# HG changeset patch
# User iuc
# Date 1530475894 14400
# Node ID c98b3fa910bf65cce901a4f217ac3c211f9bb9f0
# Parent  0cb75547ecc23312ccc3bca98ceef6aa4cdfc861
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398

diff -r 0cb75547ecc2 -r c98b3fa910bf maker.xml
--- a/maker.xml	Thu Oct 19 15:41:42 2017 -0400
+++ b/maker.xml	Sun Jul 01 16:11:34 2018 -0400
@@ -1,11 +1,19 @@
 <?xml version="1.0"?>
-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1">
     <description>genome annotation pipeline</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command><![CDATA[
+        RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries &&
+        mkdir lib &&
+        export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
+          for file in \$(ls \$RM_LIB_PATH) ; do  ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
+        #if $repeat_masking.repeat_source.source_type == "repbase":
+          cp '${repeat_masking.repeat_source.repbase_file}' 'lib/${repeat_masking.repeat_source.repbase_file_name}' &&
+        #end if
+
         maker -CTL
 
         &&
@@ -104,28 +112,41 @@
 #end if
 
 #-----Repeat Masking (leave values blank to skip repeat masking)
-#if $repeat_masking.repeatmasker.do_rm == 'simple'
-model_org=simple # select a model organism for RepBase masking in RepeatMasker
+#if $repeat_masking.repeat_source.source_type == 'repbase'
+
+#if $repeat_masking.repeat_source.species_source.species_from_list == 'yes'
+model_org=${repeat_masking.repeat_source.species_source.species_list}
+#else
+model_org=${repeat_masking.repeat_source.species_source.species_name}
+#end if
+
 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
-#else if $repeat_masking.repeatmasker.do_rm == 'lib'
+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
+#else if $repeat_masking.repeat_source.source_type == 'library'
 model_org= # select a model organism for RepBase masking in RepeatMasker
-rmlib=${repeat_masking.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
+rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
+
+#if $repeat_masking.repeat_source.repeat_protein
+repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
+#else
+repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner
+#end if
+#if $repeat_masking.repeat_source.rm_gff
+rm_gff=${repeat_masking.repeat_source.rm_gff} # pre-identified repeat elements from an external GFF3 file
+#else
+rm_gff= # pre-identified repeat elements from an external GFF3 file
+#end if
+
+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
+
 #else
 model_org= # select a model organism for RepBase masking in RepeatMasker
 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
-#end if
-#if $repeat_masking.repeat_protein
-repeat_protein=${repeat_masking.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
-#else
-repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner
+softmask=0 # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
 #end if
-#if $repeat_masking.rm_gff
-rm_gff=${repeat_masking.rm_gff} # pre-identified repeat elements from an external GFF3 file
-#else
-rm_gff= # pre-identified repeat elements from an external GFF3 file
-#end if
+
 prok_rm=0 # forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
-softmask=${repeat_masking.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
 
 #-----Gene Prediction
 #if $abinitio_gene_prediction.snaphmm
@@ -359,32 +380,69 @@
         </section>
 
         <section name="repeat_masking" title="Repeat masking" expanded="True">
-            <conditional name="repeatmasker">
-                <param name="do_rm" type="select" label="Enable repeat masking with RepeatMasker">
+            <conditional name="repeat_source">
+              <param label="Repeat library source" name="source_type" type="select">
+                <option selected="true" value="repbase">RepBase</option>
+                <option value="library">Custom library of repeats</option>
+                <option value="no">Disable repeat masking (not recommended)</option>
+              </param>
+              <when value="repbase">
+                <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />
+                <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase -->
+                <conditional name="species_source">
+                  <param label="Select species name from a list?" name="species_from_list" type="select">
+                    <option value="yes" selected="true">Yes</option>
                     <option value="no">No</option>
-                    <option value="simple" selected="true">Yes, run RepeatMasker with default simple models</option>
-                    <option value="lib">Yes, use an organism specific repeat library (fasta)</option>
-                </param>
-                <!-- full repbase cannot be redistributed (for licensing reasons, see https://hpc.nih.gov/apps/repbase_license.html),
-                    using only the default maker base
-                    model_org is ignored and replaced by 'simple' if the full RepBase is not available.
-                    model_org=simple means maker will search using the simple models shipped by default
-                    Installing RepBase requires to replace files in the RepeatMasker installation dir
-                     -->
-                <when value="no"/>
-                <when value="simple"/>
-                <when value="lib">
-                    <param name="rmlib" type="data" format="fasta" label="Organism specific repeat library for RepeatMasker (fasta)"/>
-                </when>
+                  </param>
+                  <when value="yes">
+                    <param name="species_list" type="select" label="Species">
+                      <option value="anopheles" selected="true">anopheles</option>
+                      <option value="arabidopsis">arabidopsis</option>
+                      <option value="artiodactyl">artiodactyl</option>
+                      <option value="aspergillus">aspergillus</option>
+                      <option value="carnivore">carnivore</option>
+                      <option value="cat">cat</option>
+                      <option value="chicken">chicken</option>
+                      <option value="ciona intestinalis">ciona intestinalis</option>
+                      <option value="ciona savignyi">ciona savignyi</option>
+                      <option value="cow">cow</option>
+                      <option value="danio">danio</option>
+                      <option value="diatoaea">diatomea</option>
+                      <option value="dog">dog</option>
+                      <option value="drosophila">drosophila</option>
+                      <option value="elegans">elegans</option>
+                      <option value="fugu">fugu</option>
+                      <option value="fungi" selected="true">fungi</option>
+                      <option value="human">human</option>
+                      <option value="maize">maize</option>
+                      <option value="mammal">mammal</option>
+                      <option value="mouse">mouse</option>
+                      <option value="pig">pig</option>
+                      <option value="rat">rat</option>
+                      <option value="rice">rice</option>
+                      <option value="rodentia">rodentia</option>
+                      <option value="ruminantia">ruminantia</option>
+                      <option value="wheat">wheat</option>
+                    </param>
+                  </when>
+                  <when value="no">
+                    <param name="species_name" type="text" value="homo sapiens" label="Repeat source species" help="Source species (or clade name) used to select repeats from RepBase" />
+                  </when>
+                </conditional>
+                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
+              </when>
+              <when value="library">
+                <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
+                <param name="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" />
+                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
+              </when>
+              <when value="no"/>
             </conditional>
-            <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner (fasta)" help="Leave empty to skip" optional="True"/>
-            <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" help="Leave empty to skip" optional="True"/>
-            <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
         </section>
 
         <section name="gene_prediction" title="Other predictions" expanded="True">
             <param name="pred_gff" type="data" format="gff" label="Predictions from an external GFF3 file" optional="True"/>
-            <param name="model_gff" type="data" format="gff" label="Annotated gene models an external GFF3 file" help="annotation pass-through" optional="True"/>
+            <param name="model_gff" type="data" format="gff" label="Annotated gene models from an external GFF3 file" help="annotation pass-through" optional="True"/>
             <param name="trna" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Find tRNAs with tRNAscan"/>
             <param name="snoscan_rrna" type="data" format="fasta" label="rRNA file to have Snoscan find snoRNAs" optional="True"/>
         </section>
@@ -428,6 +486,7 @@
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot.gff3"/>
             <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
         </test>
@@ -436,6 +495,7 @@
             <param name="organism_type" value="prokaryotic"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_proc.gff3"/>
             <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
         </test>
@@ -445,6 +505,7 @@
             <param name="reannotation|maker_gff" value="evidences.gff3"/>
             <param name="reannotation|est_pass" value="true"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_reuse.gff3"/>
             <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
         </test>
@@ -455,6 +516,7 @@
             <param name="abinitio_gene_prediction|aug_prediction|augustus_species" value="human"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>
             <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
         </test>
@@ -465,6 +527,7 @@
             <param name="abinitio_gene_prediction|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>
             <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
         </test>
@@ -472,10 +535,21 @@
             <param name="genome" value="genome.fasta"/>
             <param name="est_evidences|est" value="est.fasta"/>
             <param name="est_evidences|est2genome" value="1"/>
-            <param name="repeat_masking|repeatmasker|do_rm" value="no"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
             <output name="output_gff" file="annot_norm.gff3"/>
             <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
         </test>
+        <test>
+            <param name="genome" value="genome.fasta"/>
+            <param name="est_evidences|est" value="est.fasta"/>
+            <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="repbase"/>
+            <param name="repeat_masking|repeat_source|repbase_file" value="fake_repbase.embl" />
+            <param name="repeat_masking|repeat_source|repbase_file_name" value="fake.embl" />
+            <param name="repeat_masking|repeat_source|species_list" value="anopheles" />
+            <output name="output_gff" file="annot_repbase.gff3"/>
+            <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
         MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/annot.gff3
--- a/test-data/annot.gff3	Thu Oct 19 15:41:42 2017 -0400
+++ b/test-data/annot.gff3	Sun Jul 01 16:11:34 2018 -0400
@@ -17,7 +17,6 @@
 HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
 HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
 ###
-###
 HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
 HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
 HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
@@ -40,4 +39,3 @@
 HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
 HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
 ###
-###
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/annot_mapped.gff3
--- a/test-data/annot_mapped.gff3	Thu Oct 19 15:41:42 2017 -0400
+++ b/test-data/annot_mapped.gff3	Sun Jul 01 16:11:34 2018 -0400
@@ -17,7 +17,6 @@
 HS08198	maker	CDS	1587	1688	.	+	2	ID=YES000002-RA:cds;Parent=YES000002-RA;
 HS08198	maker	CDS	1772	1848	.	+	2	ID=YES000002-RA:cds;Parent=YES000002-RA;
 ###
-###
 HS04636	maker	gene	1813	6903	.	+	.	ID=YES000001;Name=YES000001;Alias=maker-HS04636-exonerate_est2genome-gene-0.0;
 HS04636	maker	mRNA	1813	6903	8728	+	.	ID=YES000001-RA;Parent=YES000001;Name=YES000001-RA;Alias=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=49|1|1|1|0|0|9|0|572;_eAED=0.00;
 HS04636	maker	exon	1813	1934	.	+	.	ID=YES000001-RA:exon:0;Parent=YES000001-RA;
@@ -40,4 +39,3 @@
 HS04636	maker	CDS	5860	6007	.	+	0	ID=YES000001-RA:cds;Parent=YES000001-RA;
 HS04636	maker	CDS	6494	6903	.	+	2	ID=YES000001-RA:cds;Parent=YES000001-RA;
 ###
-###
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/annot_repbase.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_repbase.gff3	Sun Jul 01 16:11:34 2018 -0400
@@ -0,0 +1,43 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
+HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+###
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
+HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+###
+###
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/annot_reuse.gff3
--- a/test-data/annot_reuse.gff3	Thu Oct 19 15:41:42 2017 -0400
+++ b/test-data/annot_reuse.gff3	Sun Jul 01 16:11:34 2018 -0400
@@ -17,7 +17,6 @@
 HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
 HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
 ###
-###
 HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0;score=8728
 HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
 HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
@@ -40,4 +39,3 @@
 HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
 HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
 ###
-###
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/evidences.gff3
--- a/test-data/evidences.gff3	Thu Oct 19 15:41:42 2017 -0400
+++ b/test-data/evidences.gff3	Sun Jul 01 16:11:34 2018 -0400
@@ -1,62 +1,42 @@
 ##gff-version 3
 HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
 ###
-HS08198	repeatmasker	match	578	651	13	+	.	ID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +
-HS08198	repeatmasker	match_part	578	651	13	+	.	ID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +
-###
-HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:11:3.2.0.0;Name=HS08198.g2
-HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
-HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
-HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
-HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
-HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
-HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
-HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:12:3.2.0.0;Name=HS08198.g2
-HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
-HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
-HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
-HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
-HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
-HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:26:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:27:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
 HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
 ###
-HS04636	repeatmasker	match	9419	9435	16	+	.	ID=HS04636:hit:0:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match_part	9419	9435	16	+	.	ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match	939	980	13	+	.	ID=HS04636:hit:1:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match_part	939	980	13	+	.	ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match	3791	3839	22	+	.	ID=HS04636:hit:2:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match_part	3791	3839	22	+	.	ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match	6918	6977	17	+	.	ID=HS04636:hit:3:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match_part	6918	6977	17	+	.	ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match	6028	6072	21	+	.	ID=HS04636:hit:4:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match_part	6028	6072	21	+	.	ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:5:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match_part	4518	4541	17	+	.	ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:6:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match_part	3852	3888	12	+	.	ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:7:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +
-HS04636	repeatmasker	match_part	3840	3847	17	+	.	ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
-###
-HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1
-HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
-HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
-HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
-HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
-HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
-HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
-HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
-HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
-HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1
-HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
-HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
-HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
-HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
-HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
-HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
-HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
-HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4542	4790	249	+	.	ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 802 1050 +;Gap=M249
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/evidences_reuse.gff3
--- a/test-data/evidences_reuse.gff3	Thu Oct 19 15:41:42 2017 -0400
+++ b/test-data/evidences_reuse.gff3	Sun Jul 01 16:11:34 2018 -0400
@@ -1,62 +1,42 @@
 ##gff-version 3
 HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
 ###
-HS08198	repeatmasker	match	578	651	13	+	.	ID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +
-HS08198	repeatmasker	match_part	578	651	13	+	.	ID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +
-###
-HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:11:3.12.0.0;Name=HS08198.g2;score=140
-HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140
-HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79
-HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88
-HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110
-HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:33:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104
-HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:34:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78
-HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:12:3.12.0.0;Name=HS08198.g2;score=2869
-HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:35:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46
-HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:36:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162
-HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:37:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83
-HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:38:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:39:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108
-HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:40:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102
-HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:41:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:2:3.12.0.0;Name=HS08198.g2;score=140
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:19:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:20:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:21:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:22:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:23:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:24:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:25:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:3:3.12.0.0;Name=HS08198.g2;score=2869
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:26:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:27:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:3:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77
 HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
 ###
-HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:0:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match_part	3852	3888	12	+	.	ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match	6028	6072	21	+	.	ID=HS04636:hit:1:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match_part	6028	6072	21	+	.	ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:2:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +
-HS04636	repeatmasker	match_part	3840	3847	17	+	.	ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
-HS04636	repeatmasker	match	3791	3839	22	+	.	ID=HS04636:hit:3:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match_part	3791	3839	22	+	.	ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match	9419	9435	16	+	.	ID=HS04636:hit:4:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match_part	9419	9435	16	+	.	ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match	939	980	13	+	.	ID=HS04636:hit:5:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match_part	939	980	13	+	.	ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match	6918	6977	17	+	.	ID=HS04636:hit:6:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match_part	6918	6977	17	+	.	ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:7:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match_part	4518	4541	17	+	.	ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
-###
-HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:8:3.12.0.0;Name=HS04636.g1;score=120
-HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 129 248 +;Gap=M120
-HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 50 80 +;Gap=M31
-HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:10:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146
-HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186
-HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
-HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
-HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
-HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
-HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:9:3.12.0.0;Name=HS04636.g1;score=8728
-HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 127 248 +;Gap=M122
-HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:19:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:20:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144
-HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:21:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182
-HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:22:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84
-HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:23:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
-HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:24:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
-HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:25:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
-HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:26:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:0:3.12.0.0;Name=HS04636.g1;score=120
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:0:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:1:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:2:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:6:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:1:3.12.0.0;Name=HS04636.g1;score=8728
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:10:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
diff -r 0cb75547ecc2 -r c98b3fa910bf test-data/fake_repbase.embl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fake_repbase.embl	Sun Jul 01 16:11:34 2018 -0400
@@ -0,0 +1,21 @@
+CC Fake repbase-like embl file, using data from DfamConsensus.embl*
+CC ****************************************************************
+XX
+ID   ACROBAT1     repeatmasker; DNA;  ???;  768 BP.
+CC   consensus - See RepBase for additional annotations.
+XX
+SQ   Sequence 768 BP; 178 A; 194 C; 215 G; 181 T; 0 other;
+     ggtgatgctg ccaacttact gatttagtgt atgatggtgt ttttgaggtg ctccagtggc   60
+     ttctgtttct atcagctgtc cctcctgttc agctactgac ggggtggtgc gtaacggcaa   120
+     aagcaccgcc ggacatcagc gctatctctg ctctcactgc cgtaaaacat ggcaactgca   180
+     gttcacttac accgcttctc aacccggtac gcaccagaaa atcattgata tggccatgaa   240
+     tggcgttgga tgccgggcaa cagcccgcat tatgggcgtt ggcctcaaca cgattttacg   300
+     tcacttaaaa aactcaggcc gcagtcggta acctcgcgca tacagccggg cagtgacgtc   360
+     atcgtctgcg cggaaatgga cgaacagtgg ggctatgtcg gggctaaatc gcgccagcgc   420
+     tggctgtttt acgcgtatga cagtctccgg aagacggttg ttgcgcacgt attcggtgaa   480
+     cgcactatgg cgacgctggg gcgtcttatg agcctgctgt caccctttga cgtggtgata   540
+     tggatgacgg atggctggcc gctgtatgaa tcccgcctga agggaaagct gcacgtaatc   600
+     agcaagcgat atacgcagcg aattgagcgg cataacctga atctgaggca gcacctggca   660
+     cggctgggac ggaagtcgct gtcgttctca aaatcggtgg agctgcatga caaagtcatc   720
+     gggcattatc tgaacataaa acactatcaa taagttggag tcattacc                768
+//