Mercurial > repos > greg > plant_tribes_gene_family_aligner
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 |
| 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(-) [+] |
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--- 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)