_pacbio_env/bin
-if [ -z $(check_installed $pacbio_dir) ]; then
-    cd $build_dir
-    $miniconda3_dir/conda create -y -p $build_dir/conda_pacbio_env python=3.7
-    source $miniconda3_dir/activate $build_dir/conda_pacbio_env
-    $miniconda3_dir/conda install -y hdf5=${HDF_VERSION}
-    # $miniconda3_dir/conda install -y -c bioconda samtools=${SAMTOOLS_VERSION} openssl
-    $miniconda3_dir/conda install -y -c bioconda pb-assembly=${PB_ASSEMBLY_VERSION}
-    # $miniconda3_dir/conda install -y -c bioconda bax2bam=${BAX2BAM_VERSION}
-    # $miniconda3_dir/conda install -y -c bioconda pbmm2=${PBMM2_VERSION}
-    source $miniconda3_dir/deactivate
+if [[ $lite_installation == "no" ]]
+then
+    echo ""
+    echo "[$(timestamp)] Installing pb-assembly ..."
+    pbassembly_dir=$build_dir/pbassembly_conda_env/bin
+    if [ -z $(check_installed $pbassembly_dir) ]; then
+	cd $build_dir
+	clean "$build_dir/pbassembly_conda_env"
+	$miniconda3_dir/conda create -y -p $build_dir/pbassembly_conda_env 
+	source $miniconda3_dir/activate $build_dir/pbassembly_conda_env
+	$miniconda3_dir/conda install -y -c bioconda pb-assembly=${PB_ASSEMBLY_VERSION}
+	source $miniconda3_dir/deactivate
+	note_installed $pbassembly_dir
+    fi
 fi
-note_installed $pacbio_dir
-
 
-# ------------- SRA Toolkit -------------------
-sra_dir="$build_dir/sratoolkit.${SRA_VERSION}-centos_linux64/bin"
-if [ -z $(check_installed $sra_dir) ]; then
-    cd $build_dir
-    echo "Download SRAtoolkit-v${SRA_VERSION}"
-    download_and_extract $SRA_DOWNLOAD_URL sratoolkit.${SRA_VERSION}-centos_linux64.tar.gz
-    note_installed $sra_dir
+# ----------------- BAX2BAM  ----------------------
+if [[ $lite_installation == "no" ]]
+then
+    echo ""
+    echo "[$(timestamp)] Installing bax2bam ..."
+    bax2bam_dir="$build_dir/bax2bam_conda_env/bin"
+    if [ -z $(check_installed $bax2bam_dir) ]; then
+	cd $build_dir
+	clean "$build_dir/bax2bam_conda_env"
+	$miniconda2_dir/conda create -y -p $build_dir/bax2bam_conda_env 
+	source $miniconda2_dir/activate $build_dir/bax2bam_conda_env
+	$miniconda2_dir/conda install -y -c bioconda bax2bam=${BAX2BAM_VERSION}
+	source $miniconda2_dir/deactivate
+	note_installed $bax2bam_dir
+    fi
 fi
 
 # --------------- Porechop ------------------
-porechop_dir="$build_dir/conda_porechop_env/bin"
+echo ""
+echo "[$(timestamp)] Installing Porechop ..."
+porechop_dir="$build_dir/porechop_conda_env/bin"
 if [ -z $(check_installed $porechop_dir) ]; then
     cd $build_dir
+    clean "$build_dir/porechop_conda_env"
     echo "Download Porechop-v${PORECHOP_VERSION}"
-    $miniconda3_dir/conda create -y -p $build_dir/conda_porechop_env python=3.7
-    source $miniconda3_dir/activate $build_dir/conda_porechop_env
+    $miniconda3_dir/conda create -y -p $build_dir/porechop_conda_env python=3.7
+    source $miniconda3_dir/activate $build_dir/porechop_conda_env
     $miniconda3_dir/conda install -y -c bioconda porechop=${PORECHOP_VERSION} 
     source $miniconda3_dir/deactivate
     note_installed $porechop_dir
 fi
 
 # --------------- Filtlong ------------------
+echo ""
+echo "[$(timestamp)] Installing Filtlong ..."
 filtlong_dir="$build_dir/Filtlong/bin"
 if [ -z $(check_installed $filtlong_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Filtlong"
     echo "Download Filtlong-v${FILTLONG_VERSION}"
     git clone $FILTLONG_DOWNLOAD_URL
     cd Filtlong
@@ -434,64 +609,100 @@ if [ -z $(check_installed $filtlong_dir) ]; then
 fi
 
 # --------------- minimap2 ------------------
+echo ""
+echo "[$(timestamp)] Installing minimap2 ..."
 minimap2_dir="$build_dir/minimap2-${MINIMAP2_VERSION}_x64-linux"
 if [ -z $(check_installed $minimap2_dir) ]; then
     cd $build_dir
+    clean "$build_dir/minimap2-${MINIMAP2_VERSION}_x64-linux"
     echo "Download minimap2-v${MINIMAP2_VERSION}"
-    download_and_extract $MINIMAP2_DOWNLOAD_URL "minimap2-${MINIMAP2_VERSION}.tar.bz2"
+    download $MINIMAP2_DOWNLOAD_URL "minimap2-${MINIMAP2_VERSION}.tar.bz2"
+    tar xvjf minimap2-${MINIMAP2_VERSION}.tar.bz2
+    rm minimap2-${MINIMAP2_VERSION}.tar.bz2
     note_installed $minimap2_dir
 fi
 PATH=$minimap2_dir:${PATH}
 
 # --------------- samtools -----------------
+echo ""
+echo "[$(timestamp)] Installing samtools ..."
 samtools_dir="$build_dir/samtools-${SAMTOOLS_VERSION}"
-htslib_dir="$samtools_dir/htslib-${SAMTOOLS_VERSION}"
-tabix_dir="$samtools_dir/htslib-${SAMTOOLS_VERSION}"
+htslib_dir="$samtools_dir/htslib-${HTSLIB_VERSION}"
+tabix_dir="$samtools_dir/htslib-${HTSLIB_VERSION}"
+
 if [ -z $(check_installed $samtools_dir) ]; then
     cd $build_dir
+    clean "$build_dir/samtools-${SAMTOOLS_VERSION}"
     echo "Download samtools-v${SAMTOOLS_VERSION}"
-    download_and_extract $SAMTOOLS_DOWNLOAD_URL "samtools-${SAMTOOLS_VERSION}.tar.bz2"
+    download $SAMTOOLS_DOWNLOAD_URL "samtools-${SAMTOOLS_VERSION}.tar.bz2"
+    tar xvjf samtools-${SAMTOOLS_VERSION}.tar.bz2
     cd $samtools_dir
     C_INCLUDE_PATH=""
     ./configure --without-curses;
     make -j $MAKE_JOBS
-    cd htslib-${SAMTOOLS_VERSION}
-    #autoheader
-    #autoconf
+    cd $htslib_dir
     ./configure
     make -j $MAKE_JOBS
     cd $build_dir
+    rm samtools-${SAMTOOLS_VERSION}.tar.bz2
     note_installed $samtools_dir
 fi
 PATH="$samtools_dir:$htslib_dir:$tabix_dir:${PATH}"
 
 # ------------- Canu -------------------
+echo ""
+echo "[$(timestamp)] Installing canu ..."
 canu_dir="$build_dir/canu-${CANU_VERSION}/bin"
 if [ -z $(check_installed $canu_dir) ]; then
     cd $build_dir
+    clean "$build_dir/canu-${CANU_VERSION}"
     echo "Download Canu-v${CANU_VERSION}"
-    download_and_extract $CANU_DOWNLOAD_URL "canu-${CANU_VERSION}.tar.xz"
+    download $CANU_DOWNLOAD_URL "canu-${CANU_VERSION}.tar.xz"
+    tar xvf canu-${CANU_VERSION}.tar.xz
     cd $canu_dir
     ln -s $minimap2_dir/minimap2 .
+    cd $build_dir
+    rm canu-${CANU_VERSION}.tar.xz
     note_installed $canu_dir
 fi
 
+# # --------------- WhatsHap -----------------
+# echo ""
+# echo "[$(timestamp)] Installing WhatsHap ..."
+# whatshap_dir="$build_dir/whatshap_conda_env/bin"
+# if [ -z $(check_installed $whatshap_dir) ]; then
+#     cd $build_dir
+#     # clean "$build_dir/whatshap_conda_env"
+#     echo "Download whatshap-v${WHATSHAP_VERSION}"
+#     # $miniconda3_dir/conda create -y -p $build_dir/whatshap_conda_env python=3.9
+#     source $miniconda3_dir/activate $build_dir/whatshap_conda_env
+#     $miniconda3_dir/conda install -y -c bioconda whatshap=${WHATSHAP_VERSION} nomkl 
+#     source $miniconda3_dir/deactivate
+#     note_installed $whatshap_dir
+# fi
+
+
 # ------------- Flye -------------------
-#flye_dir="$build_dir/Flye-${FLYE_VERSION}/bin"
-flye_dir="$build_dir/conda_flye_env/bin"
+echo ""
+echo "[$(timestamp)] Installing flye ..."
+flye_dir="$build_dir/flye_conda_env/bin"
 if [ -z $(check_installed $flye_dir) ]; then
     cd $build_dir
-    $miniconda3_dir/conda create -y -p $build_dir/conda_flye_env python=3.7
-    source $miniconda3_dir/activate $build_dir/conda_flye_env
+    clean "$build_dir/flye_conda_env"
+    $miniconda3_dir/conda create -y -p $build_dir/flye_conda_env python=3.7
+    source $miniconda3_dir/activate $build_dir/flye_conda_env
     $miniconda3_dir/conda install -y -c bioconda flye=${FLYE_VERSION} 
     source $miniconda3_dir/deactivate
     note_installed $flye_dir
 fi
 
 # --------------- wtdbg2 ------------------
+echo ""
+echo "[$(timestamp)] Installing wtdbg2 ..."
 wtdbg2_dir="$build_dir/wtdbg2"
 if [ -z $(check_installed $wtdbg2_dir) ]; then
     cd $build_dir
+    clean "$build_dir/wtdbg2"
     echo "Download wtdbg2-v${WTDBG2_VERSION}"
     git clone $WTDBG2_DOWNLOAD_URL
     cd wtdbg2
@@ -502,9 +713,12 @@ if [ -z $(check_installed $wtdbg2_dir) ]; then
 fi
 
 # --------------- smartdenovo ------------------
+echo ""
+echo "[$(timestamp)] Installing smartdenovo ..."
 smartdenovo_dir="$build_dir/smartdenovo"
 if [ -z $(check_installed $smartdenovo_dir) ]; then
     cd $build_dir
+    clean "$build_dir/smartdenovo"
     echo "Download smartdenovo-v${SMARTDENOVO_VERSION}"
     git clone $SMARTDENOVO_DOWNLOAD_URL
     cd smartdenovo
@@ -517,25 +731,31 @@ if [ -z $(check_installed $smartdenovo_dir) ]; then
     note_installed $smartdenovo_dir
 fi
 
-# --------------- Ra ------------------
-ra_dir="$build_dir/ra/build/bin"
-if [ -z $(check_installed $ra_dir) ]; then
-    cd $build_dir
-    echo "Download Ra-v${RA_VERSION}"
-    git clone --recursive $RA_DOWNLOAD_URL
-    cd ra
-    git checkout -f -q $RA_GITHUB_COMMIT_VERSION
-    mkdir build
-    cd build
-    cmake -DCMAKE_BUILD_TYPE=Release .. 
-    make -j $MAKE_JOBS
-    note_installed $ra_dir
-fi
+# # --------------- Raven ------------------
+# echo ""
+# echo "[$(timestamp)] Installing raven ..."
+# raven_dir="$build_dir/raven/build/bin"
+# if [ -z $(check_installed $raven_dir) ]; then
+#     cd $build_dir
+#     clean "$build_dir/raven"
+#     echo "Download Raven-v${RAVEN_VERSION}"
+#     git clone --recursive https://github.com/lbcb-sci/raven.git raven
+#     cd raven
+#     git checkout -f -q $RAVEN_GITHUB_COMMIT_VERSION
+#     mkdir build
+#     cd build
+#     cmake -DCMAKE_BUILD_TYPE=Release ..   #requires cmake >=3.11
+#     make -j $MAKE_JOBS
+#     note_installed $raven_dir
+# fi
 
 # --------------- Shasta ------------------
+echo ""
+echo "[$(timestamp)] Installing shasta ..."
 shasta_dir="$build_dir/shasta-${SHASTA_VERSION}"
 if [ -z $(check_installed $shasta_dir) ]; then
     cd $build_dir
+    clean "$build_dir/shasta-${SHASTA_VERSION}"
     echo "Download Shasta-v${SHASTA_VERSION}"
     mkdir shasta-${SHASTA_VERSION}
     cd shasta-${SHASTA_VERSION}
@@ -545,286 +765,393 @@ if [ -z $(check_installed $shasta_dir) ]; then
     note_installed $shasta_dir
 fi
 
-
 # --------------- Ragout ------------------
-
-ragout_dir="$build_dir/conda_ragout_env/bin"
+echo ""
+echo "[$(timestamp)] Installing ragout ..."
+ragout_dir="$build_dir/ragout_conda_env/bin"
+#ragout_dir="$build_dir/ragout_conda_env/Ragout/bin"
 if [ -z $(check_installed $ragout_dir) ]; then
     cd $build_dir
-    $miniconda3_dir/conda create -y -p $build_dir/conda_ragout_env python=3.7
-    source $miniconda3_dir/activate $build_dir/conda_ragout_env
-    $miniconda3_dir/conda install -c bioconda ragout=${RAGOUT_VERSION} 
+    clean "$build_dir/ragout_conda_env"
+    $miniconda3_dir/conda create -y -p $build_dir/ragout_conda_env python=3.8
+    source $miniconda3_dir/activate $build_dir/ragout_conda_env
+    $miniconda3_dir/conda install -y -c bioconda ragout=${RAGOUT_VERSION}
+
+    # cd $build_dir/ragout_conda_env
+    # git clone $RAGOUT_DOWNLOAD_URL
+    # cd Ragout
+    # git checkout -f -q $RAGOUT_GITHUB_COMMIT_VERSION 
+    # python setup.py build
+    # pip install -r requirements.txt
+    # python scripts/install-sibelia.py
+
     source $miniconda3_dir/deactivate
     note_installed $ragout_dir
 fi
 
-# --------------- RaGOO ------------------
-ragoo_dir="$build_dir/py3_virtualenv_ragoo/bin"
-if [ -z $(check_installed $ragoo_dir) ]; then
-    cd $build_dir
-    virtualenv -p $(which python3) py3_virtualenv_ragoo
-    source py3_virtualenv_ragoo/bin/activate
-    echo "Download RaGOO-v${RAGOO_VERSION}"
-    cd py3_virtualenv_ragoo
-    download_and_extract $RAGOO_DOWNLOAD_URL RaGOO-${RAGOO_VERSION}.tar.gz
-    # bugbug
-    cd RaGOO-${RAGOO_VERSION}
-    #git checkout -f -q $RAGOO_GITHUB_COMMIT_VERSION
-    pip install numpy==${NUMPY_VERSION}
-    python3 setup.py install 
-    deactivate
-    note_installed $ragoo_dir
+# --------------- Ragtag ------------------
+echo ""
+echo "[$(timestamp)] Installing ragtag ..."
+ragtag_dir="$build_dir/ragtag_conda_env/bin"
+if [ -z $(check_installed $ragtag_dir) ]; then
+    cd $build_dir
+    clean "$build_dir/ragout_ragtag_env"
+    $miniconda3_dir/conda create -y -p $build_dir/ragtag_conda_env python=3.7 pip
+    source $miniconda3_dir/activate $build_dir/ragtag_conda_env
+    #$miniconda3_dir/conda install -y -c bioconda ragtag=${RAGTAG_VERSION} 
+    $ragtag_dir/pip3 install --timeout 1000 ragtag==${RAGTAG_VERSION}
+    cd $ragtag_dir
+    ln -s $minimap2_dir/minimap2 .
+    source $miniconda3_dir/deactivate
+    note_installed $ragtag_dir
 fi
 
 # --------------- gnuplot ------------------
+echo ""
+echo "[$(timestamp)] Installing gnuplot ..."
 gnuplot_dir="$build_dir/gnuplot-${GNUPLOT_VERSION}/bin"
 if [ -z $(check_installed $gnuplot_dir) ]; then
     cd $build_dir
+    clean "$build_dir/gnuplot-${GNUPLOT_VERSION}"
     echo "Download gnuplot-v${GNUPLOT_VERSION}"
-    download_and_extract $GNUPLOT_DOWNLOAD_URL "gnuplot-${GNUPLOT_VERSION}.tar.gz"
+    download $GNUPLOT_DOWNLOAD_URL "gnuplot-${GNUPLOT_VERSION}.tar.gz"
+    tar xvzf gnuplot-${GNUPLOT_VERSION}.tar.gz
     cd "$build_dir/gnuplot-${GNUPLOT_VERSION}"
-    ./configure --prefix="$build_dir/gnuplot-${GNUPLOT_VERSION}" --disable-wxwidgets
+    ./configure --prefix="$build_dir/gnuplot-${GNUPLOT_VERSION}" --exec-prefix="$build_dir/gnuplot-${GNUPLOT_VERSION}" --disable-plugins --disable-wxwidgets --with-gd=no --without-latex --with-x=no
     make -j $MAKE_JOBS
     make install
+    cd $build_dir
+    rm gnuplot-${GNUPLOT_VERSION}.tar.gz
     note_installed $gnuplot_dir
 fi
 PATH="$gnuplot_dir:${PATH}"
 
-# --------------- Guppy --------------------
-guppy_dir="$build_dir/ont-guppy-cpu/bin"
-if [ -z $(check_installed $guppy_dir) ]; then
+# --------------- Guppy-GPU --------------------
+echo ""
+echo "[$(timestamp)] Installing guppy-GPU ..."
+guppy_gpu_dir="$build_dir/ont-guppy-gpu/bin"
+if [ -z $(check_installed $guppy_gpu_dir) ]; then
+    cd $build_dir
+    clean "$build_dir/ont-guppy-gpu"
+    echo "Download Guppy-v${GUPPY_VERSION}"
+    download $GUPPY_GPU_DOWNLOAD_URL "ont-guppy_${GUPPY_VERSION}_linux64.tar.gz"
+    tar xvzf ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
+    mv ont-guppy ont-guppy-gpu
+    rm ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
+    note_installed $guppy_gpu_dir
+fi
+
+# --------------- Guppy-CPU --------------------
+echo ""
+echo "[$(timestamp)] Installing guppy-CPU ..."
+guppy_cpu_dir="$build_dir/ont-guppy-cpu/bin"
+if [ -z $(check_installed $guppy_cpu_dir) ]; then
     cd $build_dir
+    clean "$build_dir/ont-guppy-cpu"
     echo "Download Guppy-v${GUPPY_VERSION}"
-    download_and_extract $GUPPY_DOWNLOAD_URL "ont-guppy-cpu_${GUPPY_VERSION}_linux64.tar.gz"
-    note_installed $guppy_dir
+    download $GUPPY_CPU_DOWNLOAD_URL "ont-guppy_${GUPPY_VERSION}_linux64.tar.gz"
+    tar xvzf ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
+    rm ont-guppy_${GUPPY_VERSION}_linux64.tar.gz
+    note_installed $guppy_cpu_dir
 fi
 
+
+# # --------------- Nanofilt --------------------
+# echo ""
+# echo "[$(timestamp)] Installing NanoFilt ..."
+# nanofilt_dir="$build_dir/nanofilt_conda_env/bin"
+# if [ -z $(check_installed $nanofilt_dir) ]; then
+#     cd $build_dir
+#     $miniconda3_dir/conda create -y -p $build_dir/nanofilt_conda_env 
+#     source $miniconda3_dir/activate $build_dir/nanofilt_conda_env
+#     $miniconda3_dir/conda install -y -c bioconda nanofilt=${NANOFILT_VERSION}
+#     source $miniconda3_dir/deactivate
+#     note_installed $nanofilt_dir
+# fi
+
 # --------------- Nanoplot --------------------
-nanoplot_dir="$build_dir/py3_virtualenv_nanoplot/bin"
+echo ""
+echo "[$(timestamp)] Installing NanoPlot ..."
+nanoplot_dir="$build_dir/nanoplot_conda_env/bin"
 if [ -z $(check_installed $nanoplot_dir) ]; then
     cd $build_dir
-    virtualenv -p $(which python3) py3_virtualenv_nanoplot
-    source py3_virtualenv_nanoplot/bin/activate
-    py3_virtualenv_nanoplot/bin/pip install --upgrade pip
-    py3_virtualenv_nanoplot/bin/pip install --upgrade setuptools
-    py3_virtualenv_nanoplot/bin/pip install numpy==${NUMPY_VERSION}
-    py3_virtualenv_nanoplot/bin/pip install scipy==${SCIPY_VERSION}
-    py3_virtualenv_nanoplot/bin/pip install NanoPlot==${NANOPLOT_VERSION}
-    deactivate
+    $miniconda3_dir/conda create -y -p $build_dir/nanoplot_conda_env python=3.9
+    source $miniconda3_dir/activate $build_dir/nanoplot_conda_env
+    $miniconda3_dir/conda install -y -c bioconda nanoplot=${NANOPLOT_VERSION}
+    source $miniconda3_dir/deactivate
     note_installed $nanoplot_dir
 fi
 
-# ------------- NANOPOLISH --------------------
-nanopolish_dir="$build_dir/nanopolish"
-nanopolish_virtualenv_dir="$build_dir/nanopolish/py3_virtualenv_nanopolish/bin"
+# --------------- Nanopolish --------------------
+echo ""
+echo "[$(timestamp)] Installing nanopolish ..."
+nanopolish_dir="$build_dir/nanopolish_conda_env/bin"
 if [ -z $(check_installed $nanopolish_dir) ]; then
     cd $build_dir
-    echo "Download nanopolish-v${NANOPOLISH_VERSION}"
-    git clone --recursive $NANOPOLISH_DOWNLOAD_URL
-    cd $nanopolish_dir
-    git checkout -f -q $NANOPOLISH_GITHUB_COMMIT_VERSION
-    make
-    virtualenv -p $(which python3) py3_virtualenv_nanopolish
-    source py3_virtualenv_nanopolish/bin/activate
-    py3_virtualenv_nanopolish/bin/pip install biopython
-    py3_virtualenv_nanopolish/bin/pip install pysam
-    deactivate
-    rm *.tar.gz
-    rm *.tar.bz2
+    clean "$build_dir/nanopolish_conda_env"
+    $miniconda3_dir/conda create -y -p $build_dir/nanopolish_conda_env python=3.9
+    source $miniconda3_dir/activate $build_dir/nanopolish_conda_env
+    $miniconda3_dir/conda install -y -c bioconda nanopolish=${NANOPOLISH_VERSION}
+    source $miniconda3_dir/deactivate
     note_installed $nanopolish_dir
 fi
 
-# --------------- parallel ------------------
+# --------------- Parallel ------------------
+echo ""
+echo "[$(timestamp)] Installing parallele ..."
 parallel_dir="$build_dir/parallel-${PARALLEL_VERSION}/bin"
 if [ -z $(check_installed $parallel_dir) ]; then
     cd $build_dir
     echo "Download parallel"
-    download_and_extract $PARALLEL_DOWNLOAD_URL "parallel_v${PARALLEL_VERSION}.tar.bz2"
+    clean "$build_dir/parallele-${PARALLEL_VERSION}"
+    download $PARALLEL_DOWNLOAD_URL "parallel_v${PARALLEL_VERSION}.tar.bz2"
+    tar xvjf parallel_v${PARALLEL_VERSION}.tar.bz2
     cd parallel-${PARALLEL_VERSION}
     ./configure --prefix="$build_dir/parallel-${PARALLEL_VERSION}"
     make -j $MAKE_JOBS
     make install
-    parallel_dir="$build_dir/parallel-${PARALLEL_VERSION}/bin"
+    cd $build_dir
+    rm parallel_v${PARALLEL_VERSION}.tar.bz2
     note_installed $parallel_dir
 fi
 
 # --------------- Racon -----------------
-racon_dir="$build_dir/racon-v${RACON_VERSION}/build/bin"
+echo ""
+echo "[$(timestamp)] Installing racon ..."
+racon_dir="$build_dir/racon_conda_env/bin"
 if [ -z $(check_installed $racon_dir) ]; then
     cd $build_dir
-    echo "Download racon-v${RACON_VERSION}"
-    download_and_extract $RACON_DOWNLOAD_URL "racon-v${RACON_VERSION}.tar.gz"
-    cd racon-v${RACON_VERSION}
-    mkdir build
-    cd build
-    cmake -DCMAKE_BUILD_TYPE=Release ..
-    make -j $MAKE_JOBS
+    clean "$build_dir/racon_conda_env"
+    $miniconda3_dir/conda create -y -p $build_dir/racon_conda_env python=3.7
+    source $miniconda3_dir/activate $build_dir/racon_conda_env
+    $miniconda3_dir/conda install -y -c bioconda racon=${RACON_VERSION}
+    source $miniconda3_dir/deactivate
     note_installed $racon_dir
 fi
 
 # --------------- Medaka -----------------
-medaka_dir="$build_dir/conda_medaka_env"
-if [ -z $(check_installed $conda_medaka_dir) ]; then
-    cd $build_dir
-    $miniconda3_dir/conda create -y -p $build_dir/conda_medaka_env python=3.7
-    source $miniconda3_dir/activate $build_dir/conda_medaka_env
-    $miniconda3_dir/conda install -y -c bioconda medaka=${MEDAKA_VERSION}
+echo ""
+echo "[$(timestamp)] Installing medaka ..."
+medaka_dir="$build_dir/medaka_conda_env/bin"
+if [ -z $(check_installed $medaka_dir) ]; then
+    cd $build_dir
+    clean "$build_dir/medaka_conda_env"
+    $miniconda3_dir/conda create -y -p $build_dir/medaka_conda_env 
+    source $miniconda3_dir/activate $build_dir/medaka_conda_env
+    $miniconda3_dir/conda install -y -c conda-forge -c bioconda medaka=${MEDAKA_VERSION}
+    #$miniconda3_dir/pip3 install medaka==${MEDAKA_VERSION}
     source $miniconda3_dir/deactivate
     note_installed $medaka_dir
-    medaka_dir="$build_dir/conda_medaka_env/bin"
 fi
 
-# --------------- MarginPolish -----------------
-marginpolish_dir="$build_dir/marginPolish/build"
-if [ -z $(check_installed $marginpolish_dir) ]; then
-    cd $build_dir
-    echo "Download MarginPolish-v${MARGINPOLISH_VERSION}"
-    git clone --recursive $MARGINPOLISH_DOWNLOAD_URL
-    cd marginPolish
-    git checkout -f -q $MARGINPOLISH_GITHUB_COMMIT_VERSION
-    git submodule update --init
-    mkdir build
-    cd build
-    cmake ..
-    make -j $MAKE_JOBS
-    note_installed $marginpolish_dir
-fi
+# # --------------- MarginPolish -----------------
+# echo ""
+# echo "[$(timestamp)] Installing marginpolish ..."
+# marginpolish_dir="$build_dir/marginPolish/build"
+# if [ -z $(check_installed $marginpolish_dir) ]; then
+#     cd $build_dir
+#     echo "Download MarginPolish-v${MARGINPOLISH_VERSION}"
+#     clean "$build_dir/marginPolish"
+#     download $MARGINPOLISH_DOWNLOAD_URL "marginPolish.tar.gz"
+#     tar xzf marginPolish.tar.gz
+#     cd MarginPolish-${MARGINPOLISH_VERSION}/externalTools
+#     git clone --recursive https://github.com/samtools/htslib.git
+#     cd htslib
+#     git checkout -f -q 1832d3a
+#     cd ..
+#     cd git clone --resursive https://github.com/benedictpaten/sonLib.git
+#     git checkout -f -q 8e403f6
+#     cd ..
+#     cd ..
+
+#     # git clone --recursive $MARGINPOLISH_DOWNLOAD_URL
+#     # cd marginPolish
+#     # git checkout -f -q $MARGINPOLISH_GITHUB_COMMIT_VERSION
+#     # # git submodule update --init
+#     mkdir build
+#     cd build
+#     cmake ..
+#     make -j $MAKE_JOBS
+#     note_installed $marginpolish_dir
+# fi
 
-# # --------------- PEPPER -----------------
+# # --------------- Helen -----------------
+# echo ""
+# echo "[$(timestamp)] Installing helen ..."
 # helen_dir="$build_dir/helen/build"
-# helen_virtualenv_dir="$build_dir/helen/py3_virtualenv_helen/bin"
 # if [ -z $(check_installed $helen_dir) ]; then
 #     cd $build_dir
-#     echo "Download helen-v${HELEN_VERSION}"
+#     echo "Download Helen-v${HELEN_VERSION}"
+#     clean "$build_dir/helen"
 #     git clone $HELEN_DOWNLOAD_URL
 #     cd helen
 #     git checkout -f -q $HELEN_GITHUB_COMMIT_VERSION
-#     mkdir install
-#     # virtualenv -p $(which python3) py3_virtualenv_helen
-#     # source py3_virtualenv_helen/bin/activate
-#     # py3_virtualenv_helen/bin/pip install pybind11
-#     # py3_virtualenv_helen/bin/pip install h5py
-#     # py3_virtualenv_helen/bin/pip install tqdm
-#     # py3_virtualenv_helen/bin/pip install numpy==${NUMPY_VERSION}
-#     # #py3_virtualenv_helen/bin/pip install torchnet
-#     # py3_virtualenv_helen/bin/pip install pyyaml
-#     # cd $helen_dir
-#     # cmake .. -Wno-deprecated
-#     # make -j $MAKE_JOBS
-#     # cd ..
-#     # deactivate
+#     make install
+#     . ./venv/bin/activate
+#     cd build
 #     note_installed $helen_dir
 # fi
 
-# ------------- QUAST --------------------
-# quast_dir="$build_dir/quast-${QUAST_VERSION}"
+# # --------------- PEPPER -----------------
+# pepper_dir="$build_dir/pepper_conda_env/bin"
+# if [ -z $(check_installed $pepper_dir) ]; then
+#     cd $build_dir
+#     $miniconda3_dir/conda create -y -p $build_dir/pepper_conda_env python=3.7
+#     source $miniconda3_dir/activate $build_dir/pepper_conda_env
+#     $miniconda3_dir/pip3 install pepper-polish
+#     source $miniconda3_dir/deactivate
+#     note_installed $pepper_dir
+# fi
+
+# # --------------- HOMOPOLISH -----------------
+# homopolish_dir="$build_dir/homopolish_conda_env/bin"
+# if [ -z $(check_installed $homopolish_dir) ]; then
+#     cd $build_dir
+#     clean "$build_dir/homopolish_conda_env"
+#     $miniconda3_dir/conda create -y -p $build_dir/homopolish_conda_env python=3.7
+#     source $miniconda3_dir/activate $build_dir/homopolish_conda_env
+#     $miniconda3_dir/conda install -y -c bioconda homopolish=${HOMOPOLISH_VERSION}
+#     source $miniconda3_dir/deactivate
+#     note_installed $homopolish_dir
+# fi
+
+# # ------------- QUAST --------------------
+# quast_dir="$build_dir/quast_conda_env/bin"
 # if [ -z $(check_installed $quast_dir) ]; then
 #     cd $build_dir
-#     echo "Download QUAST-v${QUAST_VERSION}"
-#     download_and_extract $QUAST_DOWNLOAD_URL "QUAST-${QUAST_VERSION}.tar.gz"
-#     cd $quast_dir
-#     virtualenv -p $(which python3) py3_virtualenv_quast
-#     source py3_virtualenv_quast/bin/activate
-#     py3_virtualenv_quast/bin/pip install joblib
-#     py3_virtualenv_quast/bin/pip install simplejson
-#     py3_virtualenv_quast/bin/python3 -mpip install -U matplotlib
-#     py3_virtualenv_quast/bin/python3 ./setup.py install
-#     deactivate
+#     $miniconda3_dir/conda create -y -p $build_dir/quast_conda_env python=3.7
+#     source $miniconda3_dir/activate $build_dir/quast_conda_env
+#     $miniconda3_dir/conda install -y -c bioconda quast=${QUAST_VERSION}
+#     source $miniconda3_dir/deactivate
 #     note_installed $quast_dir
 # fi
 
 # --------------- mummer4 ------------------
+echo ""
+echo "[$(timestamp)] Installing mummer4 ..."
 mummer4_dir="$build_dir/mummer-${MUMMER4_VERSION}"
 if [ -z $(check_installed $mummer4_dir) ]; then
     cd $build_dir
+    clean "$build_dir/mummer-${MUMMER4_VERSION}"
     echo "Download mummer-v${MUMMER4_VERSION}"
-    download_and_extract $MUMMER4_DOWNLOAD_URL "mummer-${MUMMER4_VERSION}.tar.gz"
+    download $MUMMER4_DOWNLOAD_URL "mummer-${MUMMER4_VERSION}.tar.gz"
+    tar xvzf mummer-${MUMMER4_VERSION}.tar.gz
     echo "$mummer4_dir"
     cd $mummer4_dir
     ./configure
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm mummer-${MUMMER4_VERSION}.tar.gz
     note_installed $mummer4_dir
 fi
 PATH="$mummer4_dir:${PATH}"
 
 # --------------- bedtools ------------------
+echo ""
+echo "[$(timestamp)] Installing bedtools ..."
 bedtools_dir="$build_dir/bedtools2/bin"
 if [ -z $(check_installed $bedtools_dir) ]; then
     cd $build_dir
+    clean "$build_dir/bedtools2"
     echo "Download bedtools-v${BEDTOOLS_VERSION}"
-    download_and_extract $BEDTOOLS_DOWNLOAD_URL "bedtools-${BEDTOOLS_VERSION}.tar.gz"
+    download $BEDTOOLS_DOWNLOAD_URL "bedtools-${BEDTOOLS_VERSION}.tar.gz"
+    tar xvzf bedtools-${BEDTOOLS_VERSION}.tar.gz
     cd "$build_dir/bedtools2"
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm bedtools-${BEDTOOLS_VERSION}.tar.gz
     note_installed $bedtools_dir
 fi
 
 # --------------- SPAdes ------------------
+echo ""
+echo "[$(timestamp)] Installing spades ..."                                                                                       
 spades_dir="$build_dir/SPAdes-${SPADES_VERSION}-Linux/bin"
 if [ -z $(check_installed $spades_dir) ]; then
     cd $build_dir
+    clean "$build_dir/SPAdes-${SPADES_VERSION}-Linux"
     echo "Download SPAdes-v${SPADES_VERSION}"
-    # This sometimes times out, could this be throttling from the server?
-    # Allow administrator to manually upload a copy of the tarball for installation
-    if [ ! -e "SPAdes-${SPADES_VERSION}-Linux.tar.gz" ]; then
-        download_and_extract $SPADES_DOWNLOAD_URL "SPAdes-${SPADES_VERSION}-Linux.tar.gz"
-    else
-        tar -zxf "SPAdes-${SPADES_VERSION}-Linux.tar.gz"
-    fi
+    download $SPADES_DOWNLOAD_URL "SPAdes-${SPADES_VERSION}-Linux.tar.gz"
+    tar xvzf SPAdes-${SPADES_VERSION}-Linux.tar.gz
+    rm SPAdes-${SPADES_VERSION}-Linux.tar.gz
     note_installed $spades_dir
 fi
 
 # --------------- Prodigal ------------------
 prodigal_dir="$build_dir/Prodigal-${PRODIGAL_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing Prodigal ..."
 if [ -z $(check_installed $prodigal_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Prodigal-${PRODIGAL_VERSION}"
     echo "Download Prodigal-v${PRODIGAL_VERSION}"
-    download_and_extract $PRODIGAL_DOWNLOAD_URL "v${PRODIGAL_VERSION}.tar.gz"
+    download $PRODIGAL_DOWNLOAD_URL "v${PRODIGAL_VERSION}.tar.gz"
+    tar xvzf v${PRODIGAL_VERSION}.tar.gz
     cd $prodigal_dir
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm v${PRODIGAL_VERSION}.tar.gz
     note_installed $prodigal_dir
 fi
 
 # --------------- CAP3 ------------------
-cap_dir="$build_dir/CAP3"
-if [ -z $(check_installed $cap_dir) ]; then
+cap3_dir="$build_dir/CAP3/CAP3"
+echo ""
+echo "[$(timestamp)] Installing CAP3 ..."
+if [ -z $(check_installed $cap3_dir) ]; then
     cd $build_dir
+    clean "$build_dir/CAP3"
     echo "Download CAP3-v${CAP3_VERSION}"
-    download_and_extract $CAP_DOWNLOAD_URL "cap3.linux.x86_64.tar"
-    note_installed $cap_dir
+    # download $CAP3_DOWNLOAD_URL "cap3.linux.x86_64.tar"
+    git clone $CAP3_DOWNLOAD_URL
+    cd CAP3
+    tar xvf cap3.linux.x86_64.tar
+    rm cap3.linux.x86_64.tar
+    note_installed $cap3_dir
 fi
 
 # ------------- BWA -------------------
 bwa_dir="$build_dir/bwa-${BWA_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing BWA ..."
 if [ -z $(check_installed $bwa_dir) ]; then
     cd $build_dir
+    clean "$build_dir/bwa-${BWA_VERSION}"
     echo "Download BWA-v${BWA_VERSION}"
-    download_and_extract $BWA_DOWNLOAD_URL "bwa-${BWA_VERSION}.tar.bz2"
+    download $BWA_DOWNLOAD_URL "bwa-${BWA_VERSION}.tar.bz2"
+    tar xvjf bwa-${BWA_VERSION}.tar.bz2
     cd $bwa_dir
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm bwa-${BWA_VERSION}.tar.bz2
     note_installed $bwa_dir
 fi
 
 # --------------- Circlator ------------------
-circlator_dir="$build_dir/py3_virtualenv_circlator/bin"
+circlator_dir="$build_dir/circlator_conda_env/bin"
+echo ""
+echo "[$(timestamp)] Installing Circlator ..."
 if [ -z $(check_installed $circlator_dir) ]; then
     cd $build_dir
-    echo "Creating local virtual python3 environment and install Circlator-v${CIRCLATOR_VERSION}"
-    virtualenv -p $(which python3) py3_virtualenv_circlator
-    source py3_virtualenv_circlator/bin/activate
-    py3_virtualenv_circlator/bin/pip3 install "circlator==${CIRCLATOR_VERSION}"
-    deactivate
+    clean "$build_dir/circlator_conda_env"
+    $miniconda3_dir/conda create -y -p $build_dir/circlator_conda_env
+    source $miniconda3_dir/activate $build_dir/circlator_conda_env
+    $miniconda3_dir/conda install -y -c bioconda circlator=${CIRCLATOR_VERSION}
+    source $miniconda3_dir/deactivate
     note_installed $circlator_dir
 fi
 
 # --------------- Trimmomatic -----------------
 trimmomatic_dir="$build_dir/Trimmomatic-${TRIMMOMATIC_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing Trimmomatic ..."
 if [ -z $(check_installed $trimmomatic_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Trimmomatic-${TRIMMOMATIC_VERSION}"
     echo "Download Trimmomatic-v${TRIMMOMATIC_VERSION}"
     download $TRIMMOMATIC_DOWNLOAD_URL "Trimmomatic-${TRIMMOMATIC_VERSION}.zip"
     unzip Trimmomatic-${TRIMMOMATIC_VERSION}.zip
     rm Trimmomatic-${TRIMMOMATIC_VERSION}.zip
-
     cd $trimmomatic_dir
     chmod 755 trimmomatic-${TRIMMOMATIC_VERSION}.jar
     ln -s trimmomatic-${TRIMMOMATIC_VERSION}.jar trimmomatic.jar 
@@ -833,8 +1160,11 @@ fi
 
 # --------------- Picard -----------------
 picard_dir="$build_dir/Picard-v${PICARD_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing Picard ..."
 if [ -z $(check_installed $picard_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Picard-v${PICARD_VERSION}"
     echo "Download Picard-v${PICARD_VERSION}"
     download $PICARD_DOWNLOAD_URL "picard.jar"
     mkdir Picard-v${PICARD_VERSION}
@@ -845,10 +1175,26 @@ if [ -z $(check_installed $picard_dir) ]; then
     note_installed $picard_dir
 fi
 
+# # --------------- hapo-G ------------------
+# hapog_dir="$build_dir/hapog_conda_env/bin"
+# echo ""
+# echo "[$(timestamp)] Installing hapo-G ..."
+# if [ -z $(check_installed $hapog_dir) ]; then
+#     cd $build_dir
+#     $miniconda3_dir/conda create -y -p $build_dir/hapog_conda_env
+#     source $miniconda3_dir/activate $build_dir/hapog_conda_env
+#     $miniconda3_dir/conda install -y -c lbgb_cea hapog=${HAPOG_VERSION}
+#     source $miniconda3_dir/deactivate
+#     note_installed $hapog_dir
+# fi
+
 # --------------- Pilon -----------------
 pilon_dir="$build_dir/Pilon-v${PILON_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing Pilon ..."
 if [ -z $(check_installed $pilon_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Pilon-v${PILON_VERSION}"
     echo "Download Pilon-v${PILON_VERSION}"
     download $PILON_DOWNLOAD_URL "pilon-${PILON_VERSION}.jar"
     mkdir Pilon-v${PILON_VERSION}
@@ -860,42 +1206,61 @@ fi
 
 # --------------- exonerate ------------------
 exonerate_dir="$build_dir/exonerate-${EXONERATE_VERSION}-x86_64/bin"
+echo ""
+echo "[$(timestamp)] Installing exonerate ..."
 if [ -z $(check_installed $exonerate_dir) ]; then
     cd $build_dir
+    clean "$build_dir/exonerate-${EXONERATE_VERSION}-x86_64"
     echo "Download exonerate-v${EXONERATE_VERSION}"
-    download_and_extract $EXONERATE_DOWNLOAD_URL "exonerate-${EXONERATE_VERSION}-x86_64.tar.gz"
+    download $EXONERATE_DOWNLOAD_URL "exonerate-${EXONERATE_VERSION}-x86_64.tar.gz"
+    tar xvzf exonerate-${EXONERATE_VERSION}-x86_64.tar.gz
+    rm exonerate-${EXONERATE_VERSION}-x86_64.tar.gz
     note_installed $exonerate_dir
 fi
 
 # --------------- ncbi-blast+ ------------------
 blast_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/bin"
 blast_matrices_dir="$build_dir/ncbi-blast-${BLAST_VERSION}+/matrices"
+echo ""
+echo "[$(timestamp)] Installing ncbi-blast+ ..."
 if [ -z $(check_installed $blast_dir) ]; then
     cd $build_dir
+    clean "$build_dir/ncbi-blast-${BLAST_VERSION}+"
     echo "Download ncbi-blast-v${BLAST_VERSION}"
-    download_and_extract $BLAST_DOWNLOAD_URL "ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
+    download $BLAST_DOWNLOAD_URL "ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
+    tar xvzf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
     cd "ncbi-blast-${BLAST_VERSION}+"
     mkdir matrices
     cd matrices
-    wget -nv --no-check-certificate ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/*
+    wget -c --no-check-certificate ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/*
+    cd $build_dir
+    rm ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz
     note_installed $blast_dir
 fi
 
 # --------------- ncbi-rmblast ------------------
 rmblast_dir="$build_dir/ncbi-rmblastn-${RMBLAST_VERSION}/bin"
+echo ""
+echo "[$(timestamp)] Installing rmblast ..."
 if [ -z $(check_installed $rmblast_dir) ]; then
     cd $build_dir
+    clean "$build_dir/ncbi-rmblastn-${RMBLAST_VERSION}"
     echo "Download ncbi-rmblastn-v${BLAST_VERSION}"
-    download_and_extract $RMBLAST_DOWNLOAD_URL "ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
+    download $RMBLAST_DOWNLOAD_URL "ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz"
+    tar xvzf ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz
     # copy rmblastn binary file to ncbi-blast+ directory for easy RepeatMasker configuration
     cp $rmblast_dir/rmblastn $blast_dir
+    rm ncbi-rmblastn-${RMBLAST_VERSION}-x64-linux.tar.gz
     note_installed $rmblast_dir
 fi
 
 # --------------- snap ------------------
 snap_dir="$build_dir/SNAP"
+echo ""
+echo "[$(timestamp)] Installing snap ..."
 if [ -z $(check_installed $snap_dir) ]; then
     cd $build_dir
+    clean "$build_dir/SNAP"
     echo "Download snap-v${SNAP_VERSION}"
     git clone $SNAP_DOWNLOAD_URL
     cd $snap_dir
@@ -906,23 +1271,31 @@ if [ -z $(check_installed $snap_dir) ]; then
     note_installed $snap_dir
 fi
 
-# --------------- RAPSearch2 ------------------
-rapsearch_dir="$build_dir/RAPSearch${RAPSEARCH_VERSION}_64bits/bin"
-if [ -z $(check_installed $rapsearch_dir) ]; then
-    cd $build_dir
-    echo "Download RAPsearch-v${RAPSEARCH_VERSION}"
-    download_and_extract $RAPSEARCH_DOWNLOAD_URL "RAPSearch${RAPSEARCH_VERSION}_64bits.tar.gz"
-    note_installed $rapsearch_dir
-fi
+# # --------------- RAPSearch2 ------------------
+# rapsearch_dir="$build_dir/RAPSearch${RAPSEARCH_VERSION}_64bits/bin"
+# echo ""
+# echo "[$(timestamp)] Installing RAPSearch2 ..."
+# if [ -z $(check_installed $rapsearch_dir) ]; then
+#     cd $build_dir
+#     echo "Download RAPsearch-v${RAPSEARCH_VERSION}"
+#     download $RAPSEARCH_DOWNLOAD_URL "RAPSearch${RAPSEARCH_VERSION}_64bits.tar.gz"
+#     tar xvzf RAPSearch${RAPSEARCH_VERSION}_64bits.tar.gz
+#     rm RAPSearch${RAPSEARCH_VERSION}_64bits.tar.gz
+#     note_installed $rapsearch_dir
+# fi
 
 # --------------- tRNAscan-SE ------------------
 trnascan_root="$build_dir/tRNAscan-SE-${TRNASCAN_VERSION}"
 trnascan_dir="$trnascan_root/bin"
 PERL5LIB=$trnascan_dir:$PERL5LIB
+echo ""
+echo "[$(timestamp)] Installing tRNAscan-SE ..."
 if [ -z $(check_installed $trnascan_dir) ]; then
     cd $build_dir
+    clean "$build_dir/tRNAscan-SE-${TRNASCAN_VERSION}"
     echo "Download tRNAscan-SE-v${TRNASCAN_VERSION}"
-    download_and_extract $TRNASCAN_DOWNLOAD_URL "tRNAscan-SE-${TRNASCAN_VERSION}.tar.gz"
+    download $TRNASCAN_DOWNLOAD_URL "tRNAscan-SE-${TRNASCAN_VERSION}.tar.gz"
+    tar xvzf tRNAscan-SE-${TRNASCAN_VERSION}.tar.gz
     cd $trnascan_root
     mkdir bin
     mkdir -p lib/tRNAscan-SE
@@ -930,15 +1303,21 @@ if [ -z $(check_installed $trnascan_dir) ]; then
     cp $LRSDAY_HOME/misc/tRNAscan-SE.Makefile Makefile
     make -j $MAKE_JOBS BINDIR="$trnascan_root/bin" LIBDIR="$trnascan_root/lib/tRNAscan-SE" MANDIR="$trnascan_root"
     make install BINDIR="$trnascan_root/bin" LIBDIR="$trnascan_root/lib/tRNAscan-SE" MANDIR="$trnascan_root"
+    cd $build_dir
+    rm tRNAscan-SE-${TRNASCAN_VERSION}.tar.gz
     note_installed $trnascan_dir
 fi
 
 # --------------- snoscan ------------------
 snoscan_dir="$build_dir/snoscan-${SNOSCAN_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing snoscan ..."
 if [ -z $(check_installed $snoscan_dir) ]; then
     cd $build_dir
+    clean "$build_dir/snoscan-${SNOSCAN_VERSION}"
     echo "Download snoscan-v${SNOSCAN_VERSION}"
-    download_and_extract $SNOSCAN_DOWNLOAD_URL "snoscan-${SNOSCAN_VERSION}.tar.gz"
+    download $SNOSCAN_DOWNLOAD_URL "snoscan-${SNOSCAN_VERSION}.tar.gz"
+    tar xvzf snoscan-${SNOSCAN_VERSION}.tar.gz
     cd $snoscan_dir
     cd squid-1.5.11
     rm *.o
@@ -947,27 +1326,37 @@ if [ -z $(check_installed $snoscan_dir) ]; then
     cp $LRSDAY_HOME/misc/snoscan.Makefile Makefile
     rm *.o
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm snoscan-${SNOSCAN_VERSION}.tar.gz
     note_installed $snoscan_dir
 fi
 
 # --------------- RepeatMasker ------------------
 repeatmasker_dir="$build_dir/RepeatMasker"
+echo ""
+echo "[$(timestamp)] Installing RepeatMasker ..."
 if [ -z $(check_installed $repeatmasker_dir) ]; then
     cd $build_dir
+    clean "$build_dir/RepeatMasker"
     echo "Download Repeatmasker-v${REPEATMASKER_VERSION}"
-    download_and_extract $REPEATMASKER_DOWNLOAD_URL "RepeatMasker-${REPEATMASKER_VERSION}.tar.gz"
+    download $REPEATMASKER_DOWNLOAD_URL "RepeatMasker-${REPEATMASKER_VERSION}.tar.gz"
+    tar xvzf RepeatMasker-${REPEATMASKER_VERSION}.tar.gz
     cd $repeatmasker_dir
     echo "Download and setup RepBase library"
-    REPBASE_VERSION="20170127"
-    wget -nv --no-check-certificate https://github.com/yjx1217/RMRB/raw/master/RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz
+    # download $REPBASE_DOWNLOAD_URL "RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz"
+    git clone $REPBASE_DOWNLOAD_URL
+    mv ./RMRB/RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz .
     tar xzf RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz
     rm RepBaseRepeatMaskerEdition-${REPBASE_VERSION}.tar.gz
-    cd .. 
+    cd $build_dir
+    rm RepeatMasker-${REPEATMASKER_VERSION}.tar.gz
     note_installed $repeatmasker_dir
 fi
 
 # --------------- TRF ------------------
 trf_dir=$repeatmasker_dir
+echo ""
+echo "[$(timestamp)] Installing trf ..."
 if [ ! -e "$repeatmasker_dir/trf" ]; then
     cd $repeatmasker_dir
     echo "Download TRF-v${TRF_VERSION}"
@@ -976,66 +1365,91 @@ if [ ! -e "$repeatmasker_dir/trf" ]; then
     chmod 755 trf
 fi
 
-
 # --------------- REannotate ------------------
-reannotate_dir="$build_dir/REannotate_LongQueryName-version_${REANNOTATE_VERSION}"
+reannotate_dir="$build_dir/REannotate_LongQueryName"
+echo ""
+echo "[$(timestamp)] Installing REannotate ..."
 if [ -z $(check_installed $reannotate_dir) ]; then
     cd $build_dir
+    clean "$build_dir/REannotate_LongQueryName"
     echo "Download REannotate-v${REANNOTATE_VERSION}"
-    download_and_extract $REANNOTATE_DOWNLOAD_URL "version_${REANNOTATE_VERSION}.tar.gz"
-    cd $reannotate_dir
+    git clone $REANNOTATE_DOWNLOAD_URL
+    cd REannotate_LongQueryName 
+    git checkout -f -q $REANNOTATE_GITHUB_COMMIT_VERSION
     chmod 755 REannotate_longname
     ln -s REannotate_longname REannotate
+    cd $build_dir
     note_installed $reannotate_dir
 fi
 
 # --------------- ClustalW ------------------
 clustalw_dir="$build_dir/clustalw-${CLUSTALW_VERSION}/bin"
+echo ""
+echo "[$(timestamp)] Installing ClustalW ..."
 if [ -z $(check_installed $clustalw_dir) ]; then
     cd $build_dir
+    clean "$build_dir/clustalw-${CLUSTALW_VERSION}"
     echo "Download ClustalW-v${CLUSTALW_VERSION}"
-    download_and_extract $CLUSTALW_DOWNLOAD_URL "clustalw-${CLUSTALW_VERSION}.tar.gz"
+    download $CLUSTALW_DOWNLOAD_URL "clustalw-${CLUSTALW_VERSION}.tar.gz"
+    tar xvzf clustalw-${CLUSTALW_VERSION}.tar.gz
     cd clustalw-${CLUSTALW_VERSION}
     ./configure --prefix="$build_dir/clustalw-${CLUSTALW_VERSION}"
     make -j $MAKE_JOBS
     make install
+    cd $build_dir
+    rm clustalw-${CLUSTALW_VERSION}.tar.gz
     note_installed $clustalw_dir
 fi
 
 # --------------- MUSCLE ------------------
 muscle_dir="$build_dir/muscle-${MUSCLE_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing muscle ..."
 if [ -z $(check_installed $muscle_dir) ]; then
     cd $build_dir
+    clean "$build_dir/muscle-${MUSCLE_VERSION}"
     echo "Download MUSCLE-v${MUSCLE_VERSION}"
-    download_and_extract $MUSCLE_DOWNLOAD_URL "muscle-${MUSCLE_VERSION}_i86linux64.tar.gz"
+    download $MUSCLE_DOWNLOAD_URL "muscle-${MUSCLE_VERSION}_i86linux64.tar.gz"
+    tar xvzf muscle-${MUSCLE_VERSION}_i86linux64.tar.gz
     mkdir muscle-${MUSCLE_VERSION}
     mv muscle${MUSCLE_VERSION}_i86linux64 ./muscle-${MUSCLE_VERSION}/muscle
+    cd $build_dir
+    rm muscle-${MUSCLE_VERSION}_i86linux64.tar.gz
     note_installed $muscle_dir
 fi
 
 # --------------- HMMER ------------------
-hmmer_root="$build_dir/hmmer-${HMMER_VERSION}"
 hmmer_dir="$build_dir/hmmer-${HMMER_VERSION}/bin"
+echo ""
+echo "[$(timestamp)] Installing HMMER ..."
 if [ -z $(check_installed $hmmer_dir) ]; then
     cd $build_dir
+    clean "$build_dir/hmmer-${HMMER_VERSION}"
     echo "Download hmmer-v${HMMER_VERSION}"
-    download_and_extract $HMMER_DOWNLOAD_URL "hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz"
-    cd $hmmer_root
-    ./configure --prefix=$hmmer_root
+    download $HMMER_DOWNLOAD_URL "hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz"
+    tar xvzf hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz
+    cd hmmer-${HMMER_VERSION}
+    ./configure --prefix="$build_dir/hmmer-${HMMER_VERSION}"
     make -j $MAKE_JOBS
     make install
     cd easel
     make install
+    cd $build_dir
+    rm hmmer-${HMMER_VERSION}-linux-intel-x86_64.tar.gz
     note_installed $hmmer_dir
 fi
 
 # --------------- bamtools ------------------
 bamtools_dir="$build_dir/bamtools-${BAMTOOLS_VERSION}/bin"
+echo ""
+echo "[$(timestamp)] Installing bamtools ..."
 if [ -z $(check_installed $bamtools_dir) ]; then
     cd $build_dir
+    clean "$build_dir/bamtools-${BAMTOOLS_VERSION}"
     echo "Download bamtools-v${BAMTOOLS_VERSION}"
-    download_and_extract $BAMTOOLS_DOWNLOAD_URL "v${BAMTOOLS_VERSION}.tar.gz"
-    cd $build_dir/bamtools-${BAMTOOLS_VERSION}
+    download $BAMTOOLS_DOWNLOAD_URL "v${BAMTOOLS_VERSION}.tar.gz"
+    tar xvzf v${BAMTOOLS_VERSION}.tar.gz
+    cd bamtools-${BAMTOOLS_VERSION}
     mkdir build
     cd build
     cmake -DCMAKE_INSTALL_PREFIX="$build_dir/bamtools-${BAMTOOLS_VERSION}" ..
@@ -1043,99 +1457,144 @@ if [ -z $(check_installed $bamtools_dir) ]; then
     make install
     cd $build_dir/bamtools-${BAMTOOLS_VERSION}
     ln -sf lib lib64
+    cd $build_dir
+    rm v${BAMTOOLS_VERSION}.tar.gz
     note_installed $bamtools_dir
 fi
 
 # --------------- Augustus ------------------
 augustus_dir="$build_dir/augustus-${AUGUSTUS_VERSION}/bin"
+echo ""
+echo "[$(timestamp)] Installing augustus ..."
 if [ -z $(check_installed $augustus_dir) ]; then
     cd $build_dir
+    clean "$build_dir/augustus-${AUGUSTUS_VERSION}"
     echo "Download Augustus-v${AUGUSTUS_VERSION}"
-    download_and_extract $AUGUSTUS_DOWNLOAD_URL "augustus-${AUGUSTUS_VERSION}.tar.gz"
+    download $AUGUSTUS_DOWNLOAD_URL "augustus-${AUGUSTUS_VERSION}.tar.gz"
+    tar xvzf augustus-${AUGUSTUS_VERSION}.tar.gz
     cd $build_dir/augustus-${AUGUSTUS_VERSION}/auxprogs/bam2hints/
     cp $LRSDAY_HOME/misc/bam2hints.Makefile Makefile
     cd $build_dir/augustus-${AUGUSTUS_VERSION}/auxprogs/filterBam/src/
     cp $LRSDAY_HOME/misc/filterBam.Makefile Makefile
     cd $build_dir/augustus-${AUGUSTUS_VERSION}
     make -j $MAKE_JOBS BAMTOOLS="$build_dir/bamtools-${BAMTOOLS_VERSION}"
+    cd $build_dir
+    rm augustus-${AUGUSTUS_VERSION}.tar.gz
     note_installed $augustus_dir
 fi
 export AUGUSTUS_CONFIG_PATH="$build_dir/augustus-${AUGUSTUS_VERSION}/config"
 
-# cd $build_dir
-# echo "Download Augustus-v${AUGUSTUS_VERSION}"
-# git clone $AUGUSTUS_DOWNLOAD_URL
-# cd Augustus
-# git submodule update --init
-# git checkout -f -q $AUGUSTUS_GITHUB_COMMIT_VERSION
-# cd $build_dir/augustus-${AUGUSTUS_VERSION}/auxprogs/bam2hints/
-# cp $LRSDAY_HOME/misc/bam2hints.Makefile Makefile
-# cd $build_dir/augustus-${AUGUSTUS_VERSION}/auxprogs/filterBam/src/
-# cp $LRSDAY_HOME/misc/filterBam.Makefile Makefile
-# cd $build_dir/augustus-${AUGUSTUS_VERSION}
-# make BAMTOOLS="$build_dir/bamtools-${BAMTOOLS_VERSION}"
-# augustus_dir="$build_dir/augustus-${AUGUSTUS_VERSION}/bin"
-# export AUGUSTUS_CONFIG_PATH="$build_dir/augustus-${AUGUSTUS_VERSION}/config"
-# cd $build_dir
-# rm augustus-${AUGUSTUS_VERSION}.tar.gz
-
-
 # --------------- EVidenceModeler ------------------
 evm_dir="$build_dir/EVidenceModeler-${EVM_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing EVM ..."
 if [ -z $(check_installed $evm_dir) ]; then
     cd $build_dir
+    clean "$build_dir/EVidenceModeler-${EVM_VERSION}"
     echo "Download EvidenceModeler-v${EVM_VERSION}"
-    download_and_extract $EVM_DOWNLOAD_URL "v${EVM_VERSION}.tar.gz"
+    download $EVM_DOWNLOAD_URL "v${EVM_VERSION}.tar.gz"
+    tar xvzf v${EVM_VERSION}.tar.gz
+    rm v${EVM_VERSION}.tar.gz
     note_installed $evm_dir
 fi
 
 # --------------- Proteinortho ------------------
-proteinortho_dir="$build_dir/proteinortho_v${PROTEINORTHO_VERSION}"
+proteinortho_dir="$build_dir/proteinortho_conda_env/bin"
+diamond_dir="$build_dir/proteinortho_conda_env/bin"
+echo ""
+echo "[$(timestamp)] Installing proteinortho ..."
 if [ -z $(check_installed $proteinortho_dir) ]; then
     cd $build_dir
+    clean "$build_dir/proteinortho_conda_env"
     echo "Download Porteinortho-v${PROTEINORTHO_VERSION}"
-
-    $miniconda3_dir/conda create -y -p $build_dir/proteinortho_conda_env # python=3.6 
+    $miniconda3_dir/conda create -y -p $build_dir/proteinortho_conda_env 
     source $miniconda3_dir/activate $build_dir/proteinortho_conda_env
     $miniconda3_dir/conda install -y proteinortho=${PROTEINORTHO_VERSION}
-    $miniconda3_dir/conda install -y -c bioconda diamond=${DIAMOND_VERSION}
-    $miniconda3_dir/conda install -y -c bioconda blast=2.10.1
-    $miniconda3_dir/conda install -y -c bioconda last=${LAST_VERSION}
+    # $miniconda3_dir/conda install -y -c bioconda diamond=${DIAMOND_VERSION}
+    # $miniconda3_dir/conda install -y -c bioconda blast=2.10.1
+    # $miniconda3_dir/conda install -y -c bioconda last=${LAST_VERSION}
     source $miniconda3_dir/deactivate
-    proteinortho_dir="$build_dir/proteinortho_conda_env/bin"
-    diamond_dir="$build_dir/proteinortho_conda_env/bin"
     note_installed $proteinortho_dir
 fi
 
 # --------------- GATK3 ------------------
 gatk3_dir="$build_dir/GATK3"
+echo ""
+echo "[$(timestamp)] Installing gatk3 ..."
 if [ -z $(check_installed $gatk3_dir) ]; then
     cd $build_dir
+    clean "$build_dir/GATK3"
     echo "Create the GATK3 folder for installation"
     mkdir GATK3
     cd GATK3
-    wget -nv --no-check-certificate $GATK3_DOWNLOAD_URL
+    #git clone $GATK3_DOWNLOAD_URL 
+    download $GATK3_DOWNLOAD_URL gatk3.jar.gz
+    gunzip gatk3.jar.gz 
+    mv gatk3.jar GenomeAnalysisTK.jar 
     chmod 755 GenomeAnalysisTK.jar
     note_installed $gatk3_dir
 fi
 
+# # --------------- MAKER -----------------
+# maker_dir="$build_dir/maker_conda_env/bin"
+# echo ""
+# echo "[$(timestamp)] Installing maker ..."
+# if [ -z $(check_installed $maker_dir) ]; then
+#     cd $build_dir
+#     echo "Download MAKER-${MAKER_VERSION}"
+#     $miniconda3_dir/conda create -y -p $build_dir/maker_conda_env python=3.8 
+#     source $miniconda3_dir/activate $build_dir/maker_conda_env
+#     $miniconda3_dir/conda install -y -c bioconda maker==${MAKER_VERSION}    
+#     source $miniconda3_dir/deactivate
+#     note_installed $maker_dir
+# fi
+
 # --------------- MAKER -----------------
 maker_dir="$build_dir/maker/bin"
 if [ -z $(check_installed $maker_dir) ]; then
     cd $build_dir
+    clean "$build_dir/maker"
     echo "Download MAKER"
-    download_and_extract $MAKER_DOWNLOAD_URL "maker-v${MAKER_VERSION}.tgz"
+    cp -r $LRSDAY_HOME/misc/maker-${MAKER_VERSION}.tar.gz .
+    tar xvzf maker-${MAKER_VERSION}.tar.gz
+    mv maker-${MAKER_VERSION} maker
     cd $build_dir/maker/src/
     cp $LRSDAY_HOME/misc/maker_Build.PL .
     echo "no"|perl maker_Build.PL
     ./Build install
+    cd $build_dir
+    rm maker-${MAKER_VERSION}.tar.gz
     note_installed $maker_dir
 fi
 
+
+# # --------------- Gff3toolkit ------------------
+# gff3toolkit_dir="$build_dir/gff3toolkit_conda_env/bin"
+# echo ""
+# echo "[$(timestamp)] Installing gff3toolkit ..."
+# if [ -z $(check_installed $gff3toolkit_dir) ]; then
+#     cd $build_dir
+#     clean "$build_dir/gff3toolkit_conda_env"
+#     echo "Download GFF3toolkit-v${GFF3TOOLKIT_VERSION}"
+#     $miniconda3_dir/conda create -y -p $build_dir/gff3toolkit_conda_env python=3.7
+#     source $miniconda3_dir/activate $build_dir/gff3toolkit_conda_env
+#     cd gff3toolkit_conda_env
+#     git clone $GFF3TOOLKIT_DOWNLOAD_URL
+#     cd  GFF3toolkit
+#     python setup.py install
+#     #$miniconda3_dir/conda install -y pip
+#     #pip3 install gff3tool==${GFF3TOOLKIT_VERSION}
+#     source $miniconda3_dir/deactivate
+#     note_installed $gff3toolkit_dir
+# fi
+
 # --------------- UCSC Utilities -----------------
 ucsc_dir="$build_dir/UCSC_Utilities"
+echo ""
+echo "[$(timestamp)] Installing UCSC utilities ..."
 if [ -z $(check_installed $ucsc_dir) ]; then
     cd $build_dir
+    clean "$build_dir/UCSC_Utilities"
     mkdir UCSC_Utilities
     cd $ucsc_dir
     download $BLAT_DOWNLOAD_URL "blat"
@@ -1149,55 +1608,80 @@ fi
 
 # --------------- EMBOSS ------------------
 emboss_dir="$build_dir/EMBOSS-${EMBOSS_VERSION}/emboss"
+echo ""
+echo "[$(timestamp)] Installing emboss ..."
 if [ -z $(check_installed $emboss_dir) ]; then
     cd $build_dir
+    clean "$build_dir/EMBOSS-${EMBOSS_VERSION}"
     echo "Download EMBOSS"
-    download_and_extract $EMBOSS_DOWNLOAD_URL "emboss_v${EMBOSS_VERSION}.tar.gz"
+    download $EMBOSS_DOWNLOAD_URL "emboss_v${EMBOSS_VERSION}.tar.gz"
+    tar xvzf emboss_v${EMBOSS_VERSION}.tar.gz
     cd EMBOSS-${EMBOSS_VERSION}
     ./configure --without-x
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm emboss_v${EMBOSS_VERSION}.tar.gz
     note_installed $emboss_dir
 fi
 
 # --------------- ERPIN ------------------
 erpin_dir="$build_dir/erpin${ERPIN_VERSION}.serv/bin"
+echo ""
+echo "[$(timestamp)] Installing erpin ..."
 if [ -z $(check_installed $erpin_dir) ]; then
     cd $build_dir
+    clean "$build_dir/erpin${ERPIN_VERSION}.serv"
     echo "Download ERPIN"
-    download_and_extract $ERPIN_DOWNLOAD_URL "erpin_v${ERPIN_VERSION}.tar.gz"
+    download $ERPIN_DOWNLOAD_URL "erpin_v${ERPIN_VERSION}.tar.gz"
+    tar xvzf erpin_v${ERPIN_VERSION}.tar.gz
     cd erpin${ERPIN_VERSION}.serv
     make -j $MAKE_JOBS
+    cd $build_dir
+    rm erpin_v${ERPIN_VERSION}.tar.gz
     note_installed $erpin_dir
 fi
 
 # --------------- tbl2asn ------------------
 tbl2asn_dir="$build_dir/tbl2asn_dir"
+echo ""
+echo "[$(timestamp)] Installing tbl2asn ..."
 if [ -z $(check_installed $tbl2asn_dir) ]; then
     cd $build_dir
+    clean "$build_dir/tbl2asn_dir"
     echo "Download tbl2asn"
-    download $TBL2ASN_DOWNLOAD_URL "tbl2asn.gz"
     mkdir tbl2asn_dir
+    cd tbl2asn_dir
+    wget -c  $TBL2ASN_DOWNLOAD_URL # linux64.tbl2asn.gz
+    mv linux64.tbl2asn.gz tbl2asn.gz
     gunzip tbl2asn.gz
     chmod 755 tbl2asn
-    mv tbl2asn ./tbl2asn_dir/
     note_installed $tbl2asn_dir
 fi
 
 # --------------- PirObject ----------------
 pirobject_dir="$build_dir/PirObject-${PIROBJECT_VERSION}"
+echo ""
+echo "[$(timestamp)] Installing PirObject ..."
 if [ -z $(check_installed $pirobject_dir) ]; then
     cd $build_dir
+    clean "$build_dir/PirObject-${PIROBJECT_VERSION}"
     echo "Download PirObject"
-    download_and_extract $PIROBJECT_DOWNLOAD_URL "pirobject_v${PIROBJECT_VERSION}.tar.gz"
+    download $PIROBJECT_DOWNLOAD_URL "pirobject_v${PIROBJECT_VERSION}.tar.gz"
+    tar xvzf pirobject_v${PIROBJECT_VERSION}.tar.gz
     cd PirObject-${PIROBJECT_VERSION}
     ln -s ./lib/PirObject.pm .
+    cd $build_dir
+    rm pirobject_v${PIROBJECT_VERSION}.tar.gz
     note_installed $pirobject_dir
 fi
 
 # --------------- PirModels ------------------
 pirmodels_dir="$pirobject_dir/PirModels"
+echo ""
+echo "[$(timestamp)] Installing PirModels ..."
 if [ -z $(check_installed $pirmodels_dir) ]; then
     cd $build_dir
+    clean "$pirobject_dir/PirModels"
     echo "Download PirModels"
     git clone $PIRMODELS_DOWNLOAD_URL
     cd PirModels
@@ -1207,11 +1691,13 @@ if [ -z $(check_installed $pirmodels_dir) ]; then
     note_installed $pirmodels_dir
 fi
 
-
 # --------------- Flip ------------------
 flip_dir="$build_dir/Flip"
+echo ""
+echo "[$(timestamp)] Installing Flip ..."
 if [ -z $(check_installed $flip_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Flip"
     echo "Download Flip"
     git clone $FLIP_DOWNLOAD_URL
     cd Flip
@@ -1224,8 +1710,11 @@ fi
 
 # --------------- Umac ------------------
 umac_dir="$build_dir/Umac"
+echo ""
+echo "[$(timestamp)] Installing Umac ..."
 if [ -z $(check_installed $umac_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Umac"
     echo "Download Umac"
     git clone $UMAC_DOWNLOAD_URL
     cd Umac
@@ -1236,8 +1725,11 @@ fi
 
 # --------------- HMMsearchWC ------------------
 hmmsearchwc_dir="$build_dir/HMMsearchWC"
+echo ""
+echo "[$(timestamp)] Installing HMMsearchWC ..."
 if [ -z $(check_installed $hmmsearchwc_dir) ]; then
     cd $build_dir
+    clean "$build_dir/HMMsearchWC"
     echo "Download HMMsearchWC"
     git clone $HMMSEARCHWC_DOWNLOAD_URL
     cd HMMsearchWC
@@ -1248,8 +1740,11 @@ fi
 
 # --------------- RNAfinder ------------------
 rnafinder_dir="$build_dir/RNAfinder"
+echo ""
+echo "[$(timestamp)] Installing RNAfinder ..."
 if [ -z $(check_installed $rnafinder_dir) ]; then
     cd $build_dir
+    clean "$build_dir/RNAfinder"
     echo "Download RNAfinder"
     git clone $RNAFINDER_DOWNLOAD_URL
     cd RNAfinder
@@ -1261,8 +1756,11 @@ fi
 
 # --------------- Mf2sqn ------------------
 mf2sqn_dir="$build_dir/Mf2sqn"
+echo ""
+echo "[$(timestamp)] Installing Mf2sqn ..."
 if [ -z $(check_installed $mf2sqn_dir) ]; then
     cd $build_dir
+    clean "$build_dir/Mf2sqn"
     echo "Download Mf2sqn"
     git clone $MF2SQN_DOWNLOAD_URL
     cd Mf2sqn
@@ -1273,8 +1771,11 @@ fi
 
 # --------------- grab-fasta ------------------
 grab_fasta_dir="$build_dir/grab-fasta"
+echo ""
+echo "[$(timestamp)] Installing grab-fasta ..."
 if [ -z $(check_installed $grab_fasta_dir) ]; then
     cd $build_dir
+    clean "$build_dir/grab-fasta"
     echo "Download grab-fasta"
     git clone $GRAB_FASTA_DOWNLOAD_URL
     cd grab-fasta
@@ -1284,8 +1785,11 @@ fi
 
 # --------------- MFannot_data ------------------
 mfannot_data_dir="$build_dir/MFannot_data"
+echo ""
+echo "[$(timestamp)] Installing MFannot_data ..."
 if [ -z $(check_installed $mfannot_data_dir) ]; then
     cd $build_dir
+    clean "$build_dir/MFannot_data"
     echo "Download MFannot_data"
     git clone $MFANNOT_DATA_DOWNLOAD_URL
     cd MFannot_data
@@ -1293,11 +1797,13 @@ if [ -z $(check_installed $mfannot_data_dir) ]; then
     note_installed $mfannot_data_dir
 fi
 
-
 # --------------- MFannot ------------------
 mfannot_dir="$build_dir/MFannot"
+echo ""
+echo "[$(timestamp)] Installing MFannot ..."
 if [ -z $(check_installed $mfannot_dir) ]; then
     cd $build_dir
+    clean "$build_dir/MFannot"
     echo "Download MFannot"
     git clone $MFANNOT_DOWNLOAD_URL
     cd MFannot
@@ -1314,31 +1820,40 @@ echo "export build_dir=${build_dir}" >> env.sh
 echo "export PYTHONPATH=${PYTHONPATH}" >> env.sh
 echo "export PERL5LIB=${PERL5LIB}" >> env.sh 
 echo "export cpanm_dir=${cpanm_dir}" >> env.sh
+if [[ $lite_installation == "no" ]]
+then
+    echo "export miniconda2_dir=${miniconda2_dir}" >> env.sh
+    echo "export pbassembly_dir=${pbassembly_dir}" >> env.sh
+    echo "export bax2bam_dir=${bax2bam_dir}" >> env.sh
+fi
 echo "export miniconda3_dir=${miniconda3_dir}" >> env.sh
-echo "export sra_dir=${sra_dir}" >> env.sh
+# echo "export sra_dir=${sra_dir}" >> env.sh
 echo "export porechop_dir=${porechop_dir}" >> env.sh
 echo "export filtlong_dir=${filtlong_dir}" >> env.sh
 echo "export minimap2_dir=${minimap2_dir}" >> env.sh
 echo "export canu_dir=${canu_dir}" >> env.sh
+# echo "export whatshap_dir=${whatshap_dir}" >> env.sh
 echo "export flye_dir=${flye_dir}" >> env.sh
 echo "export wtdbg2_dir=${wtdbg2_dir}" >> env.sh
 echo "export smartdenovo_dir=${smartdenovo_dir}" >> env.sh
-echo "export ra_dir=${ra_dir}" >> env.sh
+# echo "export raven_dir=${raven_dir}" >> env.sh
 echo "export shasta_dir=${shasta_dir}" >> env.sh
-echo "export pacbio_dir=${pacbio_dir}" >> env.sh
-echo "export guppy_dir=${guppy_dir}" >> env.sh
+echo "export guppy_cpu_dir=${guppy_cpu_dir}" >> env.sh
+echo "export guppy_gpu_dir=${guppy_gpu_dir}" >> env.sh
+# echo "export bonito_dir=${bonito_dir}" >> env.sh
+# echo "export nanofilt_dir=${nanofilt_dir}" >> env.sh
 echo "export nanoplot_dir=${nanoplot_dir}" >> env.sh
 echo "export nanopolish_dir=${nanopolish_dir}" >> env.sh
-echo "export nanopolish_virtualenv_dir=${nanopolish_virtualenv_dir}" >> env.sh
 echo "export parallel_dir=${parallel_dir}" >> env.sh
 echo "export medaka_dir=${medaka_dir}" >> env.sh
 echo "export racon_dir=${racon_dir}" >> env.sh
-echo "export marginpolish_dir=${marginpolish_dir}" >> env.sh
-echo "export helen_dir=${helen_dir}" >> env.sh
-echo "export helen_virtualenv_dir=${helen_virtualenv_dir}" >> env.sh
+# echo "export marginpolish_dir=${marginpolish_dir}" >> env.sh
+# echo "export helen_dir=${helen_dir}" >> env.sh
+# echo "export pepper_dir=${pepper_dir}" >> env.sh
+# echo "export homopolish_dir=${homopolish_dir}" >> env.sh
 # echo "export quast_dir=${quast_dir}" >> env.sh
 echo "export ragout_dir=${ragout_dir}" >> env.sh
-echo "export ragoo_dir=${ragoo_dir}" >> env.sh
+echo "export ragtag_dir=${ragtag_dir}" >> env.sh
 # echo "export hdf_dir=${hdf_dir}" >> env.sh
 # echo "export h5prefix=${h5prefix}" >> env.sh
 # echo "export hal_dir=${hal_dir}" >> env.sh
@@ -1347,12 +1862,13 @@ echo "export gnuplot_dir=${gnuplot_dir}" >> env.sh
 echo "export bedtools_dir=${bedtools_dir}" >> env.sh
 echo "export spades_dir=${spades_dir}" >> env.sh
 echo "export prodigal_dir=${prodigal_dir}" >> env.sh
-echo "export cap_dir=${cap_dir}" >> env.sh
+echo "export cap3_dir=${cap3_dir}" >> env.sh
 echo "export circlator_dir=${circlator_dir}" >> env.sh
 echo "export trimmomatic_dir=${trimmomatic_dir}" >> env.sh
 echo "export bwa_dir=${bwa_dir}" >> env.sh
 echo "export samtools_dir=${samtools_dir}" >> env.sh
 echo "export picard_dir=${picard_dir}" >> env.sh
+#echo "export hapog_dir=${hapog_dir}" >> env.sh
 echo "export pilon_dir=${pilon_dir}" >> env.sh
 echo "export exonerate_dir=${exonerate_dir}" >> env.sh
 echo "export blast_dir=${blast_dir}" >> env.sh
@@ -1378,6 +1894,7 @@ echo "export maker_dir=${maker_dir}" >> env.sh
 echo "export proteinortho_dir=${proteinortho_dir}" >> env.sh
 echo "export diamond_dir=${diamond_dir}" >> env.sh
 echo "export gatk3_dir=${gatk3_dir}" >> env.sh
+#echo "export gff3toolkit_dir=${gff3toolkit_dir}" >> env.sh
 echo "export ucsc_dir=${ucsc_dir}" >> env.sh
 
 ######### for Mfannot  ###########
@@ -1396,19 +1913,117 @@ echo "export mfannot_data_dir=${mfannot_data_dir}" >> env.sh
 echo "export mfannot_dir=${mfannot_dir}" >> env.sh
 
 
+# test java configuration: requireds java 1.8 
+echo ""
+echo "##########################################"
+echo "Testing java configuration ..."
+echo ""
+java_bin=""
+if type -p java
+then 
+    java_bin=$(which java)
+    echo "found java executable in PATH: $java_bin"
+elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]
+then 
+    java_bin="$JAVA_HOME/bin/java"
+    echo "found java executable in JAVA_HOME: $java_bin" 
+else 
+    echo "";
+    echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
+    echo "Failed to detect Java installation in the system!"
+    echo "Please install java 1.8, which is a dependency of RecombineX!\n";
+    echo "After the java installation, please manually set the directory path to java 1.8 executable on the last line of the env.sh file generated by this installation script!"
+    echo "export java_dir=" >> env.sh
+fi  
+
+if [[ -n "$java_bin" ]]
+then
+    java_version=$("$java_bin" -version 2>&1 | awk -F '"' '/version/ {print $2}')
+    echo "detected java_version: $java_version"
+    if [ $(tidy_version "$java_version") -eq $(tidy_version "1.8") ]
+    then
+        java_dir=$(dirname $java_bin)
+        echo "export java_dir=${java_dir}" >> env.sh
+        echo "You have the correct java version for LRSDAY! LRSDAY will take care of the configuration."
+    else
+        echo "";
+        echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
+        echo "Your java version is not the version required by LRSDAY (java v1.8)!"
+        echo "Please manually set the directory path to java 1.8 executable on the last line of the env.sh file generated by this installation script!"
+        echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
+        echo "export java_dir=" >> env.sh
+    fi
+fi
+
+
+
 echo ""
 echo "uncompress large supporting files ..."
-gunzip $LRSDAY_HOME/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz
-gunzip $LRSDAY_HOME/data/SGDref.PoFF.ffn.gz
-gunzip $LRSDAY_HOME/data/SGDref.PoFF.faa.gz
-gunzip $LRSDAY_HOME/data/te_proteins.fasta.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.assembly.final.fa.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.final.gff3.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.final.trimmed_cds.fa.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.final.cds.fa.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.final.pep.fa.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz
-gunzip $LRSDAY_HOME/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz
+if [[ -e $LRSDAY_HOME/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/data/Proteome_DB_for_annotation.CDhit_I95.fa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/data/SGDref.PoFF.ffn.gz ]]
+then
+    gunzip $LRSDAY_HOME/data/SGDref.PoFF.ffn.gz
+fi
+
+if [[ -e $LRSDAY_HOME/data/SGDref.PoFF.faa.gz ]]
+then
+    gunzip $LRSDAY_HOME/data/SGDref.PoFF.faa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/data/SGDref.PoFF.gff.gz ]]
+then
+    gunzip $LRSDAY_HOME/data/SGDref.PoFF.gff.gz
+fi
+
+if [[ -e $LRSDAY_HOME/data/te_proteins.fasta.gz ]]
+then
+    gunzip $LRSDAY_HOME/data/te_proteins.fasta.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.fa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.gff3.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.gff3.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.cds.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.cds.fa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.pep.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.nuclear_genome.tidy.pep.fa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.fa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.gff3.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.gff3.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.cds.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.cds.fa.gz
+fi
+
+if [[ -e $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.pep.fa.gz ]]
+then
+    gunzip $LRSDAY_HOME/Example_Outputs/CPG_1a.mitochondrial_genome.tidy.pep.fa.gz
+fi
+
 echo "done!"
 echo ""
 echo ""
diff --git a/misc/cpanm b/misc/cpanm
new file mode 100644
index 0000000..b72e5d8
--- /dev/null
+++ b/misc/cpanm
@@ -0,0 +1,1078 @@
+#!/usr/bin/env perl
+#
+# This is a pre-compiled source code for the cpanm (cpanminus) program.
+# For more details about how to install cpanm, go to the following URL:
+#
+#   https://github.com/miyagawa/cpanminus
+#
+# Quickstart: Run the following command and it will install itself for
+# you. You might want to run it as a root with sudo if you want to install
+# to places like /usr/local/bin.
+#
+#   % curl -L https://cpanmin.us | perl - App::cpanminus
+#
+# If you don't have curl but wget, replace `curl -L` with `wget -O -`.
+
+# DO NOT EDIT -- this is an auto generated file
+
+# This chunk of stuff was generated by App::FatPacker. To find the original
+# file's code, look for the end of this BEGIN block or the string 'FATPACK'
+BEGIN {
+my %fatpacked;
+
+$fatpacked{"App/cpanminus.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'APP_CPANMINUS';
+  package App::cpanminus;our$VERSION="1.7046";1;
+APP_CPANMINUS
+
+$fatpacked{"App/cpanminus/Dependency.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'APP_CPANMINUS_DEPENDENCY';
+  package App::cpanminus::Dependency;use strict;use CPAN::Meta::Requirements;sub from_prereqs {my($class,$prereqs,$phases,$types)=@_;my@deps;for my$type (@$types){push@deps,$class->from_versions($prereqs->merged_requirements($phases,[$type])->as_string_hash,$type,)}return@deps}sub from_versions {my($class,$versions,$type)=@_;my@deps;while (my($module,$version)=each %$versions){push@deps,$class->new($module,$version,$type)}@deps}sub merge_with {my($self,$requirements)=@_;$self->{original_version}=$self->version;eval {$requirements->add_string_requirement($self->module,$self->version)};if ($@ =~ /illegal requirements/){warn sprintf("Can't merge requirements for %s: '%s' and '%s'",$self->module,$self->version,$requirements->requirements_for_module($self->module))}$self->{version}=$requirements->requirements_for_module($self->module)}sub new {my($class,$module,$version,$type)=@_;bless {module=>$module,version=>$version,type=>$type || 'requires',},$class}sub module {$_[0]->{module}}sub version {$_[0]->{version}}sub type {$_[0]->{type}}sub requires_version {my$self=shift;if (defined$self->{original_version}){return$self->{original_version}}$self->version}sub is_requirement {$_[0]->{type}eq 'requires'}1;
+APP_CPANMINUS_DEPENDENCY
+
+$fatpacked{"App/cpanminus/script.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'APP_CPANMINUS_SCRIPT';
+  package App::cpanminus::script;use strict;use Config;use Cwd ();use App::cpanminus;use App::cpanminus::Dependency;use File::Basename ();use File::Find ();use File::Path ();use File::Spec ();use File::Copy ();use File::Temp ();use Getopt::Long ();use Symbol ();use String::ShellQuote ();use version ();use constant WIN32=>$^O eq 'MSWin32';use constant BAD_TAR=>($^O eq 'solaris' || $^O eq 'hpux');use constant CAN_SYMLINK=>eval {symlink("","");1};our$VERSION=$App::cpanminus::VERSION;if ($INC{"App/FatPacker/Trace.pm"}){require version::vpp}my$quote=WIN32 ? q/"/ : q/'/;sub agent {my$self=shift;my$agent="cpanminus/$VERSION";$agent .= " perl/$]" if$self->{report_perl_version};$agent}sub determine_home {my$class=shift;my$homedir=$ENV{HOME}|| eval {require File::HomeDir;File::HomeDir->my_home}|| join('',@ENV{qw(HOMEDRIVE HOMEPATH)});if (WIN32){require Win32;$homedir=Win32::GetShortPathName($homedir)}return "$homedir/.cpanm"}sub new {my$class=shift;bless {home=>$class->determine_home,cmd=>'install',seen=>{},notest=>undef,test_only=>undef,installdeps=>undef,force=>undef,sudo=>undef,make=>undef,verbose=>undef,quiet=>undef,interactive=>undef,log=>undef,mirrors=>[],mirror_only=>undef,mirror_index=>undef,cpanmetadb=>"http://cpanmetadb.plackperl.org/v1.0/",perl=>$^X,argv=>[],local_lib=>undef,self_contained=>undef,exclude_vendor=>undef,prompt_timeout=>0,prompt=>undef,configure_timeout=>60,build_timeout=>3600,test_timeout=>1800,try_lwp=>1,try_wget=>1,try_curl=>1,uninstall_shadows=>($] < 5.012),skip_installed=>1,skip_satisfied=>0,auto_cleanup=>7,pod2man=>1,installed_dists=>0,install_types=>['requires'],with_develop=>0,with_configure=>0,showdeps=>0,scandeps=>0,scandeps_tree=>[],format=>'tree',save_dists=>undef,skip_configure=>0,verify=>0,report_perl_version=>!$class->maybe_ci,build_args=>{},features=>{},pure_perl=>0,cpanfile_path=>'cpanfile',@_,},$class}sub env {my($self,$key)=@_;$ENV{"PERL_CPANM_" .$key}}sub maybe_ci {my$class=shift;grep$ENV{$_},qw(TRAVIS CI AUTOMATED_TESTING AUTHOR_TESTING)}sub install_type_handlers {my$self=shift;my@handlers;for my$type (qw(recommends suggests)){push@handlers,"with-$type"=>sub {my%uniq;$self->{install_types}=[grep!$uniq{$_}++,@{$self->{install_types}},$type ]};push@handlers,"without-$type"=>sub {$self->{install_types}=[grep $_ ne $type,@{$self->{install_types}}]}}@handlers}sub build_args_handlers {my$self=shift;my@handlers;for my$phase (qw(configure build test install)){push@handlers,"$phase-args=s"=>\($self->{build_args}{$phase})}@handlers}sub parse_options {my$self=shift;local@ARGV=@{$self->{argv}};push@ARGV,grep length,split /\s+/,$self->env('OPT');push@ARGV,@_;Getopt::Long::Configure("bundling");Getopt::Long::GetOptions('f|force'=>sub {$self->{skip_installed}=0;$self->{force}=1},'n|notest!'=>\$self->{notest},'test-only'=>sub {$self->{notest}=0;$self->{skip_installed}=0;$self->{test_only}=1},'S|sudo!'=>\$self->{sudo},'v|verbose'=>\$self->{verbose},'verify!'=>\$self->{verify},'q|quiet!'=>\$self->{quiet},'h|help'=>sub {$self->{action}='show_help'},'V|version'=>sub {$self->{action}='show_version'},'perl=s'=>sub {$self->diag("--perl is deprecated since it's known to be fragile in figuring out dependencies. Run `$_[1] -S cpanm` instead.\n",1);$self->{perl}=$_[1]},'l|local-lib=s'=>sub {$self->{local_lib}=$self->maybe_abs($_[1])},'L|local-lib-contained=s'=>sub {$self->{local_lib}=$self->maybe_abs($_[1]);$self->{self_contained}=1;$self->{pod2man}=undef},'self-contained!'=>\$self->{self_contained},'exclude-vendor!'=>\$self->{exclude_vendor},'mirror=s@'=>$self->{mirrors},'mirror-only!'=>\$self->{mirror_only},'mirror-index=s'=>sub {$self->{mirror_index}=$self->maybe_abs($_[1])},'M|from=s'=>sub {$self->{mirrors}=[$_[1]];$self->{mirror_only}=1},'cpanmetadb=s'=>\$self->{cpanmetadb},'cascade-search!'=>\$self->{cascade_search},'prompt!'=>\$self->{prompt},'installdeps'=>\$self->{installdeps},'skip-installed!'=>\$self->{skip_installed},'skip-satisfied!'=>\$self->{skip_satisfied},'reinstall'=>sub {$self->{skip_installed}=0},'interactive!'=>\$self->{interactive},'i|install'=>sub {$self->{cmd}='install'},'info'=>sub {$self->{cmd}='info'},'look'=>sub {$self->{cmd}='look';$self->{skip_installed}=0},'U|uninstall'=>sub {$self->{cmd}='uninstall'},'self-upgrade'=>sub {$self->{action}='self_upgrade'},'uninst-shadows!'=>\$self->{uninstall_shadows},'lwp!'=>\$self->{try_lwp},'wget!'=>\$self->{try_wget},'curl!'=>\$self->{try_curl},'auto-cleanup=s'=>\$self->{auto_cleanup},'man-pages!'=>\$self->{pod2man},'scandeps'=>\$self->{scandeps},'showdeps'=>sub {$self->{showdeps}=1;$self->{skip_installed}=0},'format=s'=>\$self->{format},'save-dists=s'=>sub {$self->{save_dists}=$self->maybe_abs($_[1])},'skip-configure!'=>\$self->{skip_configure},'dev!'=>\$self->{dev_release},'metacpan!'=>\$self->{metacpan},'report-perl-version!'=>\$self->{report_perl_version},'configure-timeout=i'=>\$self->{configure_timeout},'build-timeout=i'=>\$self->{build_timeout},'test-timeout=i'=>\$self->{test_timeout},'with-develop'=>\$self->{with_develop},'without-develop'=>sub {$self->{with_develop}=0},'with-configure'=>\$self->{with_configure},'without-configure'=>sub {$self->{with_configure}=0},'with-feature=s'=>sub {$self->{features}{$_[1]}=1},'without-feature=s'=>sub {$self->{features}{$_[1]}=0},'with-all-features'=>sub {$self->{features}{__all}=1},'pp|pureperl!'=>\$self->{pure_perl},"cpanfile=s"=>\$self->{cpanfile_path},$self->install_type_handlers,$self->build_args_handlers,);if (!@ARGV && $0 ne '-' &&!-t STDIN){push@ARGV,$self->load_argv_from_fh(\*STDIN);$self->{load_from_stdin}=1}$self->{argv}=\@ARGV}sub check_upgrade {my$self=shift;my$install_base=$ENV{PERL_LOCAL_LIB_ROOT}? $self->local_lib_target($ENV{PERL_LOCAL_LIB_ROOT}): $Config{installsitebin};if ($0 eq '-'){return}elsif ($0 !~ /^$install_base/){if ($0 =~ m!perlbrew/bin!){die <<DIE}else {die <<DIE}}}sub check_libs {my$self=shift;return if$self->{_checked}++;$self->bootstrap_local_lib}sub setup_verify {my$self=shift;my$has_modules=eval {require Module::Signature;require Digest::SHA;1};$self->{cpansign}=$self->which('cpansign');unless ($has_modules && $self->{cpansign}){warn "WARNING: Module::Signature and Digest::SHA is required for distribution verifications.\n";$self->{verify}=0}}sub parse_module_args {my($self,$module)=@_;$module =~ s/^([A-Za-z0-9_:]+)@([v\d\._]+)$/$1~== $2/;if ($module =~ /\~[v\d\._,\!<>= ]+$/){return split /\~/,$module,2}else {return$module,undef}}sub doit {my$self=shift;my$code;eval {$code=($self->_doit==0)};if (my$e=$@){warn$e;$code=1}return$code}sub _doit {my$self=shift;$self->setup_home;$self->init_tools;$self->setup_verify if$self->{verify};if (my$action=$self->{action}){$self->$action()and return 1}return$self->show_help(1)unless @{$self->{argv}}or $self->{load_from_stdin};$self->configure_mirrors;my$cwd=Cwd::cwd;my@fail;for my$module (@{$self->{argv}}){if ($module =~ s/\.pm$//i){my ($volume,$dirs,$file)=File::Spec->splitpath($module);$module=join '::',grep {$_}File::Spec->splitdir($dirs),$file}($module,my$version)=$self->parse_module_args($module);$self->chdir($cwd);if ($self->{cmd}eq 'uninstall'){$self->uninstall_module($module)or push@fail,$module}else {$self->install_module($module,0,$version)or push@fail,$module}}if ($self->{base}&& $self->{auto_cleanup}){$self->cleanup_workdirs}if ($self->{installed_dists}){my$dists=$self->{installed_dists}> 1 ? "distributions" : "distribution";$self->diag("$self->{installed_dists} $dists installed\n",1)}if ($self->{scandeps}){$self->dump_scandeps()}$self->chdir($cwd);return!@fail}sub setup_home {my$self=shift;$self->{home}=$self->env('HOME')if$self->env('HOME');unless (_writable($self->{home})){die "Can't write to cpanm home '$self->{home}': You should fix it with chown/chmod first.\n"}$self->{base}="$self->{home}/work/" .time .".$$";File::Path::mkpath([$self->{base}],0,0777);$self->{log}=File::Spec->catfile($self->{base},"build.log");my$final_log="$self->{home}/build.log";{open my$out,">$self->{log}" or die "$self->{log}: $!"}if (CAN_SYMLINK){my$build_link="$self->{home}/latest-build";unlink$build_link;symlink$self->{base},$build_link;unlink$final_log;symlink$self->{log},$final_log}else {my$log=$self->{log};my$home=$self->{home};$self->{at_exit}=sub {my$self=shift;my$temp_log="$home/build.log." .time .".$$";File::Copy::copy($log,$temp_log)&& unlink($final_log);rename($temp_log,$final_log)}}$self->chat("cpanm (App::cpanminus) $VERSION on perl $] built for $Config{archname}\n" ."Work directory is $self->{base}\n")}sub package_index_for {my ($self,$mirror)=@_;return$self->source_for($mirror)."/02packages.details.txt"}sub generate_mirror_index {my ($self,$mirror)=@_;my$file=$self->package_index_for($mirror);my$gz_file=$file .'.gz';my$index_mtime=(stat$gz_file)[9];unless (-e $file && (stat$file)[9]>= $index_mtime){$self->chat("Uncompressing index file...\n");if (eval {require Compress::Zlib}){my$gz=Compress::Zlib::gzopen($gz_file,"rb")or do {$self->diag_fail("$Compress::Zlib::gzerrno opening compressed index");return};open my$fh,'>',$file or do {$self->diag_fail("$! opening uncompressed index for write");return};my$buffer;while (my$status=$gz->gzread($buffer)){if ($status < 0){$self->diag_fail($gz->gzerror ." reading compressed index");return}print$fh $buffer}}else {if (system("gunzip -c $gz_file > $file")){$self->diag_fail("Cannot uncompress -- please install gunzip or Compress::Zlib");return}}utime$index_mtime,$index_mtime,$file}return 1}sub search_mirror_index {my ($self,$mirror,$module,$version)=@_;$self->search_mirror_index_file($self->package_index_for($mirror),$module,$version)}sub search_mirror_index_file {my($self,$file,$module,$version)=@_;open my$fh,'<',$file or return;my$found;while (<$fh>){if (m!^\Q$module\E\s+([\w\.]+)\s+(\S*)!m){$found=$self->cpan_module($module,$2,$1);last}}return$found unless$self->{cascade_search};if ($found){if ($self->satisfy_version($module,$found->{module_version},$version)){return$found}else {$self->chat("Found $module $found->{module_version} which doesn't satisfy $version.\n")}}return}sub with_version_range {my($self,$version)=@_;defined($version)&& $version =~ /(?:<|!=|==)/}sub encode_json {my($self,$data)=@_;require JSON::PP;my$json=JSON::PP::encode_json($data);$self->uri_escape($json)}sub decode_json {my($self,$json)=@_;require JSON::PP;JSON::PP::decode_json($json)}sub uri_escape {my($self,$fragment)=@_;$fragment =~ s/([^A-Za-z0-9\-\._~])/uc sprintf("%%%02X", ord($1))/eg;$fragment}sub uri_params {my($self,@params)=@_;my@param_strings;while (my$key=shift@params){my$value=shift@params;push@param_strings,join '=',map$self->uri_escape($_),$key,$value}return join '&',@param_strings}sub numify_ver {my($self,$ver)=@_;eval version->new($ver)->numify}sub search_metacpan {my($self,$module,$version,$dev_release)=@_;my$metacpan_uri='http://fastapi.metacpan.org/v1/download_url/';my$url=$metacpan_uri .$module;my$query=$self->uri_params(($version ? (version=>$version): ()),($dev_release ? (dev=>1): ()),);$url .= '?' .$query if length$query;my$dist_json=$self->get($url);my$dist_meta=eval {$self->decode_json($dist_json)};if ($dist_meta && $dist_meta->{download_url}){(my$distfile=$dist_meta->{download_url})=~ s!.+/authors/id/!!;local$self->{mirrors}=$self->{mirrors};$self->{mirrors}=['http://cpan.metacpan.org' ];return$self->cpan_module($module,$distfile,$dist_meta->{version})}$self->chat("! Could not find a release matching $module".($version?" ($version)":'')." on MetaCPAN.\n");return}sub search_database {my($self,$module,$version)=@_;my$found;if ($self->{dev_release}or $self->{metacpan}){$found=$self->search_metacpan($module,$version,$self->{dev_release})and return$found;$found=$self->search_cpanmetadb($module,$version,$self->{dev_release})and return$found}else {$found=$self->search_cpanmetadb($module,$version)and return$found;$found=$self->search_metacpan($module,$version)and return$found}}sub search_cpanmetadb {my($self,$module,$version,$dev_release)=@_;$self->chat("Searching $module ($version) on cpanmetadb ...\n");if ($self->with_version_range($version)){return$self->search_cpanmetadb_history($module,$version,$dev_release)}else {return$self->search_cpanmetadb_package($module,$version,$dev_release)}}sub search_cpanmetadb_package {my($self,$module,$version,$dev_release)=@_;require CPAN::Meta::YAML;(my$uri=$self->{cpanmetadb})=~ s{/?$}{/package/$module};my$yaml=$self->get($uri);my$meta=eval {CPAN::Meta::YAML::Load($yaml)};if ($meta && $meta->{distfile}){return$self->cpan_module($module,$meta->{distfile},$meta->{version})}$self->diag_fail("Finding $module on cpanmetadb failed.");return}sub search_cpanmetadb_history {my($self,$module,$version)=@_;(my$uri=$self->{cpanmetadb})=~ s{/?$}{/history/$module};my$content=$self->get($uri)or return;my@found;for my$line (split /\r?\n/,$content){if ($line =~ /^$module\s+(\S+)\s+(\S+)$/){push@found,{version=>$1,version_obj=>version::->parse($1),distfile=>$2,}}}return unless@found;$found[-1]->{latest}=1;my$match;for my$try (sort {$b->{version_obj}cmp $a->{version_obj}}@found){if ($self->satisfy_version($module,$try->{version_obj},$version)){local$self->{mirrors}=$self->{mirrors};unshift @{$self->{mirrors}},'http://backpan.perl.org' unless$try->{latest};return$self->cpan_module($module,$try->{distfile},$try->{version})}}$self->diag_fail("Finding $module ($version) on cpanmetadb failed.");return}sub search_module {my($self,$module,$version)=@_;if ($self->{mirror_index}){$self->mask_output(chat=>"Searching $module on mirror index $self->{mirror_index} ...\n");my$pkg=$self->search_mirror_index_file($self->{mirror_index},$module,$version);return$pkg if$pkg;unless ($self->{cascade_search}){$self->mask_output(diag_fail=>"Finding $module ($version) on mirror index $self->{mirror_index} failed.");return}}unless ($self->{mirror_only}){my$found=$self->search_database($module,$version);return$found if$found}MIRROR: for my$mirror (@{$self->{mirrors}}){$self->mask_output(chat=>"Searching $module on mirror $mirror ...\n");my$name='02packages.details.txt.gz';my$uri="$mirror/modules/$name";my$gz_file=$self->package_index_for($mirror).'.gz';unless ($self->{pkgs}{$uri}){$self->mask_output(chat=>"Downloading index file $uri ...\n");$self->mirror($uri,$gz_file);$self->generate_mirror_index($mirror)or next MIRROR;$self->{pkgs}{$uri}="!!retrieved!!"}my$pkg=$self->search_mirror_index($mirror,$module,$version);return$pkg if$pkg;$self->mask_output(diag_fail=>"Finding $module ($version) on mirror $mirror failed.")}return}sub source_for {my($self,$mirror)=@_;$mirror =~ s/[^\w\.\-]+/%/g;my$dir="$self->{home}/sources/$mirror";File::Path::mkpath([$dir ],0,0777);return$dir}sub load_argv_from_fh {my($self,$fh)=@_;my@argv;while(defined(my$line=<$fh>)){chomp$line;$line =~ s/#.+$//;$line =~ s/^\s+//;$line =~ s/\s+$//;push@argv,split ' ',$line if$line}return@argv}sub show_version {my$self=shift;print "cpanm (App::cpanminus) version $VERSION ($0)\n";print "perl version $] ($^X)\n\n";print "  \%Config:\n";for my$key (qw(archname installsitelib installsitebin installman1dir installman3dir sitearchexp sitelibexp vendorarch vendorlibexp archlibexp privlibexp)){print "    $key=$Config{$key}\n" if$Config{$key}}print "  \%ENV:\n";for my$key (grep /^PERL/,sort keys%ENV){print "    $key=$ENV{$key}\n"}print "  \@INC:\n";for my$inc (@INC){print "    $inc\n" unless ref($inc)eq 'CODE'}return 1}sub show_help {my$self=shift;if ($_[0]){print <<USAGE;return}print <<HELP;return 1}sub _writable {my$dir=shift;my@dir=File::Spec->splitdir($dir);while (@dir){$dir=File::Spec->catdir(@dir);if (-e $dir){return -w _}pop@dir}return}sub maybe_abs {my($self,$lib)=@_;if ($lib eq '_' or $lib =~ /^~/ or File::Spec->file_name_is_absolute($lib)){return$lib}else {return File::Spec->canonpath(File::Spec->catdir(Cwd::cwd(),$lib))}}sub local_lib_target {my($self,$root)=@_;(grep {$_ ne ''}split /\Q$Config{path_sep}/,$root)[0]}sub bootstrap_local_lib {my$self=shift;if ($self->{local_lib}){return$self->setup_local_lib($self->{local_lib})}if ($ENV{PERL_LOCAL_LIB_ROOT}&& $ENV{PERL_MM_OPT}){return$self->setup_local_lib($self->local_lib_target($ENV{PERL_LOCAL_LIB_ROOT}),1)}return if$self->{sudo}or (_writable($Config{installsitelib})and _writable($Config{installsitebin}));if ($ENV{PERL_MM_OPT}and ($ENV{MODULEBUILDRC}or $ENV{PERL_MB_OPT})){return}$self->setup_local_lib;$self->diag(<<DIAG,1);sleep 2}sub upgrade_toolchain {my($self,$config_deps)=@_;my%deps=map {$_->module=>$_}@$config_deps;my$reqs=CPAN::Meta::Requirements->from_string_hash({'Module::Build'=>'0.38','ExtUtils::MakeMaker'=>'6.58','ExtUtils::Install'=>'1.46',});if ($deps{"ExtUtils::MakeMaker"}){$deps{"ExtUtils::MakeMaker"}->merge_with($reqs)}elsif ($deps{"Module::Build"}){$deps{"Module::Build"}->merge_with($reqs);$deps{"ExtUtils::Install"}||= App::cpanminus::Dependency->new("ExtUtils::Install",0,'configure');$deps{"ExtUtils::Install"}->merge_with($reqs)}@$config_deps=values%deps}sub _core_only_inc {my($self,$base)=@_;require local::lib;(local::lib->resolve_path(local::lib->install_base_arch_path($base)),local::lib->resolve_path(local::lib->install_base_perl_path($base)),(!$self->{exclude_vendor}? grep {$_}@Config{qw(vendorarch vendorlibexp)}: ()),@Config{qw(archlibexp privlibexp)},)}sub _diff {my($self,$old,$new)=@_;my@diff;my%old=map {$_=>1}@$old;for my$n (@$new){push@diff,$n unless exists$old{$n}}@diff}sub _setup_local_lib_env {my($self,$base)=@_;$self->diag(<<WARN,1)if$base =~ /\s/;local$SIG{__WARN__}=sub {};local::lib->setup_env_hash_for($base,0)}sub setup_local_lib {my($self,$base,$no_env)=@_;$base=undef if$base eq '_';require local::lib;{local $0='cpanm';$base ||= "~/perl5";$base=local::lib->resolve_path($base);if ($self->{self_contained}){my@inc=$self->_core_only_inc($base);$self->{search_inc}=[@inc ]}else {$self->{search_inc}=[local::lib->install_base_arch_path($base),local::lib->install_base_perl_path($base),@INC,]}$self->_setup_local_lib_env($base)unless$no_env;$self->{local_lib}=$base}}sub prompt_bool {my($self,$mess,$def)=@_;my$val=$self->prompt($mess,$def);return lc$val eq 'y'}sub prompt {my($self,$mess,$def)=@_;my$isa_tty=-t STDIN && (-t STDOUT ||!(-f STDOUT || -c STDOUT));my$dispdef=defined$def ? "[$def] " : " ";$def=defined$def ? $def : "";if (!$self->{prompt}|| (!$isa_tty && eof STDIN)){return$def}local $|=1;local $\;my$ans;eval {local$SIG{ALRM}=sub {undef$ans;die "alarm\n"};print STDOUT "$mess $dispdef";alarm$self->{prompt_timeout}if$self->{prompt_timeout};$ans=<STDIN>;alarm 0};if (defined$ans){chomp$ans}else {print STDOUT "\n"}return (!defined$ans || $ans eq '')? $def : $ans}sub diag_ok {my($self,$msg)=@_;chomp$msg;$msg ||= "OK";if ($self->{in_progress}){$self->_diag("$msg\n");$self->{in_progress}=0}$self->log("-> $msg\n")}sub diag_fail {my($self,$msg,$always)=@_;chomp$msg;if ($self->{in_progress}){$self->_diag("FAIL\n");$self->{in_progress}=0}if ($msg){$self->_diag("! $msg\n",$always,1);$self->log("-> FAIL $msg\n")}}sub diag_progress {my($self,$msg)=@_;chomp$msg;$self->{in_progress}=1;$self->_diag("$msg ... ");$self->log("$msg\n")}sub _diag {my($self,$msg,$always,$error)=@_;my$fh=$error ? *STDERR : *STDOUT;print {$fh}$msg if$always or $self->{verbose}or!$self->{quiet}}sub diag {my($self,$msg,$always)=@_;$self->_diag($msg,$always);$self->log($msg)}sub chat {my$self=shift;print STDERR @_ if$self->{verbose};$self->log(@_)}sub mask_output {my$self=shift;my$method=shift;$self->$method($self->mask_uri_passwords(@_))}sub log {my$self=shift;open my$out,">>$self->{log}";print$out @_}sub run {my($self,$cmd)=@_;if (WIN32){$cmd=$self->shell_quote(@$cmd)if ref$cmd eq 'ARRAY';unless ($self->{verbose}){$cmd .= " >> " .$self->shell_quote($self->{log})." 2>&1"}!system$cmd}else {my$pid=fork;if ($pid){waitpid$pid,0;return!$?}else {$self->run_exec($cmd)}}}sub run_exec {my($self,$cmd)=@_;if (ref$cmd eq 'ARRAY'){unless ($self->{verbose}){open my$logfh,">>",$self->{log};open STDERR,'>&',$logfh;open STDOUT,'>&',$logfh;close$logfh}exec @$cmd}else {unless ($self->{verbose}){$cmd .= " >> " .$self->shell_quote($self->{log})." 2>&1"}exec$cmd}}sub run_timeout {my($self,$cmd,$timeout)=@_;return$self->run($cmd)if WIN32 || $self->{verbose}||!$timeout;my$pid=fork;if ($pid){eval {local$SIG{ALRM}=sub {die "alarm\n"};alarm$timeout;waitpid$pid,0;alarm 0};if ($@ && $@ eq "alarm\n"){$self->diag_fail("Timed out (> ${timeout}s). Use --verbose to retry.");local$SIG{TERM}='IGNORE';kill TERM=>0;waitpid$pid,0;return}return!$?}elsif ($pid==0){$self->run_exec($cmd)}else {$self->chat("! fork failed: falling back to system()\n");$self->run($cmd)}}sub append_args {my($self,$cmd,$phase)=@_;if (my$args=$self->{build_args}{$phase}){$cmd=join ' ',$self->shell_quote(@$cmd),$args}$cmd}sub configure {my($self,$cmd,$depth)=@_;local$ENV{PERL5_CPAN_IS_RUNNING}=local$ENV{PERL5_CPANPLUS_IS_RUNNING}=$$;local$ENV{PERL5_CPANM_IS_RUNNING}=$$;my$use_default=!$self->{interactive};local$ENV{PERL_MM_USE_DEFAULT}=$use_default;local$ENV{PERL_MM_OPT}=$ENV{PERL_MM_OPT};local$ENV{PERL_MB_OPT}=$ENV{PERL_MB_OPT};unless ($self->{pod2man}){$ENV{PERL_MM_OPT}.= " INSTALLMAN1DIR=none INSTALLMAN3DIR=none";$ENV{PERL_MB_OPT}.= " --config installman1dir= --config installsiteman1dir= --config installman3dir= --config installsiteman3dir="}if ($self->{pure_perl}){$ENV{PERL_MM_OPT}.= " PUREPERL_ONLY=1";$ENV{PERL_MB_OPT}.= " --pureperl-only"}local$ENV{PERL_USE_UNSAFE_INC}=1 unless exists$ENV{PERL_USE_UNSAFE_INC};$cmd=$self->append_args($cmd,'configure')if$depth==0;local$self->{verbose}=$self->{verbose}|| $self->{interactive};$self->run_timeout($cmd,$self->{configure_timeout})}sub build {my($self,$cmd,$distname,$depth)=@_;local$ENV{PERL_MM_USE_DEFAULT}=!$self->{interactive};local$ENV{PERL_USE_UNSAFE_INC}=1 unless exists$ENV{PERL_USE_UNSAFE_INC};$cmd=$self->append_args($cmd,'build')if$depth==0;return 1 if$self->run_timeout($cmd,$self->{build_timeout});while (1){my$ans=lc$self->prompt("Building $distname failed.\nYou can s)kip, r)etry, e)xamine build log, or l)ook ?","s");return if$ans eq 's';return$self->build($cmd,$distname,$depth)if$ans eq 'r';$self->show_build_log if$ans eq 'e';$self->look if$ans eq 'l'}}sub test {my($self,$cmd,$distname,$depth)=@_;return 1 if$self->{notest};local$ENV{PERL_MM_USE_DEFAULT}=!$self->{interactive};local$ENV{NONINTERACTIVE_TESTING}=!$self->{interactive};$cmd=$self->append_args($cmd,'test')if$depth==0;local$ENV{PERL_USE_UNSAFE_INC}=1 unless exists$ENV{PERL_USE_UNSAFE_INC};return 1 if$self->run_timeout($cmd,$self->{test_timeout});if ($self->{force}){$self->diag_fail("Testing $distname failed but installing it anyway.");return 1}else {$self->diag_fail;while (1){my$ans=lc$self->prompt("Testing $distname failed.\nYou can s)kip, r)etry, f)orce install, e)xamine build log, or l)ook ?","s");return if$ans eq 's';return$self->test($cmd,$distname,$depth)if$ans eq 'r';return 1 if$ans eq 'f';$self->show_build_log if$ans eq 'e';$self->look if$ans eq 'l'}}}sub install {my($self,$cmd,$uninst_opts,$depth)=@_;if ($depth==0 && $self->{test_only}){return 1}local$ENV{PERL_USE_UNSAFE_INC}=1 unless exists$ENV{PERL_USE_UNSAFE_INC};if ($self->{sudo}){unshift @$cmd,"sudo"}if ($self->{uninstall_shadows}&&!$ENV{PERL_MM_OPT}){push @$cmd,@$uninst_opts}$cmd=$self->append_args($cmd,'install')if$depth==0;$self->run($cmd)}sub look {my$self=shift;my$shell=$ENV{SHELL};$shell ||= $ENV{COMSPEC}if WIN32;if ($shell){my$cwd=Cwd::cwd;$self->diag("Entering $cwd with $shell\n");system$shell}else {$self->diag_fail("You don't seem to have a SHELL :/")}}sub show_build_log {my$self=shift;my@pagers=($ENV{PAGER},(WIN32 ? (): ('less')),'more');my$pager;while (@pagers){$pager=shift@pagers;next unless$pager;$pager=$self->which($pager);next unless$pager;last}if ($pager){system("$pager < $self->{log}")}else {$self->diag_fail("You don't seem to have a PAGER :/")}}sub chdir {my$self=shift;Cwd::chdir(File::Spec->canonpath($_[0]))or die "$_[0]: $!"}sub configure_mirrors {my$self=shift;unless (@{$self->{mirrors}}){$self->{mirrors}=['http://www.cpan.org' ]}for (@{$self->{mirrors}}){s!^/!file:///!;s!/$!!}}sub self_upgrade {my$self=shift;$self->check_upgrade;$self->{argv}=['App::cpanminus' ];return}sub install_module {my($self,$module,$depth,$version)=@_;$self->check_libs;if ($self->{seen}{$module}++){$self->chat("Already tried $module. Skipping.\n");return 1}if ($self->{skip_satisfied}){my($ok,$local)=$self->check_module($module,$version || 0);if ($ok){$self->diag("You have $module ($local)\n",1);return 1}}my$dist=$self->resolve_name($module,$version);unless ($dist){my$what=$module .($version ? " ($version)" : "");$self->diag_fail("Couldn't find module or a distribution $what",1);return}if ($dist->{distvname}&& $self->{seen}{$dist->{distvname}}++){$self->chat("Already tried $dist->{distvname}. Skipping.\n");return 1}if ($self->{cmd}eq 'info'){print$self->format_dist($dist),"\n";return 1}$dist->{depth}=$depth;if ($dist->{module}){unless ($self->satisfy_version($dist->{module},$dist->{module_version},$version)){$self->diag("Found $dist->{module} $dist->{module_version} which doesn't satisfy $version.\n",1);return}my$cmp=$version ? "==" : "";my$requirement=$dist->{module_version}? "$cmp$dist->{module_version}" : 0;my($ok,$local)=$self->check_module($dist->{module},$requirement);if ($self->{skip_installed}&& $ok){$self->diag("$dist->{module} is up to date. ($local)\n",1);return 1}}if ($dist->{dist}eq 'perl'){$self->diag("skipping $dist->{pathname}\n");return 1}$self->diag("--> Working on $module\n");$dist->{dir}||= $self->fetch_module($dist);unless ($dist->{dir}){$self->diag_fail("Failed to fetch distribution $dist->{distvname}",1);return}$self->chat("Entering $dist->{dir}\n");$self->chdir($self->{base});$self->chdir($dist->{dir});if ($self->{cmd}eq 'look'){$self->look;return 1}return$self->build_stuff($module,$dist,$depth)}sub uninstall_search_path {my$self=shift;$self->{local_lib}? (local::lib->install_base_arch_path($self->{local_lib}),local::lib->install_base_perl_path($self->{local_lib})): @Config{qw(installsitearch installsitelib)}}sub uninstall_module {my ($self,$module)=@_;$self->check_libs;my@inc=$self->uninstall_search_path;my($metadata,$packlist)=$self->packlists_containing($module,\@inc);unless ($packlist){$self->diag_fail(<<DIAG,1);return}my@uninst_files=$self->uninstall_target($metadata,$packlist);$self->ask_permission($module,\@uninst_files)or return;$self->uninstall_files(@uninst_files,$packlist);$self->diag("Successfully uninstalled $module\n",1);return 1}sub packlists_containing {my($self,$module,$inc)=@_;require Module::Metadata;my$metadata=Module::Metadata->new_from_module($module,inc=>$inc)or return;my$packlist;my$wanted=sub {return unless $_ eq '.packlist' && -f $_;for my$file ($self->unpack_packlist($File::Find::name)){$packlist ||= $File::Find::name if$file eq $metadata->filename}};{require File::pushd;my$pushd=File::pushd::pushd();my@search=grep -d $_,map File::Spec->catdir($_,'auto'),@$inc;File::Find::find($wanted,@search)}return$metadata,$packlist}sub uninstall_target {my($self,$metadata,$packlist)=@_;if ($self->has_shadow_install($metadata)or $self->{local_lib}){grep$self->should_unlink($_),$self->unpack_packlist($packlist)}else {$self->unpack_packlist($packlist)}}sub has_shadow_install {my($self,$metadata)=@_;my@shadow=grep defined,map Module::Metadata->new_from_module($metadata->name,inc=>[$_]),@INC;@shadow >= 2}sub should_unlink {my($self,$file)=@_;if ($self->{local_lib}){$file =~ /^\Q$self->{local_lib}\E/}else {!(grep$file =~ /^\Q$_\E/,@Config{qw(installbin installscript installman1dir installman3dir)})}}sub ask_permission {my ($self,$module,$files)=@_;$self->diag("$module contains the following files:\n\n");for my$file (@$files){$self->diag("  $file\n")}$self->diag("\n");return 'force uninstall' if$self->{force};local$self->{prompt}=1;return$self->prompt_bool("Are you sure you want to uninstall $module?",'y')}sub unpack_packlist {my ($self,$packlist)=@_;open my$fh,'<',$packlist or die "$packlist: $!";map {chomp;$_}<$fh>}sub uninstall_files {my ($self,@files)=@_;$self->diag("\n");for my$file (@files){$self->diag("Unlink: $file\n");unlink$file or $self->diag_fail("$!: $file")}$self->diag("\n");return 1}sub format_dist {my($self,$dist)=@_;return "$dist->{cpanid}/$dist->{filename}"}sub trim {local $_=shift;tr/\n/ /d;s/^\s*|\s*$//g;$_}sub fetch_module {my($self,$dist)=@_;$self->chdir($self->{base});for my$uri (@{$dist->{uris}}){$self->mask_output(diag_progress=>"Fetching $uri");my$filename=$dist->{filename}|| $uri;my$name=File::Basename::basename($filename);my$cancelled;my$fetch=sub {my$file;eval {local$SIG{INT}=sub {$cancelled=1;die "SIGINT\n"};$self->mirror($uri,$name);$file=$name if -e $name};$self->diag("ERROR: " .trim("$@")."\n",1)if $@ && $@ ne "SIGINT\n";return$file};my($try,$file);while ($try++ < 3){$file=$fetch->();last if$cancelled or $file;$self->mask_output(diag_fail=>"Download $uri failed. Retrying ... ")}if ($cancelled){$self->diag_fail("Download cancelled.");return}unless ($file){$self->mask_output(diag_fail=>"Failed to download $uri");next}$self->diag_ok;$dist->{local_path}=File::Spec->rel2abs($name);my$dir=$self->unpack($file,$uri,$dist);next unless$dir;if (my$save=$self->{save_dists}){my$path=$dist->{pathname}? "$save/authors/id/$dist->{pathname}" : "$save/vendor/$file";$self->chat("Copying $name to $path\n");File::Path::mkpath([File::Basename::dirname($path)],0,0777);File::Copy::copy($file,$path)or warn $!}return$dist,$dir}}sub unpack {my($self,$file,$uri,$dist)=@_;if ($self->{verify}){$self->verify_archive($file,$uri,$dist)or return}$self->chat("Unpacking $file\n");my$dir=$file =~ /\.zip/i ? $self->unzip($file): $self->untar($file);unless ($dir){$self->diag_fail("Failed to unpack $file: no directory")}return$dir}sub verify_archive {my($self,$file,$uri,$dist)=@_;unless ($dist->{cpanid}){$self->chat("Archive '$file' does not seem to be from PAUSE. Skip verification.\n");return 1}(my$mirror=$uri)=~ s!/authors/id.*$!!;(my$chksum_uri=$uri)=~ s!/[^/]*$!/CHECKSUMS!;my$chk_file=$self->source_for($mirror)."/$dist->{cpanid}.CHECKSUMS";$self->mask_output(diag_progress=>"Fetching $chksum_uri");$self->mirror($chksum_uri,$chk_file);unless (-e $chk_file){$self->diag_fail("Fetching $chksum_uri failed.\n");return}$self->diag_ok;$self->verify_checksum($file,$chk_file)}sub verify_checksum {my($self,$file,$chk_file)=@_;$self->chat("Verifying the SHA1 for $file\n");open my$fh,"<$chk_file" or die "$chk_file: $!";my$data=join '',<$fh>;$data =~ s/\015?\012/\n/g;require Safe;my$chksum=Safe->new->reval($data);if (!ref$chksum or ref$chksum ne 'HASH'){$self->diag_fail("! Checksum file downloaded from $chk_file is broken.\n");return}if (my$sha=$chksum->{$file}{sha256}){my$hex=$self->sha1_for($file);if ($hex eq $sha){$self->chat("Checksum for $file: Verified!\n")}else {$self->diag_fail("Checksum mismatch for $file\n");return}}else {$self->chat("Checksum for $file not found in CHECKSUMS.\n");return}}sub sha1_for {my($self,$file)=@_;require Digest::SHA;open my$fh,"<",$file or die "$file: $!";my$dg=Digest::SHA->new(256);my($data);while (read($fh,$data,4096)){$dg->add($data)}return$dg->hexdigest}sub verify_signature {my($self,$dist)=@_;$self->diag_progress("Verifying the SIGNATURE file");my$out=`$self->{cpansign} -v --skip 2>&1`;$self->log($out);if ($out =~ /Signature verified OK/){$self->diag_ok("Verified OK");return 1}else {$self->diag_fail("SIGNATURE verification for $dist->{filename} failed\n");return}}sub resolve_name {my($self,$module,$version)=@_;if ($module =~ /(?:^git:|\.git(?:@.+)?$)/){return$self->git_uri($module)}if ($module =~ /^(ftp|https?|file):/){if ($module =~ m!authors/id/(.*)!){return$self->cpan_dist($1,$module)}else {return {uris=>[$module ]}}}if ($module =~ m!^[\./]! && -d $module){return {source=>'local',dir=>Cwd::abs_path($module),}}if (-f $module){return {source=>'local',uris=>["file://" .Cwd::abs_path($module)],}}if ($module =~ s!^cpan:///distfile/!!){return$self->cpan_dist($module)}if ($module =~ m!^(?:[A-Z]/[A-Z]{2}/)?([A-Z]{2}[\-A-Z0-9]*/.*)$!){return$self->cpan_dist($1)}return$self->search_module($module,$version)}sub cpan_module {my($self,$module,$dist_file,$version)=@_;my$dist=$self->cpan_dist($dist_file);$dist->{module}=$module;$dist->{module_version}=$version if$version && $version ne 'undef';return$dist}sub cpan_dist {my($self,$dist,$url)=@_;$dist =~ s!^([A-Z]{2})!substr($1,0,1)."/".substr($1,0,2)."/".$1!e;require CPAN::DistnameInfo;my$d=CPAN::DistnameInfo->new($dist);if ($url){$url=[$url ]unless ref$url eq 'ARRAY'}else {my$id=$d->cpanid;my$fn=substr($id,0,1)."/" .substr($id,0,2)."/" .$id ."/" .$d->filename;my@mirrors=@{$self->{mirrors}};my@urls=map "$_/authors/id/$fn",@mirrors;$url=\@urls,}return {$d->properties,source=>'cpan',uris=>$url,}}sub git_uri {my ($self,$uri)=@_;($uri,my$commitish)=split /(?<=\.git)@/i,$uri,2;my$dir=File::Temp::tempdir(CLEANUP=>1);$self->mask_output(diag_progress=>"Cloning $uri");$self->run(['git','clone',$uri,$dir ]);unless (-e "$dir/.git"){$self->diag_fail("Failed cloning git repository $uri",1);return}if ($commitish){require File::pushd;my$dir=File::pushd::pushd($dir);unless ($self->run(['git','checkout',$commitish ])){$self->diag_fail("Failed to checkout '$commitish' in git repository $uri\n");return}}$self->diag_ok;return {source=>'local',dir=>$dir,}}sub setup_module_build_patch {my$self=shift;open my$out,">$self->{base}/ModuleBuildSkipMan.pm" or die $!;print$out <<EOF}sub core_version_for {my($self,$module)=@_;require Module::CoreList;unless (exists$Module::CoreList::version{$]+0}){die sprintf("Module::CoreList %s (loaded from %s) doesn't seem to have entries for perl $]. " ."You're strongly recommended to upgrade Module::CoreList from CPAN.\n",$Module::CoreList::VERSION,$INC{"Module/CoreList.pm"})}unless (exists$Module::CoreList::version{$]+0}{$module}){return -1}return$Module::CoreList::version{$]+0}{$module}}sub search_inc {my$self=shift;$self->{search_inc}||= do {if (defined$::Bin){[grep!/^\Q$::Bin\E\/..\/(?:fat)?lib$/,@INC]}else {[@INC]}}}sub check_module {my($self,$mod,$want_ver)=@_;require Module::Metadata;my$meta=Module::Metadata->new_from_module($mod,inc=>$self->search_inc)or return 0,undef;my$version=$meta->version;if ($self->{self_contained}&& $self->loaded_from_perl_lib($meta)){$version=$self->core_version_for($mod);return 0,undef if$version && $version==-1}$self->{local_versions}{$mod}=$version;if ($self->is_deprecated($meta)){return 0,$version}elsif ($self->satisfy_version($mod,$version,$want_ver)){return 1,($version || 'undef')}else {return 0,$version}}sub satisfy_version {my($self,$mod,$version,$want_ver)=@_;$want_ver='0' unless defined($want_ver)&& length($want_ver);require CPAN::Meta::Requirements;my$requirements=CPAN::Meta::Requirements->new;$requirements->add_string_requirement($mod,$want_ver);$requirements->accepts_module($mod,$version)}sub unsatisfy_how {my($self,$ver,$want_ver)=@_;if ($want_ver =~ /^[v0-9\.\_]+$/){return "$ver < $want_ver"}else {return "$ver doesn't satisfy $want_ver"}}sub is_deprecated {my($self,$meta)=@_;my$deprecated=eval {require Module::CoreList;Module::CoreList::is_deprecated($meta->{module})};return$deprecated && $self->loaded_from_perl_lib($meta)}sub loaded_from_perl_lib {my($self,$meta)=@_;require Config;my@dirs=qw(archlibexp privlibexp);if ($self->{self_contained}&&!$self->{exclude_vendor}&& $Config{vendorarch}){unshift@dirs,qw(vendorarch vendorlibexp)}for my$dir (@dirs){my$confdir=$Config{$dir};if ($confdir eq substr($meta->filename,0,length($confdir))){return 1}}return}sub should_install {my($self,$mod,$ver)=@_;$self->chat("Checking if you have $mod $ver ... ");my($ok,$local)=$self->check_module($mod,$ver);if ($ok){$self->chat("Yes ($local)\n")}elsif ($local){$self->chat("No (" .$self->unsatisfy_how($local,$ver).")\n")}else {$self->chat("No\n")}return$mod unless$ok;return}sub check_perl_version {my($self,$version)=@_;require CPAN::Meta::Requirements;my$req=CPAN::Meta::Requirements->from_string_hash({perl=>$version });$req->accepts_module(perl=>$])}sub install_deps {my($self,$dir,$depth,@deps)=@_;my(@install,%seen,@fail);for my$dep (@deps){next if$seen{$dep->module};if ($dep->module eq 'perl'){if ($dep->is_requirement &&!$self->check_perl_version($dep->version)){$self->diag("Needs perl @{[$dep->version]}, you have $]\n");push@fail,'perl'}}elsif ($self->should_install($dep->module,$dep->version)){push@install,$dep;$seen{$dep->module}=1}}if (@install){$self->diag("==> Found dependencies: " .join(", ",map $_->module,@install)."\n")}for my$dep (@install){$self->install_module($dep->module,$depth + 1,$dep->version)}$self->chdir($self->{base});$self->chdir($dir)if$dir;if ($self->{scandeps}){return 1}my@not_ok=$self->unsatisfied_deps(@deps);if (@not_ok){return 0,\@not_ok}else {return 1}}sub unsatisfied_deps {my($self,@deps)=@_;require CPAN::Meta::Check;require CPAN::Meta::Requirements;my$reqs=CPAN::Meta::Requirements->new;for my$dep (grep $_->is_requirement,@deps){$reqs->add_string_requirement($dep->module=>$dep->requires_version || '0')}my$ret=CPAN::Meta::Check::check_requirements($reqs,'requires',$self->{search_inc});grep defined,values %$ret}sub install_deps_bailout {my($self,$target,$dir,$depth,@deps)=@_;my($ok,$fail)=$self->install_deps($dir,$depth,@deps);if (!$ok){$self->diag_fail("Installing the dependencies failed: " .join(", ",@$fail),1);unless ($self->prompt_bool("Do you want to continue building $target anyway?","n")){$self->diag_fail("Bailing out the installation for $target.",1);return}}return 1}sub build_stuff {my($self,$stuff,$dist,$depth)=@_;if ($self->{verify}&& -e 'SIGNATURE'){$self->verify_signature($dist)or return}require CPAN::Meta;my($meta_file)=grep -f,qw(META.json META.yml);if ($meta_file){$self->chat("Checking configure dependencies from $meta_file\n");$dist->{cpanmeta}=eval {CPAN::Meta->load_file($meta_file)}}elsif ($dist->{dist}&& $dist->{version}){$self->chat("META.yml/json not found. Creating skeleton for it.\n");$dist->{cpanmeta}=CPAN::Meta->new({name=>$dist->{dist},version=>$dist->{version}})}$dist->{meta}=$dist->{cpanmeta}? $dist->{cpanmeta}->as_struct : {};my@config_deps;if ($dist->{cpanmeta}){push@config_deps,App::cpanminus::Dependency->from_prereqs($dist->{cpanmeta}->effective_prereqs,['configure'],$self->{install_types},)}if (-e 'Build.PL' &&!$self->should_use_mm($dist->{dist})&&!@config_deps){push@config_deps,App::cpanminus::Dependency->from_versions({'Module::Build'=>'0.38' },'configure',)}$self->merge_with_cpanfile($dist,\@config_deps);$self->upgrade_toolchain(\@config_deps);my$target=$dist->{meta}{name}? "$dist->{meta}{name}-$dist->{meta}{version}" : $dist->{dir};{$self->install_deps_bailout($target,$dist->{dir},$depth,@config_deps)or return}$self->diag_progress("Configuring $target");my$configure_state=$self->configure_this($dist,$depth);$self->diag_ok($configure_state->{configured_ok}? "OK" : "N/A");if ($dist->{cpanmeta}&& $dist->{source}eq 'cpan'){$dist->{provides}=$dist->{cpanmeta}{provides}|| $self->extract_packages($dist->{cpanmeta},".")}my$root_target=(($self->{installdeps}or $self->{showdeps})and $depth==0);$dist->{want_phases}=$self->{notest}&&!$root_target ? [qw(build runtime)]: [qw(build test runtime)];push @{$dist->{want_phases}},'develop' if$self->{with_develop}&& $depth==0;push @{$dist->{want_phases}},'configure' if$self->{with_configure}&& $depth==0;my@deps=$self->find_prereqs($dist);my$module_name=$self->find_module_name($configure_state)|| $dist->{meta}{name};$module_name =~ s/-/::/g;if ($self->{showdeps}){for my$dep (@config_deps,@deps){print$dep->module,($dep->version ? ("~".$dep->version): ""),"\n"}return 1}my$distname=$dist->{meta}{name}? "$dist->{meta}{name}-$dist->{meta}{version}" : $stuff;my$walkup;if ($self->{scandeps}){$walkup=$self->scandeps_append_child($dist)}$self->install_deps_bailout($distname,$dist->{dir},$depth,@deps)or return;if ($self->{scandeps}){unless ($configure_state->{configured_ok}){my$diag=<<DIAG;if (@config_deps){my@tree=@{$self->{scandeps_tree}};$diag .= "!\n" .join("",map "! * $_->[0]{module}\n",@tree[0..$#tree-1])if@tree}$self->diag("!\n$diag!\n",1)}$walkup->();return 1}if ($self->{installdeps}&& $depth==0){if ($configure_state->{configured_ok}){$self->diag("<== Installed dependencies for $stuff. Finishing.\n");return 1}else {$self->diag("! Configuring $distname failed. See $self->{log} for details.\n",1);return}}my$installed;if ($configure_state->{use_module_build}&& -e 'Build' && -f _){$self->diag_progress("Building " .($self->{notest}? "" : "and testing ").$distname);$self->build([$self->{perl},"./Build" ],$distname,$depth)&& $self->test([$self->{perl},"./Build","test" ],$distname,$depth)&& $self->install([$self->{perl},"./Build","install" ],["--uninst",1 ],$depth)&& $installed++}elsif ($self->{make}&& -e 'Makefile'){$self->diag_progress("Building " .($self->{notest}? "" : "and testing ").$distname);$self->build([$self->{make}],$distname,$depth)&& $self->test([$self->{make},"test" ],$distname,$depth)&& $self->install([$self->{make},"install" ],["UNINST=1" ],$depth)&& $installed++}else {my$why;my$configure_failed=$configure_state->{configured}&&!$configure_state->{configured_ok};if ($configure_failed){$why="Configure failed for $distname."}elsif ($self->{make}){$why="The distribution doesn't have a proper Makefile.PL/Build.PL"}else {$why="Can't configure the distribution. You probably need to have 'make'."}$self->diag_fail("$why See $self->{log} for details.",1);return}if ($installed && $self->{test_only}){$self->diag_ok;$self->diag("Successfully tested $distname\n",1)}elsif ($installed){my$local=$self->{local_versions}{$dist->{module}|| ''};my$version=$dist->{module_version}|| $dist->{meta}{version}|| $dist->{version};my$reinstall=$local && ($local eq $version);my$action=$local &&!$reinstall ? $self->numify_ver($version)< $self->numify_ver($local)? "downgraded" : "upgraded" : undef;my$how=$reinstall ? "reinstalled $distname" : $local ? "installed $distname ($action from $local)" : "installed $distname" ;my$msg="Successfully $how";$self->diag_ok;$self->diag("$msg\n",1);$self->{installed_dists}++;$self->save_meta($stuff,$dist,$module_name,\@config_deps,\@deps);return 1}else {my$what=$self->{test_only}? "Testing" : "Installing";$self->diag_fail("$what $stuff failed. See $self->{log} for details. Retry with --force to force install it.",1);return}}sub perl_requirements {my($self,@requires)=@_;my@perl;for my$requires (grep defined,@requires){if (exists$requires->{perl}){push@perl,App::cpanminus::Dependency->new(perl=>$requires->{perl})}}return@perl}sub should_use_mm {my($self,$dist)=@_;my%should_use_mm=map {$_=>1}qw(version ExtUtils-ParseXS ExtUtils-Install ExtUtils-Manifest);$should_use_mm{$dist}}sub configure_this {my($self,$dist,$depth)=@_;if (-e $self->{cpanfile_path}&& $self->{installdeps}&& $depth==0){require Module::CPANfile;$dist->{cpanfile}=eval {Module::CPANfile->load($self->{cpanfile_path})};$self->diag_fail($@,1)if $@;return {configured=>1,configured_ok=>!!$dist->{cpanfile},use_module_build=>0,}}if ($self->{skip_configure}){my$eumm=-e 'Makefile';my$mb=-e 'Build' && -f _;return {configured=>1,configured_ok=>$eumm || $mb,use_module_build=>$mb,}}my$state={};my$try_eumm=sub {if (-e 'Makefile.PL'){$self->chat("Running Makefile.PL\n");if ($self->configure([$self->{perl},"Makefile.PL" ],$depth)){$state->{configured_ok}=-e 'Makefile'}$state->{configured}++}};my$try_mb=sub {if (-e 'Build.PL'){$self->chat("Running Build.PL\n");if ($self->configure([$self->{perl},"Build.PL" ],$depth)){$state->{configured_ok}=-e 'Build' && -f _}$state->{use_module_build}++;$state->{configured}++}};my@try;if ($dist->{dist}&& $self->should_use_mm($dist->{dist})){@try=($try_eumm,$try_mb)}else {@try=($try_mb,$try_eumm)}for my$try (@try){$try->();last if$state->{configured_ok}}unless ($state->{configured_ok}){while (1){my$ans=lc$self->prompt("Configuring $dist->{dist} failed.\nYou can s)kip, r)etry, e)xamine build log, or l)ook ?","s");last if$ans eq 's';return$self->configure_this($dist,$depth)if$ans eq 'r';$self->show_build_log if$ans eq 'e';$self->look if$ans eq 'l'}}return$state}sub find_module_name {my($self,$state)=@_;return unless$state->{configured_ok};if ($state->{use_module_build}&& -e "_build/build_params"){my$params=do {open my$in,"_build/build_params";$self->safe_eval(join "",<$in>)};return eval {$params->[2]{module_name}}|| undef}elsif (-e "Makefile"){open my$mf,"Makefile";while (<$mf>){if (/^\#\s+NAME\s+=>\s+(.*)/){return$self->safe_eval($1)}}}return}sub list_files {my$self=shift;if (-e 'MANIFEST'){require ExtUtils::Manifest;my$manifest=eval {ExtUtils::Manifest::manifind()}|| {};return sort {lc$a cmp lc$b}keys %$manifest}else {require File::Find;my@files;my$finder=sub {my$name=$File::Find::name;$name =~ s!\.[/\\]!!;push@files,$name};File::Find::find($finder,".");return sort {lc$a cmp lc$b}@files}}sub extract_packages {my($self,$meta,$dir)=@_;my$try=sub {my$file=shift;return 0 if$file =~ m!^(?:x?t|inc|local|perl5|fatlib|_build)/!;return 1 unless$meta->{no_index};return 0 if grep {$file =~ m!^$_/!}@{$meta->{no_index}{directory}|| []};return 0 if grep {$file eq $_}@{$meta->{no_index}{file}|| []};return 1};require Parse::PMFile;my@files=grep {/\.pm(?:\.PL)?$/ && $try->($_)}$self->list_files;my$provides={};for my$file (@files){my$parser=Parse::PMFile->new($meta,{UNSAFE=>1,ALLOW_DEV_VERSION=>1 });my$packages=$parser->parse($file);while (my($package,$meta)=each %$packages){$provides->{$package}||= {file=>$meta->{infile},($meta->{version}eq 'undef')? (): (version=>$meta->{version}),}}}return$provides}sub save_meta {my($self,$module,$dist,$module_name,$config_deps,$build_deps)=@_;return unless$dist->{distvname}&& $dist->{source}eq 'cpan';my$base=($ENV{PERL_MM_OPT}|| '')=~ /INSTALL_BASE=/ ? ($self->install_base($ENV{PERL_MM_OPT})."/lib/perl5"): $Config{sitelibexp};my$provides=$dist->{provides};File::Path::mkpath("blib/meta",0,0777);my$local={name=>$module_name,target=>$module,version=>exists$provides->{$module_name}? ($provides->{$module_name}{version}|| $dist->{version}): $dist->{version},dist=>$dist->{distvname},pathname=>$dist->{pathname},provides=>$provides,};require JSON::PP;open my$fh,">","blib/meta/install.json" or die $!;print$fh JSON::PP::encode_json($local);if (-e "MYMETA.json"){File::Copy::copy("MYMETA.json","blib/meta/MYMETA.json")}my@cmd=(($self->{sudo}? 'sudo' : ()),$^X,'-MExtUtils::Install=install','-e',qq[install({ 'blib/meta' => '$base/$Config{archname}/.meta/$dist->{distvname}' })],);$self->run(\@cmd)}sub _merge_hashref {my($self,@hashrefs)=@_;my%hash;for my$h (@hashrefs){%hash=(%hash,%$h)}return \%hash}sub install_base {my($self,$mm_opt)=@_;$mm_opt =~ /INSTALL_BASE=(\S+)/ and return $1;die "Your PERL_MM_OPT doesn't contain INSTALL_BASE"}sub safe_eval {my($self,$code)=@_;eval$code}sub configure_features {my($self,$dist,@features)=@_;map $_->identifier,grep {$self->effective_feature($dist,$_)}@features}sub effective_feature {my($self,$dist,$feature)=@_;if ($dist->{depth}==0){my$value=$self->{features}{$feature->identifier};return$value if defined$value;return 1 if$self->{features}{__all}}if ($self->{interactive}){require CPAN::Meta::Requirements;$self->diag("[@{[ $feature->description ]}]\n",1);my$req=CPAN::Meta::Requirements->new;for my$phase (@{$dist->{want_phases}}){for my$type (@{$self->{install_types}}){$req->add_requirements($feature->prereqs->requirements_for($phase,$type))}}my$reqs=$req->as_string_hash;my@missing;for my$module (keys %$reqs){if ($self->should_install($module,$req->{$module})){push@missing,$module}}if (@missing){my$howmany=@missing;$self->diag("==> Found missing dependencies: " .join(", ",@missing)."\n",1);local$self->{prompt}=1;return$self->prompt_bool("Install the $howmany optional module(s)?","y")}}return}sub find_prereqs {my($self,$dist)=@_;my@deps=$self->extract_meta_prereqs($dist);if ($dist->{module}=~ /^Bundle::/i){push@deps,$self->bundle_deps($dist)}$self->merge_with_cpanfile($dist,\@deps);return@deps}sub merge_with_cpanfile {my($self,$dist,$deps)=@_;if ($self->{cpanfile_requirements}&&!$dist->{cpanfile}){for my$dep (@$deps){$dep->merge_with($self->{cpanfile_requirements})}}}sub extract_meta_prereqs {my($self,$dist)=@_;if ($dist->{cpanfile}){my@features=$self->configure_features($dist,$dist->{cpanfile}->features);my$prereqs=$dist->{cpanfile}->prereqs_with(@features);$self->{cpanfile_requirements}=$prereqs->merged_requirements($dist->{want_phases},['requires']);return App::cpanminus::Dependency->from_prereqs($prereqs,$dist->{want_phases},$self->{install_types})}require CPAN::Meta;my@deps;my($meta_file)=grep -f,qw(MYMETA.json MYMETA.yml);if ($meta_file){$self->chat("Checking dependencies from $meta_file ...\n");my$mymeta=eval {CPAN::Meta->load_file($meta_file,{lazy_validation=>1 })};if ($mymeta){$dist->{meta}{name}=$mymeta->name;$dist->{meta}{version}=$mymeta->version;return$self->extract_prereqs($mymeta,$dist)}}if (-e '_build/prereqs'){$self->chat("Checking dependencies from _build/prereqs ...\n");my$prereqs=do {open my$in,"_build/prereqs";$self->safe_eval(join "",<$in>)};my$meta=CPAN::Meta->new({name=>$dist->{meta}{name},version=>$dist->{meta}{version},%$prereqs },{lazy_validation=>1 },);@deps=$self->extract_prereqs($meta,$dist)}elsif (-e 'Makefile'){$self->chat("Finding PREREQ from Makefile ...\n");open my$mf,"Makefile";while (<$mf>){if (/^\#\s+PREREQ_PM => \{\s*(.*?)\s*\}/){my@all;my@pairs=split ', ',$1;for (@pairs){my ($pkg,$v)=split '=>',$_;push@all,[$pkg,$v ]}my$list=join ", ",map {"'$_->[0]' => $_->[1]"}@all;my$prereq=$self->safe_eval("no strict; +{ $list }");push@deps,App::cpanminus::Dependency->from_versions($prereq)if$prereq;last}}}return@deps}sub bundle_deps {my($self,$dist)=@_;my$match;if ($dist->{module}){$match=sub {my$meta=Module::Metadata->new_from_file($_[0]);$meta && ($meta->name eq $dist->{module})}}else {$match=sub {1}}my@files;File::Find::find({wanted=>sub {push@files,File::Spec->rel2abs($_)if /\.pm$/i && $match->($_)},no_chdir=>1,},'.');my@deps;for my$file (@files){open my$pod,"<",$file or next;my$in_contents;while (<$pod>){if (/^=head\d\s+CONTENTS/){$in_contents=1}elsif (/^=/){$in_contents=0}elsif ($in_contents){/^(\S+)\s*(\S+)?/ and push@deps,App::cpanminus::Dependency->new($1,$self->maybe_version($2))}}}return@deps}sub maybe_version {my($self,$string)=@_;return$string && $string =~ /^\.?\d/ ? $string : undef}sub extract_prereqs {my($self,$meta,$dist)=@_;my@features=$self->configure_features($dist,$meta->features);my$prereqs=$self->soften_makemaker_prereqs($meta->effective_prereqs(\@features)->clone);return App::cpanminus::Dependency->from_prereqs($prereqs,$dist->{want_phases},$self->{install_types})}sub soften_makemaker_prereqs {my($self,$prereqs)=@_;return$prereqs unless -e "inc/Module/Install.pm";for my$phase (qw(build test runtime)){my$reqs=$prereqs->requirements_for($phase,'requires');if ($reqs->requirements_for_module('ExtUtils::MakeMaker')){$reqs->clear_requirement('ExtUtils::MakeMaker');$reqs->add_minimum('ExtUtils::MakeMaker'=>0)}}$prereqs}sub cleanup_workdirs {my$self=shift;my$expire=time - 24 * 60 * 60 * $self->{auto_cleanup};my@targets;opendir my$dh,"$self->{home}/work";while (my$e=readdir$dh){next if$e !~ /^(\d+)\.\d+$/;my$time=$1;if ($time < $expire){push@targets,"$self->{home}/work/$e"}}if (@targets){if (@targets >= 64){$self->diag("Expiring " .scalar(@targets)." work directories. This might take a while...\n")}else {$self->chat("Expiring " .scalar(@targets)." work directories.\n")}File::Path::rmtree(\@targets,0,0)}}sub scandeps_append_child {my($self,$dist)=@_;my$new_node=[$dist,[]];my$curr_node=$self->{scandeps_current}|| [undef,$self->{scandeps_tree}];push @{$curr_node->[1]},$new_node;$self->{scandeps_current}=$new_node;return sub {$self->{scandeps_current}=$curr_node}}sub dump_scandeps {my$self=shift;if ($self->{format}eq 'tree'){$self->walk_down(sub {my($dist,$depth)=@_;if ($depth==0){print "$dist->{distvname}\n"}else {print " " x ($depth - 1);print "\\_ $dist->{distvname}\n"}},1)}elsif ($self->{format}=~ /^dists?$/){$self->walk_down(sub {my($dist,$depth)=@_;print$self->format_dist($dist),"\n"},0)}elsif ($self->{format}eq 'json'){require JSON::PP;print JSON::PP::encode_json($self->{scandeps_tree})}elsif ($self->{format}eq 'yaml'){require YAML;print YAML::Dump($self->{scandeps_tree})}else {$self->diag("Unknown format: $self->{format}\n")}}sub walk_down {my($self,$cb,$pre)=@_;$self->_do_walk_down($self->{scandeps_tree},$cb,0,$pre)}sub _do_walk_down {my($self,$children,$cb,$depth,$pre)=@_;for my$node (@$children){$cb->($node->[0],$depth)if$pre;$self->_do_walk_down($node->[1],$cb,$depth + 1,$pre);$cb->($node->[0],$depth)unless$pre}}sub DESTROY {my$self=shift;$self->{at_exit}->($self)if$self->{at_exit}}sub shell_quote {my($self,@stuff)=@_;if (WIN32){join ' ',map {/^${quote}.+${quote}$/ ? $_ : ($quote .$_ .$quote)}@stuff}else {String::ShellQuote::shell_quote_best_effort(@stuff)}}sub which {my($self,$name)=@_;if (File::Spec->file_name_is_absolute($name)){if (-x $name &&!-d _){return$name}}my$exe_ext=$Config{_exe};for my$dir (File::Spec->path){my$fullpath=File::Spec->catfile($dir,$name);if ((-x $fullpath || -x ($fullpath .= $exe_ext))&&!-d _){if ($fullpath =~ /\s/){$fullpath=$self->shell_quote($fullpath)}return$fullpath}}return}sub get {my($self,$uri)=@_;if ($uri =~ /^file:/){$self->file_get($uri)}else {$self->{_backends}{get}->(@_)}}sub mirror {my($self,$uri,$local)=@_;if ($uri =~ /^file:/){$self->file_mirror($uri,$local)}else {$self->{_backends}{mirror}->(@_)}}sub untar {$_[0]->{_backends}{untar}->(@_)};sub unzip {$_[0]->{_backends}{unzip}->(@_)};sub uri_to_file {my($self,$uri)=@_;if ($uri =~ s!file:/+!!){$uri="/$uri" unless$uri =~ m![a-zA-Z]:!}return$uri}sub file_get {my($self,$uri)=@_;my$file=$self->uri_to_file($uri);open my$fh,"<$file" or return;join '',<$fh>}sub file_mirror {my($self,$uri,$path)=@_;my$file=$self->uri_to_file($uri);my$source_mtime=(stat$file)[9];return 1 if -e $path && (stat$path)[9]>= $source_mtime;File::Copy::copy($file,$path);utime$source_mtime,$source_mtime,$path}sub has_working_lwp {my($self,$mirrors)=@_;my$https=grep /^https:/,@$mirrors;eval {require LWP::UserAgent;LWP::UserAgent->VERSION(5.802);require LWP::Protocol::https if$https;1}}sub init_tools {my$self=shift;return if$self->{initialized}++;if ($self->{make}=$self->which($Config{make})){$self->chat("You have make $self->{make}\n")}if ($self->{try_lwp}&& $self->has_working_lwp($self->{mirrors})){$self->chat("You have LWP $LWP::VERSION\n");my$ua=sub {LWP::UserAgent->new(parse_head=>0,env_proxy=>1,agent=>$self->agent,timeout=>30,@_,)};$self->{_backends}{get}=sub {my$self=shift;my$res=$ua->()->request(HTTP::Request->new(GET=>$_[0]));return unless$res->is_success;return$res->decoded_content};$self->{_backends}{mirror}=sub {my$self=shift;my$res=$ua->()->mirror(@_);die$res->content if$res->code==501;$res->code}}elsif ($self->{try_wget}and my$wget=$self->which('wget')){$self->chat("You have $wget\n");my@common=('--user-agent',$self->agent,'--retry-connrefused',($self->{verbose}? (): ('-q')),);$self->{_backends}{get}=sub {my($self,$uri)=@_;$self->safeexec(my$fh,$wget,$uri,@common,'-O','-')or die "wget $uri: $!";local $/;<$fh>};$self->{_backends}{mirror}=sub {my($self,$uri,$path)=@_;$self->safeexec(my$fh,$wget,$uri,@common,'-O',$path)or die "wget $uri: $!";local $/;<$fh>}}elsif ($self->{try_curl}and my$curl=$self->which('curl')){$self->chat("You have $curl\n");my@common=('--location','--user-agent',$self->agent,($self->{verbose}? (): '-s'),);$self->{_backends}{get}=sub {my($self,$uri)=@_;$self->safeexec(my$fh,$curl,@common,$uri)or die "curl $uri: $!";local $/;<$fh>};$self->{_backends}{mirror}=sub {my($self,$uri,$path)=@_;$self->safeexec(my$fh,$curl,@common,$uri,'-#','-o',$path)or die "curl $uri: $!";local $/;<$fh>}}else {require HTTP::Tiny;$self->chat("Falling back to HTTP::Tiny $HTTP::Tiny::VERSION\n");my%common=(agent=>$self->agent,);$self->{_backends}{get}=sub {my$self=shift;my$res=HTTP::Tiny->new(%common)->get($_[0]);return unless$res->{success};return$res->{content}};$self->{_backends}{mirror}=sub {my$self=shift;my$res=HTTP::Tiny->new(%common)->mirror(@_);return$res->{status}}}my$tar=$self->which('tar');my$tar_ver;my$maybe_bad_tar=sub {WIN32 || BAD_TAR || (($tar_ver=`$tar --version 2>/dev/null`)=~ /GNU.*1\.13/i)};if ($tar &&!$maybe_bad_tar->()){chomp$tar_ver;$self->chat("You have $tar: $tar_ver\n");$self->{_backends}{untar}=sub {my($self,$tarfile)=@_;my$xf=($self->{verbose}? 'v' : '')."xf";my$ar=$tarfile =~ /bz2$/ ? 'j' : 'z';my($root,@others)=`$tar ${ar}tf $tarfile` or return undef;FILE: {chomp$root;$root =~ s!^\./!!;$root =~ s{^(.+?)/.*$}{$1};if (!length($root)){$root=shift(@others);redo FILE if$root}}system "$tar $ar$xf $tarfile";return$root if -d $root;$self->diag_fail("Bad archive: $tarfile");return undef}}elsif ($tar and my$gzip=$self->which('gzip')and my$bzip2=$self->which('bzip2')){$self->chat("You have $tar, $gzip and $bzip2\n");$self->{_backends}{untar}=sub {my($self,$tarfile)=@_;my$x="x" .($self->{verbose}? 'v' : '')."f -";my$ar=$tarfile =~ /bz2$/ ? $bzip2 : $gzip;my($root,@others)=`$ar -dc $tarfile | $tar tf -` or return undef;FILE: {chomp$root;$root =~ s!^\./!!;$root =~ s{^(.+?)/.*$}{$1};if (!length($root)){$root=shift(@others);redo FILE if$root}}system "$ar -dc $tarfile | $tar $x";return$root if -d $root;$self->diag_fail("Bad archive: $tarfile");return undef}}elsif (eval {require Archive::Tar}){$self->chat("Falling back to Archive::Tar $Archive::Tar::VERSION\n");$self->{_backends}{untar}=sub {my$self=shift;my$t=Archive::Tar->new($_[0]);my($root,@others)=$t->list_files;FILE: {$root =~ s!^\./!!;$root =~ s{^(.+?)/.*$}{$1};if (!length($root)){$root=shift(@others);redo FILE if$root}}$t->extract;return -d $root ? $root : undef}}else {$self->{_backends}{untar}=sub {die "Failed to extract $_[1] - You need to have tar or Archive::Tar installed.\n"}}if (my$unzip=$self->which('unzip')){$self->chat("You have $unzip\n");$self->{_backends}{unzip}=sub {my($self,$zipfile)=@_;my$opt=$self->{verbose}? '' : '-q';my(undef,$root,@others)=`$unzip -t $zipfile` or return undef;FILE: {chomp$root;if ($root !~ s{^\s+testing:\s+([^/]+)/.*?\s+OK$}{$1}){$root=shift(@others);redo FILE if$root}}system "$unzip $opt $zipfile";return$root if -d $root;$self->diag_fail("Bad archive: [$root] $zipfile");return undef}}else {$self->{_backends}{unzip}=sub {eval {require Archive::Zip}or die "Failed to extract $_[1] - You need to have unzip or Archive::Zip installed.\n";my($self,$file)=@_;my$zip=Archive::Zip->new();my$status;$status=$zip->read($file);$self->diag_fail("Read of file[$file] failed")if$status!=Archive::Zip::AZ_OK();my@members=$zip->members();for my$member (@members){my$af=$member->fileName();next if ($af =~ m!^(/|\.\./)!);$status=$member->extractToFileNamed($af);$self->diag_fail("Extracting of file[$af] from zipfile[$file failed")if$status!=Archive::Zip::AZ_OK()}my ($root)=$zip->membersMatching(qr<^[^/]+/$>);$root &&= $root->fileName;return -d $root ? $root : undef}}}sub safeexec {my$self=shift;my$rdr=$_[0]||= Symbol::gensym();if (WIN32){my$cmd=$self->shell_quote(@_[1..$#_]);return open($rdr,"$cmd |")}if (my$pid=open($rdr,'-|')){return$pid}elsif (defined$pid){exec(@_[1 .. $#_ ]);exit 1}else {return}}sub mask_uri_passwords {my($self,@strings)=@_;s{ (https?://) ([^:/]+) : [^@/]+ @ }{$1$2:********@}gx for@strings;return@strings}1;
+  It appears your cpanm executable was installed via `perlbrew install-cpanm`.
+  cpanm --self-upgrade won't upgrade the version of cpanm you're running.
+  
+  Run the following command to get it upgraded.
+  
+    perlbrew install-cpanm
+  
+  DIE
+  You are running cpanm from the path where your current perl won't install executables to.
+  Because of that, cpanm --self-upgrade won't upgrade the version of cpanm you're running.
+  
+    cpanm path   : $0
+    Install path : $Config{installsitebin}
+  
+  It means you either installed cpanm globally with system perl, or use distro packages such
+  as rpm or apt-get, and you have to use them again to upgrade cpanm.
+  DIE
+  Usage: cpanm [options] Module [...]
+  
+  Try `cpanm --help` or `man cpanm` for more options.
+  USAGE
+  Usage: cpanm [options] Module [...]
+  
+  Options:
+    -v,--verbose              Turns on chatty output
+    -q,--quiet                Turns off the most output
+    --interactive             Turns on interactive configure (required for Task:: modules)
+    -f,--force                force install
+    -n,--notest               Do not run unit tests
+    --test-only               Run tests only, do not install
+    -S,--sudo                 sudo to run install commands
+    --installdeps             Only install dependencies
+    --showdeps                Only display direct dependencies
+    --reinstall               Reinstall the distribution even if you already have the latest version installed
+    --mirror                  Specify the base URL for the mirror (e.g. http://cpan.cpantesters.org/)
+    --mirror-only             Use the mirror's index file instead of the CPAN Meta DB
+    -M,--from                 Use only this mirror base URL and its index file
+    --prompt                  Prompt when configure/build/test fails
+    -l,--local-lib            Specify the install base to install modules
+    -L,--local-lib-contained  Specify the install base to install all non-core modules
+    --self-contained          Install all non-core modules, even if they're already installed.
+    --auto-cleanup            Number of days that cpanm's work directories expire in. Defaults to 7
+  
+  Commands:
+    --self-upgrade            upgrades itself
+    --info                    Displays distribution info on CPAN
+    --look                    Opens the distribution with your SHELL
+    -U,--uninstall            Uninstalls the modules (EXPERIMENTAL)
+    -V,--version              Displays software version
+  
+  Examples:
+  
+    cpanm Test::More                                          # install Test::More
+    cpanm MIYAGAWA/Plack-0.99_05.tar.gz                       # full distribution path
+    cpanm http://example.org/LDS/CGI.pm-3.20.tar.gz           # install from URL
+    cpanm ~/dists/MyCompany-Enterprise-1.00.tar.gz            # install from a local file
+    cpanm --interactive Task::Kensho                          # Configure interactively
+    cpanm .                                                   # install from local directory
+    cpanm --installdeps .                                     # install all the deps for the current directory
+    cpanm -L extlib Plack                                     # install Plack and all non-core deps into extlib
+    cpanm --mirror http://cpan.cpantesters.org/ DBI           # use the fast-syncing mirror
+    cpanm -M https://cpan.metacpan.org App::perlbrew          # use only this secure mirror and its index
+  
+  You can also specify the default options in PERL_CPANM_OPT environment variable in the shell rc:
+  
+    export PERL_CPANM_OPT="--prompt --reinstall -l ~/perl --mirror http://cpan.cpantesters.org"
+  
+  Type `man cpanm` or `perldoc cpanm` for the more detailed explanation of the options.
+  
+  HELP
+  !
+  ! Can't write to $Config{installsitelib} and $Config{installsitebin}: Installing modules to $ENV{HOME}/perl5
+  ! To turn off this warning, you have to do one of the following:
+  !   - run me as a root or with --sudo option (to install to $Config{installsitelib} and $Config{installsitebin})
+  !   - Configure local::lib in your existing shell to set PERL_MM_OPT etc.
+  !   - Install local::lib by running the following commands
+  !
+  !         cpanm --local-lib=~/perl5 local::lib && eval \$(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
+  !
+  DIAG
+  WARNING: Your lib directory name ($base) contains a space in it. It's known to cause issues with perl builder tools such as local::lib and MakeMaker. You're recommended to rename your directory.
+  WARN
+  $module is not found in the following directories and can't be uninstalled.
+  
+  @{[ join("  \n", map "  $_", @inc) ]}
+  
+  DIAG
+  package ModuleBuildSkipMan;
+  CHECK {
+    if (%Module::Build::) {
+      no warnings 'redefine';
+      *Module::Build::Base::ACTION_manpages = sub {};
+      *Module::Build::Base::ACTION_docs     = sub {};
+    }
+  }
+  1;
+  EOF
+  ! Configuring $distname failed. See $self->{log} for details.
+  ! You might have to install the following modules first to get --scandeps working correctly.
+  DIAG
+APP_CPANMINUS_SCRIPT
+
+$fatpacked{"CPAN/DistnameInfo.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_DISTNAMEINFO';
+  package CPAN::DistnameInfo;$VERSION="0.12";use strict;sub distname_info {my$file=shift or return;my ($dist,$version)=$file =~ /^
+      ((?:[-+.]*(?:[A-Za-z0-9]+|(?<=\D)_|_(?=\D))*
+       (?:
+       [A-Za-z](?=[^A-Za-z]|$)
+       |
+       \d(?=-)
+       )(?<![._-][vV])
+      )+)(.*)
+    $/xs or return ($file,undef,undef);if ($dist =~ /-undef\z/ and!length$version){$dist =~ s/-undef\z//}$version =~ s/-withoutworldwriteables$//;if ($version =~ /^(-[Vv].*)-(\d.*)/){$dist .= $1;$version=$2}if ($version =~ /(.+_.*)-(\d.*)/){$dist .= $1;$version=$2}$dist =~ s{\.pm$}{};$version=$1 if!length$version and $dist =~ s/-(\d+\w)$//;$version=$1 .$version if$version =~ /^\d+$/ and $dist =~ s/-(\w+)$//;if ($version =~ /\d\.\d/){$version =~ s/^[-_.]+//}else {$version =~ s/^[-_]+//}my$dev;if (length$version){if ($file =~ /^perl-?\d+\.(\d+)(?:\D(\d+))?(-(?:TRIAL|RC)\d+)?$/){$dev=1 if (($1 > 6 and $1 & 1)or ($2 and $2 >= 50))or $3}elsif ($version =~ /\d\D\d+_\d/ or $version =~ /-TRIAL/){$dev=1}}else {$version=undef}($dist,$version,$dev)}sub new {my$class=shift;my$distfile=shift;$distfile =~ s,//+,/,g;my%info=(pathname=>$distfile);($info{filename}=$distfile)=~ s,^(((.*?/)?authors/)?id/)?([A-Z])/(\4[A-Z])/(\5[-A-Z0-9]*)/,, and $info{cpanid}=$6;if ($distfile =~ m,([^/]+)\.(tar\.(?:g?z|bz2)|zip|tgz)$,i){$info{distvname}=$1;$info{extension}=$2}@info{qw(dist version beta)}=distname_info($info{distvname});$info{maturity}=delete$info{beta}? 'developer' : 'released';return bless \%info,$class}sub dist {shift->{dist}}sub version {shift->{version}}sub maturity {shift->{maturity}}sub filename {shift->{filename}}sub cpanid {shift->{cpanid}}sub distvname {shift->{distvname}}sub extension {shift->{extension}}sub pathname {shift->{pathname}}sub properties {%{$_[0]}}1;
+CPAN_DISTNAMEINFO
+
+$fatpacked{"CPAN/Meta.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META';
+  use 5.006;use strict;use warnings;package CPAN::Meta;our$VERSION='2.150005';use Carp qw(carp croak);use CPAN::Meta::Feature;use CPAN::Meta::Prereqs;use CPAN::Meta::Converter;use CPAN::Meta::Validator;use Parse::CPAN::Meta 1.4414 ();BEGIN {*_dclone=\&CPAN::Meta::Converter::_dclone}BEGIN {my@STRING_READERS=qw(abstract description dynamic_config generated_by name release_status version);no strict 'refs';for my$attr (@STRING_READERS){*$attr=sub {$_[0]{$attr }}}}BEGIN {my@LIST_READERS=qw(author keywords license);no strict 'refs';for my$attr (@LIST_READERS){*$attr=sub {my$value=$_[0]{$attr };croak "$attr must be called in list context" unless wantarray;return @{_dclone($value)}if ref$value;return$value}}}sub authors {$_[0]->author}sub licenses {$_[0]->license}BEGIN {my@MAP_READERS=qw(meta-spec resources provides no_index prereqs optional_features);no strict 'refs';for my$attr (@MAP_READERS){(my$subname=$attr)=~ s/-/_/;*$subname=sub {my$value=$_[0]{$attr };return _dclone($value)if$value;return {}}}}sub custom_keys {return grep {/^x_/i}keys %{$_[0]}}sub custom {my ($self,$attr)=@_;my$value=$self->{$attr};return _dclone($value)if ref$value;return$value}sub _new {my ($class,$struct,$options)=@_;my$self;if ($options->{lazy_validation}){my$cmc=CPAN::Meta::Converter->new($struct);$self=$cmc->convert(version=>2);return bless$self,$class}else {my$cmv=CPAN::Meta::Validator->new($struct);unless ($cmv->is_valid){die "Invalid metadata structure. Errors: " .join(", ",$cmv->errors)."\n"}}my$version=$struct->{'meta-spec'}{version}|| '1.0';if ($version==2){$self=$struct}else {my$cmc=CPAN::Meta::Converter->new($struct);$self=$cmc->convert(version=>2)}return bless$self,$class}sub new {my ($class,$struct,$options)=@_;my$self=eval {$class->_new($struct,$options)};croak($@)if $@;return$self}sub create {my ($class,$struct,$options)=@_;my$version=__PACKAGE__->VERSION || 2;$struct->{generated_by}||= __PACKAGE__ ." version $version" ;$struct->{'meta-spec'}{version}||= int($version);my$self=eval {$class->_new($struct,$options)};croak ($@)if $@;return$self}sub load_file {my ($class,$file,$options)=@_;$options->{lazy_validation}=1 unless exists$options->{lazy_validation};croak "load_file() requires a valid, readable filename" unless -r $file;my$self;eval {my$struct=Parse::CPAN::Meta->load_file($file);$self=$class->_new($struct,$options)};croak($@)if $@;return$self}sub load_yaml_string {my ($class,$yaml,$options)=@_;$options->{lazy_validation}=1 unless exists$options->{lazy_validation};my$self;eval {my ($struct)=Parse::CPAN::Meta->load_yaml_string($yaml);$self=$class->_new($struct,$options)};croak($@)if $@;return$self}sub load_json_string {my ($class,$json,$options)=@_;$options->{lazy_validation}=1 unless exists$options->{lazy_validation};my$self;eval {my$struct=Parse::CPAN::Meta->load_json_string($json);$self=$class->_new($struct,$options)};croak($@)if $@;return$self}sub load_string {my ($class,$string,$options)=@_;$options->{lazy_validation}=1 unless exists$options->{lazy_validation};my$self;eval {my$struct=Parse::CPAN::Meta->load_string($string);$self=$class->_new($struct,$options)};croak($@)if $@;return$self}sub save {my ($self,$file,$options)=@_;my$version=$options->{version}|| '2';my$layer=$] ge '5.008001' ? ':utf8' : '';if ($version ge '2'){carp "'$file' should end in '.json'" unless$file =~ m{\.json$}}else {carp "'$file' should end in '.yml'" unless$file =~ m{\.yml$}}my$data=$self->as_string($options);open my$fh,">$layer",$file or die "Error opening '$file' for writing: $!\n";print {$fh}$data;close$fh or die "Error closing '$file': $!\n";return 1}sub meta_spec_version {my ($self)=@_;return$self->meta_spec->{version}}sub effective_prereqs {my ($self,$features)=@_;$features ||= [];my$prereq=CPAN::Meta::Prereqs->new($self->prereqs);return$prereq unless @$features;my@other=map {;$self->feature($_)->prereqs}@$features;return$prereq->with_merged_prereqs(\@other)}sub should_index_file {my ($self,$filename)=@_;for my$no_index_file (@{$self->no_index->{file}|| []}){return if$filename eq $no_index_file}for my$no_index_dir (@{$self->no_index->{directory}}){$no_index_dir =~ s{$}{/} unless$no_index_dir =~ m{/\z};return if index($filename,$no_index_dir)==0}return 1}sub should_index_package {my ($self,$package)=@_;for my$no_index_pkg (@{$self->no_index->{package}|| []}){return if$package eq $no_index_pkg}for my$no_index_ns (@{$self->no_index->{namespace}}){return if index($package,"${no_index_ns}::")==0}return 1}sub features {my ($self)=@_;my$opt_f=$self->optional_features;my@features=map {;CPAN::Meta::Feature->new($_=>$opt_f->{$_ })}keys %$opt_f;return@features}sub feature {my ($self,$ident)=@_;croak "no feature named $ident" unless my$f=$self->optional_features->{$ident };return CPAN::Meta::Feature->new($ident,$f)}sub as_struct {my ($self,$options)=@_;my$struct=_dclone($self);if ($options->{version}){my$cmc=CPAN::Meta::Converter->new($struct);$struct=$cmc->convert(version=>$options->{version})}return$struct}sub as_string {my ($self,$options)=@_;my$version=$options->{version}|| '2';my$struct;if ($self->meta_spec_version ne $version){my$cmc=CPAN::Meta::Converter->new($self->as_struct);$struct=$cmc->convert(version=>$version)}else {$struct=$self->as_struct}my ($data,$backend);if ($version ge '2'){$backend=Parse::CPAN::Meta->json_backend();local$struct->{x_serialization_backend}=sprintf '%s version %s',$backend,$backend->VERSION;$data=$backend->new->pretty->canonical->encode($struct)}else {$backend=Parse::CPAN::Meta->yaml_backend();local$struct->{x_serialization_backend}=sprintf '%s version %s',$backend,$backend->VERSION;$data=eval {no strict 'refs';&{"$backend\::Dump"}($struct)};if ($@){croak$backend->can('errstr')? $backend->errstr : $@}}return$data}sub TO_JSON {return {%{$_[0]}}}1;
+CPAN_META
+
+$fatpacked{"CPAN/Meta/Check.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_CHECK';
+  package CPAN::Meta::Check;$CPAN::Meta::Check::VERSION='0.012';use strict;use warnings;use base 'Exporter';our@EXPORT=qw//;our@EXPORT_OK=qw/check_requirements requirements_for verify_dependencies/;our%EXPORT_TAGS=(all=>[@EXPORT,@EXPORT_OK ]);use CPAN::Meta::Prereqs '2.132830';use CPAN::Meta::Requirements 2.121;use Module::Metadata 1.000023;sub _check_dep {my ($reqs,$module,$dirs)=@_;$module eq 'perl' and return ($reqs->accepts_module($module,$])? (): sprintf "Your Perl (%s) is not in the range '%s'",$],$reqs->requirements_for_module($module));my$metadata=Module::Metadata->new_from_module($module,inc=>$dirs);return "Module '$module' is not installed" if not defined$metadata;my$version=eval {$metadata->version};return "Missing version info for module '$module'" if$reqs->requirements_for_module($module)and not $version;return sprintf 'Installed version (%s) of %s is not in range \'%s\'',$version,$module,$reqs->requirements_for_module($module)if not $reqs->accepts_module($module,$version || 0);return}sub _check_conflict {my ($reqs,$module,$dirs)=@_;my$metadata=Module::Metadata->new_from_module($module,inc=>$dirs);return if not defined$metadata;my$version=eval {$metadata->version};return "Missing version info for module '$module'" if not $version;return sprintf 'Installed version (%s) of %s is in range \'%s\'',$version,$module,$reqs->requirements_for_module($module)if$reqs->accepts_module($module,$version);return}sub requirements_for {my ($meta,$phases,$type)=@_;my$prereqs=ref($meta)eq 'CPAN::Meta' ? $meta->effective_prereqs : $meta;return$prereqs->merged_requirements(ref($phases)? $phases : [$phases ],[$type ])}sub check_requirements {my ($reqs,$type,$dirs)=@_;return +{map {$_=>$type ne 'conflicts' ? scalar _check_dep($reqs,$_,$dirs): scalar _check_conflict($reqs,$_,$dirs)}$reqs->required_modules }}sub verify_dependencies {my ($meta,$phases,$type,$dirs)=@_;my$reqs=requirements_for($meta,$phases,$type);my$issues=check_requirements($reqs,$type,$dirs);return grep {defined}values %{$issues}}1;
+CPAN_META_CHECK
+
+$fatpacked{"CPAN/Meta/Converter.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_CONVERTER';
+  use 5.006;use strict;use warnings;package CPAN::Meta::Converter;our$VERSION='2.150005';use CPAN::Meta::Validator;use CPAN::Meta::Requirements;use Parse::CPAN::Meta 1.4400 ();BEGIN {eval "use version ()";if (my$err=$@){eval "use ExtUtils::MakeMaker::version" or die$err}}*_is_qv=version->can('is_qv')? sub {$_[0]->is_qv}: sub {exists $_[0]->{qv}};sub _dclone {my$ref=shift;no warnings 'once';no warnings 'redefine';local*UNIVERSAL::TO_JSON=sub {"$_[0]"};my$json=Parse::CPAN::Meta->json_backend()->new ->utf8 ->allow_blessed ->convert_blessed;$json->decode($json->encode($ref))}my%known_specs=('2'=>'http://search.cpan.org/perldoc?CPAN::Meta::Spec','1.4'=>'http://module-build.sourceforge.net/META-spec-v1.4.html','1.3'=>'http://module-build.sourceforge.net/META-spec-v1.3.html','1.2'=>'http://module-build.sourceforge.net/META-spec-v1.2.html','1.1'=>'http://module-build.sourceforge.net/META-spec-v1.1.html','1.0'=>'http://module-build.sourceforge.net/META-spec-v1.0.html');my@spec_list=sort {$a <=> $b}keys%known_specs;my ($LOWEST,$HIGHEST)=@spec_list[0,-1];sub _keep {$_[0]}sub _keep_or_one {defined($_[0])? $_[0]: 1}sub _keep_or_zero {defined($_[0])? $_[0]: 0}sub _keep_or_unknown {defined($_[0])&& length($_[0])? $_[0]: "unknown"}sub _generated_by {my$gen=shift;my$sig=__PACKAGE__ ." version " .(__PACKAGE__->VERSION || "<dev>");return$sig unless defined$gen and length$gen;return$gen if$gen =~ /\Q$sig/;return "$gen, $sig"}sub _listify {!defined $_[0]? undef : ref $_[0]eq 'ARRAY' ? $_[0]: [$_[0]]}sub _prefix_custom {my$key=shift;$key =~ s/^(?!x_)   # Unless it already starts with x_
+               (?:x-?)? # Remove leading x- or x (if present)
+             /x_/ix;return$key}sub _ucfirst_custom {my$key=shift;$key=ucfirst$key unless$key =~ /[A-Z]/;return$key}sub _no_prefix_ucfirst_custom {my$key=shift;$key =~ s/^x_//;return _ucfirst_custom($key)}sub _change_meta_spec {my ($element,undef,undef,$version)=@_;return {version=>$version,url=>$known_specs{$version},}}my@open_source=('perl','gpl','apache','artistic','artistic_2','lgpl','bsd','gpl','mit','mozilla','open_source',);my%is_open_source=map {;$_=>1}@open_source;my@valid_licenses_1=(@open_source,'unrestricted','restrictive','unknown',);my%license_map_1=((map {$_=>$_}@valid_licenses_1),artistic2=>'artistic_2',);sub _license_1 {my ($element)=@_;return 'unknown' unless defined$element;if ($license_map_1{lc$element}){return$license_map_1{lc$element}}else {return 'unknown'}}my@valid_licenses_2=qw(agpl_3 apache_1_1 apache_2_0 artistic_1 artistic_2 bsd freebsd gfdl_1_2 gfdl_1_3 gpl_1 gpl_2 gpl_3 lgpl_2_1 lgpl_3_0 mit mozilla_1_0 mozilla_1_1 openssl perl_5 qpl_1_0 ssleay sun zlib open_source restricted unrestricted unknown);my%license_map_2=((map {$_=>$_}@valid_licenses_2),apache=>'apache_2_0',artistic=>'artistic_1',artistic2=>'artistic_2',gpl=>'open_source',lgpl=>'open_source',mozilla=>'open_source',perl=>'perl_5',restrictive=>'restricted',);sub _license_2 {my ($element)=@_;return ['unknown' ]unless defined$element;$element=[$element ]unless ref$element eq 'ARRAY';my@new_list;for my$lic (@$element){next unless defined$lic;if (my$new=$license_map_2{lc$lic}){push@new_list,$new}}return@new_list ? \@new_list : ['unknown' ]}my%license_downgrade_map=qw(agpl_3 open_source apache_1_1 apache apache_2_0 apache artistic_1 artistic artistic_2 artistic_2 bsd bsd freebsd open_source gfdl_1_2 open_source gfdl_1_3 open_source gpl_1 gpl gpl_2 gpl gpl_3 gpl lgpl_2_1 lgpl lgpl_3_0 lgpl mit mit mozilla_1_0 mozilla mozilla_1_1 mozilla openssl open_source perl_5 perl qpl_1_0 open_source ssleay open_source sun open_source zlib open_source open_source open_source restricted restrictive unrestricted unrestricted unknown unknown);sub _downgrade_license {my ($element)=@_;if (!defined$element){return "unknown"}elsif(ref$element eq 'ARRAY'){if (@$element > 1){if (grep {!$is_open_source{$license_downgrade_map{lc $_}|| 'unknown' }}@$element){return 'unknown'}else {return 'open_source'}}elsif (@$element==1){return$license_downgrade_map{lc$element->[0]}|| "unknown"}}elsif (!ref$element){return$license_downgrade_map{lc$element}|| "unknown"}return "unknown"}my$no_index_spec_1_2={'file'=>\&_listify,'dir'=>\&_listify,'package'=>\&_listify,'namespace'=>\&_listify,};my$no_index_spec_1_3={'file'=>\&_listify,'directory'=>\&_listify,'package'=>\&_listify,'namespace'=>\&_listify,};my$no_index_spec_2={'file'=>\&_listify,'directory'=>\&_listify,'package'=>\&_listify,'namespace'=>\&_listify,':custom'=>\&_prefix_custom,};sub _no_index_1_2 {my (undef,undef,$meta)=@_;my$no_index=$meta->{no_index}|| $meta->{private};return unless$no_index;if (!ref$no_index){my$item=$no_index;$no_index={dir=>[$item ],file=>[$item ]}}elsif (ref$no_index eq 'ARRAY'){my$list=$no_index;$no_index={dir=>[@$list ],file=>[@$list ]}}if (exists$no_index->{files}){$no_index->{file}=delete$no_index->{files}}if (exists$no_index->{modules}){$no_index->{module}=delete$no_index->{modules}}return _convert($no_index,$no_index_spec_1_2)}sub _no_index_directory {my ($element,$key,$meta,$version)=@_;return unless$element;if (!ref$element){my$item=$element;$element={directory=>[$item ],file=>[$item ]}}elsif (ref$element eq 'ARRAY'){my$list=$element;$element={directory=>[@$list ],file=>[@$list ]}}if (exists$element->{dir}){$element->{directory}=delete$element->{dir}}if (exists$element->{files}){$element->{file}=delete$element->{files}}if (exists$element->{modules}){$element->{module}=delete$element->{modules}}my$spec=$version==2 ? $no_index_spec_2 : $no_index_spec_1_3;return _convert($element,$spec)}sub _is_module_name {my$mod=shift;return unless defined$mod && length$mod;return$mod =~ m{^[A-Za-z][A-Za-z0-9_]*(?:::[A-Za-z0-9_]+)*$}}sub _clean_version {my ($element)=@_;return 0 if!defined$element;$element =~ s{^\s*}{};$element =~ s{\s*$}{};$element =~ s{^\.}{0.};return 0 if!length$element;return 0 if ($element eq 'undef' || $element eq '<undef>');my$v=eval {version->new($element)};if (defined$v){return _is_qv($v)? $v->normal : $element}else {return 0}}sub _bad_version_hook {my ($v)=@_;$v =~ s{^\s*}{};$v =~ s{\s*$}{};$v =~ s{[a-z]+$}{};my$vobj=eval {version->new($v)};return defined($vobj)? $vobj : version->new(0)}sub _version_map {my ($element)=@_;return unless defined$element;if (ref$element eq 'HASH'){my$new_map=CPAN::Meta::Requirements->new({bad_version_hook=>\&_bad_version_hook });while (my ($k,$v)=each %$element){next unless _is_module_name($k);if (!defined($v)||!length($v)|| $v eq 'undef' || $v eq '<undef>'){$v=0}if (_is_module_name($v)&&!version::is_lax($v)){$new_map->add_minimum($k=>0);$new_map->add_minimum($v=>0)}$new_map->add_string_requirement($k=>$v)}return$new_map->as_string_hash}elsif (ref$element eq 'ARRAY'){my$hashref={map {$_=>0}@$element };return _version_map($hashref)}elsif (ref$element eq '' && length$element){return {$element=>0 }}return}sub _prereqs_from_1 {my (undef,undef,$meta)=@_;my$prereqs={};for my$phase (qw/build configure/){my$key="${phase}_requires";$prereqs->{$phase}{requires}=_version_map($meta->{$key})if$meta->{$key}}for my$rel (qw/requires recommends conflicts/){$prereqs->{runtime}{$rel}=_version_map($meta->{$rel})if$meta->{$rel}}return$prereqs}my$prereqs_spec={configure=>\&_prereqs_rel,build=>\&_prereqs_rel,test=>\&_prereqs_rel,runtime=>\&_prereqs_rel,develop=>\&_prereqs_rel,':custom'=>\&_prefix_custom,};my$relation_spec={requires=>\&_version_map,recommends=>\&_version_map,suggests=>\&_version_map,conflicts=>\&_version_map,':custom'=>\&_prefix_custom,};sub _cleanup_prereqs {my ($prereqs,$key,$meta,$to_version)=@_;return unless$prereqs && ref$prereqs eq 'HASH';return _convert($prereqs,$prereqs_spec,$to_version)}sub _prereqs_rel {my ($relation,$key,$meta,$to_version)=@_;return unless$relation && ref$relation eq 'HASH';return _convert($relation,$relation_spec,$to_version)}BEGIN {my@old_prereqs=qw(requires configure_requires recommends conflicts);for (@old_prereqs){my$sub="_get_$_";my ($phase,$type)=split qr/_/,$_;if (!defined$type){$type=$phase;$phase='runtime'}no strict 'refs';*{$sub}=sub {_extract_prereqs($_[2]->{prereqs},$phase,$type)}}}sub _get_build_requires {my ($data,$key,$meta)=@_;my$test_h=_extract_prereqs($_[2]->{prereqs},qw(test requires))|| {};my$build_h=_extract_prereqs($_[2]->{prereqs},qw(build requires))|| {};my$test_req=CPAN::Meta::Requirements->from_string_hash($test_h);my$build_req=CPAN::Meta::Requirements->from_string_hash($build_h);$test_req->add_requirements($build_req)->as_string_hash}sub _extract_prereqs {my ($prereqs,$phase,$type)=@_;return unless ref$prereqs eq 'HASH';return scalar _version_map($prereqs->{$phase}{$type})}sub _downgrade_optional_features {my (undef,undef,$meta)=@_;return unless exists$meta->{optional_features};my$origin=$meta->{optional_features};my$features={};for my$name (keys %$origin){$features->{$name}={description=>$origin->{$name}{description},requires=>_extract_prereqs($origin->{$name}{prereqs},'runtime','requires'),configure_requires=>_extract_prereqs($origin->{$name}{prereqs},'runtime','configure_requires'),build_requires=>_extract_prereqs($origin->{$name}{prereqs},'runtime','build_requires'),recommends=>_extract_prereqs($origin->{$name}{prereqs},'runtime','recommends'),conflicts=>_extract_prereqs($origin->{$name}{prereqs},'runtime','conflicts'),};for my$k (keys %{$features->{$name}}){delete$features->{$name}{$k}unless defined$features->{$name}{$k}}}return$features}sub _upgrade_optional_features {my (undef,undef,$meta)=@_;return unless exists$meta->{optional_features};my$origin=$meta->{optional_features};my$features={};for my$name (keys %$origin){$features->{$name}={description=>$origin->{$name}{description},prereqs=>_prereqs_from_1(undef,undef,$origin->{$name}),};delete$features->{$name}{prereqs}{configure}}return$features}my$optional_features_2_spec={description=>\&_keep,prereqs=>\&_cleanup_prereqs,':custom'=>\&_prefix_custom,};sub _feature_2 {my ($element,$key,$meta,$to_version)=@_;return unless$element && ref$element eq 'HASH';_convert($element,$optional_features_2_spec,$to_version)}sub _cleanup_optional_features_2 {my ($element,$key,$meta,$to_version)=@_;return unless$element && ref$element eq 'HASH';my$new_data={};for my$k (keys %$element){$new_data->{$k}=_feature_2($element->{$k},$k,$meta,$to_version)}return unless keys %$new_data;return$new_data}sub _optional_features_1_4 {my ($element)=@_;return unless$element;$element=_optional_features_as_map($element);for my$name (keys %$element){for my$drop (qw/requires_packages requires_os excluded_os/){delete$element->{$name}{$drop}}}return$element}sub _optional_features_as_map {my ($element)=@_;return unless$element;if (ref$element eq 'ARRAY'){my%map;for my$feature (@$element){my (@parts)=%$feature;$map{$parts[0]}=$parts[1]}$element=\%map}return$element}sub _is_urlish {defined $_[0]&& $_[0]=~ m{\A[-+.a-z0-9]+:.+}i}sub _url_or_drop {my ($element)=@_;return$element if _is_urlish($element);return}sub _url_list {my ($element)=@_;return unless$element;$element=_listify($element);$element=[grep {_is_urlish($_)}@$element ];return unless @$element;return$element}sub _author_list {my ($element)=@_;return ['unknown' ]unless$element;$element=_listify($element);$element=[map {defined $_ && length $_ ? $_ : 'unknown'}@$element ];return ['unknown' ]unless @$element;return$element}my$resource2_upgrade={license=>sub {return _is_urlish($_[0])? _listify($_[0]): undef},homepage=>\&_url_or_drop,bugtracker=>sub {my ($item)=@_;return unless$item;if ($item =~ m{^mailto:(.*)$}){return {mailto=>$1 }}elsif(_is_urlish($item)){return {web=>$item }}else {return}},repository=>sub {return _is_urlish($_[0])? {url=>$_[0]}: undef},':custom'=>\&_prefix_custom,};sub _upgrade_resources_2 {my (undef,undef,$meta,$version)=@_;return unless exists$meta->{resources};return _convert($meta->{resources},$resource2_upgrade)}my$bugtracker2_spec={web=>\&_url_or_drop,mailto=>\&_keep,':custom'=>\&_prefix_custom,};sub _repo_type {my ($element,$key,$meta,$to_version)=@_;return$element if defined$element;return unless exists$meta->{url};my$repo_url=$meta->{url};for my$type (qw/git svn/){return$type if$repo_url =~ m{\A$type}}return}my$repository2_spec={web=>\&_url_or_drop,url=>\&_url_or_drop,type=>\&_repo_type,':custom'=>\&_prefix_custom,};my$resources2_cleanup={license=>\&_url_list,homepage=>\&_url_or_drop,bugtracker=>sub {ref $_[0]? _convert($_[0],$bugtracker2_spec): undef},repository=>sub {my$data=shift;ref$data ? _convert($data,$repository2_spec): undef},':custom'=>\&_prefix_custom,};sub _cleanup_resources_2 {my ($resources,$key,$meta,$to_version)=@_;return unless$resources && ref$resources eq 'HASH';return _convert($resources,$resources2_cleanup,$to_version)}my$resource1_spec={license=>\&_url_or_drop,homepage=>\&_url_or_drop,bugtracker=>\&_url_or_drop,repository=>\&_url_or_drop,':custom'=>\&_keep,};sub _resources_1_3 {my (undef,undef,$meta,$version)=@_;return unless exists$meta->{resources};return _convert($meta->{resources},$resource1_spec)}*_resources_1_4=*_resources_1_3;sub _resources_1_2 {my (undef,undef,$meta)=@_;my$resources=$meta->{resources}|| {};if ($meta->{license_url}&&!$resources->{license}){$resources->{license}=$meta->{license_url}if _is_urlish($meta->{license_url})}return unless keys %$resources;return _convert($resources,$resource1_spec)}my$resource_downgrade_spec={license=>sub {return ref $_[0]? $_[0]->[0]: $_[0]},homepage=>\&_url_or_drop,bugtracker=>sub {return $_[0]->{web}},repository=>sub {return $_[0]->{url}|| $_[0]->{web}},':custom'=>\&_no_prefix_ucfirst_custom,};sub _downgrade_resources {my (undef,undef,$meta,$version)=@_;return unless exists$meta->{resources};return _convert($meta->{resources},$resource_downgrade_spec)}sub _release_status {my ($element,undef,$meta)=@_;return$element if$element && $element =~ m{\A(?:stable|testing|unstable)\z};return _release_status_from_version(undef,undef,$meta)}sub _release_status_from_version {my (undef,undef,$meta)=@_;my$version=$meta->{version}|| '';return ($version =~ /_/)? 'testing' : 'stable'}my$provides_spec={file=>\&_keep,version=>\&_keep,};my$provides_spec_2={file=>\&_keep,version=>\&_keep,':custom'=>\&_prefix_custom,};sub _provides {my ($element,$key,$meta,$to_version)=@_;return unless defined$element && ref$element eq 'HASH';my$spec=$to_version==2 ? $provides_spec_2 : $provides_spec;my$new_data={};for my$k (keys %$element){$new_data->{$k}=_convert($element->{$k},$spec,$to_version);$new_data->{$k}{version}=_clean_version($element->{$k}{version})if exists$element->{$k}{version}}return$new_data}sub _convert {my ($data,$spec,$to_version,$is_fragment)=@_;my$new_data={};for my$key (keys %$spec){next if$key eq ':custom' || $key eq ':drop';next unless my$fcn=$spec->{$key};if ($is_fragment && $key eq 'generated_by'){$fcn=\&_keep}die "spec for '$key' is not a coderef" unless ref$fcn && ref$fcn eq 'CODE';my$new_value=$fcn->($data->{$key},$key,$data,$to_version);$new_data->{$key}=$new_value if defined$new_value}my$drop_list=$spec->{':drop'};my$customizer=$spec->{':custom'}|| \&_keep;for my$key (keys %$data){next if$drop_list && grep {$key eq $_}@$drop_list;next if exists$spec->{$key};$new_data->{$customizer->($key)}=$data->{$key}}return$new_data}my%up_convert=('2-from-1.4'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_2,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'release_status'=>\&_release_status,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_upgrade_optional_features,'provides'=>\&_provides,'resources'=>\&_upgrade_resources_2,'description'=>\&_keep,'prereqs'=>\&_prereqs_from_1,':drop'=>[qw(build_requires configure_requires conflicts distribution_type license_url private recommends requires) ],':custom'=>\&_prefix_custom,},'1.4-from-1.3'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_optional_features_1_4,'provides'=>\&_provides,'recommends'=>\&_version_map,'requires'=>\&_version_map,'resources'=>\&_resources_1_4,'configure_requires'=>\&_keep,':drop'=>[qw(license_url private)],':custom'=>\&_keep },'1.3-from-1.2'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_optional_features_as_map,'provides'=>\&_provides,'recommends'=>\&_version_map,'requires'=>\&_version_map,'resources'=>\&_resources_1_3,':drop'=>[qw(license_url private)],':custom'=>\&_keep },'1.2-from-1.1'=>{'version'=>\&_keep,'license'=>\&_license_1,'name'=>\&_keep,'generated_by'=>\&_generated_by,'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'meta-spec'=>\&_change_meta_spec,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'recommends'=>\&_version_map,'requires'=>\&_version_map,'keywords'=>\&_keep,'no_index'=>\&_no_index_1_2,'optional_features'=>\&_optional_features_as_map,'provides'=>\&_provides,'resources'=>\&_resources_1_2,':drop'=>[qw(license_url private)],':custom'=>\&_keep },'1.1-from-1.0'=>{'version'=>\&_keep,'name'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'recommends'=>\&_version_map,'requires'=>\&_version_map,'license_url'=>\&_url_or_drop,'private'=>\&_keep,':custom'=>\&_keep },);my%down_convert=('1.4-from-2'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_downgrade_license,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_get_build_requires,'configure_requires'=>\&_get_configure_requires,'conflicts'=>\&_get_conflicts,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_downgrade_optional_features,'provides'=>\&_provides,'recommends'=>\&_get_recommends,'requires'=>\&_get_requires,'resources'=>\&_downgrade_resources,':drop'=>[qw(description prereqs release_status)],':custom'=>\&_keep },'1.3-from-1.4'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_optional_features_as_map,'provides'=>\&_provides,'recommends'=>\&_version_map,'requires'=>\&_version_map,'resources'=>\&_resources_1_3,':drop'=>[qw(configure_requires)],':custom'=>\&_keep,},'1.2-from-1.3'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_1_2,'optional_features'=>\&_optional_features_as_map,'provides'=>\&_provides,'recommends'=>\&_version_map,'requires'=>\&_version_map,'resources'=>\&_resources_1_3,':custom'=>\&_keep,},'1.1-from-1.2'=>{'version'=>\&_keep,'name'=>\&_keep,'meta-spec'=>\&_change_meta_spec,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'private'=>\&_keep,'recommends'=>\&_version_map,'requires'=>\&_version_map,':drop'=>[qw(abstract author provides no_index keywords resources)],':custom'=>\&_keep,},'1.0-from-1.1'=>{'name'=>\&_keep,'meta-spec'=>\&_change_meta_spec,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'recommends'=>\&_version_map,'requires'=>\&_version_map,':custom'=>\&_keep,},);my%cleanup=('2'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_2,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'release_status'=>\&_release_status,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_cleanup_optional_features_2,'provides'=>\&_provides,'resources'=>\&_cleanup_resources_2,'description'=>\&_keep,'prereqs'=>\&_cleanup_prereqs,':drop'=>[qw(build_requires configure_requires conflicts distribution_type license_url private recommends requires) ],':custom'=>\&_prefix_custom,},'1.4'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_optional_features_1_4,'provides'=>\&_provides,'recommends'=>\&_version_map,'requires'=>\&_version_map,'resources'=>\&_resources_1_4,'configure_requires'=>\&_keep,':custom'=>\&_keep },'1.3'=>{'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'meta-spec'=>\&_change_meta_spec,'name'=>\&_keep,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'keywords'=>\&_keep,'no_index'=>\&_no_index_directory,'optional_features'=>\&_optional_features_as_map,'provides'=>\&_provides,'recommends'=>\&_version_map,'requires'=>\&_version_map,'resources'=>\&_resources_1_3,':custom'=>\&_keep },'1.2'=>{'version'=>\&_keep,'license'=>\&_license_1,'name'=>\&_keep,'generated_by'=>\&_generated_by,'abstract'=>\&_keep_or_unknown,'author'=>\&_author_list,'meta-spec'=>\&_change_meta_spec,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'recommends'=>\&_version_map,'requires'=>\&_version_map,'keywords'=>\&_keep,'no_index'=>\&_no_index_1_2,'optional_features'=>\&_optional_features_as_map,'provides'=>\&_provides,'resources'=>\&_resources_1_2,':custom'=>\&_keep },'1.1'=>{'version'=>\&_keep,'name'=>\&_keep,'meta-spec'=>\&_change_meta_spec,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'recommends'=>\&_version_map,'requires'=>\&_version_map,'license_url'=>\&_url_or_drop,'private'=>\&_keep,':custom'=>\&_keep },'1.0'=>{'name'=>\&_keep,'meta-spec'=>\&_change_meta_spec,'version'=>\&_keep,'build_requires'=>\&_version_map,'conflicts'=>\&_version_map,'distribution_type'=>\&_keep,'dynamic_config'=>\&_keep_or_one,'generated_by'=>\&_generated_by,'license'=>\&_license_1,'recommends'=>\&_version_map,'requires'=>\&_version_map,':custom'=>\&_keep,},);my%fragments_generate=('2'=>{'abstract'=>'abstract','author'=>'author','generated_by'=>'generated_by','license'=>'license','name'=>'name','version'=>'version','dynamic_config'=>'dynamic_config','release_status'=>'release_status','keywords'=>'keywords','no_index'=>'no_index','optional_features'=>'optional_features','provides'=>'provides','resources'=>'resources','description'=>'description','prereqs'=>'prereqs',},'1.4'=>{'abstract'=>'abstract','author'=>'author','generated_by'=>'generated_by','license'=>'license','name'=>'name','version'=>'version','build_requires'=>'prereqs','conflicts'=>'prereqs','distribution_type'=>'distribution_type','dynamic_config'=>'dynamic_config','keywords'=>'keywords','no_index'=>'no_index','optional_features'=>'optional_features','provides'=>'provides','recommends'=>'prereqs','requires'=>'prereqs','resources'=>'resources','configure_requires'=>'prereqs',},);$fragments_generate{$_}=$fragments_generate{'1.4'}for qw/1.3 1.2 1.1 1.0/;sub new {my ($class,$data,%args)=@_;my$self={'data'=>$data,'spec'=>_extract_spec_version($data,$args{default_version}),};return bless$self,$class}sub _extract_spec_version {my ($data,$default)=@_;my$spec=$data->{'meta-spec'};return($default || "1.0")unless defined$spec && ref$spec eq 'HASH';my$v=$spec->{version};if (defined$v && $v =~ /^\d+(?:\.\d+)?$/){return$v if defined$v && grep {$v eq $_}keys%known_specs;return$v+0 if defined$v && grep {$v==$_}keys%known_specs}return "2" if exists$data->{prereqs};return "1.4" if exists$data->{configure_requires};return($default || "1.2")}sub convert {my ($self,%args)=@_;my$args={%args };my$new_version=$args->{version}|| $HIGHEST;my$is_fragment=$args->{is_fragment};my ($old_version)=$self->{spec};my$converted=_dclone($self->{data});if ($old_version==$new_version){$converted=_convert($converted,$cleanup{$old_version},$old_version,$is_fragment);unless ($args->{is_fragment}){my$cmv=CPAN::Meta::Validator->new($converted);unless ($cmv->is_valid){my$errs=join("\n",$cmv->errors);die "Failed to clean-up $old_version metadata. Errors:\n$errs\n"}}return$converted}elsif ($old_version > $new_version){my@vers=sort {$b <=> $a}keys%known_specs;for my$i (0 .. $#vers-1){next if$vers[$i]> $old_version;last if$vers[$i+1]< $new_version;my$spec_string="$vers[$i+1]-from-$vers[$i]";$converted=_convert($converted,$down_convert{$spec_string},$vers[$i+1],$is_fragment);unless ($args->{is_fragment}){my$cmv=CPAN::Meta::Validator->new($converted);unless ($cmv->is_valid){my$errs=join("\n",$cmv->errors);die "Failed to downconvert metadata to $vers[$i+1]. Errors:\n$errs\n"}}}return$converted}else {my@vers=sort {$a <=> $b}keys%known_specs;for my$i (0 .. $#vers-1){next if$vers[$i]< $old_version;last if$vers[$i+1]> $new_version;my$spec_string="$vers[$i+1]-from-$vers[$i]";$converted=_convert($converted,$up_convert{$spec_string},$vers[$i+1],$is_fragment);unless ($args->{is_fragment}){my$cmv=CPAN::Meta::Validator->new($converted);unless ($cmv->is_valid){my$errs=join("\n",$cmv->errors);die "Failed to upconvert metadata to $vers[$i+1]. Errors:\n$errs\n"}}}return$converted}}sub upgrade_fragment {my ($self)=@_;my ($old_version)=$self->{spec};my%expected=map {;$_=>1}grep {defined}map {$fragments_generate{$old_version}{$_}}keys %{$self->{data}};my$converted=$self->convert(version=>$HIGHEST,is_fragment=>1);for my$key (keys %$converted){next if$key =~ /^x_/i || $key eq 'meta-spec';delete$converted->{$key}unless$expected{$key}}return$converted}1;
+CPAN_META_CONVERTER
+
+$fatpacked{"CPAN/Meta/Feature.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_FEATURE';
+  use 5.006;use strict;use warnings;package CPAN::Meta::Feature;our$VERSION='2.150005';use CPAN::Meta::Prereqs;sub new {my ($class,$identifier,$spec)=@_;my%guts=(identifier=>$identifier,description=>$spec->{description},prereqs=>CPAN::Meta::Prereqs->new($spec->{prereqs}),);bless \%guts=>$class}sub identifier {$_[0]{identifier}}sub description {$_[0]{description}}sub prereqs {$_[0]{prereqs}}1;
+CPAN_META_FEATURE
+
+$fatpacked{"CPAN/Meta/History.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_HISTORY';
+  use 5.006;use strict;use warnings;package CPAN::Meta::History;our$VERSION='2.150005';1;
+CPAN_META_HISTORY
+
+$fatpacked{"CPAN/Meta/Merge.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_MERGE';
+  use strict;use warnings;package CPAN::Meta::Merge;our$VERSION='2.150005';use Carp qw/croak/;use Scalar::Util qw/blessed/;use CPAN::Meta::Converter 2.141170;sub _is_identical {my ($left,$right)=@_;return (not defined$left and not defined$right)|| (defined$left and defined$right and $left eq $right)}sub _identical {my ($left,$right,$path)=@_;croak sprintf "Can't merge attribute %s: '%s' does not equal '%s'",join('.',@{$path}),$left,$right unless _is_identical($left,$right);return$left}sub _merge {my ($current,$next,$mergers,$path)=@_;for my$key (keys %{$next}){if (not exists$current->{$key}){$current->{$key}=$next->{$key}}elsif (my$merger=$mergers->{$key}){$current->{$key}=$merger->($current->{$key},$next->{$key},[@{$path},$key ])}elsif ($merger=$mergers->{':default'}){$current->{$key}=$merger->($current->{$key},$next->{$key},[@{$path},$key ])}else {croak sprintf "Can't merge unknown attribute '%s'",join '.',@{$path},$key}}return$current}sub _uniq {my%seen=();return grep {not $seen{$_}++}@_}sub _set_addition {my ($left,$right)=@_;return [+_uniq(@{$left},@{$right})]}sub _uniq_map {my ($left,$right,$path)=@_;for my$key (keys %{$right}){if (not exists$left->{$key}){$left->{$key}=$right->{$key}}elsif (_is_identical($left->{$key},$right->{$key})){1}elsif (ref$left->{$key}eq 'HASH' and ref$right->{$key}eq 'HASH'){$left->{$key}=_uniq_map($left->{$key},$right->{$key},[@{$path},$key ])}else {croak 'Duplication of element ' .join '.',@{$path},$key}}return$left}sub _improvize {my ($left,$right,$path)=@_;my ($name)=reverse @{$path};if ($name =~ /^x_/){if (ref($left)eq 'ARRAY'){return _set_addition($left,$right,$path)}elsif (ref($left)eq 'HASH'){return _uniq_map($left,$right,$path)}else {return _identical($left,$right,$path)}}croak sprintf "Can't merge '%s'",join '.',@{$path}}sub _optional_features {my ($left,$right,$path)=@_;for my$key (keys %{$right}){if (not exists$left->{$key}){$left->{$key}=$right->{$key}}else {for my$subkey (keys %{$right->{$key}}){next if$subkey eq 'prereqs';if (not exists$left->{$key}{$subkey}){$left->{$key}{$subkey}=$right->{$key}{$subkey}}else {Carp::croak "Cannot merge two optional_features named '$key' with different '$subkey' values" if do {no warnings 'uninitialized';$left->{$key}{$subkey}ne $right->{$key}{$subkey}}}}require CPAN::Meta::Prereqs;$left->{$key}{prereqs}=CPAN::Meta::Prereqs->new($left->{$key}{prereqs})->with_merged_prereqs(CPAN::Meta::Prereqs->new($right->{$key}{prereqs}))->as_string_hash}}return$left}my%default=(abstract=>\&_identical,author=>\&_set_addition,dynamic_config=>sub {my ($left,$right)=@_;return$left || $right},generated_by=>sub {my ($left,$right)=@_;return join ', ',_uniq(split(/, /,$left),split(/, /,$right))},license=>\&_set_addition,'meta-spec'=>{version=>\&_identical,url=>\&_identical },name=>\&_identical,release_status=>\&_identical,version=>\&_identical,description=>\&_identical,keywords=>\&_set_addition,no_index=>{map {($_=>\&_set_addition)}qw/file directory package namespace/ },optional_features=>\&_optional_features,prereqs=>sub {require CPAN::Meta::Prereqs;my ($left,$right)=map {CPAN::Meta::Prereqs->new($_)}@_[0,1];return$left->with_merged_prereqs($right)->as_string_hash},provides=>\&_uniq_map,resources=>{license=>\&_set_addition,homepage=>\&_identical,bugtracker=>\&_uniq_map,repository=>\&_uniq_map,':default'=>\&_improvize,},':default'=>\&_improvize,);sub new {my ($class,%arguments)=@_;croak 'default version required' if not exists$arguments{default_version};my%mapping=%default;my%extra=%{$arguments{extra_mappings}|| {}};for my$key (keys%extra){if (ref($mapping{$key})eq 'HASH'){$mapping{$key}={%{$mapping{$key}},%{$extra{$key}}}}else {$mapping{$key}=$extra{$key}}}return bless {default_version=>$arguments{default_version},mapping=>_coerce_mapping(\%mapping,[]),},$class}my%coderef_for=(set_addition=>\&_set_addition,uniq_map=>\&_uniq_map,identical=>\&_identical,improvize=>\&_improvize,);sub _coerce_mapping {my ($orig,$map_path)=@_;my%ret;for my$key (keys %{$orig}){my$value=$orig->{$key};if (ref($orig->{$key})eq 'CODE'){$ret{$key}=$value}elsif (ref($value)eq 'HASH'){my$mapping=_coerce_mapping($value,[@{$map_path},$key ]);$ret{$key}=sub {my ($left,$right,$path)=@_;return _merge($left,$right,$mapping,[@{$path}])}}elsif ($coderef_for{$value}){$ret{$key}=$coderef_for{$value}}else {croak "Don't know what to do with " .join '.',@{$map_path},$key}}return \%ret}sub merge {my ($self,@items)=@_;my$current={};for my$next (@items){if (blessed($next)&& $next->isa('CPAN::Meta')){$next=$next->as_struct}elsif (ref($next)eq 'HASH'){my$cmc=CPAN::Meta::Converter->new($next,default_version=>$self->{default_version});$next=$cmc->upgrade_fragment}else {croak "Don't know how to merge '$next'"}$current=_merge($current,$next,$self->{mapping},[])}return$current}1;
+CPAN_META_MERGE
+
+$fatpacked{"CPAN/Meta/Prereqs.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_PREREQS';
+  use 5.006;use strict;use warnings;package CPAN::Meta::Prereqs;our$VERSION='2.150005';use Carp qw(confess);use Scalar::Util qw(blessed);use CPAN::Meta::Requirements 2.121;sub __legal_phases {qw(configure build test runtime develop)}sub __legal_types {qw(requires recommends suggests conflicts)}sub new {my ($class,$prereq_spec)=@_;$prereq_spec ||= {};my%is_legal_phase=map {;$_=>1}$class->__legal_phases;my%is_legal_type=map {;$_=>1}$class->__legal_types;my%guts;PHASE: for my$phase (keys %$prereq_spec){next PHASE unless$phase =~ /\Ax_/i or $is_legal_phase{$phase};my$phase_spec=$prereq_spec->{$phase };next PHASE unless keys %$phase_spec;TYPE: for my$type (keys %$phase_spec){next TYPE unless$type =~ /\Ax_/i or $is_legal_type{$type};my$spec=$phase_spec->{$type };next TYPE unless keys %$spec;$guts{prereqs}{$phase}{$type}=CPAN::Meta::Requirements->from_string_hash($spec)}}return bless \%guts=>$class}sub requirements_for {my ($self,$phase,$type)=@_;confess "requirements_for called without phase" unless defined$phase;confess "requirements_for called without type" unless defined$type;unless ($phase =~ /\Ax_/i or grep {$phase eq $_}$self->__legal_phases){confess "requested requirements for unknown phase: $phase"}unless ($type =~ /\Ax_/i or grep {$type eq $_}$self->__legal_types){confess "requested requirements for unknown type: $type"}my$req=($self->{prereqs}{$phase}{$type}||= CPAN::Meta::Requirements->new);$req->finalize if$self->is_finalized;return$req}sub with_merged_prereqs {my ($self,$other)=@_;my@other=blessed($other)? $other : @$other;my@prereq_objs=($self,@other);my%new_arg;for my$phase ($self->__legal_phases){for my$type ($self->__legal_types){my$req=CPAN::Meta::Requirements->new;for my$prereq (@prereq_objs){my$this_req=$prereq->requirements_for($phase,$type);next unless$this_req->required_modules;$req->add_requirements($this_req)}next unless$req->required_modules;$new_arg{$phase }{$type }=$req->as_string_hash}}return (ref$self)->new(\%new_arg)}sub merged_requirements {my ($self,$phases,$types)=@_;$phases=[qw/runtime build test/]unless defined$phases;$types=[qw/requires recommends/]unless defined$types;confess "merged_requirements phases argument must be an arrayref" unless ref$phases eq 'ARRAY';confess "merged_requirements types argument must be an arrayref" unless ref$types eq 'ARRAY';my$req=CPAN::Meta::Requirements->new;for my$phase (@$phases){unless ($phase =~ /\Ax_/i or grep {$phase eq $_}$self->__legal_phases){confess "requested requirements for unknown phase: $phase"}for my$type (@$types){unless ($type =~ /\Ax_/i or grep {$type eq $_}$self->__legal_types){confess "requested requirements for unknown type: $type"}$req->add_requirements($self->requirements_for($phase,$type))}}$req->finalize if$self->is_finalized;return$req}sub as_string_hash {my ($self)=@_;my%hash;for my$phase ($self->__legal_phases){for my$type ($self->__legal_types){my$req=$self->requirements_for($phase,$type);next unless$req->required_modules;$hash{$phase }{$type }=$req->as_string_hash}}return \%hash}sub is_finalized {$_[0]{finalized}}sub finalize {my ($self)=@_;$self->{finalized}=1;for my$phase (keys %{$self->{prereqs}}){$_->finalize for values %{$self->{prereqs}{$phase}}}}sub clone {my ($self)=@_;my$clone=(ref$self)->new($self->as_string_hash)}1;
+CPAN_META_PREREQS
+
+$fatpacked{"CPAN/Meta/Requirements.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_REQUIREMENTS';
+  use strict;use warnings;package CPAN::Meta::Requirements;our$VERSION='2.133';use Carp ();BEGIN {eval "use version ()";if (my$err=$@){eval "use ExtUtils::MakeMaker::version" or die$err}}*_is_qv=version->can('is_qv')? sub {$_[0]->is_qv}: sub {exists $_[0]->{qv}};my$V0=version->new(0);my@valid_options=qw(bad_version_hook);sub new {my ($class,$options)=@_;$options ||= {};Carp::croak "Argument to $class\->new() must be a hash reference" unless ref$options eq 'HASH';my%self=map {;$_=>$options->{$_}}@valid_options;return bless \%self=>$class}sub _find_magic_vstring {my$value=shift;my$tvalue='';require B;my$sv=B::svref_2object(\$value);my$magic=ref($sv)eq 'B::PVMG' ? $sv->MAGIC : undef;while ($magic){if ($magic->TYPE eq 'V'){$tvalue=$magic->PTR;$tvalue =~ s/^v?(.+)$/v$1/;last}else {$magic=$magic->MOREMAGIC}}return$tvalue}sub _isa_version {UNIVERSAL::isa($_[0],'UNIVERSAL')&& $_[0]->isa('version')}sub _version_object {my ($self,$module,$version)=@_;my ($vobj,$err);if (not defined$version or (!ref($version)&& $version eq '0')){return$V0}elsif (ref($version)eq 'version' || _isa_version($version)){$vobj=$version}else {if ($INC{'version/vpp.pm'}|| $INC{'ExtUtils/MakeMaker/version/vpp.pm'}){my$magic=_find_magic_vstring($version);$version=$magic if length$magic}eval {local$SIG{__WARN__}=sub {die "Invalid version: $_[0]"};$vobj=version->new($version)};if (my$err=$@){my$hook=$self->{bad_version_hook};$vobj=eval {$hook->($version,$module)}if ref$hook eq 'CODE';unless (eval {$vobj->isa("version")}){$err =~ s{ at .* line \d+.*$}{};die "Can't convert '$version': $err"}}}if ($vobj =~ m{\A\.}){$vobj=version->new("0$vobj")}if (_is_qv($vobj)){$vobj=version->new($vobj->normal)}return$vobj}BEGIN {for my$type (qw(maximum exclusion exact_version)){my$method="with_$type";my$to_add=$type eq 'exact_version' ? $type : "add_$type";my$code=sub {my ($self,$name,$version)=@_;$version=$self->_version_object($name,$version);$self->__modify_entry_for($name,$method,$version);return$self};no strict 'refs';*$to_add=$code}}sub add_minimum {my ($self,$name,$version)=@_;if (not defined$version or "$version" eq '0'){return$self if$self->__entry_for($name);Carp::confess("can't add new requirements to finalized requirements")if$self->is_finalized;$self->{requirements}{$name }=CPAN::Meta::Requirements::_Range::Range->with_minimum($V0)}else {$version=$self->_version_object($name,$version);$self->__modify_entry_for($name,'with_minimum',$version)}return$self}sub add_requirements {my ($self,$req)=@_;for my$module ($req->required_modules){my$modifiers=$req->__entry_for($module)->as_modifiers;for my$modifier (@$modifiers){my ($method,@args)=@$modifier;$self->$method($module=>@args)}}return$self}sub accepts_module {my ($self,$module,$version)=@_;$version=$self->_version_object($module,$version);return 1 unless my$range=$self->__entry_for($module);return$range->_accepts($version)}sub clear_requirement {my ($self,$module)=@_;return$self unless$self->__entry_for($module);Carp::confess("can't clear requirements on finalized requirements")if$self->is_finalized;delete$self->{requirements}{$module };return$self}sub requirements_for_module {my ($self,$module)=@_;my$entry=$self->__entry_for($module);return unless$entry;return$entry->as_string}sub required_modules {keys %{$_[0]{requirements}}}sub clone {my ($self)=@_;my$new=(ref$self)->new;return$new->add_requirements($self)}sub __entry_for {$_[0]{requirements}{$_[1]}}sub __modify_entry_for {my ($self,$name,$method,$version)=@_;my$fin=$self->is_finalized;my$old=$self->__entry_for($name);Carp::confess("can't add new requirements to finalized requirements")if$fin and not $old;my$new=($old || 'CPAN::Meta::Requirements::_Range::Range')->$method($version);Carp::confess("can't modify finalized requirements")if$fin and $old->as_string ne $new->as_string;$self->{requirements}{$name }=$new}sub is_simple {my ($self)=@_;for my$module ($self->required_modules){return if$self->__entry_for($module)->as_string =~ /\s/}return 1}sub is_finalized {$_[0]{finalized}}sub finalize {$_[0]{finalized}=1}sub as_string_hash {my ($self)=@_;my%hash=map {;$_=>$self->{requirements}{$_}->as_string}$self->required_modules;return \%hash}my%methods_for_op=('=='=>[qw(exact_version) ],'!='=>[qw(add_exclusion) ],'>='=>[qw(add_minimum) ],'<='=>[qw(add_maximum) ],'>'=>[qw(add_minimum add_exclusion) ],'<'=>[qw(add_maximum add_exclusion) ],);sub add_string_requirement {my ($self,$module,$req)=@_;unless (defined$req && length$req){$req=0;$self->_blank_carp($module)}my$magic=_find_magic_vstring($req);if (length$magic){$self->add_minimum($module=>$magic);return}my@parts=split qr{\s*,\s*},$req;for my$part (@parts){my ($op,$ver)=$part =~ m{\A\s*(==|>=|>|<=|<|!=)\s*(.*)\z};if (!defined$op){$self->add_minimum($module=>$part)}else {Carp::confess("illegal requirement string: $req")unless my$methods=$methods_for_op{$op };$self->$_($module=>$ver)for @$methods}}}sub _blank_carp {my ($self,$module)=@_;Carp::carp("Undefined requirement for $module treated as '0'")}sub from_string_hash {my ($class,$hash,$options)=@_;my$self=$class->new($options);for my$module (keys %$hash){my$req=$hash->{$module};unless (defined$req && length$req){$req=0;$class->_blank_carp($module)}$self->add_string_requirement($module,$req)}return$self}{package CPAN::Meta::Requirements::_Range::Exact;sub _new {bless {version=>$_[1]}=>$_[0]}sub _accepts {return $_[0]{version}==$_[1]}sub as_string {return "== $_[0]{version}"}sub as_modifiers {return [[exact_version=>$_[0]{version}]]}sub _clone {(ref $_[0])->_new(version->new($_[0]{version}))}sub with_exact_version {my ($self,$version)=@_;return$self->_clone if$self->_accepts($version);Carp::confess("illegal requirements: unequal exact version specified")}sub with_minimum {my ($self,$minimum)=@_;return$self->_clone if$self->{version}>= $minimum;Carp::confess("illegal requirements: minimum above exact specification")}sub with_maximum {my ($self,$maximum)=@_;return$self->_clone if$self->{version}<= $maximum;Carp::confess("illegal requirements: maximum below exact specification")}sub with_exclusion {my ($self,$exclusion)=@_;return$self->_clone unless$exclusion==$self->{version};Carp::confess("illegal requirements: excluded exact specification")}}{package CPAN::Meta::Requirements::_Range::Range;sub _self {ref($_[0])? $_[0]: (bless {}=>$_[0])}sub _clone {return (bless {}=>$_[0])unless ref $_[0];my ($s)=@_;my%guts=((exists$s->{minimum}? (minimum=>version->new($s->{minimum})): ()),(exists$s->{maximum}? (maximum=>version->new($s->{maximum})): ()),(exists$s->{exclusions}? (exclusions=>[map {version->new($_)}@{$s->{exclusions}}]): ()),);bless \%guts=>ref($s)}sub as_modifiers {my ($self)=@_;my@mods;push@mods,[add_minimum=>$self->{minimum}]if exists$self->{minimum};push@mods,[add_maximum=>$self->{maximum}]if exists$self->{maximum};push@mods,map {;[add_exclusion=>$_ ]}@{$self->{exclusions}|| []};return \@mods}sub as_string {my ($self)=@_;return 0 if!keys %$self;return "$self->{minimum}" if (keys %$self)==1 and exists$self->{minimum};my@exclusions=@{$self->{exclusions}|| []};my@parts;for my$pair ([qw(>= > minimum) ],[qw(<= < maximum) ],){my ($op,$e_op,$k)=@$pair;if (exists$self->{$k}){my@new_exclusions=grep {$_!=$self->{$k }}@exclusions;if (@new_exclusions==@exclusions){push@parts,"$op $self->{ $k }"}else {push@parts,"$e_op $self->{ $k }";@exclusions=@new_exclusions}}}push@parts,map {;"!= $_"}@exclusions;return join q{, },@parts}sub with_exact_version {my ($self,$version)=@_;$self=$self->_clone;Carp::confess("illegal requirements: exact specification outside of range")unless$self->_accepts($version);return CPAN::Meta::Requirements::_Range::Exact->_new($version)}sub _simplify {my ($self)=@_;if (defined$self->{minimum}and defined$self->{maximum}){if ($self->{minimum}==$self->{maximum}){Carp::confess("illegal requirements: excluded all values")if grep {$_==$self->{minimum}}@{$self->{exclusions}|| []};return CPAN::Meta::Requirements::_Range::Exact->_new($self->{minimum})}Carp::confess("illegal requirements: minimum exceeds maximum")if$self->{minimum}> $self->{maximum}}if ($self->{exclusions}){my%seen;@{$self->{exclusions}}=grep {(!defined$self->{minimum}or $_ >= $self->{minimum})and (!defined$self->{maximum}or $_ <= $self->{maximum})and !$seen{$_}++}@{$self->{exclusions}}}return$self}sub with_minimum {my ($self,$minimum)=@_;$self=$self->_clone;if (defined (my$old_min=$self->{minimum})){$self->{minimum}=(sort {$b cmp $a}($minimum,$old_min))[0]}else {$self->{minimum}=$minimum}return$self->_simplify}sub with_maximum {my ($self,$maximum)=@_;$self=$self->_clone;if (defined (my$old_max=$self->{maximum})){$self->{maximum}=(sort {$a cmp $b}($maximum,$old_max))[0]}else {$self->{maximum}=$maximum}return$self->_simplify}sub with_exclusion {my ($self,$exclusion)=@_;$self=$self->_clone;push @{$self->{exclusions}||= []},$exclusion;return$self->_simplify}sub _accepts {my ($self,$version)=@_;return if defined$self->{minimum}and $version < $self->{minimum};return if defined$self->{maximum}and $version > $self->{maximum};return if defined$self->{exclusions}and grep {$version==$_}@{$self->{exclusions}};return 1}}1;
+CPAN_META_REQUIREMENTS
+
+$fatpacked{"CPAN/Meta/Spec.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_SPEC';
+  use 5.006;use strict;use warnings;package CPAN::Meta::Spec;our$VERSION='2.150005';1;
+CPAN_META_SPEC
+
+$fatpacked{"CPAN/Meta/Validator.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_VALIDATOR';
+  use 5.006;use strict;use warnings;package CPAN::Meta::Validator;our$VERSION='2.150005';my%known_specs=('1.4'=>'http://module-build.sourceforge.net/META-spec-v1.4.html','1.3'=>'http://module-build.sourceforge.net/META-spec-v1.3.html','1.2'=>'http://module-build.sourceforge.net/META-spec-v1.2.html','1.1'=>'http://module-build.sourceforge.net/META-spec-v1.1.html','1.0'=>'http://module-build.sourceforge.net/META-spec-v1.0.html');my%known_urls=map {$known_specs{$_}=>$_}keys%known_specs;my$module_map1={'map'=>{':key'=>{name=>\&module,value=>\&exversion }}};my$module_map2={'map'=>{':key'=>{name=>\&module,value=>\&version }}};my$no_index_2={'map'=>{file=>{list=>{value=>\&string }},directory=>{list=>{value=>\&string }},'package'=>{list=>{value=>\&string }},namespace=>{list=>{value=>\&string }},':key'=>{name=>\&custom_2,value=>\&anything },}};my$no_index_1_3={'map'=>{file=>{list=>{value=>\&string }},directory=>{list=>{value=>\&string }},'package'=>{list=>{value=>\&string }},namespace=>{list=>{value=>\&string }},':key'=>{name=>\&string,value=>\&anything },}};my$no_index_1_2={'map'=>{file=>{list=>{value=>\&string }},dir=>{list=>{value=>\&string }},'package'=>{list=>{value=>\&string }},namespace=>{list=>{value=>\&string }},':key'=>{name=>\&string,value=>\&anything },}};my$no_index_1_1={'map'=>{':key'=>{name=>\&string,list=>{value=>\&string }},}};my$prereq_map={map=>{':key'=>{name=>\&phase,'map'=>{':key'=>{name=>\&relation,%$module_map1,},},}},};my%definitions=('2'=>{'abstract'=>{mandatory=>1,value=>\&string },'author'=>{mandatory=>1,list=>{value=>\&string }},'dynamic_config'=>{mandatory=>1,value=>\&boolean },'generated_by'=>{mandatory=>1,value=>\&string },'license'=>{mandatory=>1,list=>{value=>\&license }},'meta-spec'=>{mandatory=>1,'map'=>{version=>{mandatory=>1,value=>\&version},url=>{value=>\&url },':key'=>{name=>\&custom_2,value=>\&anything },}},'name'=>{mandatory=>1,value=>\&string },'release_status'=>{mandatory=>1,value=>\&release_status },'version'=>{mandatory=>1,value=>\&version },'description'=>{value=>\&string },'keywords'=>{list=>{value=>\&string }},'no_index'=>$no_index_2,'optional_features'=>{'map'=>{':key'=>{name=>\&string,'map'=>{description=>{value=>\&string },prereqs=>$prereq_map,':key'=>{name=>\&custom_2,value=>\&anything },}}}},'prereqs'=>$prereq_map,'provides'=>{'map'=>{':key'=>{name=>\&module,'map'=>{file=>{mandatory=>1,value=>\&file },version=>{value=>\&version },':key'=>{name=>\&custom_2,value=>\&anything },}}}},'resources'=>{'map'=>{license=>{list=>{value=>\&url }},homepage=>{value=>\&url },bugtracker=>{'map'=>{web=>{value=>\&url },mailto=>{value=>\&string},':key'=>{name=>\&custom_2,value=>\&anything },}},repository=>{'map'=>{web=>{value=>\&url },url=>{value=>\&url },type=>{value=>\&string },':key'=>{name=>\&custom_2,value=>\&anything },}},':key'=>{value=>\&string,name=>\&custom_2 },}},':key'=>{name=>\&custom_2,value=>\&anything },},'1.4'=>{'meta-spec'=>{mandatory=>1,'map'=>{version=>{mandatory=>1,value=>\&version},url=>{mandatory=>1,value=>\&urlspec },':key'=>{name=>\&string,value=>\&anything },},},'name'=>{mandatory=>1,value=>\&string },'version'=>{mandatory=>1,value=>\&version },'abstract'=>{mandatory=>1,value=>\&string },'author'=>{mandatory=>1,list=>{value=>\&string }},'license'=>{mandatory=>1,value=>\&license },'generated_by'=>{mandatory=>1,value=>\&string },'distribution_type'=>{value=>\&string },'dynamic_config'=>{value=>\&boolean },'requires'=>$module_map1,'recommends'=>$module_map1,'build_requires'=>$module_map1,'configure_requires'=>$module_map1,'conflicts'=>$module_map2,'optional_features'=>{'map'=>{':key'=>{name=>\&string,'map'=>{description=>{value=>\&string },requires=>$module_map1,recommends=>$module_map1,build_requires=>$module_map1,conflicts=>$module_map2,':key'=>{name=>\&string,value=>\&anything },}}}},'provides'=>{'map'=>{':key'=>{name=>\&module,'map'=>{file=>{mandatory=>1,value=>\&file },version=>{value=>\&version },':key'=>{name=>\&string,value=>\&anything },}}}},'no_index'=>$no_index_1_3,'private'=>$no_index_1_3,'keywords'=>{list=>{value=>\&string }},'resources'=>{'map'=>{license=>{value=>\&url },homepage=>{value=>\&url },bugtracker=>{value=>\&url },repository=>{value=>\&url },':key'=>{value=>\&string,name=>\&custom_1 },}},':key'=>{name=>\&string,value=>\&anything },},'1.3'=>{'meta-spec'=>{mandatory=>1,'map'=>{version=>{mandatory=>1,value=>\&version},url=>{mandatory=>1,value=>\&urlspec },':key'=>{name=>\&string,value=>\&anything },},},'name'=>{mandatory=>1,value=>\&string },'version'=>{mandatory=>1,value=>\&version },'abstract'=>{mandatory=>1,value=>\&string },'author'=>{mandatory=>1,list=>{value=>\&string }},'license'=>{mandatory=>1,value=>\&license },'generated_by'=>{mandatory=>1,value=>\&string },'distribution_type'=>{value=>\&string },'dynamic_config'=>{value=>\&boolean },'requires'=>$module_map1,'recommends'=>$module_map1,'build_requires'=>$module_map1,'conflicts'=>$module_map2,'optional_features'=>{'map'=>{':key'=>{name=>\&string,'map'=>{description=>{value=>\&string },requires=>$module_map1,recommends=>$module_map1,build_requires=>$module_map1,conflicts=>$module_map2,':key'=>{name=>\&string,value=>\&anything },}}}},'provides'=>{'map'=>{':key'=>{name=>\&module,'map'=>{file=>{mandatory=>1,value=>\&file },version=>{value=>\&version },':key'=>{name=>\&string,value=>\&anything },}}}},'no_index'=>$no_index_1_3,'private'=>$no_index_1_3,'keywords'=>{list=>{value=>\&string }},'resources'=>{'map'=>{license=>{value=>\&url },homepage=>{value=>\&url },bugtracker=>{value=>\&url },repository=>{value=>\&url },':key'=>{value=>\&string,name=>\&custom_1 },}},':key'=>{name=>\&string,value=>\&anything },},'1.2'=>{'meta-spec'=>{mandatory=>1,'map'=>{version=>{mandatory=>1,value=>\&version},url=>{mandatory=>1,value=>\&urlspec },':key'=>{name=>\&string,value=>\&anything },},},'name'=>{mandatory=>1,value=>\&string },'version'=>{mandatory=>1,value=>\&version },'license'=>{mandatory=>1,value=>\&license },'generated_by'=>{mandatory=>1,value=>\&string },'author'=>{mandatory=>1,list=>{value=>\&string }},'abstract'=>{mandatory=>1,value=>\&string },'distribution_type'=>{value=>\&string },'dynamic_config'=>{value=>\&boolean },'keywords'=>{list=>{value=>\&string }},'private'=>$no_index_1_2,'$no_index'=>$no_index_1_2,'requires'=>$module_map1,'recommends'=>$module_map1,'build_requires'=>$module_map1,'conflicts'=>$module_map2,'optional_features'=>{'map'=>{':key'=>{name=>\&string,'map'=>{description=>{value=>\&string },requires=>$module_map1,recommends=>$module_map1,build_requires=>$module_map1,conflicts=>$module_map2,':key'=>{name=>\&string,value=>\&anything },}}}},'provides'=>{'map'=>{':key'=>{name=>\&module,'map'=>{file=>{mandatory=>1,value=>\&file },version=>{value=>\&version },':key'=>{name=>\&string,value=>\&anything },}}}},'resources'=>{'map'=>{license=>{value=>\&url },homepage=>{value=>\&url },bugtracker=>{value=>\&url },repository=>{value=>\&url },':key'=>{value=>\&string,name=>\&custom_1 },}},':key'=>{name=>\&string,value=>\&anything },},'1.1'=>{'name'=>{value=>\&string },'version'=>{mandatory=>1,value=>\&version },'license'=>{value=>\&license },'generated_by'=>{value=>\&string },'license_uri'=>{value=>\&url },'distribution_type'=>{value=>\&string },'dynamic_config'=>{value=>\&boolean },'private'=>$no_index_1_1,'requires'=>$module_map1,'recommends'=>$module_map1,'build_requires'=>$module_map1,'conflicts'=>$module_map2,':key'=>{name=>\&string,value=>\&anything },},'1.0'=>{'name'=>{value=>\&string },'version'=>{mandatory=>1,value=>\&version },'license'=>{value=>\&license },'generated_by'=>{value=>\&string },'license_uri'=>{value=>\&url },'distribution_type'=>{value=>\&string },'dynamic_config'=>{value=>\&boolean },'requires'=>$module_map1,'recommends'=>$module_map1,'build_requires'=>$module_map1,'conflicts'=>$module_map2,':key'=>{name=>\&string,value=>\&anything },},);sub new {my ($class,$data)=@_;my$self={'data'=>$data,'spec'=>eval {$data->{'meta-spec'}{'version'}}|| "1.0",'errors'=>undef,};return bless$self,$class}sub is_valid {my$self=shift;my$data=$self->{data};my$spec_version=$self->{spec};$self->check_map($definitions{$spec_version},$data);return!$self->errors}sub errors {my$self=shift;return ()unless(defined$self->{errors});return @{$self->{errors}}}my$spec_error="Missing validation action in specification. " ."Must be one of 'map', 'list', or 'value'";sub check_map {my ($self,$spec,$data)=@_;if(ref($spec)ne 'HASH'){$self->_error("Unknown META specification, cannot validate.");return}if(ref($data)ne 'HASH'){$self->_error("Expected a map structure from string or file.");return}for my$key (keys %$spec){next unless($spec->{$key}->{mandatory});next if(defined$data->{$key});push @{$self->{stack}},$key;$self->_error("Missing mandatory field, '$key'");pop @{$self->{stack}}}for my$key (keys %$data){push @{$self->{stack}},$key;if($spec->{$key}){if($spec->{$key}{value}){$spec->{$key}{value}->($self,$key,$data->{$key})}elsif($spec->{$key}{'map'}){$self->check_map($spec->{$key}{'map'},$data->{$key})}elsif($spec->{$key}{'list'}){$self->check_list($spec->{$key}{'list'},$data->{$key})}else {$self->_error("$spec_error for '$key'")}}elsif ($spec->{':key'}){$spec->{':key'}{name}->($self,$key,$key);if($spec->{':key'}{value}){$spec->{':key'}{value}->($self,$key,$data->{$key})}elsif($spec->{':key'}{'map'}){$self->check_map($spec->{':key'}{'map'},$data->{$key})}elsif($spec->{':key'}{'list'}){$self->check_list($spec->{':key'}{'list'},$data->{$key})}else {$self->_error("$spec_error for ':key'")}}else {$self->_error("Unknown key, '$key', found in map structure")}pop @{$self->{stack}}}}sub check_list {my ($self,$spec,$data)=@_;if(ref($data)ne 'ARRAY'){$self->_error("Expected a list structure");return}if(defined$spec->{mandatory}){if(!defined$data->[0]){$self->_error("Missing entries from mandatory list")}}for my$value (@$data){push @{$self->{stack}},$value || "<undef>";if(defined$spec->{value}){$spec->{value}->($self,'list',$value)}elsif(defined$spec->{'map'}){$self->check_map($spec->{'map'},$value)}elsif(defined$spec->{'list'}){$self->check_list($spec->{'list'},$value)}elsif ($spec->{':key'}){$self->check_map($spec,$value)}else {$self->_error("$spec_error associated with '$self->{stack}[-2]'")}pop @{$self->{stack}}}}sub header {my ($self,$key,$value)=@_;if(defined$value){return 1 if($value && $value =~ /^--- #YAML:1.0/)}$self->_error("file does not have a valid YAML header.");return 0}sub release_status {my ($self,$key,$value)=@_;if(defined$value){my$version=$self->{data}{version}|| '';if ($version =~ /_/){return 1 if ($value =~ /\A(?:testing|unstable)\z/);$self->_error("'$value' for '$key' is invalid for version '$version'")}else {return 1 if ($value =~ /\A(?:stable|testing|unstable)\z/);$self->_error("'$value' for '$key' is invalid")}}else {$self->_error("'$key' is not defined")}return 0}sub _uri_split {return $_[0]=~ m,(?:([^:/?#]+):)?(?://([^/?#]*))?([^?#]*)(?:\?([^#]*))?(?:#(.*))?,}sub url {my ($self,$key,$value)=@_;if(defined$value){my ($scheme,$auth,$path,$query,$frag)=_uri_split($value);unless (defined$scheme && length$scheme){$self->_error("'$value' for '$key' does not have a URL scheme");return 0}unless (defined$auth && length$auth){$self->_error("'$value' for '$key' does not have a URL authority");return 0}return 1}$value ||= '';$self->_error("'$value' for '$key' is not a valid URL.");return 0}sub urlspec {my ($self,$key,$value)=@_;if(defined$value){return 1 if($value && $known_specs{$self->{spec}}eq $value);if($value && $known_urls{$value}){$self->_error('META specification URL does not match version');return 0}}$self->_error('Unknown META specification');return 0}sub anything {return 1}sub string {my ($self,$key,$value)=@_;if(defined$value){return 1 if($value || $value =~ /^0$/)}$self->_error("value is an undefined string");return 0}sub string_or_undef {my ($self,$key,$value)=@_;return 1 unless(defined$value);return 1 if($value || $value =~ /^0$/);$self->_error("No string defined for '$key'");return 0}sub file {my ($self,$key,$value)=@_;return 1 if(defined$value);$self->_error("No file defined for '$key'");return 0}sub exversion {my ($self,$key,$value)=@_;if(defined$value && ($value || $value =~ /0/)){my$pass=1;for(split(",",$value)){$self->version($key,$_)or ($pass=0)}return$pass}$value='<undef>' unless(defined$value);$self->_error("'$value' for '$key' is not a valid version.");return 0}sub version {my ($self,$key,$value)=@_;if(defined$value){return 0 unless($value || $value =~ /0/);return 1 if($value =~ /^\s*((<|<=|>=|>|!=|==)\s*)?v?\d+((\.\d+((_|\.)\d+)?)?)/)}else {$value='<undef>'}$self->_error("'$value' for '$key' is not a valid version.");return 0}sub boolean {my ($self,$key,$value)=@_;if(defined$value){return 1 if($value =~ /^(0|1|true|false)$/)}else {$value='<undef>'}$self->_error("'$value' for '$key' is not a boolean value.");return 0}my%v1_licenses=('perl'=>'http://dev.perl.org/licenses/','gpl'=>'http://www.opensource.org/licenses/gpl-license.php','apache'=>'http://apache.org/licenses/LICENSE-2.0','artistic'=>'http://opensource.org/licenses/artistic-license.php','artistic_2'=>'http://opensource.org/licenses/artistic-license-2.0.php','lgpl'=>'http://www.opensource.org/licenses/lgpl-license.php','bsd'=>'http://www.opensource.org/licenses/bsd-license.php','gpl'=>'http://www.opensource.org/licenses/gpl-license.php','mit'=>'http://opensource.org/licenses/mit-license.php','mozilla'=>'http://opensource.org/licenses/mozilla1.1.php','open_source'=>undef,'unrestricted'=>undef,'restrictive'=>undef,'unknown'=>undef,);my%v2_licenses=map {$_=>1}qw(agpl_3 apache_1_1 apache_2_0 artistic_1 artistic_2 bsd freebsd gfdl_1_2 gfdl_1_3 gpl_1 gpl_2 gpl_3 lgpl_2_1 lgpl_3_0 mit mozilla_1_0 mozilla_1_1 openssl perl_5 qpl_1_0 ssleay sun zlib open_source restricted unrestricted unknown);sub license {my ($self,$key,$value)=@_;my$licenses=$self->{spec}< 2 ? \%v1_licenses : \%v2_licenses;if(defined$value){return 1 if($value && exists$licenses->{$value})}else {$value='<undef>'}$self->_error("License '$value' is invalid");return 0}sub custom_1 {my ($self,$key)=@_;if(defined$key){return 1 if($key && $key =~ /^[_a-z]+$/i && $key =~ /[A-Z]/)}else {$key='<undef>'}$self->_error("Custom resource '$key' must be in CamelCase.");return 0}sub custom_2 {my ($self,$key)=@_;if(defined$key){return 1 if($key && $key =~ /^x_/i)}else {$key='<undef>'}$self->_error("Custom key '$key' must begin with 'x_' or 'X_'.");return 0}sub identifier {my ($self,$key)=@_;if(defined$key){return 1 if($key && $key =~ /^([a-z][_a-z]+)$/i)}else {$key='<undef>'}$self->_error("Key '$key' is not a legal identifier.");return 0}sub module {my ($self,$key)=@_;if(defined$key){return 1 if($key && $key =~ /^[A-Za-z0-9_]+(::[A-Za-z0-9_]+)*$/)}else {$key='<undef>'}$self->_error("Key '$key' is not a legal module name.");return 0}my@valid_phases=qw/configure build test runtime develop/;sub phase {my ($self,$key)=@_;if(defined$key){return 1 if(length$key && grep {$key eq $_}@valid_phases);return 1 if$key =~ /x_/i}else {$key='<undef>'}$self->_error("Key '$key' is not a legal phase.");return 0}my@valid_relations=qw/requires recommends suggests conflicts/;sub relation {my ($self,$key)=@_;if(defined$key){return 1 if(length$key && grep {$key eq $_}@valid_relations);return 1 if$key =~ /x_/i}else {$key='<undef>'}$self->_error("Key '$key' is not a legal prereq relationship.");return 0}sub _error {my$self=shift;my$mess=shift;$mess .= ' ('.join(' -> ',@{$self->{stack}}).')' if($self->{stack});$mess .= " [Validation: $self->{spec}]";push @{$self->{errors}},$mess}1;
+CPAN_META_VALIDATOR
+
+$fatpacked{"CPAN/Meta/YAML.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'CPAN_META_YAML';
+  use 5.008001;use strict;use warnings;package CPAN::Meta::YAML;$CPAN::Meta::YAML::VERSION='0.016';;use Exporter;our@ISA=qw{Exporter};our@EXPORT=qw{Load Dump};our@EXPORT_OK=qw{LoadFile DumpFile freeze thaw};sub Dump {return CPAN::Meta::YAML->new(@_)->_dump_string}sub Load {my$self=CPAN::Meta::YAML->_load_string(@_);if (wantarray){return @$self}else {return$self->[-1]}}BEGIN {*freeze=\&Dump;*thaw=\&Load}sub DumpFile {my$file=shift;return CPAN::Meta::YAML->new(@_)->_dump_file($file)}sub LoadFile {my$file=shift;my$self=CPAN::Meta::YAML->_load_file($file);if (wantarray){return @$self}else {return$self->[-1]}}sub new {my$class=shift;bless [@_ ],$class}sub read_string {my$self=shift;$self->_load_string(@_)}sub write_string {my$self=shift;$self->_dump_string(@_)}sub read {my$self=shift;$self->_load_file(@_)}sub write {my$self=shift;$self->_dump_file(@_)}my@UNPRINTABLE=qw(0 x01 x02 x03 x04 x05 x06 a b t n v f r x0E x0F x10 x11 x12 x13 x14 x15 x16 x17 x18 x19 x1A e x1C x1D x1E x1F);my%UNESCAPES=(0=>"\x00",z=>"\x00",N=>"\x85",a=>"\x07",b=>"\x08",t=>"\x09",n=>"\x0a",v=>"\x0b",f=>"\x0c",r=>"\x0d",e=>"\x1b",'\\'=>'\\',);my%QUOTE=map {$_=>1}qw{null true false};my$re_capture_double_quoted=qr/\"([^\\"]*(?:\\.[^\\"]*)*)\"/;my$re_capture_single_quoted=qr/\'([^\']*(?:\'\'[^\']*)*)\'/;my$re_capture_unquoted_key=qr/([^:]+(?::+\S(?:[^:]*|.*?(?=:)))*)(?=\s*\:(?:\s+|$))/;my$re_trailing_comment=qr/(?:\s+\#.*)?/;my$re_key_value_separator=qr/\s*:(?:\s+(?:\#.*)?|$)/;sub _load_file {my$class=ref $_[0]? ref shift : shift;my$file=shift or $class->_error('You did not specify a file name');$class->_error("File '$file' does not exist")unless -e $file;$class->_error("'$file' is a directory, not a file")unless -f _;$class->_error("Insufficient permissions to read '$file'")unless -r _;open(my$fh,"<:unix:encoding(UTF-8)",$file);unless ($fh){$class->_error("Failed to open file '$file': $!")}if (_can_flock()){flock($fh,Fcntl::LOCK_SH())or warn "Couldn't lock '$file' for reading: $!"}my$contents=eval {use warnings FATAL=>'utf8';local $/;<$fh>};if (my$err=$@){$class->_error("Error reading from file '$file': $err")}unless (close$fh){$class->_error("Failed to close file '$file': $!")}$class->_load_string($contents)}sub _load_string {my$class=ref $_[0]? ref shift : shift;my$self=bless [],$class;my$string=$_[0];eval {unless (defined$string){die \"Did not provide a string to load"}if (utf8::is_utf8($string)&&!utf8::valid($string)){die \<<'...'}utf8::upgrade($string);$string =~ s/^\x{FEFF}//;return$self unless length$string;my@lines=grep {!/^\s*(?:\#.*)?\z/}split /(?:\015{1,2}\012|\015|\012)/,$string;@lines and $lines[0]=~ /^\%YAML[: ][\d\.]+.*\z/ and shift@lines;my$in_document=0;while (@lines){if ($lines[0]=~ /^---\s*(?:(.+)\s*)?\z/){shift@lines;if (defined $1 and $1 !~ /^(?:\#.+|\%YAML[: ][\d\.]+)\z/){push @$self,$self->_load_scalar("$1",[undef ],\@lines);next}$in_document=1}if (!@lines or $lines[0]=~ /^(?:---|\.\.\.)/){push @$self,undef;while (@lines and $lines[0]!~ /^---/){shift@lines}$in_document=0}elsif (!$in_document && @$self){die \"CPAN::Meta::YAML failed to classify the line '$lines[0]'"}elsif ($lines[0]=~ /^\s*\-(?:\s|$|-+$)/){my$document=[];push @$self,$document;$self->_load_array($document,[0 ],\@lines)}elsif ($lines[0]=~ /^(\s*)\S/){my$document={};push @$self,$document;$self->_load_hash($document,[length($1)],\@lines)}else {die \"CPAN::Meta::YAML failed to classify the line '$lines[0]'"}}};my$err=$@;if (ref$err eq 'SCALAR'){$self->_error(${$err})}elsif ($err){$self->_error($err)}return$self}sub _unquote_single {my ($self,$string)=@_;return '' unless length$string;$string =~ s/\'\'/\'/g;return$string}sub _unquote_double {my ($self,$string)=@_;return '' unless length$string;$string =~ s/\\"/"/g;$string =~ s{\\([Nnever\\fartz0b]|x([0-9a-fA-F]{2}))}
+  Read an invalid UTF-8 string (maybe mixed UTF-8 and 8-bit character set).
+  Did you decode with lax ":utf8" instead of strict ":encoding(UTF-8)"?
+  ...
+           {(length($1)>1)?pack("H2",$2):$UNESCAPES{$1}}gex;return$string}sub _load_scalar {my ($self,$string,$indent,$lines)=@_;$string =~ s/\s*\z//;return undef if$string eq '~';if ($string =~ /^$re_capture_single_quoted$re_trailing_comment\z/){return$self->_unquote_single($1)}if ($string =~ /^$re_capture_double_quoted$re_trailing_comment\z/){return$self->_unquote_double($1)}if ($string =~ /^[\'\"!&]/){die \"CPAN::Meta::YAML does not support a feature in line '$string'"}return {}if$string =~ /^{}(?:\s+\#.*)?\z/;return []if$string =~ /^\[\](?:\s+\#.*)?\z/;if ($string !~ /^[>|]/){die \"CPAN::Meta::YAML found illegal characters in plain scalar: '$string'" if$string =~ /^(?:-(?:\s|$)|[\@\%\`])/ or $string =~ /:(?:\s|$)/;$string =~ s/\s+#.*\z//;return$string}die \"CPAN::Meta::YAML failed to find multi-line scalar content" unless @$lines;$lines->[0]=~ /^(\s*)/;$indent->[-1]=length("$1");if (defined$indent->[-2]and $indent->[-1]<= $indent->[-2]){die \"CPAN::Meta::YAML found bad indenting in line '$lines->[0]'"}my@multiline=();while (@$lines){$lines->[0]=~ /^(\s*)/;last unless length($1)>= $indent->[-1];push@multiline,substr(shift(@$lines),length($1))}my$j=(substr($string,0,1)eq '>')? ' ' : "\n";my$t=(substr($string,1,1)eq '-')? '' : "\n";return join($j,@multiline).$t}sub _load_array {my ($self,$array,$indent,$lines)=@_;while (@$lines){if ($lines->[0]=~ /^(?:---|\.\.\.)/){while (@$lines and $lines->[0]!~ /^---/){shift @$lines}return 1}$lines->[0]=~ /^(\s*)/;if (length($1)< $indent->[-1]){return 1}elsif (length($1)> $indent->[-1]){die \"CPAN::Meta::YAML found bad indenting in line '$lines->[0]'"}if ($lines->[0]=~ /^(\s*\-\s+)[^\'\"]\S*\s*:(?:\s+|$)/){my$indent2=length("$1");$lines->[0]=~ s/-/ /;push @$array,{};$self->_load_hash($array->[-1],[@$indent,$indent2 ],$lines)}elsif ($lines->[0]=~ /^\s*\-\s*\z/){shift @$lines;unless (@$lines){push @$array,undef;return 1}if ($lines->[0]=~ /^(\s*)\-/){my$indent2=length("$1");if ($indent->[-1]==$indent2){push @$array,undef}else {push @$array,[];$self->_load_array($array->[-1],[@$indent,$indent2 ],$lines)}}elsif ($lines->[0]=~ /^(\s*)\S/){push @$array,{};$self->_load_hash($array->[-1],[@$indent,length("$1")],$lines)}else {die \"CPAN::Meta::YAML failed to classify line '$lines->[0]'"}}elsif ($lines->[0]=~ /^\s*\-(\s*)(.+?)\s*\z/){shift @$lines;push @$array,$self->_load_scalar("$2",[@$indent,undef ],$lines)}elsif (defined$indent->[-2]and $indent->[-1]==$indent->[-2]){return 1}else {die \"CPAN::Meta::YAML failed to classify line '$lines->[0]'"}}return 1}sub _load_hash {my ($self,$hash,$indent,$lines)=@_;while (@$lines){if ($lines->[0]=~ /^(?:---|\.\.\.)/){while (@$lines and $lines->[0]!~ /^---/){shift @$lines}return 1}$lines->[0]=~ /^(\s*)/;if (length($1)< $indent->[-1]){return 1}elsif (length($1)> $indent->[-1]){die \"CPAN::Meta::YAML found bad indenting in line '$lines->[0]'"}my$key;if ($lines->[0]=~ s/^\s*$re_capture_single_quoted$re_key_value_separator//){$key=$self->_unquote_single($1)}elsif ($lines->[0]=~ s/^\s*$re_capture_double_quoted$re_key_value_separator//){$key=$self->_unquote_double($1)}elsif ($lines->[0]=~ s/^\s*$re_capture_unquoted_key$re_key_value_separator//){$key=$1;$key =~ s/\s+$//}elsif ($lines->[0]=~ /^\s*\?/){die \"CPAN::Meta::YAML does not support a feature in line '$lines->[0]'"}else {die \"CPAN::Meta::YAML failed to classify line '$lines->[0]'"}if (exists$hash->{$key}){warn "CPAN::Meta::YAML found a duplicate key '$key' in line '$lines->[0]'"}if (length$lines->[0]){$hash->{$key}=$self->_load_scalar(shift(@$lines),[@$indent,undef ],$lines)}else {shift @$lines;unless (@$lines){$hash->{$key}=undef;return 1}if ($lines->[0]=~ /^(\s*)-/){$hash->{$key}=[];$self->_load_array($hash->{$key},[@$indent,length($1)],$lines)}elsif ($lines->[0]=~ /^(\s*)./){my$indent2=length("$1");if ($indent->[-1]>= $indent2){$hash->{$key}=undef}else {$hash->{$key}={};$self->_load_hash($hash->{$key},[@$indent,length($1)],$lines)}}}}return 1}sub _dump_file {my$self=shift;require Fcntl;my$file=shift or $self->_error('You did not specify a file name');my$fh;if (_can_flock()){my$flags=Fcntl::O_WRONLY()|Fcntl::O_CREAT();sysopen($fh,$file,$flags);unless ($fh){$self->_error("Failed to open file '$file' for writing: $!")}binmode($fh,":raw:encoding(UTF-8)");flock($fh,Fcntl::LOCK_EX())or warn "Couldn't lock '$file' for reading: $!";truncate$fh,0;seek$fh,0,0}else {open$fh,">:unix:encoding(UTF-8)",$file}print {$fh}$self->_dump_string;unless (close$fh){$self->_error("Failed to close file '$file': $!")}return 1}sub _dump_string {my$self=shift;return '' unless ref$self && @$self;my$indent=0;my@lines=();eval {for my$cursor (@$self){push@lines,'---';if (!defined$cursor){}elsif (!ref$cursor){$lines[-1].= ' ' .$self->_dump_scalar($cursor)}elsif (ref$cursor eq 'ARRAY'){unless (@$cursor){$lines[-1].= ' []';next}push@lines,$self->_dump_array($cursor,$indent,{})}elsif (ref$cursor eq 'HASH'){unless (%$cursor){$lines[-1].= ' {}';next}push@lines,$self->_dump_hash($cursor,$indent,{})}else {die \("Cannot serialize " .ref($cursor))}}};if (ref $@ eq 'SCALAR'){$self->_error(${$@})}elsif ($@){$self->_error($@)}join '',map {"$_\n"}@lines}sub _has_internal_string_value {my$value=shift;my$b_obj=B::svref_2object(\$value);return$b_obj->FLAGS & B::SVf_POK()}sub _dump_scalar {my$string=$_[1];my$is_key=$_[2];my$has_string_flag=_has_internal_string_value($string);return '~' unless defined$string;return "''" unless length$string;if (Scalar::Util::looks_like_number($string)){if ($is_key || $has_string_flag){return qq['$string']}else {return$string}}if ($string =~ /[\x00-\x09\x0b-\x0d\x0e-\x1f\x7f-\x9f\'\n]/){$string =~ s/\\/\\\\/g;$string =~ s/"/\\"/g;$string =~ s/\n/\\n/g;$string =~ s/[\x85]/\\N/g;$string =~ s/([\x00-\x1f])/\\$UNPRINTABLE[ord($1)]/g;$string =~ s/([\x7f-\x9f])/'\x' . sprintf("%X",ord($1))/ge;return qq|"$string"|}if ($string =~ /(?:^[~!@#%&*|>?:,'"`{}\[\]]|^-+$|\s|:\z)/ or $QUOTE{$string}){return "'$string'"}return$string}sub _dump_array {my ($self,$array,$indent,$seen)=@_;if ($seen->{refaddr($array)}++){die \"CPAN::Meta::YAML does not support circular references"}my@lines=();for my$el (@$array){my$line=('  ' x $indent).'-';my$type=ref$el;if (!$type){$line .= ' ' .$self->_dump_scalar($el);push@lines,$line}elsif ($type eq 'ARRAY'){if (@$el){push@lines,$line;push@lines,$self->_dump_array($el,$indent + 1,$seen)}else {$line .= ' []';push@lines,$line}}elsif ($type eq 'HASH'){if (keys %$el){push@lines,$line;push@lines,$self->_dump_hash($el,$indent + 1,$seen)}else {$line .= ' {}';push@lines,$line}}else {die \"CPAN::Meta::YAML does not support $type references"}}@lines}sub _dump_hash {my ($self,$hash,$indent,$seen)=@_;if ($seen->{refaddr($hash)}++){die \"CPAN::Meta::YAML does not support circular references"}my@lines=();for my$name (sort keys %$hash){my$el=$hash->{$name};my$line=('  ' x $indent).$self->_dump_scalar($name,1).":";my$type=ref$el;if (!$type){$line .= ' ' .$self->_dump_scalar($el);push@lines,$line}elsif ($type eq 'ARRAY'){if (@$el){push@lines,$line;push@lines,$self->_dump_array($el,$indent + 1,$seen)}else {$line .= ' []';push@lines,$line}}elsif ($type eq 'HASH'){if (keys %$el){push@lines,$line;push@lines,$self->_dump_hash($el,$indent + 1,$seen)}else {$line .= ' {}';push@lines,$line}}else {die \"CPAN::Meta::YAML does not support $type references"}}@lines}our$errstr='';sub _error {require Carp;$errstr=$_[1];$errstr =~ s/ at \S+ line \d+.*//;Carp::croak($errstr)}my$errstr_warned;sub errstr {require Carp;Carp::carp("CPAN::Meta::YAML->errstr and \$CPAN::Meta::YAML::errstr is deprecated")unless$errstr_warned++;$errstr}use B;my$HAS_FLOCK;sub _can_flock {if (defined$HAS_FLOCK){return$HAS_FLOCK}else {require Config;my$c=\%Config::Config;$HAS_FLOCK=grep {$c->{$_}}qw/d_flock d_fcntl_can_lock d_lockf/;require Fcntl if$HAS_FLOCK;return$HAS_FLOCK}}use Scalar::Util ();BEGIN {local $@;if (eval {Scalar::Util->VERSION(1.18)}){*refaddr=*Scalar::Util::refaddr}else {eval <<'END_PERL'}}delete$CPAN::Meta::YAML::{refaddr};1;
+  # Scalar::Util failed to load or too old
+  sub refaddr {
+      my $pkg = ref($_[0]) or return undef;
+      if ( !! UNIVERSAL::can($_[0], 'can') ) {
+          bless $_[0], 'Scalar::Util::Fake';
+      } else {
+          $pkg = undef;
+      }
+      "$_[0]" =~ /0x(\w+)/;
+      my $i = do { no warnings 'portable'; hex $1 };
+      bless $_[0], $pkg if defined $pkg;
+      $i;
+  }
+  END_PERL
+CPAN_META_YAML
+
+$fatpacked{"Exporter.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'EXPORTER';
+  package Exporter;require 5.006;our$Debug=0;our$ExportLevel=0;our$Verbose ||= 0;our$VERSION='5.70';our (%Cache);sub as_heavy {require Exporter::Heavy;my$c=(caller(1))[3];$c =~ s/.*:://;\&{"Exporter::Heavy::heavy_$c"}}sub export {goto &{as_heavy()}}sub import {my$pkg=shift;my$callpkg=caller($ExportLevel);if ($pkg eq "Exporter" and @_ and $_[0]eq "import"){*{$callpkg."::import"}=\&import;return}my$exports=\@{"$pkg\::EXPORT"};my$fail=${$pkg .'::'}{EXPORT_FAIL}&& \@{"$pkg\::EXPORT_FAIL"};return export$pkg,$callpkg,@_ if$Verbose or $Debug or $fail && @$fail > 1;my$export_cache=($Cache{$pkg}||= {});my$args=@_ or @_=@$exports;if ($args and not %$export_cache){s/^&//,$export_cache->{$_}=1 foreach (@$exports,@{"$pkg\::EXPORT_OK"})}my$heavy;if ($args or $fail){($heavy=(/\W/ or $args and not exists$export_cache->{$_}or $fail and @$fail and $_ eq $fail->[0]))and last foreach (@_)}else {($heavy=/\W/)and last foreach (@_)}return export$pkg,$callpkg,($args ? @_ : ())if$heavy;local$SIG{__WARN__}=sub {require Carp;&Carp::carp}if not $SIG{__WARN__};*{"$callpkg\::$_"}=\&{"$pkg\::$_"}foreach @_}sub export_fail {my$self=shift;@_}sub export_to_level {goto &{as_heavy()}}sub export_tags {goto &{as_heavy()}}sub export_ok_tags {goto &{as_heavy()}}sub require_version {goto &{as_heavy()}}1;
+EXPORTER
+
+$fatpacked{"Exporter/Heavy.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'EXPORTER_HEAVY';
+  package Exporter::Heavy;use strict;no strict 'refs';require Exporter;our$VERSION=$Exporter::VERSION;sub _rebuild_cache {my ($pkg,$exports,$cache)=@_;s/^&// foreach @$exports;@{$cache}{@$exports}=(1)x @$exports;my$ok=\@{"${pkg}::EXPORT_OK"};if (@$ok){s/^&// foreach @$ok;@{$cache}{@$ok}=(1)x @$ok}}sub heavy_export {my$oldwarn=$SIG{__WARN__};local$SIG{__WARN__}=sub {local$SIG{__WARN__}=$oldwarn;my$text=shift;if ($text =~ s/ at \S*Exporter\S*.pm line \d+.*\n//){require Carp;local$Carp::CarpLevel=1;Carp::carp($text)}else {warn$text}};local$SIG{__DIE__}=sub {require Carp;local$Carp::CarpLevel=1;Carp::croak("$_[0]Illegal null symbol in \@${1}::EXPORT")if $_[0]=~ /^Unable to create sub named "(.*?)::"/};my($pkg,$callpkg,@imports)=@_;my($type,$sym,$cache_is_current,$oops);my($exports,$export_cache)=(\@{"${pkg}::EXPORT"},$Exporter::Cache{$pkg}||= {});if (@imports){if (!%$export_cache){_rebuild_cache ($pkg,$exports,$export_cache);$cache_is_current=1}if (grep m{^[/!:]},@imports){my$tagsref=\%{"${pkg}::EXPORT_TAGS"};my$tagdata;my%imports;my($remove,$spec,@names,@allexports);unshift@imports,':DEFAULT' if$imports[0]=~ m/^!/;for$spec (@imports){$remove=$spec =~ s/^!//;if ($spec =~ s/^://){if ($spec eq 'DEFAULT'){@names=@$exports}elsif ($tagdata=$tagsref->{$spec}){@names=@$tagdata}else {warn qq["$spec" is not defined in %${pkg}::EXPORT_TAGS];++$oops;next}}elsif ($spec =~ m:^/(.*)/$:){my$patn=$1;@allexports=keys %$export_cache unless@allexports;@names=grep(/$patn/,@allexports)}else {@names=($spec)}warn "Import ".($remove ? "del":"add").": @names " if$Exporter::Verbose;if ($remove){for$sym (@names){delete$imports{$sym}}}else {@imports{@names}=(1)x @names}}@imports=keys%imports}my@carp;for$sym (@imports){if (!$export_cache->{$sym}){if ($sym =~ m/^\d/){$pkg->VERSION($sym);if (@imports==1){@imports=@$exports;last}if (@imports==2 and!$imports[1]){@imports=();last}}elsif ($sym !~ s/^&// ||!$export_cache->{$sym}){unless ($cache_is_current){%$export_cache=();_rebuild_cache ($pkg,$exports,$export_cache);$cache_is_current=1}if (!$export_cache->{$sym}){push@carp,qq["$sym" is not exported by the $pkg module\n];$oops++}}}}if ($oops){require Carp;Carp::croak("@{carp}Can't continue after import errors")}}else {@imports=@$exports}my($fail,$fail_cache)=(\@{"${pkg}::EXPORT_FAIL"},$Exporter::FailCache{$pkg}||= {});if (@$fail){if (!%$fail_cache){my@expanded=map {/^\w/ ? ($_,'&'.$_): $_}@$fail;warn "${pkg}::EXPORT_FAIL cached: @expanded" if$Exporter::Verbose;@{$fail_cache}{@expanded}=(1)x @expanded}my@failed;for$sym (@imports){push(@failed,$sym)if$fail_cache->{$sym}}if (@failed){@failed=$pkg->export_fail(@failed);for$sym (@failed){require Carp;Carp::carp(qq["$sym" is not implemented by the $pkg module ],"on this architecture")}if (@failed){require Carp;Carp::croak("Can't continue after import errors")}}}warn "Importing into $callpkg from $pkg: ",join(", ",sort@imports)if$Exporter::Verbose;for$sym (@imports){(*{"${callpkg}::$sym"}=\&{"${pkg}::$sym"},next)unless$sym =~ s/^(\W)//;$type=$1;no warnings 'once';*{"${callpkg}::$sym"}=$type eq '&' ? \&{"${pkg}::$sym"}: $type eq '$' ? \${"${pkg}::$sym"}: $type eq '@' ? \@{"${pkg}::$sym"}: $type eq '%' ? \%{"${pkg}::$sym"}: $type eq '*' ? *{"${pkg}::$sym"}: do {require Carp;Carp::croak("Can't export symbol: $type$sym")}}}sub heavy_export_to_level {my$pkg=shift;my$level=shift;(undef)=shift;my$callpkg=caller($level);$pkg->export($callpkg,@_)}sub _push_tags {my($pkg,$var,$syms)=@_;my@nontag=();my$export_tags=\%{"${pkg}::EXPORT_TAGS"};push(@{"${pkg}::$var"},map {$export_tags->{$_}? @{$export_tags->{$_}}: scalar(push(@nontag,$_),$_)}(@$syms)? @$syms : keys %$export_tags);if (@nontag and $^W){require Carp;Carp::carp(join(", ",@nontag)." are not tags of $pkg")}}sub heavy_require_version {my($self,$wanted)=@_;my$pkg=ref$self || $self;return ${pkg}->VERSION($wanted)}sub heavy_export_tags {_push_tags((caller)[0],"EXPORT",\@_)}sub heavy_export_ok_tags {_push_tags((caller)[0],"EXPORT_OK",\@_)}1;
+EXPORTER_HEAVY
+
+$fatpacked{"File/pushd.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'FILE_PUSHD';
+  use strict;use warnings;package File::pushd;our$VERSION='1.009';our@EXPORT=qw(pushd tempd);our@ISA=qw(Exporter);use Exporter;use Carp;use Cwd qw(getcwd abs_path);use File::Path qw(rmtree);use File::Temp qw();use File::Spec;use overload q{""}=>sub {File::Spec->canonpath($_[0]->{_pushd})},fallback=>1;sub pushd {my ($target_dir,$options)=@_;$options->{untaint_pattern}||= qr{^([-+@\w./]+)$};$target_dir="." unless defined$target_dir;croak "Can't locate directory $target_dir" unless -d $target_dir;my$tainted_orig=getcwd;my$orig;if ($tainted_orig =~ $options->{untaint_pattern}){$orig=$1}else {$orig=$tainted_orig}my$tainted_dest;eval {$tainted_dest=$target_dir ? abs_path($target_dir): $orig};croak "Can't locate absolute path for $target_dir: $@" if $@;my$dest;if ($tainted_dest =~ $options->{untaint_pattern}){$dest=$1}else {$dest=$tainted_dest}if ($dest ne $orig){chdir$dest or croak "Can't chdir to $dest\: $!"}my$self=bless {_pushd=>$dest,_original=>$orig },__PACKAGE__;return$self}sub tempd {my ($options)=@_;my$dir;eval {$dir=pushd(File::Temp::tempdir(CLEANUP=>0),$options)};croak $@ if $@;$dir->{_tempd}=1;return$dir}sub preserve {my$self=shift;return 1 if!$self->{"_tempd"};if (@_==0){return$self->{_preserve}=1}else {return$self->{_preserve}=$_[0]? 1 : 0}}sub DESTROY {my ($self)=@_;my$orig=$self->{_original};chdir$orig if$orig;if ($self->{_tempd}&&!$self->{_preserve}){my$err=do {local $@;eval {rmtree($self->{_pushd})};$@};carp$err if$err}}1;
+FILE_PUSHD
+
+$fatpacked{"HTTP/Tiny.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'HTTP_TINY';
+  package HTTP::Tiny;use strict;use warnings;our$VERSION='0.056';use Carp ();my@attributes;BEGIN {@attributes=qw(cookie_jar default_headers http_proxy https_proxy keep_alive local_address max_redirect max_size proxy no_proxy timeout SSL_options verify_SSL);my%persist_ok=map {;$_=>1}qw(cookie_jar default_headers max_redirect max_size);no strict 'refs';no warnings 'uninitialized';for my$accessor (@attributes){*{$accessor}=sub {@_ > 1 ? do {delete $_[0]->{handle}if!$persist_ok{$accessor}&& $_[1]ne $_[0]->{$accessor};$_[0]->{$accessor}=$_[1]}: $_[0]->{$accessor}}}}sub agent {my($self,$agent)=@_;if(@_ > 1){$self->{agent}=(defined$agent && $agent =~ / $/)? $agent .$self->_agent : $agent}return$self->{agent}}sub new {my($class,%args)=@_;my$self={max_redirect=>5,timeout=>60,keep_alive=>1,verify_SSL=>$args{verify_SSL}|| $args{verify_ssl}|| 0,no_proxy=>$ENV{no_proxy},};bless$self,$class;$class->_validate_cookie_jar($args{cookie_jar})if$args{cookie_jar};for my$key (@attributes){$self->{$key}=$args{$key}if exists$args{$key}}$self->agent(exists$args{agent}? $args{agent}: $class->_agent);$self->_set_proxies;return$self}sub _set_proxies {my ($self)=@_;if (!exists$self->{proxy}){$self->{proxy}=$ENV{all_proxy}|| $ENV{ALL_PROXY}}if (defined$self->{proxy}){$self->_split_proxy('generic proxy'=>$self->{proxy})}else {delete$self->{proxy}}if (!exists$self->{http_proxy}){local$ENV{HTTP_PROXY}if$ENV{REQUEST_METHOD};$self->{http_proxy}=$ENV{http_proxy}|| $ENV{HTTP_PROXY}|| $self->{proxy}}if (defined$self->{http_proxy}){$self->_split_proxy(http_proxy=>$self->{http_proxy});$self->{_has_proxy}{http}=1}else {delete$self->{http_proxy}}if (!exists$self->{https_proxy}){$self->{https_proxy}=$ENV{https_proxy}|| $ENV{HTTPS_PROXY}|| $self->{proxy}}if ($self->{https_proxy}){$self->_split_proxy(https_proxy=>$self->{https_proxy});$self->{_has_proxy}{https}=1}else {delete$self->{https_proxy}}unless (ref$self->{no_proxy}eq 'ARRAY'){$self->{no_proxy}=(defined$self->{no_proxy})? [split /\s*,\s*/,$self->{no_proxy}]: []}return}for my$sub_name (qw/get head put post delete/){my$req_method=uc$sub_name;no strict 'refs';eval <<"HERE"}sub post_form {my ($self,$url,$data,$args)=@_;(@_==3 || @_==4 && ref$args eq 'HASH')or Carp::croak(q/Usage: $http->post_form(URL, DATAREF, [HASHREF])/ ."\n");my$headers={};while (my ($key,$value)=each %{$args->{headers}|| {}}){$headers->{lc$key}=$value}delete$args->{headers};return$self->request('POST',$url,{%$args,content=>$self->www_form_urlencode($data),headers=>{%$headers,'content-type'=>'application/x-www-form-urlencoded' },})}sub mirror {my ($self,$url,$file,$args)=@_;@_==3 || (@_==4 && ref$args eq 'HASH')or Carp::croak(q/Usage: $http->mirror(URL, FILE, [HASHREF])/ ."\n");if (-e $file and my$mtime=(stat($file))[9]){$args->{headers}{'if-modified-since'}||= $self->_http_date($mtime)}my$tempfile=$file .int(rand(2**31));require Fcntl;sysopen my$fh,$tempfile,Fcntl::O_CREAT()|Fcntl::O_EXCL()|Fcntl::O_WRONLY()or Carp::croak(qq/Error: Could not create temporary file $tempfile for downloading: $!\n/);binmode$fh;$args->{data_callback}=sub {print {$fh}$_[0]};my$response=$self->request('GET',$url,$args);close$fh or Carp::croak(qq/Error: Caught error closing temporary file $tempfile: $!\n/);if ($response->{success}){rename$tempfile,$file or Carp::croak(qq/Error replacing $file with $tempfile: $!\n/);my$lm=$response->{headers}{'last-modified'};if ($lm and my$mtime=$self->_parse_http_date($lm)){utime$mtime,$mtime,$file}}$response->{success}||= $response->{status}eq '304';unlink$tempfile;return$response}my%idempotent=map {$_=>1}qw/GET HEAD PUT DELETE OPTIONS TRACE/;sub request {my ($self,$method,$url,$args)=@_;@_==3 || (@_==4 && ref$args eq 'HASH')or Carp::croak(q/Usage: $http->request(METHOD, URL, [HASHREF])/ ."\n");$args ||= {};my$response;for (0 .. 1){$response=eval {$self->_request($method,$url,$args)};last unless $@ && $idempotent{$method}&& $@ =~ m{^(?:Socket closed|Unexpected end)}}if (my$e=$@){if (ref$e eq 'HASH' && exists$e->{status}){return$e}$e="$e";$response={url=>$url,success=>q{},status=>599,reason=>'Internal Exception',content=>$e,headers=>{'content-type'=>'text/plain','content-length'=>length$e,}}}return$response}sub www_form_urlencode {my ($self,$data)=@_;(@_==2 && ref$data)or Carp::croak(q/Usage: $http->www_form_urlencode(DATAREF)/ ."\n");(ref$data eq 'HASH' || ref$data eq 'ARRAY')or Carp::croak("form data must be a hash or array reference\n");my@params=ref$data eq 'HASH' ? %$data : @$data;@params % 2==0 or Carp::croak("form data reference must have an even number of terms\n");my@terms;while(@params){my ($key,$value)=splice(@params,0,2);if (ref$value eq 'ARRAY'){unshift@params,map {$key=>$_}@$value}else {push@terms,join("=",map {$self->_uri_escape($_)}$key,$value)}}return join("&",(ref$data eq 'ARRAY')? (@terms): (sort@terms))}sub can_ssl {my ($self)=@_;my($ok,$reason)=(1,'');unless (eval {require IO::Socket::SSL;IO::Socket::SSL->VERSION(1.42)}){$ok=0;$reason .= qq/IO::Socket::SSL 1.42 must be installed for https support\n/}unless (eval {require Net::SSLeay;Net::SSLeay->VERSION(1.49)}){$ok=0;$reason .= qq/Net::SSLeay 1.49 must be installed for https support\n/}if (ref($self)&& ($self->{verify_SSL}|| $self->{SSL_options}{SSL_verify_mode})){my$handle=HTTP::Tiny::Handle->new(SSL_options=>$self->{SSL_options},verify_SSL=>$self->{verify_SSL},);unless (eval {$handle->_find_CA_file;1}){$ok=0;$reason .= "$@"}}wantarray ? ($ok,$reason): $ok}my%DefaultPort=(http=>80,https=>443,);sub _agent {my$class=ref($_[0])|| $_[0];(my$default_agent=$class)=~ s{::}{-}g;return$default_agent ."/" .$class->VERSION}sub _request {my ($self,$method,$url,$args)=@_;my ($scheme,$host,$port,$path_query,$auth)=$self->_split_url($url);my$request={method=>$method,scheme=>$scheme,host=>$host,port=>$port,host_port=>($port==$DefaultPort{$scheme}? $host : "$host:$port"),uri=>$path_query,headers=>{},};my$handle=delete$self->{handle};if ($handle){unless ($handle->can_reuse($scheme,$host,$port)){$handle->close;undef$handle}}$handle ||= $self->_open_handle($request,$scheme,$host,$port);$self->_prepare_headers_and_cb($request,$args,$url,$auth);$handle->write_request($request);my$response;do {$response=$handle->read_response_header}until (substr($response->{status},0,1)ne '1');$self->_update_cookie_jar($url,$response)if$self->{cookie_jar};if (my@redir_args=$self->_maybe_redirect($request,$response,$args)){$handle->close;return$self->_request(@redir_args,$args)}my$known_message_length;if ($method eq 'HEAD' || $response->{status}=~ /^[23]04/){$known_message_length=1}else {my$data_cb=$self->_prepare_data_cb($response,$args);$known_message_length=$handle->read_body($data_cb,$response)}if ($self->{keep_alive}&& $known_message_length && $response->{protocol}eq 'HTTP/1.1' && ($response->{headers}{connection}|| '')ne 'close'){$self->{handle}=$handle}else {$handle->close}$response->{success}=substr($response->{status},0,1)eq '2';$response->{url}=$url;return$response}sub _open_handle {my ($self,$request,$scheme,$host,$port)=@_;my$handle=HTTP::Tiny::Handle->new(timeout=>$self->{timeout},SSL_options=>$self->{SSL_options},verify_SSL=>$self->{verify_SSL},local_address=>$self->{local_address},keep_alive=>$self->{keep_alive});if ($self->{_has_proxy}{$scheme}&&!grep {$host =~ /\Q$_\E$/}@{$self->{no_proxy}}){return$self->_proxy_connect($request,$handle)}else {return$handle->connect($scheme,$host,$port)}}sub _proxy_connect {my ($self,$request,$handle)=@_;my@proxy_vars;if ($request->{scheme}eq 'https'){Carp::croak(qq{No https_proxy defined})unless$self->{https_proxy};@proxy_vars=$self->_split_proxy(https_proxy=>$self->{https_proxy});if ($proxy_vars[0]eq 'https'){Carp::croak(qq{Can't proxy https over https: $request->{uri} via $self->{https_proxy}})}}else {Carp::croak(qq{No http_proxy defined})unless$self->{http_proxy};@proxy_vars=$self->_split_proxy(http_proxy=>$self->{http_proxy})}my ($p_scheme,$p_host,$p_port,$p_auth)=@proxy_vars;if (length$p_auth &&!defined$request->{headers}{'proxy-authorization'}){$self->_add_basic_auth_header($request,'proxy-authorization'=>$p_auth)}$handle->connect($p_scheme,$p_host,$p_port);if ($request->{scheme}eq 'https'){$self->_create_proxy_tunnel($request,$handle)}else {$request->{uri}="$request->{scheme}://$request->{host_port}$request->{uri}"}return$handle}sub _split_proxy {my ($self,$type,$proxy)=@_;my ($scheme,$host,$port,$path_query,$auth)=eval {$self->_split_url($proxy)};unless(defined($scheme)&& length($scheme)&& length($host)&& length($port)&& $path_query eq '/'){Carp::croak(qq{$type URL must be in format http[s]://[auth@]<host>:<port>/\n})}return ($scheme,$host,$port,$auth)}sub _create_proxy_tunnel {my ($self,$request,$handle)=@_;$handle->_assert_ssl;my$agent=exists($request->{headers}{'user-agent'})? $request->{headers}{'user-agent'}: $self->{agent};my$connect_request={method=>'CONNECT',uri=>"$request->{host}:$request->{port}",headers=>{host=>"$request->{host}:$request->{port}",'user-agent'=>$agent,}};if ($request->{headers}{'proxy-authorization'}){$connect_request->{headers}{'proxy-authorization'}=delete$request->{headers}{'proxy-authorization'}}$handle->write_request($connect_request);my$response;do {$response=$handle->read_response_header}until (substr($response->{status},0,1)ne '1');unless (substr($response->{status},0,1)eq '2'){die$response}$handle->start_ssl($request->{host});return}sub _prepare_headers_and_cb {my ($self,$request,$args,$url,$auth)=@_;for ($self->{default_headers},$args->{headers}){next unless defined;while (my ($k,$v)=each %$_){$request->{headers}{lc$k}=$v}}if (exists$request->{headers}{'host'}){die(qq/The 'Host' header must not be provided as header option\n/)}$request->{headers}{'host'}=$request->{host_port};$request->{headers}{'user-agent'}||= $self->{agent};$request->{headers}{'connection'}="close" unless$self->{keep_alive};if (defined$args->{content}){if (ref$args->{content}eq 'CODE'){$request->{headers}{'content-type'}||= "application/octet-stream";$request->{headers}{'transfer-encoding'}='chunked' unless$request->{headers}{'content-length'}|| $request->{headers}{'transfer-encoding'};$request->{cb}=$args->{content}}elsif (length$args->{content}){my$content=$args->{content};if ($] ge '5.008'){utf8::downgrade($content,1)or die(qq/Wide character in request message body\n/)}$request->{headers}{'content-type'}||= "application/octet-stream";$request->{headers}{'content-length'}=length$content unless$request->{headers}{'content-length'}|| $request->{headers}{'transfer-encoding'};$request->{cb}=sub {substr$content,0,length$content,''}}$request->{trailer_cb}=$args->{trailer_callback}if ref$args->{trailer_callback}eq 'CODE'}if ($self->{cookie_jar}){my$cookies=$self->cookie_jar->cookie_header($url);$request->{headers}{cookie}=$cookies if length$cookies}if (length$auth &&!defined$request->{headers}{authorization}){$self->_add_basic_auth_header($request,'authorization'=>$auth)}return}sub _add_basic_auth_header {my ($self,$request,$header,$auth)=@_;require MIME::Base64;$request->{headers}{$header}="Basic " .MIME::Base64::encode_base64($auth,"");return}sub _prepare_data_cb {my ($self,$response,$args)=@_;my$data_cb=$args->{data_callback};$response->{content}='';if (!$data_cb || $response->{status}!~ /^2/){if (defined$self->{max_size}){$data_cb=sub {$_[1]->{content}.= $_[0];die(qq/Size of response body exceeds the maximum allowed of $self->{max_size}\n/)if length $_[1]->{content}> $self->{max_size}}}else {$data_cb=sub {$_[1]->{content}.= $_[0]}}}return$data_cb}sub _update_cookie_jar {my ($self,$url,$response)=@_;my$cookies=$response->{headers}->{'set-cookie'};return unless defined$cookies;my@cookies=ref$cookies ? @$cookies : $cookies;$self->cookie_jar->add($url,$_)for@cookies;return}sub _validate_cookie_jar {my ($class,$jar)=@_;for my$method (qw/add cookie_header/){Carp::croak(qq/Cookie jar must provide the '$method' method\n/)unless ref($jar)&& ref($jar)->can($method)}return}sub _maybe_redirect {my ($self,$request,$response,$args)=@_;my$headers=$response->{headers};my ($status,$method)=($response->{status},$request->{method});if (($status eq '303' or ($status =~ /^30[1278]/ && $method =~ /^GET|HEAD$/))and $headers->{location}and ++$args->{redirects}<= $self->{max_redirect}){my$location=($headers->{location}=~ /^\//)? "$request->{scheme}://$request->{host_port}$headers->{location}" : $headers->{location};return (($status eq '303' ? 'GET' : $method),$location)}return}sub _split_url {my$url=pop;my ($scheme,$host,$path_query)=$url =~ m<\A([^:/?#]+)://([^/?#]*)([^#]*)> or die(qq/Cannot parse URL: '$url'\n/);$scheme=lc$scheme;$path_query="/$path_query" unless$path_query =~ m<\A/>;my$auth='';if ((my$i=index$host,'@')!=-1){$auth=substr$host,0,$i,'';substr$host,0,1,'';$auth =~ s/%([0-9A-Fa-f]{2})/chr(hex($1))/eg}my$port=$host =~ s/:(\d*)\z// && length $1 ? $1 : $scheme eq 'http' ? 80 : $scheme eq 'https' ? 443 : undef;return ($scheme,(length$host ? lc$host : "localhost"),$port,$path_query,$auth)}my$DoW="Sun|Mon|Tue|Wed|Thu|Fri|Sat";my$MoY="Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec";sub _http_date {my ($sec,$min,$hour,$mday,$mon,$year,$wday)=gmtime($_[1]);return sprintf("%s, %02d %s %04d %02d:%02d:%02d GMT",substr($DoW,$wday*4,3),$mday,substr($MoY,$mon*4,3),$year+1900,$hour,$min,$sec)}sub _parse_http_date {my ($self,$str)=@_;require Time::Local;my@tl_parts;if ($str =~ /^[SMTWF][a-z]+, +(\d{1,2}) ($MoY) +(\d\d\d\d) +(\d\d):(\d\d):(\d\d) +GMT$/){@tl_parts=($6,$5,$4,$1,(index($MoY,$2)/4),$3)}elsif ($str =~ /^[SMTWF][a-z]+, +(\d\d)-($MoY)-(\d{2,4}) +(\d\d):(\d\d):(\d\d) +GMT$/){@tl_parts=($6,$5,$4,$1,(index($MoY,$2)/4),$3)}elsif ($str =~ /^[SMTWF][a-z]+ +($MoY) +(\d{1,2}) +(\d\d):(\d\d):(\d\d) +(?:[^0-9]+ +)?(\d\d\d\d)$/){@tl_parts=($5,$4,$3,$2,(index($MoY,$1)/4),$6)}return eval {my$t=@tl_parts ? Time::Local::timegm(@tl_parts): -1;$t < 0 ? undef : $t}}my%escapes=map {chr($_)=>sprintf("%%%02X",$_)}0..255;$escapes{' '}="+";my$unsafe_char=qr/[^A-Za-z0-9\-\._~]/;sub _uri_escape {my ($self,$str)=@_;if ($] ge '5.008'){utf8::encode($str)}else {$str=pack("U*",unpack("C*",$str))if (length$str==do {use bytes;length$str});$str=pack("C*",unpack("C*",$str))}$str =~ s/($unsafe_char)/$escapes{$1}/ge;return$str}package HTTP::Tiny::Handle;use strict;use warnings;use Errno qw[EINTR EPIPE];use IO::Socket qw[SOCK_STREAM];my$SOCKET_CLASS=$ENV{PERL_HTTP_TINY_IPV4_ONLY}? 'IO::Socket::INET' : eval {require IO::Socket::IP;IO::Socket::IP->VERSION(0.25)}? 'IO::Socket::IP' : 'IO::Socket::INET';sub BUFSIZE () {32768}my$Printable=sub {local $_=shift;s/\r/\\r/g;s/\n/\\n/g;s/\t/\\t/g;s/([^\x20-\x7E])/sprintf('\\x%.2X', ord($1))/ge;$_};my$Token=qr/[\x21\x23-\x27\x2A\x2B\x2D\x2E\x30-\x39\x41-\x5A\x5E-\x7A\x7C\x7E]/;sub new {my ($class,%args)=@_;return bless {rbuf=>'',timeout=>60,max_line_size=>16384,max_header_lines=>64,verify_SSL=>0,SSL_options=>{},%args },$class}sub connect {@_==4 || die(q/Usage: $handle->connect(scheme, host, port)/ ."\n");my ($self,$scheme,$host,$port)=@_;if ($scheme eq 'https'){$self->_assert_ssl}elsif ($scheme ne 'http'){die(qq/Unsupported URL scheme '$scheme'\n/)}$self->{fh}=$SOCKET_CLASS->new(PeerHost=>$host,PeerPort=>$port,$self->{local_address}? (LocalAddr=>$self->{local_address}): (),Proto=>'tcp',Type=>SOCK_STREAM,Timeout=>$self->{timeout},KeepAlive=>!!$self->{keep_alive})or die(qq/Could not connect to '$host:$port': $@\n/);binmode($self->{fh})or die(qq/Could not binmode() socket: '$!'\n/);$self->start_ssl($host)if$scheme eq 'https';$self->{scheme}=$scheme;$self->{host}=$host;$self->{port}=$port;$self->{pid}=$$;$self->{tid}=_get_tid();return$self}sub start_ssl {my ($self,$host)=@_;if (ref($self->{fh})eq 'IO::Socket::SSL'){unless ($self->{fh}->stop_SSL){my$ssl_err=IO::Socket::SSL->errstr;die(qq/Error halting prior SSL connection: $ssl_err/)}}my$ssl_args=$self->_ssl_args($host);IO::Socket::SSL->start_SSL($self->{fh},%$ssl_args,SSL_create_ctx_callback=>sub {my$ctx=shift;Net::SSLeay::CTX_set_mode($ctx,Net::SSLeay::MODE_AUTO_RETRY())},);unless (ref($self->{fh})eq 'IO::Socket::SSL'){my$ssl_err=IO::Socket::SSL->errstr;die(qq/SSL connection failed for $host: $ssl_err\n/)}}sub close {@_==1 || die(q/Usage: $handle->close()/ ."\n");my ($self)=@_;CORE::close($self->{fh})or die(qq/Could not close socket: '$!'\n/)}sub write {@_==2 || die(q/Usage: $handle->write(buf)/ ."\n");my ($self,$buf)=@_;if ($] ge '5.008'){utf8::downgrade($buf,1)or die(qq/Wide character in write()\n/)}my$len=length$buf;my$off=0;local$SIG{PIPE}='IGNORE';while (){$self->can_write or die(qq/Timed out while waiting for socket to become ready for writing\n/);my$r=syswrite($self->{fh},$buf,$len,$off);if (defined$r){$len -= $r;$off += $r;last unless$len > 0}elsif ($!==EPIPE){die(qq/Socket closed by remote server: $!\n/)}elsif ($!!=EINTR){if ($self->{fh}->can('errstr')){my$err=$self->{fh}->errstr();die (qq/Could not write to SSL socket: '$err'\n /)}else {die(qq/Could not write to socket: '$!'\n/)}}}return$off}sub read {@_==2 || @_==3 || die(q/Usage: $handle->read(len [, allow_partial])/ ."\n");my ($self,$len,$allow_partial)=@_;my$buf='';my$got=length$self->{rbuf};if ($got){my$take=($got < $len)? $got : $len;$buf=substr($self->{rbuf},0,$take,'');$len -= $take}while ($len > 0){$self->can_read or die(q/Timed out while waiting for socket to become ready for reading/ ."\n");my$r=sysread($self->{fh},$buf,$len,length$buf);if (defined$r){last unless$r;$len -= $r}elsif ($!!=EINTR){if ($self->{fh}->can('errstr')){my$err=$self->{fh}->errstr();die (qq/Could not read from SSL socket: '$err'\n /)}else {die(qq/Could not read from socket: '$!'\n/)}}}if ($len &&!$allow_partial){die(qq/Unexpected end of stream\n/)}return$buf}sub readline {@_==1 || die(q/Usage: $handle->readline()/ ."\n");my ($self)=@_;while (){if ($self->{rbuf}=~ s/\A ([^\x0D\x0A]* \x0D?\x0A)//x){return $1}if (length$self->{rbuf}>= $self->{max_line_size}){die(qq/Line size exceeds the maximum allowed size of $self->{max_line_size}\n/)}$self->can_read or die(qq/Timed out while waiting for socket to become ready for reading\n/);my$r=sysread($self->{fh},$self->{rbuf},BUFSIZE,length$self->{rbuf});if (defined$r){last unless$r}elsif ($!!=EINTR){if ($self->{fh}->can('errstr')){my$err=$self->{fh}->errstr();die (qq/Could not read from SSL socket: '$err'\n /)}else {die(qq/Could not read from socket: '$!'\n/)}}}die(qq/Unexpected end of stream while looking for line\n/)}sub read_header_lines {@_==1 || @_==2 || die(q/Usage: $handle->read_header_lines([headers])/ ."\n");my ($self,$headers)=@_;$headers ||= {};my$lines=0;my$val;while (){my$line=$self->readline;if (++$lines >= $self->{max_header_lines}){die(qq/Header lines exceeds maximum number allowed of $self->{max_header_lines}\n/)}elsif ($line =~ /\A ([^\x00-\x1F\x7F:]+) : [\x09\x20]* ([^\x0D\x0A]*)/x){my ($field_name)=lc $1;if (exists$headers->{$field_name}){for ($headers->{$field_name}){$_=[$_]unless ref $_ eq "ARRAY";push @$_,$2;$val=\$_->[-1]}}else {$val=\($headers->{$field_name}=$2)}}elsif ($line =~ /\A [\x09\x20]+ ([^\x0D\x0A]*)/x){$val or die(qq/Unexpected header continuation line\n/);next unless length $1;$$val .= ' ' if length $$val;$$val .= $1}elsif ($line =~ /\A \x0D?\x0A \z/x){last}else {die(q/Malformed header line: / .$Printable->($line)."\n")}}return$headers}sub write_request {@_==2 || die(q/Usage: $handle->write_request(request)/ ."\n");my($self,$request)=@_;$self->write_request_header(@{$request}{qw/method uri headers/});$self->write_body($request)if$request->{cb};return}my%HeaderCase=('content-md5'=>'Content-MD5','etag'=>'ETag','te'=>'TE','www-authenticate'=>'WWW-Authenticate','x-xss-protection'=>'X-XSS-Protection',);sub write_header_lines {(@_==2 || @_==3 && ref $_[1]eq 'HASH')|| die(q/Usage: $handle->write_header_lines(headers[,prefix])/ ."\n");my($self,$headers,$prefix_data)=@_;my$buf=(defined$prefix_data ? $prefix_data : '');while (my ($k,$v)=each %$headers){my$field_name=lc$k;if (exists$HeaderCase{$field_name}){$field_name=$HeaderCase{$field_name}}else {$field_name =~ /\A $Token+ \z/xo or die(q/Invalid HTTP header field name: / .$Printable->($field_name)."\n");$field_name =~ s/\b(\w)/\u$1/g;$HeaderCase{lc$field_name}=$field_name}for (ref$v eq 'ARRAY' ? @$v : $v){$_='' unless defined $_;$buf .= "$field_name: $_\x0D\x0A"}}$buf .= "\x0D\x0A";return$self->write($buf)}sub read_body {@_==3 || die(q/Usage: $handle->read_body(callback, response)/ ."\n");my ($self,$cb,$response)=@_;my$te=$response->{headers}{'transfer-encoding'}|| '';my$chunked=grep {/chunked/i}(ref$te eq 'ARRAY' ? @$te : $te);return$chunked ? $self->read_chunked_body($cb,$response): $self->read_content_body($cb,$response)}sub write_body {@_==2 || die(q/Usage: $handle->write_body(request)/ ."\n");my ($self,$request)=@_;if ($request->{headers}{'content-length'}){return$self->write_content_body($request)}else {return$self->write_chunked_body($request)}}sub read_content_body {@_==3 || @_==4 || die(q/Usage: $handle->read_content_body(callback, response, [read_length])/ ."\n");my ($self,$cb,$response,$content_length)=@_;$content_length ||= $response->{headers}{'content-length'};if (defined$content_length){my$len=$content_length;while ($len > 0){my$read=($len > BUFSIZE)? BUFSIZE : $len;$cb->($self->read($read,0),$response);$len -= $read}return length($self->{rbuf})==0}my$chunk;$cb->($chunk,$response)while length($chunk=$self->read(BUFSIZE,1));return}sub write_content_body {@_==2 || die(q/Usage: $handle->write_content_body(request)/ ."\n");my ($self,$request)=@_;my ($len,$content_length)=(0,$request->{headers}{'content-length'});while (){my$data=$request->{cb}->();defined$data && length$data or last;if ($] ge '5.008'){utf8::downgrade($data,1)or die(qq/Wide character in write_content()\n/)}$len += $self->write($data)}$len==$content_length or die(qq/Content-Length mismatch (got: $len expected: $content_length)\n/);return$len}sub read_chunked_body {@_==3 || die(q/Usage: $handle->read_chunked_body(callback, $response)/ ."\n");my ($self,$cb,$response)=@_;while (){my$head=$self->readline;$head =~ /\A ([A-Fa-f0-9]+)/x or die(q/Malformed chunk head: / .$Printable->($head)."\n");my$len=hex($1)or last;$self->read_content_body($cb,$response,$len);$self->read(2)eq "\x0D\x0A" or die(qq/Malformed chunk: missing CRLF after chunk data\n/)}$self->read_header_lines($response->{headers});return 1}sub write_chunked_body {@_==2 || die(q/Usage: $handle->write_chunked_body(request)/ ."\n");my ($self,$request)=@_;my$len=0;while (){my$data=$request->{cb}->();defined$data && length$data or last;if ($] ge '5.008'){utf8::downgrade($data,1)or die(qq/Wide character in write_chunked_body()\n/)}$len += length$data;my$chunk=sprintf '%X',length$data;$chunk .= "\x0D\x0A";$chunk .= $data;$chunk .= "\x0D\x0A";$self->write($chunk)}$self->write("0\x0D\x0A");$self->write_header_lines($request->{trailer_cb}->())if ref$request->{trailer_cb}eq 'CODE';return$len}sub read_response_header {@_==1 || die(q/Usage: $handle->read_response_header()/ ."\n");my ($self)=@_;my$line=$self->readline;$line =~ /\A (HTTP\/(0*\d+\.0*\d+)) [\x09\x20]+ ([0-9]{3}) [\x09\x20]+ ([^\x0D\x0A]*) \x0D?\x0A/x or die(q/Malformed Status-Line: / .$Printable->($line)."\n");my ($protocol,$version,$status,$reason)=($1,$2,$3,$4);die (qq/Unsupported HTTP protocol: $protocol\n/)unless$version =~ /0*1\.0*[01]/;return {status=>$status,reason=>$reason,headers=>$self->read_header_lines,protocol=>$protocol,}}sub write_request_header {@_==4 || die(q/Usage: $handle->write_request_header(method, request_uri, headers)/ ."\n");my ($self,$method,$request_uri,$headers)=@_;return$self->write_header_lines($headers,"$method $request_uri HTTP/1.1\x0D\x0A")}sub _do_timeout {my ($self,$type,$timeout)=@_;$timeout=$self->{timeout}unless defined$timeout && $timeout >= 0;my$fd=fileno$self->{fh};defined$fd && $fd >= 0 or die(qq/select(2): 'Bad file descriptor'\n/);my$initial=time;my$pending=$timeout;my$nfound;vec(my$fdset='',$fd,1)=1;while (){$nfound=($type eq 'read')? select($fdset,undef,undef,$pending): select(undef,$fdset,undef,$pending);if ($nfound==-1){$!==EINTR or die(qq/select(2): '$!'\n/);redo if!$timeout || ($pending=$timeout - (time - $initial))> 0;$nfound=0}last}$!=0;return$nfound}sub can_read {@_==1 || @_==2 || die(q/Usage: $handle->can_read([timeout])/ ."\n");my$self=shift;if (ref($self->{fh})eq 'IO::Socket::SSL'){return 1 if$self->{fh}->pending}return$self->_do_timeout('read',@_)}sub can_write {@_==1 || @_==2 || die(q/Usage: $handle->can_write([timeout])/ ."\n");my$self=shift;return$self->_do_timeout('write',@_)}sub _assert_ssl {my($ok,$reason)=HTTP::Tiny->can_ssl();die$reason unless$ok}sub can_reuse {my ($self,$scheme,$host,$port)=@_;return 0 if $self->{pid}!=$$ || $self->{tid}!=_get_tid()|| length($self->{rbuf})|| $scheme ne $self->{scheme}|| $host ne $self->{host}|| $port ne $self->{port}|| eval {$self->can_read(0)}|| $@ ;return 1}sub _find_CA_file {my$self=shift();if ($self->{SSL_options}->{SSL_ca_file}){unless (-r $self->{SSL_options}->{SSL_ca_file}){die qq/SSL_ca_file '$self->{SSL_options}->{SSL_ca_file}' not found or not readable\n/}return$self->{SSL_options}->{SSL_ca_file}}return Mozilla::CA::SSL_ca_file()if eval {require Mozilla::CA;1};for my$ca_bundle ("/etc/ssl/certs/ca-certificates.crt","/etc/pki/tls/certs/ca-bundle.crt","/etc/ssl/ca-bundle.pem","/etc/openssl/certs/ca-certificates.crt","/etc/ssl/cert.pem","/usr/local/share/certs/ca-root-nss.crt","/etc/pki/tls/cacert.pem","/etc/certs/ca-certificates.crt",){return$ca_bundle if -e $ca_bundle}die qq/Couldn't find a CA bundle with which to verify the SSL certificate.\n/ .qq/Try installing Mozilla::CA from CPAN\n/}sub _get_tid {no warnings 'reserved';return threads->can("tid")? threads->tid : 0}sub _ssl_args {my ($self,$host)=@_;my%ssl_args;if (Net::SSLeay::OPENSSL_VERSION_NUMBER()>= 0x01000000){$ssl_args{SSL_hostname}=$host,}if ($self->{verify_SSL}){$ssl_args{SSL_verifycn_scheme}='http';$ssl_args{SSL_verifycn_name}=$host;$ssl_args{SSL_verify_mode}=0x01;$ssl_args{SSL_ca_file}=$self->_find_CA_file}else {$ssl_args{SSL_verifycn_scheme}='none';$ssl_args{SSL_verify_mode}=0x00}for my$k (keys %{$self->{SSL_options}}){$ssl_args{$k}=$self->{SSL_options}{$k}if$k =~ m/^SSL_/}return \%ssl_args}1;
+      sub $sub_name {
+          my (\$self, \$url, \$args) = \@_;
+          \@_ == 2 || (\@_ == 3 && ref \$args eq 'HASH')
+          or Carp::croak(q/Usage: \$http->$sub_name(URL, [HASHREF])/ . "\n");
+          return \$self->request('$req_method', \$url, \$args || {});
+      }
+  HERE
+HTTP_TINY
+
+$fatpacked{"JSON/PP.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'JSON_PP';
+  package JSON::PP;use 5.005;use strict;use base qw(Exporter);use overload ();use Carp ();use B ();$JSON::PP::VERSION='2.27300';@JSON::PP::EXPORT=qw(encode_json decode_json from_json to_json);use constant P_ASCII=>0;use constant P_LATIN1=>1;use constant P_UTF8=>2;use constant P_INDENT=>3;use constant P_CANONICAL=>4;use constant P_SPACE_BEFORE=>5;use constant P_SPACE_AFTER=>6;use constant P_ALLOW_NONREF=>7;use constant P_SHRINK=>8;use constant P_ALLOW_BLESSED=>9;use constant P_CONVERT_BLESSED=>10;use constant P_RELAXED=>11;use constant P_LOOSE=>12;use constant P_ALLOW_BIGNUM=>13;use constant P_ALLOW_BAREKEY=>14;use constant P_ALLOW_SINGLEQUOTE=>15;use constant P_ESCAPE_SLASH=>16;use constant P_AS_NONBLESSED=>17;use constant P_ALLOW_UNKNOWN=>18;use constant OLD_PERL=>$] < 5.008 ? 1 : 0;BEGIN {my@xs_compati_bit_properties=qw(latin1 ascii utf8 indent canonical space_before space_after allow_nonref shrink allow_blessed convert_blessed relaxed allow_unknown);my@pp_bit_properties=qw(allow_singlequote allow_bignum loose allow_barekey escape_slash as_nonblessed);if ($] < 5.008){my$helper=$] >= 5.006 ? 'JSON::PP::Compat5006' : 'JSON::PP::Compat5005';eval qq| require $helper |;if ($@){Carp::croak $@}}for my$name (@xs_compati_bit_properties,@pp_bit_properties){my$flag_name='P_' .uc($name);eval qq/
+              sub $name {
+                  my \$enable = defined \$_[1] ? \$_[1] : 1;
+  
+                  if (\$enable) {
+                      \$_[0]->{PROPS}->[$flag_name] = 1;
+                  }
+                  else {
+                      \$_[0]->{PROPS}->[$flag_name] = 0;
+                  }
+  
+                  \$_[0];
+              }
+  
+              sub get_$name {
+                  \$_[0]->{PROPS}->[$flag_name] ? 1 : '';
+              }
+          /}}my%encode_allow_method =map {($_=>1)}qw/utf8 pretty allow_nonref latin1 self_encode escape_slash allow_blessed convert_blessed indent indent_length allow_bignum as_nonblessed/;my%decode_allow_method =map {($_=>1)}qw/utf8 allow_nonref loose allow_singlequote allow_bignum allow_barekey max_size relaxed/;my$JSON;sub encode_json ($) {($JSON ||= __PACKAGE__->new->utf8)->encode(@_)}sub decode_json {($JSON ||= __PACKAGE__->new->utf8)->decode(@_)}sub to_json($) {Carp::croak ("JSON::PP::to_json has been renamed to encode_json.")}sub from_json($) {Carp::croak ("JSON::PP::from_json has been renamed to decode_json.")}sub new {my$class=shift;my$self={max_depth=>512,max_size=>0,indent=>0,FLAGS=>0,fallback=>sub {encode_error('Invalid value. JSON can only reference.')},indent_length=>3,};bless$self,$class}sub encode {return $_[0]->PP_encode_json($_[1])}sub decode {return $_[0]->PP_decode_json($_[1],0x00000000)}sub decode_prefix {return $_[0]->PP_decode_json($_[1],0x00000001)}sub pretty {my ($self,$v)=@_;my$enable=defined$v ? $v : 1;if ($enable){$self->indent(1)->indent_length(3)->space_before(1)->space_after(1)}else {$self->indent(0)->space_before(0)->space_after(0)}$self}sub max_depth {my$max=defined $_[1]? $_[1]: 0x80000000;$_[0]->{max_depth}=$max;$_[0]}sub get_max_depth {$_[0]->{max_depth}}sub max_size {my$max=defined $_[1]? $_[1]: 0;$_[0]->{max_size}=$max;$_[0]}sub get_max_size {$_[0]->{max_size}}sub filter_json_object {$_[0]->{cb_object}=defined $_[1]? $_[1]: 0;$_[0]->{F_HOOK}=($_[0]->{cb_object}or $_[0]->{cb_sk_object})? 1 : 0;$_[0]}sub filter_json_single_key_object {if (@_ > 1){$_[0]->{cb_sk_object}->{$_[1]}=$_[2]}$_[0]->{F_HOOK}=($_[0]->{cb_object}or $_[0]->{cb_sk_object})? 1 : 0;$_[0]}sub indent_length {if (!defined $_[1]or $_[1]> 15 or $_[1]< 0){Carp::carp "The acceptable range of indent_length() is 0 to 15."}else {$_[0]->{indent_length}=$_[1]}$_[0]}sub get_indent_length {$_[0]->{indent_length}}sub sort_by {$_[0]->{sort_by}=defined $_[1]? $_[1]: 1;$_[0]}sub allow_bigint {Carp::carp("allow_bigint() is obsoleted. use allow_bignum() insted.")}{my$max_depth;my$indent;my$ascii;my$latin1;my$utf8;my$space_before;my$space_after;my$canonical;my$allow_blessed;my$convert_blessed;my$indent_length;my$escape_slash;my$bignum;my$as_nonblessed;my$depth;my$indent_count;my$keysort;sub PP_encode_json {my$self=shift;my$obj=shift;$indent_count=0;$depth=0;my$idx=$self->{PROPS};($ascii,$latin1,$utf8,$indent,$canonical,$space_before,$space_after,$allow_blessed,$convert_blessed,$escape_slash,$bignum,$as_nonblessed)=@{$idx}[P_ASCII .. P_SPACE_AFTER,P_ALLOW_BLESSED,P_CONVERT_BLESSED,P_ESCAPE_SLASH,P_ALLOW_BIGNUM,P_AS_NONBLESSED];($max_depth,$indent_length)=@{$self}{qw/max_depth indent_length/};$keysort=$canonical ? sub {$a cmp $b}: undef;if ($self->{sort_by}){$keysort=ref($self->{sort_by})eq 'CODE' ? $self->{sort_by}: $self->{sort_by}=~ /\D+/ ? $self->{sort_by}: sub {$a cmp $b}}encode_error("hash- or arrayref expected (not a simple scalar, use allow_nonref to allow this)")if(!ref$obj and!$idx->[P_ALLOW_NONREF ]);my$str=$self->object_to_json($obj);$str .= "\n" if ($indent);unless ($ascii or $latin1 or $utf8){utf8::upgrade($str)}if ($idx->[P_SHRINK ]){utf8::downgrade($str,1)}return$str}sub object_to_json {my ($self,$obj)=@_;my$type=ref($obj);if($type eq 'HASH'){return$self->hash_to_json($obj)}elsif($type eq 'ARRAY'){return$self->array_to_json($obj)}elsif ($type){if (blessed($obj)){return$self->value_to_json($obj)if ($obj->isa('JSON::PP::Boolean'));if ($convert_blessed and $obj->can('TO_JSON')){my$result=$obj->TO_JSON();if (defined$result and ref($result)){if (refaddr($obj)eq refaddr($result)){encode_error(sprintf("%s::TO_JSON method returned same object as was passed instead of a new one",ref$obj))}}return$self->object_to_json($result)}return "$obj" if ($bignum and _is_bignum($obj));return$self->blessed_to_json($obj)if ($allow_blessed and $as_nonblessed);encode_error(sprintf("encountered object '%s', but neither allow_blessed " ."nor convert_blessed settings are enabled",$obj))unless ($allow_blessed);return 'null'}else {return$self->value_to_json($obj)}}else{return$self->value_to_json($obj)}}sub hash_to_json {my ($self,$obj)=@_;my@res;encode_error("json text or perl structure exceeds maximum nesting level (max_depth set too low?)")if (++$depth > $max_depth);my ($pre,$post)=$indent ? $self->_up_indent(): ('','');my$del=($space_before ? ' ' : '').':' .($space_after ? ' ' : '');for my$k (_sort($obj)){if (OLD_PERL){utf8::decode($k)}push@res,string_to_json($self,$k).$del .($self->object_to_json($obj->{$k})|| $self->value_to_json($obj->{$k}))}--$depth;$self->_down_indent()if ($indent);return '{' .(@res ? $pre : '').(@res ? join(",$pre",@res).$post : '').'}'}sub array_to_json {my ($self,$obj)=@_;my@res;encode_error("json text or perl structure exceeds maximum nesting level (max_depth set too low?)")if (++$depth > $max_depth);my ($pre,$post)=$indent ? $self->_up_indent(): ('','');for my$v (@$obj){push@res,$self->object_to_json($v)|| $self->value_to_json($v)}--$depth;$self->_down_indent()if ($indent);return '[' .(@res ? $pre : '').(@res ? join(",$pre",@res).$post : '').']'}sub value_to_json {my ($self,$value)=@_;return 'null' if(!defined$value);my$b_obj=B::svref_2object(\$value);my$flags=$b_obj->FLAGS;return$value if$flags & (B::SVp_IOK | B::SVp_NOK)and!($flags & B::SVp_POK);my$type=ref($value);if(!$type){return string_to_json($self,$value)}elsif(blessed($value)and $value->isa('JSON::PP::Boolean')){return $$value==1 ? 'true' : 'false'}elsif ($type){if ((overload::StrVal($value)=~ /=(\w+)/)[0]){return$self->value_to_json("$value")}if ($type eq 'SCALAR' and defined $$value){return $$value eq '1' ? 'true' : $$value eq '0' ? 'false' : $self->{PROPS}->[P_ALLOW_UNKNOWN ]? 'null' : encode_error("cannot encode reference to scalar")}if ($self->{PROPS}->[P_ALLOW_UNKNOWN ]){return 'null'}else {if ($type eq 'SCALAR' or $type eq 'REF'){encode_error("cannot encode reference to scalar")}else {encode_error("encountered $value, but JSON can only represent references to arrays or hashes")}}}else {return$self->{fallback}->($value)if ($self->{fallback}and ref($self->{fallback})eq 'CODE');return 'null'}}my%esc=("\n"=>'\n',"\r"=>'\r',"\t"=>'\t',"\f"=>'\f',"\b"=>'\b',"\""=>'\"',"\\"=>'\\\\',"\'"=>'\\\'',);sub string_to_json {my ($self,$arg)=@_;$arg =~ s/([\x22\x5c\n\r\t\f\b])/$esc{$1}/g;$arg =~ s/\//\\\//g if ($escape_slash);$arg =~ s/([\x00-\x08\x0b\x0e-\x1f])/'\\u00' . unpack('H2', $1)/eg;if ($ascii){$arg=JSON_PP_encode_ascii($arg)}if ($latin1){$arg=JSON_PP_encode_latin1($arg)}if ($utf8){utf8::encode($arg)}return '"' .$arg .'"'}sub blessed_to_json {my$reftype=reftype($_[1])|| '';if ($reftype eq 'HASH'){return $_[0]->hash_to_json($_[1])}elsif ($reftype eq 'ARRAY'){return $_[0]->array_to_json($_[1])}else {return 'null'}}sub encode_error {my$error=shift;Carp::croak "$error"}sub _sort {defined$keysort ? (sort$keysort (keys %{$_[0]})): keys %{$_[0]}}sub _up_indent {my$self=shift;my$space=' ' x $indent_length;my ($pre,$post)=('','');$post="\n" .$space x $indent_count;$indent_count++;$pre="\n" .$space x $indent_count;return ($pre,$post)}sub _down_indent {$indent_count--}sub PP_encode_box {{depth=>$depth,indent_count=>$indent_count,}}}sub _encode_ascii {join('',map {$_ <= 127 ? chr($_): $_ <= 65535 ? sprintf('\u%04x',$_): sprintf('\u%x\u%x',_encode_surrogates($_))}unpack('U*',$_[0]))}sub _encode_latin1 {join('',map {$_ <= 255 ? chr($_): $_ <= 65535 ? sprintf('\u%04x',$_): sprintf('\u%x\u%x',_encode_surrogates($_))}unpack('U*',$_[0]))}sub _encode_surrogates {my$uni=$_[0]- 0x10000;return ($uni / 0x400 + 0xD800,$uni % 0x400 + 0xDC00)}sub _is_bignum {$_[0]->isa('Math::BigInt')or $_[0]->isa('Math::BigFloat')}my$max_intsize;BEGIN {my$checkint=1111;for my$d (5..64){$checkint .= 1;my$int=eval qq| $checkint |;if ($int =~ /[eE]/){$max_intsize=$d - 1;last}}}{my%escapes=(b=>"\x8",t=>"\x9",n=>"\xA",f=>"\xC",r=>"\xD",'\\'=>'\\','"'=>'"','/'=>'/',);my$text;my$at;my$ch;my$len;my$depth;my$encoding;my$is_valid_utf8;my$utf8_len;my$utf8;my$max_depth;my$max_size;my$relaxed;my$cb_object;my$cb_sk_object;my$F_HOOK;my$allow_bigint;my$singlequote;my$loose;my$allow_barekey;sub PP_decode_json {my ($self,$opt);($self,$text,$opt)=@_;($at,$ch,$depth)=(0,'',0);if (!defined$text or ref$text){decode_error("malformed JSON string, neither array, object, number, string or atom")}my$idx=$self->{PROPS};($utf8,$relaxed,$loose,$allow_bigint,$allow_barekey,$singlequote)=@{$idx}[P_UTF8,P_RELAXED,P_LOOSE .. P_ALLOW_SINGLEQUOTE];if ($utf8){utf8::downgrade($text,1)or Carp::croak("Wide character in subroutine entry")}else {utf8::upgrade($text);utf8::encode($text)}$len=length$text;($max_depth,$max_size,$cb_object,$cb_sk_object,$F_HOOK)=@{$self}{qw/max_depth max_size cb_object cb_sk_object F_HOOK/};if ($max_size > 1){use bytes;my$bytes=length$text;decode_error(sprintf("attempted decode of JSON text of %s bytes size, but max_size is set to %s" ,$bytes,$max_size),1)if ($bytes > $max_size)}my@octets=unpack('C4',$text);$encoding=($octets[0]and $octets[1])? 'UTF-8' : (!$octets[0]and $octets[1])? 'UTF-16BE' : (!$octets[0]and!$octets[1])? 'UTF-32BE' : ($octets[2])? 'UTF-16LE' : (!$octets[2])? 'UTF-32LE' : 'unknown';white();my$valid_start=defined$ch;my$result=value();return undef if (!$result && ($opt & 0x10000000));decode_error("malformed JSON string, neither array, object, number, string or atom")unless$valid_start;if (!$idx->[P_ALLOW_NONREF ]and!ref$result){decode_error('JSON text must be an object or array (but found number, string, true, false or null,' .' use allow_nonref to allow this)',1)}Carp::croak('something wrong.')if$len < $at;my$consumed=defined$ch ? $at - 1 : $at;white();if ($ch){return ($result,$consumed)if ($opt & 0x00000001);decode_error("garbage after JSON object")}($opt & 0x00000001)? ($result,$consumed): $result}sub next_chr {return$ch=undef if($at >= $len);$ch=substr($text,$at++,1)}sub value {white();return if(!defined$ch);return object()if($ch eq '{');return array()if($ch eq '[');return string()if($ch eq '"' or ($singlequote and $ch eq "'"));return number()if($ch =~ /[0-9]/ or $ch eq '-');return word()}sub string {my ($i,$s,$t,$u);my$utf16;my$is_utf8;($is_valid_utf8,$utf8_len)=('',0);$s='';if($ch eq '"' or ($singlequote and $ch eq "'")){my$boundChar=$ch;OUTER: while(defined(next_chr())){if($ch eq $boundChar){next_chr();if ($utf16){decode_error("missing low surrogate character in surrogate pair")}utf8::decode($s)if($is_utf8);return$s}elsif($ch eq '\\'){next_chr();if(exists$escapes{$ch}){$s .= $escapes{$ch}}elsif($ch eq 'u'){my$u='';for(1..4){$ch=next_chr();last OUTER if($ch !~ /[0-9a-fA-F]/);$u .= $ch}if ($u =~ /^[dD][89abAB][0-9a-fA-F]{2}/){$utf16=$u}elsif ($u =~ /^[dD][c-fC-F][0-9a-fA-F]{2}/){unless (defined$utf16){decode_error("missing high surrogate character in surrogate pair")}$is_utf8=1;$s .= JSON_PP_decode_surrogates($utf16,$u)|| next;$utf16=undef}else {if (defined$utf16){decode_error("surrogate pair expected")}if ((my$hex=hex($u))> 127){$is_utf8=1;$s .= JSON_PP_decode_unicode($u)|| next}else {$s .= chr$hex}}}else{unless ($loose){$at -= 2;decode_error('illegal backslash escape sequence in string')}$s .= $ch}}else{if (ord$ch > 127){unless($ch=is_valid_utf8($ch)){$at -= 1;decode_error("malformed UTF-8 character in JSON string")}else {$at += $utf8_len - 1}$is_utf8=1}if (!$loose){if ($ch =~ /[\x00-\x1f\x22\x5c]/){$at--;decode_error('invalid character encountered while parsing JSON string')}}$s .= $ch}}}decode_error("unexpected end of string while parsing JSON string")}sub white {while(defined$ch){if($ch le ' '){next_chr()}elsif($ch eq '/'){next_chr();if(defined$ch and $ch eq '/'){1 while(defined(next_chr())and $ch ne "\n" and $ch ne "\r")}elsif(defined$ch and $ch eq '*'){next_chr();while(1){if(defined$ch){if($ch eq '*'){if(defined(next_chr())and $ch eq '/'){next_chr();last}}else{next_chr()}}else{decode_error("Unterminated comment")}}next}else{$at--;decode_error("malformed JSON string, neither array, object, number, string or atom")}}else{if ($relaxed and $ch eq '#'){pos($text)=$at;$text =~ /\G([^\n]*(?:\r\n|\r|\n|$))/g;$at=pos($text);next_chr;next}last}}}sub array {my$a=$_[0]|| [];decode_error('json text or perl structure exceeds maximum nesting level (max_depth set too low?)')if (++$depth > $max_depth);next_chr();white();if(defined$ch and $ch eq ']'){--$depth;next_chr();return$a}else {while(defined($ch)){push @$a,value();white();if (!defined$ch){last}if($ch eq ']'){--$depth;next_chr();return$a}if($ch ne ','){last}next_chr();white();if ($relaxed and $ch eq ']'){--$depth;next_chr();return$a}}}decode_error(", or ] expected while parsing array")}sub object {my$o=$_[0]|| {};my$k;decode_error('json text or perl structure exceeds maximum nesting level (max_depth set too low?)')if (++$depth > $max_depth);next_chr();white();if(defined$ch and $ch eq '}'){--$depth;next_chr();if ($F_HOOK){return _json_object_hook($o)}return$o}else {while (defined$ch){$k=($allow_barekey and $ch ne '"' and $ch ne "'")? bareKey(): string();white();if(!defined$ch or $ch ne ':'){$at--;decode_error("':' expected")}next_chr();$o->{$k}=value();white();last if (!defined$ch);if($ch eq '}'){--$depth;next_chr();if ($F_HOOK){return _json_object_hook($o)}return$o}if($ch ne ','){last}next_chr();white();if ($relaxed and $ch eq '}'){--$depth;next_chr();if ($F_HOOK){return _json_object_hook($o)}return$o}}}$at--;decode_error(", or } expected while parsing object/hash")}sub bareKey {my$key;while($ch =~ /[^\x00-\x23\x25-\x2F\x3A-\x40\x5B-\x5E\x60\x7B-\x7F]/){$key .= $ch;next_chr()}return$key}sub word {my$word=substr($text,$at-1,4);if($word eq 'true'){$at += 3;next_chr;return$JSON::PP::true}elsif($word eq 'null'){$at += 3;next_chr;return undef}elsif($word eq 'fals'){$at += 3;if(substr($text,$at,1)eq 'e'){$at++;next_chr;return$JSON::PP::false}}$at--;decode_error("'null' expected")if ($word =~ /^n/);decode_error("'true' expected")if ($word =~ /^t/);decode_error("'false' expected")if ($word =~ /^f/);decode_error("malformed JSON string, neither array, object, number, string or atom")}sub number {my$n='';my$v;if($ch eq '0'){my$peek=substr($text,$at,1);my$hex=$peek =~ /[xX]/;if($hex){decode_error("malformed number (leading zero must not be followed by another digit)");($n)=(substr($text,$at+1)=~ /^([0-9a-fA-F]+)/)}else{($n)=(substr($text,$at)=~ /^([0-7]+)/);if (defined$n and length$n > 1){decode_error("malformed number (leading zero must not be followed by another digit)")}}if(defined$n and length($n)){if (!$hex and length($n)==1){decode_error("malformed number (leading zero must not be followed by another digit)")}$at += length($n)+ $hex;next_chr;return$hex ? hex($n): oct($n)}}if($ch eq '-'){$n='-';next_chr;if (!defined$ch or $ch !~ /\d/){decode_error("malformed number (no digits after initial minus)")}}while(defined$ch and $ch =~ /\d/){$n .= $ch;next_chr}if(defined$ch and $ch eq '.'){$n .= '.';next_chr;if (!defined$ch or $ch !~ /\d/){decode_error("malformed number (no digits after decimal point)")}else {$n .= $ch}while(defined(next_chr)and $ch =~ /\d/){$n .= $ch}}if(defined$ch and ($ch eq 'e' or $ch eq 'E')){$n .= $ch;next_chr;if(defined($ch)and ($ch eq '+' or $ch eq '-')){$n .= $ch;next_chr;if (!defined$ch or $ch =~ /\D/){decode_error("malformed number (no digits after exp sign)")}$n .= $ch}elsif(defined($ch)and $ch =~ /\d/){$n .= $ch}else {decode_error("malformed number (no digits after exp sign)")}while(defined(next_chr)and $ch =~ /\d/){$n .= $ch}}$v .= $n;if ($v !~ /[.eE]/ and length$v > $max_intsize){if ($allow_bigint){require Math::BigInt;return Math::BigInt->new($v)}else {return "$v"}}elsif ($allow_bigint){require Math::BigFloat;return Math::BigFloat->new($v)}return 0+$v}sub is_valid_utf8 {$utf8_len=$_[0]=~ /[\x00-\x7F]/ ? 1 : $_[0]=~ /[\xC2-\xDF]/ ? 2 : $_[0]=~ /[\xE0-\xEF]/ ? 3 : $_[0]=~ /[\xF0-\xF4]/ ? 4 : 0 ;return unless$utf8_len;my$is_valid_utf8=substr($text,$at - 1,$utf8_len);return ($is_valid_utf8 =~ /^(?:
+               [\x00-\x7F]
+              |[\xC2-\xDF][\x80-\xBF]
+              |[\xE0][\xA0-\xBF][\x80-\xBF]
+              |[\xE1-\xEC][\x80-\xBF][\x80-\xBF]
+              |[\xED][\x80-\x9F][\x80-\xBF]
+              |[\xEE-\xEF][\x80-\xBF][\x80-\xBF]
+              |[\xF0][\x90-\xBF][\x80-\xBF][\x80-\xBF]
+              |[\xF1-\xF3][\x80-\xBF][\x80-\xBF][\x80-\xBF]
+              |[\xF4][\x80-\x8F][\x80-\xBF][\x80-\xBF]
+          )$/x)? $is_valid_utf8 : ''}sub decode_error {my$error=shift;my$no_rep=shift;my$str=defined$text ? substr($text,$at): '';my$mess='';my$type=$] >= 5.008 ? 'U*' : $] < 5.006 ? 'C*' : utf8::is_utf8($str)? 'U*' : 'C*' ;for my$c (unpack($type,$str)){$mess .= $c==0x07 ? '\a' : $c==0x09 ? '\t' : $c==0x0a ? '\n' : $c==0x0d ? '\r' : $c==0x0c ? '\f' : $c < 0x20 ? sprintf('\x{%x}',$c): $c==0x5c ? '\\\\' : $c < 0x80 ? chr($c): sprintf('\x{%x}',$c);if (length$mess >= 20){$mess .= '...';last}}unless (length$mess){$mess='(end of string)'}Carp::croak ($no_rep ? "$error" : "$error, at character offset $at (before \"$mess\")")}sub _json_object_hook {my$o=$_[0];my@ks=keys %{$o};if ($cb_sk_object and @ks==1 and exists$cb_sk_object->{$ks[0]}and ref$cb_sk_object->{$ks[0]}){my@val=$cb_sk_object->{$ks[0]}->($o->{$ks[0]});if (@val==1){return$val[0]}}my@val=$cb_object->($o)if ($cb_object);if (@val==0 or @val > 1){return$o}else {return$val[0]}}sub PP_decode_box {{text=>$text,at=>$at,ch=>$ch,len=>$len,depth=>$depth,encoding=>$encoding,is_valid_utf8=>$is_valid_utf8,}}}sub _decode_surrogates {my$uni=0x10000 + (hex($_[0])- 0xD800)* 0x400 + (hex($_[1])- 0xDC00);my$un=pack('U*',$uni);utf8::encode($un);return$un}sub _decode_unicode {my$un=pack('U',hex shift);utf8::encode($un);return$un}BEGIN {unless (defined&utf8::is_utf8){require Encode;*utf8::is_utf8=*Encode::is_utf8}if ($] >= 5.008){*JSON::PP::JSON_PP_encode_ascii=\&_encode_ascii;*JSON::PP::JSON_PP_encode_latin1=\&_encode_latin1;*JSON::PP::JSON_PP_decode_surrogates=\&_decode_surrogates;*JSON::PP::JSON_PP_decode_unicode=\&_decode_unicode}if ($] >= 5.008 and $] < 5.008003){package JSON::PP;require subs;subs->import('join');eval q|
+              sub join {
+                  return '' if (@_ < 2);
+                  my $j   = shift;
+                  my $str = shift;
+                  for (@_) { $str .= $j . $_; }
+                  return $str;
+              }
+          |}sub JSON::PP::incr_parse {local$Carp::CarpLevel=1;($_[0]->{_incr_parser}||= JSON::PP::IncrParser->new)->incr_parse(@_)}sub JSON::PP::incr_skip {($_[0]->{_incr_parser}||= JSON::PP::IncrParser->new)->incr_skip}sub JSON::PP::incr_reset {($_[0]->{_incr_parser}||= JSON::PP::IncrParser->new)->incr_reset}eval q{
+          sub JSON::PP::incr_text : lvalue {
+              $_[0]->{_incr_parser} ||= JSON::PP::IncrParser->new;
+  
+              if ( $_[0]->{_incr_parser}->{incr_parsing} ) {
+                  Carp::croak("incr_text can not be called when the incremental parser already started parsing");
+              }
+              $_[0]->{_incr_parser}->{incr_text};
+          }
+      } if ($] >= 5.006)}BEGIN {eval 'require Scalar::Util';unless($@){*JSON::PP::blessed=\&Scalar::Util::blessed;*JSON::PP::reftype=\&Scalar::Util::reftype;*JSON::PP::refaddr=\&Scalar::Util::refaddr}else{eval 'sub UNIVERSAL::a_sub_not_likely_to_be_here { ref($_[0]) }';*JSON::PP::blessed=sub {local($@,$SIG{__DIE__},$SIG{__WARN__});ref($_[0])? eval {$_[0]->a_sub_not_likely_to_be_here}: undef};my%tmap=qw(B::NULL SCALAR B::HV HASH B::AV ARRAY B::CV CODE B::IO IO B::GV GLOB B::REGEXP REGEXP);*JSON::PP::reftype=sub {my$r=shift;return undef unless length(ref($r));my$t=ref(B::svref_2object($r));return exists$tmap{$t}? $tmap{$t}: length(ref($$r))? 'REF' : 'SCALAR'};*JSON::PP::refaddr=sub {return undef unless length(ref($_[0]));my$addr;if(defined(my$pkg=blessed($_[0]))){$addr .= bless $_[0],'Scalar::Util::Fake';bless $_[0],$pkg}else {$addr .= $_[0]}$addr =~ /0x(\w+)/;local $^W;hex($1)}}}$JSON::PP::true=do {bless \(my$dummy=1),"JSON::PP::Boolean"};$JSON::PP::false=do {bless \(my$dummy=0),"JSON::PP::Boolean"};sub is_bool {defined $_[0]and UNIVERSAL::isa($_[0],"JSON::PP::Boolean")}sub true {$JSON::PP::true}sub false {$JSON::PP::false}sub null {undef}package JSON::PP::Boolean;use overload ("0+"=>sub {${$_[0]}},"++"=>sub {$_[0]=${$_[0]}+ 1},"--"=>sub {$_[0]=${$_[0]}- 1},fallback=>1,);package JSON::PP::IncrParser;use strict;use constant INCR_M_WS=>0;use constant INCR_M_STR=>1;use constant INCR_M_BS=>2;use constant INCR_M_JSON=>3;use constant INCR_M_C0=>4;use constant INCR_M_C1=>5;$JSON::PP::IncrParser::VERSION='1.01';my$unpack_format=$] < 5.006 ? 'C*' : 'U*';sub new {my ($class)=@_;bless {incr_nest=>0,incr_text=>undef,incr_parsing=>0,incr_p=>0,},$class}sub incr_parse {my ($self,$coder,$text)=@_;$self->{incr_text}='' unless (defined$self->{incr_text});if (defined$text){if (utf8::is_utf8($text)and!utf8::is_utf8($self->{incr_text})){utf8::upgrade($self->{incr_text});utf8::decode($self->{incr_text})}$self->{incr_text}.= $text}my$max_size=$coder->get_max_size;if (defined wantarray){$self->{incr_mode}=INCR_M_WS unless defined$self->{incr_mode};if (wantarray){my@ret;$self->{incr_parsing}=1;do {push@ret,$self->_incr_parse($coder,$self->{incr_text});unless (!$self->{incr_nest}and $self->{incr_mode}==INCR_M_JSON){$self->{incr_mode}=INCR_M_WS if$self->{incr_mode}!=INCR_M_STR}}until (length$self->{incr_text}>= $self->{incr_p});$self->{incr_parsing}=0;return@ret}else {$self->{incr_parsing}=1;my$obj=$self->_incr_parse($coder,$self->{incr_text});$self->{incr_parsing}=0 if defined$obj;return$obj ? $obj : undef}}}sub _incr_parse {my ($self,$coder,$text,$skip)=@_;my$p=$self->{incr_p};my$restore=$p;my@obj;my$len=length$text;if ($self->{incr_mode}==INCR_M_WS){while ($len > $p){my$s=substr($text,$p,1);$p++ and next if (0x20 >= unpack($unpack_format,$s));$self->{incr_mode}=INCR_M_JSON;last}}while ($len > $p){my$s=substr($text,$p++,1);if ($s eq '"'){if (substr($text,$p - 2,1)eq '\\'){next}if ($self->{incr_mode}!=INCR_M_STR){$self->{incr_mode}=INCR_M_STR}else {$self->{incr_mode}=INCR_M_JSON;unless ($self->{incr_nest}){last}}}if ($self->{incr_mode}==INCR_M_JSON){if ($s eq '[' or $s eq '{'){if (++$self->{incr_nest}> $coder->get_max_depth){Carp::croak('json text or perl structure exceeds maximum nesting level (max_depth set too low?)')}}elsif ($s eq ']' or $s eq '}'){last if (--$self->{incr_nest}<= 0)}elsif ($s eq '#'){while ($len > $p){last if substr($text,$p++,1)eq "\n"}}}}$self->{incr_p}=$p;return if ($self->{incr_mode}==INCR_M_STR and not $self->{incr_nest});return if ($self->{incr_mode}==INCR_M_JSON and $self->{incr_nest}> 0);return '' unless (length substr($self->{incr_text},0,$p));local$Carp::CarpLevel=2;$self->{incr_p}=$restore;$self->{incr_c}=$p;my ($obj,$tail)=$coder->PP_decode_json(substr($self->{incr_text},0,$p),0x10000001);$self->{incr_text}=substr($self->{incr_text},$p);$self->{incr_p}=0;return$obj || ''}sub incr_text {if ($_[0]->{incr_parsing}){Carp::croak("incr_text can not be called when the incremental parser already started parsing")}$_[0]->{incr_text}}sub incr_skip {my$self=shift;$self->{incr_text}=substr($self->{incr_text},$self->{incr_c});$self->{incr_p}=0}sub incr_reset {my$self=shift;$self->{incr_text}=undef;$self->{incr_p}=0;$self->{incr_mode}=0;$self->{incr_nest}=0;$self->{incr_parsing}=0}1;
+JSON_PP
+
+$fatpacked{"JSON/PP/Boolean.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'JSON_PP_BOOLEAN';
+  use JSON::PP ();use strict;1;
+JSON_PP_BOOLEAN
+
+$fatpacked{"Module/CPANfile.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'MODULE_CPANFILE';
+  package Module::CPANfile;use strict;use warnings;use Cwd;use Carp ();use Module::CPANfile::Environment;use Module::CPANfile::Requirement;our$VERSION='1.1000';sub new {my($class,$file)=@_;bless {},$class}sub load {my($proto,$file)=@_;my$self=ref$proto ? $proto : $proto->new;$self->parse($file || Cwd::abs_path('cpanfile'));$self}sub save {my($self,$path)=@_;open my$out,">",$path or die "$path: $!";print {$out}$self->to_string}sub parse {my($self,$file)=@_;my$code=do {open my$fh,"<",$file or die "$file: $!";join '',<$fh>};my$env=Module::CPANfile::Environment->new($file);$env->parse($code)or die $@;$self->{_mirrors}=$env->mirrors;$self->{_prereqs}=$env->prereqs}sub from_prereqs {my($proto,$prereqs)=@_;my$self=$proto->new;$self->{_prereqs}=Module::CPANfile::Prereqs->from_cpan_meta($prereqs);$self}sub mirrors {my$self=shift;$self->{_mirrors}|| []}sub features {my$self=shift;map$self->feature($_),$self->{_prereqs}->identifiers}sub feature {my($self,$identifier)=@_;$self->{_prereqs}->feature($identifier)}sub prereq {shift->prereqs}sub prereqs {my$self=shift;$self->{_prereqs}->as_cpan_meta}sub merged_requirements {my$self=shift;$self->{_prereqs}->merged_requirements}sub effective_prereqs {my($self,$features)=@_;$self->prereqs_with(@{$features || []})}sub prereqs_with {my($self,@feature_identifiers)=@_;my$prereqs=$self->prereqs;my@others=map {$self->feature($_)->prereqs}@feature_identifiers;$prereqs->with_merged_prereqs(\@others)}sub prereq_specs {my$self=shift;$self->prereqs->as_string_hash}sub prereq_for_module {my($self,$module)=@_;$self->{_prereqs}->find($module)}sub options_for_module {my($self,$module)=@_;my$prereq=$self->prereq_for_module($module)or return;$prereq->requirement->options}sub merge_meta {my($self,$file,$version)=@_;require CPAN::Meta;$version ||= $file =~ /\.yml$/ ? '1.4' : '2';my$prereq=$self->prereqs;my$meta=CPAN::Meta->load_file($file);my$prereqs_hash=$prereq->with_merged_prereqs($meta->effective_prereqs)->as_string_hash;my$struct={%{$meta->as_struct},prereqs=>$prereqs_hash };CPAN::Meta->new($struct)->save($file,{version=>$version })}sub _dump {my$str=shift;require Data::Dumper;chomp(my$value=Data::Dumper->new([$str])->Terse(1)->Dump);$value}sub to_string {my($self,$include_empty)=@_;my$mirrors=$self->mirrors;my$prereqs=$self->prereq_specs;my$code='';$code .= $self->_dump_mirrors($mirrors);$code .= $self->_dump_prereqs($prereqs,$include_empty);for my$feature ($self->features){$code .= sprintf "feature %s, %s => sub {\n",_dump($feature->{identifier}),_dump($feature->{description});$code .= $self->_dump_prereqs($feature->{spec},$include_empty,4);$code .= "}\n\n"}$code =~ s/\n+$/\n/s;$code}sub _dump_mirrors {my($self,$mirrors)=@_;my$code="";for my$url (@$mirrors){$code .= "mirror '$url';\n"}$code =~ s/\n+$/\n/s;$code}sub _dump_prereqs {my($self,$prereqs,$include_empty,$base_indent)=@_;my$code='';for my$phase (qw(runtime configure build test develop)){my$indent=$phase eq 'runtime' ? '' : '    ';$indent=(' ' x ($base_indent || 0)).$indent;my($phase_code,$requirements);$phase_code .= "on $phase => sub {\n" unless$phase eq 'runtime';for my$type (qw(requires recommends suggests conflicts)){for my$mod (sort keys %{$prereqs->{$phase}{$type}}){my$ver=$prereqs->{$phase}{$type}{$mod};$phase_code .= $ver eq '0' ? "${indent}$type '$mod';\n" : "${indent}$type '$mod', '$ver';\n";$requirements++}}$phase_code .= "\n" unless$requirements;$phase_code .= "};\n" unless$phase eq 'runtime';$code .= $phase_code ."\n" if$requirements or $include_empty}$code =~ s/\n+$/\n/s;$code}1;
+MODULE_CPANFILE
+
+$fatpacked{"Module/CPANfile/Environment.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'MODULE_CPANFILE_ENVIRONMENT';
+  package Module::CPANfile::Environment;use strict;use warnings;use Module::CPANfile::Prereqs;use Carp ();my@bindings=qw(on requires recommends suggests conflicts feature osname mirror configure_requires build_requires test_requires author_requires);my$file_id=1;sub new {my($class,$file)=@_;bless {file=>$file,phase=>'runtime',feature=>undef,features=>{},prereqs=>Module::CPANfile::Prereqs->new,mirrors=>[],},$class}sub bind {my$self=shift;my$pkg=caller;for my$binding (@bindings){no strict 'refs';*{"$pkg\::$binding"}=sub {$self->$binding(@_)}}}sub parse {my($self,$code)=@_;my$err;{local $@;$file_id++;$self->_evaluate(<<EVAL);$err=$@}if ($err){die "Parsing $self->{file} failed: $err"};return 1}sub _evaluate {my$_environment=$_[0];eval $_[1]}sub prereqs {$_[0]->{prereqs}}sub mirrors {$_[0]->{mirrors}}sub on {my($self,$phase,$code)=@_;local$self->{phase}=$phase;$code->()}sub feature {my($self,$identifier,$description,$code)=@_;if (@_==3 && ref($description)eq 'CODE'){$code=$description;$description=$identifier}unless (ref$description eq '' && ref$code eq 'CODE'){Carp::croak("Usage: feature 'identifier', 'Description' => sub { ... }")}local$self->{feature}=$identifier;$self->prereqs->add_feature($identifier,$description);$code->()}sub osname {die "TODO"}sub mirror {my($self,$url)=@_;push @{$self->{mirrors}},$url}sub requirement_for {my($self,$module,@args)=@_;my$requirement=0;$requirement=shift@args if@args % 2;return Module::CPANfile::Requirement->new(name=>$module,version=>$requirement,@args,)}sub requires {my$self=shift;$self->add_prereq(requires=>@_)}sub recommends {my$self=shift;$self->add_prereq(recommends=>@_)}sub suggests {my$self=shift;$self->add_prereq(suggests=>@_)}sub conflicts {my$self=shift;$self->add_prereq(conflicts=>@_)}sub add_prereq {my($self,$type,$module,@args)=@_;$self->prereqs->add_prereq(feature=>$self->{feature},phase=>$self->{phase},type=>$type,module=>$module,requirement=>$self->requirement_for($module,@args),)}sub configure_requires {my($self,@args)=@_;$self->on(configure=>sub {$self->requires(@args)})}sub build_requires {my($self,@args)=@_;$self->on(build=>sub {$self->requires(@args)})}sub test_requires {my($self,@args)=@_;$self->on(test=>sub {$self->requires(@args)})}sub author_requires {my($self,@args)=@_;$self->on(develop=>sub {$self->requires(@args)})}1;
+  package Module::CPANfile::Sandbox$file_id;
+  no warnings;
+  BEGIN { \$_environment->bind }
+  
+  # line 1 "$self->{file}"
+  $code;
+  EVAL
+MODULE_CPANFILE_ENVIRONMENT
+
+$fatpacked{"Module/CPANfile/Prereq.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'MODULE_CPANFILE_PREREQ';
+  package Module::CPANfile::Prereq;use strict;sub new {my($class,%options)=@_;bless \%options,$class}sub feature {$_[0]->{feature}}sub phase {$_[0]->{phase}}sub type {$_[0]->{type}}sub module {$_[0]->{module}}sub requirement {$_[0]->{requirement}}sub match_feature {my($self,$identifier)=@_;no warnings 'uninitialized';$self->feature eq $identifier}1;
+MODULE_CPANFILE_PREREQ
+
+$fatpacked{"Module/CPANfile/Prereqs.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'MODULE_CPANFILE_PREREQS';
+  package Module::CPANfile::Prereqs;use strict;use Carp ();use CPAN::Meta::Feature;use Module::CPANfile::Prereq;sub from_cpan_meta {my($class,$prereqs)=@_;my$self=$class->new;for my$phase (keys %$prereqs){for my$type (keys %{$prereqs->{$phase}}){while (my($module,$requirement)=each %{$prereqs->{$phase}{$type}}){$self->add_prereq(phase=>$phase,type=>$type,module=>$module,requirement=>Module::CPANfile::Requirement->new(name=>$module,version=>$requirement),)}}}$self}sub new {my$class=shift;bless {prereqs=>[],features=>{},},$class}sub add_feature {my($self,$identifier,$description)=@_;$self->{features}{$identifier}={description=>$description }}sub add_prereq {my($self,%args)=@_;$self->add(Module::CPANfile::Prereq->new(%args))}sub add {my($self,$prereq)=@_;push @{$self->{prereqs}},$prereq}sub as_cpan_meta {my$self=shift;$self->{cpanmeta}||= $self->build_cpan_meta}sub build_cpan_meta {my($self,$identifier)=@_;my$prereq_spec={};$self->prereq_each($identifier,sub {my$prereq=shift;$prereq_spec->{$prereq->phase}{$prereq->type}{$prereq->module}=$prereq->requirement->version});CPAN::Meta::Prereqs->new($prereq_spec)}sub prereq_each {my($self,$identifier,$code)=@_;for my$prereq (@{$self->{prereqs}}){next unless$prereq->match_feature($identifier);$code->($prereq)}}sub merged_requirements {my$self=shift;my$reqs=CPAN::Meta::Requirements->new;for my$prereq (@{$self->{prereqs}}){$reqs->add_string_requirement($prereq->module,$prereq->requirement->version)}$reqs}sub find {my($self,$module)=@_;for my$prereq (@{$self->{prereqs}}){return$prereq if$prereq->module eq $module}return}sub identifiers {my$self=shift;keys %{$self->{features}}}sub feature {my($self,$identifier)=@_;my$data=$self->{features}{$identifier}or Carp::croak("Unknown feature '$identifier'");my$prereqs=$self->build_cpan_meta($identifier);CPAN::Meta::Feature->new($identifier,{description=>$data->{description},prereqs=>$prereqs->as_string_hash,})}1;
+MODULE_CPANFILE_PREREQS
+
+$fatpacked{"Module/CPANfile/Requirement.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'MODULE_CPANFILE_REQUIREMENT';
+  package Module::CPANfile::Requirement;use strict;sub new {my ($class,%args)=@_;$args{version}||= 0;bless +{name=>delete$args{name},version=>delete$args{version},options=>\%args,},$class}sub name {$_[0]->{name}}sub version {$_[0]->{version}}sub options {$_[0]->{options}}sub has_options {keys %{$_[0]->{options}}> 0}1;
+MODULE_CPANFILE_REQUIREMENT
+
+$fatpacked{"Module/Metadata.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'MODULE_METADATA';
+  package Module::Metadata;sub __clean_eval {eval $_[0]}use strict;use warnings;our$VERSION='1.000027';use Carp qw/croak/;use File::Spec;BEGIN {eval {require Fcntl;Fcntl->import('SEEK_SET');1}or *SEEK_SET=sub {0}}use version 0.87;BEGIN {if ($INC{'Log/Contextual.pm'}){require "Log/Contextual/WarnLogger.pm";Log::Contextual->import('log_info','-default_logger'=>Log::Contextual::WarnLogger->new({env_prefix=>'MODULE_METADATA',}),)}else {*log_info=sub (&) {warn $_[0]->()}}}use File::Find qw(find);my$V_NUM_REGEXP=qr{v?[0-9._]+};my$PKG_FIRST_WORD_REGEXP=qr{ # the FIRST word in a package name
+    [a-zA-Z_]                     # the first word CANNOT start with a digit
+      (?:
+        [\w']?                    # can contain letters, digits, _, or ticks
+        \w                        # But, NO multi-ticks or trailing ticks
+      )*
+  }x;my$PKG_ADDL_WORD_REGEXP=qr{ # the 2nd+ word in a package name
+    \w                           # the 2nd+ word CAN start with digits
+      (?:
+        [\w']?                   # and can contain letters or ticks
+        \w                       # But, NO multi-ticks or trailing ticks
+      )*
+  }x;my$PKG_NAME_REGEXP=qr{ # match a package name
+    (?: :: )?               # a pkg name can start with arisdottle
+    $PKG_FIRST_WORD_REGEXP  # a package word
+    (?:
+      (?: :: )+             ### arisdottle (allow one or many times)
+      $PKG_ADDL_WORD_REGEXP ### a package word
+    )*                      # ^ zero, one or many times
+    (?:
+      ::                    # allow trailing arisdottle
+    )?
+  }x;my$PKG_REGEXP=qr{   # match a package declaration
+    ^[\s\{;]*             # intro chars on a line
+    package               # the word 'package'
+    \s+                   # whitespace
+    ($PKG_NAME_REGEXP)    # a package name
+    \s*                   # optional whitespace
+    ($V_NUM_REGEXP)?        # optional version number
+    \s*                   # optional whitesapce
+    [;\{]                 # semicolon line terminator or block start (since 5.16)
+  }x;my$VARNAME_REGEXP=qr{ # match fully-qualified VERSION name
+    ([\$*])         # sigil - $ or *
+    (
+      (             # optional leading package name
+        (?:::|\')?  # possibly starting like just :: (a la $::VERSION)
+        (?:\w+(?:::|\'))*  # Foo::Bar:: ...
+      )?
+      VERSION
+    )\b
+  }x;my$VERS_REGEXP=qr{ # match a VERSION definition
+    (?:
+      \(\s*$VARNAME_REGEXP\s*\) # with parens
+    |
+      $VARNAME_REGEXP           # without parens
+    )
+    \s*
+    =[^=~>]  # = but not ==, nor =~, nor =>
+  }x;sub new_from_file {my$class=shift;my$filename=File::Spec->rel2abs(shift);return undef unless defined($filename)&& -f $filename;return$class->_init(undef,$filename,@_)}sub new_from_handle {my$class=shift;my$handle=shift;my$filename=shift;return undef unless defined($handle)&& defined($filename);$filename=File::Spec->rel2abs($filename);return$class->_init(undef,$filename,@_,handle=>$handle)}sub new_from_module {my$class=shift;my$module=shift;my%props=@_;$props{inc}||= \@INC;my$filename=$class->find_module_by_name($module,$props{inc});return undef unless defined($filename)&& -f $filename;return$class->_init($module,$filename,%props)}{my$compare_versions=sub {my ($v1,$op,$v2)=@_;$v1=version->new($v1)unless UNIVERSAL::isa($v1,'version');my$eval_str="\$v1 $op \$v2";my$result=eval$eval_str;log_info {"error comparing versions: '$eval_str' $@"}if $@;return$result};my$normalize_version=sub {my ($version)=@_;if ($version =~ /[=<>!,]/){}elsif (ref$version eq 'version'){$version=$version->is_qv ? $version->normal : $version->stringify}elsif ($version =~ /^[^v][^.]*\.[^.]+\./){$version="v$version"}else {}return$version};my$resolve_module_versions=sub {my$packages=shift;my($file,$version);my$err='';for my$p (@$packages){if (defined($p->{version})){if (defined($version)){if ($compare_versions->($version,'!=',$p->{version})){$err .= "  $p->{file} ($p->{version})\n"}else {}}else {$file=$p->{file};$version=$p->{version}}}$file ||= $p->{file}if defined($p->{file})}if ($err){$err="  $file ($version)\n" .$err}my%result=(file=>$file,version=>$version,err=>$err);return \%result};sub provides {my$class=shift;croak "provides() requires key/value pairs \n" if @_ % 2;my%args=@_;croak "provides() takes only one of 'dir' or 'files'\n" if$args{dir}&& $args{files};croak "provides() requires a 'version' argument" unless defined$args{version};croak "provides() does not support version '$args{version}' metadata" unless grep {$args{version}eq $_}qw/1.4 2/;$args{prefix}='lib' unless defined$args{prefix};my$p;if ($args{dir}){$p=$class->package_versions_from_directory($args{dir})}else {croak "provides() requires 'files' to be an array reference\n" unless ref$args{files}eq 'ARRAY';$p=$class->package_versions_from_directory($args{files})}if (length$args{prefix}){$args{prefix}=~ s{/$}{};for my$v (values %$p){$v->{file}="$args{prefix}/$v->{file}"}}return$p}sub package_versions_from_directory {my ($class,$dir,$files)=@_;my@files;if ($files){@files=@$files}else {find({wanted=>sub {push@files,$_ if -f $_ && /\.pm$/},no_chdir=>1,},$dir)}my(%prime,%alt);for my$file (@files){my$mapped_filename=File::Spec::Unix->abs2rel($file,$dir);my@path=split(/\//,$mapped_filename);(my$prime_package=join('::',@path))=~ s/\.pm$//;my$pm_info=$class->new_from_file($file);for my$package ($pm_info->packages_inside){next if$package eq 'main';next if$package eq 'DB';next if grep /^_/,split(/::/,$package);my$version=$pm_info->version($package);$prime_package=$package if lc($prime_package)eq lc($package);if ($package eq $prime_package){if (exists($prime{$package})){croak "Unexpected conflict in '$package'; multiple versions found.\n"}else {$mapped_filename="$package.pm" if lc("$package.pm")eq lc($mapped_filename);$prime{$package}{file}=$mapped_filename;$prime{$package}{version}=$version if defined($version)}}else {push(@{$alt{$package}},{file=>$mapped_filename,version=>$version,})}}}for my$package (keys(%alt)){my$result=$resolve_module_versions->($alt{$package});if (exists($prime{$package})){if ($result->{err}){log_info {"Found conflicting versions for package '$package'\n" ."  $prime{$package}{file} ($prime{$package}{version})\n" .$result->{err}}}elsif (defined($result->{version})){if (exists($prime{$package}{version})&& defined($prime{$package}{version})){if ($compare_versions->($prime{$package}{version},'!=',$result->{version})){log_info {"Found conflicting versions for package '$package'\n" ."  $prime{$package}{file} ($prime{$package}{version})\n" ."  $result->{file} ($result->{version})\n"}}}else {$prime{$package}{file}=$result->{file};$prime{$package}{version}=$result->{version}}}else {}}else {if ($result->{err}){log_info {"Found conflicting versions for package '$package'\n" .$result->{err}}}$prime{$package}{file}=$result->{file};$prime{$package}{version}=$result->{version}if defined($result->{version})}}for (grep defined $_->{version},values%prime){$_->{version}=$normalize_version->($_->{version})}return \%prime}}sub _init {my$class=shift;my$module=shift;my$filename=shift;my%props=@_;my$handle=delete$props{handle};my(%valid_props,@valid_props);@valid_props=qw(collect_pod inc);@valid_props{@valid_props}=delete(@props{@valid_props});warn "Unknown properties: @{[keys %props]}\n" if scalar(%props);my%data=(module=>$module,filename=>$filename,version=>undef,packages=>[],versions=>{},pod=>{},pod_headings=>[],collect_pod=>0,%valid_props,);my$self=bless(\%data,$class);if (not $handle){my$filename=$self->{filename};open$handle,'<',$filename or croak("Can't open '$filename': $!");$self->_handle_bom($handle,$filename)}$self->_parse_fh($handle);unless($self->{module}and length($self->{module})){my ($v,$d,$f)=File::Spec->splitpath($self->{filename});if($f =~ /\.pm$/){$f =~ s/\..+$//;my@candidates=grep /$f$/,@{$self->{packages}};$self->{module}=shift(@candidates)}else {if(grep /main/,@{$self->{packages}}){$self->{module}='main'}else {$self->{module}=$self->{packages}[0]|| ''}}}$self->{version}=$self->{versions}{$self->{module}}if defined($self->{module});return$self}sub _do_find_module {my$class=shift;my$module=shift || croak 'find_module_by_name() requires a package name';my$dirs=shift || \@INC;my$file=File::Spec->catfile(split(/::/,$module));for my$dir (@$dirs){my$testfile=File::Spec->catfile($dir,$file);return [File::Spec->rel2abs($testfile),$dir ]if -e $testfile and!-d _;$testfile .= '.pm';return [File::Spec->rel2abs($testfile),$dir ]if -e $testfile}return}sub find_module_by_name {my$found=shift()->_do_find_module(@_)or return;return$found->[0]}sub find_module_dir_by_name {my$found=shift()->_do_find_module(@_)or return;return$found->[1]}sub _parse_version_expression {my$self=shift;my$line=shift;my($sigil,$variable_name,$package);if ($line =~ /$VERS_REGEXP/o){($sigil,$variable_name,$package)=$2 ? ($1,$2,$3): ($4,$5,$6);if ($package){$package=($package eq '::')? 'main' : $package;$package =~ s/::$//}}return ($sigil,$variable_name,$package)}sub _handle_bom {my ($self,$fh,$filename)=@_;my$pos=tell$fh;return unless defined$pos;my$buf=' ' x 2;my$count=read$fh,$buf,length$buf;return unless defined$count and $count >= 2;my$encoding;if ($buf eq "\x{FE}\x{FF}"){$encoding='UTF-16BE'}elsif ($buf eq "\x{FF}\x{FE}"){$encoding='UTF-16LE'}elsif ($buf eq "\x{EF}\x{BB}"){$buf=' ';$count=read$fh,$buf,length$buf;if (defined$count and $count >= 1 and $buf eq "\x{BF}"){$encoding='UTF-8'}}if (defined$encoding){if ("$]" >= 5.008){binmode($fh,":encoding($encoding)")}}else {seek$fh,$pos,SEEK_SET or croak(sprintf "Can't reset position to the top of '$filename'")}return$encoding}sub _parse_fh {my ($self,$fh)=@_;my($in_pod,$seen_end,$need_vers)=(0,0,0);my(@packages,%vers,%pod,@pod);my$package='main';my$pod_sect='';my$pod_data='';my$in_end=0;while (defined(my$line=<$fh>)){my$line_num=$.;chomp($line);my$is_cut;if ($line =~ /^=([a-zA-Z].*)/){my$cmd=$1;$is_cut=$cmd =~ /^cut(?:[^a-zA-Z]|$)/;$in_pod=!$is_cut}if ($in_pod){if ($line =~ /^=head[1-4]\s+(.+)\s*$/){push(@pod,$1);if ($self->{collect_pod}&& length($pod_data)){$pod{$pod_sect}=$pod_data;$pod_data=''}$pod_sect=$1}elsif ($self->{collect_pod}){$pod_data .= "$line\n"}}elsif ($is_cut){if ($self->{collect_pod}&& length($pod_data)){$pod{$pod_sect}=$pod_data;$pod_data=''}$pod_sect=''}else {next if$in_end;next if$line =~ /^\s*#/;if ($line eq '__END__'){$in_end++;next}last if$line eq '__DATA__';my($version_sigil,$version_fullname,$version_package)=index($line,'VERSION')>= 1 ? $self->_parse_version_expression($line): ();if ($line =~ /$PKG_REGEXP/o){$package=$1;my$version=$2;push(@packages,$package)unless grep($package eq $_,@packages);$need_vers=defined$version ? 0 : 1;if (not exists$vers{$package}and defined$version){my$dwim_version=eval {_dwim_version($version)};croak "Version '$version' from $self->{filename} does not appear to be valid:\n$line\n\nThe fatal error was: $@\n" unless defined$dwim_version;$vers{$package}=$dwim_version}}elsif ($version_fullname && $version_package){push(@packages,$version_package)unless grep($version_package eq $_,@packages);$need_vers=0 if$version_package eq $package;unless (defined$vers{$version_package}&& length$vers{$version_package}){$vers{$version_package}=$self->_evaluate_version_line($version_sigil,$version_fullname,$line)}}elsif ($package eq 'main' && $version_fullname &&!exists($vers{main})){$need_vers=0;my$v=$self->_evaluate_version_line($version_sigil,$version_fullname,$line);$vers{$package}=$v;push(@packages,'main')}elsif ($package eq 'main' &&!exists($vers{main})&& $line =~ /\w/){$need_vers=1;$vers{main}='';push(@packages,'main')}elsif ($version_fullname && $need_vers){$need_vers=0;my$v=$self->_evaluate_version_line($version_sigil,$version_fullname,$line);unless (defined$vers{$package}&& length$vers{$package}){$vers{$package}=$v}}}}if ($self->{collect_pod}&& length($pod_data)){$pod{$pod_sect}=$pod_data}$self->{versions}=\%vers;$self->{packages}=\@packages;$self->{pod}=\%pod;$self->{pod_headings}=\@pod}{my$pn=0;sub _evaluate_version_line {my$self=shift;my($sigil,$variable_name,$line)=@_;$pn++;my$eval=qq{ my \$dummy = q#  Hide from _packages_inside()
+      #; package Module::Metadata::_version::p${pn};
+      use version;
+      sub {
+        local $sigil$variable_name;
+        $line;
+        \$$variable_name
+      };
+    };$eval=$1 if$eval =~ m{^(.+)}s;local $^W;my$vsub=__clean_eval($eval);if ($@ =~ /Can't locate/ && -d 'lib'){local@INC=('lib',@INC);$vsub=__clean_eval($eval)}warn "Error evaling version line '$eval' in $self->{filename}: $@\n" if $@;(ref($vsub)eq 'CODE')or croak "failed to build version sub for $self->{filename}";my$result=eval {$vsub->()};croak "Could not get version from $self->{filename} by executing:\n$eval\n\nThe fatal error was: $@\n" if $@;my$version=eval {_dwim_version($result)};croak "Version '$result' from $self->{filename} does not appear to be valid:\n$eval\n\nThe fatal error was: $@\n" unless defined$version;return$version}}{my@version_prep=(sub {return shift},sub {my$v=shift;$v =~ s{([0-9])[a-z-].*$}{$1}i;return$v},sub {my$v=shift;my$num_dots=()=$v =~ m{(\.)}g;my$num_unders=()=$v =~ m{(_)}g;my$leading_v=substr($v,0,1)eq 'v';if (!$leading_v && $num_dots < 2 && $num_unders > 1){$v =~ s{_}{}g;$num_unders=()=$v =~ m{(_)}g}return$v},sub {my$v=shift;no warnings 'numeric';return 0 + $v},);sub _dwim_version {my ($result)=shift;return$result if ref($result)eq 'version';my ($version,$error);for my$f (@version_prep){$result=$f->($result);$version=eval {version->new($result)};$error ||= $@ if $@;last if defined$version}croak$error unless defined$version;return$version}}sub name {$_[0]->{module}}sub filename {$_[0]->{filename}}sub packages_inside {@{$_[0]->{packages}}}sub pod_inside {@{$_[0]->{pod_headings}}}sub contains_pod {0+@{$_[0]->{pod_headings}}}sub version {my$self=shift;my$mod=shift || $self->{module};my$vers;if (defined($mod)&& length($mod)&& exists($self->{versions}{$mod})){return$self->{versions}{$mod}}else {return undef}}sub pod {my$self=shift;my$sect=shift;if (defined($sect)&& length($sect)&& exists($self->{pod}{$sect})){return$self->{pod}{$sect}}else {return undef}}sub is_indexable {my ($self,$package)=@_;my@indexable_packages=grep {$_ ne 'main'}$self->packages_inside;return!!grep {$_ eq $package}@indexable_packages if$package;return!!@indexable_packages}1;
+MODULE_METADATA
+
+$fatpacked{"Parse/CPAN/Meta.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'PARSE_CPAN_META';
+  use 5.008001;use strict;package Parse::CPAN::Meta;our$VERSION='1.4414';use Exporter;use Carp 'croak';our@ISA=qw/Exporter/;our@EXPORT_OK=qw/Load LoadFile/;sub load_file {my ($class,$filename)=@_;my$meta=_slurp($filename);if ($filename =~ /\.ya?ml$/){return$class->load_yaml_string($meta)}elsif ($filename =~ /\.json$/){return$class->load_json_string($meta)}else {$class->load_string($meta)}}sub load_string {my ($class,$string)=@_;if ($string =~ /^---/){return$class->load_yaml_string($string)}elsif ($string =~ /^\s*\{/){return$class->load_json_string($string)}else {return$class->load_yaml_string($string)}}sub load_yaml_string {my ($class,$string)=@_;my$backend=$class->yaml_backend();my$data=eval {no strict 'refs';&{"$backend\::Load"}($string)};croak $@ if $@;return$data || {}}sub load_json_string {my ($class,$string)=@_;my$data=eval {$class->json_backend()->new->decode($string)};croak $@ if $@;return$data || {}}sub yaml_backend {if (!defined$ENV{PERL_YAML_BACKEND}){_can_load('CPAN::Meta::YAML',0.011)or croak "CPAN::Meta::YAML 0.011 is not available\n";return "CPAN::Meta::YAML"}else {my$backend=$ENV{PERL_YAML_BACKEND};_can_load($backend)or croak "Could not load PERL_YAML_BACKEND '$backend'\n";$backend->can("Load")or croak "PERL_YAML_BACKEND '$backend' does not implement Load()\n";return$backend}}sub json_backend {if (!$ENV{PERL_JSON_BACKEND}or $ENV{PERL_JSON_BACKEND}eq 'JSON::PP'){_can_load('JSON::PP'=>2.27103)or croak "JSON::PP 2.27103 is not available\n";return 'JSON::PP'}else {_can_load('JSON'=>2.5)or croak "JSON 2.5 is required for " ."\$ENV{PERL_JSON_BACKEND} = '$ENV{PERL_JSON_BACKEND}'\n";return "JSON"}}sub _slurp {require Encode;open my$fh,"<:raw","$_[0]" or die "can't open $_[0] for reading: $!";my$content=do {local $/;<$fh>};$content=Encode::decode('UTF-8',$content,Encode::PERLQQ());return$content}sub _can_load {my ($module,$version)=@_;(my$file=$module)=~ s{::}{/}g;$file .= ".pm";return 1 if$INC{$file};return 0 if exists$INC{$file};eval {require$file;1}or return 0;if (defined$version){eval {$module->VERSION($version);1}or return 0}return 1}sub LoadFile ($) {return Load(_slurp(shift))}sub Load ($) {require CPAN::Meta::YAML;my$object=eval {CPAN::Meta::YAML::Load(shift)};croak $@ if $@;return$object}1;
+PARSE_CPAN_META
+
+$fatpacked{"Parse/PMFile.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'PARSE_PMFILE';
+  package Parse::PMFile;sub __clean_eval {eval $_[0]}use strict;use warnings;use Safe;use JSON::PP ();use Dumpvalue;use version ();use File::Spec ();our$VERSION='0.36';our$VERBOSE=0;our$ALLOW_DEV_VERSION=0;our$FORK=0;our$UNSAFE=$] < 5.010000 ? 1 : 0;sub new {my ($class,$meta,$opts)=@_;bless {%{$opts || {}},META_CONTENT=>$meta},$class}sub parse {my ($self,$pmfile)=@_;$pmfile =~ s|\\|/|g;my($filemtime)=(stat$pmfile)[9];$self->{MTIME}=$filemtime;$self->{PMFILE}=$pmfile;unless ($self->_version_from_meta_ok){my$version;unless (eval {$version=$self->_parse_version;1}){$self->_verbose(1,"error with version in $pmfile: $@");return}$self->{VERSION}=$version;if ($self->{VERSION}=~ /^\{.*\}$/){}elsif ($self->{VERSION}=~ /[_\s]/ &&!$self->{ALLOW_DEV_VERSION}&&!$ALLOW_DEV_VERSION){return}}my($ppp)=$self->_packages_per_pmfile;my@keys_ppp=$self->_filter_ppps(sort keys %$ppp);$self->_verbose(1,"Will check keys_ppp[@keys_ppp]\n");my ($package,%errors);my%checked_in;DBPACK: foreach$package (@keys_ppp){if ($package !~ /^\w[\w\:\']*\w?\z/ || $package !~ /\w\z/ || $package =~ /:/ && $package !~ /::/ || $package =~ /\w:\w/ || $package =~ /:::/){$self->_verbose(1,"Package[$package] did not pass the ultimate sanity check");delete$ppp->{$package};next}if ($self->{USERID}&& $self->{PERMISSIONS}&&!$self->_perm_check($package)){delete$ppp->{$package};next}{my (undef,$module)=split m{/lib/},$self->{PMFILE},2;if ($module){$module =~ s{\.pm\z}{};$module =~ s{/}{::}g;if (lc$module eq lc$package && $module ne $package){$errors{$package}={indexing_warning=>"Capitalization of package ($package) does not match filename!",infile=>$self->{PMFILE},}}}}my$pp=$ppp->{$package};if ($pp->{version}&& $pp->{version}=~ /^\{.*\}$/){my$err=JSON::PP::decode_json($pp->{version});if ($err->{x_normalize}){$errors{$package}={normalize=>$err->{version},infile=>$pp->{infile},};$pp->{version}="undef"}elsif ($err->{openerr}){$pp->{version}="undef";$self->_verbose(1,qq{Parse::PMFile was not able to
+          read the file. It issued the following error: C< $err->{r} >},);$errors{$package}={open=>$err->{r},infile=>$pp->{infile},}}else {$pp->{version}="undef";$self->_verbose(1,qq{Parse::PMFile was not able to
+          parse the following line in that file: C< $err->{line} >
+  
+          Note: the indexer is running in a Safe compartement and cannot
+          provide the full functionality of perl in the VERSION line. It
+          is trying hard, but sometime it fails. As a workaround, please
+          consider writing a META.yml that contains a 'provides'
+          attribute or contact the CPAN admins to investigate (yet
+          another) workaround against "Safe" limitations.)},);$errors{$package}={parse_version=>$err->{line},infile=>$err->{file},}}}for ($package,$pp->{version},){if (!defined || /^\s*$/ || /\s/){delete$ppp->{$package};next}}$checked_in{$package}=$ppp->{$package}}return (wantarray && %errors)? (\%checked_in,\%errors): \%checked_in}sub _perm_check {my ($self,$package)=@_;my$userid=$self->{USERID};my$module=$self->{PERMISSIONS}->module_permissions($package);return 1 if!$module;return 1 if defined$module->m && $module->m eq $userid;return 1 if defined$module->f && $module->f eq $userid;return 1 if defined$module->c && grep {$_ eq $userid}@{$module->c};return}sub _parse_version {my$self=shift;use strict;my$pmfile=$self->{PMFILE};my$tmpfile=File::Spec->catfile(File::Spec->tmpdir,"ParsePMFile$$" .rand(1000));my$pmcp=$pmfile;for ($pmcp){s/([^\\](\\\\)*)@/$1\\@/g}my($v);{package main;my$pid;if ($self->{FORK}|| $FORK){$pid=fork();die "Can't fork: $!" unless defined$pid}if ($pid){waitpid($pid,0);if (open my$fh,'<',$tmpfile){$v=<$fh>}}else {my($comp)=Safe->new;my$eval=qq{
+                  local(\$^W) = 0;
+                  Parse::PMFile::_parse_version_safely("$pmcp");
+              };$comp->permit("entereval");$comp->share("*Parse::PMFile::_parse_version_safely");$comp->share("*version::new");$comp->share("*version::numify");$comp->share_from('main',['*version::','*charstar::','*Exporter::','*DynaLoader::']);$comp->share_from('version',['&qv']);$comp->permit(":base_math");$comp->deny(qw/enteriter iter unstack goto/);version->import('qv')if$self->{UNSAFE}|| $UNSAFE;{no strict;$v=($self->{UNSAFE}|| $UNSAFE)? eval$eval : $comp->reval($eval)}if ($@){my$err=$@;if (ref$err){if ($err->{line}=~ /([\$*])([\w\:\']*)\bVERSION\b.*?\=(.*)/){local($^W)=0;my ($sigil,$vstr)=($1,$3);$self->_restore_overloaded_stuff(1)if$err->{line}=~ /use\s+version\b|version\->|qv\(/;$v=($self->{UNSAFE}|| $UNSAFE)? eval$vstr : $comp->reval($vstr);$v=$$v if$sigil eq '*' && ref$v}if ($@ or!$v){$self->_verbose(1,sprintf("reval failed: err[%s] for eval[%s]",JSON::PP::encode_json($err),$eval,));$v=JSON::PP::encode_json($err)}}else {$v=JSON::PP::encode_json({openerr=>$err })}}if (defined$v){$v=$v->numify if ref($v)=~ /^version(::vpp)?$/}else {$v=""}if ($self->{FORK}|| $FORK){open my$fh,'>:utf8',$tmpfile;print$fh $v;exit 0}else {utf8::encode($v);$v=undef if defined$v &&!length$v;$comp->erase;$self->_restore_overloaded_stuff}}}unlink$tmpfile if ($self->{FORK}|| $FORK)&& -e $tmpfile;return$self->_normalize_version($v)}sub _restore_overloaded_stuff {my ($self,$used_version_in_safe)=@_;return if$self->{UNSAFE}|| $UNSAFE;no strict 'refs';no warnings 'redefine';my$restored;if ($INC{'version/vxs.pm'}){*{'version::(""'}=\&version::vxs::stringify;*{'version::(0+'}=\&version::vxs::numify;*{'version::(cmp'}=\&version::vxs::VCMP;*{'version::(<=>'}=\&version::vxs::VCMP;*{'version::(bool'}=\&version::vxs::boolean;$restored=1}if ($INC{'version/vpp.pm'}){{package charstar;overload->import}if (!$used_version_in_safe){package version::vpp;overload->import}unless ($restored){*{'version::(""'}=\&version::vpp::stringify;*{'version::(0+'}=\&version::vpp::numify;*{'version::(cmp'}=\&version::vpp::vcmp;*{'version::(<=>'}=\&version::vpp::vcmp;*{'version::(bool'}=\&version::vpp::vbool}*{'version::vpp::(""'}=\&version::vpp::stringify;*{'version::vpp::(0+'}=\&version::vpp::numify;*{'version::vpp::(cmp'}=\&version::vpp::vcmp;*{'version::vpp::(<=>'}=\&version::vpp::vcmp;*{'version::vpp::(bool'}=\&version::vpp::vbool;*{'charstar::(""'}=\&charstar::thischar;*{'charstar::(0+'}=\&charstar::thischar;*{'charstar::(++'}=\&charstar::increment;*{'charstar::(--'}=\&charstar::decrement;*{'charstar::(+'}=\&charstar::plus;*{'charstar::(-'}=\&charstar::minus;*{'charstar::(*'}=\&charstar::multiply;*{'charstar::(cmp'}=\&charstar::cmp;*{'charstar::(<=>'}=\&charstar::spaceship;*{'charstar::(bool'}=\&charstar::thischar;*{'charstar::(='}=\&charstar::clone;$restored=1}if (!$restored){*{'version::(""'}=\&version::stringify;*{'version::(0+'}=\&version::numify;*{'version::(cmp'}=\&version::vcmp;*{'version::(<=>'}=\&version::vcmp;*{'version::(bool'}=\&version::boolean}}sub _packages_per_pmfile {my$self=shift;my$ppp={};my$pmfile=$self->{PMFILE};my$filemtime=$self->{MTIME};my$version=$self->{VERSION};open my$fh,"<","$pmfile" or return$ppp;local $/="\n";my$inpod=0;PLINE: while (<$fh>){chomp;my($pline)=$_;$inpod=$pline =~ /^=(?!cut)/ ? 1 : $pline =~ /^=cut/ ? 0 : $inpod;next if$inpod;next if substr($pline,0,4)eq "=cut";$pline =~ s/\#.*//;next if$pline =~ /^\s*$/;if ($pline =~ /^__(?:END|DATA)__\b/ and $pmfile !~ /\.PL$/){last PLINE}my$pkg;my$strict_version;if ($pline =~ m{
+                        # (.*) # takes too much time if $pline is long
+                        (?<![*\$\\@%&]) # no sigils
+                        \bpackage\s+
+                        ([\w\:\']+)
+                        \s*
+                        (?: $ | [\}\;] | \{ | \s+($version::STRICT) )
+                      }x){$pkg=$1;$strict_version=$2;if ($pkg eq "DB"){next PLINE}}if ($pkg){$pkg =~ s/\'/::/;next PLINE unless$pkg =~ /^[A-Za-z]/;next PLINE unless$pkg =~ /\w$/;next PLINE if$pkg eq "main";next PLINE if length($pkg)> 128;$ppp->{$pkg}{parsed}++;$ppp->{$pkg}{infile}=$pmfile;if ($self->_simile($pmfile,$pkg)){$ppp->{$pkg}{simile}=$pmfile;if ($self->_version_from_meta_ok){my$provides=$self->{META_CONTENT}{provides};if (exists$provides->{$pkg}){if (defined$provides->{$pkg}{version}){my$v=$provides->{$pkg}{version};if ($v =~ /[_\s]/ &&!$self->{ALLOW_DEV_VERSION}&&!$ALLOW_DEV_VERSION){next PLINE}unless (eval {$version=$self->_normalize_version($v);1}){$self->_verbose(1,"error with version in $pmfile: $@");next}$ppp->{$pkg}{version}=$version}else {$ppp->{$pkg}{version}="undef"}}}else {if (defined$strict_version){$ppp->{$pkg}{version}=$strict_version }else {$ppp->{$pkg}{version}=defined$version ? $version : ""}no warnings;if ($version eq 'undef'){$ppp->{$pkg}{version}=$version unless defined$ppp->{$pkg}{version}}else {$ppp->{$pkg}{version}=$version if$version > $ppp->{$pkg}{version}|| $version gt $ppp->{$pkg}{version}}}}else {$ppp->{$pkg}{version}=$version unless defined$ppp->{$pkg}{version}&& length($ppp->{$pkg}{version})}$ppp->{$pkg}{filemtime}=$filemtime}else {}}close$fh;$ppp}{no strict;sub _parse_version_safely {my($parsefile)=@_;my$result;local*FH;local $/="\n";open(FH,$parsefile)or die "Could not open '$parsefile': $!";my$inpod=0;while (<FH>){$inpod=/^=(?!cut)/ ? 1 : /^=cut/ ? 0 : $inpod;next if$inpod || /^\s*#/;last if /^__(?:END|DATA)__\b/;chop;if (my ($ver)=/package \s+ \S+ \s+ (\S+) \s* [;{]/x){return$ver if version::is_lax($ver)}next unless /(?<!\\)([\$*])(([\w\:\']*)\bVERSION)\b.*(?<![!><=])\=(?![=>])/;my$current_parsed_line=$_;my$eval=qq{
+                  package #
+                      ExtUtils::MakeMaker::_version;
+  
+                  local $1$2;
+                  \$$2=undef; do {
+                      $_
+                  }; \$$2
+              };local $^W=0;local$SIG{__WARN__}=sub {};$result=__clean_eval($eval);if ($@ or!defined$result){die +{eval=>$eval,line=>$current_parsed_line,file=>$parsefile,err=>$@,}}last}close FH;$result="undef" unless defined$result;if ((ref$result)=~ /^version(?:::vpp)?\b/){$result=$result->numify}return$result}}sub _filter_ppps {my($self,@ppps)=@_;my@res;MANI: for my$ppp (@ppps){if ($self->{META_CONTENT}){my$no_index=$self->{META_CONTENT}{no_index}|| $self->{META_CONTENT}{private};if (ref($no_index)eq 'HASH'){my%map=(package=>qr{\z},namespace=>qr{::},);for my$k (qw(package namespace)){next unless my$v=$no_index->{$k};my$rest=$map{$k};if (ref$v eq "ARRAY"){for my$ve (@$v){$ve =~ s|::$||;if ($ppp =~ /^$ve$rest/){$self->_verbose(1,"Skipping ppp[$ppp] due to ve[$ve]");next MANI}else {$self->_verbose(1,"NOT skipping ppp[$ppp] due to ve[$ve]")}}}else {$v =~ s|::$||;if ($ppp =~ /^$v$rest/){$self->_verbose(1,"Skipping ppp[$ppp] due to v[$v]");next MANI}else {$self->_verbose(1,"NOT skipping ppp[$ppp] due to v[$v]")}}}}else {$self->_verbose(1,"No keyword 'no_index' or 'private' in META_CONTENT")}}else {}push@res,$ppp}$self->_verbose(1,"Result of filter_ppps: res[@res]");@res}sub _simile {my($self,$file,$package)=@_;$file =~ s|.*/||;$file =~ s|\.pm(?:\.PL)?||;my$ret=$package =~ m/\b\Q$file\E$/;$ret ||= 0;unless ($ret){$ret=1 if lc$file eq 'version'}$self->_verbose(1,"Result of simile(): file[$file] package[$package] ret[$ret]\n");$ret}sub _normalize_version {my($self,$v)=@_;$v="undef" unless defined$v;my$dv=Dumpvalue->new;my$sdv=$dv->stringify($v,1);$self->_verbose(1,"Result of normalize_version: sdv[$sdv]\n");return$v if$v eq "undef";return$v if$v =~ /^\{.*\}$/;$v =~ s/^\s+//;$v =~ s/\s+\z//;if ($v =~ /_/){return$v }if (!version::is_lax($v)){return JSON::PP::encode_json({x_normalize=>'version::is_lax failed',version=>$v })}my$vv=eval {no warnings;version->new($v)->numify};if ($@){return JSON::PP::encode_json({x_normalize=>$@,version=>$v })}if ($vv eq $v){}else {my$forced=$self->_force_numeric($v);if ($forced eq $vv){}elsif ($forced =~ /^v(.+)/){$vv=version->new($1)->numify}else {if ($forced==$vv){$vv=$forced}}}return$vv}sub _force_numeric {my($self,$v)=@_;$v=$self->_readable($v);if ($v =~ /^(\+?)(\d*)(\.(\d*))?/ && (defined $2 && length $2 || defined $4 && length $4)){my$two=defined $2 ? $2 : "";my$three=defined $3 ? $3 : "";$v="$two$three"}$v}sub _version_from_meta_ok {my($self)=@_;return$self->{VERSION_FROM_META_OK}if exists$self->{VERSION_FROM_META_OK};my$c=$self->{META_CONTENT};return($self->{VERSION_FROM_META_OK}=0)unless$c->{provides};my ($mb_v)=(defined$c->{generated_by}? $c->{generated_by}: '')=~ /Module::Build version ([\d\.]+)/;return($self->{VERSION_FROM_META_OK}=1)unless$mb_v;return($self->{VERSION_FROM_META_OK}=1)if$mb_v eq '0.250.0';if ($mb_v >= 0.19 && $mb_v < 0.26 &&!keys %{$c->{provides}}){return($self->{VERSION_FROM_META_OK}=0)}return($self->{VERSION_FROM_META_OK}=1)}sub _verbose {my($self,$level,@what)=@_;warn@what if$level <= ((ref$self && $self->{VERBOSE})|| $VERBOSE)}sub _vcmp {my($self,$l,$r)=@_;local($^W)=0;$self->_verbose(9,"l[$l] r[$r]");return 0 if$l eq $r;for ($l,$r){s/_//g}$self->_verbose(9,"l[$l] r[$r]");for ($l,$r){next unless tr/.// > 1 || /^v/;s/^v?/v/;1 while s/\.0+(\d)/.$1/}$self->_verbose(9,"l[$l] r[$r]");if ($l=~/^v/ <=> $r=~/^v/){for ($l,$r){next if /^v/;$_=$self->_float2vv($_)}}$self->_verbose(9,"l[$l] r[$r]");my$lvstring="v0";my$rvstring="v0";if ($] >= 5.006 && $l =~ /^v/ && $r =~ /^v/){$lvstring=$self->_vstring($l);$rvstring=$self->_vstring($r);$self->_verbose(9,sprintf "lv[%vd] rv[%vd]",$lvstring,$rvstring)}return (($l ne "undef")<=> ($r ne "undef")|| $lvstring cmp $rvstring || $l <=> $r || $l cmp $r)}sub _vgt {my($self,$l,$r)=@_;$self->_vcmp($l,$r)> 0}sub _vlt {my($self,$l,$r)=@_;$self->_vcmp($l,$r)< 0}sub _vge {my($self,$l,$r)=@_;$self->_vcmp($l,$r)>= 0}sub _vle {my($self,$l,$r)=@_;$self->_vcmp($l,$r)<= 0}sub _vstring {my($self,$n)=@_;$n =~ s/^v// or die "Parse::PMFile::_vstring() called with invalid arg [$n]";pack "U*",split /\./,$n}sub _float2vv {my($self,$n)=@_;my($rev)=int($n);$rev ||= 0;my($mantissa)=$n =~ /\.(\d{1,12})/;$mantissa ||= 0;$mantissa .= "0" while length($mantissa)%3;my$ret="v" .$rev;while ($mantissa){$mantissa =~ s/(\d{1,3})// or die "Panic: length>0 but not a digit? mantissa[$mantissa]";$ret .= ".".int($1)}$ret =~ s/(\.0)+/.0/;$ret}sub _readable {my($self,$n)=@_;$n =~ /^([\w\-\+\.]+)/;return $1 if defined $1 && length($1)>0;if ($] < 5.006){$self->_verbose(9,"Suspicious version string seen [$n]\n");return$n}my$better=sprintf "v%vd",$n;$self->_verbose(9,"n[$n] better[$better]");return$better}1;
+PARSE_PMFILE
+
+$fatpacked{"String/ShellQuote.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'STRING_SHELLQUOTE';
+  package String::ShellQuote;use strict;use vars qw($VERSION @ISA @EXPORT);require Exporter;$VERSION='1.04';@ISA=qw(Exporter);@EXPORT=qw(shell_quote shell_quote_best_effort shell_comment_quote);sub croak {require Carp;goto&Carp::croak}sub _shell_quote_backend {my@in=@_;my@err=();if (0){require RS::Handy;print RS::Handy::data_dump(\@in)}return \@err,'' unless@in;my$ret='';my$saw_non_equal=0;for (@in){if (!defined $_ or $_ eq ''){$_="''";next}if (s/\x00//g){push@err,"No way to quote string containing null (\\000) bytes"}my$escape=0;if (/=/){if (!$saw_non_equal){$escape=1}}else {$saw_non_equal=1}if (m|[^\w!%+,\-./:=@^]|){$escape=1}if ($escape || (!$saw_non_equal && /=/)){s/'/'\\''/g;s|((?:'\\''){2,})|q{'"} . (q{'} x (length($1) / 4)) . q{"'}|ge;$_="'$_'";s/^''//;s/''$//}}continue {$ret .= "$_ "}chop$ret;return \@err,$ret}sub shell_quote {my ($rerr,$s)=_shell_quote_backend @_;if (@$rerr){my%seen;@$rerr=grep {!$seen{$_}++}@$rerr;my$s=join '',map {"shell_quote(): $_\n"}@$rerr;chomp$s;croak$s}return$s}sub shell_quote_best_effort {my ($rerr,$s)=_shell_quote_backend @_;return$s}sub shell_comment_quote {return '' unless @_;unless (@_==1){croak "Too many arguments to shell_comment_quote " ."(got " .@_ ." expected 1)"}local $_=shift;s/\n/\n#/g;return $_}1;
+STRING_SHELLQUOTE
+
+$fatpacked{"lib/core/only.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'LIB_CORE_ONLY';
+  package lib::core::only;use strict;use warnings FATAL=>'all';use Config;sub import {@INC=@Config{qw(privlibexp archlibexp)};return}1;
+LIB_CORE_ONLY
+
+$fatpacked{"local/lib.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'LOCAL_LIB';
+  package local::lib;use 5.006;use strict;use warnings;use Config;our$VERSION='2.000015';$VERSION=eval$VERSION;BEGIN {*_WIN32=($^O eq 'MSWin32' || $^O eq 'NetWare' || $^O eq 'symbian')? sub(){1}: sub(){0};*_USE_FSPEC=($^O eq 'MacOS' || $^O eq 'VMS' || $INC{'File/Spec.pm'})? sub(){1}: sub(){0}}our$_DIR_JOIN=_WIN32 ? '\\' : '/';our$_DIR_SPLIT=(_WIN32 || $^O eq 'cygwin')? qr{[\\/]} : qr{/};our$_ROOT=_WIN32 ? do {my$UNC=qr{[\\/]{2}[^\\/]+[\\/][^\\/]+};qr{^(?:$UNC|[A-Za-z]:|)$_DIR_SPLIT}}: qr{^/};our$_PERL;sub _cwd {my$drive=shift;if (!$_PERL){($_PERL)=$^X =~ /(.+)/;if (_is_abs($_PERL)){}elsif (-x $Config{perlpath}){$_PERL=$Config{perlpath}}else {($_PERL)=map {/(.*)/}grep {-x $_}map {join($_DIR_JOIN,$_,$_PERL)}split /\Q$Config{path_sep}\E/,$ENV{PATH}}}local@ENV{qw(PATH IFS CDPATH ENV BASH_ENV)};my$cmd=$drive ? "eval { Cwd::getdcwd(q($drive)) }" : 'getcwd';my$cwd=`"$_PERL" -MCwd -le "print $cmd"`;chomp$cwd;if (!length$cwd && $drive){$cwd=$drive}$cwd =~ s/$_DIR_SPLIT?$/$_DIR_JOIN/;$cwd}sub _catdir {if (_USE_FSPEC){require File::Spec;File::Spec->catdir(@_)}else {my$dir=join($_DIR_JOIN,@_);$dir =~ s{($_DIR_SPLIT)(?:\.?$_DIR_SPLIT)+}{$1}g;$dir}}sub _is_abs {if (_USE_FSPEC){require File::Spec;File::Spec->file_name_is_absolute($_[0])}else {$_[0]=~ $_ROOT}}sub _rel2abs {my ($dir,$base)=@_;return$dir if _is_abs($dir);$base=_WIN32 && $dir =~ s/^([A-Za-z]:)// ? _cwd("$1"): $base ? $base : _cwd;return _catdir($base,$dir)}sub import {my ($class,@args)=@_;push@args,@ARGV if $0 eq '-';my@steps;my%opts;my$shelltype;while (@args){my$arg=shift@args;if ($arg =~ /\xE2\x88\x92/ or $arg =~ /−/){die <<'DEATH'}elsif ($arg eq '--self-contained'){die <<'DEATH'}elsif($arg =~ /^--deactivate(?:=(.*))?$/){my$path=defined $1 ? $1 : shift@args;push@steps,['deactivate',$path]}elsif ($arg eq '--deactivate-all'){push@steps,['deactivate_all']}elsif ($arg =~ /^--shelltype(?:=(.*))?$/){$shelltype=defined $1 ? $1 : shift@args}elsif ($arg eq '--no-create'){$opts{no_create}=1}elsif ($arg =~ /^--/){die "Unknown import argument: $arg"}else {push@steps,['activate',$arg]}}if (!@steps){push@steps,['activate',undef]}my$self=$class->new(%opts);for (@steps){my ($method,@args)=@$_;$self=$self->$method(@args)}if ($0 eq '-'){print$self->environment_vars_string($shelltype);exit 0}else {$self->setup_local_lib}}sub new {my$class=shift;bless {@_},$class}sub clone {my$self=shift;bless {%$self,@_},ref$self}sub inc {$_[0]->{inc}||= \@INC}sub libs {$_[0]->{libs}||= [\'PERL5LIB' ]}sub bins {$_[0]->{bins}||= [\'PATH' ]}sub roots {$_[0]->{roots}||= [\'PERL_LOCAL_LIB_ROOT' ]}sub extra {$_[0]->{extra}||= {}}sub no_create {$_[0]->{no_create}}my$_archname=$Config{archname};my$_version=$Config{version};my@_inc_version_list=reverse split / /,$Config{inc_version_list};my$_path_sep=$Config{path_sep};sub _as_list {my$list=shift;grep length,map {!(ref $_ && ref $_ eq 'SCALAR')? $_ : (defined$ENV{$$_}? split(/\Q$_path_sep/,$ENV{$$_}): ())}ref$list ? @$list : $list}sub _remove_from {my ($list,@remove)=@_;return @$list if!@remove;my%remove=map {$_=>1}@remove;grep!$remove{$_},_as_list($list)}my@_lib_subdirs=([$_version,$_archname],[$_version],[$_archname],(@_inc_version_list ? \@_inc_version_list : ()),[],);sub install_base_bin_path {my ($class,$path)=@_;return _catdir($path,'bin')}sub install_base_perl_path {my ($class,$path)=@_;return _catdir($path,'lib','perl5')}sub install_base_arch_path {my ($class,$path)=@_;_catdir($class->install_base_perl_path($path),$_archname)}sub lib_paths_for {my ($class,$path)=@_;my$base=$class->install_base_perl_path($path);return map {_catdir($base,@$_)}@_lib_subdirs}sub _mm_escape_path {my$path=shift;$path =~ s/\\/\\\\/g;if ($path =~ s/ /\\ /g){$path=qq{"$path"}}return$path}sub _mb_escape_path {my$path=shift;$path =~ s/\\/\\\\/g;return qq{"$path"}}sub installer_options_for {my ($class,$path)=@_;return (PERL_MM_OPT=>defined$path ? "INSTALL_BASE="._mm_escape_path($path): undef,PERL_MB_OPT=>defined$path ? "--install_base "._mb_escape_path($path): undef,)}sub active_paths {my ($self)=@_;$self=ref$self ? $self : $self->new;return grep {my$active_ll=$self->install_base_perl_path($_);grep {$_ eq $active_ll}@{$self->inc}}_as_list($self->roots)}sub deactivate {my ($self,$path)=@_;$self=$self->new unless ref$self;$path=$self->resolve_path($path);$path=$self->normalize_path($path);my@active_lls=$self->active_paths;if (!grep {$_ eq $path}@active_lls){warn "Tried to deactivate inactive local::lib '$path'\n";return$self}my%args=(bins=>[_remove_from($self->bins,$self->install_base_bin_path($path))],libs=>[_remove_from($self->libs,$self->install_base_perl_path($path))],inc=>[_remove_from($self->inc,$self->lib_paths_for($path))],roots=>[_remove_from($self->roots,$path)],);$args{extra}={$self->installer_options_for($args{roots}[0])};$self->clone(%args)}sub deactivate_all {my ($self)=@_;$self=$self->new unless ref$self;my@active_lls=$self->active_paths;my%args;if (@active_lls){%args=(bins=>[_remove_from($self->bins,map$self->install_base_bin_path($_),@active_lls)],libs=>[_remove_from($self->libs,map$self->install_base_perl_path($_),@active_lls)],inc=>[_remove_from($self->inc,map$self->lib_paths_for($_),@active_lls)],roots=>[_remove_from($self->roots,@active_lls)],)}$args{extra}={$self->installer_options_for(undef)};$self->clone(%args)}sub activate {my ($self,$path)=@_;$self=$self->new unless ref$self;$path=$self->resolve_path($path);$self->ensure_dir_structure_for($path)unless$self->no_create;$path=$self->normalize_path($path);my@active_lls=$self->active_paths;if (grep {$_ eq $path}@active_lls[1 .. $#active_lls]){$self=$self->deactivate($path)}my%args;if (!@active_lls || $active_lls[0]ne $path){%args=(bins=>[$self->install_base_bin_path($path),@{$self->bins}],libs=>[$self->install_base_perl_path($path),@{$self->libs}],inc=>[$self->lib_paths_for($path),@{$self->inc}],roots=>[$path,@{$self->roots}],)}$args{extra}={$self->installer_options_for($path)};$self->clone(%args)}sub normalize_path {my ($self,$path)=@_;$path=(Win32::GetShortPathName($path)|| $path)if $^O eq 'MSWin32';return$path}sub build_environment_vars_for {my$self=$_[0]->new->activate($_[1]);$self->build_environment_vars}sub build_activate_environment_vars_for {my$self=$_[0]->new->activate($_[1]);$self->build_environment_vars}sub build_deactivate_environment_vars_for {my$self=$_[0]->new->deactivate($_[1]);$self->build_environment_vars}sub build_deact_all_environment_vars_for {my$self=$_[0]->new->deactivate_all;$self->build_environment_vars}sub build_environment_vars {my$self=shift;(PATH=>join($_path_sep,_as_list($self->bins)),PERL5LIB=>join($_path_sep,_as_list($self->libs)),PERL_LOCAL_LIB_ROOT=>join($_path_sep,_as_list($self->roots)),%{$self->extra},)}sub setup_local_lib_for {my$self=$_[0]->new->activate($_[1]);$self->setup_local_lib}sub setup_local_lib {my$self=shift;require Carp::Heavy if$INC{'Carp.pm'};$self->setup_env_hash;@INC=@{$self->inc}}sub setup_env_hash_for {my$self=$_[0]->new->activate($_[1]);$self->setup_env_hash}sub setup_env_hash {my$self=shift;my%env=$self->build_environment_vars;for my$key (keys%env){if (defined$env{$key}){$ENV{$key}=$env{$key}}else {delete$ENV{$key}}}}sub print_environment_vars_for {print $_[0]->environment_vars_string_for(@_[1..$#_])}sub environment_vars_string_for {my$self=$_[0]->new->activate($_[1]);$self->environment_vars_string}sub environment_vars_string {my ($self,$shelltype)=@_;$shelltype ||= $self->guess_shelltype;my$extra=$self->extra;my@envs=(PATH=>$self->bins,PERL5LIB=>$self->libs,PERL_LOCAL_LIB_ROOT=>$self->roots,map {$_=>$extra->{$_}}sort keys %$extra,);$self->_build_env_string($shelltype,\@envs)}sub _build_env_string {my ($self,$shelltype,$envs)=@_;my@envs=@$envs;my$build_method="build_${shelltype}_env_declaration";my$out='';while (@envs){my ($name,$value)=(shift(@envs),shift(@envs));if (ref$value && @$value==1 && ref$value->[0]&& ref$value->[0]eq 'SCALAR' && ${$value->[0]}eq $name){next}$out .= $self->$build_method($name,$value)}my$wrap_method="wrap_${shelltype}_output";if ($self->can($wrap_method)){return$self->$wrap_method($out)}return$out}sub build_bourne_env_declaration {my ($class,$name,$args)=@_;my$value=$class->_interpolate($args,'${%s}',qr/["\\\$!`]/,'\\%s');if (!defined$value){return qq{unset $name;\n}}$value =~ s/(^|\G|$_path_sep)\$\{$name\}$_path_sep/$1\${$name}\${$name+$_path_sep}/g;$value =~ s/$_path_sep\$\{$name\}$/\${$name+$_path_sep}\${$name}/;qq{${name}="$value"; export ${name};\n}}sub build_csh_env_declaration {my ($class,$name,$args)=@_;my ($value,@vars)=$class->_interpolate($args,'${%s}','"','"\\%s"');if (!defined$value){return qq{unsetenv $name;\n}}my$out='';for my$var (@vars){$out .= qq{if ! \$?$name setenv $name '';\n}}my$value_without=$value;if ($value_without =~ s/(?:^|$_path_sep)\$\{$name\}(?:$_path_sep|$)//g){$out .= qq{if "\${$name}" != '' setenv $name "$value";\n};$out .= qq{if "\${$name}" == '' }}$out .= qq{setenv $name "$value_without";\n};return$out}sub build_cmd_env_declaration {my ($class,$name,$args)=@_;my$value=$class->_interpolate($args,'%%%s%%',qr(%),'%s');if (!$value){return qq{\@set $name=\n}}my$out='';my$value_without=$value;if ($value_without =~ s/(?:^|$_path_sep)%$name%(?:$_path_sep|$)//g){$out .= qq{\@if not "%$name%"=="" set "$name=$value"\n};$out .= qq{\@if "%$name%"=="" }}$out .= qq{\@set "$name=$value_without"\n};return$out}sub build_powershell_env_declaration {my ($class,$name,$args)=@_;my$value=$class->_interpolate($args,'$env:%s','"','`%s');if (!$value){return qq{Remove-Item -ErrorAction 0 Env:\\$name;\n}}my$maybe_path_sep=qq{\$(if("\$env:$name"-eq""){""}else{"$_path_sep"})};$value =~ s/(^|\G|$_path_sep)\$env:$name$_path_sep/$1\$env:$name"+$maybe_path_sep+"/g;$value =~ s/$_path_sep\$env:$name$/"+$maybe_path_sep+\$env:$name+"/;qq{\$env:$name = \$("$value");\n}}sub wrap_powershell_output {my ($class,$out)=@_;return$out || " \n"}sub build_fish_env_declaration {my ($class,$name,$args)=@_;my$value=$class->_interpolate($args,'$%s',qr/[\\"' ]/,'\\%s');if (!defined$value){return qq{set -e $name;\n}}$value =~ s/$_path_sep/ /g;qq{set -x $name $value;\n}}sub _interpolate {my ($class,$args,$var_pat,$escape,$escape_pat)=@_;return unless defined$args;my@args=ref$args ? @$args : $args;return unless@args;my@vars=map {$$_}grep {ref $_ eq 'SCALAR'}@args;my$string=join$_path_sep,map {ref $_ eq 'SCALAR' ? sprintf($var_pat,$$_): do {s/($escape)/sprintf($escape_pat, $1)/ge;$_}}@args;return wantarray ? ($string,\@vars): $string}sub pipeline;sub pipeline {my@methods=@_;my$last=pop(@methods);if (@methods){\sub {my ($obj,@args)=@_;$obj->${pipeline@methods}($obj->$last(@args))}}else {\sub {shift->$last(@_)}}}sub resolve_path {my ($class,$path)=@_;$path=$class->${pipeline qw(resolve_relative_path resolve_home_path resolve_empty_path)}($path);$path}sub resolve_empty_path {my ($class,$path)=@_;if (defined$path){$path}else {'~/perl5'}}sub resolve_home_path {my ($class,$path)=@_;$path =~ /^~([^\/]*)/ or return$path;my$user=$1;my$homedir=do {if (!length($user)&& defined$ENV{HOME}){$ENV{HOME}}else {require File::Glob;File::Glob::bsd_glob("~$user",File::Glob::GLOB_TILDE())}};unless (defined$homedir){require Carp;require Carp::Heavy;Carp::croak("Couldn't resolve homedir for " .(defined$user ? $user : 'current user'))}$path =~ s/^~[^\/]*/$homedir/;$path}sub resolve_relative_path {my ($class,$path)=@_;_rel2abs($path)}sub ensure_dir_structure_for {my ($class,$path)=@_;unless (-d $path){warn "Attempting to create directory ${path}\n"}require File::Basename;my@dirs;while(!-d $path){push@dirs,$path;$path=File::Basename::dirname($path)}mkdir $_ for reverse@dirs;return}sub guess_shelltype {my$shellbin =defined$ENV{SHELL}? ($ENV{SHELL}=~ /([\w.]+)$/)[-1]: ($^O eq 'MSWin32' && exists$ENV{'!EXITCODE'})? 'bash' : ($^O eq 'MSWin32' && $ENV{PROMPT}&& $ENV{COMSPEC})? ($ENV{COMSPEC}=~ /([\w.]+)$/)[-1]: ($^O eq 'MSWin32' &&!$ENV{PROMPT})? 'powershell.exe' : 'sh';for ($shellbin){return /csh$/ ? 'csh' : /fish/ ? 'fish' : /command(?:\.com)?$/i ? 'cmd' : /cmd(?:\.exe)?$/i ? 'cmd' : /4nt(?:\.exe)?$/i ? 'cmd' : /powershell(?:\.exe)?$/i ? 'powershell' : 'bourne'}}1;
+  WHOA THERE! It looks like you've got some fancy dashes in your commandline!
+  These are *not* the traditional -- dashes that software recognizes. You
+  probably got these by copy-pasting from the perldoc for this module as
+  rendered by a UTF8-capable formatter. This most typically happens on an OS X
+  terminal, but can happen elsewhere too. Please try again after replacing the
+  dashes with normal minus signs.
+  DEATH
+  FATAL: The local::lib --self-contained flag has never worked reliably and the
+  original author, Mark Stosberg, was unable or unwilling to maintain it. As
+  such, this flag has been removed from the local::lib codebase in order to
+  prevent misunderstandings and potentially broken builds. The local::lib authors
+  recommend that you look at the lib::core::only module shipped with this
+  distribution in order to create a more robust environment that is equivalent to
+  what --self-contained provided (although quite possibly not what you originally
+  thought it provided due to the poor quality of the documentation, for which we
+  apologise).
+  DEATH
+LOCAL_LIB
+
+$fatpacked{"parent.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'PARENT';
+  package parent;use strict;use vars qw($VERSION);$VERSION='0.228';sub import {my$class=shift;my$inheritor=caller(0);if (@_ and $_[0]eq '-norequire'){shift @_}else {for (my@filename=@_){if ($_ eq $inheritor){warn "Class '$inheritor' tried to inherit from itself\n"};s{::|'}{/}g;require "$_.pm"}}{no strict 'refs';push @{"$inheritor\::ISA"},@_}};"All your base are belong to us" 
+PARENT
+
+$fatpacked{"version.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'VERSION';
+  package version;use 5.006002;use strict;use warnings::register;if ($] >= 5.015){warnings::register_categories(qw/version/)}use vars qw(@ISA $VERSION $CLASS $STRICT $LAX *declare *qv);$VERSION=0.9912;$CLASS='version';{local$SIG{'__DIE__'};if (1){eval "use version::vpp $VERSION";die "$@" if ($@);push@ISA,"version::vpp";local $^W;*version::qv=\&version::vpp::qv;*version::declare=\&version::vpp::declare;*version::_VERSION=\&version::vpp::_VERSION;*version::vcmp=\&version::vpp::vcmp;*version::new=\&version::vpp::new;*version::numify=\&version::vpp::numify;*version::normal=\&version::vpp::normal;if ($] >= 5.009000){no strict 'refs';*version::stringify=\&version::vpp::stringify;*{'version::(""'}=\&version::vpp::stringify;*{'version::(<=>'}=\&version::vpp::vcmp;*version::parse=\&version::vpp::parse}}else {push@ISA,"version::vxs";local $^W;*version::declare=\&version::vxs::declare;*version::qv=\&version::vxs::qv;*version::_VERSION=\&version::vxs::_VERSION;*version::vcmp=\&version::vxs::VCMP;*version::new=\&version::vxs::new;*version::numify=\&version::vxs::numify;*version::normal=\&version::vxs::normal;if ($] >= 5.009000){no strict 'refs';*version::stringify=\&version::vxs::stringify;*{'version::(""'}=\&version::vxs::stringify;*{'version::(<=>'}=\&version::vxs::VCMP;*version::parse=\&version::vxs::parse}}}require version::regex;*version::is_lax=\&version::regex::is_lax;*version::is_strict=\&version::regex::is_strict;*LAX=\$version::regex::LAX;*STRICT=\$version::regex::STRICT;sub import {no strict 'refs';my ($class)=shift;unless ($class eq $CLASS){local $^W;*{$class.'::declare'}=\&{$CLASS.'::declare'};*{$class.'::qv'}=\&{$CLASS.'::qv'}}my%args;if (@_){map {$args{$_}=1}@_}else {%args=(qv=>1,'UNIVERSAL::VERSION'=>1,)}my$callpkg=caller();if (exists($args{declare})){*{$callpkg.'::declare'}=sub {return$class->declare(shift)}unless defined(&{$callpkg.'::declare'})}if (exists($args{qv})){*{$callpkg.'::qv'}=sub {return$class->qv(shift)}unless defined(&{$callpkg.'::qv'})}if (exists($args{'UNIVERSAL::VERSION'})){local $^W;*UNIVERSAL::VERSION =\&{$CLASS.'::_VERSION'}}if (exists($args{'VERSION'})){*{$callpkg.'::VERSION'}=\&{$CLASS.'::_VERSION'}}if (exists($args{'is_strict'})){*{$callpkg.'::is_strict'}=\&{$CLASS.'::is_strict'}unless defined(&{$callpkg.'::is_strict'})}if (exists($args{'is_lax'})){*{$callpkg.'::is_lax'}=\&{$CLASS.'::is_lax'}unless defined(&{$callpkg.'::is_lax'})}}1;
+VERSION
+
+$fatpacked{"version/regex.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'VERSION_REGEX';
+  package version::regex;use strict;use vars qw($VERSION $CLASS $STRICT $LAX);$VERSION=0.9912;my$FRACTION_PART=qr/\.[0-9]+/;my$STRICT_INTEGER_PART=qr/0|[1-9][0-9]*/;my$LAX_INTEGER_PART=qr/[0-9]+/;my$STRICT_DOTTED_DECIMAL_PART=qr/\.[0-9]{1,3}/;my$LAX_DOTTED_DECIMAL_PART=qr/\.[0-9]+/;my$LAX_ALPHA_PART=qr/_[0-9]+/;my$STRICT_DECIMAL_VERSION=qr/ $STRICT_INTEGER_PART $FRACTION_PART? /x;my$STRICT_DOTTED_DECIMAL_VERSION=qr/ v $STRICT_INTEGER_PART $STRICT_DOTTED_DECIMAL_PART{2,} /x;$STRICT=qr/ $STRICT_DECIMAL_VERSION | $STRICT_DOTTED_DECIMAL_VERSION /x;my$LAX_DECIMAL_VERSION=qr/ $LAX_INTEGER_PART (?: \. | $FRACTION_PART $LAX_ALPHA_PART? )?
+  	  |
+  	  $FRACTION_PART $LAX_ALPHA_PART?
+      /x;my$LAX_DOTTED_DECIMAL_VERSION=qr/
+      v $LAX_INTEGER_PART (?: $LAX_DOTTED_DECIMAL_PART+ $LAX_ALPHA_PART? )?
+      |
+      $LAX_INTEGER_PART? $LAX_DOTTED_DECIMAL_PART{2,} $LAX_ALPHA_PART?
+      /x;$LAX=qr/ undef | $LAX_DECIMAL_VERSION | $LAX_DOTTED_DECIMAL_VERSION /x;sub is_strict {defined $_[0]&& $_[0]=~ qr/ \A $STRICT \z /x}sub is_lax {defined $_[0]&& $_[0]=~ qr/ \A $LAX \z /x}1;
+VERSION_REGEX
+
+$fatpacked{"version/vpp.pm"} = '#line '.(1+__LINE__).' "'.__FILE__."\"\n".<<'VERSION_VPP';
+  package charstar;use overload ('""'=>\&thischar,'0+'=>\&thischar,'++'=>\&increment,'--'=>\&decrement,'+'=>\&plus,'-'=>\&minus,'*'=>\&multiply,'cmp'=>\&cmp,'<=>'=>\&spaceship,'bool'=>\&thischar,'='=>\&clone,);sub new {my ($self,$string)=@_;my$class=ref($self)|| $self;my$obj={string=>[split(//,$string)],current=>0,};return bless$obj,$class}sub thischar {my ($self)=@_;my$last=$#{$self->{string}};my$curr=$self->{current};if ($curr >= 0 && $curr <= $last){return$self->{string}->[$curr]}else {return ''}}sub increment {my ($self)=@_;$self->{current}++}sub decrement {my ($self)=@_;$self->{current}--}sub plus {my ($self,$offset)=@_;my$rself=$self->clone;$rself->{current}+= $offset;return$rself}sub minus {my ($self,$offset)=@_;my$rself=$self->clone;$rself->{current}-= $offset;return$rself}sub multiply {my ($left,$right,$swapped)=@_;my$char=$left->thischar();return$char * $right}sub spaceship {my ($left,$right,$swapped)=@_;unless (ref($right)){$right=$left->new($right)}return$left->{current}<=> $right->{current}}sub cmp {my ($left,$right,$swapped)=@_;unless (ref($right)){if (length($right)==1){return$left->thischar cmp $right}$right=$left->new($right)}return$left->currstr cmp $right->currstr}sub bool {my ($self)=@_;my$char=$self->thischar;return ($char ne '')}sub clone {my ($left,$right,$swapped)=@_;$right={string=>[@{$left->{string}}],current=>$left->{current},};return bless$right,ref($left)}sub currstr {my ($self,$s)=@_;my$curr=$self->{current};my$last=$#{$self->{string}};if (defined($s)&& $s->{current}< $last){$last=$s->{current}}my$string=join('',@{$self->{string}}[$curr..$last]);return$string}package version::vpp;use 5.006002;use strict;use warnings::register;use Config;use vars qw($VERSION $CLASS @ISA $LAX $STRICT $WARN_CATEGORY);$VERSION=0.9912;$CLASS='version::vpp';if ($] > 5.015){warnings::register_categories(qw/version/);$WARN_CATEGORY='version'}else {$WARN_CATEGORY='numeric'}require version::regex;*version::vpp::is_strict=\&version::regex::is_strict;*version::vpp::is_lax=\&version::regex::is_lax;*LAX=\$version::regex::LAX;*STRICT=\$version::regex::STRICT;use overload ('""'=>\&stringify,'0+'=>\&numify,'cmp'=>\&vcmp,'<=>'=>\&vcmp,'bool'=>\&vbool,'+'=>\&vnoop,'-'=>\&vnoop,'*'=>\&vnoop,'/'=>\&vnoop,'+='=>\&vnoop,'-='=>\&vnoop,'*='=>\&vnoop,'/='=>\&vnoop,'abs'=>\&vnoop,);sub import {no strict 'refs';my ($class)=shift;unless ($class eq $CLASS){local $^W;*{$class.'::declare'}=\&{$CLASS.'::declare'};*{$class.'::qv'}=\&{$CLASS.'::qv'}}my%args;if (@_){map {$args{$_}=1}@_}else {%args=(qv=>1,'UNIVERSAL::VERSION'=>1,)}my$callpkg=caller();if (exists($args{declare})){*{$callpkg.'::declare'}=sub {return$class->declare(shift)}unless defined(&{$callpkg.'::declare'})}if (exists($args{qv})){*{$callpkg.'::qv'}=sub {return$class->qv(shift)}unless defined(&{$callpkg.'::qv'})}if (exists($args{'UNIVERSAL::VERSION'})){no warnings qw/redefine/;*UNIVERSAL::VERSION =\&{$CLASS.'::_VERSION'}}if (exists($args{'VERSION'})){*{$callpkg.'::VERSION'}=\&{$CLASS.'::_VERSION'}}if (exists($args{'is_strict'})){*{$callpkg.'::is_strict'}=\&{$CLASS.'::is_strict'}unless defined(&{$callpkg.'::is_strict'})}if (exists($args{'is_lax'})){*{$callpkg.'::is_lax'}=\&{$CLASS.'::is_lax'}unless defined(&{$callpkg.'::is_lax'})}}my$VERSION_MAX=0x7FFFFFFF;use constant TRUE=>1;use constant FALSE=>0;sub isDIGIT {my ($char)=shift->thischar();return ($char =~ /\d/)}sub isALPHA {my ($char)=shift->thischar();return ($char =~ /[a-zA-Z]/)}sub isSPACE {my ($char)=shift->thischar();return ($char =~ /\s/)}sub BADVERSION {my ($s,$errstr,$error)=@_;if ($errstr){$$errstr=$error}return$s}sub prescan_version {my ($s,$strict,$errstr,$sqv,$ssaw_decimal,$swidth,$salpha)=@_;my$qv=defined$sqv ? $$sqv : FALSE;my$saw_decimal=defined$ssaw_decimal ? $$ssaw_decimal : 0;my$width=defined$swidth ? $$swidth : 3;my$alpha=defined$salpha ? $$salpha : FALSE;my$d=$s;if ($qv && isDIGIT($d)){goto dotted_decimal_version}if ($d eq 'v'){$d++;if (isDIGIT($d)){$qv=TRUE}else {return BADVERSION($s,$errstr,"Invalid version format (dotted-decimal versions require at least three parts)")}dotted_decimal_version: if ($strict && $d eq '0' && isDIGIT($d+1)){return BADVERSION($s,$errstr,"Invalid version format (no leading zeros)")}while (isDIGIT($d)){$d++}if ($d eq '.'){$saw_decimal++;$d++}else {if ($strict){return BADVERSION($s,$errstr,"Invalid version format (dotted-decimal versions require at least three parts)")}else {goto version_prescan_finish}}{my$i=0;my$j=0;while (isDIGIT($d)){$i++;while (isDIGIT($d)){$d++;$j++;if ($strict && $j > 3){return BADVERSION($s,$errstr,"Invalid version format (maximum 3 digits between decimals)")}}if ($d eq '_'){if ($strict){return BADVERSION($s,$errstr,"Invalid version format (no underscores)")}if ($alpha){return BADVERSION($s,$errstr,"Invalid version format (multiple underscores)")}$d++;$alpha=TRUE}elsif ($d eq '.'){if ($alpha){return BADVERSION($s,$errstr,"Invalid version format (underscores before decimal)")}$saw_decimal++;$d++}elsif (!isDIGIT($d)){last}$j=0}if ($strict && $i < 2){return BADVERSION($s,$errstr,"Invalid version format (dotted-decimal versions require at least three parts)")}}}else {my$j=0;if ($strict){if ($d eq '.'){return BADVERSION($s,$errstr,"Invalid version format (0 before decimal required)")}if ($d eq '0' && isDIGIT($d+1)){return BADVERSION($s,$errstr,"Invalid version format (no leading zeros)")}}if ($d eq '-'){return BADVERSION($s,$errstr,"Invalid version format (negative version number)")}while (isDIGIT($d)){$d++}if ($d eq '.'){$saw_decimal++;$d++}elsif (!$d || $d eq ';' || isSPACE($d)|| $d eq '}'){if ($d==$s){return BADVERSION($s,$errstr,"Invalid version format (version required)")}goto version_prescan_finish}elsif ($d==$s){return BADVERSION($s,$errstr,"Invalid version format (non-numeric data)")}elsif ($d eq '_'){if ($strict){return BADVERSION($s,$errstr,"Invalid version format (no underscores)")}elsif (isDIGIT($d+1)){return BADVERSION($s,$errstr,"Invalid version format (alpha without decimal)")}else {return BADVERSION($s,$errstr,"Invalid version format (misplaced underscore)")}}elsif ($d){return BADVERSION($s,$errstr,"Invalid version format (non-numeric data)")}if ($d &&!isDIGIT($d)&& ($strict ||!($d eq ';' || isSPACE($d)|| $d eq '}'))){return BADVERSION($s,$errstr,"Invalid version format (fractional part required)")}while (isDIGIT($d)){$d++;$j++;if ($d eq '.' && isDIGIT($d-1)){if ($alpha){return BADVERSION($s,$errstr,"Invalid version format (underscores before decimal)")}if ($strict){return BADVERSION($s,$errstr,"Invalid version format (dotted-decimal versions must begin with 'v')")}$d=$s;$qv=TRUE;goto dotted_decimal_version}if ($d eq '_'){if ($strict){return BADVERSION($s,$errstr,"Invalid version format (no underscores)")}if ($alpha){return BADVERSION($s,$errstr,"Invalid version format (multiple underscores)")}if (!isDIGIT($d+1)){return BADVERSION($s,$errstr,"Invalid version format (misplaced underscore)")}$width=$j;$d++;$alpha=TRUE}}}version_prescan_finish: while (isSPACE($d)){$d++}if ($d &&!isDIGIT($d)&& (!($d eq ';' || $d eq '}'))){return BADVERSION($s,$errstr,"Invalid version format (non-numeric data)")}if ($saw_decimal > 1 && ($d-1)eq '.'){return BADVERSION($s,$errstr,"Invalid version format (trailing decimal)")}if (defined$sqv){$$sqv=$qv}if (defined$swidth){$$swidth=$width}if (defined$ssaw_decimal){$$ssaw_decimal=$saw_decimal}if (defined$salpha){$$salpha=$alpha}return$d}sub scan_version {my ($s,$rv,$qv)=@_;my$start;my$pos;my$last;my$errstr;my$saw_decimal=0;my$width=3;my$alpha=FALSE;my$vinf=FALSE;my@av;$s=new charstar$s;while (isSPACE($s)){$s++}$last=prescan_version($s,FALSE,\$errstr,\$qv,\$saw_decimal,\$width,\$alpha);if ($errstr){if ($s ne 'undef'){require Carp;Carp::croak($errstr)}}$start=$s;if ($s eq 'v'){$s++}$pos=$s;if ($qv){$$rv->{qv}=$qv}if ($alpha){$$rv->{alpha}=$alpha}if (!$qv && $width < 3){$$rv->{width}=$width}while (isDIGIT($pos)){$pos++}if (!isALPHA($pos)){my$rev;for (;;){$rev=0;{my$end=$pos;my$mult=1;my$orev;if (!$qv && $s > $start && $saw_decimal==1){$mult *= 100;while ($s < $end){$orev=$rev;$rev += $s * $mult;$mult /= 10;if ((abs($orev)> abs($rev))|| (abs($rev)> $VERSION_MAX)){warn("Integer overflow in version %d",$VERSION_MAX);$s=$end - 1;$rev=$VERSION_MAX;$vinf=1}$s++;if ($s eq '_'){$s++}}}else {while (--$end >= $s){$orev=$rev;$rev += $end * $mult;$mult *= 10;if ((abs($orev)> abs($rev))|| (abs($rev)> $VERSION_MAX)){warn("Integer overflow in version");$end=$s - 1;$rev=$VERSION_MAX;$vinf=1}}}}push@av,$rev;if ($vinf){$s=$last;last}elsif ($pos eq '.'){$pos++;if ($qv){while ($pos eq '0'){$pos++}}$s=$pos}elsif ($pos eq '_' && isDIGIT($pos+1)){$s=++$pos}elsif ($pos eq ',' && isDIGIT($pos+1)){$s=++$pos}elsif (isDIGIT($pos)){$s=$pos}else {$s=$pos;last}if ($qv){while (isDIGIT($pos)){$pos++}}else {my$digits=0;while ((isDIGIT($pos)|| $pos eq '_')&& $digits < 3){if ($pos ne '_'){$digits++}$pos++}}}}if ($qv){my$len=$#av;$len=2 - $len;while ($len-- > 0){push@av,0}}if ($vinf){$$rv->{original}="v.Inf";$$rv->{vinf}=1}elsif ($s > $start){$$rv->{original}=$start->currstr($s);if ($qv && $saw_decimal==1 && $start ne 'v'){$$rv->{original}='v' .$$rv->{original}}}else {$$rv->{original}='0';push(@av,0)}$$rv->{version}=\@av;if ($s eq 'undef'){$s += 5}return$s}sub new {my$class=shift;unless (defined$class or $#_ > 1){require Carp;Carp::croak('Usage: version::new(class, version)')}my$self=bless ({},ref ($class)|| $class);my$qv=FALSE;if ($#_==1){$qv=TRUE}my$value=pop;if (ref($value)&& eval('$value->isa("version")')){$self->{version}=[@{$value->{version}}];$self->{qv}=1 if$value->{qv};$self->{alpha}=1 if$value->{alpha};$self->{original}=''.$value->{original};return$self}if (not defined$value or $value =~ /^undef$/){push @{$self->{version}},0;$self->{original}="0";return ($self)}if (ref($value)=~ m/ARRAY|HASH/){require Carp;Carp::croak("Invalid version format (non-numeric data)")}$value=_un_vstring($value);if ($Config{d_setlocale}){use POSIX qw/locale_h/;use if$Config{d_setlocale},'locale';my$currlocale=setlocale(LC_ALL);if (localeconv()->{decimal_point}eq ','){$value =~ tr/,/./}}if ($value =~ /\d+.?\d*e[-+]?\d+/){$value=sprintf("%.9f",$value);$value =~ s/(0+)$//}my$s=scan_version($value,\$self,$qv);if ($s){warn("Version string '%s' contains invalid data; " ."ignoring: '%s'",$value,$s)}return ($self)}*parse=\&new;sub numify {my ($self)=@_;unless (_verify($self)){require Carp;Carp::croak("Invalid version object")}my$width=$self->{width}|| 3;my$alpha=$self->{alpha}|| "";my$len=$#{$self->{version}};my$digit=$self->{version}[0];my$string=sprintf("%d.",$digit);if ($alpha and warnings::enabled()){warnings::warn($WARN_CATEGORY,'alpha->numify() is lossy')}for (my$i=1 ;$i < $len ;$i++ ){$digit=$self->{version}[$i];if ($width < 3){my$denom=10**(3-$width);my$quot=int($digit/$denom);my$rem=$digit - ($quot * $denom);$string .= sprintf("%0".$width."d_%d",$quot,$rem)}else {$string .= sprintf("%03d",$digit)}}if ($len > 0){$digit=$self->{version}[$len];if ($alpha && $width==3){$string .= "_"}$string .= sprintf("%0".$width."d",$digit)}else {$string .= sprintf("000")}return$string}sub normal {my ($self)=@_;unless (_verify($self)){require Carp;Carp::croak("Invalid version object")}my$alpha=$self->{alpha}|| "";my$qv=$self->{qv}|| "";my$len=$#{$self->{version}};my$digit=$self->{version}[0];my$string=sprintf("v%d",$digit);for (my$i=1 ;$i < $len ;$i++ ){$digit=$self->{version}[$i];$string .= sprintf(".%d",$digit)}if ($len > 0){$digit=$self->{version}[$len];if ($alpha){$string .= sprintf("_%0d",$digit)}else {$string .= sprintf(".%0d",$digit)}}if ($len <= 2){for ($len=2 - $len;$len!=0;$len-- ){$string .= sprintf(".%0d",0)}}return$string}sub stringify {my ($self)=@_;unless (_verify($self)){require Carp;Carp::croak("Invalid version object")}return exists$self->{original}? $self->{original}: exists$self->{qv}? $self->normal : $self->numify}sub vcmp {require UNIVERSAL;my ($left,$right,$swap)=@_;my$class=ref($left);unless (UNIVERSAL::isa($right,$class)){$right=$class->new($right)}if ($swap){($left,$right)=($right,$left)}unless (_verify($left)){require Carp;Carp::croak("Invalid version object")}unless (_verify($right)){require Carp;Carp::croak("Invalid version format")}my$l=$#{$left->{version}};my$r=$#{$right->{version}};my$m=$l < $r ? $l : $r;my$lalpha=$left->is_alpha;my$ralpha=$right->is_alpha;my$retval=0;my$i=0;while ($i <= $m && $retval==0){$retval=$left->{version}[$i]<=> $right->{version}[$i];$i++}if ($retval==0 && $l==$r && $left->{version}[$m]==$right->{version}[$m]&& ($lalpha || $ralpha)){if ($lalpha &&!$ralpha){$retval=-1}elsif ($ralpha &&!$lalpha){$retval=+1}}if ($retval==0 && $l!=$r){if ($l < $r){while ($i <= $r && $retval==0){if ($right->{version}[$i]!=0){$retval=-1}$i++}}else {while ($i <= $l && $retval==0){if ($left->{version}[$i]!=0){$retval=+1}$i++}}}return$retval}sub vbool {my ($self)=@_;return vcmp($self,$self->new("0"),1)}sub vnoop {require Carp;Carp::croak("operation not supported with version object")}sub is_alpha {my ($self)=@_;return (exists$self->{alpha})}sub qv {my$value=shift;my$class=$CLASS;if (@_){$class=ref($value)|| $value;$value=shift}$value=_un_vstring($value);$value='v'.$value unless$value =~ /(^v|\d+\.\d+\.\d)/;my$obj=$CLASS->new($value);return bless$obj,$class}*declare=\&qv;sub is_qv {my ($self)=@_;return (exists$self->{qv})}sub _verify {my ($self)=@_;if (ref($self)&& eval {exists$self->{version}}&& ref($self->{version})eq 'ARRAY'){return 1}else {return 0}}sub _is_non_alphanumeric {my$s=shift;$s=new charstar$s;while ($s){return 0 if isSPACE($s);return 1 unless (isALPHA($s)|| isDIGIT($s)|| $s =~ /[.-]/);$s++}return 0}sub _un_vstring {my$value=shift;if (length($value)>= 1 && $value !~ /[,._]/ && _is_non_alphanumeric($value)){my$tvalue;if ($] >= 5.008_001){$tvalue=_find_magic_vstring($value);$value=$tvalue if length$tvalue}elsif ($] >= 5.006_000){$tvalue=sprintf("v%vd",$value);if ($tvalue =~ /^v\d+(\.\d+)*$/){$value=$tvalue}}}return$value}sub _find_magic_vstring {my$value=shift;my$tvalue='';require B;my$sv=B::svref_2object(\$value);my$magic=ref($sv)eq 'B::PVMG' ? $sv->MAGIC : undef;while ($magic){if ($magic->TYPE eq 'V'){$tvalue=$magic->PTR;$tvalue =~ s/^v?(.+)$/v$1/;last}else {$magic=$magic->MOREMAGIC}}return$tvalue}sub _VERSION {my ($obj,$req)=@_;my$class=ref($obj)|| $obj;no strict 'refs';if (exists$INC{"$class.pm"}and not %{"$class\::"}and $] >= 5.008){require Carp;Carp::croak("$class defines neither package nor VERSION" ."--version check failed")}my$version=eval "\$$class\::VERSION";if (defined$version){local $^W if $] <= 5.008;$version=version::vpp->new($version)}if (defined$req){unless (defined$version){require Carp;my$msg=$] < 5.006 ? "$class version $req required--this is only version " : "$class does not define \$$class\::VERSION" ."--version check failed";if ($ENV{VERSION_DEBUG}){Carp::confess($msg)}else {Carp::croak($msg)}}$req=version::vpp->new($req);if ($req > $version){require Carp;if ($req->is_qv){Carp::croak(sprintf ("%s version %s required--"."this is only version %s",$class,$req->normal,$version->normal))}else {Carp::croak(sprintf ("%s version %s required--"."this is only version %s",$class,$req->stringify,$version->stringify))}}}return defined$version ? $version->stringify : undef}1;
+VERSION_VPP
+
+s/^  //mg for values %fatpacked;
+
+my $class = 'FatPacked::'.(0+\%fatpacked);
+no strict 'refs';
+*{"${class}::files"} = sub { keys %{$_[0]} };
+
+if ($] < 5.008) {
+  *{"${class}::INC"} = sub {
+    if (my $fat = $_[0]{$_[1]}) {
+      my $pos = 0;
+      my $last = length $fat;
+      return (sub {
+        return 0 if $pos == $last;
+        my $next = (1 + index $fat, "\n", $pos) || $last;
+        $_ .= substr $fat, $pos, $next - $pos;
+        $pos = $next;
+        return 1;
+      });
+    }
+  };
+}
+
+else {
+  *{"${class}::INC"} = sub {
+    if (my $fat = $_[0]{$_[1]}) {
+      open my $fh, '<', \$fat
+        or die "FatPacker error loading $_[1] (could be a perl installation issue?)";
+      return $fh;
+    }
+    return;
+  };
+}
+
+unshift @INC, bless \%fatpacked, $class;
+  } # END OF FATPACK CODE
+
+
+
+use strict;
+use App::cpanminus::script;
+
+
+unless (caller) {
+    my $app = App::cpanminus::script->new;
+    $app->parse_options(@ARGV);
+    exit $app->doit;
+}
+
+__END__
+
+=head1 NAME
+
+cpanm - get, unpack build and install modules from CPAN
+
+=head1 SYNOPSIS
+
+  cpanm Test::More                                 # install Test::More
+  cpanm MIYAGAWA/Plack-0.99_05.tar.gz              # full distribution path
+  cpanm http://example.org/LDS/CGI.pm-3.20.tar.gz  # install from URL
+  cpanm ~/dists/MyCompany-Enterprise-1.00.tar.gz   # install from a local file
+  cpanm --interactive Task::Kensho                 # Configure interactively
+  cpanm .                                          # install from local directory
+  cpanm --installdeps .                            # install all the deps for the current directory
+  cpanm -L extlib Plack                            # install Plack and all non-core deps into extlib
+  cpanm --mirror http://cpan.cpantesters.org/ DBI  # use the fast-syncing mirror
+  cpanm --from https://cpan.metacpan.org/ Plack    # use only the HTTPS mirror
+
+=head1 COMMANDS
+
+=over 4
+
+=item (arguments)
+
+Command line arguments can be either a module name, distribution file,
+local file path, HTTP URL or git repository URL. Following commands
+will all work as you expect.
+
+    cpanm Plack
+    cpanm Plack/Request.pm
+    cpanm MIYAGAWA/Plack-1.0000.tar.gz
+    cpanm /path/to/Plack-1.0000.tar.gz
+    cpanm http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/Plack-0.9990.tar.gz
+    cpanm git://github.com/plack/Plack.git
+
+Additionally, you can use the notation using C<~> and C<@> to specify
+version for a given module. C<~> specifies the version requirement in
+the L<CPAN::Meta::Spec> format, while C<@> pins the exact version, and
+is a shortcut for C<~"== VERSION">.
+
+    cpanm Plack~1.0000                 # 1.0000 or later
+    cpanm Plack~">= 1.0000, < 2.0000"  # latest of 1.xxxx
+    cpanm Plack@0.9990                 # specific version. same as Plack~"== 0.9990"
+
+The version query including specific version or range will be sent to
+L<MetaCPAN> to search for previous releases. The query will search for
+BackPAN archives by default, unless you specify C<--dev> option, in
+which case, archived versions will be filtered out.
+
+For a git repository, you can specify a branch, tag, or commit SHA to
+build. The default is C<master>
+
+    cpanm git://github.com/plack/Plack.git@1.0000        # tag
+    cpanm git://github.com/plack/Plack.git@devel         # branch
+
+=item -i, --install
+
+Installs the modules. This is a default behavior and this is just a
+compatibility option to make it work like L<cpan> or L<cpanp>.
+
+=item --self-upgrade
+
+Upgrades itself. It's just an alias for:
+
+  cpanm App::cpanminus
+
+=item --info
+
+Displays the distribution information in
+C<AUTHOR/Dist-Name-ver.tar.gz> format in the standard out.
+
+=item --installdeps
+
+Installs the dependencies of the target distribution but won't build
+itself. Handy if you want to try the application from a version
+controlled repository such as git.
+
+  cpanm --installdeps .
+
+=item --look
+
+Download and unpack the distribution and then open the directory with
+your shell. Handy to poke around the source code or do manual
+testing.
+
+=item -h, --help
+
+Displays the help message.
+
+=item -V, --version
+
+Displays the version number.
+
+=back
+
+=head1 OPTIONS
+
+You can specify the default options in C<PERL_CPANM_OPT> environment variable.
+
+=over 4
+
+=item -f, --force
+
+Force install modules even when testing failed.
+
+=item -n, --notest
+
+Skip the testing of modules. Use this only when you just want to save
+time for installing hundreds of distributions to the same perl and
+architecture you've already tested to make sure it builds fine.
+
+Defaults to false, and you can say C<--no-notest> to override when it
+is set in the default options in C<PERL_CPANM_OPT>.
+
+=item --test-only
+
+Run the tests only, and do not install the specified module or
+distributions. Handy if you want to verify the new (or even old)
+releases pass its unit tests without installing the module.
+
+Note that if you specify this option with a module or distribution
+that has dependencies, these dependencies will be installed if you
+don't currently have them.
+
+=item -S, --sudo
+
+Switch to the root user with C<sudo> when installing modules. Use this
+if you want to install modules to the system perl include path.
+
+Defaults to false, and you can say C<--no-sudo> to override when it is
+set in the default options in C<PERL_CPANM_OPT>.
+
+=item -v, --verbose
+
+Makes the output verbose. It also enables the interactive
+configuration. (See --interactive)
+
+=item -q, --quiet
+
+Makes the output even more quiet than the default. It only shows the
+successful/failed dependencies to the output.
+
+=item -l, --local-lib
+
+Sets the L<local::lib> compatible path to install modules to. You
+don't need to set this if you already configure the shell environment
+variables using L<local::lib>, but this can be used to override that
+as well.
+
+=item -L, --local-lib-contained
+
+Same with C<--local-lib> but with L<--self-contained> set.  All
+non-core dependencies will be installed even if they're already
+installed.
+
+For instance,
+
+  cpanm -L extlib Plack
+
+would install Plack and all of its non-core dependencies into the
+directory C<extlib>, which can be loaded from your application with:
+
+  use local::lib '/path/to/extlib';
+
+Note that this option does B<NOT> reliably work with perl installations
+supplied by operating system vendors that strips standard modules from perl,
+such as RHEL, Fedora and CentOS, B<UNLESS> you also install packages supplying
+all the modules that have been stripped.  For these systems you will probably
+want to install the C<perl-core> meta-package which does just that.
+
+=item --self-contained
+
+When examining the dependencies, assume no non-core modules are
+installed on the system. Handy if you want to bundle application
+dependencies in one directory so you can distribute to other machines.
+
+=item --exclude-vendor
+
+Don't include modules installed under the 'vendor' paths when searching for
+core modules when the C<--self-contained> flag is in effect.  This restores
+the behaviour from before version 1.7023
+
+=item --mirror
+
+Specifies the base URL for the CPAN mirror to use, such as
+C<http://cpan.cpantesters.org/> (you can omit the trailing slash). You
+can specify multiple mirror URLs by repeating the command line option.
+
+You can use a local directory that has a CPAN mirror structure
+(created by tools such as L<OrePAN> or L<Pinto>) by using a special
+URL scheme C<file://>. If the given URL begins with `/` (without any
+scheme), it is considered as a file scheme as well.
+
+  cpanm --mirror file:///path/to/mirror
+  cpanm --mirror ~/minicpan      # Because shell expands ~ to /home/user
+
+Defaults to C<http://www.cpan.org/>.
+
+=item --mirror-only
+
+Download the mirror's 02packages.details.txt.gz index file instead of
+querying the CPAN Meta DB. This will also effectively opt out sending
+your local perl versions to backend database servers such as CPAN Meta
+DB and MetaCPAN.
+
+Select this option if you are using a local mirror of CPAN, such as
+minicpan when you're offline, or your own CPAN index (a.k.a darkpan).
+
+=item --from, -M
+
+  cpanm -M https://cpan.metacpan.org/
+  cpanm --from https://cpan.metacpan.org/
+
+Use the given mirror URL and its index as the I<only> source to search
+and download modules from.
+
+It works similar to C<--mirror> and C<--mirror-only> combined, with a
+small difference: unlike C<--mirror> which I<appends> the URL to the
+list of mirrors, C<--from> (or C<-M> for short) uses the specified URL
+as its I<only> source to download index and modules from. This makes
+the option always override the default mirror, which might have been
+set via global options such as the one set by C<PERL_CPANM_OPT>
+environment variable.
+
+B<Tip:> It might be useful if you name these options with your shell
+aliases, like:
+
+  alias minicpanm='cpanm --from ~/minicpan'
+  alias darkpan='cpanm --from http://mycompany.example.com/DPAN'
+
+=item --mirror-index
+
+B<EXPERIMENTAL>: Specifies the file path to C<02packages.details.txt>
+for module search index.
+
+=item --cpanmetadb
+
+B<EXPERIMENTAL>: Specifies an alternate URI for CPAN MetaDB index lookups.
+
+=item --metacpan
+
+Prefers MetaCPAN API over CPAN MetaDB.
+
+=item --cpanfile
+
+B<EXPERIMENTAL>: Specified an alternate path for cpanfile to search for,
+when C<--installdeps> command is in use. Defaults to C<cpanfile>.
+
+=item --prompt
+
+Prompts when a test fails so that you can skip, force install, retry
+or look in the shell to see what's going wrong. It also prompts when
+one of the dependency failed if you want to proceed the installation.
+
+Defaults to false, and you can say C<--no-prompt> to override if it's
+set in the default options in C<PERL_CPANM_OPT>.
+
+=item --dev
+
+B<EXPERIMENTAL>: search for a newer developer release as well. Defaults to false.
+
+=item --reinstall
+
+cpanm, when given a module name in the command line (i.e. C<cpanm
+Plack>), checks the locally installed version first and skips if it is
+already installed. This option makes it skip the check, so:
+
+  cpanm --reinstall Plack
+
+would reinstall L<Plack> even if your locally installed version is
+latest, or even newer (which would happen if you install a developer
+release from version control repositories).
+
+Defaults to false.
+
+=item --interactive
+
+Makes the configuration (such as C<Makefile.PL> and C<Build.PL>)
+interactive, so you can answer questions in the distribution that
+requires custom configuration or Task:: distributions.
+
+Defaults to false, and you can say C<--no-interactive> to override
+when it's set in the default options in C<PERL_CPANM_OPT>.
+
+=item --pp, --pureperl
+
+Prefer Pure perl build of modules by setting C<PUREPERL_ONLY=1> for
+MakeMaker and C<--pureperl-only> for Build.PL based
+distributions. Note that not all of the CPAN modules support this
+convention yet.
+
+=item --with-recommends, --with-suggests
+
+B<EXPERIMENTAL>: Installs dependencies declared as C<recommends> and
+C<suggests> respectively, per META spec. When these dependencies fail
+to install, cpanm continues the installation, since they're just
+recommendation/suggestion.
+
+Enabling this could potentially make a circular dependency for a few
+modules on CPAN, when C<recommends> adds a module that C<recommends>
+back the module in return.
+
+There's also C<--without-recommend> and C<--without-suggests> to
+override the default decision made earlier in C<PERL_CPANM_OPT>.
+
+Defaults to false for both.
+
+=item --with-develop
+
+B<EXPERIMENTAL>: Installs develop phase dependencies in META files or
+C<cpanfile> when used with C<--installdeps>. Defaults to false.
+
+=item --with-configure
+
+B<EXPERIMENTAL>: Installs configure phase dependencies in C<cpanfile>
+when used with C<--installdeps>. Defaults to false.
+
+=item --with-feature, --without-feature, --with-all-features
+
+B<EXPERIMENTAL>: Specifies the feature to enable, if a module supports
+optional features per META spec 2.0.
+
+    cpanm --with-feature=opt_csv Spreadsheet::Read
+
+the features can also be interactively chosen when C<--interactive>
+option is enabled.
+
+C<--with-all-features> enables all the optional features, and
+C<--without-feature> can select a feature to disable.
+
+=item --configure-timeout, --build-timeout, --test-timeout
+
+Specify the timeout length (in seconds) to wait for the configure,
+build and test process. Current default values are: 60 for configure,
+3600 for build and 1800 for test.
+
+=item --configure-args, --build-args, --test-args, --install-args
+
+B<EXPERIMENTAL>: Pass arguments for configure/build/test/install
+commands respectively, for a given module to install.
+
+    cpanm DBD::mysql --configure-args="--cflags=... --libs=..."
+
+The argument is only enabled for the module passed as a command line
+argument, not dependencies.
+
+=item --scandeps
+
+B<DEPRECATED>: Scans the depencencies of given modules and output the
+tree in a text format. (See C<--format> below for more options)
+
+Because this command doesn't actually install any distributions, it
+will be useful that by typing:
+
+  cpanm --scandeps Catalyst::Runtime
+
+you can make sure what modules will be installed.
+
+This command takes into account which modules you already have
+installed in your system. If you want to see what modules will be
+installed against a vanilla perl installation, you might want to
+combine it with C<-L> option.
+
+=item --format
+
+B<DEPRECATED>: Determines what format to display the scanned
+dependency tree. Available options are C<tree>, C<json>, C<yaml> and
+C<dists>.
+
+=over 8
+
+=item tree
+
+Displays the tree in a plain text format. This is the default value.
+
+=item json, yaml
+
+Outputs the tree in a JSON or YAML format. L<JSON> and L<YAML> modules
+need to be installed respectively. The output tree is represented as a
+recursive tuple of:
+
+  [ distribution, dependencies ]
+
+and the container is an array containing the root elements. Note that
+there may be multiple root nodes, since you can give multiple modules
+to the C<--scandeps> command.
+
+=item dists
+
+C<dists> is a special output format, where it prints the distribution
+filename in the I<depth first order> after the dependency resolution,
+like:
+
+  GAAS/MIME-Base64-3.13.tar.gz
+  GAAS/URI-1.58.tar.gz
+  PETDANCE/HTML-Tagset-3.20.tar.gz
+  GAAS/HTML-Parser-3.68.tar.gz
+  GAAS/libwww-perl-5.837.tar.gz
+
+which means you can install these distributions in this order without
+extra dependencies. When combined with C<-L> option, it will be useful
+to replay installations on other machines.
+
+=back
+
+=item --save-dists
+
+Specifies the optional directory path to copy downloaded tarballs in
+the CPAN mirror compatible directory structure
+i.e. I<authors/id/A/AU/AUTHORS/Foo-Bar-version.tar.gz>
+
+If the distro tarball did not come from CPAN, for example from a local
+file or from GitHub, then it will be saved under
+I<vendor/Foo-Bar-version.tar.gz>.
+
+=item --uninst-shadows
+
+Uninstalls the shadow files of the distribution that you're
+installing. This eliminates the confusion if you're trying to install
+core (dual-life) modules from CPAN against perl 5.10 or older, or
+modules that used to be XS-based but switched to pure perl at some
+version.
+
+If you run cpanm as root and use C<INSTALL_BASE> or equivalent to
+specify custom installation path, you SHOULD disable this option so
+you won't accidentally uninstall dual-life modules from the core
+include path.
+
+Defaults to true if your perl version is smaller than 5.12, and you
+can disable that with C<--no-uninst-shadows>.
+
+B<NOTE>: Since version 1.3000 this flag is turned off by default for
+perl newer than 5.12, since with 5.12 @INC contains site_perl directory
+I<before> the perl core library path, and uninstalling shadows is not
+necessary anymore and does more harm by deleting files from the core
+library path.
+
+=item --uninstall, -U
+
+Uninstalls a module from the library path. It finds a packlist for
+given modules, and removes all the files included in the same
+distribution.
+
+If you enable local::lib, it only removes files from the local::lib
+directory.
+
+If you try to uninstall a module in C<perl> directory (i.e. core
+module), an error will be thrown.
+
+A dialog will be prompted to confirm the files to be deleted. If you pass
+C<-f> option as well, the dialog will be skipped and uninstallation
+will be forced.
+
+=item --cascade-search
+
+B<EXPERIMENTAL>: Specifies whether to cascade search when you specify
+multiple mirrors and a mirror doesn't have a module or has a lower
+version of the module than requested. Defaults to false.
+
+=item --skip-installed
+
+Specifies whether a module given in the command line is skipped if its latest
+version is already installed. Defaults to true.
+
+B<NOTE>: The C<PERL5LIB> environment variable have to be correctly set
+for this to work with modules installed using L<local::lib>, unless
+you always use the C<-l> option.
+
+=item --skip-satisfied
+
+B<EXPERIMENTAL>: Specifies whether a module (and version) given in the
+command line is skipped if it's already installed.
+
+If you run:
+
+  cpanm --skip-satisfied CGI DBI~1.2
+
+cpanm won't install them if you already have CGI (for whatever
+versions) or have DBI with version higher than 1.2. It is similar to
+C<--skip-installed> but while C<--skip-installed> checks if the
+I<latest> version of CPAN is installed, C<--skip-satisfied> checks if
+a requested version (or not, which means any version) is installed.
+
+Defaults to false.
+
+=item --verify
+
+Verify the integrity of distribution files retrieved from CPAN using CHECKSUMS
+file, and SIGNATURES file (if found in the distribution). Defaults to false.
+
+Using this option does not verify the integrity of the CHECKSUMS file, and it's
+unsafe to rely on this option if you're using a CPAN mirror that you do not trust.
+
+=item --report-perl-version
+
+Whether it reports the locally installed perl version to the various
+web server as part of User-Agent. Defaults to true unless CI related
+environment variables such as C<TRAVIS>, C<CI> or C<AUTOMATED_TESTING>
+is enabled. You can disable it by using C<--no-report-perl-version>.
+
+=item --auto-cleanup
+
+Specifies the number of days in which cpanm's work directories
+expire. Defaults to 7, which means old work directories will be
+cleaned up in one week.
+
+You can set the value to C<0> to make cpan never cleanup those
+directories.
+
+=item --man-pages
+
+Generates man pages for executables (man1) and libraries (man3).
+
+Defaults to true (man pages generated) unless C<-L|--local-lib-contained>
+option is supplied in which case it's set to false. You can disable
+it with C<--no-man-pages>.
+
+=item --lwp
+
+Uses L<LWP> module to download stuff over HTTP. Defaults to true, and
+you can say C<--no-lwp> to disable using LWP, when you want to upgrade
+LWP from CPAN on some broken perl systems.
+
+=item --wget
+
+Uses GNU Wget (if available) to download stuff. Defaults to true, and
+you can say C<--no-wget> to disable using Wget (versions of Wget older
+than 1.9 don't support the C<--retry-connrefused> option used by cpanm).
+
+=item --curl
+
+Uses cURL (if available) to download stuff. Defaults to true, and
+you can say C<--no-curl> to disable using cURL.
+
+Normally with C<--lwp>, C<--wget> and C<--curl> options set to true
+(which is the default) cpanm tries L<LWP>, Wget, cURL and L<HTTP::Tiny>
+(in that order) and uses the first one available.
+
+=back
+
+=head1 ENVIRONMENT VARIABLES
+
+=over 4
+
+=item PERL_CPANM_HOME
+
+The directory cpanm should use to store downloads and build and test
+modules. Defaults to the C<.cpanm> directory in your user's home
+directory.
+
+=item PERL_CPANM_OPT
+
+If set, adds a set of default options to every cpanm command. These
+options come first, and so are overridden by command-line options.
+
+=back
+
+=head1 SEE ALSO
+
+L<App::cpanminus>
+
+=head1 COPYRIGHT
+
+Copyright 2010- Tatsuhiko Miyagawa.
+
+=head1 AUTHOR
+
+Tatsuhiko Miyagawa
+
+=cut
diff --git a/misc/gnuplot.Makefile b/misc/gnuplot.Makefile
new file mode 100644
index 0000000..70f7d51
--- /dev/null
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+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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+
+
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+
+
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+QT_LIBS = 
+RCC = 
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = 
+TERMLIBS =  -lreadline  -lncurses  -lz
+TERMXLIBS = 
+TEXDIR = no
+TEXHASH = texhash
+TROFF = troff
+TUTORIAL = notutorial
+UIC = 
+VERSION = 4.6.6
+VERSION_MAJOR = 4.6
+WX_CONFIG = 
+WX_LIBS = 
+X11_APPDEFAULTS_DIR = /etc/X11/app-defaults/
+XMKMF = 
+X_CFLAGS = 
+X_EXTRA_LIBS = 
+X_LIBS = 
+X_PRE_LIBS =  -lSM -lICE
+abs_builddir = /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6/src
+abs_srcdir = /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6/src
+abs_top_builddir = /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6
+abs_top_srcdir = /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6
+ac_ct_CC = gcc
+ac_ct_CXX = 
+ac_ct_OBJC = gcc
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = $${TAR-tar} chof - "$$tardir"
+am__untar = $${TAR-tar} xf -
+bindir = ${exec_prefix}/bin
+build_alias = 
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6
+host_alias = 
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+lispdir = ${datarootdir}/emacs/site-lisp
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = $(MKDIR_P)
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /public/jxyue/Projects/LRSDAY_dev/build/gnuplot-4.6.6
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+subdirs =  lisp
+sysconfdir = ${prefix}/etc
+target_alias = 
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+AUTOMAKE_OPTIONS = foreign subdir-objects
+
+# Where to send email about bugs and comments (locally)
+EMAIL = gnuplot-bugs@lists.sourceforge.net
+
+# Default help file location
+HELPFILE = ${datarootdir}/gnuplot/4.6/gnuplot.gih
+
+# Location of X11 app defaults
+XAPPLRESDIR = /etc/X11/app-defaults/
+
+# Default X11 driver location
+X11_DRIVER_DIR = $(pkglibexecdir)
+
+# Default Qt driver location
+QT_DRIVER_DIR = $(pkglibexecdir)
+
+# Default lua driver location
+GNUPLOT_LUA_DIR = $(pkgdatadir)/$(VERSION_MAJOR)/lua
+
+# Default javascript location
+GNUPLOT_JS_DIR = $(pkgdatadir)/$(VERSION_MAJOR)/js
+
+# Default Postscript prologues location
+GNUPLOT_PS_DIR = $(pkgdatadir)/$(VERSION_MAJOR)/PostScript
+
+# System-wide initialization file
+GNUPLOT_SHARE_DIR = $(pkgdatadir)/$(VERSION_MAJOR)
+GNUPLOT_X11 = `echo gnuplot_x11 | sed '$(transform)'`$(EXEEXT)
+AM_CPPFLAGS = -I../term -I$(top_srcdir)/term -DBINDIR=\"$(bindir)\" \
+	-DX11_DRIVER_DIR=\"$(X11_DRIVER_DIR)\" \
+	-DQT_DRIVER_DIR=\"$(QT_DRIVER_DIR)\" \
+	-DGNUPLOT_SHARE_DIR=\"$(GNUPLOT_SHARE_DIR)\" \
+	-DGNUPLOT_PS_DIR=\"$(GNUPLOT_PS_DIR)\" \
+	-DGNUPLOT_JS_DIR=\"$(GNUPLOT_JS_DIR)\" \
+	-DGNUPLOT_LUA_DIR=\"$(GNUPLOT_LUA_DIR)\" \
+	-DCONTACT=\"$(EMAIL)\" -DHELPFILE=\"$(HELPFILE)\" \
+	-DGNUPLOT_X11=\"$(GNUPLOT_X11)\" \
+	-DXAPPLRESDIR=\"$(XAPPLRESDIR)\" $(am__append_5)
+gnuplot_SOURCES = alloc.c alloc.h ansichek.h axis.c axis.h binary.c \
+	breaders.c breaders.h bitmap.h color.c color.h command.c \
+	command.h contour.c contour.h datafile.c datafile.h dynarray.c \
+	dynarray.h eval.c eval.h fit.c fit.h gadgets.c gadgets.h \
+	getcolor.c getcolor.h gp_hist.h gp_time.h gp_types.h \
+	gplt_x11.h graph3d.c graph3d.h graphics.c graphics.h help.c \
+	help.h hidden3d.c hidden3d.h history.c internal.c internal.h \
+	interpol.c interpol.h matrix.c matrix.h misc.c misc.h mouse.c \
+	mouse.h mousecmn.h national.h parse.c parse.h plot.c plot.h \
+	plot2d.c plot2d.h plot3d.c plot3d.h pm3d.c pm3d.h readline.c \
+	readline.h save.c save.h scanner.c scanner.h set.c setshow.h \
+	show.c specfun.c specfun.h standard.c standard.h stats.h \
+	stats.c stdfn.c stdfn.h syscfg.h tables.c tables.h tabulate.c \
+	tabulate.h template.h term_api.h term.c term.h time.c unset.c \
+	util.c util.h util3d.c util3d.h variable.c variable.h \
+	version.c version.h $(am__append_2) $(am__append_3) \
+	$(am__append_4) $(am__append_6) $(am__append_7)
+gnuplot_LDADD = $(TERMLIBS) $(TERMXLIBS) $(WX_LIBS) $(QT_LIBS)
+gnuplot_x11_SOURCES = gplt_x11.c gplt_x11.h gpexecute.c gpexecute.h mousecmn.h version.c version.h
+XLIBS =  -lX11 
+gnuplot_x11_LDADD = getcolor_x11.o $(XLIBS)
+bf_test_SOURCES = bf_test.c binary.c binary.h alloc.c
+#d_beos = beos
+SUBDIRS = $(d_beos) wxterminal qtterminal
+EXTRA_gnuplot_SOURCES = corplot.c os9.c strftime.c vms.c
+EXTRA_DIST = GNUmakefile Makefile.maint NeXT OpenStep README \
+corgraph.asm genopt.com gnuplot.opt header.mac \
+hrcgraph.asm intergra.x11 lasergnu lineproc.mac linkopt.vms \
+makefile.all makefile.awc os2 pcgraph.asm win x11.opt \
+$(EXTRA_gnuplot_SOURCES)
+
+
+# List of compiles translation files
+#TRANSLATIONS = qtgnuplot_fr.qm qtgnuplot_ja.qm
+
+# Install translation files
+#qtgnuplotdir = $(pkgdatadir)/$(VERSION_MAJOR)/qt
+#qtgnuplot_DATA = $(TRANSLATIONS)
+#nodist_gnuplot_qt_SOURCES = moc_QtGnuplotWindow.cpp moc_QtGnuplotApplication.cpp \
+#                            moc_QtGnuplotWidget.cpp moc_QtGnuplotScene.cpp \
+#                            moc_QtGnuplotEvent.cpp qrc_QtGnuplotResource.cpp
+
+#gnuplot_qt_SOURCES = qtterminal/gnuplot_qt.cpp qtterminal/QtGnuplotWindow.cpp \
+#qtterminal/QtGnuplotApplication.cpp qtterminal/QtGnuplotWidget.cpp \
+#qtterminal/QtGnuplotScene.cpp qtterminal/QtGnuplotItems.cpp \
+#qtterminal/QtGnuplotEvent.cpp
+
+#gnuplot_qt_LDADD = $(QT_LIBS)
+
+# embed example (uncomment to build it)
+
+# bin_PROGRAMS += embed_example
+# 
+# nodist_embed_example_SOURCES = moc_embed_example.cpp moc_QtGnuplotInstance.cpp \
+#                          moc_QtGnuplotWidget.cpp moc_QtGnuplotScene.cpp \
+#                          moc_QtGnuplotEvent.cpp qrc_QtGnuplotResource.cpp
+# 
+# embed_example_SOURCES = qtterminal/embed_example.cpp \
+# qtterminal/QtGnuplotWidget.cpp qtterminal/QtGnuplotEvent.cpp \
+# qtterminal/QtGnuplotScene.cpp qtterminal/QtGnuplotItems.cpp \
+# qtterminal/QtGnuplotInstance.cpp
+# 
+# embed_example_LDADD = $(QT_LIBS)
+O = o
+T = $(top_srcdir)/term/
+
+# List of core object files except version.$(O)
+COREOBJS = alloc.$(O) axis.$(O) binary.$(O) bitmap.$(O) breaders.$(O) \
+color.$(O) command.$(O) contour.$(O) datafile.$(O) dynarray.$(O) eval.$(O) \
+fit.$(O) gadgets.$(O) getcolor.$(O) graph3d.$(O) graphics.$(O) help.$(O) \
+hidden3d.$(O) history.$(O) internal.$(O) interpol.$(O) matrix.$(O) \
+misc.$(O) mouse.$(O) parse.$(O) plot.$(O) plot2d.$(O) plot3d.$(O) \
+pm3d.$(O) readline.$(O) save.$(O) scanner.$(O) set.$(O) show.$(O) \
+specfun.$(O) standard.$(O) stats.$(O) stdfn.$(O) tables.$(O) tabulate.$(O) \
+term.$(O) time.$(O) unset.$(O) util.$(O) util3d.$(O) variable.$(O)
+
+
+# List of terminal driver sources
+CORETERM = $(T)aed.trm $(T)ai.trm $(T)aquaterm.trm $(T)be.trm \
+$(T)cairo.trm $(T)canvas.trm $(T)cgi.trm $(T)cgm.trm $(T)context.trm \
+$(T)corel.trm $(T)debug.trm $(T)djsvga.trm $(T)dumb.trm $(T)dxf.trm \
+$(T)dxy.trm $(T)eepic.trm $(T)emf.trm $(T)emxvga.trm $(T)epson.trm \
+$(T)estimate.trm $(T)excl.trm $(T)fig.trm $(T)gd.trm $(T)ggi.trm \
+$(T)gpic.trm $(T)grass.trm $(T)hp2648.trm $(T)hp26.trm $(T)hp500c.trm \
+$(T)hpgl.trm $(T)hpljii.trm $(T)hppj.trm $(T)imagen.trm $(T)kyo.trm \
+$(T)latex.trm $(T)linux.trm $(T)lua.trm $(T)mac.trm $(T)metafont.trm \
+$(T)metapost.trm $(T)mif.trm $(T)next.trm $(T)openstep.trm $(T)pbm.trm \
+$(T)pc.trm $(T)pdf.trm $(T)pm.trm $(T)post.trm $(T)pslatex.trm \
+$(T)pstricks.trm $(T)qms.trm $(T)qt.trm $(T)regis.trm $(T)sun.trm \
+$(T)svg.trm $(T)t410x.trm $(T)tek.trm $(T)texdraw.trm $(T)tgif.trm \
+$(T)tkcanvas.trm $(T)tpic.trm $(T)unixpc.trm $(T)v384.trm $(T)vgagl.trm \
+$(T)vws.trm $(T)win.trm $(T)wxt.trm $(T)x11.trm $(T)xlib.trm
+
+all: all-recursive
+
+.SUFFIXES:
+.SUFFIXES: .c .cpp .m .o .obj
+$(srcdir)/Makefile.in: # $(srcdir)/Makefile.am $(srcdir)/makefile.all $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+$(srcdir)/makefile.all:
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: # $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): # $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-binPROGRAMS: $(bin_PROGRAMS)
+	@$(NORMAL_INSTALL)
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
+	fi; \
+	for p in $$list; do echo "$$p $$p"; done | \
+	sed 's/$(EXEEXT)$$//' | \
+	while read p p1; do if test -f $$p \
+	  ; then echo "$$p"; echo "$$p"; else :; fi; \
+	done | \
+	sed -e 'p;s,.*/,,;n;h' \
+	    -e 's|.*|.|' \
+	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+	sed 'N;N;N;s,\n, ,g' | \
+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
+	    else { print "f", $$3 "/" $$4, $$1; } } \
+	  END { for (d in files) print "f", d, files[d] }' | \
+	while read type dir files; do \
+	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+	    test -z "$$files" || { \
+	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+	    } \
+	; done
+
+uninstall-binPROGRAMS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	files=`for p in $$list; do echo "$$p"; done | \
+	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+	      -e 's/$$/$(EXEEXT)/' \
+	`; \
+	test -n "$$list" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+clean-binPROGRAMS:
+	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
+clean-noinstPROGRAMS:
+	-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+install-pkglibexecPROGRAMS: $(pkglibexec_PROGRAMS)
+	@$(NORMAL_INSTALL)
+	@list='$(pkglibexec_PROGRAMS)'; test -n "$(pkglibexecdir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(pkglibexecdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(pkglibexecdir)" || exit 1; \
+	fi; \
+	for p in $$list; do echo "$$p $$p"; done | \
+	sed 's/$(EXEEXT)$$//' | \
+	while read p p1; do if test -f $$p \
+	  ; then echo "$$p"; echo "$$p"; else :; fi; \
+	done | \
+	sed -e 'p;s,.*/,,;n;h' \
+	    -e 's|.*|.|' \
+	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+	sed 'N;N;N;s,\n, ,g' | \
+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
+	    else { print "f", $$3 "/" $$4, $$1; } } \
+	  END { for (d in files) print "f", d, files[d] }' | \
+	while read type dir files; do \
+	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+	    test -z "$$files" || { \
+	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(pkglibexecdir)$$dir'"; \
+	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(pkglibexecdir)$$dir" || exit $$?; \
+	    } \
+	; done
+
+uninstall-pkglibexecPROGRAMS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(pkglibexec_PROGRAMS)'; test -n "$(pkglibexecdir)" || list=; \
+	files=`for p in $$list; do echo "$$p"; done | \
+	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+	      -e 's/$$/$(EXEEXT)/' \
+	`; \
+	test -n "$$list" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(pkglibexecdir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(pkglibexecdir)" && rm -f $$files
+
+clean-pkglibexecPROGRAMS:
+	-test -z "$(pkglibexec_PROGRAMS)" || rm -f $(pkglibexec_PROGRAMS)
+bf_test$(EXEEXT): $(bf_test_OBJECTS) $(bf_test_DEPENDENCIES) $(EXTRA_bf_test_DEPENDENCIES) 
+	@rm -f bf_test$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(bf_test_OBJECTS) $(bf_test_LDADD) $(LIBS)
+wxterminal/$(am__dirstamp):
+	@$(MKDIR_P) wxterminal
+	@: > wxterminal/$(am__dirstamp)
+wxterminal/$(DEPDIR)/$(am__dirstamp):
+	@$(MKDIR_P) wxterminal/$(DEPDIR)
+	@: > wxterminal/$(DEPDIR)/$(am__dirstamp)
+wxterminal/wxt_gui.$(OBJEXT): wxterminal/$(am__dirstamp) \
+	wxterminal/$(DEPDIR)/$(am__dirstamp)
+wxterminal/gp_cairo.$(OBJEXT): wxterminal/$(am__dirstamp) \
+	wxterminal/$(DEPDIR)/$(am__dirstamp)
+wxterminal/gp_cairo_helpers.$(OBJEXT): wxterminal/$(am__dirstamp) \
+	wxterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/$(am__dirstamp):
+	@$(MKDIR_P) qtterminal
+	@: > qtterminal/$(am__dirstamp)
+qtterminal/$(DEPDIR)/$(am__dirstamp):
+	@$(MKDIR_P) qtterminal/$(DEPDIR)
+	@: > qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/qt_term.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/qt_term_mac.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+gnuplot$(EXEEXT): $(gnuplot_OBJECTS) $(gnuplot_DEPENDENCIES) $(EXTRA_gnuplot_DEPENDENCIES) 
+	@rm -f gnuplot$(EXEEXT)
+	$(AM_V_CXXLD)$(CXXLINK) $(gnuplot_OBJECTS) $(gnuplot_LDADD) $(LIBS)
+qtterminal/gnuplot_qt.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/QtGnuplotWindow.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/QtGnuplotApplication.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/QtGnuplotWidget.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/QtGnuplotScene.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/QtGnuplotItems.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+qtterminal/QtGnuplotEvent.$(OBJEXT): qtterminal/$(am__dirstamp) \
+	qtterminal/$(DEPDIR)/$(am__dirstamp)
+gnuplot_qt$(EXEEXT): $(gnuplot_qt_OBJECTS) $(gnuplot_qt_DEPENDENCIES) $(EXTRA_gnuplot_qt_DEPENDENCIES) 
+	@rm -f gnuplot_qt$(EXEEXT)
+	$(AM_V_CXXLD)$(CXXLINK) $(gnuplot_qt_OBJECTS) $(gnuplot_qt_LDADD) $(LIBS)
+gnuplot_x11$(EXEEXT): $(gnuplot_x11_OBJECTS) $(gnuplot_x11_DEPENDENCIES) $(EXTRA_gnuplot_x11_DEPENDENCIES) 
+	@rm -f gnuplot_x11$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(gnuplot_x11_OBJECTS) $(gnuplot_x11_LDADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+	-rm -f qtterminal/*.$(OBJEXT)
+	-rm -f wxterminal/*.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+include ./$(DEPDIR)/alloc.Po
+include ./$(DEPDIR)/axis.Po
+include ./$(DEPDIR)/bf_test.Po
+include ./$(DEPDIR)/binary.Po
+include ./$(DEPDIR)/bitmap.Po
+include ./$(DEPDIR)/breaders.Po
+include ./$(DEPDIR)/color.Po
+include ./$(DEPDIR)/command.Po
+include ./$(DEPDIR)/contour.Po
+include ./$(DEPDIR)/corplot.Po
+include ./$(DEPDIR)/datafile.Po
+include ./$(DEPDIR)/dynarray.Po
+include ./$(DEPDIR)/eval.Po
+include ./$(DEPDIR)/fit.Po
+include ./$(DEPDIR)/gadgets.Po
+include ./$(DEPDIR)/getcolor.Po
+include ./$(DEPDIR)/gpexecute.Po
+include ./$(DEPDIR)/gplt_x11.Po
+include ./$(DEPDIR)/graph3d.Po
+include ./$(DEPDIR)/graphics.Po
+include ./$(DEPDIR)/help.Po
+include ./$(DEPDIR)/hidden3d.Po
+include ./$(DEPDIR)/history.Po
+include ./$(DEPDIR)/internal.Po
+include ./$(DEPDIR)/interpol.Po
+include ./$(DEPDIR)/matrix.Po
+include ./$(DEPDIR)/misc.Po
+include ./$(DEPDIR)/moc_QtGnuplotApplication.Po
+include ./$(DEPDIR)/moc_QtGnuplotEvent.Po
+include ./$(DEPDIR)/moc_QtGnuplotScene.Po
+include ./$(DEPDIR)/moc_QtGnuplotWidget.Po
+include ./$(DEPDIR)/moc_QtGnuplotWindow.Po
+include ./$(DEPDIR)/mouse.Po
+include ./$(DEPDIR)/os9.Po
+include ./$(DEPDIR)/parse.Po
+include ./$(DEPDIR)/plot.Po
+include ./$(DEPDIR)/plot2d.Po
+include ./$(DEPDIR)/plot3d.Po
+include ./$(DEPDIR)/pm3d.Po
+include ./$(DEPDIR)/qrc_QtGnuplotResource.Po
+include ./$(DEPDIR)/readline.Po
+include ./$(DEPDIR)/save.Po
+include ./$(DEPDIR)/scanner.Po
+include ./$(DEPDIR)/set.Po
+include ./$(DEPDIR)/show.Po
+include ./$(DEPDIR)/specfun.Po
+include ./$(DEPDIR)/standard.Po
+include ./$(DEPDIR)/stats.Po
+include ./$(DEPDIR)/stdfn.Po
+include ./$(DEPDIR)/strftime.Po
+include ./$(DEPDIR)/tables.Po
+include ./$(DEPDIR)/tabulate.Po
+include ./$(DEPDIR)/term.Po
+include ./$(DEPDIR)/time.Po
+include ./$(DEPDIR)/unset.Po
+include ./$(DEPDIR)/util.Po
+include ./$(DEPDIR)/util3d.Po
+include ./$(DEPDIR)/variable.Po
+include ./$(DEPDIR)/version.Po
+include ./$(DEPDIR)/vms.Po
+include qtterminal/$(DEPDIR)/QtGnuplotApplication.Po
+include qtterminal/$(DEPDIR)/QtGnuplotEvent.Po
+include qtterminal/$(DEPDIR)/QtGnuplotItems.Po
+include qtterminal/$(DEPDIR)/QtGnuplotScene.Po
+include qtterminal/$(DEPDIR)/QtGnuplotWidget.Po
+include qtterminal/$(DEPDIR)/QtGnuplotWindow.Po
+include qtterminal/$(DEPDIR)/gnuplot_qt.Po
+include qtterminal/$(DEPDIR)/qt_term.Po
+include qtterminal/$(DEPDIR)/qt_term_mac.Po
+include wxterminal/$(DEPDIR)/gp_cairo.Po
+include wxterminal/$(DEPDIR)/gp_cairo_helpers.Po
+include wxterminal/$(DEPDIR)/wxt_gui.Po
+
+.c.o:
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+
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+	    echo "$(subdir)/$$i"; \
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+	    echo "$$sdir/$$i"; \
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+	done
+install: install-recursive
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+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	if test -z '$(STRIP)'; then \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
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+mostlyclean-generic:
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+clean-generic:
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+distclean-generic:
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+
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+	@echo "it deletes files that may require special tools to rebuild."
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+
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+	clean-noinstPROGRAMS clean-pkglibexecPROGRAMS mostlyclean-am
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+	-rm -rf ./$(DEPDIR) qtterminal/$(DEPDIR) wxterminal/$(DEPDIR)
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+	check-am clean clean-binPROGRAMS clean-generic clean-local \
+	clean-noinstPROGRAMS clean-pkglibexecPROGRAMS cscopelist-am \
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+	install-data-am install-dvi install-dvi-am install-exec \
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+getcolor_x11.o: getcolor.c
+	$(COMPILE) -c -DGPLT_X11_MODE -o getcolor_x11.o $(srcdir)/getcolor.c
+
+# Call the moc preprocessor
+#moc_%.cpp : qtterminal/%.h
+#	$(MOC) -o $@ $<
+
+# Call the Qt resource compiler
+#qrc_%.cpp: qtterminal/%.qrc
+#	$(RCC) -name QtGnuplotResource -o $@ $<
+
+# Call the Qt ui compiler
+#ui_%.h: qtterminal/%.ui
+#	$(UIC) -o $@ $<
+
+# Generate translation files
+#%.qm: qtterminal/po/%.ts
+#	$(LRELEASE) $< -qm $@
+
+# Clean moc & qrc files
+#clean-qt-extra:
+#	rm -vf moc_*.cpp qrc_*.cpp qrc_*.o ui_*.h qtgnuplot*.qm
+
+# Clean transform gnuplot_x11 for demo
+#clean-demo:
+#	rm -f $(GNUPLOT_X11)
+
+#clean-local: clean-qt-extra clean-demo
+
+#$(gnuplot_qt_OBJECTS) : ui_QtGnuplotSettings.h
+# begin makefile.all
+# end makefile.all
+term$U.o: $(CORETERM)
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/misc/maker-3.00.0-beta.tar.gz b/misc/maker-3.00.0-beta.tar.gz
new file mode 100644
index 0000000..556f8d9
Binary files /dev/null and b/misc/maker-3.00.0-beta.tar.gz differ
diff --git a/misc/proteinortho5_better_robustness.pl b/misc/proteinortho5_better_robustness.pl
deleted file mode 100755
index dec173a..0000000
--- a/misc/proteinortho5_better_robustness.pl
+++ /dev/null
@@ -1,1154 +0,0 @@
-#!/usr/bin/perl
-
-##########################################################################################
-#	  This file is part of Proteinortho.
-#	  (C) 2009/2010 Marcus Lechner
-# 
-#	  Proteinortho is free software; you can redistribute it and/or modify
-#	  it under the terms of the GNU General Public License as published
-#	  by the Free Software Foundation; either version 2, or (at your
-#	  option) any later version.
-#
-#	  Proteinortho is distributed in the hope that it will be useful, but
-#	  WITHOUT ANY WARRANTY; without even the implied warranty of
-#	  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#	  General Public License for more details.
-#
-#	  You should have received a copy of the GNU General Public License
-#	  along with Proteinortho; see the file COPYING.  If not, write to the
-#	  Free Software Foundation, Inc., 59 Temple Place - Suite 330,
-#	  Boston, MA 02111-1307, USA.	
-##########################################################################################
-
-##########################################################################################
-# About
-##########################################################################################
-# Proteinortho
-# input fasta files with proteins
-# output matrix with orthologous proteins
-# 
-# @authors Marcus Lechner, Clemens Elias Thoelken
-# @email lechner@staff.uni-marburg.de
-# @company University of Maruburg
-# @date 2017-04-18
-#
-##########################################################################################
-
-##########################################################################################
-# Imports
-##########################################################################################
-use strict;
-use warnings "all";
-use File::Basename;
-use threads;
-use threads::shared;
-use Thread::Queue;
-
-##########################################################################################
-# Variables
-##########################################################################################
-our $version = "5.16b";
-our $step = 0;		# 0/1/2/3	-> do all / only apply step 1 / only apply step 2 / only apply step 3
-our $verbose = 1;	# 0/1		-> don't / be verbose
-our $debug = 0;		# 0/1		-> don't / show debug data
-#our $reflexiv = 0;	# 0/1		-> check sets against themselves
-our $synteny = 0;	# 0/1		-> Apply synteny algorithm
-our $neighbourjoin = 0;	# 0/1		-> Merge neighbours
-our $duplication = 2;	# 0-9 not 1	-> Repeats for duplication extension
-our $cs = 3;	# int		-> cs-value
-our $alpha = 0.5;	# Alpha value for ffadj_mcs.py
-our $connectivity = 0.1;# Algebr. connectivity threshold
-our $cpus   = 0;	# 0 = autodetect
-our $evalue = "1e-05";
-our $purity = 0.75;
-our $coverage = 50;	# Percent coverage threshold for two proteins
-our $identity = 25;	# Percent identity threshold for two proteins
-our $blastmode = "blastp+";
-#our $tmpdir = "./";	# Dir for tmp-files
-our $sim = 0.95;
-our $report = 3;
-our $startat = undef;	# removed 5.16
-our $stopat = undef;	# removed 5.16
-our $keep = 0;
-our $force = 0;
-our $selfblast = 0;
-our $twilight = 0;
-our $singles = 0;
-our $clean = 0;
-our $blastOptions = "";
-our $nograph = 0;
-our $desc = 0;
-our $tmp_path = "";
-
-# Internal
-our $blastversion = "unknown";	# Auto-detected blast version
-our $blastpath = "";
-our $makedb = "";		# makedb command
-our $blast = "";		# blast command
-our $jobque = Thread::Queue->new();	# Jobs todo
-our $jobs_done:shared = 0;		# Counter
-our $jobs_todo = 0;			# Sum of jobs
-our $project = "myproject";		# Project name
-our $graph_lock :shared;
-our $syn_lock :shared;
-our $all_jobs_submitted :shared = 0;
-our $po_path = &get_po_path();		# Determine local path
-our $last_i = -1;
-our $last_j = -1;
-our $run_id = "";
-our %gene_counter;		# Holds the number of genes for each data file (for sorting)
-our $threads_per_process :shared = 1;	# Number of subthreads for blast
-
-# Split work
-our $split_to_X_jobs = -1;
-our $jobnumber = -1;
-our $part = -1;
-
-
-##########################################################################################
-# Parameters
-##########################################################################################
-our @files = ();
-foreach my $option (@ARGV) {
-  if ($option =~ m/^--?step=(0|1|2|3)$/)  		{ $step = $1;   }
-  elsif ($option =~ m/^--?verbose$/) 			{ $verbose = 1;  }
-  elsif ($option =~ m/^--?verbose=(0|1)$/) 		{ $verbose = $1;  }
-  elsif ($option =~ m/^--?te?mp=(.+)$/)	 		{ $tmp_path = $1; 
-								 # make sure it ends with /
-								unless ($tmp_path =~ /\/$/) {$tmp_path .= "/";}
-							}
-  elsif ($option =~ m/^--?debug$/)     			{ $debug = 1;  }
-  elsif ($option =~ m/^--?debug=(0|1)$/)     		{ $debug = $1;  }
-  elsif ($option =~ m/^--?p=(.*)$/)     		{ $blastmode = $1; }
-  elsif ($option =~ m/^--?e=(.*)$/)  			{ $evalue = $1; }
-  elsif ($option =~ m/^--?cpus=(\d*)$/)    		{ $cpus = $1; }
-  elsif ($option =~ m/^--?cpus=auto$/)	     		{ $cpus = 0; }
-  elsif ($option =~ m/^--?alpha=([0-9\.]+)$/)    	{ $alpha = $1; }
-  elsif ($option =~ m/^--?purity=([0-9\.]+)$/)    	{ $purity = $1; }
-  elsif ($option =~ m/^--?report=([0-9]+)$/)   		{ $report = $1; }  
-  elsif ($option =~ m/^--?conn=([0-9\.]+)$/)   		{ $connectivity = $1; }
-  elsif ($option =~ m/^--?cov=([0-9]+)$/)    		{ $coverage = $1; }
-  elsif ($option =~ m/^--?blastpath=(.+)$/)  		{ $blastpath  = $1."/"; }
-  elsif ($option =~ m/^--?identity=([0-9]+)$/)    	{ $identity = $1; }
-  elsif ($option =~ m/^--?identity=twilight$/)   	{ $twilight = 1; }
-  elsif ($option =~ m/^--?sim=([0-9\.]+)$/)    		{ $sim = $1; }
-  elsif ($option =~ m/^--?startat=([0-9]+)$/)    	{ $startat = $1; }
-  elsif ($option =~ m/^--?stopat=([0-9]+)$/)    	{ $stopat = $1; }
-  elsif ($option =~ m/^--?jobs?=([\d]+)\/([\d]+)$/) 	{ $jobnumber = $1; $split_to_X_jobs = $2; }  
-  elsif ($option =~ m/^--?selfblast$/) 			{ $selfblast = 1; }  
-  elsif ($option =~ m/^--?selfblast=(0|1)$/) 		{ $selfblast = $1; }  
-  elsif ($option =~ m/^--?singles$/) 			{ $singles = 1; }  
-  elsif ($option =~ m/^--?singles=(0|1)$/) 		{ $singles = $1; }  
-  elsif ($option =~ m/^--?poff$/) 			{ $synteny = 1; }  
-  elsif ($option =~ m/^--?synteny$/) 			{ $synteny = 1; }  
-  elsif ($option =~ m/^--?synteny=(0|1)$/) 		{ $synteny = $1; }
-  elsif ($option =~ m/^--?dups=0$/)			{ $duplication = 0; } 
-  elsif ($option =~ m/^--?dups=([1-8])$/)		{ $duplication = $1+1;}
-  elsif ($option =~ m/^--?neighbourjoin$/)		{ $neighbourjoin = 1; }  
-  elsif ($option =~ m/^--?neighbourjoin=(0|1)$/)	{ $neighbourjoin = $1; }
-  elsif ($option =~ m/^--?cs=([0-9]+)$/)		{ $cs = $1; }  
-  elsif ($option =~ m/^--?keep/)			{ $keep = 1; }  
-  elsif ($option =~ m/^--?force/)			{ $force = 1; }  
-  elsif ($option =~ m/^--?clean/)			{ $clean = 1; }  
-  elsif ($option =~ m/^--?nograph/)			{ $nograph = 1; }  
-  elsif ($option =~ m/^--?graph/)			{ $nograph = 0; }  
-  elsif ($option =~ m/^--?desc/)			{ $desc = 1; }  
-  elsif ($option =~ m/^--?project=(.*)$/)		{ $project = $1; }
-  elsif ($option =~ m/^--?subpara=(.*)$/i)	{ $blastOptions = $1;}
-  elsif ($option !~ /^-/)				{ push(@files,$option); }
-  else  {&print_usage(); die "Invalid command line option: \'$option\'!\n"; }
-}
-
-##########################################################################################
-# Check parameters
-##########################################################################################
-if (defined($startat) || defined($stopat)) {
-	&Error("Sorry, -startat and -stopat were removed. Please use -jobs=M/N for more flexible job splitting.");	
-}
-
-if ($split_to_X_jobs == 0) {
-	&Error("Job parameter use incorrectly. Number of jobs cannot be 0. Valid format: M/N");
-}
-
-if ($jobnumber != -1 && ($jobnumber == 0 || $jobnumber > $split_to_X_jobs)) {
-	&Error("Job parameter use incorrectly. Job number cannot be 0 or greater than number of jobs. Valid format: M/N");
-}
-if ($jobnumber != -1) {
-	if ($step != 2) {&Error("Parameter -jobs only works for step 2!");}
-	$run_id = "_$jobnumber"."_".$split_to_X_jobs;
-}
-
-
-our $simgraph = "$project.blast-graph$run_id";		# Output file graph
-our $syngraph = "$project.ffadj-graph$run_id";		# Output file synteny
-
-our $rm_simgraph = "$tmp_path$project.removed_blast-graph";		# Output remove graph
-our $rm_syngraph = "$tmp_path$project.removed_ffadj-graph";		# Output remove graph
-
-our $csimgraph = "$project.proteinortho-graph";		# Output file graph
-our $csyngraph = "$project.poff-graph";				# Output file synteny
-our $simtable = "$project.proteinortho";			# Output file graph
-our $syntable = "$project.poff";					# Output file synteny
-our $desctable = "$project.descriptions";			# Output file seq descriptions
-
-
-if (-e "$project.proteinortho") {
-	print STDERR "!!!\nWarning: Data files for project '$project' already exists. Previous output files might be overwritten.\n";
-	print STDERR "Press CTRL + C to prevent me from proceeding\nWaiting for 10 seconds...\n!!!\n";
-	sleep(10);
-	print STDERR "\nWell then, proceeding...\n\n";
-}
-
-##########################################################################################
-# Run
-##########################################################################################
-&print_header;		# Show Proteinortho Header
-&auto_cpus;		# Set number of CPUs
-&check_blast;		# Check blast version
-
-# Always do
-&check_files;		# Check files, count sequences
-@files = ();
-foreach my $file (sort { if ($gene_counter{$a} == $gene_counter{$b}) {$a cmp $b;} else {$gene_counter{$b} <=> $gene_counter{$a};} } keys %gene_counter) {push(@files,$file);}	# Biggest first # Alphabet otherwise 5.16
-
-
-# Step 1, check files and make indices
-if ($step == 0 || $step == 1) {
-	print STDERR "\n**Step 1**\n";
-	&generate_indices;	# Generate index files for blast
-	if ($desc) {
-		&write_descriptions;	# Write sequence description file
-	}
-}
-
-# Step 2, run blast and synteny algorithm
-if ($step == 0 || $step == 2) {
-	print STDERR "\n**Step 2**\n";
-	&init_graph_output;	# Initiate Output file(s)
-	&run_blast;		# Run blasts
-}
-
-# Step 3, spacial clustering
-if ($step == 0 || $step == 3) {
-	print STDERR "\n**Step 3**\n";
-	&cluster;							# form clusters and write outputs
-	if ($clean) {&clean;}						# remove blast indices
-	print STDERR "\nAll finished.\n";
-}
-
-
-##########################################################################################
-# Functions
-##########################################################################################
-sub clean {
-	print STDERR "Removing temporary files...\n";
-	if ($blastmode =~ /blastp/) {
-		foreach my $file (@files) {
-			unlink("$file.phr");
-			unlink("$file.pin");
-			unlink("$file.psq");
-		}
-	}
-	else {
-		foreach my $file (@files) {
-			unlink("$file.nhr");
-			unlink("$file.nin");
-			unlink("$file.nsq");
-		}
-	}
-
-	if ($nograph) {
-		unlink($simgraph);
-		if ($synteny) {unlink($syngraph);}
-	}
-}
-
-sub cluster {
-	print STDERR "Clustering by similarity (Proteinortho mode)\n";
-	system("$po_path/proteinortho5_clustering -verbose $verbose -conn $connectivity -purity $purity -rmgraph '$rm_simgraph' $simgraph* >'$simtable'");
-	if ($singles) {
-		print STDERR "Adding singles...\n";
-		my $fastas = "'".join("' '",@files)."'";
-		system("$po_path/proteinortho5_singletons.pl $fastas <'$simtable' >>'$simtable'");
-	}
-        print STDERR "[OUTPUT] -> written to $simtable\n";
-	unless ($nograph) {
-		print STDERR "Writing graph...\n";
-#		system("$po_path/proteinortho5_clean_edges -e '$rm_simgraph' $simgraph* >'$csimgraph'");
-		system("$po_path/proteinortho5_clean_edges2.pl '$rm_simgraph' $simgraph* >'$csimgraph'");
-		unless ($keep) {unlink($rm_simgraph);}
-		print STDERR "[OUTPUT] -> written to $csimgraph\n";
-	}
-
-	if ($synteny) {
-		print STDERR "\nClustering by gene-order (POFF mode)\n";
-		system("$po_path/proteinortho5_clustering -verbose $verbose -conn $connectivity -purity $purity -rmgraph '$rm_syngraph' $syngraph* >'$syntable'");
-		if ($singles) {
-		print STDERR "Adding singles...\n";
-			my $fastas = "'".join("' '",@files)."'";
-			system("$po_path/proteinortho5_singletons.pl $fastas <'$syntable' >>'$syntable'");
-		}
-		print STDERR "[OUTPUT] -> written to $syntable\n";
-		unless ($nograph) {
-			print STDERR "Writing graph...\n";
-#			system("$po_path/proteinortho5_clean_edges -e '$rm_syngraph' $syngraph* >'$csyngraph'");
-			system("$po_path/proteinortho5_clean_edges2.pl '$rm_syngraph' $syngraph* >'$csyngraph'");
-			unless ($keep) {unlink($rm_syngraph);}
-			print STDERR "[OUTPUT] -> written to $csyngraph\n";
-		}
-	}
-}
-
-sub print_header {
-	print STDERR "*****************************************************************\n",
-		     "Proteinortho with PoFF version $version - An orthology detection tool\n",
-	             "*****************************************************************\n";
-}
-
-sub print_usage {
-print STDERR << "JUS";
-
-Usage: proteinortho5.pl [OPTIONS] FASTA1 FASTA2 [FASTA...]
-Options:
-         [General options]
-         -project=    prefix for all result file names [default: myproject]
-         -cpus=       number of processors to use [default: auto]
-         -verbose     keeps you informed about the progress
-         -temp=       path for temporary files [default: working directory]
-         -keep        stores temporary blast results for reuse
-         -force       forces recalculation of blast results in any case
-         -clean       remove all unnecessary files after processing
-         -step=       1 -> generate indices
-                      2 -> run blast (and ff-adj, if -synteny is set)
-                      3 -> clustering
-                      0 -> all (default)
-
-         [Search options]
-         -p=          blast program [default: blastp+]
-         -e=          E-value for blast [default: 1e-05]
-                      {blastn|blastp|tblastx|blastn+|blastp+|tblastx+}
-         -selfblast   apply selfblast, detects paralogs without orthologs
-         -sim=        min. similarity for additional hits (0..1) [default: 0.95]
-         -identity=   min. percent identity of best blast hits [default: 25]
-         -cov=        min. coverage of best blast alignments in % [default: 50]
-         -subpara=    additional parameters for the search tool
-                      example -subpara='-seg no'
-
-         [Synteny options]
-         -synteny     activate PoFF extension to separate similar sequences
-                      by contextual adjacencies (requires .gff for each .fasta)
-         -dups=       PoFF: number of reiterations for adjacencies heuristic,
-                      to determine duplicated regions (default: 0)
-         -cs=         PoFF: Size of a maximum common substring (MCS) for
-                      adjacency matches (default: 3)
-         -alpha=      PoFF: weight of adjacencies vs. sequence similarity
-                      (default: 0.5)
-
-         [Clustering options]
-         -singles     report singleton genes without any hit
-         -purity=     avoid spurious graph assignments [0.01-1, default 0.75]
-         -conn=       min. algebraic connectivity [default: 0.1]
-         -nograph     do not generate .graph file (pairwise orthology relations)
-
-         [Misc options]
-         -desc        write description files (for NCBI FASTA input only)
-         -blastpath=  path to your local blast (if not installed globally)
-         -debug       gives detailed information for bug tracking
-
-         [Large compute jobs]
-          In case jobs should be distributed onto several machines, use
-         -jobs=M/N    N defines the number of defined job groups (e.g. PCs)
-                      M defines the set of jobs to run in this process
-
-         Example:     run with 
-                        -step=1
-                      to prepare data then to split a run on two machines use
-                        -jobs=1/2 -step=2 on PC one and
-                        -jobs=2/2 -step=2 on PC two
-                      finally run with
-                        -step=3 to finalize
-JUS
-}
-
-sub init_graph_output {
-#	if (-e $graph) {
-#		&Error("Graph output file '$graph' already exists.");
-#	}
-	open(GRAPH,">$simgraph") || die("Could not open graph '$simgraph': $!");
-	print GRAPH "# file_a\tfile_b\n# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba\n";
-	close(GRAPH);
-
-	unless ($synteny) {return;}
-#	if (-e $syn) {
-#		&Error("Synteny Graph output file '$syn' already exists.");
-#	}
-	open(SYN,">$syngraph") || die("Could not open graph '$syngraph': $!");
-	print SYN "# file_a\tfile_b\n# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba\tsame_strand\tsimscore\n";
-	close(SYN);
-}
-
-sub set_threads_per_process {
-	lock($jobs_done);
-	my $willdo = ($jobs_todo-$jobs_done+$_[0]);
-
-	if ($debug) {
-		print STDERR "\nTODO: $jobs_todo DONE: $jobs_done Running: $_[0] -> $willdo\n";
-	}
-
-	if ($willdo < 1) {return;}
-
-	my $optimal = int($cpus/$willdo);
-	lock($threads_per_process);
-	if ($optimal > $threads_per_process) {
-		$threads_per_process = $optimal;
-		if ($debug) {
-			print STDERR "\nBlast subthreads was set to $threads_per_process\n";
-		}
-	}
-}
-
-sub run_blast {
-	# Jobs todo
-	$jobs_todo = 0;
-	for (my $i = 0; $i < scalar(@files)-1+$selfblast; $i++) {$jobs_todo += scalar(@files)-$i-1+$selfblast;}
-
-	# Divide 5.16
-	$part = int($jobs_todo/$split_to_X_jobs);	# Round up to not miss anything
-#	print STDERR "$jobs_todo/$split_to_X_jobs = $part\n";
-	my $from = ($jobnumber-1)*($part)+1;
-	if ($jobnumber == 1) {$from = 1;}
-	my $to = ($jobnumber-1)*($part)+$part;
-	if ($jobnumber == $split_to_X_jobs) {$to = $jobs_todo;}
-
-	$part = 1+$to-$from;	# real part
-
-	if ($split_to_X_jobs != -1 && $part < 1) {&Error("I have problems coordinating $split_to_X_jobs groups for $jobs_todo jobs.");}
-	if ($split_to_X_jobs <= 1) {$from = -1; $to = -1; $split_to_X_jobs = -1; $part = -1;}
-
-#	print STDERR "$from - $to (TODO: $jobs_todo)\n";
-
-	&set_threads_per_process(0);	# Check if we can apply more threads, nothing is running so far
-	&print_blast_stats();
-
-	# Spawn worker threads
-	for (my $i = 0; $i < $cpus; $i++) {threads->create('workerthread');}
-
-	# For each file against each other file
-	my $job_number = 0;
-	SPEC: for (my $i = 0; $i < scalar(@files)-1+$selfblast; $i++) {
-		for (my $j = $i+1-$selfblast; $j < scalar(@files); $j++) {
-			$job_number++;
-			if ($from != -1 && $job_number < $from) {next;}
-			# Wait for queque to get empty (with some buffer)
-			while ($jobque->pending() > 32 + 2*$cpus) {sleep(1);}
-			# Syncronize with other processes
-			$jobque->enqueue("$i $j");
-#			print STDERR "EN: $job_number -> $i $j\n";
-			if ($to != -1 && $job_number >= $to) {last SPEC;}
-		}
-	}
-	# Tell all threads they can stop
-	{lock($all_jobs_submitted); $all_jobs_submitted = 1;}
-
-	# Wait until all jobs are done
-	foreach (threads->list()) 	{$_->join();}
-	&print_blast_stats();		print STDERR "\n";
-	print STDERR "[OUTPUT] -> written to $simgraph\n";
-}
-
-sub workerthread {
-	my $thread_id = threads->tid();
-	my $temp_file = "$tmp_path$project-$run_id-$thread_id";
-
-	# Clean up, just to be safe
-	unlink("$temp_file.tmp");
-	unlink("$temp_file.log");
-	unlink("$temp_file.matching");
-
-	while (1) {
-		my ($i, $j);
-		while (1) {
-			# Fetch new jobs
-			my $job = $jobque->dequeue_nb();
-			# If there is nothing
-			unless (defined($job)) {
-				# Check if more jobs need to be done
-
-				{
-				lock($jobs_done);							# 	Productive
-				if ($jobs_done >= $jobs_todo || ($part != -1 && $jobs_done >= $part)) {	# 	Productive
-#				lock($all_jobs_submitted);						# 	DEBUGGING
-#				if ($all_jobs_submitted) {						# 	DEBUGGING
-					if ($debug) {print STDERR "Thread $thread_id\tis leaving\n";}
-					return;
-				}}
-				# If so, wait
-					if ($debug) {print STDERR "Thread $thread_id\tis seeking work ($jobs_done / $jobs_todo)\n";}
-				sleep(1);
-			}
-			else {
-				# Parse job
-				($i, $j) = split(" ",$job);
-				# Break the fetch loop
-				last;
-			}
-		}
-
-		my $file_i = $files[$i];
-		my $file_j = $files[$j];
-		my $short_file_i = $file_i;	$short_file_i =~ s/^.*\///;
-		my $short_file_j = $file_j;	$short_file_j =~ s/^.*\///;
-
-		# Work
-		&set_threads_per_process(scalar(threads->list()));
-		my $result_ij = &blast($file_i,$file_j);
-
-		my $result_ji;
-		if ($file_i eq $file_j) {
-			# One run is enough (selfblast)
-			$result_ji = $result_ij;
-		}
-		else {
-			$result_ji = &blast($file_j,$file_i);
-		}
-
-		if ($file_i eq $file_j && !$selfblast) {die("Selfblast is disabled but I want to check $file_i vs $file_j");}
-
-		my %lengths;
-		if ($file_i eq $file_j) {
-			# Get lengths once is enough (selfblast)
-			%lengths = %{&get_gene_lengths($file_i)};
-		}
-		else {
-			%lengths = %{&get_gene_lengths($file_i,$file_j)};
-		}
-		my %reciprocal_matches = %{&match(\%lengths,$result_ij,$result_ji)};
-
-		# Remove secondary hits if better exist	(test here instead of later)
-		%reciprocal_matches = %{&adaptive_best_blast_matches(\%reciprocal_matches)};
-
-		if ($synteny) {
-			my ($ordered_matches, $track_pointer, $close_copies_pointer) = &synteny_matches(\%reciprocal_matches,$file_i,$file_j);
-			open(PREGRAPH,">>$temp_file.tmp") || die("Could not open temp file '$temp_file.tmp': $!");
-			print PREGRAPH $ordered_matches;
-			close(PREGRAPH);
-			my $cmd = "python2 $po_path/ffadj_mcs.py '$temp_file.tmp' $alpha";
-			if ($duplication) {
-				$cmd .= " --repeat-matching $duplication --min-cs-size $cs";
-			}
-			if ($debug) {print STDERR "$cmd\n";}
-			my $synt_stats = qx($cmd);
-			chomp $synt_stats;
-			$synt_stats =~ s/#.+\n//;
-
-			# Reverse mapping of full gene ids, two seperate maps in case of overlapps in short ids
-			my %full_id_map_i;
-			my %full_id_map_j;
-			foreach (sort keys %reciprocal_matches) {
-				my ($a, $b) = split(/\s/,$_);
-				my $aa = &convertNCBI($a);
-				my $bb = &convertNCBI($b);
-				if ($aa ne $a) {
-					if ($debug) {print STDERR "j_map: $aa -> $a\n";}
-					$full_id_map_j{$aa} = $a;}
-				if ($bb ne $b) {
-					if ($debug) {print STDERR "i_map: $bb -> $b\n";}
-					$full_id_map_i{$bb} = $b;}
-			}
-
-			# Reverse mapping of gene position to short id
-			my %track = %{$track_pointer};
-			my %close = %{$close_copies_pointer};
-			# Generate hash for synteny hits
-			my %synteny;
-			unless (-s "$temp_file.matching") {
-				print STDERR "Error: Failed to run $po_path/ffadj_mcs.py for\n$file_i vs $file_j\nMoving source to $temp_file.err for debugging\nI will continue, but results may be insufficient.\n";
-				system("mv $temp_file.tmp $temp_file.err");
-				next;
-			}
-			open(OSYNGRAPH,"<$temp_file.matching") || die("Could not open temp file $temp_file.matching: $!'");
-			while(<OSYNGRAPH>) {
-					chomp;
-					my ($i, $j, $score) = split(/\s+/,$_,3);
-					if (!defined($score) || $i =~ /[^0-9]/ || $i == 0 || length($i) > 10) {next;}
-					unless (defined($track{$file_i.$i})) {
-						print STDERR "Could not find i: ".$file_i.$i."\n";	next;
-					}
-					unless (defined($track{$file_j.$j})) {
-						print STDERR "Could not find j: ".$file_j.$j."\n";	next;
-					}
-					# Remap to full ID
-					my $a = $track{$file_i.$i};
-					if (defined($full_id_map_i{$a})) {$a = $full_id_map_i{$a};}
-					my $b = $track{$file_j.$j};
-					if (defined($full_id_map_j{$b})) {$b = $full_id_map_j{$b};}
-					# Store
-					$synteny{"$b $a"} = $score;
-
-					# Close copies
-					if ($neighbourjoin && defined($close{$i})) {
-						my @partners = split(',',$close{$i});
-						foreach (@partners) {
-							my $c = $track{$file_i.$_};
-							if (defined($full_id_map_i{$c})) {$c = $full_id_map_i{$c};}
-							# Store
-							$synteny{"$b $c"} = $score;
-							if ($debug) {print STDERR "Storing addional proximity edge $a & $b -> $c\n";}
-						}
-					}
-				}
-				close(OSYNGRAPH);
-				unlink("$temp_file.tmp");
-				unlink("$temp_file.log");
-				unlink("$temp_file.matching");
-
-			{
-			lock($syn_lock);
-
-			open(SYN,">>$syngraph") || die("Could not open file '$syngraph': $!");
-			print SYN "# $short_file_j\t$short_file_i\n";
-			print SYN "# Scores: $synt_stats\n";
-			foreach (sort keys %reciprocal_matches) {
-				if (!defined($synteny{$_})) {if ($debug) {print STDERR "FAIL: $_\n";} next;}		# Not reported by gene-order algo
-				my $line = "$_ ".$reciprocal_matches{$_}." $synteny{$_}";
-				$line =~ s/ /\t/g;
-				print SYN "$line\n";
-			}
-			close(SYN);
-			}
-
-		}
-
-		{
-			lock($graph_lock);
-			open(GRAPH,">>$simgraph") || die("Could not open file '$simgraph': $!");
-			print GRAPH "# $short_file_j\t$short_file_i\n";
-			foreach (sort keys %reciprocal_matches) {
-				my $line = "$_ ".$reciprocal_matches{$_};
-				$line =~ s/ /\t/g;
-				print GRAPH "$line\n";
-			}
-			close(GRAPH);
-		}
-		# Count
-		{
-			lock($jobs_done);
-			$jobs_done++;
-		}
-		&print_blast_stats();	# Needs jobs_done to be free
-	}
-}
-
-sub identitybylength {
-        # Accoding to the formula of Rost, 1999 (Twilight-zone)
-	if($_[0] <= 11)		{return 100;}
-	if($_[0] <= 450)	{return 480*$_[0]**(-0.32*(1+exp(-$_[0]/1000)));}
-	return 19.5;
-}
-
-sub adaptive_best_blast_matches {
-	my %reciprocal_matches = %{(shift)};
-
-	if ($debug) {
-		print STDERR "\nStart with ";
-		print STDERR scalar(keys %reciprocal_matches);
-		print STDERR " edges\n";
-	}
-
-	my %best;
-	my %best_gen;
-	# Gather best
-	foreach (keys %reciprocal_matches) {
-		my ($a,$b) = split(" ",$_);
-		my ($evalue_ab,$bitscore_ab,$evalue_ba,$bitscore_ba) = split(" ",$reciprocal_matches{$_});
-		if (!defined($best{$a}) || $best{$a} < $bitscore_ab) {
-			$best{$a} = $bitscore_ab;
-			$best_gen{$a} = $b;
-		}
-		if (!defined($best{$b}) || $best{$b} < $bitscore_ba) {
-			$best{$b} = $bitscore_ba;
-			$best_gen{$b} = $a;
-		}
-	}
-
-	if ($debug) {
-		my %gene_num;
-		# Count gene number
-		foreach (keys %reciprocal_matches) {
-			my ($a,$b) = split(" ",$_);
-			$gene_num{$a}++;
-			$gene_num{$b}++;
-		}
-		print STDERR "Number of genes: ".scalar(keys %gene_num)."\n";
-
-	#	foreach (keys %best) {
-	#		print STDERR "Best score for $_ is $best{$_} ($best_gen{$_})\n";
-	#	}
-	}
-
-	# Remove worse
-	foreach (keys %reciprocal_matches) {
-		my ($a,$b) = split(" ",$_);
-		my ($evalue_ab,$bitscore_ab,$evalue_ba,$bitscore_ba) = split(" ",$reciprocal_matches{$_});
-		if 	($best{$a}*$sim > $bitscore_ab) {delete $reciprocal_matches{$_}; if ($debug) {my $v = $bitscore_ab/$best{$a}; print STDERR "Removed $_ because:\t$best{$a} vs $bitscore_ab ($v)\n";}}
-		elsif 	($best{$b}*$sim > $bitscore_ba) {delete $reciprocal_matches{$_}; if ($debug) {my $v = $bitscore_ba/$best{$b}; print STDERR "Removed $_ because:\t$best{$b} vs $bitscore_ba ($v)\n";}}
-	}
-
-	if ($debug) {
-	print STDERR "\nEnd with ";
-	print STDERR scalar(keys %reciprocal_matches);
-	print STDERR " edges\n";
-
-	my %gene_num;
-	# Count gene number
-	foreach (keys %reciprocal_matches) {
-		my ($a,$b) = split(" ",$_);
-		$gene_num{$a}++;
-		$gene_num{$b}++;
-	}
-	print STDERR "Number of genes: ".scalar(keys %gene_num)."\n";}
-
-	return \%reciprocal_matches;
-}
-
-sub synteny_matches {
-	my %reciprocal_matches = %{(shift)};
-	my $file_i = shift;
-	my $file_j = shift;
-
-	# Get order for both species (same hash as ids are non overlapping)
-	my %order;
-	my %track;
-	for my $file ($file_i, $file_j) {
-		# Get Coordinates for all genes
-		my %coords = %{&read_details($file)};
-		my $counter = 0;
-		# Number them according to their order
-		foreach my $id (sort
-			{
-				my @a = split("\t",$coords{$a});
-				my @b = split("\t",$coords{$b});
-
-#				#chr strand pos
-#				if ($a[0] ne $b[0]) {return $a[0] cmp $b[0];}
-#				if ($a[1] ne $b[1]) {return $a[1] cmp $b[1];}
-#				return $a[2] <=> $b[2];
-
-				#chr pos
-				if ($a[0] ne $b[0]) {return $a[0] cmp $b[0];}
-				return $a[2] <=> $b[2];
-			}	(keys(%coords))) {
-			my @v = split("\t",$coords{$id});
-			$order{$id} = ++$counter."\t".$v[1];	# Store strand info
-			$track{$file.$counter} = $id;		# Reverse Mapping
-		}
-	}
-
-	my $output = "";
-
-	my @multis;	# array that contains all multi-edges
-	# Convert reciprocal matches to ffadj input
-	foreach (keys %reciprocal_matches) {
-		my @values = split(/\s/,$reciprocal_matches{$_});
-		my ($a, $b) = split(/\s/,$_);
-		unless (defined($order{$a})) {$a = &convertNCBI($a);}
-		unless (defined($order{$b})) {$b = &convertNCBI($b);}
-		my @a = split(/\s/,$order{$a});
-		my @b = split(/\s/,$order{$b});
-		unless (defined($a[0])) {die("Failed parsing gene IDs from blast output/gff input\n");}
-
-		unless (defined($multis[$a[0]])) {$multis[$a[0]] = $b[0];}
-		else 				 {$multis[$a[0]] .= ','.$b[0];}
-
-		$output .= "$b[0]\t$a[0]\t";			# Positions
-		if ($a[1] eq $b[1]) 	{$output .= "1\t";}	# Same strand?
-		else 			{$output .= "-1\t";}
-		my $score = (&edgeweight($values[0])+&edgeweight($values[2]))/2;	# Score made from e-values
-		$output .= $score."\n";
-	}
-
-	# Check multis
-	my %close_copies;
-	if ($neighbourjoin) {
-		for (my $i = 1; $i < scalar(@multis); $i++) {
-			unless (defined($multis[$i])) {next;}
-			my @partners = sort { $a <=> $b } split(',',$multis[$i]);
-			if (scalar(@partners) <= 1) {next;}
-			my $dist_limit = 2;	# How far can tandem copies be away from each other? (0/1 = off, 2 = immediate, ...
-			my $last = 999999999999999;
-			foreach my $new (@partners) {
-				if (abs($last-$new) < $dist_limit) {
-					if (!defined($close_copies{$last}))  	{$close_copies{$last} = $new;}
-					else 					{$close_copies{$last} .= ','.$new;}
-					$close_copies{$new} = $last;		# The list is sortet, so we are here for the frist time
-				}
-				$last = $new;
-			}
-		}
-	}
-
-	return ($output, \%track, \%close_copies);
-}
-
-# Read the length of all genes in a given set of fasta files
-sub get_gene_lengths {
-	my %lengths;
-	while (my $file = shift @_) {
-		my $last_gene = "";
-		open(FASTA,"<$file") || &Error("Could not open '$file': $!");
-		while (<FASTA>) {
-			chomp;
-			if ($_ =~ />/) {
-				$_ =~ s/^>//;	$_ =~ s/\s.*//;
-				$lengths{$_} = 0;
-				$last_gene = $_;
-			}
-			else {
-				$lengths{$last_gene} += length($_);
-			}
-		}
-		close(FASTA);
-	}
-
-	return \%lengths;
-}
-
-sub print_blast_stats {
-	if (!$verbose) {return;}
-	{
-		if ($jobs_todo == 0) {die("Nothing to do. This should not happen!");}
-		lock($jobs_done);
-		my $percent = int($jobs_done/$jobs_todo*10000)/100;
-		print STDERR "\r                                                                               ";
-	
-		if ($split_to_X_jobs == -1) {
-			print STDERR "\rRunning blast analysis: $percent% ($jobs_done/$jobs_todo)";
-		}
-		else {	# 5.16
-			$percent = int($jobs_done/$part*10000)/100;
-			print STDERR "\rRunning blast analysis: $percent% ($jobs_done/$part, $jobs_todo in total)";
-		}
-	}
-}
-
-sub match {
-	my %length = %{(shift)};
-	my @i = @{(shift)};
-	my @j = @{(shift)};
-
-	my %legal_i = &get_legal_matches(\%length,@i);
-	my %legal_j = &get_legal_matches(\%length,@j);
-
-	return &get_reciprocal_matches(\%legal_i,\%legal_j);
-}
-
-sub get_reciprocal_matches {
-	my %i = %{(shift)};
-	my %j = %{(shift)};
-	my %reciprocal;
-
-	foreach (keys %i) {
-		my ($i, $j) = split(" ",$_);
-
-		# Reciprocal hit?
-		if (!defined($j{"$j $i"})) {next;}
-
-		# Merge both
-		$reciprocal{$_} = $i{$_}." ".$j{"$j $i"};	# evalue_ij, bitscore_ij, evalue_ji, bitscore_ji
-	}
-
-	return \%reciprocal;
-}
-
-sub get_legal_matches {
-	my %length = %{(shift)};
-
-	my %result;
-	foreach (@_) {
-		my ($query_id,$subject_id,$local_identity,$alignment_length,$mismatches,$openings,$query_start,$query_end,$subject_start,$subject_end,$local_evalue,$local_bitscore) = split(/\s+/);
-
-		if ($debug) {print STDERR "?$query_id -> $subject_id ($local_evalue,$local_bitscore)\n";}
-
-
-		# Bug tracking
-		unless (defined($length{$query_id})) 	{print STDERR "ERROR: Query gene ID '$query_id' is present in blast output but was not present in FASTA input! Skipping line.\n"; next;}
-		unless (defined($length{$subject_id})) 	{print STDERR "ERROR: Subject gene ID '$subject_id' is present in blast output but was not present in FASTA input! Skipping line.\n"; next;}
-
-		## Check for criteria
-		# Well formatted
-		if (!defined($local_bitscore)) 							{next;}
-
-		# Percent identity
-		if (!$twilight && $local_identity < $identity) 					{next;}
-		if ( $twilight && $local_identity < &identitybylength($alignment_length))	{next;} 
-		# Min. length
-		if ($blastmode eq "tblastx+" || $blastmode eq "tblastx") {$alignment_length *= 3;}
-		if ($alignment_length < $length{$query_id}*($coverage/100)+0.5) 		{next;}
-		if ($alignment_length < $length{$subject_id}*($coverage/100)+0.5) 		{next;}
-
-		# It hit itself (only during selfblast)
-		# if ($selfblast && $query_id eq $subject_id) 					{next;}	# 5.16 reuse IDs
-		## Listing them in the graph is okay, clustering will ignore them
-
-		# Similar hits? Take the better one
-		if (defined($result{"$query_id $subject_id"})) {
-			my ($remote_evalue, $remote_bitscore) = split(" ",$result{"$query_id $subject_id"});
-			if ($local_evalue > $remote_evalue) {next;}
-			if ($local_bitscore < $remote_bitscore) {next;}
-		}
-
-		# Store data
-		if ($debug) {print STDERR "!$query_id -> $subject_id ($local_evalue,$local_bitscore)\n";}
-		$result{"$query_id $subject_id"} = "$local_evalue $local_bitscore";
-	}
-
-	return %result;
-}
-
-# Auto set the number of CPUs
-sub auto_cpus {
-	if ($cpus == 0) {
-		my $cpu_x = qx(getconf _NPROCESSORS_ONLN); 		$cpu_x =~ s/[^0-9]//g;
-		# Fallback
-		if (length($cpu_x) == 0 || $cpu_x == 0) {
-			# Linux
-			if (-e "/proc/cpuinfo") {
-				$cpu_x = qx(grep processor /proc/cpuinfo | wc -l);
-			}
-			# Try Mac
-			else {
-				$cpu_x = qx(system_profiler | grep CPUs:);
-			}
-			$cpu_x =~ s/[^0-9]//g;
-		}
-		if (length($cpu_x) == 0 || $cpu_x == 0) {
-			print STDERR "failed! Use 1 core only\n";$cpu_x = 1;
-		}
-		print STDERR "Detected $cpu_x available CPU threads, ";
-		$cpus = $cpu_x;
-	}
-	else {
-		print STDERR "Using $cpus CPU threads, ";
-	}
-}
-
-sub generate_indices {
-	print STDERR "Generating indices\n";
-	foreach my $file (@files) {
-		if ($file =~ /\s/) {die("File name '$file' contains whitespaces. This might lead to undesired effects. Please change file name!\n");}
-		if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
-		system("$makedb '$file' >/dev/null");
-	}
-	unlink('formatdb.log');
-}
-
-sub blast {
-	my $command = "";
-	if 	($blastmode eq "blastp" || $blastmode eq "blastn" || $blastmode eq "tblastx") {
-			lock($threads_per_process);
-			$command = $blastpath."blastall -a $threads_per_process -d '$_[0]' -i '$_[1]' -p $blastmode -m8 -e $evalue $blastOptions";
-	}
-	elsif	($blastmode eq "blastp+") 				{lock($threads_per_process); $command = $blastpath."blastp -num_threads $threads_per_process -db '$_[0]' -query '$_[1]' -evalue $evalue -outfmt 6 $blastOptions";}
-	elsif	($blastmode eq "blastn+") 				{lock($threads_per_process); $command = $blastpath."blastn -num_threads $threads_per_process -db '$_[0]' -query '$_[1]' -evalue $evalue -outfmt 6 $blastOptions";}
-	elsif	($blastmode eq "tblastx+") 				{lock($threads_per_process); $command = $blastpath."tblastx -num_threads $threads_per_process -db '$_[0]' -query '$_[1]' -evalue $evalue -outfmt 6 $blastOptions";}
-	else	{die("This should not happen!");}
-
-	my $a = $_[0];
-	my $b = $_[1];
-	$a =~ s/^.*\///;
-	$b =~ s/^.*\///;
-	my $bla = "$tmp_path$a.vs.$b.bla";
-
-	# File does not exists yet or I am forced to rewrite it
-	if (!(-s $bla) || $force) {
-		if ($debug) {print STDERR "$command >$bla.tmp\n";}											# 5.16
-		system("$command | sort -k11,11g >'$bla.tmp'");		# run blast and presort (speeds up best alignment search but is NOT mandatory)	# 5.16
-		system("mv '$bla.tmp' '$bla'");				# move when done, aids when job fails (no half bla files)			# 5.16
-		my @data = &readFile($bla);
-		unless ($keep) {unlink($bla);}				# delete tmp file
-		return \@data;
-	}
-	# Otherwise, use existing data
-	if ($verbose) {print STDERR "\nNote: '$bla' exists, using pre-calculated data\n";}
-	my @data = &readFile($bla);
-	return \@data;
-}
-
-sub readFile {
-	open(FILE,"<$_[0]") || die("Error, could not open file $_[0]: $!");
-	my @data = <FILE>;
-	close(FILE);
-	chomp @data;
-	return @data;
-}
-
-sub check_blast {
-	if ($blastmode eq "blastp+" || $blastmode eq "blastn+" || $blastmode eq "tblastx+") {
-		my $tmp = $blastmode;
-		$tmp =~ s/\+//g;
-		my $cmd = $blastpath."$tmp -h";
-		my $out = qx($cmd);
-		if ($out =~ /DESCRIPTION.*?\n\s*(.+)\n/) {
-			my @version = split(/\s+/,$1);
-			$blastversion = pop @version;
-
-			# Commands
-			if 	($blastmode eq "blastp+") {$makedb = $blastpath."makeblastdb -dbtype prot -in";}
-			elsif 	($blastmode eq "blastn+" || $blastmode eq "tblastx+") {$makedb = $blastpath."makeblastdb -dbtype nucl -in";}
-			else	{die("This should not happen!");}
-
-			print STDERR "Detected NCBI BLAST version $blastversion\n";
-			return;
-		}
-		&Error("Failed to detect '$blastmode'! Tried to call '$tmp'.");
-	}
-	elsif ($blastmode eq "blastp" || $blastmode eq "blastn" || $blastmode eq "tblastx") {
-		my $cmd = $blastpath."blastall";
-		my @blastv = qx($cmd);
-		foreach (@blastv) {
-			chomp;
-			if ($_ =~ /blastall.+?([^\s]+)/) {
-				$blastversion = $1;
-				if 	($blastmode eq "blastp") {$makedb = $blastpath."formatdb -p T -o F -i";}
-				elsif 	($blastmode eq "blastn") {$makedb = $blastpath."formatdb -p F -o F -i";}
-				elsif 	($blastmode eq "tblastx") {$makedb = $blastpath."formatdb -p F -o F -i";}
-				else	{die("This should not happen!");}
-
-				print STDERR "Detected NCBI BLAST version $blastversion\n";
-				return;
-			}
-		}
-		&Error("Failed to detect '$blastmode'! Tried to call 'blastall'.");
-	}
-
-	&Error("Blast mode '$blastmode' is not supported. Feel free to ask the author to add it.");
-}
-
-# Check plausibility of files
-sub check_files {
-	if (scalar(@files) < 2 && $step != 3)		{&print_usage; &Error("I need at least two files to compare something!");}
-	print STDERR "Checking input files\n";
-	foreach my $file (@files) {
-		if ($verbose) {print STDERR "Checking $file... ";}
-		&read_details($file,1);
-		if ($verbose) {print STDERR "ok\n";}
-	}
-}
-
-sub convertNCBI {
-	my $long_id = shift;
-	$long_id =~ s/\|$//g;
-	my @tmp = split(/\|/,$long_id);	# take the last column for NCBI format like patterns (e.g. gi|158333234|ref|YP_001514406.1|)
-	return pop(@tmp);
-}
-
-sub read_details {
-	my %ids;				# local test for duplicated IDs
-	my %genes;
-	my $file = shift;
-	my $test = 0;
-	if (defined($_[0])) {$test = 1;}	# if no ID Hash is give, we do not want to test but to fetch the gff data
-
-#	print STDERR "TEST: $test\n";
-	if (!-e $file)		{&Error("File '$file' not found!");}
-	open(FASTA,"<$file") || &Error("Could not open '$file': $!");
-	while (<FASTA>) {
-		if ($_ =~ />/) {
-			$gene_counter{$file}++;
-			chomp;
-			$_ =~ s/^>//;
-			$_ =~ s/\s.*//;
-			if ($test) {
-#				print STDERR "ID: $_\n";
-				if (defined($ids{$_}))	{&Error("Gene ID '$_' is defined at least twice in $file");}
-				$ids{$_} = $file;
-			}
-			if ($synteny) {
-				my $short_id = &convertNCBI($_);
-				$genes{$short_id} = 1;
-			}
-		}
-	}
-	close(FASTA);
-
-	unless ($synteny) {return;}
-
-	my %coordinates;
-	if ($verbose && $test) {print STDERR "$file\t".scalar(keys %genes)." genes\t";}
-	my $gff = &gff4fasta($file);
-	open(GFF,"<$gff") || &Error("Could not open '$gff': $!");
-	while (<GFF>) {
-		if ($_ =~ /^##FASTA/) {last;}	# deal with prokka gffs, thx 2 Ben Woodcroft
-		if ($_ =~ /^#/) {next;}
-		# e.g. NC_009925.1	RefSeq	CDS	9275	10096	.	-	0	ID=cds8;Name=YP_001514414.1;Parent=gene9;Dbxref=Genbank:YP_001514414.1,GeneID:5678848;gbkey=CDS;product=signal peptide peptidase SppA;protein_id=YP_001514414.1;transl_table=11
-		my @col = split(/\t+/,$_);
-		if ($col[2] ne "CDS") {next;}
-		if ($col[8] =~ /Name=([^;]+)/i && defined($genes{$1})) {
-			delete $genes{$1};
-#			if (!$test) {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";}	# store
-			if (!$test && $col[6] eq "+") {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";}	# store
-			if (!$test && $col[6] eq "-") {$coordinates{$1} = "$col[0]\t$col[6]\t$col[4]";}	# store
-		}
-		elsif ($col[8] =~ /ID=([^;]+)/i && defined($genes{$1})) {
-			delete $genes{$1};
-#			if (!$test) {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";}	# store
-			if (!$test && $col[6] eq "+") {$coordinates{$1} = "$col[0]\t$col[6]\t$col[3]";}	# store
-			if (!$test && $col[6] eq "-") {$coordinates{$1} = "$col[0]\t$col[6]\t$col[4]";}	# store
-		}
-	}
-	close(GFF);
-
-	if (scalar(keys %genes)) {
-		my @tmp = keys %genes;
-		&Error("No coordinate found for these gene(s): ".join(",",@tmp)."\nusing '$gff' and '$file'");
-	}
-
-	if (!$test) {return \%coordinates;}		# store
-}
-
-sub Error {
-	print STDERR "\n[ERROR] ".$_[0]."\n";
-	exit 0;
-}
-
-# Remove .fasta/.faa etc. and change it to .gff
-sub gff4fasta {
-	my $gff = shift;
-	$gff =~ s/\.[^.]+$/.gff/;
-	return $gff;
-}
-
-sub get_po_path {
-	my @tmppath = fileparse($0); # path to the C++-part of this program
-	return $tmppath[1];
-}
-
-sub edgeweight {
-	# 1e-10 = 0.15, 1e-20 = 0.3, 1e-40 = 0.6, 1e-66+ = 1.0
-	if ($_[0] == 0) {return 1;}
-	my $x = -1*&log10($_[0])/100*1.5;
-	if ($x > 1) {return 1;}
-	if ($x <= 0) {return 0.0001;}
-	return $x;
-}
-
-sub log10 {
-	return log($_[0])/log(10);
-}
-
-sub write_descriptions {
-	print STDERR "Writing sequence descriptions\n";
-	open DESC, '>', $desctable;
-	foreach my $file (@files) {
-		if ($verbose) {print STDERR "Extracting descriptions from '$file'\t(".$gene_counter{$file}." entries)\n";}
-		open FASTA, '<', $file;
-		while (<FASTA>) {
-			chomp;
-			if (m/^>(\S+)(\s+(.*))?$/) {
-				print DESC $1, "\t", ($3 || "unannotated sequence"), "\n";
-			}
-		}
-	}
-	print STDERR "[OUTPUT] -> written to $desctable\n";
-
-}
diff --git a/pipelines/LRSDAY.00.Long_Reads_Preprocessing.sh b/pipelines/LRSDAY.00.Long_Reads_Preprocessing.sh
index 926db3f..c0347d6 100755
--- a/pipelines/LRSDAY.00.Long_Reads_Preprocessing.sh
+++ b/pipelines/LRSDAY.00.Long_Reads_Preprocessing.sh
@@ -1,19 +1,19 @@
 #!/bin/bash
 set -e -o pipefail
 #######################################
-# load environment variables for LRSDAY
+# load environment variables
 source ./../../env.sh
 
 #######################################
 # set project-specific variables
 
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-reads="./../00.Long_Reads/$prefix.filtered_subreads.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format).
-reads_type="pacbio-raw" # The long reads data type: "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected".
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.
+reads="./../00.Long_Reads/nanopore_basecalled_fastq_files/$prefix/$prefix.basecalled_reads.Q5.pass.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format).
+reads_type="nanopore-raw" # The long reads data type: "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected".
 run_filtering="yes" # Whether to filter and downsample the reads: "yes" or "no". Default = "yes".
 genome_size="12500000" # The haploid genome size (in bp) of sequenced organism. Default = "12500000" (i.e. 12.5 Mb for the budding yeast S. cereviaie genome). This is used to calculate targeted sequencing coverage after read filtering (see below). 
 post_filtering_coverage="60" # Targeted sequencing coverage after read filtering and downsampling. Default = "60" (i.e. 60x coverage).
-threads=4 # The number of threads to use. Default = "1".
+threads=24 # The number of threads to use. Default = "4".
 
 #######################################
 # process the pipeline
@@ -27,7 +27,7 @@ then
 	echo ""
 	echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
 	echo ""
-	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --target_bases $filtlong_target_bases $prefix.porechop.fastq.gz | gzip > $prefix.filtlong.fastq.gz
+	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --window_q_weight 5 --target_bases $filtlong_target_bases $prefix.porechop.fastq.gz | gzip > $prefix.filtlong.fastq.gz
     fi
 else
     if [[ "$run_filtering" == "yes" ]]
@@ -36,7 +36,7 @@ else
 	echo ""
 	echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
 	echo ""
-	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --target_bases $filtlong_target_bases $reads | gzip > $prefix.filtlong.fastq.gz
+	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --window_q_weight 5 --target_bases $filtlong_target_bases $reads | gzip > $prefix.filtlong.fastq.gz
     fi
 fi
 
diff --git a/pipelines/LRSDAY.00.Nanopore_Reads_Basecalling.sh b/pipelines/LRSDAY.00.Nanopore_Reads_Basecalling.sh
new file mode 100755
index 0000000..4ce407f
--- /dev/null
+++ b/pipelines/LRSDAY.00.Nanopore_Reads_Basecalling.sh
@@ -0,0 +1,222 @@
+#!/bin/bash
+set -e -o pipefail
+#######################################
+# load environment variables
+source ./../../env.sh
+
+########################
+guppy_run_mode="cpu" # The running mode of Guppy basecalling: "gpu" or "cpu". Default = "cpu".
+if [[ $guppy_run_mode == "gpu" ]]
+then
+    # set CUDA environment for GPU
+    gpu_bin_path="/public/software/cuda-11.4/bin" # The path of CUDA's bin directory. Default = "/public/software/cuda-11.4/bin".
+    gpu_lib_path="/public/software/cuda-11.4/lib64" # The path of CUDA's lib directory. Default = "/public/software/cuda-11.4/lib64".
+    gpu_include_path="/public/software/cuda-11.4/include" # The path of CUDA's include directory. Default = "/public/software/cuda-11.4/include".
+fi
+##########################3
+export PATH=$gpu_bin_path:$PATH
+export LD_LIBRARY_PATH=$gpu_lib_path:$LD_LIBRARY_PATH
+export C_INCLUDE_PATH=$gpu_include_path:$C_INCLUDE_PATH
+export CPLUS_INCLUDE_PATH=$C_INCLUDE_PATH
+
+##k#####################################
+# set project-specific variables
+
+sample_id="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.              
+raw_fast5_dir="./nanopore_raw_fast5_files/$sample_id" # The directory containing the raw nanopore reads before basecalling. Default = "./raw_fast5/$sample_id".
+flowcell_version="FLO-MIN106" # The flowcell version of the nanopore run. Default = "FLO-MIN106".
+sequencing_kit_version="SQK-LSK108" # The sequencing kit version of the nanopore run. Default = "SQK-LSK109". 
+barcode_kit_version="EXP-NBD104" # The barcode kit version of the nanopore run if barcoding has been introduced during library preparation. Default = "EXP-NBD104". For the testing example, we have not applied barcoding. So this information will not be used when we set run_demultiplexing="no" below.
+
+run_basecalling="yes" # Whether to perform basecalling: "yes" or "no". Default = "yes". 
+run_demultiplexing="no" # Whether to perform demultiplexing: "yes" or "no". Default = "no". For the testing example, we have not applied barcoding. So no need to run this step. 
+run_nanoplotting="yes" # Whether to perform nanoplotting: "yes" or "no". Default = "yes". 
+
+threads=16 # The number of CPU threads to use. Default = 16.
+debug="no" # Whether to keep intermediate files for debugging: "yes" or "no". Default = "no".
+
+#############################
+# Normally no need to change the following parameter settings.
+basecalled_fast5_dir="./nanopore_basecalled_fast5_files/$sample_id" # The directory containing the basecalled fast5 reads. This directory will be automatically generated when running basecalling.
+basecalled_fastq_dir="./nanopore_basecalled_fastq_files/$sample_id" # The directory containing the basecalled fastq reads. This directory will be automatically generated when running basecalling.
+basecalled_qc_dir="./nanopore_basecalled_qc_files/$sample_id" # The directory containing nanoplot QC outputs. This directory will be automatically generated when running nanoplot.
+trim_strategy="dna" # Trimming strategy to apply: 'dna' or 'rna' or 'none' (to disable trimming). Default = "rna".
+gpu_device="auto" # Which GPU device to use. Default = "auto". 
+qual=5 # read quality filter for guppy basecalling. Default = 5.
+num_callers_in_cpu_mode=$threads # The number of callers for guppy basecalling in the CPU mode. Default = "$threads".
+num_callers_in_gpu_mode=$threads # The number of callers for guppy basecalling in the GPU mode. Default = "1".
+gpu_runners_per_device=1 # The number of GPU runners per device for guppy basecalling in the GPU mode. Default = "1".
+threads_per_caller=1 # The number of threads per caller for guppy basecalling. Default = "1".
+demultiplexing_threads=$threads # The number of threads to use for guppy demultiplexing. Default = "$threads".
+demultiplexed_fastq_dir="$basecalled_fastq_dir/demultiplexed_fastq" # The directory containing the demultiplexed basecalled nanopore reads. This directory will be automatically generated when running demultiplexing. 
+
+##############################
+
+wkdir=$(pwd)
+if [[ "$run_demultiplexing" == "yes" && "barcode_kit_version" == "" ]]
+then
+    echo "The variable run_demultiplexing has been set to \"yes\" but the barcode_kit_version variable has not been specified!"
+    echo "Please specified barcode_kit_version if you want to run demultiplexing."
+    exit;
+fi
+
+
+if [[ "$run_basecalling" == "yes" ]]
+then
+    echo "Check if $basecalled_fast5_dir is empty for running basecalling."
+    if [[ -d $basecalled_fast5_dir && "$(ls $basecalled_fast5_dir)" ]]
+    then
+	echo "Warning! The basecalled fast5 directory $basecalled_fast5_dir exists and it is not empty! Please empty its content if you want to run basecalling."
+	echo "Exit!!!"
+	exit
+    elif [[ -d $basecalled_fastq_dir && "$(ls $basecalled_fastq_dir)" ]]
+    then
+        echo "Warning! The basecalled fastq directory $basecalled_fastq_dir exists and it is not empty! Please empty its content if you want to run basecalling."
+        echo "Exit!!!"
+        exit
+    else
+	echo "Check passed!"
+	echo "Running basecalling .."
+	if [[ ! -d $basecalled_fast5_dir ]]
+	then
+	    mkdir -p $basecalled_fast5_dir
+	fi
+	if [[ ! -d $basecalled_fastq_dir ]]
+	then
+	    mkdir -p $basecalled_fastq_dir
+	fi
+
+	if [[ "$guppy_run_mode" == "gpu" ]]
+	then
+	    $guppy_gpu_dir/guppy_basecaller \
+		--flowcell $flowcell_version \
+		--kit $sequencing_kit_version \
+		--recursive \
+		--trim_strategy $trim_strategy \
+		--input_path $raw_fast5_dir \
+		--save_path $basecalled_fast5_dir \
+		--fast5_out \
+		--min_qscore $qual \
+		--device $gpu_device \
+		--num_callers $num_callers_in_gpu_mode \
+		--gpu_runners_per_device $gpu_runners_per_device \
+		--compress_fastq	    
+	else
+	    $guppy_cpu_dir/guppy_basecaller \
+		--flowcell $flowcell_version \
+		--kit $sequencing_kit_version \
+		--recursive \
+		--trim_strategy $trim_strategy \
+		--input_path $raw_fast5_dir \
+		--save_path $basecalled_fast5_dir \
+		--fast5_out \
+		--min_qscore $qual \
+		--num_callers $num_callers_in_cpu_mode \
+		--cpu_threads_per_caller $threads_per_caller \
+		--compress_fastq	    
+	fi
+	cat $basecalled_fast5_dir/pass/*.fastq.gz  > $basecalled_fastq_dir/$sample_id.basecalled_reads.Q${qual}.pass.fastq.gz
+	# cat $basecalled_fast5_dir/fail/*.fastq.gz  > $basecalled_fastq_dir/$sample_id.basecalled_reads.Q${qual}.fail.fastq.gz
+	if [[ $debug != "yes" ]]
+	then
+	    rm -r $basecalled_fast5_dir/pass
+	    rm -r $basecalled_fast5_dir/fail
+	fi
+    fi
+fi
+
+cd $wkdir
+if [[ "$run_demultiplexing" == "yes" ]]
+then
+    echo "Check if $basecalled_fastq_dir has basecalled reads for running demultiplexing."
+    if [[ "$(ls $basecalled_fastq_dir)" ]]
+    then
+	echo "Running demultiplexing."
+	if [[ "$guppy_run_mode" == "gpu" ]]
+	then
+	    $guppy_gpu_dir/guppy_barcoder \
+		--barcode_kits $barcode_kit_version \
+		--recursive \
+		--input_path $basecalled_fastq_dir \
+		--save_path $demultiplexed_fastq_dir \
+		--worker_threads $demultiplexing_threads
+	else
+	    $guppy_cpu_dir/guppy_barcoder \
+		--barcode_kits $barcode_kit_version \
+		--recursive \
+		--input_path $basecalled_fastq_dir \
+		--save_path $demultiplexed_fastq_dir \
+		--worker_threads $demultiplexing_threads
+	fi
+
+	cd $demultiplexed_fastq_dir
+	for b in barcode*
+	do 
+	    echo "for demultiplexing: barcode=$b"
+	    cat ./$b/*.fastq |gzip -c > $sample_id.basecalled_reads.Q${qual}.pass.$b.fastq.gz
+	done
+	cat ./unclassified/*.fastq |gzip -c > $sample_id.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz
+    else
+	echo "There is no reads in $basecalled_fastq_dir!"
+	echo "Please put the basecalled reads in $basecalled_fastq_dir for demultiplexing!"
+	echo "Exit!!!"
+	exit
+    fi
+fi
+
+set +oe pipefail 
+
+cd $wkdir
+if [[ "$run_nanoplotting" == "yes" ]]
+then
+    echo "Check if $basecalled_fastq_dir has basecalled reads for running nanoplotting."
+    if [[ "$(ls $basecalled_fastq_dir)" ]]
+    then
+	echo "Running nanoplotting."
+	mkdir -p $basecalled_qc_dir
+	fastq_input="$basecalled_fastq_dir/$sample_id.basecalled_reads.Q${qual}.pass.fastq.gz"
+	$nanoplot_dir/NanoPlot \
+	    --threads $threads \
+	    --fastq $fastq_input \
+	    --N50 \
+	    -o "$basecalled_qc_dir/${sample_id}_basecalled_reads_Q${qual}_pass_NanoPlot_out"
+    fi
+    if [[ "$run_demultiplexing" == "yes" ]]
+    then
+	cd $demultiplexed_fastq_dir
+	for b in barcode*
+	do
+	    echo "for nanoplotting: barcode=$b"
+	    fastq_input="./$sample_id.basecalled_reads.Q${qual}.pass.$b.fastq.gz"
+	    $nanoplot_dir/NanoPlot \
+		--threads $threads \
+		--fastq $fastq_input \
+		--N50 \
+		-o "./../../../$basecalled_qc_dir/${sample_id}_basecalled_reads_Q${qual}_pass_${b}_NanoPlot_out"
+	done
+	echo "for nanoplotting: unclassified"
+	fastq_input="./$sample_id.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz"
+	$nanoplot_dir/NanoPlot \
+            --threads $threads \
+            --fastq $fastq_input \
+            --N50 \
+            -o "./../../../$basecalled_qc_dir/${sample_id}_basecalled_reads_Q${qual}_pass_unclassified_NanoPlot_out" 
+    fi
+fi
+
+
+
+############################
+# checking bash exit status
+if [[ $? -eq 0 ]]
+then
+    echo "" 
+    echo "##########################################################################"
+    echo "" 
+    echo "LRSDAY message: This bash script has been successfully processed! :)"
+    echo ""
+    echo "##########################################################################"
+    echo ""
+    exit 0
+fi
+############################
diff --git a/pipelines/LRSDAY.00.Nanopore_Reads_Basecalling_and_Demultiplexing.sh b/pipelines/LRSDAY.00.Nanopore_Reads_Basecalling_and_Demultiplexing.sh
deleted file mode 100755
index 6c1c640..0000000
--- a/pipelines/LRSDAY.00.Nanopore_Reads_Basecalling_and_Demultiplexing.sh
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/bin/bash
-set -e -o pipefail
-#######################################
-# load environment variables for LRSDAY
-source ./../../env.sh
-
-#######################################
-# set project-specific variables
-project_name="Project_Example" # LRSDAY Project name. Default = "Project_Example".
-run_basecalling="yes" # Whether to perform basecalling: "yes" or "no". Default = "yes". 
-run_demultiplexing="yes" # Whether to perform demultiplexing: "yes" or "no". Default = "yes". 
-run_nanoplotting="yes" # Whether to perform nanoplotting: "yes" or "no". Default = "yes". 
-
-flowcell_id="FAKXXXXX" # The flowcell ID of the nanopore run. Default = "FAKXXXXX".
-flowcell_version="FLO-MIN106" # The flowcell version of the nanopore run. Default = "FLO-MIN106".
-sequencing_kit_version="SQK-LSK108" # The sequencing kit version of the nanopore run. Default = "SQK-LSK108".
-barcode_kit_version="EXP-NBD103" # The barcode kit version of the nanopore run. Default = "EXP-NBD103".
-
-raw_reads_directory="$LRSDAY_HOME/$project_name/00.Long_Reads/nanopore_raw_fast5_files" # The directory containing the raw nanopore reads before basecalling
-basecalling_output_directory="$LRSDAY_HOME/$project_name/00.Long_Reads/nanopore_basecalled_fast5_files" # The directory containing the basecalled nanopore reads. This directory will be automatically generated when running basecalling.
-threads=8 # The number of threads to use. Default = 8.
-
-#############################
-# normally no need to change the following
-qual=5 # read quality filter for guppy basecalling
-num_callers=$threads # num_callers for guppy
-threads_per_caller=1 # threads_per_caller for guppy
-demultiplexing_threads=$threads # threads to use for demultiplexing
-demultiplexing_output_directory="$LRSDAY_HOME/$project_name/00.Long_Reads/nanopore_demultiplexed_fastq_files" # The directory containing the demultiplexed basecalled nanopore reads. This directory will be automatically generated when running demultiplexing. 
-
-if [[ "$run_basecalling" == "yes" ]]
-then
-    echo "Check if $basecalling_output_directory is empty for running basecalling."
-    if [[ "$(ls $basecalling_output_directory)" ]]
-    then
-	echo "Warning! The basecalling directory is not empty! Please empty its content if you want to run basecalling."
-	echo "Exit!!!"
-	exit
-    else
-	echo "Running basecalling."
-	$guppy_dir/guppy_basecaller \
-	    --flowcell $flowcell_version \
-	    --kit $sequencing_kit_version \
-	    --recursive \
-	    --input_path $raw_reads_directory \
-	    --save_path $basecalling_output_directory \
-	    --fast5_out \
-	    --qscore_filtering \
-	    --min_qscore $qual \
-	    --num_callers $num_callers \
-	    --cpu_threads_per_caller $threads_per_caller 
-	cd $basecalling_output_directory
-	cat ./pass/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.pass.fastq.gz
-	cat ./fail/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.fail.fastq.gz
-    fi
-fi
-
-if [[ "$run_demultiplexing" == "yes" ]]
-then
-    echo "Check if $basecalling_output_directory/pass has basecalled reads for running demultiplexing."
-    if [[ "$(ls $basecalling_output_directory/pass)" ]]
-    then
-	echo "Running demultiplexing."
-	$guppy_dir/guppy_barcoder \
-	    --barcode_kit $barcode_kit_version \
-	    --recursive \
-	    --input_path $basecalling_output_directory/pass \
-	    --save_path $demultiplexing_output_directory \
-	    --worker_threads $demultiplexing_threads
-	
-	cd $demultiplexing_output_directory
-	for b in barcode*
-	do 
-	    echo "for demultiplexing: barcode=$b"
-	    cat ./$b/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.pass.$b.fastq.gz
-	done
-	cat ./unclassified/*.fastq |gzip -c > $project_name.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz
-    else
-	echo "There is no reads in $basecalling_output_directory/pass!"
-	echo "Please put the basecalled reads in $basecalling_output_directory/pass for demultiplexing!"
-	echo "Exit!!!"
-	exit
-    fi
-fi
-
-set +oe pipefail 
-
-if [[ "$run_nanoplotting" == "yes" ]]
-then
-    echo "Check if $basecalling_output_directory/pass has basecalled reads for running nanoplotting."
-    if [[ "$(ls $basecalling_output_directory/pass)" ]]
-    then
-	echo "Running nanoplotting."
-	cd $basecalling_output_directory
-	fastq_input="$project_name.basecalled_reads.Q${qual}.pass.fastq.gz"
-	source $nanoplot_dir/activate
-	$nanoplot_dir/NanoPlot \
-	    --threads $threads \
-	    --fastq $fastq_input \
-	    --N50 \
-	    -o "${project_name}_Q${qual}_pass_NanoPlot_out"
-    fi
-    if [[ "$run_demultiplexing" == "yes" ]]
-    then
-	cd $demultiplexing_output_directory
-	for b in barcode*
-	do
-	    echo "for nanoplotting: barcode=$b"
-	    fastq_input="$project_name.basecalled_reads.Q${qual}.pass.$b.fastq.gz"
-	    source $nanoplot_dir/activate
-	    $nanoplot_dir/NanoPlot \
-		--threads $threads \
-		--fastq $fastq_input \
-		--N50 \
-		-o "${project_name}_Q${qual}_pass_${b}_NanoPlot_out"
-	done
-	echo "for nanoplotting: unclassified"
-	fastq_input="$project_name.basecalled_reads.Q${qual}.pass.unclassified.fastq.gz"
-	$nanoplot_dir/NanoPlot \
-            --threads $threads \
-            --fastq $fastq_input \
-            --N50 \
-            -o "${project_name}_Q${qual}_pass_unclassified_NanoPlot_out" 
-    fi
-fi
-
-
-
-############################
-# checking bash exit status
-if [[ $? -eq 0 ]]
-then
-    echo "" 
-    echo "LRSDAY message: This bash script has been successfully processed! :)"
-    echo ""
-    echo ""
-    exit 0
-fi
-############################
diff --git a/pipelines/LRSDAY.00.Retrieve_Sample_Illumina_Reads.sh b/pipelines/LRSDAY.00.Retrieve_Sample_Illumina_Reads.sh
deleted file mode 100755
index fe91af9..0000000
--- a/pipelines/LRSDAY.00.Retrieve_Sample_Illumina_Reads.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-set -e -o pipefail
-
-#######################################
-# load environment variables for LRSDAY
-source ./../../env.sh
-
-#######################################
-# set project-specific variables
-sra_id="SRR4074258" # the SRA Run ID for the reads that you want to retrieve, e.g. "SRR4074258 for S. cerevisiae strain SK1 generated by Yue et al. (2017) Nature Genetics"
-
-#######################################
-# process the pipeline
-echo "retrieve reads by the SRR_id: $sra_id ..."
-$sra_dir/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+$sn[_$rn]/$ri' \
-      --gzip --split-files -skip-technical --dumpbase --read-filter pass --clip $sra_id
-
-# if the fastq-dump doesn't work due to connection problems, please run the following two wget commands to directly download the reads.
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR407/008/SRR4074258/SRR4074258_1.fastq.gz 
-# ln -s SRR4074258_1.fastq.gz SRR4074258_pass_1.fastq.gz
-#  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR407/008/SRR4074258/SRR4074258_2.fastq.gz
-# ln -s SRR4074258_2.fastq.gz SRR4074258_pass_2.fastq.gz
-
-############################
-# checking bash exit status
-if [[ $? -eq 0 ]]
-then
-    echo ""
-    echo "LRSDAY message: This bash script has been successfully processed! :)"
-    echo ""
-    echo ""
-    exit 0
-fi
-############################
diff --git a/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh b/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh
index e471900..3dbdf41 100755
--- a/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh
+++ b/pipelines/LRSDAY.01.Long-read-based_Genome_Assembly.sh
@@ -1,19 +1,20 @@
 #!/bin/bash
 set -e -o pipefail
 ##########################################
-# load environment variables for LRSDAY
+# load environment variables
 source ./../../env.sh
 PATH=$gnuplot_dir:$PATH
 
 ###########################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 long_reads="./../00.Long_Reads/$prefix.filtlong.fastq.gz" # The file path of the long reads file (in fastq or fastq.gz format).
-long_reads_type="pacbio-raw" # The long reads data type. Use "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected". Default = "pacbio-raw" for the testing example
+long_reads_type="nanopore-raw" # The long reads data type. Use "pacbio-raw" or "pacbio-corrected" or "pacbio-hifi" or "nanopore-raw" or "nanopore-corrected" or "nanopore-hq" (QV20 reads). Default = "nanopore-raw" for the testing example.
 genome_size="12.5m" # The estimated genome size with the format of <number>[g|m|k], e.g. 12.5m for 12.5 Mb. Default = "12.5m".
-assembler="canu" # The long-read assembler to use. Use "canu" or "flye" or "wtdbg2" or "smartdenovo" or "ra" or "shasta" or "canu-flye" or "canu-wtdbg2" or "canu-smartdenovo" or "canu-ra" or "canu-shasta". For "canu-flye", "canu-wtdbg2", "canu-smartdenovo", "canu-ra", or "canu-shasta", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/wtdbg2/smartdenovo/ra/shasta is used to assemble the genome. Default = "canu".
-customized_canu_parameters="" # When assembler="canu" or "canu-flye", "canu-wtdbg2", "canu-smartdenovo", "canu-ra", or "canu-shasta", users can set customized Canu assembly parameters here when needed. If users want to keep Canu's default parameters or when other assembler is used, simply leave it empty like customized_canu_parameters="". For example users could set customized_canu_parameters="correctedErrorRate=0.04" for high coverage (>60X) PacBio data and customized_canu_parameters="overlapper=mhap;utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. When assembling genomes with high heterozygosity, you can could set customized_canu_parameters="corOutCoverage=200;batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50" to avoid collasping haplotypes. As shown in these examples, more than one customized parameters can be set here as long as they are separeted by a semicolon and contained in a pair of double quotes (e.g. customized_canu_parameters="option1=XXX;option2=YYY;option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "" for the testing example.
-threads=4 # The number of threads to use. Default = 4.
+assembler="canu" # The long-read assembler to use. Use "canu" or "flye" or "wtdbg2" or "smartdenovo" or "shasta" or "canu-flye" or "canu-wtdbg2" or "canu-smartdenovo" or "canu-shasta". For "canu-flye", "canu-wtdbg2", "canu-smartdenovo", or "canu-shasta", the assembler canu is used first to generate error-corrected reads from the raw reads and then the assembler flye/wtdbg2/smartdenovo/shasta is used to assemble the genome. Default = "canu".
+customized_canu_parameters="" # When assembler="canu" or "canu-flye", "canu-wtdbg2", "canu-smartdenovo", or "canu-shasta", users can set customized Canu assembly parameters here when needed. If users want to keep Canu's default parameters or when other assembler is used, simply leave it empty like customized_canu_parameters="". For example users could set customized_canu_parameters="correctedErrorRate=0.04" for high coverage (>60X) PacBio data and customized_canu_parameters="overlapper=mhap;utgReAlign=true" for high coverage (>60X) Nanopore data to improve the assembly speed. When assembling genomes with high heterozygosity, you can could set customized_canu_parameters="corOutCoverage=200;batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50" to avoid collasping haplotypes. As shown in these examples, more than one customized parameters can be set here as long as they are separeted by a semicolon and contained in a pair of double quotes (e.g. customized_canu_parameters="option1=XXX;option2=YYY;option3=ZZZ"). Please consult Canu's manual "http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak" for advanced customization settings. Default = "" for the testing example.
+threads=8 # The number of threads to use. Default = 8.
 vcf="yes" # Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Otherwise use "no". Default = "yes".
 dotplot="yes" # Use "yes" if prefer to plot genome-wide dotplot based on the comparison with the reference genome below. Otherwise use "no". Default = "yes".
 
@@ -23,11 +24,11 @@ then
     ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The file path of the raw reference genome. This is only needed when the option "dotplot" or "vcf" has been set as "yes".
 else
     parent1_tag="Parent1" # The name tag for parent1. Default = "Parent1".
-    parent1_short_reads="./../00.Short_Reads/$parent1_tag.illumina.fastq.gz" # The relative path to Illumina reads of parent1 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
+    parent1_short_reads="./../00.Short_Reads/$parent1_tag.fq.gz" # The relative path to Illumina reads of parent1 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
     parent1_ref_genome_raw="./../00.Reference_Genome/$parent1_tag.genome.raw.fa" # The relative path to the reference genome of parent1 of the hybrid. This is only needed when the options "canu_triobinning_mode" and "dotplot" (or "canu_triobinning_mode" and "vcf") have been set as "yes". When not available, it can be set to a general reference genome of the organism. 
 
     parent2_tag="Parent2" # The name tag for parent2. Default = "Parent2".
-    parent2_short_reads="./../00.Short_Reads/$parent2_tag.illumina.fastq.gz" # The relative path to Illumina reads of parent2 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
+    parent2_short_reads="./../00.Short_Reads/$parent2_tag.fq.gz" # The relative path to Illumina reads of parent2 of the long-read sequenced hybrid. This is only needed when the "canu_triobinning_mode" option has been set as "yes". You can combine the R1 and R2 reads into a single fastq file here.
     parent2_ref_genome_raw="./../00.Reference_Genome/$parent2_tag.genome.raw.fa" # The relative path to the reference genome of parent1 of the hybrid. This is only needed when the options "canu_triobinning_mode" and "dotplot" (or "canu_triobinning_mode" and "vcf") have been set as "yes". When not available, it can be set to a general reference genome of the organism. 
 fi
 
@@ -155,21 +156,33 @@ then
     fi
 elif [[ "$assembler" == "flye" ]]
 then
-    if [[ "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-raw" ]]
+    then
+	long_reads_type="pacbio-raw"
+    elif [[ "$long_reads_type" == "pacbio-corrected" ]]
     then
 	long_reads_type="pacbio-corr"
+    elif [[ "$long_reads_type" == "pacbio-hifi" ]]
+    then
+	long_reads_type="pacbio-hifi"
     elif [[ "$long_reads_type" == "nanopore-raw" ]]
     then
         long_reads_type="nano-raw"
     elif [[ "$long_reads_type" == "nanopore-corrected" ]]
     then
         long_reads_type="nano-corr"
+    elif [[ "$long_reads_type" == "nanopore-hq" ]]
+    then
+        long_reads_type="nano-hq"
     fi
+    source $miniconda3_dir/activate $build_dir/flye_conda_env
     $flye_dir/flye -o $out_dir \
 	-t $threads \
 	-g $genome_size \
+	--keep-haplotypes \
 	--${long_reads_type} $long_reads \
 	-i 2
+    source $miniconda3_dir/deactivate
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/assembly.fasta -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "wtdbg2" ]]
 then
@@ -188,33 +201,22 @@ then
     make -f $prefix.mak
     cd ..
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.dmo.cns  -o $prefix.assembly.$assembler.fa
-elif [[ "$assembler" == "ra" ]]
-then
-    mkdir $out_dir
-    cd $out_dir
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
-    then
-        long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
-    then
-        long_reads_type="ont"
-    fi
-    $ra_dir/ra -x $long_reads_type -t $threads ./../$long_reads > $prefix.assembly.$assembler.fa
-    cd ..
-    perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/$prefix.assembly.$assembler.fa -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "shasta" ]]
 then
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-hifi" ]] 
     then
-        long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
+        long_reads_type="HiFi-Oct2021"
+    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "pacbio-raw" ]]
     then
-        long_reads_type="ont"
+        long_reads_type="Nanopore-Dec2019"
+    elif [[ "$long_reads_type" == "nanopore-corrected" || "$long_reads_type" == "pacbio-corrected" || "$long_reads_type" == "nanopore-hq" ]]
+    then
+	long_reads_type="R10-Slow-Nov2022"
     fi
-    perl $LRSDAY_HOME/scripts/fastq2fasta.pl -i $long_reads -o $prefix.long_reads.fasta
-    $shasta_dir/shasta --input $prefix.long_reads.fasta  --output $out_dir
+    perl $LRSDAY_HOME/scripts/fastq2fasta.pl -i $long_reads -o $prefix.long_reads.fa
+    $shasta_dir/shasta --input $prefix.long_reads.fa --assemblyDirectory $out_dir --config $long_reads_type
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/Assembly.fasta -o $prefix.assembly.$assembler.fa
-    rm $prefix.long_reads.fasta
+    rm $prefix.long_reads.fa
 elif [[ "$assembler" == "canu-flye" ]]
 then
     OLDIFS=$IFS;
@@ -230,18 +232,21 @@ then
 	gnuplot=$gnuplot_dir/gnuplot \
 	-${long_reads_type} $long_reads
     mv $prefix.customized_canu_parameters.spec ./$out_dir/canu
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" || "$long_reads_type" == "pacbio-hifi"  ]]
     then
 	long_reads_type="pacbio-corr"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
+    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" || "$long_reads_type" == "nanopore-hq" ]]
     then
         long_reads_type="nano-corr"
     fi
+    source $miniconda3_dir/activate $build_dir/flye_conda_env
     $flye_dir/flye -o $out_dir/flye \
 	-t $threads \
 	-g $genome_size \
+	--keep-haplotypes \
 	--${long_reads_type} $out_dir/canu/$prefix.correctedReads.fasta.gz \
 	-i 2
+    source $miniconda3_dir/deactivate
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/flye/assembly.fasta -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "canu-wtdbg2" ]]
 then
@@ -286,34 +291,6 @@ then
     make -f $prefix.mak
     cd ../..
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/smartdenovo/$prefix.dmo.cns  -o $prefix.assembly.$assembler.fa
-elif [[ "$assembler" == "canu-ra" ]]
-then
-    OLDIFS=$IFS;
-    IFS=";"
-    customized_canu_parameters_array=($customized_canu_parameters)
-    IFS=$OLDIFS;
-    printf "%s\n" "${customized_canu_parameters_array[@]}" > $prefix.customized_canu_parameters.spec
-
-    $canu_dir/canu -correct -p $prefix -d $out_dir/canu \
-	-s $prefix.customized_canu_parameters.spec \
-        useGrid=false \
-        maxThreads=$threads \
-        genomeSize=$genome_size \
-        gnuplot=$gnuplot_dir/gnuplot \
-        -${long_reads_type} $long_reads 
-    mv $prefix.customized_canu_parameters.spec ./$out_dir/canu
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
-    then
-	long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
-    then
-        long_reads_type="ont"
-    fi
-    mkdir -p $out_dir/ra
-    cd $out_dir/ra
-    $ra_dir/ra -x $long_reads_type -t $threads ./../canu/$prefix.correctedReads.fasta.gz > $prefix.assembly.$assembler.fa
-    cd ../..
-    perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/ra/$prefix.assembly.$assembler.fa -o $prefix.assembly.$assembler.fa
 elif [[ "$assembler" == "canu-shasta" ]]
 then
     OLDIFS=$IFS;
@@ -330,15 +307,14 @@ then
         gnuplot=$gnuplot_dir/gnuplot \
         -${long_reads_type} $long_reads 
     mv $prefix.customized_canu_parameters.spec ./$out_dir/canu
-    if [[ "$long_reads_type" == "pacbio-raw" || "$long_reads_type" == "pacbio-corrected" ]]
+    if [[ "$long_reads_type" == "pacbio-hifi" ]]
     then
-	long_reads_type="pb"
-    elif [[ "$long_reads_type" == "nanopore-raw" || "$long_reads_type" == "nanopore-corrected" ]]
-    then
-        long_reads_type="ont"
+	long_reads_type="HiFi-Oct2021"
+    else
+	long_reads_type="R10-Slow-Nov2022"
     fi
     gunzip < $out_dir/canu/$prefix.correctedReads.fasta.gz > $out_dir/$prefix.correctedReads.fasta
-    $shasta_dir/shasta --input $out_dir/$prefix.correctedReads.fasta  --output $out_dir/shasta
+    $shasta_dir/shasta --input $out_dir/$prefix.correctedReads.fasta --assemblyDirectory $out_dir/shasta --config $long_reads_type
     rm $out_dir/$prefix.correctedReads.fasta
     perl $LRSDAY_HOME/scripts/simplify_seq_name.pl -i $out_dir/shasta/Assembly.fasta -o $prefix.assembly.$assembler.fa
 fi
@@ -441,9 +417,11 @@ fi
 # checking bash exit status
 if [[ $? -eq 0 ]]
 then
+    echo "#########################################################"
     echo ""
     echo "LRSDAY message: This bash script has been successfully processed! :)"
     echo ""
+    echo "#########################################################"
     echo ""
     exit 0
 fi
diff --git a/pipelines/LRSDAY.02.Long-read-based_Assembly_Polishing.sh b/pipelines/LRSDAY.02.Long-read-based_Assembly_Polishing.sh
index 49dece7..ac99721 100755
--- a/pipelines/LRSDAY.02.Long-read-based_Assembly_Polishing.sh
+++ b/pipelines/LRSDAY.02.Long-read-based_Assembly_Polishing.sh
@@ -7,17 +7,18 @@ source ./../../env.sh
 ###########################################
 # set project-specific variables
 
-prefix="SK1" # The file name prefix for the processing sample. Please avoid the character '.' in prefix. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 input_assembly="./../01.Long-read-based_Genome_Assembly/$prefix.assembly.raw.fa" # The file path of the input raw long-read-based assembly for polishing.
 long_reads_in_fastq="./../00.Long_Reads/$prefix.filtlong.fastq.gz" # The file path of the long-read fastq file. 
 
-polisher="quiver" # The long-read-based polisher to use: "quiver" (for PacBio RSII reads), "arrow" (for PacBio Sequel reads), "nanopolish" (for raw nanopore fast5 reads), "racon-medaka" (for basecalled nanopore fastq reads), or "marginpolish" (for basecalled nanopore fastq reads). Default = "quiver" for the testing example.
+polisher="racon-medaka" # The long-read-based polisher to use: "none" for (PacBio HiFi Reads), "arrow" (for PacBio Sequel reads), "quiver" (for PacBio RSII reads), "nanopolish" (for raw nanopore fast5 reads), "racon-medaka" (for basecalled nanopore fastq reads), or "marginpolish" (for basecalled nanopore fastq reads). Default = "racon-medaka" for the testing example.
 pacbio_bam_fofn_file="./../00.Long_Reads/pacbio_fofn_files/$prefix.merged.bam.fofn" # The file path to the fofn file containing the absolute path to the PacBio bam files. BAM file is the native output format for PacBio Sequel platform but this is not the case for the RSII platform. For RSII data, the bax2bam file conversion is needed. This can be done by running the LRSDAY.00.Retrieve_Sample_PacBio_Reads.sh script in the 00.Long_Reads directory. This is only needed when polisher="quiver" or "arrow".
 nanopore_basecalled_fast5_files="./../00.Long_Reads/nanopore_basecalled_fast5_files" # The file path to the directory containing the basecalled Oxford Nanopore FAST5 files. This option is only needed when polisher="nanopolish".
-guppy_basecalling_model="r941_flip235" # The guppy basecalling model to use for medaka. Supported values include: "r941_min_fast" for guppy (version_number >= 3.0.3) in fast mode, "r941_min_high" for guppy (version_number >= 3.0.3) in high accuracy mode, "r941_flip235" for guppy (2.3.5 <= version_number <3.0.3), "r941_flip213" for guppy (2.1.3 <= version_number <2.3.5), and "r941_trans" for albacore or guppy (version_number < 2.1.3). This option is only needed when polisher="racon-medaka".
-threads=1  # The number of threads to use. Default = "1".
+guppy_basecalling_model="r941_min_hac_g507" # The guppy basecalling model to use for medaka. Some supported values include: "r941_min_fast_g507" for guppy in fast mode for MinION R9.4.1 flowcell, "r941_min_hac_g507" for guppy in high accuracy mode for MinION R9.4.1 flowcell, "r941_prom_fast_g507" for guppy in fast mode for PromethION R9.4.1, "r941_prom_hac_g507" for guppy in high accuracy mode for PromethION R9.4.1. See here (https://github.com/nanoporetech/medaka/tree/master/medaka/data) for a complete list of supported models. This option is only needed when polisher="racon-medaka". Default = "r941_min_hac_g507".
+threads=8  # The number of threads to use. Default = "8".
 ploidy=1 # The ploidy status of the sequenced genome. Use "1" for haploid genome and "2" for diploid genome. Currently not supported when "polisher="racon-medaka". Default = "1" for the testing example.
-rounds_of_successive_polishing=1 # The number of total rounds of long-read-based assembly polishing. Default = "1" for the testing example.
+rounds_of_successive_polishing=3 # The number of total rounds of long-read-based assembly polishing. Default = "3".
 debug="no" # Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no"
 
 ###########################################
@@ -27,7 +28,10 @@ cp $input_assembly $prefix.assembly.tmp.fa
 
 mkdir tmp
 
-if [[ $polisher == "quiver" || $polisher == "arrow" ]]
+if [[ $polisher == "none" ]]
+then
+    cp $prefix.assembly.tmp.fa $prefix.assembly.long_read_polished.fa
+elif [[ $polisher == "quiver" || $polisher == "arrow" ]]
 then
     # perform correction using PacBio's pbalign-arrow pipeline
     source $miniconda2_dir/activate $build_dir/conda_pacbio_env
@@ -77,9 +81,9 @@ then
     $nanopolish_dir/nanopolish index -d $nanopore_basecalled_fast5_files $long_reads_in_fastq
     for i in $(seq 1 1 $rounds_of_successive_polishing)
     do
-	java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary -REFERENCE $prefix.assembly.tmp.fa -OUTPUT $prefix.assembly.tmp.dict
+	$java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary -REFERENCE $prefix.assembly.tmp.fa -OUTPUT $prefix.assembly.tmp.dict
 	$minimap2_dir/minimap2 -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
-	java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000  
+	$java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000  
 	$samtools_dir/samtools index $prefix.minimap2.round_${i}.bam
 	rm $prefix.minimap2.round_${i}.sam
 	python3 $nanopolish_dir/scripts/nanopolish_makerange.py $prefix.assembly.tmp.fa | $parallel_dir/parallel --results ${prefix}_nanopolish_round_${i}_results -P 1 \
@@ -94,7 +98,7 @@ then
     rm $prefix.assembly.tmp.fa
 elif [[ $polisher == "racon-medaka" ]]
 then
-    source $miniconda2_dir/activate $conda_medaka_dir/../../conda_medaka_env
+    source $miniconda3_dir/activate $medaka_dir/../../medaka_conda_env
     for i in $(seq 1 1 $rounds_of_successive_polishing)
     do
 	$minimap2_dir/minimap2 -t $threads -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
@@ -108,9 +112,9 @@ then
     done
     for i in $(seq 1 1 $rounds_of_successive_polishing)
     do
-	$conda_medaka_dir/medaka_consensus -i $long_reads_in_fastq -d $prefix.assembly.tmp.fa -o ${prefix}_medaka_out_round_${i} -t $threads -m $guppy_basecalling_model
+	$medaka_dir/medaka_consensus -i $long_reads_in_fastq -d $prefix.assembly.tmp.fa -o ${prefix}_medaka_out_round_${i} -t $threads -m $guppy_basecalling_model
 	rm $prefix.assembly.tmp.fa
-	rm $prefix.assembly.tmp.fa.mmi
+	rm $prefix.assembly.tmp.fa.map-ont.mmi
 	rm $prefix.assembly.tmp.fa.fai
         perl $LRSDAY_HOME/scripts/tidy_fasta_for_medaka.pl -i ${prefix}_medaka_out_round_${i}/consensus.fasta -o $prefix.assembly.medaka.round_${i}.fa 
 	cp $prefix.assembly.medaka.round_${i}.fa $prefix.assembly.tmp.fa
@@ -121,28 +125,28 @@ then
     done
     ln -s $prefix.assembly.medaka.round_${rounds_of_successive_polishing}.fa $prefix.assembly.long_read_polished.fa
     rm $prefix.assembly.tmp.fa
-    source $miniconda2_dir/deactivate
-elif [[ $polisher == "marginpolish" ]]
-then
-    source $miniconda2_dir/activate $conda_medaka_dir/../../conda_medaka_env
-    for i in $(seq 1 1 $rounds_of_successive_polishing)
-    do
-	$minimap2_dir/minimap2 -t $threads -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
-	java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000
-	$samtools_dir/samtools index $prefix.minimap2.round_${i}.bam
-	$marginpolish_dir/marginPolish $prefix.minimap2.round_${i}.bam $prefix.assembly.tmp.fa $marginpolish_dir/../params/allParams.np.json -t $threads -o ${prefix}.assembly.marginpolish.round_${i}
-	if [[ $debug == "no" ]]
-        then
-	    rm $prefix.minimap2.round_${i}.sam
-	    rm $prefix.minimap2.round_${i}.bam
-	    rm $prefix.minimap2.round_${i}.bam.bai
-	fi
-	rm $prefix.assembly.tmp.fa
-	cp $prefix.assembly.marginpolish.round_${i}.fa $prefix.assembly.tmp.fa
-    done
-    ln -s $prefix.assembly.marginpolish.round_${rounds_of_successive_polishing}.fa $prefix.assembly.long_read_polished.fa
-    rm $prefix.assembly.tmp.fa
-    source $miniconda2_dir/deactivate
+    source $miniconda3_dir/deactivate
+# elif [[ $polisher == "marginpolish" ]]
+# then
+#     source $miniconda3_dir/activate $conda_medaka_dir/../../conda_marginPolish_env
+#     for i in $(seq 1 1 $rounds_of_successive_polishing)
+#     do
+# 	$minimap2_dir/minimap2 -t $threads -ax map-ont $prefix.assembly.tmp.fa $long_reads_in_fastq > $prefix.minimap2.round_${i}.sam
+# 	$java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam -INPUT $prefix.minimap2.round_${i}.sam -OUTPUT $prefix.minimap2.round_${i}.bam -SORT_ORDER coordinate -VALIDATION_STRINGENCY LENIENT -MAX_RECORDS_IN_RAM 50000
+# 	$samtools_dir/samtools index $prefix.minimap2.round_${i}.bam
+# 	$marginpolish_dir/marginPolish $prefix.minimap2.round_${i}.bam $prefix.assembly.tmp.fa $marginpolish_dir/../params/allParams.np.json -t $threads -o ${prefix}.assembly.marginpolish.round_${i}
+# 	if [[ $debug == "no" ]]
+#         then
+# 	    rm $prefix.minimap2.round_${i}.sam
+# 	    rm $prefix.minimap2.round_${i}.bam
+# 	    rm $prefix.minimap2.round_${i}.bam.bai
+# 	fi
+# 	rm $prefix.assembly.tmp.fa
+# 	cp $prefix.assembly.marginpolish.round_${i}.fa $prefix.assembly.tmp.fa
+#     done
+#     ln -s $prefix.assembly.marginpolish.round_${rounds_of_successive_polishing}.fa $prefix.assembly.long_read_polished.fa
+#     rm $prefix.assembly.tmp.fa
+#     source $miniconda3_dir/deactivate
 fi
 
 rm -r tmp
@@ -158,9 +162,11 @@ fi
 # checking bash exit status
 if [[ $? -eq 0 ]]
 then
+    echo "#########################################################"
     echo ""
     echo "LRSDAY message: This bash script has been successfully processed! :)"
     echo ""
+    echo "#########################################################"
     echo ""
     exit 0
 fi
diff --git a/pipelines/LRSDAY.03.Short-read-based_Assembly_Polishing.sh b/pipelines/LRSDAY.03.Short-read-based_Assembly_Polishing.sh
index ebfeacb..a82ed7d 100755
--- a/pipelines/LRSDAY.03.Short-read-based_Assembly_Polishing.sh
+++ b/pipelines/LRSDAY.03.Short-read-based_Assembly_Polishing.sh
@@ -7,20 +7,22 @@ source ./../../env.sh
 ###########################################
 # set project-specific variables
 
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a"  # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 input_assembly="./../02.Long-read-based_Assembly_Polishing/$prefix.assembly.long_read_polished.fa" # The file path of the input assembly before Illumina-based correction
 trim_illumina_reads="yes" # Whether to trim the input Illumina reads. Use "yes" if prefer to perform trimming, otherwise use "no". Default = "yes". 
-rounds_of_successive_polishing=1 # The number of total rounds of Illumina-read-based assembly polishing. Default = "1" for the testing example.
-threads=1 # The number of threads to use. Default = "1".
+rounds_of_successive_polishing=3 # The number of total rounds of Illumina-read-based assembly polishing. Default = "3" for the testing example.
+threads=8 # The number of threads to use. Default = "8".
 mode="PE" # Illumina sequencing mode, "PE" for paired-end sequencing and "SE" for single-end sequencing. Default = "PE".
-fixlist="snps,indels" # The types of errors for Illumina-read-based correction by Pilon; see Pilon's manual for more details. Default = "snps,indels".
 if [[ $mode == "PE" ]]
 then
-    reads_PE1="./../00.Short_Reads/SRR4074258_pass_1.fastq.gz" # Please replace the PE reads file name for your own project
-    reads_PE2="./../00.Short_Reads/SRR4074258_pass_2.fastq.gz" # Please replace the PE reads file name for your own project
+    reads_PE1="./../00.Short_Reads/$prefix.R1.fastq.gz" # Please replace the PE reads file name for your own project
+    reads_PE2="./../00.Short_Reads/$prefix.R2.fastq.gz" # Please replace the PE reads file name for your own project
 else
-    reads_SE="./../00.Short_Reads/sample_pass_1.fastq.gz" # Please replace the SE reads file name for your own project if you only have SE data
+    reads_SE="./../00.Short_Reads/$prefix.fastq.gz" # Please replace the SE reads file name for your own project if you only have SE data
 fi
+
+fixlist="snps,indels" # The types of errors for Illumina-read-based correction by Pilon; see Pilon's manual for more details. Default = "snps,indels".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ###########################################
@@ -29,11 +31,8 @@ debug="no" # Whether to keep intermediate files for debugging. Use "yes" if pref
 if [[ $mode == "PE" ]]
 then
     adapter="$trimmomatic_dir/adapters/TruSeq3-PE-2.fa" # adapter for PE reads
-    ln -s $reads_PE1 raw.R1.fq.gz;
-    ln -s $reads_PE2 raw.R2.fq.gz;
 else
     adpater="$trimmomatic_dir/adapters/TruSeq3-SE.fa" # adapter for SE reads
-    ln -s $reads_SE raw.fq.gz;
 fi
 
 cp  $input_assembly refseq.tmp.fa
@@ -45,22 +44,22 @@ if [[ $trim_illumina_reads == "yes" ]]
 then
     if [[ $mode == "PE" ]]
     then
-	java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar PE -threads $threads -phred33  raw.R1.fq.gz  raw.R2.fq.gz  trimmed.R1.fq.gz trimmed.unpaired.R1.fq.gz trimmed.R2.fq.gz trimmed.unpaired.R2.fq.gz ILLUMINACLIP:adapter.fa:2:30:10  SLIDINGWINDOW:5:20 MINLEN:36
-	rm trimmed.unpaired.R1.fq.gz
-	rm trimmed.unpaired.R2.fq.gz 
-	mv trimmed.R1.fq.gz clean.R1.fq.gz
-	mv trimmed.R2.fq.gz clean.R2.fq.gz
+	$java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar PE -threads $threads -phred33  $reads_PE1 $reads_PE2  $prefix.trimmed.R1.fq.gz $prefix.trimmed.unpaired.R1.fq.gz $prefix.trimmed.R2.fq.gz $prefix.trimmed.unpaired.R2.fq.gz ILLUMINACLIP:adapter.fa:2:30:10  SLIDINGWINDOW:5:20 MINLEN:36
+	rm $prefix.trimmed.unpaired.R1.fq.gz
+	rm $prefix.trimmed.unpaired.R2.fq.gz 
+	mv $prefix.trimmed.R1.fq.gz $prefix.clean.R1.fq.gz
+	mv $prefix.trimmed.R2.fq.gz $prefix.clean.R2.fq.gz
     else
-	java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar SE -threads $threads -phred33  raw.fq.gz  trimmed.fq.gz ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:36
-	mv trimmed.fq.gz clean.fq.gz
+	$java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $trimmomatic_dir/trimmomatic.jar SE -threads $threads -phred33 $reads_SE  $prefix.trimmed.fq.gz ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 MINLEN:36
+	mv $prefix.trimmed.fq.gz $prefix.clean.fq.gz
     fi
 else
     if [[ $mode == "PE" ]]
     then
-	cp raw.R1.fq.gz clean.R1.fq.gz
-	cp raw.R2.fq.gz clean.R2.fq.gz
+	cp $prefix.raw.R1.fq.gz $prefix.clean.R1.fq.gz
+	cp $prefix.raw.R2.fq.gz $prefix.clean.R2.fq.gz
     else
-	cp raw.fq.gz clean.fq.gz
+	cp $prefix.raw.fq.gz $prefix.clean.fq.gz
     fi
 fi
 
@@ -71,30 +70,30 @@ do
 
     if [[ $mode == "PE" ]]
     then
-	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa clean.R1.fq.gz clean.R2.fq.gz >$prefix.round_${i}.sam
+	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa $prefix.clean.R1.fq.gz $prefix.clean.R2.fq.gz >$prefix.round_${i}.sam
     else
-	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa clean.fq.gz >$prefix.round_${i}.sam
+	$bwa_dir/bwa mem -t $threads -M refseq.tmp.fa $prefix.clean.fq.gz >$prefix.round_${i}.sam
     fi
 
     # index reference sequence
     $samtools_dir/samtools faidx refseq.tmp.fa
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar CreateSequenceDictionary \
 	-REFERENCE refseq.tmp.fa \
 	-OUTPUT refseq.tmp.dict
 
     # sort bam file by picard-tools SortSam
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar SortSam \
 	-INPUT $prefix.round_${i}.sam \
 	-OUTPUT $prefix.round_${i}.sort.bam \
 	-SORT_ORDER coordinate
 
     # fixmate
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar FixMateInformation \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar FixMateInformation \
 	-INPUT $prefix.round_${i}.sort.bam \
 	-OUTPUT $prefix.round_${i}.fixmate.bam
 
     # add or replace read groups and sort
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar AddOrReplaceReadGroups \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar AddOrReplaceReadGroups \
 	-INPUT $prefix.round_${i}.fixmate.bam \
 	-OUTPUT $prefix.round_${i}.rdgrp.bam \
 	-SORT_ORDER coordinate \
@@ -106,7 +105,7 @@ do
 	-RGCN "RGCN"
 
     # remove duplicates
-    java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar MarkDuplicates \
+    $java_dir/java -Djava.io.tmpdir=./tmp -Dpicard.useLegacyParser=false -XX:ParallelGCThreads=$threads -jar $picard_dir/picard.jar MarkDuplicates \
 	-INPUT $prefix.round_${i}.rdgrp.bam \
 	-REMOVE_DUPLICATES true \
 	-METRICS_FILE $prefix.round_${i}.dedup.matrics \
@@ -117,13 +116,13 @@ do
 
     # GATK local realign
     # find realigner targets
-    java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
+    $java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
 	-R refseq.tmp.fa \
 	-T RealignerTargetCreator \
 	-I $prefix.round_${i}.dedup.bam \
 	-o $prefix.round_${i}.realn.intervals
     # run realigner
-    java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
+    $java_dir/java -Djava.io.tmpdir=./tmp -XX:ParallelGCThreads=$threads -jar $gatk3_dir/GenomeAnalysisTK.jar \
 	-R refseq.tmp.fa \
 	-T IndelRealigner \
 	-I $prefix.round_${i}.dedup.bam \
@@ -136,7 +135,7 @@ do
     # for PE sequencing
     if [[ $mode == "PE" ]]
     then
-	java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
+	$java_dir/java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
 	    --genome refseq.tmp.fa \
 	    --frags $prefix.round_${i}.realn.bam \
 	    --fix $fixlist \
@@ -145,7 +144,7 @@ do
 	    --output $prefix.assembly.pilon.round_${i} \
 	    >$prefix.pilon.round_${i}.log
     else
-	java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
+	$java_dir/java -Djava.io.tmpdir=./tmp -Xmx16G -XX:ParallelGCThreads=$threads -jar $pilon_dir/pilon.jar \
 	    --genome refseq.tmp.fa \
 	    --unpaired $prefix.round_${i}.realn.bam \
 	    --fix $fixlist \
@@ -184,9 +183,11 @@ fi
 # checking bash exit status
 if [[ $? -eq 0 ]]
 then
+    echo "#########################################################"
     echo ""
     echo "LRSDAY message: This bash script has been successfully processed! :)"
     echo ""
+    echo "#########################################################"
     echo ""
     exit 0
 fi
diff --git a/pipelines/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh b/pipelines/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh
index bf74dc1..40fc8e1 100755
--- a/pipelines/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh
+++ b/pipelines/LRSDAY.04.Reference-guided_Assembly_Scaffolding.sh
@@ -3,18 +3,19 @@ set -e -o pipefail
 #######################################
 # load environment variables for LRSDAY
 source ./../../env.sh
-PATH=$gnuplot_dir:$hal_dir:$PATH
+PATH=$gnuplot_dir:$PATH
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for processing sample. Please avoid the character '.' in prefix. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 input_assembly="./../03.Short-read-based_Assembly_Polishing/$prefix.assembly.short_read_polished.fa" # The file path of the input genome assembly.
 ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The file path of the raw reference genome.
 ref_genome_noncore_masked="./../00.Reference_Genome/S288C.ASM205763v1.noncore_masked.fa" # The file path of the specially masked reference genome where subtelomeres and chromosome-ends were hard masked. When the subtelomere/chromosome-end information is unavailable for the organism that you are interested in, you can just put the path of the raw reference genome assembly here.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the raw reference genome file, if there are multiple reference mitochondrial genomes that you want to check, use a single ';' to separate them. e.g. "Sc_chrMT;Sp_chrMT". Default = "chrMT".
 gap_size=5000 # The number of Ns to insert between adjacent contigs during scaffolding. Default = "5000".
-scaffolder="ragout" # The reference-based assembly scaffolder to use: "ragout" or "ragoo". Default = "ragout". If the reference genome size is large (e.g. > 100 Mb), please use "ragoo" since extra dependency is needed for "ragout" to handle large genomes.
-threads=1 # The number of threads to use. Default = "1".
+scaffolder="ragtag" # The reference-based assembly scaffolder to use: "ragout" or "ragtag". Default = "ragtag". If the reference genome size is large (e.g. > 100 Mb), please use "ragtag" since extra dependency is needed for "ragout" to handle large genomes.
+threads=8 # The number of threads to use. Default = "8".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ######################################
@@ -26,28 +27,28 @@ sed -e '/^[^>]/s/[^ATGCatgc]/N/g' $ref_genome_noncore_masked > ref_genome_noncor
 
 if [[ $scaffolder == "ragout" ]]
 then
-    echo ".references = ref_genome" > ragout.recipe.txt
-    echo ".target = $prefix" >> ragout.recipe.txt
-    echo "ref_genome.fasta = ./ref_genome_noncore_masked.fa" >> ragout.recipe.txt
-    echo "$prefix.fasta = $input_assembly" >> ragout.recipe.txt
-    echo ".naming_ref = ref_genome" >> ragout.recipe.txt
-    source $miniconda2_dir/activate $build_dir/conda_ragout_env
-    python2 $ragout_dir/ragout -o ${prefix}_ragout_out --solid-scaffolds  -t $threads  ragout.recipe.txt
-    source $miniconda2_dir/deactivate
+    echo ".references = ref_genome" > $prefix.ragout.recipe.txt
+    echo ".target = $prefix" >>$prefix.ragout.recipe.txt
+    echo "ref_genome.fasta = ./ref_genome_noncore_masked.fa" >> $prefix.ragout.recipe.txt
+    echo "$prefix.fasta = $input_assembly" >> $prefix.ragout.recipe.txt
+    echo ".naming_ref = ref_genome" >> $prefix.ragout.recipe.txt
+    source $miniconda3_dir/activate $build_dir/ragout_conda_env
+    python3 $ragout_dir/ragout -o ${prefix}_ragout_out --solid-scaffolds --overwrite -t $threads  $prefix.ragout.recipe.txt
+    source $miniconda3_dir/deactivate
     cat ./${prefix}_ragout_out/${prefix}_scaffolds.fasta | sed "s/^>chr_/>/g" > ./${prefix}_ragout_out/${prefix}_scaffolds.renamed.fasta 
     cat ./${prefix}_ragout_out/${prefix}_scaffolds.renamed.fasta ./${prefix}_ragout_out/${prefix}_unplaced.fasta > ./${prefix}_ragout_out/${prefix}.ragout.raw.fa    
     perl $LRSDAY_HOME/scripts/adjust_assembly_by_ragoutAGP.pl -i $input_assembly -p $prefix -a ./${prefix}_ragout_out/${prefix}_scaffolds.agp -g $gap_size
-    ln -s ${prefix}.ragout.fa $prefix.assembly.ref_based_scaffolded.fa
-elif [[ $scaffolder == "ragoo" ]]
+    mv ${prefix}.ragout.fa $prefix.assembly.ref_based_scaffolded.fa
+elif [[ $scaffolder == "ragtag" ]]
 then
-    source $build_dir/py3_virtualenv_ragoo/bin/activate
-    python3 $ragoo_dir/ragoo.py -t $threads -g $gap_size  -C -m $minimap2_dir/minimap2 $input_assembly ref_genome_noncore_masked.fa
-    mv ragoo_output ${prefix}_ragoo_out
-    cp ${prefix}_ragoo_out/ragoo.fasta ${prefix}.ragoo.fa
-    ln -s ${prefix}.ragoo.fa $prefix.assembly.ref_based_scaffolded.fa
+    source $miniconda3_dir/activate $build_dir/ragtag_conda_env
+    $ragtag_dir/ragtag.py scaffold -t $threads -f 500 -g $gap_size -r -u -o ${prefix}_ragtag_out ref_genome_noncore_masked.fa $input_assembly 
+    source $miniconda3_dir/deactivate
+    cat ./${prefix}_ragtag_out/ragtag.scaffold.fasta  |sed "s/_RagTag$//g" > ${prefix}.ragtag.fa
+    mv ${prefix}.ragtag.fa $prefix.assembly.ref_based_scaffolded.fa 
 else
     echo "Unrecognized scaffolder: $scaffolder";
-    echo "Please set scaffolder=\"ragout\" or \"ragoo\".";
+    echo "Please set scaffolder=\"ragout\" or \"ragtag\".";
     echo "LRSDAY Exit!";
     exit;
 fi
@@ -66,20 +67,25 @@ perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.ref_based_sca
 $gnuplot_dir/gnuplot < $prefix.assembly.ref_based_scaffolded.filter_adjust.gp
 
 # generate dotplot for the mitochondrial genome only
-perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal -o ref.chrMT.fa
-perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.ref_based_scaffolded.fa -l $prefix.assembly.ref_based_scaffolded.mt_contig.list -m normal -o $prefix.assembly.ref_based_scaffolded.mt_contig.fa
-$mummer4_dir/nucmer --maxmatch --nosimplify  -p $prefix.assembly.ref_based_scaffolded.chrMT ref.chrMT.fa $prefix.assembly.ref_based_scaffolded.mt_contig.fa
-$mummer4_dir/delta-filter -m  $prefix.assembly.ref_based_scaffolded.chrMT.delta > $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter
-$mummer4_dir/mummerplot --large --postscript $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter -p $prefix.assembly.ref_based_scaffolded.chrMT.filter
-perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.ref_based_scaffolded.chrMT.filter.gp -o $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp -r ref.chrMT.fa -q $prefix.assembly.ref_based_scaffolded.mt_contig.fa
-$gnuplot_dir/gnuplot < $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp
+if [ -s $prefix.assembly.ref_based_scaffolded.mt_contig.list ]
+then
+    perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal -o ref.chrMT.fa
+    perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.ref_based_scaffolded.fa -l $prefix.assembly.ref_based_scaffolded.mt_contig.list -m normal -o $prefix.assembly.ref_based_scaffolded.mt_contig.fa
+    $mummer4_dir/nucmer --maxmatch --nosimplify  -p $prefix.assembly.ref_based_scaffolded.chrMT ref.chrMT.fa $prefix.assembly.ref_based_scaffolded.mt_contig.fa
+    $mummer4_dir/delta-filter -m  $prefix.assembly.ref_based_scaffolded.chrMT.delta > $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter
+    $mummer4_dir/mummerplot --large --postscript $prefix.assembly.ref_based_scaffolded.chrMT.delta_filter -p $prefix.assembly.ref_based_scaffolded.chrMT.filter
+    perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.ref_based_scaffolded.chrMT.filter.gp -o $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp -r ref.chrMT.fa -q $prefix.assembly.ref_based_scaffolded.mt_contig.fa
+    $gnuplot_dir/gnuplot < $prefix.assembly.ref_based_scaffolded.chrMT.filter_adjust.gp
+else 
+    echo "no chrMT contig detected, therefore no chrMT plotting will be performed."
+fi
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
     if [[ $scaffolder == "ragout" ]]
     then
-	rm ragout.recipe.txt
+	rm $prefix.ragout.recipe.txt
     fi
     rm ref_genome_noncore_masked.fa
     rm *.filter.fplot
@@ -89,8 +95,11 @@ then
     rm *.filter.gp
     rm *.filter_adjust.gp
     rm *.filter.ps
-    rm ref.chrMT.list
-    rm ref.chrMT.fa
+    if [ -e ref.chrMT.fa ]
+    then
+	rm ref.chrMT.list
+	rm ref.chrMT.fa
+    fi
 fi
 
 ############################
diff --git a/pipelines/LRSDAY.05.Centromere_Identity_Profiling.sh b/pipelines/LRSDAY.05.Centromere_Identity_Profiling.sh
index 663c004..25389d7 100755
--- a/pipelines/LRSDAY.05.Centromere_Identity_Profiling.sh
+++ b/pipelines/LRSDAY.05.Centromere_Identity_Profiling.sh
@@ -6,7 +6,8 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a"  # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 genome="./../04.Reference-guided_Assembly_Scaffolding/$prefix.assembly.ref_based_scaffolded.fa" # The file path of the input genome assembly
 query="$LRSDAY_HOME/data/S288C.centromere.fa" # S. cerevisiae S288C reference centromere sequences based on Yue et al. (2017) Nature Genetics. 
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
diff --git a/pipelines/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh b/pipelines/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh
index 97b06c0..2b793af 100755
--- a/pipelines/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh
+++ b/pipelines/LRSDAY.06.Mitochondrial_Genome_Assembly_Improvement.sh
@@ -3,17 +3,18 @@ set -e
 ##########################################
 # load environment variables for LRSDAY
 source ./../../env.sh
-PATH=$bwa_dir:$samtools_dir:$gnuplot_dir:$canu_dir:$mummer_dir:$spades_dir:$prodigal_dir:$PATH
+PATH=$bwa_dir:$samtools_dir:$gnuplot_dir:$mummer4_dir:$spades_dir:$prodigal_dir:$PATH
 
 ###########################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a"  # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 genome="./../04.Reference-guided_Assembly_Scaffolding/$prefix.assembly.ref_based_scaffolded.fa" # The file path of the input genome assembly
 mt_contig_list="./../04.Reference-guided_Assembly_Scaffolding/$prefix.assembly.ref_based_scaffolded.mt_contig.list" # The mitochodnrial contig list generated by the module 04.Reference-guided_Assembly_Scaffolding.
 gene_start="$LRSDAY_HOME/data/ATP6.cds.fa" # A FASTA file containing the CDS sequence of the mitochodnrial gene to be used as the starting point of the mitochondrial assembly. This can be set to any gene as long as a fasta file containing the DNA sequence of the gene is provided.
 ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The file path of the raw reference genome 
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the raw reference genome file, if there are multiple reference mitochondrial genomes that you want to check, use a single ';' to separate them. e.g. "Sc_chrMT;Sp_chrMT". Default = "chrMT".
-threads=1 # The number of threads to use. Default = "1".
+threads=8 # The number of threads to use. Default = "8".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ##########################################
@@ -21,6 +22,9 @@ debug="no" # Whether to keep intermediate files for debugging. Use "yes" if pref
 $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $mt_contig_list -m reverse -o $prefix.assembly.non_mt_contig.fa
 $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $mt_contig_list -m normal -o $prefix.assembly.mt_contig.fa
 
+echo $chrMT_tag | sed -e "s/;/\n/g" > ref.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal  -o ref.chrMT.fa
+
 if [[ $(egrep -c "^>" "$prefix.assembly.mt_contig.fa") -eq 0 ]]
 then
     echo "no chrMT contig was found in the assembly, skip this step and just output the input assembly ..."
@@ -39,12 +43,13 @@ else
     perl $LRSDAY_HOME/scripts/break_contig_by_blast.pl -i $prefix.assembly.mt_contig.descaffold.fa -b $prefix.assembly.mt_contig.descaffold.tblastx.filtered.out -o $prefix.assembly.mt_contig.break_by_blast.fa
 
     # reassemble the mitochondrial genome using CAP3 to collapse smaller fragments
-    $cap_dir/cap3 $prefix.assembly.mt_contig.break_by_blast.fa -k 0 
+    $cap3_dir/cap3 $prefix.assembly.mt_contig.break_by_blast.fa -k 0 
     if [[ $(egrep -c "^>" "$prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs") -eq 0 ]]
     then
         cat $prefix.assembly.mt_contig.break_by_blast.fa | sed "s/>/>chrMT_/" > $prefix.assembly.mt_contig.for_clean.fa
     else
-        cat $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs| sed "s/>/>chrMT_/" > $prefix.assembly.mt_contig.for_clean.fa
+	cat $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs $prefix.assembly.mt_contig.break_by_blast.fa.cap.singlets > $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs_singlets
+        cat $prefix.assembly.mt_contig.break_by_blast.fa.cap.contigs_singlets| sed "s/>/>chrMT_/" > $prefix.assembly.mt_contig.for_clean.fa
     fi
 
     $circlator_dir/circlator clean --verbose $prefix.assembly.mt_contig.for_clean.fa  ${prefix}.assembly.mt_contig.for_fixstart.fa 
@@ -64,16 +69,15 @@ else
 
     $circlator_dir/circlator fixstart --verbose --genes_fa $gene_start --min_id 90 --ignore $prefix.assembly.for_fixstart.for_skip.list $prefix.assembly.mt_contig.for_fixstart.fa  $prefix.assembly.mt_contig.circlator
 
-    mv $prefix.assembly.mt_contig.circlator.fasta $prefix.assembly.mt_contig.circlator.fa
+    source $miniconda3_dir/activate $build_dir/ragtag_conda_env
+    $ragtag_dir/ragtag.py scaffold -t $threads -f 1 -u -o ${prefix}_chrMT_ragtag_out ref.chrMT.fa $prefix.assembly.mt_contig.circlator.fasta
+    cat ${prefix}_chrMT_ragtag_out/ragtag.scaffold.fasta |sed "s/>chrMT_RagTag/>${prefix}.chrMT/"|sed -r "s/N{100}//gi" >  ${prefix}.assembly.mt_contig.ragtag.fa
     cat $prefix.assembly.non_mt_contig.fa |egrep "^>"|egrep -v "^>chr" |sed "s/>//" > $prefix.assembly.non_primary_contig.list
     $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.non_mt_contig.fa -l $prefix.assembly.non_primary_contig.list -m reverse -o $prefix.assembly.primary_contig.fa
     $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.assembly.non_mt_contig.fa -l $prefix.assembly.non_primary_contig.list -m normal -o $prefix.assembly.non_primary_contig.fa
-    cat $prefix.assembly.primary_contig.fa $prefix.assembly.mt_contig.circlator.fa $prefix.assembly.non_primary_contig.fa > $prefix.assembly.mt_improved.fa
-
+    cat $prefix.assembly.primary_contig.fa $prefix.assembly.mt_contig.ragtag.fa $prefix.assembly.non_primary_contig.fa > $prefix.assembly.mt_improved.fa
     # generate dotplot for the mitochondrial genome only
-    echo $chrMT_tag | sed -e "s/;/\n/g" > ref.chrMT.list
-    perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $ref_genome_raw -l ref.chrMT.list -m normal  -o ref.chrMT.fa
-    $mummer4_dir/nucmer -t $threads --maxmatch --nosimplify  -p $prefix.assembly.mt_improved.chrMT ref.chrMT.fa $prefix.assembly.mt_contig.circlator.fa
+    $mummer4_dir/nucmer -t $threads --maxmatch --nosimplify  -p $prefix.assembly.mt_improved.chrMT ref.chrMT.fa $prefix.assembly.mt_contig.ragtag.fa
     $mummer4_dir/delta-filter -m  $prefix.assembly.mt_improved.chrMT.delta > $prefix.assembly.mt_improved.chrMT.delta_filter
     $mummer4_dir/mummerplot --large --postscript $prefix.assembly.mt_improved.chrMT.delta_filter -p $prefix.assembly.mt_improved.chrMT.filter
     perl $LRSDAY_HOME/scripts/fine_tune_gnuplot.pl -i $prefix.assembly.mt_improved.chrMT.filter.gp -o $prefix.assembly.mt_improved.chrMT.filter_adjust.gp -r ref.chrMT.fa -q $prefix.assembly.mt_contig.final.fa
@@ -106,6 +110,10 @@ then
 	rm $prefix.assembly.for_fixstart.for_skip.fa
 	rm $prefix.assembly.for_fixstart.for_skip.list
     fi
+    if [ -d "${prefix}_chrMT_ragtag_out" ]
+    then
+	rm -r ${prefix}_chrMT_ragtag_out
+    fi
 fi
 
 ############################
diff --git a/pipelines/LRSDAY.07.Supervised_Final_Assembly.1.sh b/pipelines/LRSDAY.07.Supervised_Final_Assembly.1.sh
index f1a95ab..97b3e2a 100755
--- a/pipelines/LRSDAY.07.Supervised_Final_Assembly.1.sh
+++ b/pipelines/LRSDAY.07.Supervised_Final_Assembly.1.sh
@@ -6,7 +6,8 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.         
+
 genome="./../06.Mitochondrial_Genome_Assembly_Improvement/$prefix.assembly.mt_improved.fa" # The file name of the input genome assembly.
 
 
diff --git a/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh b/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh
index 1d342a1..3d2eb44 100755
--- a/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh
+++ b/pipelines/LRSDAY.07.Supervised_Final_Assembly.2.sh
@@ -7,20 +7,23 @@ PATH=$gnuplot_dir:$PATH
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
 genome="./../06.Mitochondrial_Genome_Assembly_Improvement/$prefix.assembly.mt_improved.fa" # The file path of the input genome assembly.
-vcf="yes" # Whether to generate a vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome. Default = "yes".
 dotplot="yes" # Whether to plot genome-wide dotplot based on the comparison with the reference genome below. Use "yes" if prefer to plot, otherwise use "no". Default = "yes".
 ref_genome_raw="./../00.Reference_Genome/S288C.ASM205763v1.fa" # The path of the raw reference genome, only needed when dotplot="yes" or vcf="yes".
-threads=1 # The number of threads to use. Default = 1.
+threads=8 # The number of threads to use. Default = 8.
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
 # process the pipeline
 # Please mark desiarable changes in the $prefix.modification.list file and comment the command lines for Step 1 before proceeding with Step 2.
+
+vcf="no" # Whether to generate a vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome for their uniquely alignable regions. Use "yes" if prefer to have vcf file generated to show SNP and INDEL differences between the assembled genome and the reference genome. Default = "no".
 # Step 2:
-perl $LRSDAY_HOME/scripts/relabel_and_reorder_sequences.pl  -i $genome -m $prefix.assembly.modification.list -o $prefix.assembly.final.fa
+perl $LRSDAY_HOME/scripts/relabel_and_reorder_sequences.pl -i $genome -m $prefix.assembly.modification.list -o $prefix.assembly.relabel_and_reorder.fa
 # generate assembly statistics
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.relabel_and_reorder.fa -o $prefix.assembly.final.fa
 perl $LRSDAY_HOME/scripts/cal_assembly_stats.pl -i $prefix.assembly.final.fa -o $prefix.assembly.final.stats.txt
 
 # check project-specific variables
@@ -77,6 +80,8 @@ then
     rm *.delta
     rm *.delta_filter
     rm ref_genome.fa
+    rm $prefix.assembly.relabel_and_reorder.fa
+
     if [[ $vcf == "yes" ]] 
     then
 	rm ref_genome.fa.fai
diff --git a/pipelines/LRSDAY.08.Centromere_Annotation.sh b/pipelines/LRSDAY.08.Centromere_Annotation.sh
index 8a731c7..0951eff 100755
--- a/pipelines/LRSDAY.08.Centromere_Annotation.sh
+++ b/pipelines/LRSDAY.08.Centromere_Annotation.sh
@@ -6,20 +6,28 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example. 
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The path of the input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
 query="$LRSDAY_HOME/data/S288C.centromere.fa" # The S. cerevisiae S288C reference centromere sequences based on Yue et al. (2017) Nature Genetics.
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 ######################################
 # process the pipeline
-$exonerate_dir/exonerate --showvulgar no --showcigar no --showalignment no --showtargetgff yes --bestn 1 $query $genome >$prefix.centromere.exonerate.gff
+
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+
+$exonerate_dir/exonerate --showvulgar no --showcigar no --showalignment no --showtargetgff yes --bestn 1 $query $prefix.assembly.nuclear_genome.tidy.fa  >$prefix.centromere.exonerate.gff
 perl $LRSDAY_HOME/scripts/exonerate_gff2gff3.pl  -i $prefix.centromere.exonerate.gff -o $prefix.centromere.gff3.tmp -t $prefix
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r $genome -i  $prefix.centromere.gff3.tmp -o  $prefix.centromere.gff3 -t $prefix
+perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r $prefix.assembly.nuclear_genome.tidy.fa -i $prefix.centromere.gff3.tmp -o $prefix.nuclear_genome.centromere.gff3 -t $prefix
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
+    rm $prefix.assembly.nuclear_genome.fa
+    rm $prefix.assembly.nuclear_genome.tidy.fa
     rm $prefix.centromere.exonerate.gff
     rm $prefix.centromere.gff3.tmp
 fi
diff --git a/pipelines/LRSDAY.09.Nuclear_Gene_Annotation.sh b/pipelines/LRSDAY.09.Nuclear_Gene_Annotation.sh
index 444ef7a..65cb69d 100755
--- a/pipelines/LRSDAY.09.Nuclear_Gene_Annotation.sh
+++ b/pipelines/LRSDAY.09.Nuclear_Gene_Annotation.sh
@@ -6,10 +6,11 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
-threads=1 # The number of threads to use. Default = "1".
+threads=8 # The number of threads to use. Default = "8".
 maker_opts="$LRSDAY_HOME/misc/maker_opts.customized.ctl" # The configuration file for MAKER. You can edit this file if you have native transciptome/EST data for the strain/species that you sequenced or if you want to adapt it to annotate other eukaryotic organisms. Otherwise, please keep it unchanged. Please note that if this file is in the same directory where this bash script is executed, the file name cannot be "maker_opts.ctl".
 EVM_weights="$LRSDAY_HOME/misc/EVM_weights.customized.txt" # The configuration file for EVM. A list of numeric weight values to be applied to each type of evidence.
 debug="no" # use "yes" if prefer to keep intermediate files, otherwise use "no".
@@ -24,17 +25,16 @@ echo "genome_assembly=$genome_assembly"
 # convert the genome assembly file to all uppercases
 
 echo $chrMT_tag | sed -e "s/;/\n/g" > $genome_tag.assembly.chrMT.list
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m reverse -o $genome_tag.assembly.nuclear_genome.fa
-#$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m normal -o $genome_tag.assembly.mitochondrial_genome.fa
-
-perl $LRSDAY_HOME/scripts/switch_letter_cases_in_fasta.pl -i $genome_tag.assembly.nuclear_genome.fa -o genome.uppercase.fa -c upper
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m reverse -o $genome_tag.assembly.nuclear_genome.fa
+# perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $genome_tag.assembly.chrMT.list -m normal -o $genome_tag.assembly.mitochondrial_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $genome_tag.assembly.nuclear_genome.fa -o $genome_tag.assembly.nuclear_genome.tidy.fa
 
 cp $maker_opts maker_opts.ctl
 cp $LRSDAY_HOME/misc/maker_exe.ctl .
 cp $LRSDAY_HOME/misc/maker_bopts.ctl .
 cp $LRSDAY_HOME/misc/maker_evm.ctl .
 
-$maker_dir/maker -fix_nucleotides -genome genome.uppercase.fa -cpus $threads -base $genome_tag
+$maker_dir/maker -fix_nucleotides -genome $genome_tag.assembly.nuclear_genome.tidy.fa -cpus $threads -base $genome_tag
 
 # $maker_dir/fasta_merge -d $genome_tag.maker.output/${genome_tag}_master_datastore_index.log -o $genome_tag.nuclear_genome.maker.fasta
 $maker_dir/gff3_merge -d $genome_tag.maker.output/${genome_tag}_master_datastore_index.log -n -g -o $genome_tag.nuclear_genome.maker.raw.gff3
@@ -64,7 +64,7 @@ cat $genome_tag.nuclear_genome.maker.raw.protein_coding_gene.gff3 $genome_tag.nu
 mkdir $genome_tag.nuclear_genome.EVM.output
 cd $genome_tag.nuclear_genome.EVM.output
 $EVM_HOME/EvmUtils/partition_EVM_inputs.pl \
-    --genome ./../genome.uppercase.fa \
+    --genome ./../$genome_tag.assembly.nuclear_genome.tidy.fa \
     --gene_predictions ./../$genome_tag.nuclear_genome.maker.combined.gff3 \
     --protein_alignments ./../$genome_tag.nuclear_genome.protein_evidence.gff3 \
     --transcript_alignments ./../$genome_tag.nuclear_genome.est_evidence.gff3 \
@@ -73,7 +73,7 @@ $EVM_HOME/EvmUtils/partition_EVM_inputs.pl \
     --partition_listing $genome_tag.nuclear_genome.partitions_list.out
 
 $EVM_HOME/EvmUtils/write_EVM_commands.pl \
-    --genome ./../genome.uppercase.fa \
+    --genome ./../$genome_tag.assembly.nuclear_genome.tidy.fa \
     --weights $EVM_weights  \
     --gene_predictions ./../$genome_tag.nuclear_genome.maker.combined.gff3 \
     --output_file_name $genome_tag.nuclear_genome.evm.out \
@@ -87,40 +87,51 @@ $EVM_HOME/EvmUtils/recombine_EVM_partial_outputs.pl \
 $EVM_HOME/EvmUtils/convert_EVM_outputs_to_GFF3.pl \
     --partitions $genome_tag.nuclear_genome.partitions_list.out \
     --output $genome_tag.nuclear_genome.evm.out \
-    --genome ./../genome.uppercase.fa
+    --genome ./../$genome_tag.assembly.nuclear_genome.tidy.fa
 
-perl $LRSDAY_HOME/scripts/collect_EVM_gff3.pl -p $genome_tag.nuclear_genome  -r ./../genome.uppercase.fa
+perl $LRSDAY_HOME/scripts/collect_EVM_gff3.pl -p $genome_tag.nuclear_genome  -r ./../$genome_tag.assembly.nuclear_genome.tidy.fa
 
 cat $genome_tag.nuclear_genome.EVM.raw.gff3 ./../$genome_tag.nuclear_genome.maker.raw.tRNA.gff3 > $genome_tag.nuclear_genome.EVM.raw.with_tRNA.gff3
 perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl \
     -i $genome_tag.nuclear_genome.EVM.raw.with_tRNA.gff3 \
-    -r ./../genome.uppercase.fa \
+    -r ./../$genome_tag.assembly.nuclear_genome.tidy.fa \
     -t $genome_tag \
     -o $genome_tag.nuclear_genome.EVM.gff3
-cp $genome_tag.nuclear_genome.EVM.gff3 ./../$genome_tag.nuclear_genome.EVM.gff3
+cp $genome_tag.nuclear_genome.EVM.gff3 ./../$genome_tag.nuclear_genome.gff3
 cd ..
 
 perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl \
-    -r $genome_assembly \
-    -g $genome_tag.nuclear_genome.EVM.gff3 \
-    -o $genome_tag.nuclear_genome.EVM.cds.fa
+    -r $genome_tag.assembly.nuclear_genome.tidy.fa \
+    -g $genome_tag.nuclear_genome.gff3 \
+    -o $genome_tag.nuclear_genome.cds.fa
 perl $LRSDAY_HOME/scripts/cds2protein.pl \
-    -i $genome_tag.nuclear_genome.EVM.cds.fa \
-    -p $genome_tag.nuclear_genome.EVM \
+    -i $genome_tag.nuclear_genome.cds.fa \
+    -p $genome_tag.nuclear_genome \
     -t 1
 
-perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $genome_tag.nuclear_genome.EVM.gff3 -o $genome_tag.nuclear_genome.EVM.PoFF.gff 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.EVM.trimmed_cds.fa -o $genome_tag.nuclear_genome.EVM.PoFF.ffn 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.EVM.pep.fa -o $genome_tag.nuclear_genome.EVM.PoFF.faa
 
 # filtered out snoRNA annotation since it is still an experimental features suffering from redundant annotations
-cp $genome_tag.nuclear_genome.EVM.gff3 $genome_tag.nuclear_genome.EVM.gff3.tmp
-cat $genome_tag.nuclear_genome.EVM.gff3.tmp | egrep -v "snoRNA" > $genome_tag.nuclear_genome.EVM.gff3
+cp $genome_tag.nuclear_genome.gff3 $genome_tag.nuclear_genome.gff3.tmp
+cat $genome_tag.nuclear_genome.gff3.tmp | egrep -v "snoRNA" > $genome_tag.nuclear_genome.snoRNA_filtered.gff3
+perl $LRSDAY_HOME/scripts/label_pseudogene_in_gff3.pl -i $genome_tag.nuclear_genome.snoRNA_filtered.gff3 -l $genome_tag.nuclear_genome.manual_check.list -o $genome_tag.nuclear_genome.gff3
+
+perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl \
+    -r $genome_tag.assembly.nuclear_genome.tidy.fa \
+    -g $genome_tag.nuclear_genome.gff3 \
+    -o $genome_tag.nuclear_genome.cds.fa
+perl $LRSDAY_HOME/scripts/cds2protein.pl \
+    -i $genome_tag.nuclear_genome.cds.fa \
+    -p $genome_tag.nuclear_genome \
+    -t 1
+
+perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $genome_tag.nuclear_genome.gff3 -o $genome_tag.nuclear_genome.PoFF.gff 
+perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.trimmed_cds.fa -o $genome_tag.nuclear_genome.PoFF.ffn 
+perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $genome_tag.nuclear_genome.pep.fa -o $genome_tag.nuclear_genome.PoFF.faa
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
-    rm genome.uppercase.fa
+    rm $genome_tag.assembly.nuclear_genome.fa
     rm $genome_tag.nuclear_genome.maker.raw.tRNA.gff3
     rm $genome_tag.nuclear_genome.maker.raw.protein_coding_gene.gff3
     rm $genome_tag.nuclear_genome.maker.raw.protein_coding_gene.single_exon_gene.gff3
@@ -129,9 +140,11 @@ then
     rm $genome_tag.nuclear_genome.est_evidence.for_gene_model_refinement.gff3
     rm $genome_tag.nuclear_genome.protein_evidence.complementary_gene_model.gff3
     rm $genome_tag.nuclear_genome.est_evidence.complementary_gene_model.gff3
-    rm $genome_tag.nuclear_genome.EVM.gff3.tmp
+    rm $genome_tag.nuclear_genome.gff3.tmp
     rm $genome_tag.nuclear_genome.maker.combined.gff3
+    rm $genome_tag.nuclear_genome.snoRNA_filtered.gff3
     rm -rf _Inline
+    rm *.ctl
 fi
 
 ############################
diff --git a/pipelines/LRSDAY.10.Mitochondrial_Gene_Annotation.sh b/pipelines/LRSDAY.10.Mitochondrial_Gene_Annotation.sh
index b37fec6..6e6be2e 100755
--- a/pipelines/LRSDAY.10.Mitochondrial_Gene_Annotation.sh
+++ b/pipelines/LRSDAY.10.Mitochondrial_Gene_Annotation.sh
@@ -18,8 +18,9 @@ export PATH="$flip_dir:$blast_dir:$muscle_dir:$umac_dir:$hmmer_dir:$erpin_dir:$t
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the input genome assembly, if there are multiple corresponding contigs/scaffolds, use a single ';' to separate them. e.g. "chrMT_1;chrMT_2". Default = "chrMT". 
 genetic_code_table=3 # The NCBI genetic code table (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) for the annotated mitochondrial genome. Default = 3 (i.e. Yeast Mitochondria)
 debug="no" # Whehter to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
@@ -27,32 +28,47 @@ debug="no" # Whehter to keep intermediate files for debugging. Use "yes" if pref
 ######################################
 # process the pipeline
 
+
 echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
 
-#$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m normal -o $prefix.assembly.mitochondrial_genome.fa
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m normal -o $prefix.assembly.mitochondrial_genome.fa
 
-mkdir tmp
+if [[ $(egrep -c "^>" "$prefix.assembly.mitochondrial_genome.fa") -eq 0 ]]
+then
+    echo "No mitochondrial genome assembly was detected! Skip mitochondrial genome annotation!"
+else
+    
+    perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.mitochondrial_genome.fa -o $prefix.assembly.mitochondrial_genome.tidy.fa
 
-$mfannot_dir/mfannot \
-    --genetic $genetic_code_table \
-    --outputfile $prefix.mitochondrial_genome.mfannot.out \
-    --logfile $prefix.mitochondrial_genome.mfannot.log \
-    --T $(pwd)/tmp \
-    $prefix.assembly.mitochondrial_genome.fa
+    mkdir tmp
 
-perl $LRSDAY_HOME/scripts/mfannot2gff3.pl -i $prefix.mitochondrial_genome.mfannot.out -o $prefix.mitochondrial_genome.mfannot.gff3 -m lite
-perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.mitochondrial_genome.fa -g $prefix.mitochondrial_genome.mfannot.gff3 -o $prefix.mitochondrial_genome.mfannot.cds.fa
-perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.mfannot.cds.fa -t $genetic_code_table -p $prefix.mitochondrial_genome.mfannot
+    $mfannot_dir/mfannot \
+	--genetic $genetic_code_table \
+	--outputfile $prefix.mitochondrial_genome.mfannot.out.txt \
+	--logfile $prefix.mitochondrial_genome.mfannot.log \
+	--T $(pwd)/tmp \
+	$prefix.assembly.mitochondrial_genome.tidy.fa
 
-perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $prefix.mitochondrial_genome.mfannot.gff3 -o $prefix.mitochondrial_genome.mfannot.PoFF.gff 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.mfannot.trimmed_cds.fa -o $prefix.mitochondrial_genome.mfannot.PoFF.ffn 
-perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.mfannot.pep.fa -o $prefix.mitochondrial_genome.mfannot.PoFF.faa
+    $trnascan_dir/tRNAscan-SE -D -g $trnascan_dir/../gcode.ystmito $prefix.assembly.mitochondrial_genome.tidy.fa  -o $prefix.assembly.mitochondrial_genome.trnascan.out.txt
 
-# clean up intermediate files
-if [[ $debug == "no" ]]
-then
-    rm -r tmp
+
+    perl $LRSDAY_HOME/scripts/mfannot2gff3.pl -mfannot_out $prefix.mitochondrial_genome.mfannot.out.txt -trnascan_out $prefix.assembly.mitochondrial_genome.trnascan.out.txt -o $prefix.mitochondrial_genome.pre_sort.gff3 -m lite -t $prefix
+    perl $LRSDAY_HOME/scripts/sort_gff3.pl -i $prefix.mitochondrial_genome.pre_sort.gff3 -t $prefix -o $prefix.mitochondrial_genome.gff3 -r $prefix.assembly.mitochondrial_genome.tidy.fa
+
+    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.mitochondrial_genome.tidy.fa -g $prefix.mitochondrial_genome.gff3 -o $prefix.mitochondrial_genome.cds.fa
+    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.cds.fa -t $genetic_code_table -p $prefix.mitochondrial_genome
+
+    perl $LRSDAY_HOME/scripts/prepare_PoFFgff_simple.pl -i $prefix.mitochondrial_genome.gff3 -o $prefix.mitochondrial_genome.PoFF.gff 
+    perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.trimmed_cds.fa -o $prefix.mitochondrial_genome.PoFF.ffn 
+    perl $LRSDAY_HOME/scripts/prepare_PoFFfaa_simple.pl -i $prefix.mitochondrial_genome.pep.fa -o $prefix.mitochondrial_genome.PoFF.faa
+
+    # clean up intermediate files
+    if [[ $debug == "no" ]]
+    then
+	rm -r tmp
+	rm -r $prefix.mitochondrial_genome.pre_sort.gff3
+	rm -r $prefix.assembly.mitochondrial_genome.fa
+    fi
 fi
 
 ############################
diff --git a/pipelines/LRSDAY.11.TE_Annotation.sh b/pipelines/LRSDAY.11.TE_Annotation.sh
index 7613f5e..44c2731 100755
--- a/pipelines/LRSDAY.11.TE_Annotation.sh
+++ b/pipelines/LRSDAY.11.TE_Annotation.sh
@@ -6,24 +6,32 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
-threads=1 # The number of threads to use. Default = "1".
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The path of the final input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
+threads=8 # The number of threads to use. Default = "8".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
 # process the pipeline
 
-ln -s $genome genome.fa
-$repeatmasker_dir/RepeatMasker -pa $threads -lib $LRSDAY_HOME/data/TY_lib.Yue_et_al_2017_NG.fa  genome.fa  -xsmall  -gff
-$reannotate_dir/REannotate_longname  -g -f $LRSDAY_HOME/data/fuzzy_defragmentation.txt  -k $clustalw_dir/clustalw2 -r 0.48764  -d 10000  -t genome.fa.out  genome.fa
+TE_lib="$LRSDAY_HOME/data/TE_lib.v20221221.tidy.fa"
+TE_lib_LTRonly="$LRSDAY_HOME/data/TE_lib.v20221221.LTRonly.tidy.fa"
+
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+ln -s $prefix.assembly.nuclear_genome.tidy.fa  $prefix.genome.fa
+
+$repeatmasker_dir/RepeatMasker -pa $threads -lib $TE_lib  $prefix.genome.fa  -xsmall  -gff
+$reannotate_dir/REannotate_longname  -g -f $LRSDAY_HOME/data/fuzzy_defragmentation.txt  -k $clustalw_dir/clustalw2 -r 0.48764  -d 10000  -t $prefix.genome.fa.out  $prefix.genome.fa
 mv REannotate_output ${prefix}_REannotate_out
 
 cd ${prefix}_REannotate_out 
 
 perl $LRSDAY_HOME/scripts/parse_REannotate_gff.pl -o $prefix.REannotate.raw.gff
 mv $prefix.REannotate.raw.gff $prefix.REannotate.gff
-perl $LRSDAY_HOME/scripts/parse_REannotate_out.pl -i genome.fa.REannotation -p $prefix.TY_REannotate -r ./../genome.fa
+perl $LRSDAY_HOME/scripts/parse_REannotate_out.pl -i $prefix.genome.fa.REannotation -p $prefix.TY_REannotate -r ./../$prefix.genome.fa
 
 cat $prefix.TY_REannotate.complete.raw.fa  |egrep ">" |egrep  '(TY1|TY2)' |sed "s/>//g" >$prefix.TY_REannotate.complete.TY1TY2.raw.list
 perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.TY_REannotate.complete.raw.fa -l $prefix.TY_REannotate.complete.TY1TY2.raw.list  -o $prefix.TY_REannotate.complete.TY1TY2.raw.fa
@@ -31,12 +39,13 @@ perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.TY_REannotate.compl
 cat $prefix.TY_REannotate.truncated.raw.fa  |egrep ">" |egrep  '(TY1|TY2)' |sed "s/>//g" >$prefix.TY_REannotate.truncated.TY1TY2.raw.list
 perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $prefix.TY_REannotate.truncated.raw.fa -l $prefix.TY_REannotate.truncated.TY1TY2.raw.list  -o $prefix.TY_REannotate.truncated.TY1TY2.raw.fa
 
-for i in {3..5}
+for i in TY3 TY4 TY5 TSU4
 do
-    cat $prefix.TY_REannotate.complete.raw.fa  |egrep ">" |egrep "TY${i}" |sed "s/>//g"  >$prefix.TY_REannotate.complete.TY${i}.final.list
-    cat $prefix.TY_REannotate.truncated.raw.fa  |egrep ">" |egrep "TY${i}" |sed "s/>//g"  >$prefix.TY_REannotate.truncated.TY${i}.final.list
+    cat $prefix.TY_REannotate.complete.raw.fa  |egrep ">" |egrep "$i" |sed "s/>//g"  >$prefix.TY_REannotate.complete.$i.final.list
+    cat $prefix.TY_REannotate.truncated.raw.fa  |egrep ">" |egrep "$i" |sed "s/>//g"  >$prefix.TY_REannotate.truncated.$i.final.list
 done
 
+
 TY2_query="$LRSDAY_HOME/data/TY2_specific_region.fa"
 
 
@@ -74,25 +83,25 @@ else
     cat $prefix.TY_REannotate.truncated.TY2.list |sed "s/TY1/TY2/g" >$prefix.TY_REannotate.truncated.TY2.final.list
 fi
 
-db="$LRSDAY_HOME/data/TY_lib.Yue_et_al_2017_NG.LTRonly.fa"
+LTR_query="$prefix.TY_REannotate.soloLTR.raw.fa"
+db=$TE_lib_LTRonly
 db_tag="soloLTR_db";
-if [ ! -s "$db" ]
+if [ ! -s "$LTR_query" ]
 then
-    echo "$db is empty, skip .."
+    echo "$LTR_query is empty, skip .."
     touch $prefix.TY_soloLTR.refined.nr.gff
 else
-    LTR_query="$prefix.TY_REannotate.soloLTR.raw.fa"
-    $blast_dir/makeblastdb  -in $db  -dbtype nucl -title $db_tag -hash_index -out $db_tag
-    $blast_dir/blastn  -task blastn -query $LTR_query -num_threads $threads -db $db_tag -outfmt 7 >$prefix.$db_tag.soloLTR.blastn.fmt7.out
-    perl $LRSDAY_HOME/scripts/trim_soloLTR_by_blast.pl -q $LTR_query -b  $prefix.$db_tag.soloLTR.blastn.fmt7.out -p $prefix  -i 70 -l 100
+    $blast_dir/makeblastdb -in $db -dbtype nucl -title $db_tag -hash_index -out $db_tag
+    $blast_dir/blastn -task blastn -query $LTR_query -num_threads $threads -db $db_tag -outfmt 7 >$prefix.$db_tag.soloLTR.blastn.fmt7.out
+    perl $LRSDAY_HOME/scripts/trim_soloLTR_by_blast.pl -q $LTR_query -b  $prefix.$db_tag.soloLTR.blastn.fmt7.out -p $prefix  -i 75 -l 100
     $bedtools_dir/bedtools sort  -i  $prefix.TY_REannotate.soloLTR.refined.gff > $prefix.TY_REannotate.soloLTR.refined.sorted.gff
-    perl $LRSDAY_HOME/scripts/rm_overlap_features_from_gff_simple.pl  -r ./../genome.fa  -i $prefix.TY_REannotate.soloLTR.refined.sorted.gff -o $prefix.TY_soloLTR.refined.nr.gff 
+    perl $LRSDAY_HOME/scripts/rm_overlap_features_from_gff_simple.pl  -r ./../$prefix.genome.fa  -i $prefix.TY_REannotate.soloLTR.refined.sorted.gff -o $prefix.TY_soloLTR.refined.nr.gff 
 fi
 
-for i in {1..5}
+for i in TY1 TY2 TY3 TY4 TY5 TSU4
 do
-    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.complete.TY${i}.final.list -o $prefix.TY_REannotate.complete.TY${i}.final.gff -t $prefix
-    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.truncated.TY${i}.final.list -o $prefix.TY_REannotate.truncated.TY${i}.final.gff -t $prefix
+    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.complete.$i.final.list -o $prefix.TY_REannotate.complete.$i.final.gff -t $prefix
+    perl $LRSDAY_HOME/scripts/TY_list2gff3.pl -i $prefix.TY_REannotate.truncated.$i.final.list -o $prefix.TY_REannotate.truncated.$i.final.gff -t $prefix
 done
 
 cat $prefix.TY_REannotate.*.final.gff > $prefix.TY.complete_plus_truncated.final.gff
@@ -102,17 +111,22 @@ $bedtools_dir/bedtools intersect -v -a $prefix.TY_soloLTR.refined.nr.gff -b $pre
 
 cat $prefix.TY.complete_plus_truncated.final.gff $prefix.TY.soloLTR.final.gff > $prefix.TY.all.final.gff
 
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r ./../genome.fa -i $prefix.TY.all.final.gff -o $prefix.TE.gff3 -t $prefix 
+#perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -r ./../$prefix.genome.fa -i $prefix.TY.all.final.gff -o $prefix.TE.gff3 -t $prefix 
+perl $LRSDAY_HOME/scripts/tidy_TE_gff3.pl -r ./../$prefix.genome.fa -i $prefix.TY.all.final.gff -o ./../$prefix.nuclear_genome.TE.gff3 -t $prefix 
+
+
+if [[ $debug == "no" ]]
+then
+    rm $prefix.*.final.gff
+fi
 
-cp $prefix.TE.gff3 ./../
-cp $prefix.REannotate.gff ./../
-rm $prefix.*.final.gff
 cd ..
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
-    rm genome.fa*
+    rm $prefix.assembly.nuclear_genome*
+    rm $prefix.genome.fa*
 fi
 
 ############################
diff --git a/pipelines/LRSDAY.12.Core_X_Element_Annotation.sh b/pipelines/LRSDAY.12.Core_X_Element_Annotation.sh
index 5c4f6f6..15c64b4 100755
--- a/pipelines/LRSDAY.12.Core_X_Element_Annotation.sh
+++ b/pipelines/LRSDAY.12.Core_X_Element_Annotation.sh
@@ -6,25 +6,34 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
 # process the pipeline
 feature_type="X_element"
 length_cutoff_for_completeness=300
-$hmmer_dir/nhmmer -E 1 --tblout $prefix.$feature_type.nhmmer.out $LRSDAY_HOME/data/S288C.$feature_type.hmm $genome
-perl $LRSDAY_HOME/scripts/nhmer2seq.pl  -r $genome -i $prefix.$feature_type.nhmmer.out -e 0.0001 -p $prefix -ft $feature_type -l $length_cutoff_for_completeness
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $genome -o $prefix.$feature_type.gff3 -t $prefix
-perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $genome -g $prefix.$feature_type.gff3 -o $prefix.$feature_type.fa 
-$muscle_dir/muscle -in $prefix.$feature_type.fa -out $prefix.$feature_type.aln.fa
+
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+
+
+$hmmer_dir/nhmmer -E 1 --tblout $prefix.$feature_type.nhmmer.out $LRSDAY_HOME/data/S288C.$feature_type.hmm $prefix.assembly.nuclear_genome.tidy.fa
+perl $LRSDAY_HOME/scripts/nhmer2seq.pl -r $prefix.assembly.nuclear_genome.tidy.fa -i $prefix.$feature_type.nhmmer.out -e 0.0001 -p $prefix -ft $feature_type -l $length_cutoff_for_completeness
+perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $prefix.assembly.nuclear_genome.tidy.fa -o $prefix.nuclear_genome.$feature_type.gff3 -t $prefix
+perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $prefix.assembly.nuclear_genome.tidy.fa -g $prefix.nuclear_genome.$feature_type.gff3 -o $prefix.nuclear_genome.$feature_type.fa 
+$muscle_dir/muscle -in $prefix.nuclear_genome.$feature_type.fa -out $prefix.nuclear_genome.$feature_type.aln.fa
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
     rm $prefix.$feature_type.raw.gff3
     rm $prefix.$feature_type.raw.fa
+    rm $prefix.assembly.nuclear_genome.fa
+    rm $prefix.assembly.nuclear_genome.tidy.fa
 fi
 
 ############################
diff --git a/pipelines/LRSDAY.13.Y_Prime_Element_Annotation.sh b/pipelines/LRSDAY.13.Y_Prime_Element_Annotation.sh
index 52fcfd5..3c5b590 100755
--- a/pipelines/LRSDAY.13.Y_Prime_Element_Annotation.sh
+++ b/pipelines/LRSDAY.13.Y_Prime_Element_Annotation.sh
@@ -6,8 +6,9 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
+chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the final assembly. If there are multiple sequences, use a single ';' to separate them. e.g. "chrMT_part1;chrMT_part2". Default = "chrMT".
 debug="no" # Whether to keep intermediate files for debugging. Use "yes" if prefer to keep intermediate files, otherwise use "no". Default = "no".
 
 #######################################
@@ -16,13 +17,17 @@ feature_type="Y_prime_element"
 query="$LRSDAY_HOME/data/query.Y_prime_element.long.fa"
 length_cutoff_for_completeness=3500
 
-$ucsc_dir/blat -maxIntron=1000 $genome $query  $prefix.$feature_type.blat.psl
+echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.assembly.nuclear_genome.fa -o $prefix.assembly.nuclear_genome.tidy.fa
+
+$ucsc_dir/blat -maxIntron=1000 $prefix.assembly.nuclear_genome.tidy.fa $query  $prefix.$feature_type.blat.psl
 $ucsc_dir/pslCDnaFilter  -minId=0.9 -minAlnSize=1000 -bestOverlap -filterWeirdOverlapped   $prefix.$feature_type.blat.psl  $prefix.$feature_type.blat.filtered.psl
 $ucsc_dir/pslScore  $prefix.$feature_type.blat.filtered.psl | sort -nk5 -r > $prefix.$feature_type.blat.filtered.pslScore.out
-perl $LRSDAY_HOME/scripts/psl2gff3.pl -i $prefix.$feature_type.blat.filtered.psl -o $prefix.$feature_type.raw.gff3 -ft $feature_type -t $prefix -r $genome -l $length_cutoff_for_completeness
-perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $genome -o $prefix.$feature_type.gff3 -t $prefix
-perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $genome -g $prefix.$feature_type.gff3 -o $prefix.$feature_type.fa
-$muscle_dir/muscle -in $prefix.$feature_type.fa -out $prefix.$feature_type.aln.fa
+perl $LRSDAY_HOME/scripts/psl2gff3.pl -i $prefix.$feature_type.blat.filtered.psl -o $prefix.$feature_type.raw.gff3 -ft $feature_type -t $prefix -r $prefix.assembly.nuclear_genome.tidy.fa  -l $length_cutoff_for_completeness
+perl $LRSDAY_HOME/scripts/tidy_maker_gff3.pl -i $prefix.$feature_type.raw.gff3 -r $prefix.assembly.nuclear_genome.tidy.fa -o $prefix.nuclear_genome.$feature_type.gff3 -t $prefix
+perl $LRSDAY_HOME/scripts/gff2seq_simple.pl -r $prefix.assembly.nuclear_genome.tidy.fa -g $prefix.nuclear_genome.$feature_type.gff3 -o $prefix.nuclear_genome.$feature_type.fa
+$muscle_dir/muscle -in $prefix.nuclear_genome.$feature_type.fa -out $prefix.nuclear_genome.$feature_type.aln.fa
 
 # clean up intermediate files
 if [[ $debug == "no" ]]
@@ -31,6 +36,8 @@ then
     rm $prefix.Y_prime_element.blat.psl
     rm $prefix.Y_prime_element.blat.filtered.psl
     rm $prefix.Y_prime_element.blat.filtered.pslScore.out
+    rm $prefix.assembly.nuclear_genome.fa
+    rm $prefix.assembly.nuclear_genome.tidy.fa
 fi
 
  
diff --git a/pipelines/LRSDAY.14.Gene_Orthology_Identification.sh b/pipelines/LRSDAY.14.Gene_Orthology_Identification.sh
index 2fc5a3d..0fe8c04 100755
--- a/pipelines/LRSDAY.14.Gene_Orthology_Identification.sh
+++ b/pipelines/LRSDAY.14.Gene_Orthology_Identification.sh
@@ -6,16 +6,17 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-threads=1 # The number of threads to use. Default = "1".
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
 
-input_nuclear_gene_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.EVM.gff3" # The file path of the input nuclear gene gff3 file generated in the task 09.Nuclear_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the nuclear gene annotation. 
-query_nuclear_gene_PoFF_faa="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.EVM.PoFF.faa" # The file path of the PoFF.faa file generated in the task 09.Nuclear_Gene_Annotation.
-query_nuclear_gene_PoFF_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.EVM.PoFF.gff" # The file path of the PoFF.gff file generated in the task 09.Nuclear_Gene_Annotation.
+threads=8 # The number of threads to use. Default = "8".
 
-input_mitochondrial_gene_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.mfannot.gff3" # The file path of the input mitochondrial gene gff3 file generated in the task 10.Mitochondrial_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the mitochondrial gene annotation. 
-query_mitochondrial_gene_PoFF_faa="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.mfannot.PoFF.faa" # The file path of the PoFF.faa file generated in the task 10.Mitochondrial_Gene_Annotation.
-query_mitochondrial_gene_PoFF_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.mfannot.PoFF.gff" # The file path of the PoFF.gff file generated in the task 10.Mitochondrial_Gene_Annotation.
+input_nuclear_genome_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.gff3" # The file path of the input nuclear gene gff3 file generated in the task 09.Nuclear_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the nuclear gene annotation. 
+query_nuclear_genome_PoFF_faa="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.PoFF.faa" # The file path of the PoFF.faa file generated in the task 09.Nuclear_Gene_Annotation.Po
+query_nuclear_genome_PoFF_gff="./../09.Nuclear_Gene_Annotation/$prefix.nuclear_genome.PoFF.gff" # The file path of the PoFF.gff file generated in the task 09.Nuclear_Gene_Annotation.
+
+input_mitochondrial_genome_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.gff3" # The file path of the input mitochondrial gene gff3 file generated in the task 10.Mitochondrial_Gene_Annotation. Set this variable as well as the following two variables to "" if you want to skip this step for the mitochondrial gene annotation. 
+query_mitochondrial_genome_PoFF_faa="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.PoFF.faa" # The file path of the PoFF.faa file generated in the task 10.Mitochondrial_Gene_Annotation.
+query_mitochondrial_genome_PoFF_gff="./../10.Mitochondrial_Gene_Annotation/$prefix.mitochondrial_genome.PoFF.gff" # The file path of the PoFF.gff file generated in the task 10.Mitochondrial_Gene_Annotation.
 
 ref_PoFF_faa="$LRSDAY_HOME/data/SGDref.PoFF.faa" # The file path of the reference proteome file in FASTA format: for S. cerevisiae and its close relatives, you can directly use the pre-shipped file: SGDref.PoFF.faa; if you work with other organisms, you can check ProteinOrtho's manual for details on how to prepare such file.
 ref_PoFF_gff="$LRSDAY_HOME/data/SGDref.PoFF.gff" # The path of the reference gene GFF file in GFF format: for S. cerevisiae and its close relatives, you can directly use the pre-shipped file: SGDref.PoFF.gff; if you work with other organisms, you can check ProteinOrtho's manual for details on how to prepare such file.
@@ -41,46 +42,45 @@ cp $ref_PoFF_faa ref.PoFF.faa
 cp $ref_PoFF_gff ref.PoFF.gff
 
 # process nuclear gene annotation
-if [[ ! -z $input_nuclear_gene_gff ]]
+if [[ ! -z $input_nuclear_genome_gff ]]
 then 
-    echo "The variable input_nuclear_gene_gff has been specified, so expecting input files specified for query_nuclear_gene_PoFF_faa and query_nuclear_gene_PoFF_gff"
-    test_file_existence $query_nuclear_gene_PoFF_faa
-    test_file_existence $query_nuclear_gene_PoFF_gff
-    cp $query_nuclear_gene_PoFF_faa query.nuclear_gene.PoFF.faa
-    cp $query_nuclear_gene_PoFF_gff query.nuclear_gene.PoFF.gff
-    output_nuclear_gene_gff="$prefix.nuclear_gene.orthology_map.gff3"
-    proteinortho_nuclear_gene_input="query.nuclear_gene.PoFF.faa ref.PoFF.faa"
-    perl $proteinortho_dir/proteinortho5.pl -cpus=$threads -blastpath=$blast_dir -singles -synteny -project="$prefix.nuclear_gene" $proteinortho_nuclear_gene_input  
-    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_nuclear_gene_gff -x $prefix.nuclear_gene.poff -r ref.PoFF.faa -q query.nuclear_gene.PoFF.faa -o $prefix.nuclear_gene.updated.gff3
+    echo "The variable input_nuclear_genome_gff has been specified, so expecting input files specified for query_nuclear_genome_PoFF_faa and query_nuclear_genome_PoFF_gff"
+    test_file_existence $query_nuclear_genome_PoFF_faa
+    test_file_existence $query_nuclear_genome_PoFF_gff
+    cp $query_nuclear_genome_PoFF_faa query.nuclear_genome.PoFF.faa
+    cp $query_nuclear_genome_PoFF_gff query.nuclear_genome.PoFF.gff
+    proteinortho_nuclear_genome_input="query.nuclear_genome.PoFF.faa ref.PoFF.faa"
+    $proteinortho_dir/proteinortho -cpus=$threads -p=blastp -binpath=$blast_dir -singles -synteny -project="$prefix.nuclear_genome" $proteinortho_nuclear_genome_input
+    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_nuclear_genome_gff -x $prefix.nuclear_genome.proteinortho.tsv -r ref.PoFF.faa -q query.nuclear_genome.PoFF.faa -o $prefix.nuclear_genome.SGD_orthology_mapped.gff3
+
 
     if [[ $debug == "no" ]]
     then
-	rm $prefix.nuclear_gene.ffadj-graph
-	rm $prefix.nuclear_gene.blast-graph
-	rm $prefix.nuclear_gene.proteinortho-graph
-	rm $prefix.nuclear_gene.poff-graph
+	rm $prefix.nuclear_genome.ffadj-graph
+	rm $prefix.nuclear_genome.blast-graph
+	rm $prefix.nuclear_genome.proteinortho-graph
+	rm $prefix.nuclear_genome.poff-graph
     fi
 fi
 
 # process mitochondrial gene annotation
-if [[ ! -z $input_mitochondrial_gene_gff ]]
+if [[ ! -z $input_mitochondrial_genome_gff ]]
 then 
-    echo "The variable input_mitochondrial_gene_gff has been specified, so expecting input files specified for query_mitochondrial_gene_PoFF_faa and query_mitochondrial_gene_PoFF_gff"
-    test_file_existence $query_mitochondrial_gene_PoFF_faa
-    test_file_existence $query_mitochondrial_gene_PoFF_gff
-    cp $query_mitochondrial_gene_PoFF_faa query.mitochondrial_gene.PoFF.faa
-    cp $query_mitochondrial_gene_PoFF_gff query.mitochondrial_gene.PoFF.gff
-    output_mitochondrial_gene_gff="$prefix.mitochondrial_gene.orthology_map.gff3"
-    proteinortho_mitochondrial_gene_input="query.mitochondrial_gene.PoFF.faa ref.PoFF.faa"
-    perl $proteinortho_dir/proteinortho5.pl -cpus=$threads -blastpath=$blast_dir -singles -synteny -project="$prefix.mitochondrial_gene"  $proteinortho_mitochondrial_gene_input  
-    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_mitochondrial_gene_gff -x $prefix.mitochondrial_gene.poff -r ref.PoFF.faa -q query.mitochondrial_gene.PoFF.faa -o $prefix.mitochondrial_gene.updated.gff3
+    echo "The variable input_mitochondrial_genome_gff has been specified, so expecting input files specified for query_mitochondrial_genome_PoFF_faa and query_mitochondrial_genome_PoFF_gff"
+    test_file_existence $query_mitochondrial_genome_PoFF_faa
+    test_file_existence $query_mitochondrial_genome_PoFF_gff
+    cp $query_mitochondrial_genome_PoFF_faa query.mitochondrial_genome.PoFF.faa
+    cp $query_mitochondrial_genome_PoFF_gff query.mitochondrial_genome.PoFF.gff
+    proteinortho_mitochondrial_genome_input="query.mitochondrial_genome.PoFF.faa ref.PoFF.faa"
+    perl $proteinortho_dir/proteinortho -cpus=$threads -p=blastp -binpath=$blast_dir -singles -synteny -project="$prefix.mitochondrial_genome"  $proteinortho_mitochondrial_genome_input  
+    perl $LRSDAY_HOME/scripts/update_gff3_by_proteinortho.pl -i $input_mitochondrial_genome_gff -x $prefix.mitochondrial_genome.proteinortho.tsv -r ref.PoFF.faa -q query.mitochondrial_genome.PoFF.faa -o $prefix.mitochondrial_genome.SGD_orthology_mapped.gff3
 
     if [[ $debug == "no" ]]
     then
-	rm $prefix.mitochondrial_gene.ffadj-graph
-	rm $prefix.mitochondrial_gene.blast-graph
-	rm $prefix.mitochondrial_gene.proteinortho-graph
-	rm $prefix.mitochondrial_gene.poff-graph
+	rm $prefix.mitochondrial_genome.ffadj-graph
+	rm $prefix.mitochondrial_genome.blast-graph
+	rm $prefix.mitochondrial_genome.proteinortho-graph
+	rm $prefix.mitochondrial_genome.poff-graph
     fi
 fi
 
@@ -90,6 +90,7 @@ if [[ $debug == "no" ]]
 then
     rm query.*
     rm ref.*
+    rm proteinortho_cache_${prefix}.log
 fi
     
 ############################
diff --git a/pipelines/LRSDAY.15.Annotation_Integration.sh b/pipelines/LRSDAY.15.Annotation_Integration.sh
index 306f7e8..695d896 100755
--- a/pipelines/LRSDAY.15.Annotation_Integration.sh
+++ b/pipelines/LRSDAY.15.Annotation_Integration.sh
@@ -6,14 +6,15 @@ source ./../../env.sh
 
 #######################################
 # set project-specific variables
-prefix="SK1" # The file name prefix for the processing sample. Default = "SK1" for the testing example.
-genome="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the input genome assembly.
-centromere_gff3="./../08.Centromere_Annotation/$prefix.centromere.gff3" # The path of the final centromere annotation gff3 generated by task 08.Centromere_Annotation_for_FinalAssembly, use "" if not existing.
-TE_gff3="./../11.TE_Annotation/$prefix.TE.gff3" # The file path of the TE annotation gff3 generated by task 11.TE_Annotation, use "" if not existing.
-X_element_gff3="./../12.Core_X_Element_Annotation/$prefix.X_element.gff3" # The file path of the X_element annotation gff3 generated by task 12.CoreX_Annotation, use "" if not existing.
-Y_prime_element_gff3="./../13.Y_Prime_Element_Annotation/$prefix.Y_prime_element.gff3" # The file path of the Y_prime_element annotation gff3 generated by task 13.Yprime_Annotation, use "" if not existing.
-nuclear_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.nuclear_gene.updated.gff3" # The file path of the nuclear gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 09.Nuclear_Gene_Annotation, use "" if not existing.
-mitochondrial_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.mitochondrial_gene.updated.gff3" # The file path of the mitochondrial gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 10.Mitochondrial_Gene_Annotation, use "" if not existing.
+prefix="CPG_1a" # The file name prefix (only allowing strings of alphabetical letters, numbers, and underscores) for the processing sample. Default = "CPG_1a" for the testing example.          
+
+genome_assembly="./../07.Supervised_Final_Assembly/$prefix.assembly.final.fa" # The file path of the final input genome assembly.
+centromere_gff3="./../08.Centromere_Annotation/$prefix.nuclear_genome.centromere.gff3" # The path of the final centromere annotation gff3 generated by task 08.Centromere_Annotation_for_FinalAssembly, use "" if not existing.
+TE_gff3="./../11.TE_Annotation/$prefix.nuclear_genome.TE.gff3" # The file path of the TE annotation gff3 generated by task 11.TE_Annotation, use "" if not existing.
+X_element_gff3="./../12.Core_X_Element_Annotation/$prefix.nuclear_genome.X_element.gff3" # The file path of the X_element annotation gff3 generated by task 12.CoreX_Annotation, use "" if not existing.
+Y_prime_element_gff3="./../13.Y_Prime_Element_Annotation/$prefix.nuclear_genome.Y_prime_element.gff3" # The file path of the Y_prime_element annotation gff3 generated by task 13.Yprime_Annotation, use "" if not existing.
+nuclear_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.nuclear_genome.SGD_orthology_mapped.gff3" # The file path of the nuclear gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 09.Nuclear_Gene_Annotation, use "" if not existing.
+mitochondrial_gene_gff3="./../14.Gene_Orthology_Identification/$prefix.mitochondrial_genome.SGD_orthology_mapped.gff3" # The file path of the mitochondrial gene annotation gff3 generated by task 14.GeneOrthology_Identification (which is better) or 10.Mitochondrial_Gene_Annotation, use "" if not existing.
 chrMT_tag="chrMT" # The sequence name for the mitochondrial genome in the input genome assembly, if there are multiple corresponding contigs/scaffolds, use a single ';' to separate them. e.g. "chrMT_1;chrMT_2". Default = "chrMT". 
 chrMT_genetic_code_table=3 # The NCBI genetic code table (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) for the annotated mitochondrial genome. Default = 3 (i.e. Yeast Mitochondria)
 
@@ -21,38 +22,52 @@ debug="no" # use "yes" if prefer to keep intermediate files, otherwise use "no".
 
 ######################################
 # process the pipeline
-cat $centromere_gff3 $TE_gff3 $X_element_gff3 $Y_prime_element_gff3 $nuclear_gene_gff3 $mitochondrial_gene_gff3  >$prefix.concatenated.gff3
-perl $LRSDAY_HOME/scripts/sort_gff3.pl -i $prefix.concatenated.gff3 -t $prefix -o $prefix.final.gff3 -r $genome
-perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $genome -g $prefix.final.gff3 -o $prefix.final.cds.fa
 
-cp $genome $prefix.assembly.final.fa
 echo $chrMT_tag | sed -e "s/;/\n/g" > $prefix.assembly.chrMT.list
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m reverse -o $prefix.assembly.nuclear_genome.fa
-$LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome -l $prefix.assembly.chrMT.list -m normal -o $prefix.assembly.mitochondrial_genome.fa
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m reverse -o $prefix.nuclear_genome.fa
+perl $LRSDAY_HOME/scripts/select_fasta_by_list.pl -i $genome_assembly -l $prefix.assembly.chrMT.list -m normal -o $prefix.mitochondrial_genome.fa
+
+perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.nuclear_genome.fa -o $prefix.nuclear_genome.tidy.fa
+
+cat $centromere_gff3 $TE_gff3 $X_element_gff3 $Y_prime_element_gff3 $nuclear_gene_gff3  >$prefix.nuclear_genome.concatenated.gff3
+perl $LRSDAY_HOME/scripts/sort_gff3.pl -i $prefix.nuclear_genome.concatenated.gff3 -t $prefix -o $prefix.nuclear_genome.tidy.gff3 -r $prefix.nuclear_genome.tidy.fa
 
 if [[ ! -z $nuclear_gene_gff3 ]]
 then
-    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.nuclear_genome.fa -g $prefix.final.gff3 -o $prefix.nuclear_genome.cds.fa
-    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.nuclear_genome.cds.fa -p $prefix.nuclear_genome -t 1
+    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.nuclear_genome.tidy.fa -g $prefix.nuclear_genome.tidy.gff3 -o $prefix.nuclear_genome.tidy.cds.fa
+    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.nuclear_genome.tidy.cds.fa -p $prefix.nuclear_genome.tidy -t 1
 fi
 
-if [[ ! -z $mitochondrial_gene_gff3 ]]
+if [[ $(egrep -c "^>" "$prefix.mitochondrial_genome.fa") -eq 0 ]]
 then
-    perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.assembly.mitochondrial_genome.fa -g $prefix.final.gff3 -o $prefix.mitochondrial_genome.cds.fa
-    perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.cds.fa -p $prefix.mitochondrial_genome -t $chrMT_genetic_code_table
-fi
+    echo "No mitochondrial genome assembly was detected! Skip final annotation aggregation for the mitochondrial genome!"
+else
+    perl $LRSDAY_HOME/scripts/tidy_fasta.pl -i $prefix.mitochondrial_genome.fa -o $prefix.mitochondrial_genome.tidy.fa
+    cp $mitochondrial_gene_gff3 $prefix.mitochondrial_genome.tidy.gff3
+    if [[ ! -z $mitochondrial_gene_gff3 ]]
+    then
+	perl $LRSDAY_HOME/scripts/extract_cds_from_tidy_gff3.pl -r $prefix.mitochondrial_genome.tidy.fa -g $prefix.mitochondrial_genome.tidy.gff3 -o $prefix.mitochondrial_genome.tidy.cds.fa
+	perl $LRSDAY_HOME/scripts/cds2protein.pl -i $prefix.mitochondrial_genome.tidy.cds.fa -p $prefix.mitochondrial_genome.tidy -t $chrMT_genetic_code_table
+    fi
 
-if [[ ! -z $nuclear_gene_gff3 && ! -z $mitochondrial_gene_gff3 ]]
-then
-    cat $prefix.nuclear_genome.trimmed_cds.fa $prefix.mitochondrial_genome.trimmed_cds.fa > $prefix.final.trimmed_cds.fa
-    cat $prefix.nuclear_genome.pep.fa $prefix.mitochondrial_genome.pep.fa >$prefix.final.pep.fa
-    cat $prefix.nuclear_genome.manual_check.list  $prefix.mitochondrial_genome.manual_check.list > $prefix.final.manual_check.list
 fi
 
+
+
 # clean up intermediate files
 if [[ $debug == "no" ]]
 then
-    rm $prefix.concatenated.gff3
+    rm $prefix.nuclear_genome.concatenated.gff3
+
+    if [[ -e $prefix.nuclear_genome.fa ]]
+    then
+	rm $prefix.nuclear_genome.fa
+    fi
+
+    if [[ -e $prefix.mitochondrial_genome.fa ]]
+    then
+	rm $prefix.mitochondrial_genome.fa
+    fi
 fi
 
 ############################
diff --git a/prerequisite.txt b/prerequisite.txt
index 85a0240..044f5b0 100644
--- a/prerequisite.txt
+++ b/prerequisite.txt
@@ -3,7 +3,7 @@
 #######################################################
 # Hardware, operating system and network requirements
 #######################################################
-This protocol is designed for a desktop or computing server running an x86-64-bit Linux operating system. Multithreaded processors are preferred to speed up the process since many steps can be configured to use multiple threads in parallel. For assembling and analyzing the budding yeast genomes (genome size = ~12.5 Mb), at least 16 Gb of RAM and 100 Gb of free disk space are reccomended. When adapted for other eukaryotic organisms with larger genome sizes, the RAM and disk space consumption will scale up, majorly during de novo genome assembly (performed by Canu). Plese refer to Canu’s manual (http://canu.readthedocs.io/en/latest/) for suggested RAM and disk space consumption for assembling large genomes. Stable Internet connection is required for the installation and configuration of LRSDAY as well as for retrieving the testing data.
+This protocol is designed for a desktop or computing server running an x86-64-bit Linux operating system. Multithreaded processors are preferred to speed up the process since many steps can be configured to use multiple threads in parallel. For assembling and analyzing the budding yeast genomes (genome size = ~12.5 Mb), at least 16 Gb of RAM and 100 Gb of free disk space are reccomended. More disk space is needed if you want to use LRSDAY to do Nanopore basecalling. When adapted for other eukaryotic organisms with larger genome sizes, the RAM and disk space consumption will scale up, majorly during de novo genome assembly (performed by Canu). Plese refer to Canu’s manual (http://canu.readthedocs.io/en/latest/) for suggested RAM and disk space consumption for assembling large genomes. Stable Internet connection is required for the installation and configuration of LRSDAY as well as for retrieving the testing data.
 
 ########################
 # Software requirements
@@ -20,7 +20,7 @@ This protocol is designed for a desktop or computing server running an x86-64-bi
 ● perl v5.12 or newer (https://www.perl.org/)
 ● python v2.7.9 or newer (https://www.python.org/)
 ● python-devel 
-● python v3.4 or newer (https://www.python.org/)
+● python v3.7 or newer (https://www.python.org/)
 ● python3-devel 
 ● tar (https://www.gnu.org/software/tar/)
 ● unzip (http://infozip.sourceforge.net/UnZip.html)
diff --git a/scripts/TY_list2gff3.pl b/scripts/TY_list2gff3.pl
index 8ba2fe0..872f264 100755
--- a/scripts/TY_list2gff3.pl
+++ b/scripts/TY_list2gff3.pl
@@ -6,7 +6,7 @@
 ##############################################################
 #  script: TY_list2gff3.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2017.06.17
+#  last edited: 2022.12.11
 #  description: covert TY_list to GFF3
 #  example: perl TY_list2gff3.pl -i ty.list -o ty.gff3 -t genome_tag
 ##############################################################
@@ -35,6 +35,7 @@
     }
     my $new_id = "$type:$chr:$start-$end:$strand";
     print $output_fh "$chr\t$tag\t$type\t$start\t$end\t.\t$strand\t.\tID=${new_id};Name=${new_id}\n";
+    # print $output_fh "$chr\t$tag\tmobile_element\t$start\t$end\t.\t$strand\t.\tID=${new_id};Name=${new_id};mobile_element_type=$type\n";
 }
 
 sub read_file {
diff --git a/scripts/break_contig_by_blast.pl b/scripts/break_contig_by_blast.pl
index c0c9bb7..3cd42cc 100755
--- a/scripts/break_contig_by_blast.pl
+++ b/scripts/break_contig_by_blast.pl
@@ -6,7 +6,7 @@
 ##############################################################
 #  script: break_contig_by_blast.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2018.01.24
+#  last edited: 2022.03.04
 #  description: break contigs containing blast hit into multiple contigs
 #  example: perl break_contig_by_blast.pl -i input.fa(.gz) -o output.fa(.gz) -b blast.result.outfmt7.txt 
 ##############################################################
@@ -101,10 +101,18 @@ sub parse_blast_file {
 	    $blast{$subject}{'part2'} = substr $input{$subject}, $subject_start - 1;
 	} else {
 	    # hit on the negative strand
-	    $blast{$subject}{'part1'} = substr $input{$subject}, 0, $subject_end;
-	    $blast{$subject}{'part2'} = substr $input{$subject}, $subject_end;
+	    $blast{$subject}{'part1'} = substr $input{$subject}, 0, $subject_start;
+	    $blast{$subject}{'part1'} = revcom($blast{$subject}{'part1'});
+	    $blast{$subject}{'part2'} = substr $input{$subject}, $subject_start;
+	    $blast{$subject}{'part2'} = revcom($blast{$subject}{'part2'});
 	}
     }
     return %blast;
 }
 
+sub revcom {
+    my $seq = shift @_;
+    my $seq_revcom = reverse $seq;
+    $seq_revcom =~ tr/ATGCNatgcn/TACGNtacgn/;
+    return $seq_revcom;
+}
diff --git a/scripts/cal_assembly_stats.pl b/scripts/cal_assembly_stats.pl
index b4feffa..2e7bc35 100755
--- a/scripts/cal_assembly_stats.pl
+++ b/scripts/cal_assembly_stats.pl
@@ -7,7 +7,7 @@
 ##############################################################
 #  script: cal_assembly_stats.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2017.06.19
+#  last edited: 2022.07.22
 #  description: calculate basice statistics for genome assemblies, such as GC%, N50, N90, etc ...
 #  example: perl cal_assembly_stats.pl -i input.fa(.gz) -o output.txt
 ##############################################################
@@ -59,10 +59,17 @@
     my $base_pct = $base_count{$base} * 100 / $total_sequence_length;
     $base_pct{$base} =  sprintf("%.2f", $base_pct);
 }
-$base_pct{'AT'} =  ($base_count{'A'} + $base_count{'T'}) * 100 / $total_sequence_length;
-$base_pct{'GC'} =  ($base_count{'G'} + $base_count{'C'}) * 100 / $total_sequence_length;
+
+$base_count{'AT'} = $base_count{'A'} + $base_count{'T'};
+$base_count{'GC'} = $base_count{'G'} + $base_count{'C'};
+$base_pct{'AT'} =  ($base_count{'AT'} * 100) / $total_sequence_length;
+$base_pct{'GC'} =  ($base_count{'GC'} * 100) / $total_sequence_length;
 $base_pct{'AT'} =  sprintf("%.2f", $base_pct{'AT'});
 $base_pct{'GC'} =  sprintf("%.2f", $base_pct{'GC'});
+$base_pct{'AT_adjusted'} = ($base_count{'AT'} * 100)/($base_count{'AT'} + $base_count{'GC'});
+$base_pct{'GC_adjusted'} = ($base_count{'GC'} * 100)/($base_count{'AT'} + $base_count{'GC'});
+$base_pct{'AT_adjusted'} =  sprintf("%.2f", $base_pct{'AT_adjusted'});
+$base_pct{'GC_adjusted'} =  sprintf("%.2f", $base_pct{'GC_adjusted'});
 
 print $output_fh "total sequence count: $total_sequence_count\n";
 print $output_fh "total sequence length: $total_sequence_length\n";
@@ -70,18 +77,29 @@
 print $output_fh "max sequence length: $max_length\n";
 print $output_fh "mean sequence length: $mean_length\n";
 print $output_fh "median sequence length: $median_length\n";
+print $output_fh "###################\n";
 print $output_fh "N50: $N50\n";
 print $output_fh "L50: $L50\n";
 print $output_fh "N90: $N90\n";
 print $output_fh "L90: $L90\n";
-
+print $output_fh "###################\n";
+print $output_fh "A count: $base_count{'A'}\n";
+print $output_fh "T count: $base_count{'T'}\n";
+print $output_fh "G count: $base_count{'G'}\n";
+print $output_fh "C count: $base_count{'C'}\n";
+print $output_fh "(A+T) count: $base_count{'AT'}\n";
+print $output_fh "(G+C) count: $base_count{'GC'}\n";
+print $output_fh "N count: $base_count{'N'}\n";
+print $output_fh "###################\n";
 print $output_fh "A%: $base_pct{'A'}\n";
 print $output_fh "T%: $base_pct{'T'}\n";
 print $output_fh "G%: $base_pct{'G'}\n";
 print $output_fh "C%: $base_pct{'C'}\n";
-print $output_fh "AT%: $base_pct{'AT'}\n";
-print $output_fh "GC%: $base_pct{'GC'}\n";
+print $output_fh "(A+T)%: $base_pct{'AT'}\n";
+print $output_fh "(G+C)%: $base_pct{'GC'}\n";
 print $output_fh "N%: $base_pct{'N'}\n";
+print $output_fh "((A+T)/(A+T+G+C))%: $base_pct{'AT_adjusted'}\n";
+print $output_fh "((G+C)/(A+T+G+C))%: $base_pct{'GC_adjusted'}\n";
 
 
 sub read_file {
@@ -155,6 +173,24 @@ sub cal_median {
 	return $median;
 }
 
+sub cal_stdev {
+    my $data_arrayref = shift @_;
+    my $data_num = scalar @$data_arrayref;
+    my $stdev;
+    if ($data_num == 1){
+        $stdev = 0;
+    } else {
+        my $mean = cal_mean($data_arrayref);
+        my $sq_sum = 0;
+        foreach my $i (@$data_arrayref) {
+            $sq_sum += ($mean -$i) ** 2;
+        }
+        $stdev = ($sq_sum / ($data_num - 1)) ** 0.5;
+    }
+    return $stdev;
+}
+
+
 
 
 sub cal_N50 {
diff --git a/scripts/extract_cds_from_tidy_gff3.pl b/scripts/extract_cds_from_tidy_gff3.pl
index ce7037e..d2b1340 100755
--- a/scripts/extract_cds_from_tidy_gff3.pl
+++ b/scripts/extract_cds_from_tidy_gff3.pl
@@ -6,7 +6,7 @@
 ##############################################################
 #  script: extract_cds_from_tidy_gff3.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2020.01.07
+#  last edited: 2022.12.11
 #  description: extract CDS sequences from GFF3 file
 #  example: perl extract_cds_from_tidy_gff3.pl -r genome.fa.gz -g genome.gff3 -o genome.cds.fa
 ##############################################################
@@ -36,6 +36,7 @@
 	}
     }
     foreach my $gene_id (sort {$gff{$a}{'gene_start'} <=> $gff{$b}{'gene_start'} or $gff{$a}{'gene_end'} <=> $gff{$b}{'gene_end'}} @genes_on_chr) {
+	my $gene_name = $gff{$gene_id}{'gene_name'};
 	foreach my $mRNA_id (sort {$gff{$gene_id}{'mRNA'}{$a}{'mRNA_index'} <=> $gff{$gene_id}{'mRNA'}{$b}{'mRNA_index'}} keys %{$gff{$gene_id}{'mRNA'}}) {
 	    my $mRNA_index = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_index'};
 	    my $mRNA_strand = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_strand'};
@@ -56,7 +57,7 @@
 	    if ($mRNA_strand eq '-') {
 		$mRNA_seq = revcom($mRNA_seq);
 	    }
-	    print $output_fh ">$gene_id|$mRNA_id\n$mRNA_seq\n";
+	    print $output_fh ">$gene_id|$mRNA_id|$gene_name\n$mRNA_seq\n";
 	}
     }
 }
@@ -130,6 +131,7 @@ sub parse_gff_file {
 		$gene_type = "gene";
 	    }
 	    $gff{$gene_id}{'gene_type'} = $gene_type;
+	    $gff{$gene_id}{'gene_name'} = $gene_name;
 	    $gff{$gene_id}{'gene_chr'} = $chr;
 	    $gff{$gene_id}{'gene_start'} = $start;
 	    $gff{$gene_id}{'gene_end'} = $end;
@@ -143,7 +145,7 @@ sub parse_gff_file {
 	    $gene_type = $type;
 	    $gene_id = "$gene_type:$chr:${start}-${end}:$strand";
 	    $gff{$gene_id}{'gene_type'} = $gene_type;
-	    $gff{$gene_id}{'gene_type'} = $type;
+	    $gff{$gene_id}{'gene_name'} = $gene_name;
 	    $gff{$gene_id}{'gene_chr'} = $chr;
 	    $gff{$gene_id}{'gene_start'} = $start;
 	    $gff{$gene_id}{'gene_end'} = $end;
diff --git a/scripts/label_pseudogene_in_gff3.pl b/scripts/label_pseudogene_in_gff3.pl
new file mode 100755
index 0000000..6c28fa1
--- /dev/null
+++ b/scripts/label_pseudogene_in_gff3.pl
@@ -0,0 +1,132 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+use Getopt::Long;
+
+##############################################################
+#  script: label_pseudogene_in_gff3.pl
+#  author: Jia-Xing Yue (GitHub ID: yjx1217)
+#  last edited: 2022.12.12
+#  description: label pseudogenes in gff3 by manual_check_list generated by cds2protein.pl
+#  example: perl label_pseudogene_in_gff3.pl -i input.gff3 -o output.gff3 -l check_list
+##############################################################
+
+my ($input, $output, $check_list);
+
+GetOptions('input|i:s' => \$input,
+	   'output|o:s' => \$output,
+	   'check_list|l:s' => \$check_list);
+
+my $list_fh = read_file($check_list);
+my %list = parse_list_file($list_fh);
+close $list_fh;
+
+my $input_fh = read_file($input);
+my $output_fh = write_file($output);
+
+my $gene_id;
+my $gene_name;
+my $new_gene_id;
+my $new_gene_name;
+my $new_gene_type;
+my $new_gene_attributes;
+
+while (<$input_fh>) {
+    chomp;
+    if (/^#/) {
+	print $output_fh "$_\n";
+    } else {
+	my ($chr, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split /\t/, $_;
+        if ($type eq "gene") {
+            ($gene_id, $gene_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+	    if (exists $list{'gene_id'}{$gene_id}) {
+		$new_gene_type = "pseudogene";
+		$new_gene_id = "${new_gene_type}:${chr}:${start}-${end}:$strand";
+		$new_gene_name = $new_gene_id;
+		$new_gene_attributes = "ID=$new_gene_id;Name=$new_gene_name";
+		print $output_fh "$chr\t$source\t$new_gene_type\t$start\t$end\t$score\t$strand\t$phase\t$new_gene_attributes\n";
+	    } else {
+		print $output_fh "$_\n";
+	    }
+	} elsif ($type eq "mRNA") {
+	    my ($mrna_id) = ($attributes =~ /ID=([^;]+)/);
+            if (exists $list{'mrna_id'}{$mrna_id}) {
+		my $new_mrna_type = "pseudogenic_transcript";
+		my $new_mrna_id = "${new_mrna_type}:${chr}:${start}-${end}:$strand";
+		my $new_mrna_name = $new_mrna_id;
+		my $new_mrna_attributes = "ID=$new_mrna_id;Name=$new_mrna_name;Parent=$new_gene_id";
+		print $output_fh "$chr\t$source\t$new_mrna_type\t$start\t$end\t$score\t$strand\t$phase\t$new_mrna_attributes\n";
+            } else {
+		print $output_fh "$_\n";
+            }
+	} elsif ($type =~ /(exon|CDS)/)  { 
+	    my ($parent_id) = ($attributes =~ /Parent=([^;]+)/);
+	    if (not exists $list{'mrna_id'}{$parent_id}) {
+		print $output_fh "$_\n";
+	    }
+	} else {
+	    print $output_fh "$_\n";
+	}
+    }
+}
+
+
+
+sub read_file {
+    my $file = shift @_;
+    my $fh;
+    if ($file =~ /\.gz$/) {
+        open($fh, "gunzip -c $file |") or die "can't open pipe to $file";
+    } else {
+        open($fh, $file) or die "can't open $file";
+    }
+    return $fh;
+}
+
+sub write_file {
+    my $file = shift @_;
+    my $fh;
+    if ($file =~ /.gz$/) {
+        open($fh, "| gzip -c >$file") or die "can't open $file\n";
+    } else {
+        open($fh, ">$file") or die "can't open $file\n";
+    }
+    return $fh;
+}  
+
+sub parse_fasta_file {
+    my ($fh, $input_hashref, $input_arrayref) = @_;
+    my $seq_name = "";
+    while (<$fh>) {
+        chomp;
+        if (/^\s*$/) {
+            next;
+        } elsif (/^\s*#/) {
+            next;
+        } elsif (/^>(.*)/) {
+            $seq_name = $1;
+            push @$input_arrayref, $seq_name;
+            $$input_hashref{$seq_name} = "";
+        } else {
+            $$input_hashref{$seq_name} .= $_;
+        }
+    }
+}
+
+sub parse_list_file {
+    my $fh = shift @_;
+    my %list = ();
+    while (<$fh>) {
+	chomp;
+	/^##FASTA/ and last;
+	/^#/ and next;
+	/^\s*$/ and next;
+	my ($transcript, $cause) = split /\t/, $_;
+	my ($gene_id, $transcript_id) = ($transcript =~ /([^\|]+)\|([^\|]+)/);
+	print "gene_id=$gene_id, transcript_id = $transcript_id\n";
+	$list{'gene_id'}{$gene_id} = $cause;
+	$list{'mrna_id'}{$transcript_id} = $cause;
+
+    }
+    return %list;
+}
diff --git a/scripts/mfannot2gff3.pl b/scripts/mfannot2gff3.pl
index 55395ff..c99bebd 100755
--- a/scripts/mfannot2gff3.pl
+++ b/scripts/mfannot2gff3.pl
@@ -6,19 +6,23 @@
 ##############################################################
 #  script: mfannot2gff3.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2018.09.01
-#  description: converting the mfannot output to the GFF3 format 
-#  example: perl mfannot2gff3.pl -i genome.mfannot.out -o genome.mfannot.gff3 -m lite 
+#  last edited: 2022.12.09
+#  description: converting the mfannot and trnascan output files into a final GFF3 output 
+#  example: perl mfannot2gff3.pl -tag strain_id -mfannot_out genome.mfannot.out.txt -trnascan_out genome.trnascan.out.txt -o genome.mfannot.gff3 -m lite 
 ##############################################################
 
-my ($input, $output, $mode);
+my ($mfannot_out, $trnascan_out, $tag, $output, $mode);
 $mode = "lite"; # use lite to filter out gene models annotated within introns
-GetOptions('input|i:s' => \$input,
+GetOptions('mfannot_out|mfannot_out:s' => \$mfannot_out,
+	   'trnascan_out|trnascan_out:s' => \$trnascan_out,
+	   'tag|t:s' => \$tag,
            'output|o:s' => \$output,
            'mode|m:s' => \$mode); # "full" or "lite"
 
-my $input_fh = read_file($input);
+my $trnascan_out_fh = read_file($trnascan_out);
+my %trnascan_out = parse_trnascan_out_file($trnascan_out_fh);
 
+my $mfannot_out_fh = read_file($mfannot_out);
 my %chr = ();
 my @chr = ();
 my %features = ();
@@ -26,7 +30,7 @@
 my $feature = "";
 my %gene2exon_intron = ();
 
-while (<$input_fh>) {
+while (<$mfannot_out_fh>) {
     chomp;
     /^\s*$/ and next;
     /^#/ and next;
@@ -36,6 +40,8 @@
 	$chr{$chr}{'genetic_code'} = $2;
 	print "chr=$chr, genetic_code=$chr{$chr}{'genetic_code'}\n";
 	push @chr, $chr;
+    } elsif (/^;\s+G-orf/) {
+	next;
     } elsif (/^;\s+G-(\S+)\s+(\S+)\s+(start|end)\s*(\S?\.*)/) {
 	$feature = $1;
 	my $feature_type;
@@ -43,10 +49,10 @@
 	my $feature_mark = $3;
 	my $feature_note = $4;
 	if ($feature =~ /(\S+)-E(\d+)$/) {
-	    $gene2exon_intron{$1}{'exon'}{$2} = $feature;
+	    $gene2exon_intron{$1}{'exon'}{$2}{'feature'} = $feature;
 	    $feature_type = "exon";
 	} elsif ($feature =~ /(\S+)-I(\d+)$/) {
-	    $gene2exon_intron{$1}{'intron'}{$2} = $feature;
+	    $gene2exon_intron{$1}{'intron'}{$2}{'feature'} = $feature;
             $feature_type = "intron";
 	} else {
 	    $feature_type = "gene";
@@ -114,6 +120,18 @@
 }   
 
 
+foreach my $f (sort keys %trnascan_out) {
+    print "trn-$f\n";
+    my ($chr, $start_end, $strand) = split /:/, $f;
+    my ($start, $end) = split /-/, $start_end;
+    $features{"trn-$f"}{'type'} = "gene";
+    $features{"trn-$f"}{'start'} = $start;
+    $features{"trn-$f"}{'end'} = $end;
+    $features{"trn-$f"}{'strand'} = $strand;
+}
+
+
+
 
 my $output_fh = write_file($output);
 print $output_fh "##gff-version 3\n";
@@ -129,26 +147,47 @@
 	}
     }
     # begin to output
+    my %gene2cds_phase = ();
     foreach my $feature (@features) {
         print "output feature=$feature\n";
 	if ($features{$feature}{'type'} eq "gene") {
-	    if ($feature =~ /(rnl|rns|rps)/) {
-		print $output_fh "$chr\tmfannot\trRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${feature};Name=${feature}\n";
+	    if ($feature =~ /^(rnl|rns|rps)/) {
+		print $output_fh "$chr\t$tag\trRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${tag}_${feature};Name=${tag}_${feature}\n";
+	    } elsif ($feature =~ /^rnpB/) {
+		print $output_fh "$chr\t$tag\trnpB\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${tag}_RPM1;Name=${tag}_RPM1\n";
+	    } elsif ($feature =~ /^trn/) {
+		if (exists $trnascan_out{"$chr:$features{$feature}{'start'}-$features{$feature}{'end'}:$features{$feature}{'strand'}"}) {
+		    my $id = "${tag}_tRNA:$chr:$features{$feature}{'start'}-$features{$feature}{'end'}:$features{$feature}{'strand'}";
+		    my $name = $trnascan_out{"$chr:$features{$feature}{'start'}-$features{$feature}{'end'}:$features{$feature}{'strand'}"}{"name"};
+		    $trnascan_out{"$chr:$features{$feature}{'start'}-$features{$feature}{'end'}:$features{$feature}{'strand'}"}{"flag"} = 1;
+		    print $output_fh "$chr\t$tag\ttRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=$id;Name=$name\n";
+		} else {
+		    print "skip feature: $feature!\n";
+		}
 	    } else {
 		if ($mode eq "lite") {
 		    if ($feature =~ /-I(\d+)-/) {
 			next;
 		    }
+		    if ($feature =~ /^orf/) {
+			next;
+		    }
 		}
+		my $gene_name = uc $feature;
+		$gene_name = $tag . "_" . $gene_name;
 		if (not exists $gene2exon_intron{$feature}) {
+		    
 		    # single exon gene
-		    print $output_fh "$chr\tmfannot\tgene\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=$feature;Name=$feature\n";
-		    print $output_fh "$chr\tmfannot\tmRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${feature}.mRNA.1;Name=${feature}.mRNA.1;Parent=$feature\n";
+		    print $output_fh "$chr\t$tag\tgene\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=$gene_name;Name=$gene_name\n";
+		    print $output_fh "$chr\t$tag\tmRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_name}.mRNA.1;Name=${gene_name}.mRNA.1;Parent=$gene_name\n";
 		    # add back exon/CDS annotation
 		    my $gene_id = $feature;
 		    my $exon_index = 1;
-		    print $output_fh "$chr\tmfannot\texon\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_id}.exon.$exon_index;Name=${gene_id}.exon.$exon_index;Parent=${gene_id}.mRNA.1\n";
-		    print $output_fh "$chr\tmfannot\tCDS\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_id}.CDS.$exon_index;Name=${gene_id}.CDS.$exon_index;Parent=${gene_id}.mRNA.1\n";
+ 		    $gene2cds_phase{$feature}{'phase'} = 0;
+		    $gene2cds_phase{$feature}{'cds_walk'} = $features{$feature}{'end'} - $features{$feature}{'start'} + 1;
+
+		    print $output_fh "$chr\t$tag\texon\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_name}.exon.$exon_index;Name=${gene_name}.exon.$exon_index;Parent=${gene_name}.mRNA.1\n";
+		    print $output_fh "$chr\t$tag\tCDS\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t0\tID=${gene_name}.CDS.$exon_index;Name=${gene_name}.CDS.$exon_index;Parent=${gene_name}.mRNA.1\n";
 		} else {
 		    # multi-exon gene
 		    # add back gene annotation
@@ -165,17 +204,45 @@
 			$features{$feature}{'start'} = $gene_end;
                         $features{$feature}{'end'} = $gene_start;
 		    }
-		    print $output_fh "$chr\tmfannot\tgene\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=$feature;Name=$feature\n";
-		    print $output_fh "$chr\tmfannot\tmRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${feature}.mRNA.1;Name=${feature}.mRNA.1;Parent=$feature\n";
+		    $gene2cds_phase{$feature}{'phase'} = 0;
+		    $gene2cds_phase{$feature}{'cds_walk'} = 0;
+
+		    print $output_fh "$chr\t$tag\tgene\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=$gene_name;Name=$gene_name\n";
+		    print $output_fh "$chr\t$tag\tmRNA\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_name}.mRNA.1;Name=${gene_name}.mRNA.1;Parent=$gene_name\n";
 		}
 	    }
 	} elsif ($features{$feature}{'type'} eq "exon") {
 	    my ($gene_id, $exon_index) = ($feature =~ /(\S+)-E(\d+)/);
-	    print $output_fh "$chr\tmfannot\texon\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_id}.exon.$exon_index;Name=${gene_id}.exon.$exon_index;Parent=${gene_id}.mRNA.1\n";
-	    print $output_fh "$chr\tmfannot\tCDS\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_id}.CDS.$exon_index;Name=${gene_id}.CDS.$exon_index;Parent=${gene_id}.mRNA.1\n";
-	}	
+	    my $gene_name = uc $gene_id;
+	    $gene_name = $tag . "_" . $gene_name;
+	    print $output_fh "$chr\t$tag\texon\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t.\tID=${gene_name}.exon.$exon_index;Name=${gene_name}.exon.$exon_index;Parent=${gene_name}.mRNA.1\n";
+	    if ($exon_index == 1) {
+		$gene2cds_phase{$gene_id}{'phase'} = 0;
+		$gene2cds_phase{$gene_id}{'cds_walk'} = $features{$feature}{'end'} - $features{$feature}{'start'} + 1;
+		print $output_fh "$chr\t$tag\tCDS\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t0\tID=${gene_name}.CDS.$exon_index;Name=${gene_name}.CDS.$exon_index;Parent=${gene_name}.mRNA.1\n";
+	    } else {
+		if ($gene2cds_phase{$gene_id}{'cds_walk'} % 3 != 0) {
+		    $gene2cds_phase{$gene_id}{'phase'} = 3 - $gene2cds_phase{$gene_id}{'cds_walk'} % 3;
+		} else {
+		    $gene2cds_phase{$gene_id}{'phase'} = 0;
+		}
+		$gene2cds_phase{$gene_id}{'cds_walk'} = $gene2cds_phase{$gene_id}{'cds_walk'} + $features{$feature}{'end'} - $features{$feature}{'start'} + 1;
+		print $output_fh "$chr\t$tag\tCDS\t$features{$feature}{'start'}\t$features{$feature}{'end'}\t.\t$features{$feature}{'strand'}\t$gene2cds_phase{$gene_id}{'phase'}\tID=${gene_name}.CDS.$exon_index;Name=${gene_name}.CDS.$exon_index;Parent=${gene_name}.mRNA.1\n";
+	    }
+	}
     }
 }
+foreach my $f (sort keys %trnascan_out) {
+    if ($trnascan_out{$f}{"flag"} == 0) {
+	my ($chr, $start_end, $strand) = split /:/, $f;
+	my ($start, $end) = split /-/, $start_end;
+	my $name = $trnascan_out{$f}{"name"};
+	my $id = "${tag}_tRNA:$chr:$start_end:$strand";
+	print $output_fh "$chr\t$tag\ttRNA\t$start\t$end\t.\t$strand\t.\tID=$id;Name=$name\n";
+    }
+}
+
+
 
 
 sub read_file {
@@ -206,3 +273,26 @@ sub revcom {
     $seq_revcom =~ tr/ATGCNatgcn/TACGNtacgn/;
     return $seq_revcom;
 }
+
+
+sub parse_trnascan_out_file {
+    my $fh = shift @_;
+    my %trnascan = ();
+    while (<$fh>) {
+        chomp;
+        /^Sequence/ and next;
+        /^Name/ and next;
+        /^------/ and next;
+        my ($chr, $id, $start, $end, $trna_type, $anti_codon, $intron_start, $intron_end, $cov_score) = split /\s+/, $_;
+        my $strand;
+        if ($start < $end) {
+            $strand = "+";
+        } else {
+            ($start, $end) = ($end, $start);
+            $strand = "-";
+        }
+        $trnascan{"$chr:$start-$end:$strand"}{'name'} = "tRNA_${trna_type}(${anti_codon})";
+	$trnascan{"$chr:$start-$end:$strand"}{'flag'} = 0;
+    }
+    return %trnascan;
+}
diff --git a/scripts/parse_REannotate_gff.pl b/scripts/parse_REannotate_gff.pl
index e89286c..021bf67 100755
--- a/scripts/parse_REannotate_gff.pl
+++ b/scripts/parse_REannotate_gff.pl
@@ -31,7 +31,7 @@
 	    /^#/ and next;
 	    /^\s*$/ and next;
 	    my @line = split /\t/, $_;
-	    if ($line[0] =~ /_TY/) {
+	    if ($line[0] =~ /(_TY|_TSU4)/) {
 		$index++;
 		$line[0] = $chr;
 		($line[1], $line[2]) = ($line[1] =~ /(REannotate)_(\S+)/);
diff --git a/scripts/psl2gff3.pl b/scripts/psl2gff3.pl
index a393d4b..246c533 100755
--- a/scripts/psl2gff3.pl
+++ b/scripts/psl2gff3.pl
@@ -27,7 +27,6 @@
 my $input_fh = read_file($input);
 my $output_fh = write_file($output);
 
-my $length_cutoff = 0;
 while (<$input_fh>) {
     chomp;
     if (/^\d+/) {
@@ -40,7 +39,7 @@
 	    ($start, $end) = ($end, $start);
 	}
 	my $feature_length = $end - $start + 1;
-	if ($feature_length >= $length_cutoff) {
+	if ($feature_length >= $length_cutoff_for_completeness) {
 	    my $new_feature_type = $feature_type;
 	    if ($feature_length < $length_cutoff_for_completeness) {
 		$new_feature_type = "${feature_type}_partial";
diff --git a/scripts/rm_overlap_features_from_gff_simple.pl b/scripts/rm_overlap_features_from_gff_simple.pl
index 82ce2f8..fe8634f 100755
--- a/scripts/rm_overlap_features_from_gff_simple.pl
+++ b/scripts/rm_overlap_features_from_gff_simple.pl
@@ -65,7 +65,6 @@
 my $refseq_fh = read_file($refseq);
 my @chr = get_chr_list($refseq_fh);
 
-
 foreach my $record (@output) {
     my ($chr, $source, $type, $start, $end, $score, $strand, $frame, $attributes) = split /\t/, $record;
     $gff{$type}{$chr}{$start} = $record;
diff --git a/scripts/sort_gff3.pl b/scripts/sort_gff3.pl
index 32cf49f..9a308af 100755
--- a/scripts/sort_gff3.pl
+++ b/scripts/sort_gff3.pl
@@ -6,7 +6,7 @@
 ##############################################################
 #  script: sort_gff3.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2018.10.15
+#  last edited: 2022.12.11
 #  description: sort gff3 file by the input multi-fasta genome file
 #  example: perl sort_gff3.pl -i raw.gff3 -t genome_tag -o sorted.gff3 -r genome.fa(.gz)
 ##############################################################
@@ -189,7 +189,7 @@ sub parse_gff_file {
 	    $gff{$gene_id}{'gene_score'} = $score;
 	    $gff{$gene_id}{'gene_phase'} = $phase;
 	    $mRNA_index = 0;
-	} elsif (($type eq "centromere") or ($type eq "rRNA")) {
+	} elsif ($type =~ /(centromere|rRNA|tRNA)/) {
 	    $gene_type = $type;
 	    ($gene_id, $gene_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
 	    $gff{$gene_id}{'gene_name'} = $gene_name;
diff --git a/scripts/tidy_TE_gff3.pl b/scripts/tidy_TE_gff3.pl
new file mode 100755
index 0000000..7c3fa0b
--- /dev/null
+++ b/scripts/tidy_TE_gff3.pl
@@ -0,0 +1,131 @@
+#!/usr/bin/perl
+use warnings;
+#use warnings FATAL => 'all';
+use strict;
+use Getopt::Long;
+
+##############################################################
+#  script: tidy_TE_gff3.pl
+#  author: Jia-Xing Yue (GitHub ID: yjx1217)
+#  last edited: 2022.12.11
+#  description: tidy TE gff3 by re-sorting and re-naming feature IDs
+#  example: perl tidy_TE_gff3.pl -i raw.gff3 -t genome_tag -o tidy.gff3 -r genome.fa(.gz)
+##############################################################
+
+my ($refseq, $input, $output, $tag);
+GetOptions('refseq|r:s' => \$refseq, # reference genome file in fasta format; can be compressed by gzip
+	   'input|i:s' => \$input, # input raw gff3
+	   'output|o:s' => \$output, # output tidy gff3
+	   'tag|t:s' => \$tag); # genome tag
+
+my $refseq_fh = read_file($refseq);
+my %refseq = ();
+my @refseq = ();
+parse_fasta_file($refseq_fh, \%refseq, \@refseq);
+
+my $input_fh = read_file($input);
+my %gff = parse_gff_file($input_fh);
+close $input_fh;
+
+my $output_fh = write_file($output);
+
+print $output_fh "##gff-version 3\n";
+
+foreach my $chr (@refseq) {
+    my $chr_length = length $refseq{$chr};
+    print $output_fh "##sequence-region $chr 1 $chr_length\n";
+}
+
+my $feature_index = 0;
+foreach my $chr (@refseq) { 
+    my @features_on_chr = ();
+    foreach my $feature_id (sort keys %gff) {
+	if ($gff{$feature_id}{'chr'} eq $chr) {
+	    push @features_on_chr, $feature_id;
+	}
+    }
+    foreach my $feature_id (sort {$gff{$a}{'start'} <=> $gff{$b}{'start'} or $gff{$a}{'end'} <=> $gff{$b}{'end'}} @features_on_chr) {
+	my $feature_name = $gff{$feature_id}{'feature_name'};
+	my $feature_note = $gff{$feature_id}{'feature_note'};
+	my $feature_type = $gff{$feature_id}{'feature_type'};
+	my $feature_start = $gff{$feature_id}{'start'};
+	my $feature_end = $gff{$feature_id}{'end'};
+	my $feature_score = $gff{$feature_id}{'score'};
+	my $feature_strand = $gff{$feature_id}{'strand'};
+	my $feature_phase = $gff{$feature_id}{'phase'};
+	print $output_fh "$chr\t$tag\t$feature_type\t$feature_start\t$feature_end\t$feature_score\t$feature_strand\t$feature_phase\tID=$feature_id;Name=$feature_name;$feature_note\n";
+    }
+}
+
+
+
+
+
+sub read_file {
+    my $file = shift @_;
+    my $fh;
+    if ($file =~ /\.gz$/) {
+        open($fh, "gunzip -c $file |") or die "can't open pipe to $file";
+    } else {
+        open($fh, $file) or die "can't open $file";
+    }
+    return $fh;
+}
+
+sub write_file {
+    my $file = shift @_;
+    my $fh;
+    if ($file =~ /.gz$/) {
+        open($fh, "| gzip -c >$file") or die "can't open $file\n";
+    } else {
+        open($fh, ">$file") or die "can't open $file\n";
+    }
+    return $fh;
+}  
+
+sub parse_fasta_file {
+    my ($fh, $input_hashref, $input_arrayref) = @_;
+    my $seq_name = "";
+    while (<$fh>) {
+        chomp;
+        if (/^\s*$/) {
+            next;
+        } elsif (/^\s*#/) {
+            next;
+        } elsif (/^>(.*)/) {
+            $seq_name = $1;
+            push @$input_arrayref, $seq_name;
+            $$input_hashref{$seq_name} = "";
+        } else {
+            $$input_hashref{$seq_name} .= $_;
+        }
+    }
+}
+
+sub parse_gff_file {
+    my $fh = shift @_;
+    my %gff = ();
+    my $feature_id;
+    my $feature_name;
+    my $feature_type;
+    while (<$fh>) {
+	chomp;
+	/^##FASTA/ and last;
+	/^#/ and next;
+	my ($chr, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split /\t/, $_;
+	# print "$_\n";
+	($feature_id, $feature_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+	$gff{$feature_id}{'feature_type'} = "mobile_element";
+	$gff{$feature_id}{'feature_name'} = $feature_name;
+	$gff{$feature_id}{'feature_note'} = "mobile_element_type=$type";
+	$gff{$feature_id}{'chr'} = $chr;
+	$gff{$feature_id}{'start'} = $start;
+	$gff{$feature_id}{'end'} = $end;
+	$gff{$feature_id}{'strand'} = $strand;
+	$gff{$feature_id}{'source'} = $source;
+	$gff{$feature_id}{'score'} = $score;
+	$gff{$feature_id}{'phase'} = $phase;
+    }
+    return %gff;
+}
+
diff --git a/scripts/tidy_maker_gff3.pl b/scripts/tidy_maker_gff3.pl
index a1bfbbb..6bea04b 100755
--- a/scripts/tidy_maker_gff3.pl
+++ b/scripts/tidy_maker_gff3.pl
@@ -1,12 +1,13 @@
 #!/usr/bin/perl
 use warnings;
+#use warnings FATAL => 'all';
 use strict;
 use Getopt::Long;
 
 ##############################################################
 #  script: tidy_maker_gff3.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2017.06.17
+#  last edited: 2022.12.09
 #  description: tidy maker gff3 by re-sorting and re-naming feature IDs
 #  example: perl tidy_maker_gff3.pl -i raw.gff3 -t genome_tag -o tidy.gff3 -r genome.fa(.gz)
 ##############################################################
@@ -35,44 +36,39 @@
     print $output_fh "##sequence-region $chr 1 $chr_length\n";
 }
 
-my $gene_index = 0;
+my $feature_index = 0;
 foreach my $chr (@refseq) { 
-    my @genes_on_chr = ();
-    foreach my $gene_id (sort keys %gff) {
-	if ($gff{$gene_id}{'gene_chr'} eq $chr) {
-	    push @genes_on_chr, $gene_id;
+    my @features_on_chr = ();
+    foreach my $feature_id (sort keys %gff) {
+	if ($gff{$feature_id}{'chr'} eq $chr) {
+	    push @features_on_chr, $feature_id;
 	}
     }
-    foreach my $gene_id (sort {$gff{$a}{'gene_start'} <=> $gff{$b}{'gene_start'} or $gff{$a}{'gene_end'} <=> $gff{$b}{'gene_end'}} @genes_on_chr) {
-	my $gene_type = $gff{$gene_id}{'gene_type'};
-	my $gene_start = $gff{$gene_id}{'gene_start'};
-	my $gene_end = $gff{$gene_id}{'gene_end'};
-	my $gene_score = $gff{$gene_id}{'gene_score'};
-	my $gene_strand = $gff{$gene_id}{'gene_strand'};
-	my $gene_phase = $gff{$gene_id}{'gene_phase'};
-	if ($gene_type ne "gene") {
-	    my $new_gene_id;
-	    if ($gene_type eq "centromere") {
-		$new_gene_id = $gene_id;
-	    } else {
-		$new_gene_id = "$gene_type:$chr:$gene_start-$gene_end:$gene_strand";
-	    }
-	    print $output_fh "$chr\t$tag\t$gene_type\t$gene_start\t$gene_end\t$gene_score\t$gene_strand\t$gene_phase\tID=$new_gene_id;Name=$new_gene_id\n";
+    foreach my $feature_id (sort {$gff{$a}{'start'} <=> $gff{$b}{'start'} or $gff{$a}{'end'} <=> $gff{$b}{'end'}} @features_on_chr) {
+	my $feature_name = $gff{$feature_id}{'feature_name'};
+	my $feature_type = $gff{$feature_id}{'feature_type'};
+	my $feature_start = $gff{$feature_id}{'start'};
+	my $feature_end = $gff{$feature_id}{'end'};
+	my $feature_score = $gff{$feature_id}{'score'};
+	my $feature_strand = $gff{$feature_id}{'strand'};
+	my $feature_phase = $gff{$feature_id}{'phase'};
+	if ($feature_type ne "gene") {
+	    print $output_fh "$chr\t$tag\t$feature_type\t$feature_start\t$feature_end\t$feature_score\t$feature_strand\t$feature_phase\tID=$feature_id;Name=$feature_name\n";
 	} else {
-	    $gene_index += 10;
-	    my $new_gene_id = sprintf("%07d", $gene_index);
-	    $new_gene_id = "${tag}_" . "G" . $new_gene_id;
-	    print $output_fh "$chr\t$tag\tgene\t$gene_start\t$gene_end\t$gene_score\t$gene_strand\t$gene_phase\tID=$new_gene_id;Name=$new_gene_id\n";
-	    foreach my $mRNA_id (sort {$gff{$gene_id}{'mRNA'}{$a}{'mRNA_index'} <=> $gff{$gene_id}{'mRNA'}{$b}{'mRNA_index'}} keys %{$gff{$gene_id}{'mRNA'}}) {
-		my $mRNA_index = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_index'};
-		my $mRNA_start = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_start'};
-		my $mRNA_end = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_end'};
-		my $mRNA_score = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_score'};
-		my $mRNA_strand = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_strand'};
-		my $mRNA_phase = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_phase'};
-		my $new_mRNA_id = "$new_gene_id.mRNA.$mRNA_index";
-		print $output_fh "$chr\t$tag\tmRNA\t$mRNA_start\t$mRNA_end\t$mRNA_score\t$mRNA_strand\t$mRNA_phase\tID=$new_mRNA_id;Name=$new_mRNA_id;Parent=$new_gene_id\n";
-		my @exon_indices = sort {$a <=> $b} keys %{$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}};
+	    $feature_index += 10;
+	    my $new_feature_id = sprintf("%07d", $feature_index);
+	    $new_feature_id = "${tag}_" . "G" . $new_feature_id;
+	    print $output_fh "$chr\t$tag\t$feature_type\t$feature_start\t$feature_end\t$feature_score\t$feature_strand\t$feature_phase\tID=$new_feature_id;Name=$new_feature_id\n";
+	    foreach my $mRNA_id (sort {$gff{$feature_id}{'mRNA'}{$a}{'mRNA_index'} <=> $gff{$feature_id}{'mRNA'}{$b}{'mRNA_index'}} keys %{$gff{$feature_id}{'mRNA'}}) {
+		my $mRNA_index = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'mRNA_index'};
+		my $mRNA_start = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'start'};
+		my $mRNA_end = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'end'};
+		my $mRNA_score = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'score'};
+		my $mRNA_strand = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'strand'};
+		my $mRNA_phase = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'phase'};
+		my $new_mRNA_id = "$new_feature_id.mRNA.$mRNA_index";
+		print $output_fh "$chr\t$tag\tmRNA\t$mRNA_start\t$mRNA_end\t$mRNA_score\t$mRNA_strand\t$mRNA_phase\tID=$new_mRNA_id;Name=$new_mRNA_id;Parent=$new_feature_id\n";
+		my @exon_indices = sort {$a <=> $b} keys %{$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}};
 		my $exon_num = scalar @exon_indices;
 		my $new_exon_index;
 		if ($mRNA_strand eq '+') {
@@ -81,11 +77,11 @@
 		    $new_exon_index = $exon_num + 1;
 		}
 		foreach my $exon_index (@exon_indices) {
-		    my $exon_start = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_start'};
-		    my $exon_end = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_end'};
-		    my $exon_score = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_score'};
-		    my $exon_strand = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_strand'};
-		    my $exon_phase = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_phase'};
+		    my $exon_start = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'start'};
+		    my $exon_end = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'end'};
+		    my $exon_score = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'score'};
+		    my $exon_strand = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'strand'};
+		    my $exon_phase = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'phase'};
 		    if ($mRNA_strand eq '+') {
 			$new_exon_index++;
 		    } else {
@@ -94,7 +90,7 @@
 		    my $new_exon_id = "$new_mRNA_id.exon.$new_exon_index";
 		    print $output_fh "$chr\t$tag\texon\t$exon_start\t$exon_end\t$exon_score\t$exon_strand\t$exon_phase\tID=$new_exon_id;Name=$new_exon_id;Parent=$new_mRNA_id\n";
 		}
-		my @cds_indices = sort {$a <=> $b} keys %{$gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}};
+		my @cds_indices = sort {$a <=> $b} keys %{$gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}};
 		my $cds_num = scalar @cds_indices;
 		my $new_cds_index;
 		if ($mRNA_strand eq '+') {
@@ -103,11 +99,11 @@
 		    $new_cds_index = $cds_num + 1;
 		}
 		foreach my $cds_index (@cds_indices) {
-		    my $cds_start = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_start'};
-		    my $cds_end = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_end'};
-		    my $cds_score = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_score'};
-		    my $cds_strand = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_strand'};
-		    my $cds_phase = $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_phase'};
+		    my $cds_start = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'start'};
+		    my $cds_end = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'end'};
+		    my $cds_score = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'score'};
+		    my $cds_strand = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'strand'};
+		    my $cds_phase = $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'phase'};
 		    if ($mRNA_strand eq '+') {
 			$new_cds_index++;
 		    } else {
@@ -169,72 +165,109 @@ sub parse_fasta_file {
 sub parse_gff_file {
     my $fh = shift @_;
     my %gff = ();
-    my $gene_id;
-    my $gene_name;
-    my $gene_type;
+    my $feature_id;
+    my $feature_name;
+    my $feature_type;
     my $mRNA_index;
     while (<$fh>) {
 	chomp;
 	/^##FASTA/ and last;
 	/^#/ and next;
 	my ($chr, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split /\t/, $_;
+	# print "$_\n";
 	if ($type eq "gene") {
-	    ($gene_id, $gene_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
-	    if ($gene_id =~ /^trnascan/) {
-		$gene_type = "tRNA";
+	    ($feature_id, $feature_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+	    if ($feature_id =~ /^trnascan/) {
+		$feature_type = "tRNA";
 		next;
-	    } elsif ($gene_id =~ /^snoscan/) {
-		$gene_type = "snoRNA";
+	    } elsif ($feature_id =~ /^snoscan/) {
+		$feature_type = "snoRNA";
 		next;
 	    } else {
-		$gene_type = "gene";
+		$feature_type = "gene";
 	    }
-	    $gff{$gene_id}{'gene_type'} = $gene_type;
-	    $gff{$gene_id}{'gene_chr'} = $chr;
-	    $gff{$gene_id}{'gene_start'} = $start;
-	    $gff{$gene_id}{'gene_end'} = $end;
-	    $gff{$gene_id}{'gene_strand'} = $strand;
-	    $gff{$gene_id}{'gene_source'} = $source;
-	    $gff{$gene_id}{'gene_score'} = $score;
-	    $gff{$gene_id}{'gene_phase'} = $phase;
+	    $gff{$feature_id}{'feature_type'} = $feature_type;
+	    $gff{$feature_id}{'feature_name'} = $feature_name;
+	    $gff{$feature_id}{'chr'} = $chr;
+	    $gff{$feature_id}{'start'} = $start;
+	    $gff{$feature_id}{'end'} = $end;
+	    $gff{$feature_id}{'strand'} = $strand;
+	    $gff{$feature_id}{'source'} = $source;
+	    $gff{$feature_id}{'score'} = $score;
+	    $gff{$feature_id}{'phase'} = $phase;
 	    $mRNA_index = 0;
 	} elsif ($type eq "centromere") {
-	    $gene_type = $type;
-	    ($gene_id, $gene_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
-	    $gff{$gene_id}{'gene_type'} = $gene_type;
-            $gff{$gene_id}{'gene_chr'} = $chr;
-            $gff{$gene_id}{'gene_start'} = $start;
-            $gff{$gene_id}{'gene_end'} = $end;
-            $gff{$gene_id}{'gene_strand'} = $strand;
-            $gff{$gene_id}{'gene_source'} = $source;
-            $gff{$gene_id}{'gene_score'} = $score;
-            $gff{$gene_id}{'gene_phase'} = $phase;
+	    $feature_type = $type;
+	    ($feature_id, $feature_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+	    $gff{$feature_id}{'feature_type'} = $feature_type;
+	    $gff{$feature_id}{'feature_name'} = $feature_name;
+            $gff{$feature_id}{'chr'} = $chr;
+            $gff{$feature_id}{'start'} = $start;
+            $gff{$feature_id}{'end'} = $end;
+            $gff{$feature_id}{'strand'} = $strand;
+            $gff{$feature_id}{'source'} = $source;
+            $gff{$feature_id}{'score'} = $score;
+            $gff{$feature_id}{'phase'} = $phase;
+	# } elsif ($type eq "mobile_element") {
+	#     $feature_type = $type;
+	#     ($feature_id, $feature_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+\S*mobile_element_type=[^;]+)/);
+	#     $gff{$feature_id}{'feature_type'} = $feature_type;
+	#     $gff{$feature_id}{'feature_name'} = $feature_name;
+        #     $gff{$feature_id}{'chr'} = $chr;
+        #     $gff{$feature_id}{'start'} = $start;
+        #     $gff{$feature_id}{'end'} = $end;
+        #     $gff{$feature_id}{'strand'} = $strand;
+        #     $gff{$feature_id}{'source'} = $source;
+        #     $gff{$feature_id}{'score'} = $score;
+        #     $gff{$feature_id}{'phase'} = $phase;
+	} elsif ($type eq "tRNA") {
+	    $feature_type = $type;
+	    ($feature_id, $feature_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+	    # print "feature_id=$feature_id\n";
+	    # print "feature_name=$feature_name\n";
+	    my ($aa, $anticodon) = ($feature_id =~ /noncoding\-([^\_]+)\_([^\_]+)\-gene/);
+	    # print "aa=$aa\n";
+	    # print "anticodon=$anticodon\n";
+	    $feature_id = "$feature_type:$chr:${start}-${end}:$strand";
+	    $feature_name = "tRNA_${aa}($anticodon)";
+	    # print "feature_id=$feature_id, feature_name=$feature_name";
+	    $gff{$feature_id}{'feature_type'} = $feature_type;
+	    $gff{$feature_id}{'feature_name'} = $feature_name;
+            $gff{$feature_id}{'chr'} = $chr;
+            $gff{$feature_id}{'start'} = $start;
+            $gff{$feature_id}{'end'} = $end;
+            $gff{$feature_id}{'strand'} = $strand;
+            $gff{$feature_id}{'source'} = $source;
+            $gff{$feature_id}{'score'} = $score;
+            $gff{$feature_id}{'phase'} = $phase;
 	} elsif ($type !~ /(exon|CDS|mRNA|UTR)/) {
 	    # e.g. type = TY, X-element, Y_prime_element ...
-	    $gene_type = $type;
-	    $gene_id = "$gene_type:$chr:${start}-${end}:$strand";
-	    $gff{$gene_id}{'gene_type'} = $gene_type;
-	    $gff{$gene_id}{'gene_chr'} = $chr;
-	    $gff{$gene_id}{'gene_start'} = $start;
-	    $gff{$gene_id}{'gene_end'} = $end;
-	    $gff{$gene_id}{'gene_strand'} = $strand;
-	    $gff{$gene_id}{'gene_source'} = $source;
-	    $gff{$gene_id}{'gene_score'} = $score;
-	    $gff{$gene_id}{'gene_phase'} = $phase;
+	    $feature_type = $type;
+	    $feature_id = "$feature_type:$chr:${start}-${end}:$strand";
+	    $feature_name = "$feature_type:$chr:${start}-${end}:$strand";
+	    $gff{$feature_id}{'feature_type'} = $feature_type;
+	    $gff{$feature_id}{'feature_name'} = $feature_name;
+	    $gff{$feature_id}{'chr'} = $chr;
+	    $gff{$feature_id}{'start'} = $start;
+	    $gff{$feature_id}{'end'} = $end;
+	    $gff{$feature_id}{'strand'} = $strand;
+	    $gff{$feature_id}{'source'} = $source;
+	    $gff{$feature_id}{'score'} = $score;
+	    $gff{$feature_id}{'phase'} = $phase;
 	} elsif ($type eq "mRNA") {
-	    my ($mRNA_id, $gene_id) = ($attributes =~ /ID=([^;]+);\S*Parent=([^;]+)/);
-	    if (exists $gff{$gene_id}) {
+	    my ($mRNA_id, $feature_id) = ($attributes =~ /ID=([^;]+);\S*Parent=([^;]+)/);
+	    if (exists $gff{$feature_id}) {
 		$mRNA_index++;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_index'} = $mRNA_index;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_chr'} = $chr;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_start'} = $start;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_end'} = $end;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_strand'} = $strand;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_source'} = $source;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_score'} = $score;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'mRNA_phase'} = $phase;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'mRNA_index'} = $mRNA_index;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'chr'} = $chr;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'start'} = $start;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'end'} = $end;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'strand'} = $strand;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'source'} = $source;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'score'} = $score;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'phase'} = $phase;
 	    } else {
-		die "cannot find matching gene record for the mRNA $mRNA_id derived from the gene $gene_id\n"
+		die "cannot find matching gene record for the mRNA $mRNA_id derived from the gene $feature_id\n"
 	    }
 	} elsif ($type eq "exon") {
 	    my ($exon_id, $mRNA_id) = ($attributes =~ /ID=([^;]+);\S*Parent=([^;]+)/);
@@ -242,29 +275,29 @@ sub parse_gff_file {
 		next;
 	    } elsif ($exon_id =~ /^snoscan/) {
 		next;
-	    } elsif (exists $gff{$gene_id}{'mRNA'}{$mRNA_id}) {
+	    } elsif (exists $gff{$feature_id}{'mRNA'}{$mRNA_id}) {
 		my $exon_index = $start;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_chr'} = $chr;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_start'} = $start;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_end'} = $end;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_strand'} = $strand;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_source'} = $source;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_score'} = $score;
-		$gff{$gene_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'exon_phase'} = $phase;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'chr'} = $chr;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'start'} = $start;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'end'} = $end;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'strand'} = $strand;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'source'} = $source;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'score'} = $score;
+		$gff{$feature_id}{'mRNA'}{$mRNA_id}{'exon'}{$exon_index}{'phase'} = $phase;
 	    } else {
 		die "cannot find matching mRNA record for the exon $exon_id derived from the mRNA $mRNA_id\n"
 	    }
 	} elsif ($type eq "CDS") {
             my ($cds_id, $mRNA_id) = ($attributes =~ /ID=([^;]+);\S*Parent=([^;]+)/);
-            if (exists $gff{$gene_id}{'mRNA'}{$mRNA_id}) {
+            if (exists $gff{$feature_id}{'mRNA'}{$mRNA_id}) {
                 my $cds_index = $start;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_chr'} = $chr;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_start'} = $start;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_end'} = $end;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_strand'} = $strand;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_source'} = $source;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_score'} = $score;
-                $gff{$gene_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'cds_phase'} = $phase;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'chr'} = $chr;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'start'} = $start;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'end'} = $end;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'strand'} = $strand;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'source'} = $source;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'score'} = $score;
+                $gff{$feature_id}{'mRNA'}{$mRNA_id}{'cds'}{$cds_index}{'phase'} = $phase;
             } else {
                 die "cannot find matching mRNA record for the CDS $cds_id derived from the mRNA $mRNA_id\n"
             }
diff --git a/scripts/tidy_truncated_TY_gff.pl b/scripts/tidy_truncated_TY_gff.pl
index bc288f0..b1fb922 100755
--- a/scripts/tidy_truncated_TY_gff.pl
+++ b/scripts/tidy_truncated_TY_gff.pl
@@ -24,7 +24,7 @@
     /^#/ and next;
     /^\s*$/ and next;
     my ($chr, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split /\t/, $_;
-    my ($new_type) = ($type =~ /(TY\d+)/);
+    my ($new_type) = ($type =~ /(TY\d+|TSU4)/);
     $new_type .= "_truncated";
     my $new_id = "$new_type:$chr:$start-$end:$strand";
     print $output_fh "$chr\t$tag\t$new_type\t$start\t$end\t.\t$strand\t.\tID=${new_id};Name=${new_id}\n";
diff --git a/scripts/update_gff3_by_proteinortho.pl b/scripts/update_gff3_by_proteinortho.pl
index be931f1..0c3270b 100755
--- a/scripts/update_gff3_by_proteinortho.pl
+++ b/scripts/update_gff3_by_proteinortho.pl
@@ -1,12 +1,13 @@
 #!/usr/bin/perl
-use warnings;
+#use warnings;
+use warnings FATAL => 'all';
 use strict;
 use Getopt::Long;
 
 ##############################################################
 #  script: update_gff3_by_proteinortho.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
-#  last edited: 2017.06.17
+#  last edited: 2022.12.11
 #  description: update gff3 file based on proteinortho result: attach gene name based on gene orthology 
 #  example: perl update_gff3_by_proteinortho.pl -i query.maker.gff3 -x query.poff -r ref.PoFF.faa -q query.maker.PoFF.faa -o query.final.gff
 ##############################################################
@@ -60,12 +61,43 @@
 
 while (<$input_fh>) {
     chomp;
-    /^#/ and next;
     /^\s*$/ and next;
+    if (/^#/) {
+	print $output_fh "$_\n";
+	next;
+    }
     my ($chr, $source, $type, $start, $end, $score, $strand, $phase, $attributes) = split '\t', $_;
-    my ($id, $name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+    my ($id, $original_name) = ($attributes =~ /ID=([^;]+);\S*Name=([^;]+)/);
+    # print "$_\n";
+    my @original_name = ();
+    if ($original_name =~ /\//) {
+	@original_name = split /\//, $original_name;
+    } else {
+	@original_name = ($original_name);
+    }
+    my %name = ();
+
+    # foreach my $n (@original_name) {
+    # 	if ($n !~ /\d+$/) {
+    # 	    $name{$n} = 1;
+    # 	}
+    # }
+
     if (($type eq "gene") and (exists $ortho_map{$id})) {
-	$name = $ortho_map{$id};
+	my $new_name = $ortho_map{$id};
+	my @new_name =();
+	if ($new_name =~ /\//){
+	    @new_name = split /\//, $new_name;
+	} else {
+	    @new_name = ($new_name);
+	}
+	foreach my $n (@new_name) {
+	    if (not exists $name{$n}) {
+		$name{$n} = 1;
+	    }
+	}
+	my @name = sort keys %name;
+	my $name = join '/', @name;
         print $output_fh "$chr\t$source\t$type\t$start\t$end\t$score\t$strand\t$phase\tID=$id;Name=$name\n";
     } else {
         print $output_fh "$_\n";