changeset 11:1c5a484fc06f draft default tip

planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner commit f7690d10e0515911ee00455806e457bc53f145c7-dirty
author greg
date Thu, 13 Jun 2024 11:54:31 +0000 (6 months ago)
parents 79ea0eef1942
children
files .shed.yml gene_family_aligner.xml macros.xml test-data/3722.faa.aln test-data/3722.fna.aln test-data/38889.faa.aln test-data/38889.fna.aln test-data/39614.faa.aln test-data/39614.fna.aln utils.py
diffstat 10 files changed, 69 insertions(+), 1492 deletions(-) [+]
line wrap: on
line diff
--- a/.shed.yml	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-name: plant_tribes_gene_family_aligner
-owner: greg
-description: |
-  Contains a tool that integrates de novo assembly sequences with scaffold gene family sequences.
-homepage_url: https://github.com/dePamphilis/PlantTribes
-long_description: |
-  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/phylogenetics/plant_tribes/gene_family_aligner
-type: unrestricted
-categories:
-- Phylogenetics
--- a/gene_family_aligner.xml	Tue Sep 04 08:51:38 2018 -0400
+++ b/gene_family_aligner.xml	Thu Jun 13 11:54:31 2024 +0000
@@ -1,10 +1,10 @@
-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">
+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@TOOL_VERSION@.4.0+galaxy0">
     <description>aligns integrated orthologous gene family clusters</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.0.3">plant_tribes_gene_family_aligner</requirement>
+        <requirement type="package" version="1.0.4">plant_tribes_gene_family_aligner</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set alignment_method = $alignment_method_cond.alignment_method
@@ -138,7 +138,7 @@
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input">
                 <collection type="list">
                     <element name="3722.faa" value="3722.faa"/>
@@ -151,14 +151,62 @@
             </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"/>
+                <element name="3722.faa.aln" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">gnl_Glyma1.01_PACid_16266208"/>
+                        <has_text text=">gnl_Vitvi12X_PACid_17827068"/>
+                        <has_text text=">gnl_Selmo1.0_PACid_15401289"/>
+                        <has_text text=">gnl_Orysa6.0_PACid_16864430"/>
+                        <has_text text=">contig_7"/>
+                    </assert_contents>
+                </element>
+                <element name="38889.faa.aln" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
+                        <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
+                        <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
+                        <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
+                        <has_text text=">contig_2"/>
+                    </assert_contents>
+                </element>
+                <element name="39614.faa.aln" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
+                        <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
+                        <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
+                        <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
+                        <has_text text=">contig_3"/>
+                    </assert_contents>
+                </element>
             </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"/>
+                <element name="3722.fna.aln" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">gnl_Glyma1.01_PACid_16266208"/>
+                        <has_text text=">gnl_Glyma1.01_PACid_16266209"/>
+                        <has_text text=">gnl_Glyma1.01_PACid_16266210"/>
+                        <has_text text=">gnl_Glyma1.01_PACid_16301083"/>
+                        <has_text text=">contig_7"/>
+                    </assert_contents>
+                </element>
+                <element name="38889.fna.aln" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
+                        <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
+                        <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
+                        <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
+                        <has_text text=">contig_2"/>
+                    </assert_contents>
+                </element>
+                <element name="39614.fna.aln" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
+                        <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
+                        <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
+                        <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
+                        <has_text text=">contig_3"/>
+                    </assert_contents>
+                </element>
             </output_collection>
         </test>
     </tests>
@@ -199,65 +247,16 @@
 
     </help>
     <citations>
-        <expand macro="citation1" />
-        <citation type="bibtex">
-            @article{Wall2008,
-            journal = {Nucleic Acids Research},
-            author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
-            title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
-            year = {2008},
-            volume = {36},
-            number = {suppl 1},
-            pages = {D970-D976},}
-        </citation>
-        <citation type="bibtex">
-            @article{Katoh2013,
-            journal = {Molecular biology and evolution},
-            author = {3. Katoh K, Standley DM},
-            title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
-            year = {2013},
-            volume = {30},
-            number = {4},
-            pages = {772-780},}
-        </citation>
-        <citation type="bibtex">
-            @article{Mirarab2014,
-            journal = {Research in Computational Molecular Biology (RECOMB)},
-            author = {4. Mirarab S, Nguyen N, Warnow T},
-            title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
-            year = {2014},
-            pages = {177–191},
-            url = {https://github.com/smirarab/pasta},}
-        </citation>
-        <citation type="bibtex">
-            @article{Capella-Gutierrez2009,
-            journal = {Bioinformatics,},
-            author = {5. Capella-Gutierrez S, Silla-Martínez JM, Gabaldón T},
-            title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
-            year = {2009},
-            volume = {25},
-            number = {15},
-            pages = {1972-1973},}
-        </citation>
-        <citation type="bibtex">
-            @article{Yachdav2016,
-            journal = {Bioinformatics,},
-            author = {6. Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T},
-            title = {MSAViewer: interactive JavaScript visualization of multiple sequence alignments},
-            year = {2016},
-            volume = {32},
-            number = {22},
-            pages = {3501-3503},}
-        </citation>
-        <citation type="bibtex">
-            @article{Clamp2004,
-            journal = {Bioinformatics,},
-            author = {7. Clamp M, Cuff J, Searle SM, Barton GJ},
-            title = {The jalview java alignment editor},
-            year = {2004},
-            volume = {20},
-            number = {3},
-            pages = {426-427},}
-        </citation>
+        <citation type="doi">10.3389/fpls.2022.1011199</citation>
+        <citation type="doi">10.1371/journal.pone.0146062</citation>
+        <citation type="doi">10.1038/nprot.2013.084</citation>
+        <citation type="doi">10.1101/gr.9.9.868</citation>
+        <citation type="doi">10.1142/9781848165632_0019</citation>
+        <citation type="doi">10.1093/molbev/mst010</citation>
+        <citation type="doi">10.1093/nar/gks631</citation>
+        <citation type="doi">10.1101/gr.1224503</citation>
+        <citation type="doi">10.1186/s13059-015-0721-2</citation>
+        <citation type="doi">10.1093/bioinformatics/btp348</citation>
+        <citation type="doi">10.1109/TCBB.2013.68</citation>
     </citations>
 </tool>
--- a/macros.xml	Tue Sep 04 08:51:38 2018 -0400
+++ b/macros.xml	Thu Jun 13 11:54:31 2024 +0000
@@ -1,28 +1,4 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <token name="@WRAPPER_VERSION@">1.0</token>
-    <xml name="param_method">
-        <param name="method" type="select" label="Protein clustering method" dynamic_options="get_clustering_method_options(scaffold)"/>
-    </xml>
-    <xml name="param_scaffold">
-        <param name="scaffold" type="select" label="Gene family scaffold" refresh_on_change="True">
-            <options from_data_table="plant_tribes_scaffolds">
-                <column name="name" index="1"/>
-                <column name="value" index="2"/>
-                <column name="path" index="2"/>
-                <filter type="sort_by" column="1"/>
-                <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."/>
-            </options>
-        </param>
-    </xml>
-    <xml name="citation1">
-        <citation type="bibtex">
-            @misc{None,
-            journal = {None},
-            author = {1. Wafula EK},
-            title = {Manuscript in preparation},
-            year = {None},
-            url = {https://github.com/dePamphilis/PlantTribes},}
-        </citation>
-    </xml>
+    <token name="@TOOL_VERSION@">1.0</token>
 </macros>
--- a/test-data/3722.faa.aln	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,312 +0,0 @@
->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-------------------------------
--- a/test-data/3722.fna.aln	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,819 +0,0 @@
->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---------------------------------
-------------------------------------------------------------
--- a/test-data/38889.faa.aln	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
->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
--- a/test-data/38889.fna.aln	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
->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
--- a/test-data/39614.faa.aln	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
->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-
--- a/test-data/39614.fna.aln	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
->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	Tue Sep 04 08:51:38 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-import os
-import shutil
-import subprocess
-import sys
-
-FSTDERR = 'stderr.txt'
-FSTDOUT = 'stdout.txt'
-
-
-def check_execution_errors(rc, fstderr, fstdout):
-    if rc != 0:
-        fh = open(fstdout, 'rb')
-        out_msg = fh.read()
-        fh.close()
-        fh = open(fstderr, 'rb')
-        err_msg = fh.read()
-        fh.close()
-        msg = '%s\n%s\n' % (str(out_msg), str(err_msg))
-        stop_err(msg)
-
-
-def get_response_buffers():
-    fstderr = os.path.join(os.getcwd(), FSTDERR)
-    fherr = open(fstderr, 'wb')
-    fstdout = os.path.join(os.getcwd(), FSTDOUT)
-    fhout = open(fstdout, 'wb')
-    return fstderr, fherr, fstdout, fhout
-
-
-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):
-        os.makedirs(destination_directory)
-    for dir_entry in os.listdir(source_directory):
-        source_entry = os.path.join(source_directory, dir_entry)
-        if copy:
-            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):
-    fstderr, fherr, fstdout, fhout = get_response_buffers()
-    proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True)
-    rc = proc.wait()
-    # Check results.
-    fherr.close()
-    fhout.close()
-    check_execution_errors(rc, fstderr, fstdout)
-
-
-def stop_err(msg):
-    sys.exit(msg)