changeset 6:3384b6a842b0 draft

Uploaded
author greg
date Mon, 30 Oct 2017 09:52:00 -0400 (2017-10-30)
parents a73c2e65098e
children 2ac7090847f9
files .shed.yml gene_family_aligner.py gene_family_aligner.xml macros.xml test-data/3722.faa test-data/3722.faa.aln test-data/3722.fna test-data/3722.fna.aln test-data/38889.faa test-data/38889.faa.aln test-data/38889.fna test-data/38889.fna.aln test-data/39614.faa test-data/39614.faa.aln test-data/39614.fna test-data/39614.fna.aln utils.py
diffstat 17 files changed, 2094 insertions(+), 281 deletions(-) [+]
line wrap: on
line diff
--- a/.shed.yml	Fri Aug 25 13:01:25 2017 -0400
+++ b/.shed.yml	Mon Oct 30 09:52:00 2017 -0400
@@ -7,7 +7,7 @@
   Contains a tool that tool is one of the PlantTribes collection of automated modular analysis pipelines that
   utilize objective classifications of complete protein sequences from sequenced plant genomes to perform
   comparative evolutionary studies.  This tool aligns gene family sequences.
-remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/gene_family_aligner
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner
 type: unrestricted
 categories:
 - Phylogenetics
--- a/gene_family_aligner.py	Fri Aug 25 13:01:25 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import os
-
-import utils
-
-OUTPUT_DIR = 'geneFamilyAlignments_dir'
-
-parser = argparse.ArgumentParser()
-parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method')
-parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help='Trims alignments using trimAls ML heuristic trimming approach')
-parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help='Flag for constructing orthogroup multiple codon alignments')
-parser.add_argument('--gap_trimming', dest='gap_trimming', default=0, type=float, help='Remove sites in alignments with gaps of')
-parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='Maximum number of iterations')
-parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
-parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets')
-parser.add_argument('--output', dest='output', help='Output dataset')
-parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory')
-parser.add_argument('--output_dataset_collection', dest='output_dataset_collection', default=None, help='Output additional dataset collection of files.')
-parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='Maximum number of iteration that the PASTA algorithm will execute')
-parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
-parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of')
-
-args = parser.parse_args()
-
-# Build the command line.
-cmd = 'GeneFamilyAligner'
-cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
-cmd += ' --alignment_method %s' % args.alignment_method
-if args.alignment_method == 'pasta':
-    if args.pasta_script_path is not None:
-        cmd += ' --pasta_script_path %s' % args.pasta_script_path
-    if args.pasta_iter_limit is not None:
-        cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
-cmd += ' --num_threads %d' % args.num_threads
-if args.codon_alignments is not None:
-    cmd += ' --codon_alignments'
-if args.automated_trimming is not None:
-    cmd += ' --automated_trimming'
-if args.gap_trimming > 0:
-    cmd += ' --gap_trimming %4f' % args.gap_trimming
-if args.remove_sequences > 0:
-    cmd += ' --remove_sequences %4f' % args.remove_sequences
-if args.iterative_realignment > 0:
-    cmd += ' --iterative_realignment %d' % args.iterative_realignment
-
-# Run the command.
-utils.run_command(cmd)
-
-# Handle outputs.
-if args.codon_alignments is None:
-    src_output_dir = OUTPUT_DIR
-else:
-    src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
-if args.output_dataset_collection is not None:
-    utils.move_directory_files(src_output_dir, args.output_dataset_collection, copy=True)
-utils.move_directory_files(src_output_dir, args.output_dir)
-utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)
--- a/gene_family_aligner.xml	Fri Aug 25 13:01:25 2017 -0400
+++ b/gene_family_aligner.xml	Mon Oct 30 09:52:00 2017 -0400
@@ -1,36 +1,30 @@
-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.2">
+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">
     <description>aligns integrated orthologous gene family clusters</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements_gene_family_aligner" />
+    <requirements>
+        <requirement type="package" version="1.0.3">plant_tribes_gene_family_aligner</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#set input_format = $input_format_cond.input_format
-#set alignment_method_cond = $input_format_cond.alignment_method_cond
 #set alignment_method = $alignment_method_cond.alignment_method
-#if str($input_format_cond.input_format) == 'ptortho':
-    #set output_codon_alignments = False
-#else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
-    #set output_codon_alignments = False
-#else:
-    #set output_codon_alignments = True
-#end if
-
-python '$__tool_directory__/gene_family_aligner.py'
+#set input_dir = 'input_dir'
+mkdir $input_dir &&
+#for $i in $input:
+    #set filename = $i.file_name
+    #set name = $i.name
+    ln -s $filename $input_dir/$name &&
+#end for
+GeneFamilyAligner
 --alignment_method $alignment_method
 #if str($alignment_method) == 'pasta':
     --pasta_script_path '$__tool_directory__/run_pasta.py'
     --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
 #end if
 --num_threads \${GALAXY_SLOTS:-4}
-#if str($input_format) == 'ptortho':
-    --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
-#else:
-    ## str($input_format) == 'ptorthocs'
-    --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
-    #if str($input_format_cond.codon_alignments) == 'yes':
-        --codon_alignments true
-    #end if
+--orthogroup_faa '$input_dir'
+#if str($codon_alignments) == 'yes':
+    --codon_alignments
 #end if
 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
 #if str($remove_gappy_sequences) == 'yes':
@@ -40,7 +34,7 @@
         --gap_trimming $trim_type_cond.gap_trimming
     #else:
         ## str($trim_type) == 'automated_trimming'
-        --automated_trimming true
+        --automated_trimming
     #end if
     #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
     #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
@@ -51,90 +45,116 @@
         #if str($remove_sequences_with_gaps_cond.iterative_realignment):
             --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
         #end if
-        #if $output_codon_alignments:
-            --output '$output_aln_filtered_ca'
-            --output_dir '$output_aln_filtered_ca.files_path'
-        #else:
-            --output '$output_aln_filtered'
-            --output_dir '$output_aln_filtered.files_path'
-        #end if
-    #else:
-        #if $output_codon_alignments:
-            --output '$output_aln_trimmed_ca'
-            --output_dir '$output_aln_trimmed_ca.files_path'
-        #else:
-            --output '$output_aln_trimmed'
-            --output_dir '$output_aln_trimmed.files_path'
-        #end if
-    #end if
-#else:
-    #if $output_codon_alignments:
-        --output '$output_aln_ca'
-        --output_dir '$output_aln_ca.files_path'
-    #else:
-        --output '$output_aln'
-        --output_dir '$output_aln.files_path'
     #end if
 #end if
-#if str($output_dataset_collection) == 'yes':
-    --output_dataset_collection dataset_collection
-#end if
+&>proc.log
     ]]></command>
     <inputs>
-        <conditional name="input_format_cond">
-            <param name="input_format" type="select" label="Classified orthogroup fasta files">
-                <option value="ptortho">Proteins orthogroup fasta files</option>
-                <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
+        <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
+        <conditional name="alignment_method_cond">
+            <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
+                <option value="mafft" selected="true">MAFFT</option>
+                <option value="pasta">PASTA</option>
             </param>
-            <when value="ptortho">
-                <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
-                    <validator type="empty_extra_files_path" />
-                </param>
-                <expand macro="cond_alignment_method" />
-            </when>
-            <when value="ptorthocs">
-                <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
-                    <validator type="empty_extra_files_path" />
-                </param>
-                <expand macro="cond_alignment_method" />
-                <expand macro="param_codon_alignments" />
+            <when value="mafft" />
+            <when value="pasta">
+                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
             </when>
         </conditional>
-        <expand macro="cond_remove_gappy_sequences" />
-        <param name="output_dataset_collection" type="select" display="radio" label="Output additional dataset collection of files?">
+        <param name="codon_alignments" type="select" label="Codon alignments">
             <option value="no" selected="true">No</option>
             <option value="yes">Yes</option>
         </param>
+        <conditional name="remove_gappy_sequences_cond">
+            <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <conditional name="trim_type_cond">
+                    <param name="trim_type" type="select" label="Trimming method">
+                        <option value="gap_trimming" selected="true">Gap score based trimming</option>
+                        <option value="automated_trimming">Automated heuristic trimming</option>
+                    </param>
+                    <when value="gap_trimming">
+                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
+                    </when>
+                    <when value="automated_trimming" />
+                </conditional>
+                <conditional name="remove_sequences_with_gaps_cond">
+                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
+                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
+                    </when>
+                </conditional>
+                <param name="output_pristine_alignments" type="select" display="radio" label="Output primary and intermediate alignments?" help="In addition to trimmed/filtered alignments">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
-        </data>
-        <data name="output_aln_ca" format="ptalignca" label="${tool.name} (protein and coding sequences orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
-        </data>
-        <data name="output_aln_filtered" format="ptalignfiltered" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
-        </data>
-        <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="${tool.name} (filtered protein and coding sequences orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter>
-        </data>
-        <data name="output_aln_trimmed" format="ptaligntrimmed" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
-        </data>
-        <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}">
-            <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
-        </data>
-        <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" />
-            <filter>output_dataset_collection == 'yes'</filter>
+        <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
+        </collection>
+        <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" />
+            <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
+        </collection>
+        <collection name="pristine" type="list" label="${tool.name} (intermediate alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
         </collection>
+        <collection name="trimmed_faa" type="list" label="${tool.name} (trimmed orthogroup protein alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_faa" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+        </collection>
+        <collection name="trimmed_fna" type="list" label="${tool.name} (trimmed orthogroup codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" />
+            <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
+        </collection>
+        <collection name="filtered_faa" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
+            <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+        </collection>
+        <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
+            <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
+        </collection>
+
     </outputs>
     <tests>
-        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
         <test>
+            <param name="input">
+                <collection type="list">
+                    <element name="3722.faa" value="3722.faa"/>
+                    <element name="3722.fna" value="3722.fna"/>
+                    <element name="38889.faa" value="38889.faa"/>
+                    <element name="38889.fna" value="38889.fna"/>
+                    <element name="39614.faa" value="39614.faa"/>
+                    <element name="39614.fna" value="39614.fna"/>
+                </collection>
+            </param>
+            <param name="codon_alignments" value="yes"/>
+            <output_collection name="primary_faa" type="list">
+                <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/>
+                <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/>
+                <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/>
+            </output_collection>
+            <output_collection name="primary_fna" type="list">
+                <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
+                <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
+                <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
+            </output_collection>
         </test>
-        -->
     </tests>
     <help>
 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
@@ -145,13 +165,13 @@
 
 **Required options**
 
- * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history.  Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
+ * **Integrated orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyIntegrator tool selected from your history.  Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
 
  * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments.  PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.
 
   - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
 
- * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments.  This option requires protein and their corresponding coding sequences to be provided as input data.
+ * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments.  This option requires both protein and their corresponding coding sequence orthogroup fasta files to be present in the GeneFamilyAligner input data that was produced by the GeneFamilyIntegrator.
 
 **Other options**
 
@@ -167,7 +187,7 @@
 
     - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences.  Zero value has no effect.
 
- * **Output additional dataset collection of files** - selecting 'Yes' will produce an additional output dataset collection whose elements are copies of the directories of files (these elements can be viewed with visualization tools).
+ * **Output primary and intermediate alignments** - selecting 'Yes' will produce a dataset collection of primary and intermediate alignments, the elements of which can be viewed with viaula tools, in addition to the final trimmed and/or filtered alignments dataset collection.
 
 .. _trimAl: http://trimal.cgenomics.org
 
--- a/macros.xml	Fri Aug 25 13:01:25 2017 -0400
+++ b/macros.xml	Mon Oct 30 09:52:00 2017 -0400
@@ -1,47 +1,6 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
     <token name="@WRAPPER_VERSION@">1.0</token>
-    <xml name="requirements_assembly_post_processor">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_assembly_post_processor</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_aligner">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_aligner</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_classifier">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_classifier</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_integrator">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_integrator</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_kaks_analysis">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_kaks_analysis</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_ks_distribution">
-        <requirements>
-            <requirement type="package" version="1.3.2">r-optparse</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_phylogeny_builder">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_phylogeny_builder</requirement>
-        </requirements>
-    </xml>
-    <xml name="param_codon_alignments">
-        <param name="codon_alignments" type="select" label="Codon alignments">
-            <option value="yes" selected="true">Yes</option>
-            <option value="no">No</option>
-        </param>
-    </xml>
     <xml name="param_method">
         <param name="method" type="select" label="Protein clustering method">
             <option value="gfam" selected="true">GFam</option>
@@ -49,74 +8,12 @@
             <option value="orthomcl">OrthoMCL</option>
         </param>
     </xml>
-    <xml name="param_options_type">
-        <param name="options_type" type="select" label="Options Configuration">
-            <option value="basic" selected="true">Basic</option>
-            <option value="advanced">Advanced</option>
-        </param>
-    </xml>
-    <xml name="param_orthogroup_fna">
-        <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences">
-            <option value="yes" selected="true">Yes</option>
-            <option value="no">No</option>
-        </param>
-    </xml>
     <xml name="param_scaffold">
         <param name="scaffold" type="select" label="Gene family scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
         </param>
     </xml>
-    <xml name="param_sequence_type">
-        <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
-            <option value="protein" selected="true">Amino acid based</option>
-            <option value="dna">Nucleotide based</option>
-        </param>
-    </xml>
-    <xml name="cond_alignment_method">
-        <conditional name="alignment_method_cond">
-            <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
-                <option value="mafft" selected="true">MAFFT</option>
-                <option value="pasta">PASTA</option>
-            </param>
-            <when value="mafft" />
-            <when value="pasta">
-                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
-            </when>
-        </conditional>
-    </xml>
-    <xml name="cond_remove_gappy_sequences">
-        <conditional name="remove_gappy_sequences_cond">
-            <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <conditional name="trim_type_cond">
-                    <param name="trim_type" type="select" label="Trimming method">
-                        <option value="gap_trimming" selected="true">Gap score based trimming</option>
-                        <option value="automated_trimming">Automated heuristic trimming</option>
-                    </param>
-                    <when value="gap_trimming">
-                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
-                    </when>
-                    <when value="automated_trimming" />
-                </conditional>
-                <conditional name="remove_sequences_with_gaps_cond">
-                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
-                        <option value="no" selected="true">No</option>
-                        <option value="yes">Yes</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
-                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-    </xml>
     <xml name="citation1">
         <citation type="bibtex">
             @misc{None,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3722.faa	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,161 @@
+>gnl_Glyma1.01_PACid_16266208
+MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG
+VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK
+RNSSEMNFGKAENSSVFDASYQNFCFGVNQLQDIKKGKGGILGGGGRSRHRSGRKQKMFYGHDV
+>gnl_Glyma1.01_PACid_16266209
+MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG
+VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK
+RNSSEMNFGKAENSSVFDASYQNFCFGTGEPTPRYKEGKGGNSRRRR
+>gnl_Glyma1.01_PACid_16266210
+MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG
+VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK
+RNSSEMNFGKAENSSVFDASYQNFCFGVGHVNYHYQ
+>gnl_Glyma1.01_PACid_16301083
+MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG
+VYDSDDDENGMGDFLDEMLTMMSQTKSNENGEESFEELQQLFEDMFEADIGLDGGPSLASSDCSTSSAYMTYSESSSSNK
+HNSSEMNFGKAENSSVFDAGYQNFCFGVNQLQDIKKKKGGILGGGRSRHRNGRKQNMSYGHDVSSNDYPGISTK
+>gnl_Glyma1.01_PACid_16301085
+MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG
+VYDSDDDENGMGDFLDEMLTMMSQTKSNENGEESFEELQQLFEDMFEADIGLDGGPSLASSDCSTSSAYMTYSESSSSNK
+HNSSEMNFGKAENSSVFDAGYQNFCFGVGHVNYHYQ
+>gnl_Glyma1.01_PACid_16301084
+MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG
+VYDSDDDENGMGDFLDEMLTMMSQTKSNENGEESFEELQQLFEDMFEADIGLDGGPSLASSDCSTSSAYMTYSESSSSNK
+HNSSEMNFGKAENSSVFDAGYQNFCFGTGEPTPRYKEEKGGNSRRR
+>gnl_Medtr3.5_Medtr8g022310.1
+MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG
+VYDSDDDENGMGDFLNEMVTMMSQTKSNENGEESFEELQQLFDDMFQADIGLNGSTSLNASGCSTSSTFMTFSESSNSNK
+RNSTQMNFGKAEDSSSFGANYQNFCFGMKHLQEDVEKEKGGILEGGGSKKQRKGRKQKISCGHVSSNDHPGISAN
+>gnl_Medtr3.5_Medtr8g022310.2
+MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG
+VYDSDDDENGMGDFLNEMVTMMSQTKSNENGEESFEELQQLFDDMFQADIGLNGSTSLNASGCSTSSTFMTFSESSNSNK
+RNSTQMNFGKAEDSSSFGANYQNFCFGVNLVNYHYQ
+>gnl_Musac1.0_GSMUA_Achr6T31040_001
+MAAEEDKSGDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASGNAQIVGEAKEKFQEIQKAYSVLSDSNKRFLYDVG
+VYDNDDDNDENGMGDFIGEMLEMMSQTKPNENSQDSFQELQELFVEMFQDDLDAGFGGSIFHDCPWAQPTNGQDCWTSSG
+LHFANGRSKCGNKRGNSAVNLGKVNLEELEHGTSDFYFGLNDAAQPSQGKGGSNNKRRNGRKQKVSSNHDVSS
+>gnl_Musac1.0_GSMUA_Achr9T18140_001
+MAAGEEKIGDFYTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASGNHRRMEEAKEKFQEIQKAYSVLSDSSKRFLYDVG
+IYDNEDDNDEKGMGDFIGEIAQMMSQTKSGENGHDSFEELQRMFLDMFQDDLDAGFGDSSIHSGPQARPTDGLNCSMPSG
+LQFADGGNNGSNKRGNSEKAKLDGLENSSTGFCFGLNDAGQSSKGKGSANSKRRNGRKQKVSSKHDVSSSDAEVSF
+>gnl_Musac1.0_GSMUA_Achr8T23700_001
+MASDMDASGDFYSVLGLKKECSEAELRNAYKKLALKWHPDKCSASGNEIRMKEAKQQFQEIQKAYSVLSDSNKRFLYDVG
+AYDKDDDKDEEGMVEFLGEMAQMMRQTKCCGSGQESFEQLQQMFVEMFHDDLDAGFCGHSSATSGAASCGNKRDNSAMDS
+GKRKPDELDPAAIGFCLGTKDAGQSSKGRGSNSKRRNRRKQKASSKHDNSSHNAKVSA
+>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001
+MEGDEEKSGDFYAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASGNKIRMDKAKEKFQEIQKAYSVLSDSNKRFLYDVG
+VYDKDDEEDEEGMGDFIGEIAQMMSQSKPSGSGHESLEELHRQVVEMFLDELDAGDRFSSANQGASSCDGRDDGGGNKRG
+NWAVDWGKEKLNELGPGTGGFCFGVSRRVHSFDLMIDVVHLIHSDLTLE
+>gnl_Orysa6.0_PACid_16843526
+MADGGEKCRDAAGEGGGGGDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSSSAKHMEEAKEKFQEIQGAYSVLSD
+SNKRFLYDVGVYDDDDNDDDNLQGMGDFIGEMAQMMSQARPTRQESFKELQQLFVDMFQADLDSGFCNGPSKCYHTQAQS
+QTRTSSTSPSMSPSPPPPVATEAESPSCNGINKRGSSAMDSGKPPRASEVGSGQSQSGFCFGKSDAKQAAKTRSGNTASR
+RRNGRKQKVSSKHDVSSEDEMPGSQWHGVA
+>gnl_Orysa6.0_PACid_16843528
+MADGGEKCRDAAGEGGGGGDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSSSAKHMEEAKEKFQEIQGAYSVLSD
+SNKRFLYDVGVYDDDDNDDDNLQGMGDFIGEMAQMMSQARPTRQESFKELQQLFVDMFQADLDSGFCNGPSKCYHTQAQS
+QTRTSSTSPSMSPSPPPPVATEAESPSCNGINKRGSSAMDSGKPPRASEVGSGQSQSGFCFGQKSDAKQAAKTRSGNTAS
+RRRNGRKQKVSSKHDVSSEDEMPGSQWHGVA
+>gnl_Poptr2.2_PACid_18217800
+MANGGEDKWKSNDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASGNSKFVEEAKKKFQAIQQAYSVLSDTNKRFLY
+DVGVDDSDDDENGMGDFLNEMAVMMSQTKPSENMEESLEELQELFDEMFQEDLHSFGIDSQAAPSCPPSYVSYSESSNSN
+NKRVSADMNLGKTKVDDSSSFNSHFEKFCLGTGGTAATFQEGEGGSKRRNSRRSQRQTKARQETKSFFGL
+>gnl_Poptr2.2_PACid_18234651
+MENGGEEKGKSNDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASENSRFVDEAKKKFQTIQQAYSVLSDTNKRFLY
+DVGVYDSEDDENGMGGFMNEMAAMMSQTKPHENVEESFEELQGLFEEMFQEDLDSFGIACQATTCVSYSESSNSNDKRVS
+VDMNLKKTKVDDSSGFNSHVEKFCLGVSGTPAIFQEGEGSKRRSSRRNRR
+>gnl_Poptr2.2_PACid_18234649
+MLRMENGGEEKGKSNDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASENSRFVDEAKKKFQTIQQAYSVLSDTNKR
+FLYDVGVYDSEDDENGMGGFMNEMAAMMSQTKPHENVEESFEELQGLFEEMFQEDLDSFGIACQATTCVSYSESSNSNDK
+RVSVDMNLKKTKVDDSSGFNSHVEKFCLGVEHQQSFKKGKGVRGGVQGGTGGRERKGRKQEVSSGYDVSSHDHGISAS
+>gnl_Poptr2.2_PACid_18234650
+MENGGEEKGKSNDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASENSRFVDEAKKKFQTIQQAYSVLSDTNKRFLY
+DVGVYDSEDDENGMGGFMNEMAAMMSQTKPHENVEESFEELQGLFEEMFQEDLDSFGIACQATTCVSYSESSNSNDKRVS
+VDMNLKKTKVDDSSGFNSHVEKFCLGVEHQQSFKKGKGVRGGVQGGTGGRERKGRKQEVSSGYDVSSHDHGISAS
+>gnl_Soltu3.4_PGSC0003DMP400016105
+MGNDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASGNSKFVDEAKKKFQAIQEAYSVLSDANKRFLYDVGVYDSGD
+DDDENGMGDFLNEMAAMMSQNKSNENQEETFEELQDMFDEIFNSDNGMSSSSSSSSRTGTPSMCSTTSSTSSSETFFTFS
+NKRSSGEMKSGKGDSCQFQGFCEGTGGASGKSNERERSRRKNSKSGRKQ
+>gnl_Soltu3.4_PGSC0003DMP400016106
+MGNDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASGNSKFVDEAKKKFQAIQEAYSVLSDANKRFLYDVGVYDSGD
+DDDENGMGDFLNEMAAMMSQNKSNENQEETFEELQDMFDEIFNSDNGMSSSSSSSSRTGTPSMCSTTSSTSSSETFFTFS
+NKRSSGEMKSGKGDSCQFQGFCEGVEHLEKAMKENGVGGKIPRVDGSNRMDAKRQKVLS
+>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329
+MAPRGEKDSDFYAILGLKKECSASDLRNAYKRLALRWHPDRCSASGNTKFVEECKKKFQAIQQAYSVLSDANKRFLYDVG
+AYGSDDDDQGMGEFLGEMAVMMSQTKPSEKGPESFEDLQNLFQEMFERDLDMFKSSTSHNNNNDNNNNNHRSSDNNNCSS
+VHCFSNTNKRNCSDMNAGEASEVGRFAFSCYATEFLHKQTFSVGADDVRSESSNKRRNGRKQKSTSSSRKS
+>gnl_Aquco1.0_PACid_18141277
+MASEEEASDFYKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASGNSKFVEEAKKNFQAIQEAYSVLSDEQKRFMYDVGV
+YDKDDDDENEDMGDFLGEMMSMMKQENTSADGQQSFEDLQNLFQEMVQNDKEFYNPASQNSSIYNASNNMFSFSNNENLN
+NASNNTFSSFYNENLNSSNKKSCSSMSAENTKVDFNMESLDFRSFSIGLEGGTSFQNSKGRGVTGRRTGRKQKGSSCNDM
+SSHDSKILA
+>gnl_Arath10_AT3G14200.1
+MASSNSEKINENLYAVLGLKKECSKTELRSAYKKLALRWHPDRCSSMEFVEEAKKKFQAIQEAYSVLSDSNKRFLYDVGA
+YNTDDDDDQNGMGDFLNEMATMMNQSKPSDNNTGDSFEQLQDLFNEMFQGDAAAFPSSSSCSTSNFTSSRSFVFDTNSQR
+SSSFATSSMGMNNDPFGYDPRAHSFSLGVDHQQEFKKGKNNGGRRNRRKNNVPSAGHETSSSNNYGVPTS
+>gnl_Bradi1.2_Bradi3g60090.1
+MATGGDKCGGKPAAAGVGGGDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSSSTKHMEEAKEKFQEIQGAYSVLS
+DANKRFLYDVGVYEEHEEEDDDTLQGMGDFLGEMAHMMSQTQPARQESFEELQQLFVDMFQSDIESGFCNGPAKDHDPVQ
+RQTRTFSTPPSPSPSPPPPLATVDEAASCNGINKRGSSAMGSGKPPRAGEVSGGHGQSEFCFGMSDAKQAPKARGGNASR
+RRNGQKQKLSSKHDVSSGDEMPRPHAAV
+>gnl_Carpa1.181_PACid_16420351
+MADGEDKNNSDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASGNSMFVEEAKKKFQAIQEAYSVLSDANKRFLYDV
+GAYESDDDENGMGDFLNEMAAMMSQTKPNENGNAQESFEELQELFQEMFQGDMGFNTFGSSSQPTTSSCSASSAYATCSE
+TSNPNNNKRNSSEMNYGKKKVDDSSGFHAHFQTFCLGVEQQQDFKKGKEARGGIRGKPGGSRRQGRKQKVSSRHNVSSND
+LGISAS
+>gnl_Frave2.0_gene05408
+MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNRRMEEKGNDFYAVMGLKKECSDSELRNAYKKLA
+LIWHPDRCSASGNSKFVEEAKKKFQDIQQAYSVLSDANKRFLYDVGAYESDDDENGMGDFLNEMAVMMSQTKPNENGGES
+FEQLQELFEEMFQGDIEGFSSCSQPPTSCSTSSSSYALYCENSTPSNKRNSSAMNYGNATLDSSGFDAHFHNFCVGTGGK
+PAKDREGDARKRKDSRRSNR
+>gnl_Mimgu1.0_PACid_17694730
+MAADEEKSSDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASGNLKYVEEAKNKFQAVQQAYSVLSDANKRFLYDVG
+IYDSEDDADENGMGDFLNEMVAMMGQSKPNENKNESFQELQDLFEEIFNNDAEEVFKIPPPHFPYQDSCSETRTASNKRN
+AREMGSVNFSNIEATPFEGFCIGENVIFGGERIQTRPGGGSRRTKPKISTSIDGLIS
+>gnl_Nelnu1.0_NNU_010544-RA
+MNLLLQKWHPDRCSSSGNSKFVEDSKKKFQAIQEAYSVLSDENKRFLYDVGVYDCDDDDDDENGMGEFLGEMATMMSQIK
+PSENGPESLEKLQELFEEMFQRDMDDGFFSPSPQCASFSSSCSSSSSSTTYFSYNNNKHDNKRNCSDISSMDDFYTFGTD
+SIQFSNFCIGVEGGEDSKVRGGKSRRKSNRRQKVSSSKHDPSCR
+>gnl_Solly2.3_Solyc03g123560.2.1
+MEDKSNDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASGNLKFVDEAKKQFQAIQEAYSVLSDANKKFLYDVGVYD
+SGDDDDENGMGDFLNEMAAMMSQNKSNENQGEETFEELQDMFNEMFNSDNGTFSSSSSSSSSWTGTPSMCSTTSSTSSSE
+TFLTFPNKRSSGEMKSGSSVRGDSCQFQGFCVGAGGTSGKCNERERSWRKNSKSGRKH
+>gnl_Sorbi1.4_PACid_1968370
+MDAGGEKFSDAAAAEGGEGGGDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSSSVKHMEEAKEKFQEIQGAYSVL
+SDANKRLLYDVGVYDDEDDEDSMQGMGDFIGEMAQMMSQVRPTRQESFEELQQLFVDMFQSDIDSGFCNGSAKDQVQGQA
+KSRTCSTSPSSSPSPPPPPTIVKEAEVSSCNGFNKRGSSAMDSGKPPRPVEGGAGQAGFCFGVSDTKQTPKPRGPNTSRR
+RNGRKQKLSSKHDVSSEDETAGS
+>gnl_Thepa2.0_Tp3g12470
+MASNNSEKGNDDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMGTPEFVDEAKKKFQAIQEAYSVLSDSNKRFLYD
+VGAYNSDDEDQNGMGDFLNEMAAMMNQSKPSENNSGDSFEQLQDLFNEMFQGDAAAFSSSSSSSCSASTFTSSCSFVFDT
+NSQRSPFETSSMGTNDLFGFDHSAHTFSLGVEHQQDFKKGKNSGGRRNRRKNNAQSAAHETASSNNYGVPTS
+>gnl_Theca1.0_Tc06_g010450
+MANGEEKNNDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASGNSKFVEEAKKKFQAIQQAYSVLSDSNKRFLYDVG
+AYDSDDDENGMGDFLNEMAGMMSQTKSNENGGESFEELQELFEEMFQADIDSFESTGQSTPSCSASSSFGSYGESSSSNK
+RNSSEMSSVETRLESSSSFDAQFHSFCLGVEHRQDIKQHRGARGGMRGAAGGSRRRNGRKQKVSSGHDVTSNDCGISAS
+>gnl_Vitvi12X_PACid_17827068
+MAAGEEKSNDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSGNSKFVEEAKKKFQAIQEAYSVLSDANKRFLYDVG
+AYDSDDDENGMGDFLNEMAVMMSQTKSNENGKESFEELQELFEDMFQRDVDAFNSASHHPMNSFPSSTSTSSYCESSNAN
+NKRNSAEMGSGRMMSAGESSAFDAHFQSFCFGTGGTPGRFQEGERSKRRNSRRSQR
+>gnl_Selmo1.0_PACid_15401289
+MEKRKEDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDKQHSLEDQAKAKFQGIQEAYSVLSDDKKRVLYDSGLYDEGDDE
+VS
+>gnl_Orysa6.0_PACid_16864430
+MARGGGGGGGADADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAYSVLSDSNK
+RFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATPAESFEELQQLFVDMFQDDIDAGLCQSTPPPPSWPSPPA
+AANARSPAAAATSRKGVNKRCSPAAMDMDSGLSSLLGISGFCFEAPWTSQDASTAAGGGGGKRRKQRPPPASHNV
+>gnl_Sorbi1.4_PACid_1982925
+MAATSHCGNIQDQDEEASAPGAADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASGSSPARMEEAKERFQEIQGAY
+SVLSDSNKRLLYDVGVYDSDDDEADLSGMGDFLGEMADMMSQATPTETFEELQQVFVDMFQDDLDDAGFFGGLPTTGRRA
+QAPSTSLPPSVSSSPLRPTPAAGRSKGPQATPSSSFKGVERRGSTSTAKRPRPNGSAGLESDLGLSGFCFMVSKEMSKSK
+ERQAVWASDDGDRSTDGKQRLSTSRDVSGGGMSRSLQGQSSKNLLQCMASKS
+>gnl_Medtr3.5_Medtr8g022310.3
+MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG
+VYDSDDDENVRHLFHTIHELGTLFCVMFCFFISLRGEKRSNLNLTFSLSH
+>gnl_Nelnu1.0_NNU_000115-RA
+MEVDSHRSSPSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTPSLLEKAKSKFQQIQEAYSGGLLVFMLSDQGKRT
+LYDVGLYDPDDETNDEVGLRRFHAGDDISHERCEETGEEIQLGGTTGDVSGNVTRAGVEDGECWWCVVVRWSCSLKEELK
+EGQMGIISESDDAGHDTPSLPHLHGSELELLGRTGCCN
+>contig_7
+ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG
+NESGEISGKKNTRKGKGDX
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3722.faa.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,312 @@
+>gnl_Glyma1.01_PACid_16266208
+---MANE-------------------------------------------------GKKS
+NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY
+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG
+--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------
+----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM
+NFGK---AENSSVFDASY------QNFCFG-VN--QLQDIKKGK---GGILGGGGRSRHR
+SGRKQKMFY-GHDV--------------------------
+>gnl_Glyma1.01_PACid_16266209
+---MANE-------------------------------------------------GKKS
+NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY
+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG
+--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------
+----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM
+NFGK---AENSSVFDASY------QNFCFG-TG--EPTPRYKEG--------KGGNSRRR
+R---------------------------------------
+>gnl_Glyma1.01_PACid_16266210
+---MANE-------------------------------------------------GKKS
+NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY
+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG
+--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------
+----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM
+NFGK---AENSSVFDASY------QNFCFG-VG--HVNYHYQ------------------
+----------------------------------------
+>gnl_Glyma1.01_PACid_16301083
+---MADE-------------------------------------------------GNKS
+NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY
+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG
+--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------
+----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM
+NFGK---AENSSVFDAGY------QNFCFG-VN--QLQDIKKKK---GGIL-GGGRSRHR
+NGRKQNMSY-GHDVSSNDYPGISTK---------------
+>gnl_Glyma1.01_PACid_16301085
+---MADE-------------------------------------------------GNKS
+NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY
+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG
+--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------
+----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM
+NFGK---AENSSVFDAGY------QNFCFG-VG--HVNYHYQ------------------
+----------------------------------------
+>gnl_Glyma1.01_PACid_16301084
+---MADE-------------------------------------------------GNKS
+NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY
+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG
+--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------
+----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM
+NFGK---AENSSVFDAGY------QNFCFG-TG--EPTPRYKEE--------KGGNSRRR
+----------------------------------------
+>gnl_Medtr3.5_Medtr8g022310.1
+---MANE-------------------------------------------------GNKS
+NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY
+S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG
+--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL-------------
+----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM
+NFGK---AEDSSSFGANY------QNFCFG-MK--HLQEDVEKE--KGGILEGGGSKKQR
+KGRKQKISC-GH-VSSNDHPGISAN---------------
+>gnl_Medtr3.5_Medtr8g022310.2
+---MANE-------------------------------------------------GNKS
+NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY
+S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG
+--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL-------------
+----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM
+NFGK---AEDSSSFGANY------QNFCFG-VN--LVNYHYQ------------------
+----------------------------------------
+>gnl_Musac1.0_GSMUA_Achr6T31040_001
+---MAAE-------------------------------------------------EDKS
+GDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAY
+S------VLSDSNKRFLYDVGVYDND------DDNDENGMGDFIGEMLEMMSQTKPNENS
+--QDSFQELQ------ELFVEMFQDDL--DAG---------FGGSIFH-DCPWAQP----
+---TNGQDCWTSSG------------------LHFANGRSK--------CGNKRGNS-AV
+NLGK----VNLEELEHGT------SDFYFG-LN--DAAQPSQGKGGS--------NNKRR
+NGRKQKVSS-NHDVSS------------------------
+>gnl_Musac1.0_GSMUA_Achr9T18140_001
+---MAAG-------------------------------------------------EEKI
+GDFYTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASG---NHRRMEEAKEKFQEIQKAY
+S------VLSDSSKRFLYDVGIYDNE------DDNDEKGMGDFIGEIAQMMSQTKSGENG
+--HDSFEELQ------RMFLDMFQDDL--DAG---------FGDSSIH-SGPQARP----
+---TDGLNCSMPSG------------------LQFADGGNN--------GSNKRGNS-EK
+--------AKLDGLENSS------TGFCFG-LN--DAGQSSKGKGSA--------NSKRR
+NGRKQKVSS-KHDVSSSD-AEVSF----------------
+>gnl_Musac1.0_GSMUA_Achr8T23700_001
+---MASD-------------------------------------------------MDAS
+GDFYSVLGLKKECSEAELRNAYKKLALKWHPDKCSASG---NEIRMKEAKQQFQEIQKAY
+S------VLSDSNKRFLYDVGAYDKD------DDKDEEGMVEFLGEMAQMMRQTKCCGSG
+--QESFEQLQ------QMFVEMFHDDL--DAG---------F------------------
+--------CGHSSA---------------------TSGAAS--------CGNKRDNS-AM
+DSGK----RKPDELDPAA------IGFCLG-TK--DAGQSSKGRGS---------NSKRR
+NRRKQKASS-KHDNSSHN-AKVSA----------------
+>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001
+---MEGD-------------------------------------------------EEKS
+GDFYAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASG---NKIRMDKAKEKFQEIQKAY
+S------VLSDSNKRFLYDVGVYDKD------DEEDEEGMGDFIGEIAQMMSQSKPSGSG
+--HESLEELH------RQVVEMFLDEL--DAGD-------RFSSANQ-------------
+----GASSCDGRDD----------------------------------GGGNKRGNW-AV
+DWGK----EKLNELGPGT------GGFCFG-VS------------------------RRV
+HSFDLMIDV-VHLIHSDL-------------------TLE
+>gnl_Orysa6.0_PACid_16843526
+---MADGG-------------------------------------EKC-RDAAG-EGGGG
+GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY
+S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR--
+--QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT
+SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM
+DSGK-PPRASEVGSGQSQ------SGFCFG-KS--DAKQAAKTRSGNT-------ASRRR
+NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA
+>gnl_Orysa6.0_PACid_16843528
+---MADGG-------------------------------------EKC-RDAAG-EGGGG
+GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY
+S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR--
+--QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT
+SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM
+DSGK-PPRASEVGSGQSQ------SGFCFGQKS--DAKQAAKTRSGNT-------ASRRR
+NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA
+>gnl_Poptr2.2_PACid_18217800
+---MANGGE----------------------------------------------DKWKS
+NDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY
+S------VLSDTNKRFLYDVGVDDS--------DDDENGMGDFLNEMAVMMSQTKPSENM
+--EESLEELQ------ELFDEMFQEDL--HS----------FGIDSQ-------------
+----AAPSC--PPS------------------YVSYSESSN--------SNNKRVSA-DM
+NLGK-TKVDDSSSFNSHF------EKFCLG-T-----------GGTAATFQEGEGGSKRR
+NSRRSQRQT-KARQETKSFFGL------------------
+>gnl_Poptr2.2_PACid_18234651
+---MENGGE----------------------------------------------EKGKS
+NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY
+S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV
+--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ-------------
+----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM
+NLKK-TKVDDSSGFNSHV------EKFCLG-V-----------SGTPAIFQEGE-GSKRR
+SSRRNRR---------------------------------
+>gnl_Poptr2.2_PACid_18234649
+MLRMENGGE----------------------------------------------EKGKS
+NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY
+S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV
+--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ-------------
+----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM
+NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER
+KGRKQEVSS-GYDVSSHD-HGISAS---------------
+>gnl_Poptr2.2_PACid_18234650
+---MENGGE----------------------------------------------EKGKS
+NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY
+S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV
+--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ-------------
+----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM
+NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER
+KGRKQEVSS-GYDVSSHD-HGISAS---------------
+>gnl_Soltu3.4_PGSC0003DMP400016105
+---M-------------------------------------------------------G
+NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY
+S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ
+--EETFEELQ------DMFDEIFNSDN--GM------------SSSS-------------
+----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM
+KSGK--------GDSCQF------QGFCEG-T-----------GGASGKSNERE-RSRRK
+NSKSGRKQ--------------------------------
+>gnl_Soltu3.4_PGSC0003DMP400016106
+---M-------------------------------------------------------G
+NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY
+S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ
+--EETFEELQ------DMFDEIFNSDN--GM------------SSSS-------------
+----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM
+KSGK--------GDSCQF------QGFCEG-VE--HLEKAMKENGVGGKIPRVD-GSNRM
+DAKRQKVLS-------------------------------
+>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329
+---MAPR-------------------------------------------------GEKD
+SDFYAILGLKKECSASDLRNAYKRLALRWHPDRCSASG---NTKFVEECKKKFQAIQQAY
+S------VLSDANKRFLYDVGAYGS--------DDDDQGMGEFLGEMAVMMSQTKPSEKG
+--PESFEDLQ------NLFQEMFERDL--DM----------FKSSTSH------------
+----NNNNDNNNNN------------------HRSSDNNNCSSVH-CFSNTNKRNCS-DM
+NAGE-ASEVGRFAFSCYATEFLHKQTFSVG-AD------DVRSES----------SNKRR
+NGRKQKSTS-SSRKS-------------------------
+>gnl_Aquco1.0_PACid_18141277
+---MAS--------------------------------------------------EEEA
+SDFYKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASG---NSKFVEEAKKNFQAIQEAY
+S------VLSDEQKRFMYDVGVYDKD------DDDENEDMGDFLGEMMSMMKQENTSADG
+--QQSFEDLQ------NLFQEMVQNDK--EF----------YNPASQ-------------
+----NSSIYNASNNMFSFSNNENLNNASNNTFSSFYNENLN--------SSNKKSCS-SM
+SAEN--TKVDFNMESLDF------RSFSIG-LE--GGTSFQNSKGRG--------VTGRR
+TGRKQKGSS-CNDMSSHD-SKILA----------------
+>gnl_Arath10_AT3G14200.1
+---MASSN-----------------------------------------------SEKIN
+ENLYAVLGLKKECSKTELRSAYKKLALRWHPDRCSS------MEFVEEAKKKFQAIQEAY
+S------VLSDSNKRFLYDVGAYNTD------DDDDQNGMGDFLNEMATMMNQSKPSDNN
+-TGDSFEQLQ------DLFNEMFQGDA--AA----------FPSS---------------
+------SSCSTSNF------------------TSSRSFVFD--------TNSQRSSSFAT
+SSMG--MNNDPFGYDPRA------HSFSLG-VD--HQQEFKKGKN----------NGGRR
+NRRKNNVPSAGHETSSSNNYGVPTS---------------
+>gnl_Bradi1.2_Bradi3g60090.1
+---MATGG-------------------------------------DKCGGKPAA-AGVGG
+GDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSS---STKHMEEAKEKFQEIQGAY
+S------VLSDANKRFLYDVGVYEEHEE---EDDDTLQGMGDFLGEMAHMMSQTQPAR--
+--QESFEELQ------QLFVDMFQSDI--ESG---------FCNGPAK-DHDPVQRQTRT
+FSTPPSPSPSPPPP------------------LATVDEAAS------CNGINKRGSS-AM
+GSGK-PPRAGEVSGGHGQ------SEFCFG-MS--DAKQAPKARGGN--------ASRRR
+NGQKQKLSS-KHDVSSGDEMPRP-------------HAAV
+>gnl_Carpa1.181_PACid_16420351
+---MADG------------------------------------------------EDKNN
+SDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASG---NSMFVEEAKKKFQAIQEAY
+S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAAMMSQTKPNENG
+NAQESFEELQ------ELFQEMFQGDMGFNT----------FGSSSQP------------
+----TTSSCSASSA------------------YATCSETSN-------PNNNKRNSS-EM
+NYGK-KKVDDSSGFHAHF------QTFCLG-VE--QQQDFKKGKEARGGIRGKP-GGSRR
+QGRKQKVSS-RHNVSSND-LGISAS---------------
+>gnl_Frave2.0_gene05408
+---MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNR---RMEEKG
+NDFYAVMGLKKECSDSELRNAYKKLALIWHPDRCSASG---NSKFVEEAKKKFQDIQQAY
+S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAVMMSQTKPNENG
+--GESFEQLQ------ELFEEMFQGDI--EG----------FSSCSQP------------
+----PTSCSTSSSS------------------YALYCENST--------PSNKRNSS-AM
+NYGN--ATLDSSGFDAHF------HNFCVG-T-----------GGKPAKDREGD-ARKRK
+DSRRSNR---------------------------------
+>gnl_Mimgu1.0_PACid_17694730
+---MAAD-------------------------------------------------EEKS
+SDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASG---NLKYVEEAKNKFQAVQQAY
+S------VLSDANKRFLYDVGIYDSE------DDADENGMGDFLNEMVAMMGQSKPNENK
+--NESFQELQ------DLFEEIFNNDA--EEV---------FKIPPPH------------
+--FPYQDSCSETRT-----------------------------------ASNKRNAR-EM
+GSVN-----FSNIEATPF------EGFCIG-ENVIFGGERIQTRPG---------GGSRR
+T--KPKIST-SID-----------------------GLIS
+>gnl_Nelnu1.0_NNU_010544-RA
+------------------------------------------------------------
+---------------------MNLLLQKWHPDRCSSSG---NSKFVEDSKKKFQAIQEAY
+S------VLSDENKRFLYDVGVYDCDD-----DDDDENGMGEFLGEMATMMSQIKPSENG
+--PESLEKLQ------ELFEEMFQRDM--DDG---------FFSPSPQCA----------
+---SFSSSCSSSSS---------------STTYFSYNNNKH---------DNKRNCS-DI
+SSMD--DFYTFGTDSIQF------SNFCIG-VE--GGE-DSKVRGGK---------SRRK
+SNRRQKVSSSKHDPSCR-----------------------
+>gnl_Solly2.3_Solyc03g123560.2.1
+---M----------------------------------------------------EDKS
+NDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASG---NLKFVDEAKKQFQAIQEAY
+S------VLSDANKKFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ
+-GEETFEELQ------DMFNEMFNSDN--GT----------FSSSSS-------------
+----SSSSWTGTPS------------------MCSTTSSTSSSET-FLTFPNKRSSG-EM
+KSGS-----SVRGDSCQF------QGFCVG-A-----------GGTSGKCNERE-RSWRK
+NSKSGRKH--------------------------------
+>gnl_Sorbi1.4_PACid_1968370
+---MDAGG-------------------------------------EKFSDAAAAEGGEGG
+GDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSS---SVKHMEEAKEKFQEIQGAY
+S------VLSDANKRLLYDVGVYDDED-----DEDSMQGMGDFIGEMAQMMSQVRPTR--
+--QESFEELQ------QLFVDMFQSDI--DSG---------FCNGSAK-DQVQGQAKSRT
+CSTSPSSSPSPPPP----------------PTIVKEAEVSS------CNGFNKRGSS-AM
+DSGK-PPRP--VEGGAGQ------AGFCFG-VS--DTKQTPKPRGPN--------TSRRR
+NGRKQKLSS-KHDVSSEDETAGS-----------------
+>gnl_Thepa2.0_Tp3g12470
+---MASNN-----------------------------------------------SEKGN
+DDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAY
+S------VLSDSNKRFLYDVGAYNS-------DDEDQNGMGDFLNEMAAMMNQSKPSENN
+-SGDSFEQLQ------DLFNEMFQGDA--AA----------FSSSSS-------------
+------SSCSASTF------------------TSSCSFVFD--------TNSQRSPF-ET
+SSMG---TNDLFGFDHSA------HTFSLG-VE--HQQDFKKGKN----------SGGRR
+NRRKNNAQSAAHETASSNNYGVPTS---------------
+>gnl_Theca1.0_Tc06_g010450
+---MANG-------------------------------------------------EEKN
+NDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY
+S------VLSDSNKRFLYDVGAYDS--------DDDENGMGDFLNEMAGMMSQTKSNENG
+--GESFEELQ------ELFEEMFQADI--DS----------FESTGQ-------------
+----STPSCSASSS------------------FGSYGESSS---------SNKRNSS-EM
+SSVE-TRLESSSSFDAQF------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGGSRRR
+NGRKQKVSS-GHDVTSND-CGISAS---------------
+>gnl_Vitvi12X_PACid_17827068
+---MAAG-------------------------------------------------EEKS
+NDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAY
+S------VLSDANKRFLYDVGAYDS--------DDDENGMGDFLNEMAVMMSQTKSNENG
+--KESFEELQ------ELFEDMFQRDV--DA----------FNSASHH------------
+----PMNSFPSSTS------------------TSSYCESSN--------ANNKRNSA-EM
+GSGRMMSAGESSAFDAHF------QSFCFG-T-----------GGTPGRFQEGE-RSKRR
+NSRRSQR---------------------------------
+>gnl_Selmo1.0_PACid_15401289
+---M----------------------------------------------------EKRK
+EDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAY
+S------VLSDDKKRVLYDSGLYDEG------DDE-------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------VS---------------------------
+----------------------------------------
+>gnl_Orysa6.0_PACid_16864430
+---MARGGG-----------------------------------G----------GGGAD
+ADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAY
+S------VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP----
+--AESFEELQ------QLFVDMFQDDI--DAG---------LCQSTP-------------
+----PPPSWPSPPA-------------------AANARSPAAAAT-SRKGVNKRCSP-AA
+MDMD-----SGLSSLLGI------SGFCFE-AP--WTSQDASTAAGGG-------GGKRR
+KQRPPPA---SHNV--------------------------
+>gnl_Sorbi1.4_PACid_1982925
+---MAATSH-----------------------------------CGNIQDQDEEASAPGA
+ADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAY
+S------VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP----
+--TETFEELQ------QVFVDMFQDDLD-DAG---------FFGGLPT-TGRRAQA--PS
+TSLPPSVSSSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-ST
+AKRPRPNGSAGLESDLGL------SGFCFM-VS--KEMSKSKERQAV---WASD-DGDRS
+TDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS
+>gnl_Medtr3.5_Medtr8g022310.3
+---MANE-------------------------------------------------GNKS
+NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY
+S------VLSDSNKRLMYDVGVYDS--------DDDENVRHLF-----------------
+---HTIHELG------TLFCVMFCFFISLR------------GE----------------
+---------KRSNL------------------NLTFSLSH--------------------
+------------------------------------------------------------
+----------------------------------------
+>gnl_Nelnu1.0_NNU_000115-RA
+---MEVD------------------------------------------------SHRSS
+PSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAY
+SGGLLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC----
+--EETGEEIQLGGTTGDVSGNVTRAGV--EDGECWWCVVVRWSCSLKE------------
+----------------------------------------------------------EL
+KEGQ--------------------MGIISE-SD--DA-----------------------
+----------GHDTPSLPHLHGSEL-----ELLGRTGCCN
+>contig_7
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------ENEWSGAEFLNEMAAMMTQNKSNENG
+--TGTFEELQ------QLFDEMFQSDI--ES----------FNGCSSS------------
+----SNETCS---------------------------------------NSNKRNSI-ES
+SSAN----------------FRPENGNESG-----------------------E-ISGKK
+NTRKGKGDX-------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3722.fna	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,378 @@
+>gnl_Glyma1.01_PACid_16266208
+ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA
+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG
+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA
+GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC
+AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG
+GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA
+CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG
+GGTGAACCAACTCCAAGATATAAAGAAGGGAAAGGGGGGAATTCTAGGAGGAGGAGGTAGAAGTAGACACAGAAGTGGCA
+GAAAGCAAAAAATGTTCTATGGCCATGATGTT
+>gnl_Glyma1.01_PACid_16266209
+ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA
+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG
+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA
+GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC
+AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG
+GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA
+CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG
+GACAGGTGAACCAACTCCAAGATATAAAGAAGGGAAAGGGGGGAATTCTAGGAGGAGGAGG
+>gnl_Glyma1.01_PACid_16266210
+ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA
+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG
+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA
+GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC
+AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG
+GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA
+CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG
+GGTCGGTCATGTAAACTATCATTACCAA
+>gnl_Glyma1.01_PACid_16301083
+ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA
+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG
+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA
+GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC
+GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG
+GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA
+CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG
+GGTGAACCAACTCCAAGATATAAAGAAGAAAAAGGGGGGAATTCTAGGAGGAGGTAGAAGTAGACACAGAAATGGCAGAA
+AGCAAAATATGTCCTATGGCCATGATGTTTCATCGAATGACTACCCTGGAATTTCCACAAAG
+>gnl_Glyma1.01_PACid_16301085
+ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA
+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG
+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA
+GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC
+GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG
+GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA
+CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG
+GGTAGGTCATGTAAACTATCATTACCAA
+>gnl_Glyma1.01_PACid_16301084
+ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA
+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG
+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA
+GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC
+GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG
+GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA
+CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG
+GACAGGTGAACCAACTCCAAGATATAAAGAAGAAAAAGGGGGGAATTCTAGGAGGAGG
+>gnl_Medtr3.5_Medtr8g022310.1
+ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG
+GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG
+CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA
+GTTTACGACAGTGATGATGACGAAAATGGTATGGGAGACTTTCTGAATGAAATGGTTACAATGATGAGCCAAACTAAATC
+AAATGAAAATGGAGAGGAGAGCTTCGAGGAGTTACAACAGTTGTTTGATGATATGTTTCAAGCGGATATCGGATTAAATG
+GAAGCACCTCTCTTAATGCTTCGGGTTGCTCCACTTCATCGACTTTCATGACGTTCAGTGAAAGCTCGAATTCAAATAAG
+CGCAATTCCACTCAAATGAATTTTGGGAAGGCAGAGGATTCTTCTAGTTTTGGTGCAAATTACCAGAACTTCTGTTTTGG
+GATGAAGCACCTTCAAGAAGATGTGGAGAAGGAAAAAGGGGGAATTCTAGAAGGAGGAGGTAGCAAAAAACAAAGAAAAG
+GAAGAAAACAAAAAATTTCATGTGGACATGTTTCCTCTAATGACCATCCTGGTATTTCTGCTAAT
+>gnl_Medtr3.5_Medtr8g022310.2
+ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG
+GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG
+CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA
+GTTTACGACAGTGATGATGACGAAAATGGTATGGGAGACTTTCTGAATGAAATGGTTACAATGATGAGCCAAACTAAATC
+AAATGAAAATGGAGAGGAGAGCTTCGAGGAGTTACAACAGTTGTTTGATGATATGTTTCAAGCGGATATCGGATTAAATG
+GAAGCACCTCTCTTAATGCTTCGGGTTGCTCCACTTCATCGACTTTCATGACGTTCAGTGAAAGCTCGAATTCAAATAAG
+CGCAATTCCACTCAAATGAATTTTGGGAAGGCAGAGGATTCTTCTAGTTTTGGTGCAAATTACCAGAACTTCTGTTTTGG
+GGTCAATCTTGTAAATTATCATTACCAA
+>gnl_Musac1.0_GSMUA_Achr6T31040_001
+ATGGCGGCCGAAGAGGACAAAAGCGGCGACTTCTACGCCGTGTTGGGGCTCAGGAAGGAGTGCTCCGAAACCGAGCTGAG
+GAATGCGTACAAGAAGCTTGCCATGAGGTGGCATCCGGATAAGTGCTTGGCTTCGGGAAATGCTCAAATCGTGGGGGAAG
+CCAAGGAGAAGTTTCAGGAGATCCAGAAAGCCTACTCTGTTCTCTCAGACTCCAATAAGAGATTCCTGTACGATGTGGGA
+GTCTACGACAACGATGATGACAATGACGAAAACGGTATGGGAGACTTTATAGGGGAGATGTTGGAGATGATGAGCCAAAC
+GAAACCCAATGAGAACAGCCAAGATAGCTTCCAGGAGCTGCAGGAGCTGTTTGTGGAGATGTTCCAGGACGACCTGGATG
+CCGGATTTGGTGGTTCCATCTTCCACGATTGCCCCTGGGCTCAACCGACCAATGGCCAAGATTGCTGGACTTCATCGGGA
+CTGCACTTTGCTAATGGAAGGAGTAAGTGTGGCAACAAGCGGGGCAACTCAGCTGTGAACTTGGGAAAGGTCAATCTTGA
+AGAGTTGGAACATGGTACCAGCGACTTCTATTTTGGGCTAAATGATGCAGCACAGCCATCACAAGGGAAAGGAGGCAGTA
+ATAACAAGAGAAGGAATGGAAGAAAGCAAAAGGTTTCATCCAATCATGATGTCTCATCC
+>gnl_Musac1.0_GSMUA_Achr9T18140_001
+ATGGCCGCCGGGGAGGAAAAGATCGGCGATTTCTACACGGTGCTGGGGCTCAGGAAGGAGTGCTCGGAGGCGGAGCTGAG
+GATCGCGTACAAGAAGCTGGCTATGAGATGGCATCCGGATAAGTGCTCGGCTTCGGGAAACCATCGAAGGATGGAGGAAG
+CGAAGGAGAAGTTCCAGGAAATCCAAAAAGCCTACTCTGTTCTCTCGGACTCCAGCAAGAGATTTCTGTATGATGTGGGA
+ATCTACGATAACGAGGATGATAATGACGAAAAAGGAATGGGGGATTTTATTGGGGAGATAGCTCAGATGATGAGCCAAAC
+GAAATCTGGGGAGAATGGTCATGATAGCTTTGAGGAGCTGCAGCGGATGTTCCTGGATATGTTCCAGGACGACCTGGACG
+CCGGATTCGGTGATTCTTCCATCCACAGTGGCCCCCAAGCTCGGCCAACCGACGGTCTCAATTGCTCGATGCCATCAGGA
+CTGCAGTTTGCTGATGGAGGGAACAATGGCAGCAACAAGAGAGGCAACTCGGAGAAGGCAAAGCTGGATGGGTTGGAAAA
+CAGTTCCACTGGCTTCTGCTTCGGGTTGAATGATGCAGGGCAGTCATCAAAAGGAAAAGGAAGCGCTAATAGCAAGAGAA
+GGAATGGAAGAAAGCAGAAGGTCTCATCCAAACATGATGTCTCATCCAGTGATGCTGAGGTCTCATTT
+>gnl_Musac1.0_GSMUA_Achr8T23700_001
+ATGGCGAGCGACATGGATGCAAGCGGCGATTTCTACTCGGTGCTGGGGCTGAAGAAGGAGTGCTCCGAGGCGGAGCTCAG
+GAATGCGTACAAGAAGCTCGCTTTGAAGTGGCATCCCGATAAGTGCTCGGCGTCGGGTAATGAGATTCGCATGAAGGAAG
+CGAAGCAGCAGTTCCAGGAGATCCAGAAAGCCTACTCTGTTCTCTCCGACTCCAACAAGAGATTTCTGTACGATGTTGGA
+GCCTACGACAAAGACGACGACAAAGACGAAGAGGGGATGGTGGAGTTTCTTGGGGAGATGGCGCAAATGATGAGGCAAAC
+CAAATGCTGTGGGAGCGGCCAGGAGAGCTTCGAGCAGCTGCAGCAGATGTTCGTGGAGATGTTCCACGACGATCTGGACG
+CGGGATTCTGCGGCCACTCCTCGGCCACCTCGGGCGCGGCGTCCTGCGGCAACAAACGGGACAACTCGGCGATGGACTCG
+GGCAAGCGGAAGCCGGACGAGTTGGACCCGGCCGCCATTGGGTTCTGCCTCGGGACAAAGGATGCAGGGCAATCCTCAAA
+AGGAAGAGGTAGCAACAGCAAGAGAAGGAACAGAAGAAAGCAAAAGGCATCATCCAAGCATGACAACTCATCTCACAATG
+CTAAGGTCTCAGCT
+>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001
+ATGGAGGGGGACGAGGAGAAGAGCGGGGATTTCTACGCGGTGCTGGGGCTGAAGAAAGAGGGCTCCATGGCGGAGCTCAA
+GAATGCGTACAAGAAGCTGGCGATGAAGTGGCATCCCGATAAGTGTCCTGCGTCAGGCAATAAGATACGCATGGATAAAG
+CGAAGGAGAAGTTCCAGGAGATCCAAAAAGCCTACTCTGTTCTCTCCGACTCCAACAAGCGATTCCTGTACGATGTCGGA
+GTTTACGACAAAGACGATGAGGAAGATGAAGAGGGGATGGGGGACTTCATTGGGGAGATCGCGCAAATGATGAGCCAGTC
+CAAACCCAGCGGGAGCGGCCACGAGAGCTTGGAGGAGCTGCATCGGCAGGTCGTGGAGATGTTCCTCGACGAACTGGACG
+CCGGAGATCGCTTCTCCTCGGCCAACCAAGGCGCGTCGTCCTGCGACGGCAGGGACGACGGCGGCGGTAACAAGCGTGGC
+AACTGGGCGGTGGACTGGGGCAAGGAGAAGCTGAACGAGTTGGGCCCGGGCACCGGCGGGTTCTGCTTCGGGGTGAGTCG
+CCGAGTCCACTCCTTTGATCTTATGATAGACGTAGTCCACCTCATCCATTCTGATCTGACTCTGGAA
+>gnl_Orysa6.0_PACid_16843526
+ATGGCCGACGGGGGAGAGAAGTGCCGGGACGCGGCCGGCGAGGGCGGCGGCGGCGGCGACCTGTACGCCGTGCTCGGGCT
+CAAGAAGGAGTGCTCCGACGCCGACCTCAAGCTCGCGTACCGGAAGCTCGCCATGAGATGGCATCCGGACAAATGCTCAT
+CCTCCAGCAGTGCAAAGCACATGGAGGAAGCCAAGGAGAAGTTCCAGGAGATCCAGGGCGCCTATTCCGTCCTCTCAGAC
+TCAAACAAGCGGTTCCTCTACGACGTGGGGGTATATGATGATGACGACAATGACGATGACAACCTGCAGGGGATGGGGGA
+CTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGCACGGCCAACGAGGCAGGAGAGCTTTAAAGAACTGCAGCAGCTAT
+TCGTAGACATGTTCCAAGCTGATCTTGATTCGGGTTTCTGCAATGGACCCTCAAAGTGCTACCATACCCAGGCCCAAAGC
+CAGACTCGAACATCCTCAACCTCCCCTTCGATGTCACCGTCTCCACCGCCTCCAGTAGCTACTGAGGCAGAATCGCCATC
+ATGTAATGGTATTAATAAGCGTGGTTCATCAGCAATGGACTCTGGGAAGCCTCCAAGAGCCAGCGAAGTCGGTTCTGGAC
+AGAGTCAATCAGGGTTTTGTTTCGGGAAGAGTGATGCTAAACAAGCGGCGAAGACGCGAAGCGGGAACACGGCCAGCCGG
+AGGAGGAACGGCCGGAAGCAGAAGGTGTCGTCGAAGCACGACGTCTCGTCTGAGGACGAGATGCCAGGTTCGCAGTGGCA
+CGGCGTGGCC
+>gnl_Orysa6.0_PACid_16843528
+ATGGCCGACGGGGGAGAGAAGTGCCGGGACGCGGCCGGCGAGGGCGGCGGCGGCGGCGACCTGTACGCCGTGCTCGGGCT
+CAAGAAGGAGTGCTCCGACGCCGACCTCAAGCTCGCGTACCGGAAGCTCGCCATGAGATGGCATCCGGACAAATGCTCAT
+CCTCCAGCAGTGCAAAGCACATGGAGGAAGCCAAGGAGAAGTTCCAGGAGATCCAGGGCGCCTATTCCGTCCTCTCAGAC
+TCAAACAAGCGGTTCCTCTACGACGTGGGGGTATATGATGATGACGACAATGACGATGACAACCTGCAGGGGATGGGGGA
+CTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGCACGGCCAACGAGGCAGGAGAGCTTTAAAGAACTGCAGCAGCTAT
+TCGTAGACATGTTCCAAGCTGATCTTGATTCGGGTTTCTGCAATGGACCCTCAAAGTGCTACCATACCCAGGCCCAAAGC
+CAGACTCGAACATCCTCAACCTCCCCTTCGATGTCACCGTCTCCACCGCCTCCAGTAGCTACTGAGGCAGAATCGCCATC
+ATGTAATGGTATTAATAAGCGTGGTTCATCAGCAATGGACTCTGGGAAGCCTCCAAGAGCCAGCGAAGTCGGTTCTGGAC
+AGAGTCAATCAGGGTTTTGTTTCGGGCAGAAGAGTGATGCTAAACAAGCGGCGAAGACGCGAAGCGGGAACACGGCCAGC
+CGGAGGAGGAACGGCCGGAAGCAGAAGGTGTCGTCGAAGCACGACGTCTCGTCTGAGGACGAGATGCCAGGTTCGCAGTG
+GCACGGCGTGGCC
+>gnl_Poptr2.2_PACid_18217800
+ATGGCAAACGGAGGAGAAGATAAATGGAAAAGCAATGACTTATATCAAGTCTTGGGGTTGAATAAGGAATGCACTGATAC
+AGAGCTCAGGAGTGCTTATAAGAAACTTGCACTGAGATGGCATCCAGATCGATGTTCAGCTTCAGGAAATTCTAAGTTCG
+TTGAAGAAGCCAAAAAGAAGTTTCAGGCAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGGTTTCTTTAC
+GACGTTGGTGTTGATGACAGTGATGACGACGAAAATGGAATGGGTGATTTTCTGAATGAAATGGCTGTCATGATGAGCCA
+AACGAAGCCTAGCGAAAACATGGAGGAGAGCCTAGAGGAACTGCAAGAATTATTTGACGAGATGTTCCAAGAGGATCTGC
+ATTCGTTTGGGATTGACAGTCAGGCTGCTCCTTCATGTCCTCCTTCTTATGTATCCTACAGCGAAAGTTCCAACTCAAAT
+AACAAACGTGTTTCTGCTGATATGAACTTGGGGAAGACTAAAGTGGATGATTCTTCTAGCTTCAACTCTCACTTTGAGAA
+ATTCTGTTTAGGGACAGGTGGAACAGCAGCAACCTTTCAAGAAGGTGAAGGTGGGAGTAAGAGGAGGAATTCAAGGAGGA
+GCCAGCGGCAGACGAAGGCAAGACAAGAAACAAAGAGTTTCTTCGGGCTA
+>gnl_Poptr2.2_PACid_18234651
+ATGGAAAATGGAGGAGAAGAGAAAGGGAAAAGCAATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCAC
+AGAGCTGAGGAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAAAATTCCAGGTTCG
+TTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGGTTTCTTTAC
+GACGTTGGTGTTTATGACAGTGAAGACGACGAAAATGGAATGGGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCA
+AACAAAGCCCCACGAAAACGTGGAGGAGAGCTTTGAGGAATTGCAAGGATTGTTTGAGGAGATGTTCCAAGAGGATTTGG
+ATTCGTTTGGGATTGCCTGTCAGGCTACTACCTGTGTGTCATACAGCGAAAGCTCCAACTCAAATGATAAACGTGTTTCT
+GTCGATATGAACTTGAAGAAGACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTCGAGAAGTTCTGTTTAGGGGT
+AAGTGGAACACCAGCAATCTTTCAAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACCGGCGG
+>gnl_Poptr2.2_PACid_18234649
+ATGCTAAGAATGGAAAATGGAGGAGAAGAGAAAGGGAAAAGCAATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTG
+CACTGCCACAGAGCTGAGGAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAAAATT
+CCAGGTTCGTTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGG
+TTTCTTTACGACGTTGGTGTTTATGACAGTGAAGACGACGAAAATGGAATGGGCGGATTTATGAATGAAATGGCTGCTAT
+GATGAGCCAAACAAAGCCCCACGAAAACGTGGAGGAGAGCTTTGAGGAATTGCAAGGATTGTTTGAGGAGATGTTCCAAG
+AGGATTTGGATTCGTTTGGGATTGCCTGTCAGGCTACTACCTGTGTGTCATACAGCGAAAGCTCCAACTCAAATGATAAA
+CGTGTTTCTGTCGATATGAACTTGAAGAAGACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTCGAGAAGTTCTG
+TTTAGGGGTGGAACACCAGCAATCTTTCAAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACCGGCGGTAGAG
+AGAGGAAAGGCAGGAAACAAGAAGTTTCATCTGGCTATGATGTCTCCTCCCATGACCATGGTATTTCTGCTTCA
+>gnl_Poptr2.2_PACid_18234650
+ATGGAAAATGGAGGAGAAGAGAAAGGGAAAAGCAATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCAC
+AGAGCTGAGGAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAAAATTCCAGGTTCG
+TTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGGTTTCTTTAC
+GACGTTGGTGTTTATGACAGTGAAGACGACGAAAATGGAATGGGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCA
+AACAAAGCCCCACGAAAACGTGGAGGAGAGCTTTGAGGAATTGCAAGGATTGTTTGAGGAGATGTTCCAAGAGGATTTGG
+ATTCGTTTGGGATTGCCTGTCAGGCTACTACCTGTGTGTCATACAGCGAAAGCTCCAACTCAAATGATAAACGTGTTTCT
+GTCGATATGAACTTGAAGAAGACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTCGAGAAGTTCTGTTTAGGGGT
+GGAACACCAGCAATCTTTCAAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACCGGCGGTAGAGAGAGGAAAG
+GCAGGAAACAAGAAGTTTCATCTGGCTATGATGTCTCCTCCCATGACCATGGTATTTCTGCTTCA
+>gnl_Soltu3.4_PGSC0003DMP400016105
+ATGGGCAATGATTATTATGCAGTTTTGGGATTGAAAAAGGAATGCACTGAAACAGAGCTTAGGAATGCTTATAAGAAGCT
+TGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGGAATTCGAAGTTTGTAGATGAAGCAAAGAAGAAATTTCAGG
+CAATTCAAGAAGCATATTCTGTGTTATCGGATGCAAACAAAAGGTTTCTGTACGATGTAGGAGTTTATGACTCTGGTGAT
+GATGACGACGAAAATGGCATGGGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCA
+GGAAGAAACCTTTGAGGAATTGCAGGATATGTTTGACGAAATTTTCAATAGTGATAATGGGATGTCTTCTTCTTCTTCTT
+CTTCTTCTCGGACTGGAACTCCTTCAATGTGTTCTACTACATCGTCTACATCTTCCAGTGAGACCTTTTTTACCTTTTCC
+AACAAAAGAAGTTCAGGTGAAATGAAGTCGGGTAAAGGCGATTCTTGCCAATTCCAAGGATTTTGTGAAGGGACAGGTGG
+AGCATCTGGAAAAAGCAATGAAAGAGAACGGAGTCGGAGGAAAAATTCCAAGAGTGGACGGAAGCAA
+>gnl_Soltu3.4_PGSC0003DMP400016106
+ATGGGCAATGATTATTATGCAGTTTTGGGATTGAAAAAGGAATGCACTGAAACAGAGCTTAGGAATGCTTATAAGAAGCT
+TGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGGAATTCGAAGTTTGTAGATGAAGCAAAGAAGAAATTTCAGG
+CAATTCAAGAAGCATATTCTGTGTTATCGGATGCAAACAAAAGGTTTCTGTACGATGTAGGAGTTTATGACTCTGGTGAT
+GATGACGACGAAAATGGCATGGGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCA
+GGAAGAAACCTTTGAGGAATTGCAGGATATGTTTGACGAAATTTTCAATAGTGATAATGGGATGTCTTCTTCTTCTTCTT
+CTTCTTCTCGGACTGGAACTCCTTCAATGTGTTCTACTACATCGTCTACATCTTCCAGTGAGACCTTTTTTACCTTTTCC
+AACAAAAGAAGTTCAGGTGAAATGAAGTCGGGTAAAGGCGATTCTTGCCAATTCCAAGGATTTTGTGAAGGGGTGGAGCA
+TCTGGAAAAAGCAATGAAAGAGAACGGAGTCGGAGGAAAAATTCCAAGAGTGGACGGAAGCAATAGGATGGATGCTAAAA
+GGCAAAAGGTTCTATCA
+>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329
+ATGGCACCCCGAGGAGAGAAAGACAGTGATTTTTATGCAATTTTAGGGTTGAAGAAGGAGTGCTCTGCTTCAGATCTCAG
+AAATGCGTACAAAAGGCTCGCACTTCGGTGGCATCCAGATAGGTGCTCTGCCTCAGGGAACACAAAGTTTGTGGAGGAAT
+GCAAGAAAAAGTTCCAGGCCATTCAGCAGGCTTATTCCGTGCTCTCGGATGCAAATAAGAGGTTTTTGTACGATGTTGGA
+GCATATGGAAGTGACGATGACGATCAGGGAATGGGTGAATTTCTTGGGGAGATGGCGGTAATGATGAGCCAGACAAAGCC
+CAGTGAAAAAGGGCCGGAGAGCTTTGAGGATCTACAGAACTTGTTTCAGGAGATGTTCGAAAGGGATCTGGACATGTTTA
+AGTCATCGACCTCCCACAACAACAACAATGATAACAACAATAATAATCATAGGAGTAGTGACAATAATAATTGTAGTAGT
+GTTCATTGTTTTAGTAACACCAACAAGAGGAATTGCTCGGATATGAATGCCGGAGAAGCCTCGGAGGTCGGGCGCTTTGC
+TTTCTCATGCTATGCGACAGAGTTCCTGCACAAGCAAACTTTCTCCGTCGGGGCGGATGATGTGCGATCGGAGTCGAGCA
+ACAAGAGACGAAACGGGAGGAAACAGAAATCCACCTCCTCTTCAAGGAAAAGT
+>gnl_Aquco1.0_PACid_18141277
+ATGGCTAGTGAAGAAGAAGCAAGTGATTTCTATAAAGTTTTGGGATTGAAAAATAACTGTTCTTCCTTGGAGCTCAGGAA
+CGCTTATAAGAAGCTTGCACTGAAATGGCATCCGGATCGTTGTGCTGCTTCAGGAAACTCAAAGTTTGTTGAAGAAGCAA
+AGAAGAATTTTCAAGCAATACAAGAAGCTTATTCTGTTCTTTCAGATGAGCAGAAACGATTTATGTATGACGTTGGTGTC
+TACGATAAAGATGATGATGACGAAAATGAAGATATGGGCGATTTTTTAGGTGAAATGATGTCTATGATGAAGCAAGAAAA
+TACTAGTGCGGATGGACAACAAAGTTTTGAAGACCTTCAAAACCTATTCCAGGAAATGGTTCAAAATGACAAAGAATTTT
+ATAATCCAGCCTCTCAAAACTCGTCGATATATAATGCTAGTAACAACATGTTCTCCTTCTCTAATAACGAGAACTTAAAC
+AATGCTAGCAACAACACATTCTCCTCTTTTTATAATGAGAACCTAAACAGCAGCAACAAGAAAAGTTGCTCAAGTATGAG
+CGCAGAAAATACCAAGGTGGACTTTAACATGGAATCATTGGACTTCCGCAGCTTTTCTATTGGGTTAGAAGGCGGTACAT
+CATTTCAAAACTCCAAAGGGAGAGGAGTAACGGGTAGGCGGACAGGAAGGAAACAGAAGGGGTCGTCCTGTAATGATATG
+TCTTCCCATGATTCTAAGATTTTGGCG
+>gnl_Arath10_AT3G14200.1
+ATGGCGTCCAGTAATAGCGAGAAGATCAACGAGAATCTGTACGCTGTTCTGGGTTTGAAGAAGGAATGTTCTAAGACGGA
+GCTCCGTTCTGCTTATAAGAAGCTTGCTCTCAGATGGCATCCAGATCGTTGTTCGTCAATGGAGTTTGTAGAAGAAGCAA
+AGAAGAAATTTCAGGCAATCCAAGAAGCCTACTCTGTTCTGTCTGACTCCAACAAGAGGTTCCTGTATGATGTTGGTGCT
+TATAATACTGATGATGATGATGACCAAAACGGAATGGGAGATTTCTTGAACGAAATGGCGACTATGATGAATCAATCCAA
+GCCTAGTGATAATAACACAGGGGACAGTTTTGAACAACTACAAGATCTGTTTAATGAGATGTTTCAAGGAGACGCTGCAG
+CATTCCCATCATCATCGTCCTGCTCCACTTCAAATTTCACTTCATCTCGTAGTTTTGTATTCGATACAAATTCTCAGCGG
+TCATCTTCGTTTGCGACAAGTTCGATGGGGATGAATAATGATCCTTTCGGATATGACCCGAGAGCTCATTCCTTCTCTTT
+AGGGGTGGACCATCAGCAAGAGTTCAAGAAAGGGAAAAACAATGGCGGAAGAAGAAACAGGAGAAAGAACAATGTTCCAT
+CGGCTGGTCACGAAACGTCGTCGTCAAACAACTATGGAGTCCCCACCTCA
+>gnl_Bradi1.2_Bradi3g60090.1
+ATGGCCACCGGGGGCGACAAGTGCGGCGGAAAGCCGGCGGCCGCGGGGGTGGGCGGCGGTGACCTGTACTCTGTGCTGGG
+CGTCAACAAGGAGTGCTCCGACGCCGACCTCAAGGTCGCCTACCGGAAGCTCGCCATGAGATGGCATCCGGATAGATGCT
+CCTCCTCCAGCAGCACCAAGCACATGGAGGAAGCAAAAGAGAAGTTCCAGGAGATCCAGGGCGCCTATTCCGTCCTCTCC
+GATGCCAACAAGCGCTTCCTCTATGACGTGGGGGTATATGAAGAACATGAAGAAGAAGATGATGACACTCTGCAGGGGAT
+GGGGGACTTCCTTGGTGAGATGGCCCATATGATGAGCCAGACGCAGCCAGCGAGACAGGAAAGCTTTGAGGAGCTCCAGC
+AGCTCTTCGTGGACATGTTCCAGTCTGATATTGAATCGGGATTCTGCAACGGACCTGCCAAGGACCATGACCCAGTCCAA
+AGACAGACGCGAACATTCTCGACCCCTCCTTCGCCATCGCCATCTCCACCGCCTCCACTAGCTACAGTGGACGAAGCGGC
+ATCATGTAATGGCATCAATAAGCGTGGCTCATCAGCAATGGGCTCTGGGAAGCCTCCAAGAGCTGGTGAAGTGAGTGGGG
+GTCACGGCCAGTCTGAGTTCTGTTTCGGGATGAGCGACGCCAAGCAAGCGCCGAAGGCGCGAGGCGGGAACGCTAGCAGG
+AGAAGGAACGGCCAGAAGCAGAAACTGTCGTCGAAGCACGACGTCTCCTCCGGCGATGAGATGCCGAGACCACATGCAGC
+AGTA
+>gnl_Carpa1.181_PACid_16420351
+ATGGCGGATGGAGAAGACAAGAACAACAGTGATTTGTATGCGGTTCTTGGATTGAATAAGGAATGTACTCCAGCAGAGCT
+CAGGAACGCTTATAAGAAACTTGCAATGAGATGGCATCCAGATCGCTGTTCCGCGTCGGGGAATTCAATGTTTGTGGAAG
+AAGCAAAGAAGAAATTTCAGGCAATCCAAGAAGCCTACTCTGTTCTTTCTGACGCAAACAAGAGGTTTCTGTACGACGTC
+GGAGCTTACGAAAGTGATGACGACGAAAATGGAATGGGTGATTTTTTAAACGAAATGGCAGCCATGATGAGCCAAACAAA
+GCCTAATGAGAATGGGAATGCACAAGAGAGCTTTGAAGAATTGCAAGAGTTGTTTCAAGAGATGTTTCAAGGGGATATGG
+GATTCAACACATTTGGATCTAGTTCTCAGCCTACTACTTCTTCGTGTTCTGCTTCCTCTGCATATGCAACCTGTAGCGAA
+ACCTCCAATCCTAACAACAACAAGCGCAATTCATCAGAAATGAATTATGGCAAGAAAAAGGTAGATGATTCTTCAGGGTT
+TCATGCTCATTTCCAAACCTTTTGTTTAGGGGTGGAACAGCAGCAAGATTTCAAGAAGGGGAAGGAAGCAAGAGGAGGAA
+TTCGAGGAAAACCCGGAGGTAGTAGGAGGCAGGGAAGGAAACAGAAGGTTTCATCTCGCCACAATGTCTCATCCAATGAC
+TTGGGCATTTCTGCTTCC
+>gnl_Frave2.0_gene05408
+ATGGCGGGGGGAAAGTGGGTCCCCCCACCCCTGTCCCAGTTTCATCTTCACATAAAGAGGTTCCGTCGACGTCAGAAAGT
+CTCTGGATCCAGTGGAAACACAGAACCTTCTGGATACACAGACTGCAAAAATATCTCCAATCGAAGAATGGAAGAGAAAG
+GCAATGACTTTTATGCTGTTATGGGGTTGAAGAAGGAATGCTCTGACTCGGAGCTCAGGAATGCTTATAAGAAACTTGCA
+CTGATATGGCACCCAGATCGTTGCTCTGCCTCAGGAAATTCAAAGTTCGTGGAAGAAGCCAAGAAGAAGTTTCAGGACAT
+TCAACAAGCCTATTCTGTTCTGTCCGACGCCAACAAGAGGTTTCTGTACGATGTAGGAGCTTATGAAAGTGATGATGACG
+AAAATGGAATGGGTGATTTTTTAAACGAGATGGCGGTGATGATGAGCCAGACTAAGCCGAATGAAAATGGAGGAGAGAGC
+TTCGAACAATTGCAGGAGCTCTTTGAAGAAATGTTTCAGGGGGATATTGAGGGCTTTAGCTCCTGCTCTCAGCCTCCTAC
+TTCCTGTTCTACTTCCTCATCTTCATACGCATTGTACTGTGAAAATTCTACTCCCAGTAACAAACGTAATTCCTCCGCAA
+TGAATTATGGCAACGCAACCCTGGACAGTTCTGGTTTTGATGCTCATTTTCACAATTTCTGTGTAGGGACAGGCGGGAAG
+CCAGCAAAGGATCGGGAAGGGGATGCCAGGAAGAGAAAGGATTCCAGGAGGAGTAACCGG
+>gnl_Mimgu1.0_PACid_17694730
+ATGGCTGCTGATGAAGAGAAAAGCAGCGATTTTTACGGCGTTCTGGGGCTGAGGAAAGAATGTACGGCGGCGGAGCTCAG
+GGTTGCCTACAAGAAACTTGCAATGAAATGGCATCCAGATCGTTGCTCTGCTTCTGGGAATTTAAAGTATGTGGAGGAAG
+CAAAGAACAAGTTTCAAGCTGTCCAACAGGCCTATTCTGTGCTTTCCGATGCCAACAAAAGGTTTCTCTACGACGTAGGA
+ATCTACGATTCTGAAGACGATGCTGACGAAAACGGTATGGGTGATTTCTTGAATGAAATGGTAGCAATGATGGGCCAAAG
+TAAACCAAATGAAAATAAAAACGAGAGCTTCCAAGAATTGCAAGATCTATTCGAGGAAATATTCAACAATGACGCGGAAG
+AGGTTTTCAAGATTCCTCCTCCGCACTTTCCGTACCAAGATTCTTGCAGCGAGACCCGCACCGCATCGAACAAGAGGAAC
+GCCCGCGAAATGGGCTCCGTAAATTTCAGTAATATCGAAGCCACACCATTTGAAGGGTTCTGCATAGGGGAAAATGTAAT
+TTTTGGGGGAGAGAGAATACAAACGAGGCCCGGAGGAGGTAGTAGGAGGACGAAGCCGAAGATTTCGACATCGATCGATG
+GTTTAATTAGT
+>gnl_Nelnu1.0_NNU_010544-RA
+ATGAACCTGTTGTTGCAGAAATGGCATCCGGATCGATGCTCCTCGTCGGGAAACTCTAAGTTCGTGGAAGATTCAAAGAA
+GAAATTTCAGGCAATTCAAGAGGCTTATTCTGTTCTATCCGACGAGAATAAGCGATTTCTTTACGACGTTGGAGTTTACG
+ACTGCGACGACGATGACGATGACGAAAACGGAATGGGAGAATTTTTGGGGGAAATGGCGACTATGATGAGCCAAATTAAA
+CCCAGCGAGAACGGGCCGGAGAGTTTGGAGAAGCTGCAGGAACTGTTCGAGGAAATGTTCCAAAGGGACATGGATGATGG
+TTTCTTCTCCCCCTCCCCCCAATGCGCTTCTTTTTCTTCGTCTTGCTCATCTTCTTCGTCGTCGACGACTTATTTTTCAT
+ATAATAACAACAAGCACGACAATAAAAGGAATTGCTCCGACATCAGTTCTATGGACGATTTCTACACATTTGGCACGGAT
+TCTATACAATTCAGCAATTTCTGCATTGGGGTGGAAGGAGGAGAAGATTCAAAAGTAAGAGGAGGAAAGTCAAGGCGGAA
+GAGCAACAGGAGACAAAAAGTTTCATCGTCTAAACACGATCCGTCGTGCCGT
+>gnl_Solly2.3_Solyc03g123560.2.1
+ATGGAAGACAAAAGCAATGATTATTATGCAGTTTTGGGGTTGAAGAAGGAATGCACTGACACAGAACTTAGGAATGCCTA
+TAAGAAGCTTGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGGAATTTGAAGTTTGTAGATGAAGCAAAGAAGC
+AATTTCAGGCAATTCAAGAAGCATATTCTGTGTTATCGGATGCAAACAAAAAGTTTTTGTACGATGTAGGAGTTTATGAC
+TCTGGTGATGATGACGACGAAAATGGCATGGGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAA
+TGAAAATCAGGGAGAAGAAACCTTTGAGGAATTGCAGGATATGTTTAATGAAATGTTCAACAGTGATAATGGAACGTTTT
+CTTCTTCTTCTTCTTCTTCTTCTTCTTGGACTGGAACTCCTTCAATGTGCTCTACTACATCATCTACATCTTCAAGTGAG
+ACTTTTTTAACCTTTCCCAACAAGAGAAGTTCAGGTGAAATGAAGTCGGGTAGTAGTGTAAGAGGCGATTCTTGCCAATT
+CCAAGGATTTTGTGTAGGGGCAGGTGGAACTTCTGGAAAATGCAATGAAAGAGAACGAAGTTGGAGGAAAAATTCCAAGA
+GTGGACGGAAGCAT
+>gnl_Sorbi1.4_PACid_1968370
+ATGGACGCCGGGGGAGAGAAGTTCAGCGACGCGGCGGCGGCGGAGGGCGGTGAGGGCGGCGGCGACCTCTACGCCGTCCT
+CGGGCTCAAGAAGGAGTGCTCCGACGCCGACCTCAAGGTCGCTTACCGGAAGCTCGCCAAGAAATGGCACCCGGACAAAT
+GCTCCTCCTCCAGCAGCGTGAAACACATGGAGGAAGCCAAGGAGAAGTTCCAAGAGATCCAGGGCGCCTATTCCGTACTC
+TCTGACGCCAATAAACGGCTCCTCTACGATGTTGGAGTATACGACGATGAGGACGACGAGGATAGCATGCAGGGGATGGG
+TGACTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGTGCGGCCGACGAGGCAGGAAAGCTTTGAGGAGCTGCAGCAGC
+TTTTTGTGGACATGTTCCAGTCTGATATTGATTCAGGATTCTGCAACGGGTCTGCTAAGGATCAAGTTCAGGGGCAAGCC
+AAAAGTAGAACATGCTCGACCTCACCTTCATCATCACCGTCCCCACCTCCTCCTCCTACTATAGTAAAGGAGGCAGAGGT
+GTCATCATGTAATGGCTTCAATAAGCGGGGTTCATCAGCAATGGACTCAGGGAAGCCTCCAAGGCCTGTTGAAGGCGGTG
+CTGGTCAGGCTGGATTTTGTTTTGGGGTGAGCGATACGAAGCAAACGCCGAAGCCGAGAGGTCCGAACACCAGCCGGAGG
+AGGAACGGCCGGAAACAGAAGCTGTCATCCAAGCACGATGTTTCATCTGAAGATGAAACGGCCGGTTCC
+>gnl_Thepa2.0_Tp3g12470
+ATGGCGTCGAACAATAGCGAGAAAGGAAACGATGATTTGTATGGTGTTCTGGGCTTGAAGAAGGAATGTACGACGACGGA
+GCTCCGTACTGCTTATAAGAAGCTTGCTCTAAGATGGCATCCAGATCGTTGTTCGTCAATGGGGACTCCAGAGTTTGTAG
+ACGAAGCAAAGAAGAAGTTTCAGGCAATCCAAGAGGCCTATTCTGTTCTGTCTGACTCCAACAAGAGGTTCCTCTATGAT
+GTTGGAGCTTATAACAGTGATGATGAAGACCAAAACGGTATGGGAGATTTCTTGAACGAAATGGCGGCAATGATGAATCA
+GTCCAAGCCTAGTGAGAATAACTCAGGGGACAGTTTTGAGCAGCTACAAGATCTGTTTAATGAGATGTTTCAAGGAGACG
+CTGCAGCATTCTCATCATCATCATCATCATCTTGCTCTGCTTCGACTTTTACTTCCTCTTGTAGCTTTGTCTTTGACACA
+AATAGTCAGCGGTCACCGTTTGAGACAAGCTCAATGGGGACTAATGATCTTTTTGGATTCGATCACAGTGCTCACACCTT
+CTCTTTAGGGGTGGAACATCAGCAGGATTTCAAGAAGGGGAAGAACAGTGGTGGAAGAAGAAACAGAAGGAAGAACAATG
+CTCAATCGGCTGCTCACGAGACGGCGTCGTCCAACAACTATGGAGTCCCCACTTCA
+>gnl_Theca1.0_Tc06_g010450
+ATGGCAAATGGAGAAGAGAAAAACAATGATTTTTATGCAGTTTTGGGGTTGAATAAAGAATGCACTCCGACAGAGCTCAG
+GACTGCTTATAAGAAACTTGCCCTGAGATGGCACCCTGATCGTTGCTCAGCTTCGGGAAATTCAAAGTTCGTGGAAGAAG
+CCAAGAAGAAATTTCAGGCCATTCAACAAGCCTATTCTGTTCTGTCTGACTCAAACAAGAGGTTTCTGTACGACGTAGGA
+GCTTATGACAGTGATGATGACGAAAATGGAATGGGAGATTTTTTGAACGAAATGGCAGGGATGATGAGCCAGACAAAATC
+TAATGAAAATGGAGGGGAAAGCTTCGAGGAACTACAGGAATTGTTTGAAGAAATGTTCCAAGCGGACATTGATTCATTTG
+AGTCTACTGGTCAGTCCACTCCTTCCTGCTCTGCTTCATCTTCGTTTGGGTCATATGGTGAAAGTTCCAGCTCCAACAAG
+CGGAATTCCTCTGAAATGAGTTCTGTGGAGACTAGGCTGGAGAGTTCTTCTAGCTTCGATGCACAATTTCACAGTTTTTG
+TCTCGGGGTGGAACACAGGCAAGATATCAAGCAACACAGAGGAGCCAGAGGAGGAATGCGAGGAGCAGCCGGCGGTAGTA
+GACGGAGAAATGGCAGGAAACAAAAGGTTTCATCTGGCCATGATGTTACTTCCAACGACTGTGGCATTTCTGCTTCA
+>gnl_Vitvi12X_PACid_17827068
+ATGGCCGCCGGAGAAGAGAAGAGCAATGATTTTTATGCCGTTCTAGGGTTGAAAAAGGAATGCACCGCCTCCGAGCTCAG
+AAATGCGTACAAGAGACTTGCCCTGATGTGGCACCCAGATCGTTGCTCCTCGTCGGGAAACTCGAAATTCGTGGAAGAAG
+CGAAGAAGAAATTTCAGGCCATACAAGAAGCCTATTCAGTTCTCTCTGATGCGAATAAAAGGTTTCTGTACGACGTTGGA
+GCCTACGACAGCGATGATGACGAAAACGGAATGGGGGATTTTTTGAATGAGATGGCGGTTATGATGAGCCAAACCAAGTC
+CAATGAAAATGGGAAGGAGAGCTTTGAGGAGTTGCAGGAGCTCTTTGAGGATATGTTCCAAAGGGATGTCGACGCATTCA
+ACTCTGCCTCTCATCACCCCATGAACTCTTTCCCCAGTTCTACTTCCACTTCTTCCTACTGCGAAAGCTCCAATGCCAAC
+AACAAGCGGAATTCGGCTGAAATGGGCTCTGGAAGGATGATGAGTGCAGGGGAGTCCTCTGCTTTTGATGCCCACTTTCA
+GAGCTTCTGCTTTGGGACAGGCGGCACGCCAGGGAGATTTCAGGAGGGGGAAAGGAGCAAGAGGAGGAATTCCAGGAGGA
+GCCAACGG
+>gnl_Selmo1.0_PACid_15401289
+ATGGAGAAGAGGAAAGAGGATCCCTACACTGTTCTTGGTGTCCAAAAGTCGAGTTCTAGCTCGGAAATTCGCTCCGCTTA
+TCGGAAGCTCGCCATGAAATGGCATCCAGATAAGCAACACTCTTTAGAGGATCAAGCAAAAGCGAAGTTCCAGGGCATTC
+AAGAAGCTTATTCAGTGCTATCCGACGACAAAAAAAGAGTTCTTTATGATTCGGGACTTTATGACGAGGGAGATGACGAG
+GTGAGT
+>gnl_Orysa6.0_PACid_16864430
+ATGGCCCGCGGCGGCGGCGGCGGCGGCGGCGCGGACGCCGACCTGTACGCCGTCCTCGGCCTCAGCAGGGAGTGCACCGA
+CGCCGACCTCAGGCTCGCCTACCGCAAGCTCGCCATGATATGGCATCCGGACAGGTGCTCGGTGGCCGGCGGCAGCGCGA
+GCGCGGCGGGCGTCGACGAGGCCAAGGAGCGATTCCAGGAGATCCAGGGCGCCTACTCCGTGCTCTCCGACTCCAACAAG
+CGCTTCCTCTACGACGTCGGCGTCTACGACGGCAACGACGGCGACGACGACGACGACGAAGCAGATCTGTCGGGGATGGG
+CGATTTCCTCGGCGAGATGGCGCAGATGATGAGCCAGGCGACGCCTGCGGAGAGCTTCGAGGAGTTGCAGCAGCTGTTCG
+TGGACATGTTCCAGGACGACATCGACGCCGGCCTCTGCCAGTCGACGCCGCCGCCGCCGTCATGGCCGTCGCCTCCGGCG
+GCCGCCAATGCACGATCGCCGGCGGCGGCGGCGACTTCACGCAAGGGCGTGAACAAGCGGTGCTCACCGGCGGCGATGGA
+CATGGACTCCGGTTTGAGCAGCCTGCTGGGCATTTCGGGCTTCTGTTTCGAGGCGCCATGGACGTCGCAGGACGCGAGCA
+CTGCCGCCGGCGGTGGCGGCGGCAAGAGGAGAAAGCAGAGGCCGCCGCCGGCGAGCCACAACGTG
+>gnl_Sorbi1.4_PACid_1982925
+ATGGCTGCTACAAGTCACTGCGGCAACATCCAGGACCAGGACGAAGAAGCTTCGGCTCCTGGCGCCGCCGACCTCTACGC
+CGTGCTCGGGCTCAACAGGGAGTGCACCGACGCCGAGCTCAGGGTCGCGTACCGGCGGCTCGCCATGATATGGCATCCGG
+ACAGGTGCTCGGCGTCCGGCAGCTCGCCGGCGCGCATGGAGGAGGCCAAGGAGCGGTTCCAGGAGATCCAGGGCGCCTAC
+TCCGTGCTCTCCGACTCCAACAAGCGGCTCCTCTACGACGTCGGCGTCTACGACAGCGACGACGACGAGGCTGACCTGTC
+GGGGATGGGCGACTTCCTCGGAGAGATGGCCGACATGATGAGCCAGGCCACGCCAACGGAGACCTTCGAGGAGCTGCAGC
+AGGTGTTCGTGGACATGTTCCAGGACGACCTGGACGACGCCGGCTTCTTCGGCGGGCTTCCGACGACGGGCCGCAGGGCC
+CAGGCACCCAGCACCTCGCTGCCGCCGTCGGTGTCGTCGTCGCCGTTGCGGCCGACGCCTGCCGCTGGAAGAAGCAAGGG
+TCCGCAAGCGACGCCGTCGTCGTCGTTTAAAGGCGTCGAGAGGCGGGGTTCGACGTCGACGGCGAAACGGCCGAGGCCCA
+ACGGGTCGGCGGGCCTGGAATCGGACCTGGGCCTCTCCGGATTCTGCTTCATGGTGAGTAAGGAGATGAGCAAGTCGAAG
+GAGAGGCAAGCGGTATGGGCCAGTGACGACGGTGACAGGAGCACCGATGGCAAGCAGAGGTTGTCGACGAGCCGCGATGT
+CTCCGGTGGTGGGATGTCACGCTCACTGCAGGGCCAAAGCAGCAAAAACTTGTTGCAGTGTATGGCCTCTAAGTCT
+>gnl_Medtr3.5_Medtr8g022310.3
+ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG
+GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG
+CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA
+GTTTACGACAGTGATGATGACGAAAATGTAAGGCACTTGTTTCACACCATTCATGAGTTGGGGACCCTCTTTTGCGTTAT
+GTTTTGTTTCTTCATTTCCTTGAGGGGAGAGAAGAGAAGCAACCTTAATTTAACCTTTTCACTTTCACAT
+>gnl_Nelnu1.0_NNU_000115-RA
+ATGGAGGTGGACTCCCATCGATCATCTCCATCTTACTACACCATCCTTGGTGTAGATCAGAATTCCTCCGCTTCCGAGAT
+ACGCAATGCTTACAGGAAGCTCGCGATGCAATGGCATCCAGACAAATGGACGAAAACTCCGTCGCTCTTAGAGAAAGCCA
+AGAGTAAATTCCAGCAAATCCAGGAGGCTTATTCGGGTGGGTTACTCGTTTTCATGTTATCGGATCAGGGGAAGAGAACA
+CTGTATGATGTCGGTCTGTATGACCCGGACGATGAAACGAATGACGAGGTGGGGCTTCGCAGATTTCATGCAGGAGATGA
+TATCTCTCATGAACGATGTGAAGAAACAGGAGAAGAAATACAGCTTGGAGGAACTACAGGAGATGTTAGTGGAAATGTCA
+CAAGGGCTGGAGTTGAAGATGGAGAGTGCTGGTGGTGTGTGGTTGTTAGATGGAGCTGCAGCCTCAAGGAGGAGCTCAAA
+GAGGGCCAGATGGGAATCATCAGCGAGTCCGACGACGCTGGACACGACACACCTTCTCTCCCCCACTTGCACGGTTCAGA
+GCTGGAATTGTTAGGAAGAACCGGCTGTTGCAAT
+>contig_7
+GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC
+CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT
+CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA
+AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3722.fna.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,819 @@
+>gnl_Glyma1.01_PACid_16266208
+---------ATGGCTAATGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAAGAAAAGC
+AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT
+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------
+---AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT
+TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG
+GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG
+GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA
+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA
+GACATGTTTCAAGCGGATATT------GGATTG---------------------------
+---GATGGAGGCCCTTCTCTT---------------------------------------
+------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------
+------------------------------------TACATGACTTACAGTGAAAGTTCT
+AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG
+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------
+------------CAGAATTTCTGTTTTGGG---GTGAAC------CAACTCCAAGATATA
+AAGAAGGGAAAG---------GGGGGAATTCTAGGAGGAGGAGGTAGAAGTAGACACAGA
+AGTGGCAGAAAGCAAAAAATGTTCTAT---GGCCATGATGTT------------------
+------------------------------------------------------------
+>gnl_Glyma1.01_PACid_16266209
+---------ATGGCTAATGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAAGAAAAGC
+AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT
+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------
+---AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT
+TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG
+GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG
+GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA
+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA
+GACATGTTTCAAGCGGATATT------GGATTG---------------------------
+---GATGGAGGCCCTTCTCTT---------------------------------------
+------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------
+------------------------------------TACATGACTTACAGTGAAAGTTCT
+AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG
+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------
+------------CAGAATTTCTGTTTTGGG---ACAGGT------GAACCAACTCCAAGA
+TATAAAGAAGGG------------------------AAAGGGGGGAATTCTAGGAGGAGG
+AGG---------------------------------------------------------
+------------------------------------------------------------
+>gnl_Glyma1.01_PACid_16266210
+---------ATGGCTAATGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAAGAAAAGC
+AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT
+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------
+---AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT
+TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG
+GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG
+GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA
+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA
+GACATGTTTCAAGCGGATATT------GGATTG---------------------------
+---GATGGAGGCCCTTCTCTT---------------------------------------
+------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------
+------------------------------------TACATGACTTACAGTGAAAGTTCT
+AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG
+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------
+------------CAGAATTTCTGTTTTGGG---GTCGGT------CATGTAAACTATCAT
+TACCAA------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+>gnl_Glyma1.01_PACid_16301083
+---------ATGGCCGATGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAACAAAAGC
+AATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAAGAAT
+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGG------
+---AATTCAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT
+TCA------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG
+GGAGTCTACGACAGT------------------------GATGACGACGAGAACGGCATG
+GGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATCGAATGAAAACGGA
+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGTTGTTTGAA
+GACATGTTTGAAGCAGATATT------GGATTG---------------------------
+---GACGGAGGCCCTTCTCTT---------------------------------------
+------------GCTTCTTCTGATTGCTCAACTTCATCTGCT------------------
+------------------------------------TACATGACTTATAGTGAAAGTTCT
+AGT---------------------------TCAAATAAACACAATTCCTCT---GAGATG
+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCTGGTTAC------
+------------CAGAATTTCTGTTTTGGG---GTGAAC------CAACTCCAAGATATA
+AAGAAGAAAAAG---------GGGGGAATTCTA---GGAGGAGGTAGAAGTAGACACAGA
+AATGGCAGAAAGCAAAATATGTCCTAT---GGCCATGATGTTTCATCGAATGACTACCCT
+GGAATTTCCACAAAG---------------------------------------------
+>gnl_Glyma1.01_PACid_16301085
+---------ATGGCCGATGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAACAAAAGC
+AATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAAGAAT
+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGG------
+---AATTCAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT
+TCA------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG
+GGAGTCTACGACAGT------------------------GATGACGACGAGAACGGCATG
+GGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATCGAATGAAAACGGA
+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGTTGTTTGAA
+GACATGTTTGAAGCAGATATT------GGATTG---------------------------
+---GACGGAGGCCCTTCTCTT---------------------------------------
+------------GCTTCTTCTGATTGCTCAACTTCATCTGCT------------------
+------------------------------------TACATGACTTATAGTGAAAGTTCT
+AGT---------------------------TCAAATAAACACAATTCCTCT---GAGATG
+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCTGGTTAC------
+------------CAGAATTTCTGTTTTGGG---GTAGGT------CATGTAAACTATCAT
+TACCAA------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+>gnl_Glyma1.01_PACid_16301084
+---------ATGGCCGATGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAACAAAAGC
+AATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAAGAAT
+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGG------
+---AATTCAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT
+TCA------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG
+GGAGTCTACGACAGT------------------------GATGACGACGAGAACGGCATG
+GGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATCGAATGAAAACGGA
+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGTTGTTTGAA
+GACATGTTTGAAGCAGATATT------GGATTG---------------------------
+---GACGGAGGCCCTTCTCTT---------------------------------------
+------------GCTTCTTCTGATTGCTCAACTTCATCTGCT------------------
+------------------------------------TACATGACTTATAGTGAAAGTTCT
+AGT---------------------------TCAAATAAACACAATTCCTCT---GAGATG
+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCTGGTTAC------
+------------CAGAATTTCTGTTTTGGG---ACAGGT------GAACCAACTCCAAGA
+TATAAAGAAGAA------------------------AAAGGGGGGAATTCTAGGAGGAGG
+------------------------------------------------------------
+------------------------------------------------------------
+>gnl_Medtr3.5_Medtr8g022310.1
+---------ATGGCTAACGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAACAAAAGC
+AATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAGGAAT
+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGG------
+---AATGTGAAGTTTGTGGAAGAAGCTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTAT
+TCT------------------GTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTT
+GGAGTTTACGACAGT------------------------GATGATGACGAAAATGGTATG
+GGAGACTTTCTGAATGAAATGGTTACAATGATGAGCCAAACTAAATCAAATGAAAATGGA
+------GAGGAGAGCTTCGAGGAGTTACAA------------------CAGTTGTTTGAT
+GATATGTTTCAAGCGGATATC------GGATTA---------------------------
+---AATGGAAGCACCTCTCTT---------------------------------------
+------------AATGCTTCGGGTTGCTCCACTTCATCGACT------------------
+------------------------------------TTCATGACGTTCAGTGAAAGCTCG
+AAT---------------------------TCAAATAAGCGCAATTCCACT---CAAATG
+AATTTTGGGAAG---------GCAGAGGATTCTTCTAGTTTTGGTGCAAATTAC------
+------------CAGAACTTCTGTTTTGGG---ATGAAG------CACCTTCAAGAAGAT
+GTGGAGAAGGAA------AAAGGGGGAATTCTAGAAGGAGGAGGTAGCAAAAAACAAAGA
+AAAGGAAGAAAACAAAAAATTTCATGT---GGACAT---GTTTCCTCTAATGACCATCCT
+GGTATTTCTGCTAAT---------------------------------------------
+>gnl_Medtr3.5_Medtr8g022310.2
+---------ATGGCTAACGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAACAAAAGC
+AATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAGGAAT
+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGG------
+---AATGTGAAGTTTGTGGAAGAAGCTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTAT
+TCT------------------GTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTT
+GGAGTTTACGACAGT------------------------GATGATGACGAAAATGGTATG
+GGAGACTTTCTGAATGAAATGGTTACAATGATGAGCCAAACTAAATCAAATGAAAATGGA
+------GAGGAGAGCTTCGAGGAGTTACAA------------------CAGTTGTTTGAT
+GATATGTTTCAAGCGGATATC------GGATTA---------------------------
+---AATGGAAGCACCTCTCTT---------------------------------------
+------------AATGCTTCGGGTTGCTCCACTTCATCGACT------------------
+------------------------------------TTCATGACGTTCAGTGAAAGCTCG
+AAT---------------------------TCAAATAAGCGCAATTCCACT---CAAATG
+AATTTTGGGAAG---------GCAGAGGATTCTTCTAGTTTTGGTGCAAATTAC------
+------------CAGAACTTCTGTTTTGGG---GTCAAT------CTTGTAAATTATCAT
+TACCAA------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+>gnl_Musac1.0_GSMUA_Achr6T31040_001
+---------ATGGCGGCCGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAGGACAAAAGC
+GGCGACTTCTACGCCGTGTTGGGGCTCAGGAAGGAGTGCTCCGAAACCGAGCTGAGGAAT
+GCGTACAAGAAGCTTGCCATGAGGTGGCATCCGGATAAGTGCTTGGCTTCGGGA------
+---AATGCTCAAATCGTGGGGGAAGCCAAGGAGAAGTTTCAGGAGATCCAGAAAGCCTAC
+TCT------------------GTTCTCTCAGACTCCAATAAGAGATTCCTGTACGATGTG
+GGAGTCTACGACAACGAT------------------GATGACAATGACGAAAACGGTATG
+GGAGACTTTATAGGGGAGATGTTGGAGATGATGAGCCAAACGAAACCCAATGAGAACAGC
+------CAAGATAGCTTCCAGGAGCTGCAG------------------GAGCTGTTTGTG
+GAGATGTTCCAGGACGACCTG------GATGCCGGA------------------------
+---TTTGGTGGTTCCATCTTCCAC---GATTGCCCCTGGGCTCAACCG------------
+---------ACCAATGGCCAAGATTGCTGGACTTCATCGGGA------------------
+------------------------------------CTGCACTTTGCTAATGGAAGGAGT
+AAG------------------------TGTGGCAACAAGCGGGGCAACTCA---GCTGTG
+AACTTGGGAAAG------------GTCAATCTTGAAGAGTTGGAACATGGTACC------
+------------AGCGACTTCTATTTTGGG---CTAAAT------GATGCAGCACAGCCA
+TCACAAGGGAAAGGAGGCAGT------------------------AATAACAAGAGAAGG
+AATGGAAGAAAGCAAAAGGTTTCATCC---AATCATGATGTCTCATCC------------
+------------------------------------------------------------
+>gnl_Musac1.0_GSMUA_Achr9T18140_001
+---------ATGGCCGCCGGG---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAGGAAAAGATC
+GGCGATTTCTACACGGTGCTGGGGCTCAGGAAGGAGTGCTCGGAGGCGGAGCTGAGGATC
+GCGTACAAGAAGCTGGCTATGAGATGGCATCCGGATAAGTGCTCGGCTTCGGGA------
+---AACCATCGAAGGATGGAGGAAGCGAAGGAGAAGTTCCAGGAAATCCAAAAAGCCTAC
+TCT------------------GTTCTCTCGGACTCCAGCAAGAGATTTCTGTATGATGTG
+GGAATCTACGATAACGAG------------------GATGATAATGACGAAAAAGGAATG
+GGGGATTTTATTGGGGAGATAGCTCAGATGATGAGCCAAACGAAATCTGGGGAGAATGGT
+------CATGATAGCTTTGAGGAGCTGCAG------------------CGGATGTTCCTG
+GATATGTTCCAGGACGACCTG------GACGCCGGA------------------------
+---TTCGGTGATTCTTCCATCCAC---AGTGGCCCCCAAGCTCGGCCA------------
+---------ACCGACGGTCTCAATTGCTCGATGCCATCAGGA------------------
+------------------------------------CTGCAGTTTGCTGATGGAGGGAAC
+AAT------------------------GGCAGCAACAAGAGAGGCAACTCG---GAGAAG
+------------------------GCAAAGCTGGATGGGTTGGAAAACAGTTCC------
+------------ACTGGCTTCTGCTTCGGG---TTGAAT------GATGCAGGGCAGTCA
+TCAAAAGGAAAAGGAAGCGCT------------------------AATAGCAAGAGAAGG
+AATGGAAGAAAGCAGAAGGTCTCATCC---AAACATGATGTCTCATCCAGTGAT---GCT
+GAGGTCTCATTT------------------------------------------------
+>gnl_Musac1.0_GSMUA_Achr8T23700_001
+---------ATGGCGAGCGAC---------------------------------------
+------------------------------------------------------------
+------------------------------------------------ATGGATGCAAGC
+GGCGATTTCTACTCGGTGCTGGGGCTGAAGAAGGAGTGCTCCGAGGCGGAGCTCAGGAAT
+GCGTACAAGAAGCTCGCTTTGAAGTGGCATCCCGATAAGTGCTCGGCGTCGGGT------
+---AATGAGATTCGCATGAAGGAAGCGAAGCAGCAGTTCCAGGAGATCCAGAAAGCCTAC
+TCT------------------GTTCTCTCCGACTCCAACAAGAGATTTCTGTACGATGTT
+GGAGCCTACGACAAAGAC------------------GACGACAAAGACGAAGAGGGGATG
+GTGGAGTTTCTTGGGGAGATGGCGCAAATGATGAGGCAAACCAAATGCTGTGGGAGCGGC
+------CAGGAGAGCTTCGAGCAGCTGCAG------------------CAGATGTTCGTG
+GAGATGTTCCACGACGATCTG------GACGCGGGA------------------------
+---TTC------------------------------------------------------
+------------------------TGCGGCCACTCCTCGGCC------------------
+---------------------------------------------ACCTCGGGCGCGGCG
+TCC------------------------TGCGGCAACAAACGGGACAACTCG---GCGATG
+GACTCGGGCAAG------------CGGAAGCCGGACGAGTTGGACCCGGCCGCC------
+------------ATTGGGTTCTGCCTCGGG---ACAAAG------GATGCAGGGCAATCC
+TCAAAAGGAAGAGGTAGC---------------------------AACAGCAAGAGAAGG
+AACAGAAGAAAGCAAAAGGCATCATCC---AAGCATGACAACTCATCTCACAAT---GCT
+AAGGTCTCAGCT------------------------------------------------
+>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001
+---------ATGGAGGGGGAC---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAGGAGAAGAGC
+GGGGATTTCTACGCGGTGCTGGGGCTGAAGAAAGAGGGCTCCATGGCGGAGCTCAAGAAT
+GCGTACAAGAAGCTGGCGATGAAGTGGCATCCCGATAAGTGTCCTGCGTCAGGC------
+---AATAAGATACGCATGGATAAAGCGAAGGAGAAGTTCCAGGAGATCCAAAAAGCCTAC
+TCT------------------GTTCTCTCCGACTCCAACAAGCGATTCCTGTACGATGTC
+GGAGTTTACGACAAAGAC------------------GATGAGGAAGATGAAGAGGGGATG
+GGGGACTTCATTGGGGAGATCGCGCAAATGATGAGCCAGTCCAAACCCAGCGGGAGCGGC
+------CACGAGAGCTTGGAGGAGCTGCAT------------------CGGCAGGTCGTG
+GAGATGTTCCTCGACGAACTG------GACGCCGGAGAT---------------------
+CGCTTCTCCTCGGCCAACCAA---------------------------------------
+------------GGCGCGTCGTCCTGCGACGGCAGGGACGAC------------------
+------------------------------------------------------------
+------------------------GGCGGCGGTAACAAGCGTGGCAACTGG---GCGGTG
+GACTGGGGCAAG------------GAGAAGCTGAACGAGTTGGGCCCGGGCACC------
+------------GGCGGGTTCTGCTTCGGG---GTGAGT---------------------
+---------------------------------------------------CGCCGAGTC
+CACTCCTTTGATCTTATGATAGACGTA---GTCCACCTCATCCATTCTGATCTG------
+---------------------------------------------------ACTCTGGAA
+>gnl_Orysa6.0_PACid_16843526
+---------ATGGCCGACGGGGGA------------------------------------
+------------------------------------------------------------
+---------------GAGAAGTGC---CGGGACGCGGCCGGC---GAGGGCGGCGGCGGC
+GGCGACCTGTACGCCGTGCTCGGGCTCAAGAAGGAGTGCTCCGACGCCGACCTCAAGCTC
+GCGTACCGGAAGCTCGCCATGAGATGGCATCCGGACAAATGCTCATCCTCCAGC------
+---AGTGCAAAGCACATGGAGGAAGCCAAGGAGAAGTTCCAGGAGATCCAGGGCGCCTAT
+TCC------------------GTCCTCTCAGACTCAAACAAGCGGTTCCTCTACGACGTG
+GGGGTATATGATGATGACGAC------------AATGACGATGACAACCTGCAGGGGATG
+GGGGACTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGCACGGCCAACGAGG------
+------CAGGAGAGCTTTAAAGAACTGCAG------------------CAGCTATTCGTA
+GACATGTTCCAAGCTGATCTT------GATTCGGGT------------------------
+---TTCTGCAATGGACCCTCAAAGTGCTACCATACCCAGGCCCAAAGCCAGACTCGAACA
+TCCTCAACCTCCCCTTCGATGTCACCGTCTCCACCGCCTCCA------------------
+------------------------------------GTAGCTACTGAGGCAGAATCGCCA
+TCA------------------TGTAATGGTATTAATAAGCGTGGTTCATCA---GCAATG
+GACTCTGGGAAG---CCTCCAAGAGCCAGCGAAGTCGGTTCTGGACAGAGTCAA------
+------------TCAGGGTTTTGTTTCGGG---AAGAGT------GATGCTAAACAAGCG
+GCGAAGACGCGAAGCGGGAACACG---------------------GCCAGCCGGAGGAGG
+AACGGCCGGAAGCAGAAGGTGTCGTCG---AAGCACGACGTCTCGTCTGAGGACGAGATG
+CCAGGTTCGCAGTGG---------------------------------CACGGCGTGGCC
+>gnl_Orysa6.0_PACid_16843528
+---------ATGGCCGACGGGGGA------------------------------------
+------------------------------------------------------------
+---------------GAGAAGTGC---CGGGACGCGGCCGGC---GAGGGCGGCGGCGGC
+GGCGACCTGTACGCCGTGCTCGGGCTCAAGAAGGAGTGCTCCGACGCCGACCTCAAGCTC
+GCGTACCGGAAGCTCGCCATGAGATGGCATCCGGACAAATGCTCATCCTCCAGC------
+---AGTGCAAAGCACATGGAGGAAGCCAAGGAGAAGTTCCAGGAGATCCAGGGCGCCTAT
+TCC------------------GTCCTCTCAGACTCAAACAAGCGGTTCCTCTACGACGTG
+GGGGTATATGATGATGACGAC------------AATGACGATGACAACCTGCAGGGGATG
+GGGGACTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGCACGGCCAACGAGG------
+------CAGGAGAGCTTTAAAGAACTGCAG------------------CAGCTATTCGTA
+GACATGTTCCAAGCTGATCTT------GATTCGGGT------------------------
+---TTCTGCAATGGACCCTCAAAGTGCTACCATACCCAGGCCCAAAGCCAGACTCGAACA
+TCCTCAACCTCCCCTTCGATGTCACCGTCTCCACCGCCTCCA------------------
+------------------------------------GTAGCTACTGAGGCAGAATCGCCA
+TCA------------------TGTAATGGTATTAATAAGCGTGGTTCATCA---GCAATG
+GACTCTGGGAAG---CCTCCAAGAGCCAGCGAAGTCGGTTCTGGACAGAGTCAA------
+------------TCAGGGTTTTGTTTCGGGCAGAAGAGT------GATGCTAAACAAGCG
+GCGAAGACGCGAAGCGGGAACACG---------------------GCCAGCCGGAGGAGG
+AACGGCCGGAAGCAGAAGGTGTCGTCG---AAGCACGACGTCTCGTCTGAGGACGAGATG
+CCAGGTTCGCAGTGG---------------------------------CACGGCGTGGCC
+>gnl_Poptr2.2_PACid_18217800
+---------ATGGCAAACGGAGGAGAA---------------------------------
+------------------------------------------------------------
+---------------------------------------------GATAAATGGAAAAGC
+AATGACTTATATCAAGTCTTGGGGTTGAATAAGGAATGCACTGATACAGAGCTCAGGAGT
+GCTTATAAGAAACTTGCACTGAGATGGCATCCAGATCGATGTTCAGCTTCAGGA------
+---AATTCTAAGTTCGTTGAAGAAGCCAAAAAGAAGTTTCAGGCAATTCAACAGGCCTAT
+TCT------------------GTTCTTTCTGACACCAACAAGAGGTTTCTTTACGACGTT
+GGTGTTGATGACAGT------------------------GATGACGACGAAAATGGAATG
+GGTGATTTTCTGAATGAAATGGCTGTCATGATGAGCCAAACGAAGCCTAGCGAAAACATG
+------GAGGAGAGCCTAGAGGAACTGCAA------------------GAATTATTTGAC
+GAGATGTTCCAAGAGGATCTG------CATTCG---------------------------
+---TTTGGGATTGACAGTCAG---------------------------------------
+------------GCTGCTCCTTCATGT------CCTCCTTCT------------------
+------------------------------------TATGTATCCTACAGCGAAAGTTCC
+AAC------------------------TCAAATAACAAACGTGTTTCTGCT---GATATG
+AACTTGGGGAAG---ACTAAAGTGGATGATTCTTCTAGCTTCAACTCTCACTTT------
+------------GAGAAATTCTGTTTAGGG---ACA------------------------
+---------GGTGGAACAGCAGCAACCTTTCAAGAAGGTGAAGGTGGGAGTAAGAGGAGG
+AATTCAAGGAGGAGCCAGCGGCAGACG---AAGGCAAGACAAGAAACAAAGAGTTTCTTC
+GGGCTA------------------------------------------------------
+>gnl_Poptr2.2_PACid_18234651
+---------ATGGAAAATGGAGGAGAA---------------------------------
+------------------------------------------------------------
+---------------------------------------------GAGAAAGGGAAAAGC
+AATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCACAGAGCTGAGGAAT
+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAA------
+---AATTCCAGGTTCGTTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTAT
+TCT------------------GTTCTTTCTGACACCAACAAGAGGTTTCTTTACGACGTT
+GGTGTTTATGACAGT------------------------GAAGACGACGAAAATGGAATG
+GGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCAAACAAAGCCCCACGAAAACGTG
+------GAGGAGAGCTTTGAGGAATTGCAA------------------GGATTGTTTGAG
+GAGATGTTCCAAGAGGATTTG------GATTCG---------------------------
+---TTTGGGATTGCCTGTCAG---------------------------------------
+------------GCTACTACC---------------------------------------
+------------------------------------TGTGTGTCATACAGCGAAAGCTCC
+AAC------------------------TCAAATGATAAACGTGTTTCTGTC---GATATG
+AACTTGAAGAAG---ACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTC------
+------------GAGAAGTTCTGTTTAGGG---GTA------------------------
+---------AGTGGAACACCAGCAATCTTTCAAGAAGGGGAA---GGGAGTAAGAGGAGG
+AGTTCAAGGAGGAACCGGCGG---------------------------------------
+------------------------------------------------------------
+>gnl_Poptr2.2_PACid_18234649
+ATGCTAAGAATGGAAAATGGAGGAGAA---------------------------------
+------------------------------------------------------------
+---------------------------------------------GAGAAAGGGAAAAGC
+AATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCACAGAGCTGAGGAAT
+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAA------
+---AATTCCAGGTTCGTTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTAT
+TCT------------------GTTCTTTCTGACACCAACAAGAGGTTTCTTTACGACGTT
+GGTGTTTATGACAGT------------------------GAAGACGACGAAAATGGAATG
+GGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCAAACAAAGCCCCACGAAAACGTG
+------GAGGAGAGCTTTGAGGAATTGCAA------------------GGATTGTTTGAG
+GAGATGTTCCAAGAGGATTTG------GATTCG---------------------------
+---TTTGGGATTGCCTGTCAG---------------------------------------
+------------GCTACTACC---------------------------------------
+------------------------------------TGTGTGTCATACAGCGAAAGCTCC
+AAC------------------------TCAAATGATAAACGTGTTTCTGTC---GATATG
+AACTTGAAGAAG---ACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTC------
+------------GAGAAGTTCTGTTTAGGG---GTGGAA------CACCAGCAATCTTTC
+AAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACC---GGCGGTAGAGAGAGG
+AAAGGCAGGAAACAAGAAGTTTCATCT---GGCTATGATGTCTCCTCCCATGAC---CAT
+GGTATTTCTGCTTCA---------------------------------------------
+>gnl_Poptr2.2_PACid_18234650
+---------ATGGAAAATGGAGGAGAA---------------------------------
+------------------------------------------------------------
+---------------------------------------------GAGAAAGGGAAAAGC
+AATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCACAGAGCTGAGGAAT
+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAA------
+---AATTCCAGGTTCGTTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTAT
+TCT------------------GTTCTTTCTGACACCAACAAGAGGTTTCTTTACGACGTT
+GGTGTTTATGACAGT------------------------GAAGACGACGAAAATGGAATG
+GGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCAAACAAAGCCCCACGAAAACGTG
+------GAGGAGAGCTTTGAGGAATTGCAA------------------GGATTGTTTGAG
+GAGATGTTCCAAGAGGATTTG------GATTCG---------------------------
+---TTTGGGATTGCCTGTCAG---------------------------------------
+------------GCTACTACC---------------------------------------
+------------------------------------TGTGTGTCATACAGCGAAAGCTCC
+AAC------------------------TCAAATGATAAACGTGTTTCTGTC---GATATG
+AACTTGAAGAAG---ACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTC------
+------------GAGAAGTTCTGTTTAGGG---GTGGAA------CACCAGCAATCTTTC
+AAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACC---GGCGGTAGAGAGAGG
+AAAGGCAGGAAACAAGAAGTTTCATCT---GGCTATGATGTCTCCTCCCATGAC---CAT
+GGTATTTCTGCTTCA---------------------------------------------
+>gnl_Soltu3.4_PGSC0003DMP400016105
+---------ATG------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------GGC
+AATGATTATTATGCAGTTTTGGGATTGAAAAAGGAATGCACTGAAACAGAGCTTAGGAAT
+GCTTATAAGAAGCTTGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGG------
+---AATTCGAAGTTTGTAGATGAAGCAAAGAAGAAATTTCAGGCAATTCAAGAAGCATAT
+TCT------------------GTGTTATCGGATGCAAACAAAAGGTTTCTGTACGATGTA
+GGAGTTTATGACTCTGGT------------------GATGATGACGACGAAAATGGCATG
+GGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCAG
+------GAAGAAACCTTTGAGGAATTGCAG------------------GATATGTTTGAC
+GAAATTTTCAATAGTGATAAT------GGGATG---------------------------
+---------TCTTCTTCTTCT---------------------------------------
+------------TCTTCTTCTTCTCGGACTGGAACTCCTTCA------------------
+------------------------------------ATGTGTTCTACTACATCGTCTACA
+TCTTCCAGTGAGACC---TTTTTTACCTTTTCCAACAAAAGAAGTTCAGGT---GAAATG
+AAGTCGGGTAAA------------------------GGCGATTCTTGCCAATTC------
+------------CAAGGATTTTGTGAAGGG---ACA------------------------
+---------GGTGGAGCATCTGGAAAAAGCAATGAAAGAGAA---CGGAGTCGGAGGAAA
+AATTCCAAGAGTGGACGGAAGCAA------------------------------------
+------------------------------------------------------------
+>gnl_Soltu3.4_PGSC0003DMP400016106
+---------ATG------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------GGC
+AATGATTATTATGCAGTTTTGGGATTGAAAAAGGAATGCACTGAAACAGAGCTTAGGAAT
+GCTTATAAGAAGCTTGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGG------
+---AATTCGAAGTTTGTAGATGAAGCAAAGAAGAAATTTCAGGCAATTCAAGAAGCATAT
+TCT------------------GTGTTATCGGATGCAAACAAAAGGTTTCTGTACGATGTA
+GGAGTTTATGACTCTGGT------------------GATGATGACGACGAAAATGGCATG
+GGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCAG
+------GAAGAAACCTTTGAGGAATTGCAG------------------GATATGTTTGAC
+GAAATTTTCAATAGTGATAAT------GGGATG---------------------------
+---------TCTTCTTCTTCT---------------------------------------
+------------TCTTCTTCTTCTCGGACTGGAACTCCTTCA------------------
+------------------------------------ATGTGTTCTACTACATCGTCTACA
+TCTTCCAGTGAGACC---TTTTTTACCTTTTCCAACAAAAGAAGTTCAGGT---GAAATG
+AAGTCGGGTAAA------------------------GGCGATTCTTGCCAATTC------
+------------CAAGGATTTTGTGAAGGG---GTGGAG------CATCTGGAAAAAGCA
+ATGAAAGAGAACGGAGTCGGAGGAAAAATTCCAAGAGTGGAC---GGAAGCAATAGGATG
+GATGCTAAAAGGCAAAAGGTTCTATCA---------------------------------
+------------------------------------------------------------
+>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329
+---------ATGGCACCCCGA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAGAGAAAGAC
+AGTGATTTTTATGCAATTTTAGGGTTGAAGAAGGAGTGCTCTGCTTCAGATCTCAGAAAT
+GCGTACAAAAGGCTCGCACTTCGGTGGCATCCAGATAGGTGCTCTGCCTCAGGG------
+---AACACAAAGTTTGTGGAGGAATGCAAGAAAAAGTTCCAGGCCATTCAGCAGGCTTAT
+TCC------------------GTGCTCTCGGATGCAAATAAGAGGTTTTTGTACGATGTT
+GGAGCATATGGAAGT------------------------GACGATGACGATCAGGGAATG
+GGTGAATTTCTTGGGGAGATGGCGGTAATGATGAGCCAGACAAAGCCCAGTGAAAAAGGG
+------CCGGAGAGCTTTGAGGATCTACAG------------------AACTTGTTTCAG
+GAGATGTTCGAAAGGGATCTG------GACATG---------------------------
+---TTTAAGTCATCGACCTCCCAC------------------------------------
+------------AACAACAACAATGATAACAACAATAATAAT------------------
+------------------------------------CATAGGAGTAGTGACAATAATAAT
+TGTAGTAGTGTTCAT---TGTTTTAGTAACACCAACAAGAGGAATTGCTCG---GATATG
+AATGCCGGAGAA---GCCTCGGAGGTCGGGCGCTTTGCTTTCTCATGCTATGCGACAGAG
+TTCCTGCACAAGCAAACTTTCTCCGTCGGG---GCGGAT------------------GAT
+GTGCGATCGGAGTCG------------------------------AGCAACAAGAGACGA
+AACGGGAGGAAACAGAAATCCACCTCC---TCTTCAAGGAAAAGT---------------
+------------------------------------------------------------
+>gnl_Aquco1.0_PACid_18141277
+---------ATGGCTAGT------------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAAGAAGAAGCA
+AGTGATTTCTATAAAGTTTTGGGATTGAAAAATAACTGTTCTTCCTTGGAGCTCAGGAAC
+GCTTATAAGAAGCTTGCACTGAAATGGCATCCGGATCGTTGTGCTGCTTCAGGA------
+---AACTCAAAGTTTGTTGAAGAAGCAAAGAAGAATTTTCAAGCAATACAAGAAGCTTAT
+TCT------------------GTTCTTTCAGATGAGCAGAAACGATTTATGTATGACGTT
+GGTGTCTACGATAAAGAT------------------GATGATGACGAAAATGAAGATATG
+GGCGATTTTTTAGGTGAAATGATGTCTATGATGAAGCAAGAAAATACTAGTGCGGATGGA
+------CAACAAAGTTTTGAAGACCTTCAA------------------AACCTATTCCAG
+GAAATGGTTCAAAATGACAAA------GAATTT---------------------------
+---TATAATCCAGCCTCTCAA---------------------------------------
+------------AACTCGTCGATATATAATGCTAGTAACAACATGTTCTCCTTCTCTAAT
+AACGAGAACTTAAACAATGCTAGCAACAACACATTCTCCTCTTTTTATAATGAGAACCTA
+AAC------------------------AGCAGCAACAAGAAAAGTTGCTCA---AGTATG
+AGCGCAGAAAAT------ACCAAGGTGGACTTTAACATGGAATCATTGGACTTC------
+------------CGCAGCTTTTCTATTGGG---TTAGAA------GGCGGTACATCATTT
+CAAAACTCCAAAGGGAGAGGA------------------------GTAACGGGTAGGCGG
+ACAGGAAGGAAACAGAAGGGGTCGTCC---TGTAATGATATGTCTTCCCATGAT---TCT
+AAGATTTTGGCG------------------------------------------------
+>gnl_Arath10_AT3G14200.1
+---------ATGGCGTCCAGTAAT------------------------------------
+------------------------------------------------------------
+---------------------------------------------AGCGAGAAGATCAAC
+GAGAATCTGTACGCTGTTCTGGGTTTGAAGAAGGAATGTTCTAAGACGGAGCTCCGTTCT
+GCTTATAAGAAGCTTGCTCTCAGATGGCATCCAGATCGTTGTTCGTCA------------
+------ATGGAGTTTGTAGAAGAAGCAAAGAAGAAATTTCAGGCAATCCAAGAAGCCTAC
+TCT------------------GTTCTGTCTGACTCCAACAAGAGGTTCCTGTATGATGTT
+GGTGCTTATAATACTGAT------------------GATGATGATGACCAAAACGGAATG
+GGAGATTTCTTGAACGAAATGGCGACTATGATGAATCAATCCAAGCCTAGTGATAATAAC
+---ACAGGGGACAGTTTTGAACAACTACAA------------------GATCTGTTTAAT
+GAGATGTTTCAAGGAGACGCT------GCAGCA---------------------------
+---TTCCCATCATCA---------------------------------------------
+------------------TCGTCCTGCTCCACTTCAAATTTC------------------
+------------------------------------ACTTCATCTCGTAGTTTTGTATTC
+GAT------------------------ACAAATTCTCAGCGGTCATCTTCGTTTGCGACA
+AGTTCGATGGGG------ATGAATAATGATCCTTTCGGATATGACCCGAGAGCT------
+------------CATTCCTTCTCTTTAGGG---GTGGAC------CATCAGCAAGAGTTC
+AAGAAAGGGAAAAAC------------------------------AATGGCGGAAGAAGA
+AACAGGAGAAAGAACAATGTTCCATCGGCTGGTCACGAAACGTCGTCGTCAAACAACTAT
+GGAGTCCCCACCTCA---------------------------------------------
+>gnl_Bradi1.2_Bradi3g60090.1
+---------ATGGCCACCGGGGGC------------------------------------
+------------------------------------------------------------
+---------------GACAAGTGCGGCGGAAAGCCGGCGGCC---GCGGGGGTGGGCGGC
+GGTGACCTGTACTCTGTGCTGGGCGTCAACAAGGAGTGCTCCGACGCCGACCTCAAGGTC
+GCCTACCGGAAGCTCGCCATGAGATGGCATCCGGATAGATGCTCCTCCTCCAGC------
+---AGCACCAAGCACATGGAGGAAGCAAAAGAGAAGTTCCAGGAGATCCAGGGCGCCTAT
+TCC------------------GTCCTCTCCGATGCCAACAAGCGCTTCCTCTATGACGTG
+GGGGTATATGAAGAACATGAAGAA---------GAAGATGATGACACTCTGCAGGGGATG
+GGGGACTTCCTTGGTGAGATGGCCCATATGATGAGCCAGACGCAGCCAGCGAGA------
+------CAGGAAAGCTTTGAGGAGCTCCAG------------------CAGCTCTTCGTG
+GACATGTTCCAGTCTGATATT------GAATCGGGA------------------------
+---TTCTGCAACGGACCTGCCAAG---GACCATGACCCAGTCCAAAGACAGACGCGAACA
+TTCTCGACCCCTCCTTCGCCATCGCCATCTCCACCGCCTCCA------------------
+------------------------------------CTAGCTACAGTGGACGAAGCGGCA
+TCA------------------TGTAATGGCATCAATAAGCGTGGCTCATCA---GCAATG
+GGCTCTGGGAAG---CCTCCAAGAGCTGGTGAAGTGAGTGGGGGTCACGGCCAG------
+------------TCTGAGTTCTGTTTCGGG---ATGAGC------GACGCCAAGCAAGCG
+CCGAAGGCGCGAGGCGGGAAC------------------------GCTAGCAGGAGAAGG
+AACGGCCAGAAGCAGAAACTGTCGTCG---AAGCACGACGTCTCCTCCGGCGATGAGATG
+CCGAGACCA---------------------------------------CATGCAGCAGTA
+>gnl_Carpa1.181_PACid_16420351
+---------ATGGCGGATGGA---------------------------------------
+------------------------------------------------------------
+---------------------------------------------GAAGACAAGAACAAC
+AGTGATTTGTATGCGGTTCTTGGATTGAATAAGGAATGTACTCCAGCAGAGCTCAGGAAC
+GCTTATAAGAAACTTGCAATGAGATGGCATCCAGATCGCTGTTCCGCGTCGGGG------
+---AATTCAATGTTTGTGGAAGAAGCAAAGAAGAAATTTCAGGCAATCCAAGAAGCCTAC
+TCT------------------GTTCTTTCTGACGCAAACAAGAGGTTTCTGTACGACGTC
+GGAGCTTACGAAAGT------------------------GATGACGACGAAAATGGAATG
+GGTGATTTTTTAAACGAAATGGCAGCCATGATGAGCCAAACAAAGCCTAATGAGAATGGG
+AATGCACAAGAGAGCTTTGAAGAATTGCAA------------------GAGTTGTTTCAA
+GAGATGTTTCAAGGGGATATGGGATTCAACACA---------------------------
+---TTTGGATCTAGTTCTCAGCCT------------------------------------
+------------ACTACTTCTTCGTGTTCTGCTTCCTCTGCA------------------
+------------------------------------TATGCAACCTGTAGCGAAACCTCC
+AAT---------------------CCTAACAACAACAAGCGCAATTCATCA---GAAATG
+AATTATGGCAAG---AAAAAGGTAGATGATTCTTCAGGGTTTCATGCTCATTTC------
+------------CAAACCTTTTGTTTAGGG---GTGGAA------CAGCAGCAAGATTTC
+AAGAAGGGGAAGGAAGCAAGAGGAGGAATTCGAGGAAAACCC---GGAGGTAGTAGGAGG
+CAGGGAAGGAAACAGAAGGTTTCATCT---CGCCACAATGTCTCATCCAATGAC---TTG
+GGCATTTCTGCTTCC---------------------------------------------
+>gnl_Frave2.0_gene05408
+---------ATGGCGGGGGGAAAGTGGGTCCCCCCACCCCTGTCCCAGTTTCATCTTCAC
+ATAAAGAGGTTCCGTCGACGTCAGAAAGTCTCTGGATCCAGTGGAAACACAGAACCTTCT
+GGATACACAGACTGCAAAAATATCTCCAATCGA---------AGAATGGAAGAGAAAGGC
+AATGACTTTTATGCTGTTATGGGGTTGAAGAAGGAATGCTCTGACTCGGAGCTCAGGAAT
+GCTTATAAGAAACTTGCACTGATATGGCACCCAGATCGTTGCTCTGCCTCAGGA------
+---AATTCAAAGTTCGTGGAAGAAGCCAAGAAGAAGTTTCAGGACATTCAACAAGCCTAT
+TCT------------------GTTCTGTCCGACGCCAACAAGAGGTTTCTGTACGATGTA
+GGAGCTTATGAAAGT------------------------GATGATGACGAAAATGGAATG
+GGTGATTTTTTAAACGAGATGGCGGTGATGATGAGCCAGACTAAGCCGAATGAAAATGGA
+------GGAGAGAGCTTCGAACAATTGCAG------------------GAGCTCTTTGAA
+GAAATGTTTCAGGGGGATATT------GAGGGC---------------------------
+---TTTAGCTCCTGCTCTCAGCCT------------------------------------
+------------CCTACTTCCTGTTCTACTTCCTCATCTTCA------------------
+------------------------------------TACGCATTGTACTGTGAAAATTCT
+ACT------------------------CCCAGTAACAAACGTAATTCCTCC---GCAATG
+AATTATGGCAAC------GCAACCCTGGACAGTTCTGGTTTTGATGCTCATTTT------
+------------CACAATTTCTGTGTAGGG---ACA------------------------
+---------GGCGGGAAGCCAGCAAAGGATCGGGAAGGGGAT---GCCAGGAAGAGAAAG
+GATTCCAGGAGGAGTAACCGG---------------------------------------
+------------------------------------------------------------
+>gnl_Mimgu1.0_PACid_17694730
+---------ATGGCTGCTGAT---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAAGAGAAAAGC
+AGCGATTTTTACGGCGTTCTGGGGCTGAGGAAAGAATGTACGGCGGCGGAGCTCAGGGTT
+GCCTACAAGAAACTTGCAATGAAATGGCATCCAGATCGTTGCTCTGCTTCTGGG------
+---AATTTAAAGTATGTGGAGGAAGCAAAGAACAAGTTTCAAGCTGTCCAACAGGCCTAT
+TCT------------------GTGCTTTCCGATGCCAACAAAAGGTTTCTCTACGACGTA
+GGAATCTACGATTCTGAA------------------GACGATGCTGACGAAAACGGTATG
+GGTGATTTCTTGAATGAAATGGTAGCAATGATGGGCCAAAGTAAACCAAATGAAAATAAA
+------AACGAGAGCTTCCAAGAATTGCAA------------------GATCTATTCGAG
+GAAATATTCAACAATGACGCG------GAAGAGGTT------------------------
+---TTCAAGATTCCTCCTCCGCAC------------------------------------
+------TTTCCGTACCAAGATTCTTGCAGCGAGACCCGCACC------------------
+------------------------------------------------------------
+---------------------------GCATCGAACAAGAGGAACGCCCGC---GAAATG
+GGCTCCGTAAAT---------------TTCAGTAATATCGAAGCCACACCATTT------
+------------GAAGGGTTCTGCATAGGG---GAAAATGTAATTTTTGGGGGAGAGAGA
+ATACAAACGAGGCCCGGA---------------------------GGAGGTAGTAGGAGG
+ACG------AAGCCGAAGATTTCGACA---TCGATCGAT---------------------
+------------------------------------------------GGTTTAATTAGT
+>gnl_Nelnu1.0_NNU_010544-RA
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---ATGAACCTGTTGTTGCAGAAATGGCATCCGGATCGATGCTCCTCGTCGGGA------
+---AACTCTAAGTTCGTGGAAGATTCAAAGAAGAAATTTCAGGCAATTCAAGAGGCTTAT
+TCT------------------GTTCTATCCGACGAGAATAAGCGATTTCTTTACGACGTT
+GGAGTTTACGACTGCGACGAC---------------GATGACGATGACGAAAACGGAATG
+GGAGAATTTTTGGGGGAAATGGCGACTATGATGAGCCAAATTAAACCCAGCGAGAACGGG
+------CCGGAGAGTTTGGAGAAGCTGCAG------------------GAACTGTTCGAG
+GAAATGTTCCAAAGGGACATG------GATGATGGT------------------------
+---TTCTTCTCCCCCTCCCCCCAATGCGCT------------------------------
+---------TCTTTTTCTTCGTCTTGCTCATCTTCTTCGTCG------------------
+---------------------------TCGACGACTTATTTTTCATATAATAACAACAAG
+CAC---------------------------GACAATAAAAGGAATTGCTCC---GACATC
+AGTTCTATGGAC------GATTTCTACACATTTGGCACGGATTCTATACAATTC------
+------------AGCAATTTCTGCATTGGG---GTGGAA------GGAGGAGAA---GAT
+TCAAAAGTAAGAGGAGGAAAG---------------------------TCAAGGCGGAAG
+AGCAACAGGAGACAAAAAGTTTCATCGTCTAAACACGATCCGTCGTGCCGT---------
+------------------------------------------------------------
+>gnl_Solly2.3_Solyc03g123560.2.1
+---------ATG------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAAGACAAAAGC
+AATGATTATTATGCAGTTTTGGGGTTGAAGAAGGAATGCACTGACACAGAACTTAGGAAT
+GCCTATAAGAAGCTTGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGG------
+---AATTTGAAGTTTGTAGATGAAGCAAAGAAGCAATTTCAGGCAATTCAAGAAGCATAT
+TCT------------------GTGTTATCGGATGCAAACAAAAAGTTTTTGTACGATGTA
+GGAGTTTATGACTCTGGT------------------GATGATGACGACGAAAATGGCATG
+GGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCAG
+---GGAGAAGAAACCTTTGAGGAATTGCAG------------------GATATGTTTAAT
+GAAATGTTCAACAGTGATAAT------GGAACG---------------------------
+---TTTTCTTCTTCTTCTTCT---------------------------------------
+------------TCTTCTTCTTCTTGGACTGGAACTCCTTCA------------------
+------------------------------------ATGTGCTCTACTACATCATCTACA
+TCTTCAAGTGAGACT---TTTTTAACCTTTCCCAACAAGAGAAGTTCAGGT---GAAATG
+AAGTCGGGTAGT---------------AGTGTAAGAGGCGATTCTTGCCAATTC------
+------------CAAGGATTTTGTGTAGGG---GCA------------------------
+---------GGTGGAACTTCTGGAAAATGCAATGAAAGAGAA---CGAAGTTGGAGGAAA
+AATTCCAAGAGTGGACGGAAGCAT------------------------------------
+------------------------------------------------------------
+>gnl_Sorbi1.4_PACid_1968370
+---------ATGGACGCCGGGGGA------------------------------------
+------------------------------------------------------------
+---------------GAGAAGTTCAGCGACGCGGCGGCGGCGGAGGGCGGTGAGGGCGGC
+GGCGACCTCTACGCCGTCCTCGGGCTCAAGAAGGAGTGCTCCGACGCCGACCTCAAGGTC
+GCTTACCGGAAGCTCGCCAAGAAATGGCACCCGGACAAATGCTCCTCCTCCAGC------
+---AGCGTGAAACACATGGAGGAAGCCAAGGAGAAGTTCCAAGAGATCCAGGGCGCCTAT
+TCC------------------GTACTCTCTGACGCCAATAAACGGCTCCTCTACGATGTT
+GGAGTATACGACGATGAGGAC---------------GACGAGGATAGCATGCAGGGGATG
+GGTGACTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGTGCGGCCGACGAGG------
+------CAGGAAAGCTTTGAGGAGCTGCAG------------------CAGCTTTTTGTG
+GACATGTTCCAGTCTGATATT------GATTCAGGA------------------------
+---TTCTGCAACGGGTCTGCTAAG---GATCAAGTTCAGGGGCAAGCCAAAAGTAGAACA
+TGCTCGACCTCACCTTCATCATCACCGTCCCCACCTCCTCCT------------------
+------------------------------CCTACTATAGTAAAGGAGGCAGAGGTGTCA
+TCA------------------TGTAATGGCTTCAATAAGCGGGGTTCATCA---GCAATG
+GACTCAGGGAAG---CCTCCAAGGCCT------GTTGAAGGCGGTGCTGGTCAG------
+------------GCTGGATTTTGTTTTGGG---GTGAGC------GATACGAAGCAAACG
+CCGAAGCCGAGAGGTCCGAAC------------------------ACCAGCCGGAGGAGG
+AACGGCCGGAAACAGAAGCTGTCATCC---AAGCACGATGTTTCATCTGAAGATGAAACG
+GCCGGTTCC---------------------------------------------------
+>gnl_Thepa2.0_Tp3g12470
+---------ATGGCGTCGAACAAT------------------------------------
+------------------------------------------------------------
+---------------------------------------------AGCGAGAAAGGAAAC
+GATGATTTGTATGGTGTTCTGGGCTTGAAGAAGGAATGTACGACGACGGAGCTCCGTACT
+GCTTATAAGAAGCTTGCTCTAAGATGGCATCCAGATCGTTGTTCGTCAATGGGG------
+---ACTCCAGAGTTTGTAGACGAAGCAAAGAAGAAGTTTCAGGCAATCCAAGAGGCCTAT
+TCT------------------GTTCTGTCTGACTCCAACAAGAGGTTCCTCTATGATGTT
+GGAGCTTATAACAGT---------------------GATGATGAAGACCAAAACGGTATG
+GGAGATTTCTTGAACGAAATGGCGGCAATGATGAATCAGTCCAAGCCTAGTGAGAATAAC
+---TCAGGGGACAGTTTTGAGCAGCTACAA------------------GATCTGTTTAAT
+GAGATGTTTCAAGGAGACGCT------GCAGCA---------------------------
+---TTCTCATCATCATCATCA---------------------------------------
+------------------TCATCTTGCTCTGCTTCGACTTTT------------------
+------------------------------------ACTTCCTCTTGTAGCTTTGTCTTT
+GAC------------------------ACAAATAGTCAGCGGTCACCGTTT---GAGACA
+AGCTCAATGGGG---------ACTAATGATCTTTTTGGATTCGATCACAGTGCT------
+------------CACACCTTCTCTTTAGGG---GTGGAA------CATCAGCAGGATTTC
+AAGAAGGGGAAGAAC------------------------------AGTGGTGGAAGAAGA
+AACAGAAGGAAGAACAATGCTCAATCGGCTGCTCACGAGACGGCGTCGTCCAACAACTAT
+GGAGTCCCCACTTCA---------------------------------------------
+>gnl_Theca1.0_Tc06_g010450
+---------ATGGCAAATGGA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAAGAGAAAAAC
+AATGATTTTTATGCAGTTTTGGGGTTGAATAAAGAATGCACTCCGACAGAGCTCAGGACT
+GCTTATAAGAAACTTGCCCTGAGATGGCACCCTGATCGTTGCTCAGCTTCGGGA------
+---AATTCAAAGTTCGTGGAAGAAGCCAAGAAGAAATTTCAGGCCATTCAACAAGCCTAT
+TCT------------------GTTCTGTCTGACTCAAACAAGAGGTTTCTGTACGACGTA
+GGAGCTTATGACAGT------------------------GATGATGACGAAAATGGAATG
+GGAGATTTTTTGAACGAAATGGCAGGGATGATGAGCCAGACAAAATCTAATGAAAATGGA
+------GGGGAAAGCTTCGAGGAACTACAG------------------GAATTGTTTGAA
+GAAATGTTCCAAGCGGACATT------GATTCA---------------------------
+---TTTGAGTCTACTGGTCAG---------------------------------------
+------------TCCACTCCTTCCTGCTCTGCTTCATCTTCG------------------
+------------------------------------TTTGGGTCATATGGTGAAAGTTCC
+AGC---------------------------TCCAACAAGCGGAATTCCTCT---GAAATG
+AGTTCTGTGGAG---ACTAGGCTGGAGAGTTCTTCTAGCTTCGATGCACAATTT------
+------------CACAGTTTTTGTCTCGGG---GTGGAA------CACAGGCAAGATATC
+AAGCAACACAGAGGAGCCAGAGGAGGAATGCGAGGAGCAGCCGGCGGTAGTAGACGGAGA
+AATGGCAGGAAACAAAAGGTTTCATCT---GGCCATGATGTTACTTCCAACGAC---TGT
+GGCATTTCTGCTTCA---------------------------------------------
+>gnl_Vitvi12X_PACid_17827068
+---------ATGGCCGCCGGA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAAGAGAAGAGC
+AATGATTTTTATGCCGTTCTAGGGTTGAAAAAGGAATGCACCGCCTCCGAGCTCAGAAAT
+GCGTACAAGAGACTTGCCCTGATGTGGCACCCAGATCGTTGCTCCTCGTCGGGA------
+---AACTCGAAATTCGTGGAAGAAGCGAAGAAGAAATTTCAGGCCATACAAGAAGCCTAT
+TCA------------------GTTCTCTCTGATGCGAATAAAAGGTTTCTGTACGACGTT
+GGAGCCTACGACAGC------------------------GATGATGACGAAAACGGAATG
+GGGGATTTTTTGAATGAGATGGCGGTTATGATGAGCCAAACCAAGTCCAATGAAAATGGG
+------AAGGAGAGCTTTGAGGAGTTGCAG------------------GAGCTCTTTGAG
+GATATGTTCCAAAGGGATGTC------GACGCA---------------------------
+---TTCAACTCTGCCTCTCATCAC------------------------------------
+------------CCCATGAACTCTTTCCCCAGTTCTACTTCC------------------
+------------------------------------ACTTCTTCCTACTGCGAAAGCTCC
+AAT------------------------GCCAACAACAAGCGGAATTCGGCT---GAAATG
+GGCTCTGGAAGGATGATGAGTGCAGGGGAGTCCTCTGCTTTTGATGCCCACTTT------
+------------CAGAGCTTCTGCTTTGGG---ACA------------------------
+---------GGCGGCACGCCAGGGAGATTTCAGGAGGGGGAA---AGGAGCAAGAGGAGG
+AATTCCAGGAGGAGCCAACGG---------------------------------------
+------------------------------------------------------------
+>gnl_Selmo1.0_PACid_15401289
+---------ATG------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------GAGAAGAGGAAA
+GAGGATCCCTACACTGTTCTTGGTGTCCAAAAGTCGAGTTCTAGCTCGGAAATTCGCTCC
+GCTTATCGGAAGCTCGCCATGAAATGGCATCCAGATAAG---------------------
+---CAACACTCTTTAGAGGATCAAGCAAAAGCGAAGTTCCAGGGCATTCAAGAAGCTTAT
+TCA------------------GTGCTATCCGACGACAAAAAAAGAGTTCTTTATGATTCG
+GGACTTTATGACGAGGGA------------------GATGACGAG---------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------GTGAGT---------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+>gnl_Orysa6.0_PACid_16864430
+---------ATGGCCCGCGGCGGCGGC---------------------------------
+------------------------------------------------------------
+------------GGC------------------------------GGCGGCGGCGCGGAC
+GCCGACCTGTACGCCGTCCTCGGCCTCAGCAGGGAGTGCACCGACGCCGACCTCAGGCTC
+GCCTACCGCAAGCTCGCCATGATATGGCATCCGGACAGGTGCTCGGTGGCCGGCGGCAGC
+GCGAGCGCGGCGGGCGTCGACGAGGCCAAGGAGCGATTCCAGGAGATCCAGGGCGCCTAC
+TCC------------------GTGCTCTCCGACTCCAACAAGCGCTTCCTCTACGACGTC
+GGCGTCTACGACGGCAACGACGGCGACGACGACGACGACGAAGCAGATCTGTCGGGGATG
+GGCGATTTCCTCGGCGAGATGGCGCAGATGATGAGCCAGGCGACGCCT------------
+------GCGGAGAGCTTCGAGGAGTTGCAG------------------CAGCTGTTCGTG
+GACATGTTCCAGGACGACATC------GACGCCGGC------------------------
+---CTCTGCCAGTCGACGCCG---------------------------------------
+------------CCGCCGCCGTCATGGCCGTCGCCTCCGGCG------------------
+---------------------------------------GCCGCCAATGCACGATCGCCG
+GCGGCGGCGGCGACT---TCACGCAAGGGCGTGAACAAGCGGTGCTCACCG---GCGGCG
+ATGGACATGGAC---------------TCCGGTTTGAGCAGCCTGCTGGGCATT------
+------------TCGGGCTTCTGTTTCGAG---GCGCCA------TGGACGTCGCAGGAC
+GCGAGCACTGCCGCCGGCGGTGGC---------------------GGCGGCAAGAGGAGA
+AAGCAGAGGCCGCCGCCGGCG---------AGCCACAACGTG------------------
+------------------------------------------------------------
+>gnl_Sorbi1.4_PACid_1982925
+---------ATGGCTGCTACAAGTCAC---------------------------------
+------------------------------------------------------------
+------------TGCGGCAACATCCAGGACCAGGACGAAGAAGCTTCGGCTCCTGGCGCC
+GCCGACCTCTACGCCGTGCTCGGGCTCAACAGGGAGTGCACCGACGCCGAGCTCAGGGTC
+GCGTACCGGCGGCTCGCCATGATATGGCATCCGGACAGGTGCTCGGCGTCCGGC------
+AGCTCGCCGGCGCGCATGGAGGAGGCCAAGGAGCGGTTCCAGGAGATCCAGGGCGCCTAC
+TCC------------------GTGCTCTCCGACTCCAACAAGCGGCTCCTCTACGACGTC
+GGCGTCTACGACAGCGACGAC---------------GACGAGGCTGACCTGTCGGGGATG
+GGCGACTTCCTCGGAGAGATGGCCGACATGATGAGCCAGGCCACGCCA------------
+------ACGGAGACCTTCGAGGAGCTGCAG------------------CAGGTGTTCGTG
+GACATGTTCCAGGACGACCTGGAC---GACGCCGGC------------------------
+---TTCTTCGGCGGGCTTCCGACG---ACGGGCCGCAGGGCCCAGGCA------CCCAGC
+ACCTCGCTGCCGCCGTCGGTGTCGTCGTCGCCGTTGCGGCCG------------------
+------------------------------ACGCCTGCCGCTGGAAGAAGCAAGGGTCCG
+CAAGCGACGCCGTCGTCGTCGTTTAAAGGCGTCGAGAGGCGGGGTTCGACG---TCGACG
+GCGAAACGGCCGAGGCCCAACGGGTCGGCGGGCCTGGAATCGGACCTGGGCCTC------
+------------TCCGGATTCTGCTTCATG---GTGAGT------AAGGAGATGAGCAAG
+TCGAAGGAGAGGCAAGCGGTA---------TGGGCCAGTGAC---GACGGTGACAGGAGC
+ACCGATGGCAAGCAGAGGTTGTCGACG---AGCCGCGATGTCTCCGGTGGTGGG---ATG
+TCACGCTCACTGCAGGGCCAAAGCAGCAAAAACTTGTTGCAGTGTATGGCCTCTAAGTCT
+>gnl_Medtr3.5_Medtr8g022310.3
+---------ATGGCTAACGAA---------------------------------------
+------------------------------------------------------------
+------------------------------------------------GGAAACAAAAGC
+AATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAGGAAT
+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGG------
+---AATGTGAAGTTTGTGGAAGAAGCTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTAT
+TCT------------------GTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTT
+GGAGTTTACGACAGT------------------------GATGATGACGAAAATGTAAGG
+CACTTGTTT---------------------------------------------------
+---------CACACCATTCATGAGTTGGGG------------------ACCCTCTTTTGC
+GTTATGTTTTGTTTCTTCATTTCCTTGAGG------------------------------
+------GGAGAG------------------------------------------------
+---------------------------AAGAGAAGCAACCTT------------------
+------------------------------------AATTTAACCTTTTCACTTTCACAT
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+>gnl_Nelnu1.0_NNU_000115-RA
+---------ATGGAGGTGGAC---------------------------------------
+------------------------------------------------------------
+---------------------------------------------TCCCATCGATCATCT
+CCATCTTACTACACCATCCTTGGTGTAGATCAGAATTCCTCCGCTTCCGAGATACGCAAT
+GCTTACAGGAAGCTCGCGATGCAATGGCATCCAGACAAATGGACGAAAACTCCG------
+---------TCGCTCTTAGAGAAAGCCAAGAGTAAATTCCAGCAAATCCAGGAGGCTTAT
+TCGGGTGGGTTACTCGTTTTCATGTTATCGGATCAGGGGAAGAGAACACTGTATGATGTC
+GGTCTGTATGACCCGGACGAT---------------GAAACGAATGACGAGGTGGGGCTT
+CGCAGATTT------CATGCAGGAGATGATATCTCTCATGAACGATGT------------
+------GAAGAAACAGGAGAAGAAATACAGCTTGGAGGAACTACAGGAGATGTTAGTGGA
+AATGTCACAAGGGCTGGAGTT------GAAGATGGAGAGTGCTGGTGGTGTGTGGTTGTT
+AGATGGAGCTGCAGCCTCAAGGAG------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------GAGCTC
+AAAGAGGGCCAG------------------------------------------------
+------------ATGGGAATCATCAGCGAG---TCCGAC------GACGCT---------
+------------------------------------------------------------
+------------------------------GGACACGACACACCTTCTCTCCCCCACTTG
+CACGGTTCAGAGCTG---------------GAATTGTTAGGAAGAACCGGCTGTTGCAAT
+>contig_7
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------GAGAATGAGTGGTCTGGG
+GCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGA
+------ACCGGAACTTTTGAAGAACTGCAA------------------CAATTGTTCGAT
+GAAATGTTTCAGAGCGACATC------GAGTCC---------------------------
+---TTCAATGGTTGTTCTTCATCA------------------------------------
+------------TCCAATGAAACATGTAGC------------------------------
+------------------------------------------------------------
+---------------------------AACTCGAACAAGAGGAATTCCATT---GAGTCG
+AGCTCGGCTAAT------------------------------------------------
+TTCAGACCCGAAAATGGAAACGAAAGCGGC------------------------------
+---------------------------------------GAG---ATTAGCGGGAAGAAG
+AATACTAGGAAAGGTAAAGGTGACGNN---------------------------------
+------------------------------------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/38889.faa	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,14 @@
+>gnl_Mimgu1.0_PACid_17675619
+MAETKTKVLKFDAEEDVAVALAKYTAYLSEKYIKEKNSFSVVLSGGTLIDTLRKLVEFPYKDSVDWSKWLIFWVDERVVP
+LDHEDSNYLLAYRGFLSKVPIPPSNIYAINDKKSPEGAADDYEERIKNLVEEKTLPISDSGFPKFDLMLLGMGPDGHVAS
+LFPSHNQRYEKKRWVTFITDSPKPPPPRITFTFPVINSASDIAMVVTGAELADTTKKALGNEKHTLPPLPCTEVSAEREL
+TWFLDKDAASKL
+>gnl_Solly2.3_Solyc06g053200.2.1
+MATQKGKKTVLKFDSEEDVSKALAKYTAELSEKFIKQKGSFTVVLSGGSLIDTMRKLVEPPYKDSIDWSKWWIFWVDERV
+VPLGHDDSNYKLASDGFLSKVPIPSSNIYAINDKESPEGAAADYEARLKQLIESKVLPLSAITGFPKFDLMLLGMGPDGH
+VASLFPLHPHRHEKERLVTFITDSPKPPPPRITFTFPVINSASEIAMVVTGAELAHMVDVALGNAPPPDGIPPPCTEVSA
+EEELTWFLDKDAASELQTSR
+>contig_2
+XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK
+WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS
+QLLNYVRFDD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/38889.faa.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,18 @@
+>gnl_Mimgu1.0_PACid_17675619
+MAETKTK--VLKFDAEEDVAVALAKYTAYLSEKYIKEKNSFSVVLSGGTLIDTLRKLVEF
+PYKDSVDWSKWLIFWVDERVVPLDHEDSNYLLAYRGFLSKVPIPPSNIYAINDKKSPEGA
+ADDYEERIKNLVEEKTLPISD-SGFPKFDLMLLGMGPDGHVASLFPSHNQRYEKKRWVTF
+ITDSPKPPPPRITFTFPVINSASDIAMVVTGAELADTTKKALGNEKHTLP---PLPCTEV
+SAERELTWFLDKDAASKL--------
+>gnl_Solly2.3_Solyc06g053200.2.1
+MATQKGKKTVLKFDSEEDVSKALAKYTAELSEKFIKQKGSFTVVLSGGSLIDTMRKLVEP
+PYKDSIDWSKWWIFWVDERVVPLGHDDSNYKLASDGFLSKVPIPSSNIYAINDKESPEGA
+AADYEARLKQLIESKVLPLSAITGFPKFDLMLLGMGPDGHVASLFPLHPHRHEKERLVTF
+ITDSPKPPPPRITFTFPVINSASEIAMVVTGAELAHMVDVALGNAP--PPDGIPPPCTEV
+SAEEELTWFLDKDAASEL----QTSR
+>contig_2
+------------------------------------------------------------
+------------------------------------XLSKVPIPSNNIYAINDKKSPEDA
+ADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTF
+ITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEV
+SAEGEVTWFLDKDAASQLLNYVRFDD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/38889.fna	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,30 @@
+>gnl_Mimgu1.0_PACid_17675619
+ATGGCCGAAACCAAAACAAAAGTACTGAAATTCGACGCGGAGGAAGATGTGGCCGTCGCTCTAGCAAAGTACACCGCCTA
+TCTCTCCGAAAAGTACATCAAGGAAAAGAATTCTTTCTCGGTGGTTCTCTCCGGCGGCACCCTAATAGATACACTCAGGA
+AACTAGTAGAGTTTCCATACAAGGATTCTGTGGATTGGTCGAAATGGCTGATATTTTGGGTTGACGAGAGAGTGGTTCCT
+CTTGATCATGAAGACAGCAACTACTTACTTGCATACCGTGGTTTTCTTTCAAAGGTACCTATTCCTCCAAGCAACATTTA
+CGCAATCAACGACAAGAAGTCTCCGGAAGGTGCAGCCGATGATTACGAGGAGCGTATCAAGAATCTGGTCGAGGAAAAAA
+CCCTACCTATTTCAGACAGTGGCTTCCCTAAATTCGACCTTATGCTTCTCGGAATGGGGCCCGATGGCCACGTGGCGTCT
+CTTTTCCCCTCTCACAATCAACGGTACGAAAAGAAACGGTGGGTGACATTCATAACTGACTCTCCCAAACCGCCGCCACC
+TAGGATCACTTTCACATTCCCAGTCATCAACTCTGCTTCGGACATTGCAATGGTGGTCACTGGTGCTGAGCTGGCGGATA
+CTACGAAGAAAGCATTGGGAAACGAGAAGCATACTCTTCCTCCTCTTCCTTGTACTGAAGTTTCGGCTGAGAGAGAGCTC
+ACTTGGTTCTTGGACAAAGATGCTGCTTCTAAACTG
+>gnl_Solly2.3_Solyc06g053200.2.1
+ATGGCAACCCAGAAAGGGAAGAAGACGGTGCTAAAATTCGACTCCGAAGAAGATGTATCAAAGGCACTTGCTAAATACAC
+TGCTGAGCTATCGGAAAAATTCATCAAACAAAAAGGTTCTTTCACTGTTGTGCTCTCTGGTGGTTCTCTTATCGATACCA
+TGAGGAAATTGGTAGAGCCGCCGTACAAAGACTCAATTGATTGGTCGAAATGGTGGATTTTTTGGGTAGACGAAAGAGTG
+GTTCCTCTAGGTCACGATGATAGCAATTATAAACTTGCTTCGGATGGGTTTCTTTCTAAGGTTCCGATCCCCTCTTCTAA
+CATTTATGCGATTAATGACAAGGAGTCACCTGAGGGTGCAGCTGCTGATTACGAAGCTCGTCTGAAACAATTGATTGAGA
+GCAAAGTTCTTCCGTTATCAGCAATTACTGGATTCCCCAAATTTGATCTTATGCTATTAGGTATGGGGCCAGATGGACAT
+GTAGCGTCTTTGTTTCCTTTGCATCCTCACCGCCACGAGAAGGAGCGGCTGGTCACCTTCATTACAGACTCACCAAAACC
+TCCTCCACCAAGGATTACTTTCACCTTTCCGGTAATTAATTCGGCTTCAGAGATAGCAATGGTGGTCACAGGAGCAGAGT
+TAGCTCATATGGTTGATGTCGCTTTGGGTAATGCGCCTCCTCCTGATGGAATTCCTCCCCCTTGTACTGAGGTTTCAGCT
+GAAGAGGAACTGACCTGGTTTTTAGACAAGGATGCTGCATCAGAACTACAGACCTCTAGA
+>contig_2
+NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA
+CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC
+TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA
+TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC
+GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC
+CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA
+CAACTGTTAAATTATGTGCGCTTTGATGAT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/38889.fna.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,45 @@
+>gnl_Mimgu1.0_PACid_17675619
+ATGGCCGAAACCAAAACAAAA------GTACTGAAATTCGACGCGGAGGAAGATGTGGCC
+GTCGCTCTAGCAAAGTACACCGCCTATCTCTCCGAAAAGTACATCAAGGAAAAGAATTCT
+TTCTCGGTGGTTCTCTCCGGCGGCACCCTAATAGATACACTCAGGAAACTAGTAGAGTTT
+CCATACAAGGATTCTGTGGATTGGTCGAAATGGCTGATATTTTGGGTTGACGAGAGAGTG
+GTTCCTCTTGATCATGAAGACAGCAACTACTTACTTGCATACCGTGGTTTTCTTTCAAAG
+GTACCTATTCCTCCAAGCAACATTTACGCAATCAACGACAAGAAGTCTCCGGAAGGTGCA
+GCCGATGATTACGAGGAGCGTATCAAGAATCTGGTCGAGGAAAAAACCCTACCTATTTCA
+GAC---AGTGGCTTCCCTAAATTCGACCTTATGCTTCTCGGAATGGGGCCCGATGGCCAC
+GTGGCGTCTCTTTTCCCCTCTCACAATCAACGGTACGAAAAGAAACGGTGGGTGACATTC
+ATAACTGACTCTCCCAAACCGCCGCCACCTAGGATCACTTTCACATTCCCAGTCATCAAC
+TCTGCTTCGGACATTGCAATGGTGGTCACTGGTGCTGAGCTGGCGGATACTACGAAGAAA
+GCATTGGGAAACGAGAAGCATACTCTTCCT---------CCTCTTCCTTGTACTGAAGTT
+TCGGCTGAGAGAGAGCTCACTTGGTTCTTGGACAAAGATGCTGCTTCTAAACTG------
+------------------
+>gnl_Solly2.3_Solyc06g053200.2.1
+ATGGCAACCCAGAAAGGGAAGAAGACGGTGCTAAAATTCGACTCCGAAGAAGATGTATCA
+AAGGCACTTGCTAAATACACTGCTGAGCTATCGGAAAAATTCATCAAACAAAAAGGTTCT
+TTCACTGTTGTGCTCTCTGGTGGTTCTCTTATCGATACCATGAGGAAATTGGTAGAGCCG
+CCGTACAAAGACTCAATTGATTGGTCGAAATGGTGGATTTTTTGGGTAGACGAAAGAGTG
+GTTCCTCTAGGTCACGATGATAGCAATTATAAACTTGCTTCGGATGGGTTTCTTTCTAAG
+GTTCCGATCCCCTCTTCTAACATTTATGCGATTAATGACAAGGAGTCACCTGAGGGTGCA
+GCTGCTGATTACGAAGCTCGTCTGAAACAATTGATTGAGAGCAAAGTTCTTCCGTTATCA
+GCAATTACTGGATTCCCCAAATTTGATCTTATGCTATTAGGTATGGGGCCAGATGGACAT
+GTAGCGTCTTTGTTTCCTTTGCATCCTCACCGCCACGAGAAGGAGCGGCTGGTCACCTTC
+ATTACAGACTCACCAAAACCTCCTCCACCAAGGATTACTTTCACCTTTCCGGTAATTAAT
+TCGGCTTCAGAGATAGCAATGGTGGTCACAGGAGCAGAGTTAGCTCATATGGTTGATGTC
+GCTTTGGGTAATGCGCCT------CCTCCTGATGGAATTCCTCCCCCTTGTACTGAGGTT
+TCAGCTGAAGAGGAACTGACCTGGTTTTTAGACAAGGATGCTGCATCAGAACTA------
+------CAGACCTCTAGA
+>contig_2
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------NNCCTTTCCAAG
+GTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCA
+GCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCA
+ACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCAT
+GTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTC
+ATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAAC
+TCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATA
+GCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTT
+TCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAAT
+TATGTGCGCTTTGATGAT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.faa	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,19 @@
+>gnl_Orysa6.0_PACid_16878968
+MSHMEAFQNVVLLHKANSNSTLEDISSLSAASCCSLDQLLACVEGEAQKIFGDIQNLLADHRSEVAHFTQELRESFRISL
+DRTKDMSSFILGLFDKYVEETSKLQSHSNHTHEAQVKSLEDFQKAYEEQSKSEEQKLLADITSLVSKHVTRQRELVGGRL
+NSLGDAARGNKAFLDEHTSAMEVVTKDAKRKWEMFAEQAENDCKVGSNFSAAKHCRMETILQECACTVDTAAQQWKASHA
+TVNDLCRKQIAEVEALVRSAIETNEQHEAEIASSRATAEEHASNSSKDLLQDVDNMLQEARNSSSRVVSTVEAHLGESQH
+LQESHSSHTAGINTHADNAFQSSYKDYEPTGETPVRSEPEVPSKDAIESLRAMPMESLMDEFRENHPYEPSKDRRPSLIP
+RSPLATINN
+>gnl_Phoda3.0_PDK_30s1023721g001
+VNQKMMKCTLIKDLYGEIERLKAEVYAAREKVGVYIPKERYHQEESERKAMAEQIEQMGVLLENNQKQIEDLQERYNTQL
+QQSDDLSKKLDATEILCVSLSKKLDATEKSLEHTSKLLAAAREDLKQAQYTLKEKDFVISEQRKAAREDKLNTANRSIVN
+NFRADLATRVGTLCNTVVASLDRQNEHLQSVEKLCQSSLDFHDKAVSELKRKVSASRALYTSHMEALQNVVRLHKASSNA
+SLEEMSSMISANTCSLDQLLALGQSEADLIFSDLQSILSIHRGEIANFTRELREKFQVNLDRTKEMSNFILELLEKIGKG
+TKEFQNDSTLVHEAQVKSIGDFQKAYEVEVRLTGLGDAARDSKAIMDNHASSMDIVTTDAKRKWEEYSKQAEQDSEDGSN
+FSAAKHCRMELMLQQCVNSVDATSQQWKKTHASVSEMSSKHVAEIEALVRSAIESNDQHDAEVASARMAAEEDVAKNSKD
+VLQHFDTVIDHERNSAAGVMAAVEAHSATLHKLQEEQSSQATEINSHAEDTFQNTYMDYEPTGETPTRSEPDIPSRGTIE
+SLRAMPIEALLEEFRENHPYESKEPKPSLIPRSPLVQLN
+>contig_3
+XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG
+TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.faa.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,36 @@
+>gnl_Orysa6.0_PACid_16878968
+M-----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------SHMEAFQNVVLLHKANSNS
+TLEDISSLSAASCCSLDQLLACVEGEAQKIFGDIQNLLADHRSEVAHFTQELRESFRISL
+DRTKDMSSFILGLFDKYVEETSKLQSHSNHTHEAQVKSLEDFQKAYEEQSKSEEQKLLAD
+ITSLVSKHVTRQRELVGGRLNSLGDAARGNKAFLDEHTSAMEVVTKDAKRKWEMFAEQAE
+NDCKVGSNFSAAKHCRMETILQECACTVDTAAQQWKASHATVNDLCRKQIAEVEALVRSA
+IETNEQHEAEIASSRATAEEHASNSSKDLLQDVDNMLQEARNSSSRVVSTVEAHLGESQH
+LQESHSSHTAGINTHADNAFQSSYKDYEPTGETPVRSEPEVPSKDAIESLRAMPMESLMD
+EFRENHPYEPS---KDRRPSLIPRSPLATINN
+>gnl_Phoda3.0_PDK_30s1023721g001
+VNQKMMKCTLIKDLYGEIERLKAEVYAAREKVGVYIPKERYHQEESERKAMAEQIEQMGV
+LLENNQKQIEDLQERYNTQLQQSDDLSKKLDATEILCVSLSKKLDATEKSLEHTSKLLAA
+AREDLKQAQYTLKEKDFVISEQRKAAREDKLNTANRSIVNNFRADLATRVGTLCNTVVAS
+LDRQNEHLQSVEKLCQSSLDFHDKAVSELKRKVSASRALYTSHMEALQNVVRLHKASSNA
+SLEEMSSMISANTCSLDQLLALGQSEADLIFSDLQSILSIHRGEIANFTRELREKFQVNL
+DRTKEMSNFILELLEKIGKGTKEFQNDSTLVHEAQVKSIGDFQKAYE-------------
+---------------VEVRLTGLGDAARDSKAIMDNHASSMDIVTTDAKRKWEEYSKQAE
+QDSEDGSNFSAAKHCRMELMLQQCVNSVDATSQQWKKTHASVSEMSSKHVAEIEALVRSA
+IESNDQHDAEVASARMAAEEDVAKNSKDVLQHFDTVIDHERNSAAGVMAAVEAHSATLHK
+LQEEQSSQATEINSHAEDTFQNTYMDYEPTGETPTRSEPDIPSRGTIESLRAMPIEALLE
+EFRENHPYES----KEPKPSLIPRSPLVQLN-
+>contig_3
+X-----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------VD------------------------EGVV---
+--------------------------------VAGLSEQEKASVSEILTTARAHSETIEN
+LKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEE
+EFRENHSYESAVTGKELMPSVTTRAPFSQIN-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.fna	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,47 @@
+>gnl_Orysa6.0_PACid_16878968
+ATGTCACATATGGAAGCCTTCCAAAATGTTGTGCTCCTGCATAAAGCAAATTCAAATTCTACACTAGAGGATATATCATC
+CCTATCTGCTGCAAGCTGTTGCAGCCTTGATCAGCTTCTAGCTTGTGTCGAGGGAGAGGCACAGAAGATATTTGGTGATA
+TCCAGAATTTGCTAGCTGATCATCGAAGCGAAGTGGCACATTTCACTCAAGAGTTGCGGGAGAGTTTCCGCATTAGCTTG
+GATAGGACGAAGGACATGTCTAGTTTCATCCTTGGGTTGTTCGATAAGTATGTGGAGGAAACTTCGAAGTTGCAGAGCCA
+CTCCAATCACACACATGAAGCACAAGTCAAAAGCCTTGAAGATTTCCAGAAGGCTTATGAGGAGCAATCAAAATCAGAAG
+AACAAAAGCTTCTGGCGGACATCACCAGTTTGGTTTCTAAACACGTTACTCGACAACGAGAACTGGTGGGTGGTAGACTA
+AACTCTCTTGGTGACGCCGCTCGTGGAAACAAAGCATTTTTGGATGAGCACACGTCCGCCATGGAGGTGGTCACGAAGGA
+CGCCAAGAGAAAGTGGGAAATGTTTGCAGAGCAGGCAGAGAATGACTGCAAAGTTGGGTCCAACTTCTCTGCAGCTAAGC
+ATTGTCGCATGGAAACCATTCTGCAGGAATGTGCATGCACCGTCGACACTGCTGCTCAACAATGGAAAGCATCACATGCA
+ACTGTTAACGATCTATGCAGAAAACAAATAGCTGAAGTTGAAGCACTCGTCAGGAGTGCAATCGAAACCAACGAGCAGCA
+CGAAGCAGAGATTGCATCTTCCCGTGCCACGGCCGAGGAGCATGCGTCCAACAGCAGCAAGGACCTACTCCAAGATGTTG
+ACAATATGCTGCAGGAGGCGCGCAATTCGTCGTCGAGAGTGGTGTCGACGGTGGAAGCTCATTTGGGAGAGAGCCAGCAT
+CTACAGGAGAGCCACTCCAGCCATACCGCCGGCATCAACACCCACGCCGACAACGCTTTCCAGAGCAGCTACAAGGACTA
+CGAGCCGACCGGCGAAACTCCGGTGAGGTCGGAGCCGGAGGTGCCGAGCAAAGACGCGATCGAGTCGCTGCGAGCGATGC
+CGATGGAGTCCCTGATGGACGAGTTCCGCGAGAACCACCCCTACGAGCCGAGCAAGGACCGCAGGCCATCGCTCATCCCT
+CGCTCGCCGCTCGCCACCATCAACAAC
+>gnl_Phoda3.0_PDK_30s1023721g001
+GTAAACCAAAAAATGATGAAATGTACATTAATCAAAGATCTCTATGGAGAAATTGAGCGTCTAAAAGCAGAGGTGTATGC
+TGCTCGTGAGAAAGTTGGAGTTTACATACCAAAAGAACGCTACCATCAAGAAGAGAGCGAACGGAAGGCAATGGCAGAAC
+AAATTGAACAAATGGGGGTCTTGCTCGAAAACAATCAAAAGCAAATTGAGGATCTACAAGAAAGGTATAATACTCAACTT
+CAACAGTCTGATGACCTGAGCAAAAAGCTTGATGCCACCGAGATTCTCTGTGTTTCTCTGAGCAAAAAGCTTGATGCCAC
+CGAGAAAAGTTTGGAGCACACTAGCAAGTTATTGGCTGCTGCCAGAGAAGATCTGAAGCAAGCTCAGTATACTCTGAAGG
+AGAAAGATTTTGTTATATCAGAGCAGAGGAAAGCAGCTAGAGAAGACAAACTGAATACTGCCAACAGATCTATTGTGAAC
+AATTTTCGGGCTGATCTTGCAACAAGGGTTGGAACACTTTGTAATACTGTTGTTGCATCCTTGGATCGGCAAAATGAACA
+CCTTCAGTCTGTTGAGAAACTATGTCAATCTAGCCTTGATTTCCATGACAAGGCAGTATCAGAGCTGAAAAGGAAAGTGT
+CAGCTTCAAGAGCTTTGTATACTTCCCATATGGAAGCACTACAAAATGTAGTGCGTTTGCATAAGGCAAGCAGCAATGCC
+AGCTTAGAAGAGATGTCATCCATGATTTCTGCCAATACCTGCTCTCTTGATCAGTTACTTGCCTTGGGGCAAAGCGAAGC
+AGATCTGATTTTTAGTGATCTGCAAAGCATATTGTCAATTCACCGAGGAGAGATTGCAAATTTCACCCGTGAACTTCGTG
+AGAAATTTCAAGTTAATTTGGATCGGACAAAGGAGATGTCCAATTTTATTCTTGAGCTGCTTGAAAAGATAGGGAAGGGA
+ACAAAAGAATTTCAGAATGACTCAACTTTGGTACATGAGGCTCAGGTGAAGAGCATTGGTGATTTCCAAAAGGCATATGA
+GGTGGAAGTGAGGCTCACTGGACTGGGAGATGCTGCTCGAGATAGCAAAGCAATTATGGATAACCATGCATCATCAATGG
+ACATCGTCACAACTGATGCTAAGAGGAAGTGGGAAGAATATTCCAAGCAGGCAGAGCAAGATTCAGAGGACGGTTCTAAC
+TTTTCAGCAGCAAAACATTGTCGCATGGAACTCATGCTCCAACAGTGTGTAAACTCTGTTGATGCTACTTCTCAACAGTG
+GAAGAAGACACATGCATCTGTTAGTGAGATGAGCAGCAAACACGTTGCTGAAATTGAAGCACTTGTAAGGAGTGCCATTG
+AGAGCAATGATCAGCATGATGCTGAGGTTGCTTCAGCAAGAATGGCAGCAGAAGAGGATGTAGCGAAAAATAGCAAAGAT
+GTTCTTCAGCATTTTGATACTGTGATTGATCATGAGCGCAACTCAGCCGCTGGAGTGATGGCAGCAGTCGAAGCTCACTC
+AGCAACCCTGCATAAACTGCAAGAGGAACAATCAAGCCAGGCAACAGAGATTAATAGCCATGCGGAGGACACATTCCAAA
+ACACCTACATGGACTATGAACCAACGGGAGAAACCCCAACAAGGTCGGAACCAGATATACCAAGCAGGGGAACAATCGAA
+TCTCTTCGAGCCATGCCGATAGAAGCCCTCCTTGAAGAGTTCCGGGAGAACCATCCATACGAGTCCAAGGAGCCCAAACC
+GTCTCTCATACCACGCTCTCCACTCGTCCAGCTCAAC
+>contig_3
+NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG
+AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA
+CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC
+ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT
+TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.fna.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,99 @@
+>gnl_Orysa6.0_PACid_16878968
+ATG---------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---TCACATATGGAAGCCTTCCAAAATGTTGTGCTCCTGCATAAAGCAAATTCAAATTCT
+ACACTAGAGGATATATCATCCCTATCTGCTGCAAGCTGTTGCAGCCTTGATCAGCTTCTA
+GCTTGTGTCGAGGGAGAGGCACAGAAGATATTTGGTGATATCCAGAATTTGCTAGCTGAT
+CATCGAAGCGAAGTGGCACATTTCACTCAAGAGTTGCGGGAGAGTTTCCGCATTAGCTTG
+GATAGGACGAAGGACATGTCTAGTTTCATCCTTGGGTTGTTCGATAAGTATGTGGAGGAA
+ACTTCGAAGTTGCAGAGCCACTCCAATCACACACATGAAGCACAAGTCAAAAGCCTTGAA
+GATTTCCAGAAGGCTTATGAGGAGCAATCAAAATCAGAAGAACAAAAGCTTCTGGCGGAC
+ATCACCAGTTTGGTTTCTAAACACGTTACTCGACAACGAGAACTGGTGGGTGGTAGACTA
+AACTCTCTTGGTGACGCCGCTCGTGGAAACAAAGCATTTTTGGATGAGCACACGTCCGCC
+ATGGAGGTGGTCACGAAGGACGCCAAGAGAAAGTGGGAAATGTTTGCAGAGCAGGCAGAG
+AATGACTGCAAAGTTGGGTCCAACTTCTCTGCAGCTAAGCATTGTCGCATGGAAACCATT
+CTGCAGGAATGTGCATGCACCGTCGACACTGCTGCTCAACAATGGAAAGCATCACATGCA
+ACTGTTAACGATCTATGCAGAAAACAAATAGCTGAAGTTGAAGCACTCGTCAGGAGTGCA
+ATCGAAACCAACGAGCAGCACGAAGCAGAGATTGCATCTTCCCGTGCCACGGCCGAGGAG
+CATGCGTCCAACAGCAGCAAGGACCTACTCCAAGATGTTGACAATATGCTGCAGGAGGCG
+CGCAATTCGTCGTCGAGAGTGGTGTCGACGGTGGAAGCTCATTTGGGAGAGAGCCAGCAT
+CTACAGGAGAGCCACTCCAGCCATACCGCCGGCATCAACACCCACGCCGACAACGCTTTC
+CAGAGCAGCTACAAGGACTACGAGCCGACCGGCGAAACTCCGGTGAGGTCGGAGCCGGAG
+GTGCCGAGCAAAGACGCGATCGAGTCGCTGCGAGCGATGCCGATGGAGTCCCTGATGGAC
+GAGTTCCGCGAGAACCACCCCTACGAGCCGAGC---------AAGGACCGCAGGCCATCG
+CTCATCCCTCGCTCGCCGCTCGCCACCATCAACAAC
+>gnl_Phoda3.0_PDK_30s1023721g001
+GTAAACCAAAAAATGATGAAATGTACATTAATCAAAGATCTCTATGGAGAAATTGAGCGT
+CTAAAAGCAGAGGTGTATGCTGCTCGTGAGAAAGTTGGAGTTTACATACCAAAAGAACGC
+TACCATCAAGAAGAGAGCGAACGGAAGGCAATGGCAGAACAAATTGAACAAATGGGGGTC
+TTGCTCGAAAACAATCAAAAGCAAATTGAGGATCTACAAGAAAGGTATAATACTCAACTT
+CAACAGTCTGATGACCTGAGCAAAAAGCTTGATGCCACCGAGATTCTCTGTGTTTCTCTG
+AGCAAAAAGCTTGATGCCACCGAGAAAAGTTTGGAGCACACTAGCAAGTTATTGGCTGCT
+GCCAGAGAAGATCTGAAGCAAGCTCAGTATACTCTGAAGGAGAAAGATTTTGTTATATCA
+GAGCAGAGGAAAGCAGCTAGAGAAGACAAACTGAATACTGCCAACAGATCTATTGTGAAC
+AATTTTCGGGCTGATCTTGCAACAAGGGTTGGAACACTTTGTAATACTGTTGTTGCATCC
+TTGGATCGGCAAAATGAACACCTTCAGTCTGTTGAGAAACTATGTCAATCTAGCCTTGAT
+TTCCATGACAAGGCAGTATCAGAGCTGAAAAGGAAAGTGTCAGCTTCAAGAGCTTTGTAT
+ACTTCCCATATGGAAGCACTACAAAATGTAGTGCGTTTGCATAAGGCAAGCAGCAATGCC
+AGCTTAGAAGAGATGTCATCCATGATTTCTGCCAATACCTGCTCTCTTGATCAGTTACTT
+GCCTTGGGGCAAAGCGAAGCAGATCTGATTTTTAGTGATCTGCAAAGCATATTGTCAATT
+CACCGAGGAGAGATTGCAAATTTCACCCGTGAACTTCGTGAGAAATTTCAAGTTAATTTG
+GATCGGACAAAGGAGATGTCCAATTTTATTCTTGAGCTGCTTGAAAAGATAGGGAAGGGA
+ACAAAAGAATTTCAGAATGACTCAACTTTGGTACATGAGGCTCAGGTGAAGAGCATTGGT
+GATTTCCAAAAGGCATATGAG---------------------------------------
+---------------------------------------------GTGGAAGTGAGGCTC
+ACTGGACTGGGAGATGCTGCTCGAGATAGCAAAGCAATTATGGATAACCATGCATCATCA
+ATGGACATCGTCACAACTGATGCTAAGAGGAAGTGGGAAGAATATTCCAAGCAGGCAGAG
+CAAGATTCAGAGGACGGTTCTAACTTTTCAGCAGCAAAACATTGTCGCATGGAACTCATG
+CTCCAACAGTGTGTAAACTCTGTTGATGCTACTTCTCAACAGTGGAAGAAGACACATGCA
+TCTGTTAGTGAGATGAGCAGCAAACACGTTGCTGAAATTGAAGCACTTGTAAGGAGTGCC
+ATTGAGAGCAATGATCAGCATGATGCTGAGGTTGCTTCAGCAAGAATGGCAGCAGAAGAG
+GATGTAGCGAAAAATAGCAAAGATGTTCTTCAGCATTTTGATACTGTGATTGATCATGAG
+CGCAACTCAGCCGCTGGAGTGATGGCAGCAGTCGAAGCTCACTCAGCAACCCTGCATAAA
+CTGCAAGAGGAACAATCAAGCCAGGCAACAGAGATTAATAGCCATGCGGAGGACACATTC
+CAAAACACCTACATGGACTATGAACCAACGGGAGAAACCCCAACAAGGTCGGAACCAGAT
+ATACCAAGCAGGGGAACAATCGAATCTCTTCGAGCCATGCCGATAGAAGCCCTCCTTGAA
+GAGTTCCGGGAGAACCATCCATACGAGTCC------------AAGGAGCCCAAACCGTCT
+CTCATACCACGCTCTCCACTCGTCCAGCTCAAC---
+>contig_3
+NNT---------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------GTGGAT---------------------------------
+---------------------------------------GAAGGAGTTGTT---------
+------------------------------------------------------------
+------------------------------------GTTGCTGGCTTGTCAGAGCAGGAG
+AAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAAC
+CTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTC
+AGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGAT
+ATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAA
+GAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCT
+GTTACGACTCGTGCACCATTTTCACAGATCAAC---
--- a/utils.py	Fri Aug 25 13:01:25 2017 -0400
+++ b/utils.py	Mon Oct 30 09:52:00 2017 -0400
@@ -27,7 +27,7 @@
     return fstderr, fherr, fstdout, fhout
 
 
-def move_directory_files(source_dir, destination_dir, copy=False):
+def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
     source_directory = os.path.abspath(source_dir)
     destination_directory = os.path.abspath(destination_dir)
     if not os.path.isdir(destination_directory):
@@ -38,6 +38,8 @@
             shutil.copy(source_entry, destination_directory)
         else:
             shutil.move(source_entry, destination_directory)
+    if remove_source_dir:
+        os.rmdir(source_directory)
 
 
 def run_command(cmd):
@@ -52,29 +54,3 @@
 
 def stop_err(msg):
     sys.exit(msg)
-
-
-def write_html_output(output, title, dir):
-    with open(output, 'w') as fh:
-        dir_items = sorted(os.listdir(dir))
-        # Directories can only contain either files or directories,
-        # but not both.
-        if len(dir_items) > 0:
-            item_path = os.path.join(dir, dir_items[0])
-            if os.path.isdir(item_path):
-                header = 'Directories'
-            else:
-                header = 'Datasets'
-        else:
-            header = ''
-        fh.write('<html><head><h3>%s: %d items</h3></head>\n' % (title, len(dir_items)))
-        fh.write('<body><p/><table cellpadding="2">\n')
-        fh.write('<tr><b>%s</th></b>\n' % header)
-        for index, fname in enumerate(dir_items):
-            if index % 2 == 0:
-                bgcolor = '#D8D8D8'
-            else:
-                bgcolor = '#FFFFFF'
-            link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
-            fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, link))
-        fh.write('</table></body></html>\n')