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‎.gitmodules

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[submodule "qscore"]
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path = qscore
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url = https://github.com/malabz/qscore.git

‎README.md

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# QuanTest2 using Q score and TC score
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modified by [wym6912](wym6912@outlook.com)
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Using this repository by testing protein sequences provided by `QuanTest2`.
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## How to clone
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Please clone this repository use the following command:
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```bash
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git clone https://github.com/malabz/QuanTest2 --recurse-submodules
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```
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## How to test
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Before testing, please check the varibles in script: `program_name`, `cmd`, `prog_alias`.
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Then run the following command:
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```bash
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bash run.[program].sh # change the [program] to your program name
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```
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Result file is `[program].txt`.
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## `Test_hasunknown` folder
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We checked all input sequences, found one sequence has unknown character `U`. We put this file into `Test_hasunknown` folder.
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If you want to test the file into standard test, please run the following command:
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```bash
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cp Test_hasunknown/AhpC-TSA.vie Test/
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```
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## References
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QuanTest2: Sievers, F. & Higgins, D. G. Fabian Sievers, Desmond G Higgins, **QuanTest2**: benchmarking multiple sequence alignments using secondary structure prediction, *Bioinformatics*, Volume 36, Issue 1, January 2020, Pages 90–95, https://doi.org/10.1093/bioinformatics/btz552
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PREFAB Q score: Robert C. Edgar, **MUSCLE**: multiple sequence alignment with high accuracy and high throughput, *Nucleic Acids Research*, Volume 32, Issue 5, 1 March 2004, Pages 1792–1797, https://doi.org/10.1093/nar/gkh340
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SP and TC scores: J D Thompson and others, **BAliBASE**: a benchmark alignment database for the evaluation of multiple alignment programs., *Bioinformatics*, Volume 15, Issue 1, January 1999, Pages 87–88, https://doi.org/10.1093/bioinformatics/15.1.87

‎Ref/AAA.ref

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>seq0001
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-----E-DYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSD-----RTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIG-----FSETAKCQAMKKIFDDAYK----------------------------------------------------------------------------------------------------SQLSCVVVDDIERLLDYVPIGPR-FS---NLVLQALLVLLKKAPPQ--------GRKLLIIGTTS----RKDVLQEMEMLN--AFSTTIHVPNIATGEQLLEALEL----LG--------------NFKDKE-RTTIAQQVKG---KKVWIGIKKLLMLIEMSLQMD-----------------PEY------RVRKFLALLREEGASPLD-----
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>seq0002
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REDEEE-SLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFK--AIGVKPPRGILLYGPPGTGKTLIARAVANETGA-FFFLINGPEIMS-----KLAGESESNLRKAFEEAEK----------------------------------------------------------------------------------------------------NAPAIIFIDELDAIAP--KREKT-HGEVERRIVSQLLTLMDGLK-Q--------RAHVIVMAATN----RPNSIDP-ALRRFGRFDREVDIGIP-DATGRLEILQI----HTK-----------NMKLADDVDLEQVANETH-------GHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNS-LAVTMDDFRWALSQ------------
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>seq0003
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HSEMTPREIVSELDKHIIGQDNAKRSVAIALR-NRWRRMQLNEELRHEVTPKNILMIGPTGVGKTEIARRLAKLANA-PFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKMVRVQAIEKNRYRAEELAEERILDVLIPPAKNNWGQTEQQQEPSAARQAFRKKLREGQLDDKEIEKQKARKLKIKDAMKLLIEEEAAKLVNPEELKQDAIDAVEQHGIVFIDEIDKICKRG--ESSGPDVSREGVQRDLLPLVEGCTVSTKHGMVKTDH-ILFIASGAFQIAKPSDLIP-ELQG--RLPIRVELQAL-TTSDFERILTEPNASITVQYKALMATEGVNIEFTDSG-IKRIAEAAWQVNESTENIGARRLHTVLERLMEEISYDASDLS------------GQNITIDADYVSKHLDALVADEDLSRFIL

‎Ref/ACPS.ref

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>seq0001
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GIYGIGLDITELKRIASMAGRQKRFAERILTRSELDQYYELS-EKRKNEFLAGRFAAKEAFSKAFGTGIGRQLSFQDIEIRKDQNGKPYIICTKLSPAAVHVSITH-TKEYAAAQVVIER--
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>seq0002
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----MKIYGIYMDRPLS--QEENERFMTFISPEKREKCRRFYHKEDAHRTLLGDVLVRSVISRQYQ------LDKSDIRFSTQEYGKPCI--PDL--PDAHFNISH-SGRWVIGAFDSQPI-
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>seq0003
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-----GIDIEKTK-PIS-----LEIAKRFFSKTEYSDLLAKD-KDEQTDYFYHLWSMKESFIKQEGKG--LSLPLDSFSVRLHQDGQVSIELPDS-HSPCYIKTYEVDPGYKMAVCAAHPDF

‎Ref/AP_endonuc_2.ref

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>seq0001
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--KLCFNEATTLENSNLKLDLELCEKHGYDYIEIRTDKLPEYLK----DHSLDDLAEYFQTHHIK---PLALNALV--------FFNNRDEKGHNEIITEFKG--ETCKTLGVKYVVAVPLVTEQKIVKEEIKKSSVDVLTELSDIAEPYGVKIALEFVGH---PQCTVNTFEQAYEIVNTVN-RDNVGLVLDSFHFHAGS-N----------IESLKQ-ADGKKIFIYHIDDTEDFPIGFLTDEDRVWPGQGAIDLDAHLSALKEIGF-SDVVSVELFRPEYYKLTAEEAIQTAKKTTVDVVSKYFS
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>seq0002
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-PRFAANLSFT--EVPFIERFAAARKAGFDAVEFLF-PYN---------YSTLQIQKQLEQNHLT---LALFNTAPGDINAGEWGLSALPG-REHEAHADIDLALEYALALNCEQVHVAGVVPA-GEDAERYRAVFIDNIRYAADRFAPHGKRILVEALSPGVKPHYLFSSQYQALAIVEEVA-RDNVFIQLDTFHAQKVDGN----------LTHLIR-DYAGKYAHVQIAGLP----------DRHEPDDGEINYPWLFRLFDEVGY-QGWIGCEYKPR----GLTEEGLGWFDAWRG-------S
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>seq0003
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MKYIGAHVSAAG---GLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQ-ILPHDSY------LINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQ--GVTAVIENTAGQ--GSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAK-STFGSRVDR-HHSLGEGNIGHDAFRWIMQDDRFDGIPLILETINPDI----WAEEIAWLKAQQTE---KAVA

‎Ref/ARM.ref

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>seq0001
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--------LPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQCNAMEPILGLFNSN-----KPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINAGVLPALRLLLSSP--KENIKKEACWTISNITAGN--TEQIQAVIDANLIPPLVKLLE-VAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIA--------DNRIIEVTLDALENILKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIETYFG--------------------------------------
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>seq0002
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NQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNP--KTNIQKEATWTMSNITAGR--QDQIQQVVNHGLVPFLVGVLS-KADFKTQKEAAWAITNYTSGG--TVEQIVYLVHCGIIEPLMNLLSAK--------DTKIIQVILDAISNIFQAAEKLG-----ETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYF---------------------------------------
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>seq0003
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-------QVSAIVRTQNTNDVETARCTAGTLHNLSHHR--EGLLAIFKSGGIPALVK-LGSP-VDSVLFYAITTLHNLLLHQE-GAKAVRLAGGLQKV-ALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIRTYT-----YEKLLWTTSRVLKVLSVCS--SNKPAIVEAGGQALGLHLTDPSQRLVQNCLWTLRNLSDAA-TKQE---GEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNK--VCQVGGIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALC----PANHAPLREQGAIPRLVQLLVRAHQDTQRGVREEIVEGCTGALHILARD------------VHNRIVIRGLNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFR

‎Ref/Adenylsucc_synt.ref

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>seq0001
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---IGSLSQVSGVLGCQWGDEGKGKLVDILAQHFDIVARCQGGANAGHTIYNSEGKKFALHLVPSGILNEDTTCVIGNGVVVHLPGLFKEIDGLESNGVSCKGRILVSDRAHLLFDFHQEVDGLRESELAKSFIGTTKRGIGPAYSSKVIRNGIRVGDLRHMDTLPQKLDLLLSDAAARFQ---GFKYTPEMLREEVEAYKRYADRLEPYITDTVHFINDSISQKKKVLVEGGQATMLDIDFGTYPFVTSSSPSAGGICTGLGIAPSVVGDLIGVVKAYTTRVGSGPFPTENLGTGGDLLRLAGQEFGTTTGRPRRCGWLDIVALKFSCQINGFASLNLTKLDVLSDLNEIQLGVAYKRSDGTPVKSFPGDLRLLEELHVEYEVLPGWKSDISSVRNYSDLPKAAQQYVERIEELVGVPIHYIGIGPGRDALIYK------
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>seq0002
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ADRVSSLSNVSGVLGSQWGDEGKGKLVDVLAPRFDIVARCQGGANAGHTIYNSEGKKFALHLVPSGILHEGTLCVVGNGAVIHVPGFFGEIDGLQSNGVSCDGRILVSDRAHLLFDLHQTVDGLREAELANSFIGTTKRGIGPCYSSKVTRNGLRVCDLRHMDTFGDKLDVLFEDAAARFE---GFKYSKGMLKEEVERYKKFAERLEPFIADTVHVLNESIRQKKKILVEGGQATMLDIDFGTYPFVTSSSPSAGGICTGLGIAPRVIGDLIGVVKAYTTRVGSGPFPTELLGEEGDVLRKAGMEFGTTTGRPRRCGWLDIVALKYCCDINGFSSLNLTKLDVLSGLPEIKLGVSYNQMDGEKLQSFPGDLDTLEQVQVNYEVLPGWDSDISSVRSYSELPQAARRYVERIEELAGVPVHYIGVGPGRDALIYK------
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>seq0003
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-------GNNVVVLGTQWGDEGKGKIVDLLTERAKYVVRYQGGHNAGHTLVIN-GEKTVLHLIPSGILRENVTSIIGNGVVLSPAALMKEMKELEDRGIPVRERLLLSEACPLILDYHVALDNAREKARGAKAIGTTGRGIGPAYEDKVARRGLRVGDLFDKETFAEKLKEVMEYHNFQLVNYYKAEAV--DYQKVLDDTMAVADILTSMVVDVSDLLDQARQRGDFVMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVATGSGLGPRYVDYVLGILKAYSTRVGAGPFPTELFDETGEFLCKQGNEFGATTGRRRRTGWLDTVAVRRAVQLNSLSGFCLTKLDVLDGLKEVKLCVAYRMPDGREVTTTPLAADDWKGVEPIYETMPGWSESTFGVKDRSGLPQAALNYIKRIEELTGVPIDIISTGPDRTETMILRDPFDA

‎Ref/AhpC-TSA.ref

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>seq0001
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---LLLGDVAPNFEANTTV-----GRIRFHDFLGDSWGILFSHPRDFTP-VTTELGRAAKLAPEFAKRNVKLIALSIDSVEDHLAWSKDINAYNSEEPTE-KLPFPIIDDRNRELAILLGMLDPAEKDEKGMPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP
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>seq0002
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SGNARIGKPAPDFKATAVV-DGAFKEVKLSD-YKGKYVVLFFYPLDFTF-VPTEIIAFSNRAEDFRKLGCEVLGVSVDSQFTHLAWINTPRKE----GGLGPLNIPLLADVTRRLSEDYGVLKT----DEGIA--YRGLFIIDGKGVLRQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDTIKP---NVDDSKEYFSKHN------------------
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>seq0003
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SGNAKIGHPAPSFKATAVMPDGQFKDISLSD-YKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWINTPKKQ----GGLGPMNIPLVSDPKRTIAQDYGVLKA----DEGIS--FRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPA---------------------------------------------

‎Ref/Asp_Glu_race_D.ref

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>seq0001
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-MKIGIFDS-G-VGGLTVLKAIRNRYR------KVDIVYLG---DTARVPYGI--R---SKDTIIRYSLECAGFLKDKGVDIIVVACNTASAYALERLKKEI-NVPVFGVIEPGVKEALKKSR
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>seq0002
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NKKIGVIGTPATVKSGAYQRKLEEG--------GADVFAKACPLFAPLAEEGLLE-----GEITRKVVEHYLKEFK-GKIDTLILGCTHYPL-LKKEIKKFLGDAEVVDSSEALSLSLHNFIK
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>seq0003
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MKTIGILGGMGPLATAELFRRIVIKTPAKRDQEHPKVIIFN---NPQIPDRTA--YILGKGEDPRPQLIWTAKRLEECGADFIIMPCNTAHA-FVEDIRKAI-KIPIISMIEETAKKVKELG-

‎Ref/Bac_DNA_binding.ref

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>seq0001
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ALTKAEMSEYLFDKLG-LSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK----
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>seq0002
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-MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG------
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>seq0003
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-MNKTELIKAIAQDTE-LTQVSVSKMLASFEKITTETVAKGDKVQLTGFLNIKPVARQARKGFNPQTQEALEIAPSVGVSVKPGESLKKAAEGLKYEDFAK

‎Ref/C2.ref

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>seq0001
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--ERRGRIYIQAHIDR---EVLIVVVRDAKNLVPMDP--NGLSDPYVKLKLIPDPKSESKQKTKTIKCSL-NPEWNETFRFQLK-ESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQ-KAGVDGWFKLLSQEEGEYFNV
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>seq0002
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DQHPSATLFVKISIQDWRPERLRVRIISGQQLPKVNKNKNSIVDPKVIVEIHGVGRDTGSRQTAVITNNGFNPRWDMEFEFEVT--VPDLALVRFMVEDYDSSSKNDFIGQSTIPWNSLKQ---GYRHVHLLSKNG------
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>seq0003
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--EKLGKLQYSLDYDFQN-NQLLVGIIQAAELPALDM--GGTSDPYVKVFLLP--DKKKKFETKVHRKTL-NPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSA--------

‎Ref/CBS.ref

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>seq0001
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QGFIT-DPVVLSPKDRVR-----------CGIPITDTGRMGSRLVGII------------------
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>seq0002
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IMTKREDLVVAPAGITLKEANEILQRSKKGKLPIVN---EDDELVAIIARTDLKK---------NR
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>seq0003
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NGVI-IDPFFLTPEHKVSEAEE-LQRYRISGVPIVETL-ANRKLVGIITNRD-RFISDYNAPISEH

‎Ref/CH.ref

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>seq0001
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-----YSEEEKYAFVNWINKALENDPDCRHVIPMNPNTDDLFKAVGDGIVLCKMINLSVP----DTIDERAINKKKLTPFIIQENLNLALNSASAI-GCHVVNIGAEDLR--AGKPHLVLGLLWQIIKIGLFADIELSRNEAL
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>seq0002
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TLEELMKLSPEELLLRWANFHLENSGWQ----KIN----NFSADIKDSKAYFHLLNQIAPKGQKEGEPRIDINMSGFNETDDLKRAESMLQQADKL-GCRQ-FVTPADVV--SGNPKLNLAFVANLFN---------------
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>seq0003
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----LQQTNSEKILLSWVRQTTRPYSQV----NVL----NFTTSWTDGLAFNAVLHRHKP----DLFSWDKVVKM-----SPIERLEHAFSKAQTYLGIEK-LLDPEDVAVRLPDKKSIIMYLTSLFEVL-------------

‎Ref/COX3.ref

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>seq0001
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--------------------------------------------------------------------------------HDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNG------------TAGGPTGKDI-FELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGA
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>seq0002
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AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGE-TGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVL-EGDRKTTINGLIVAVILGVCFTGLQAYEYSHA--AFGL-ADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR
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>seq0003
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MTHQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHF--------NSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPT-PELG---GCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLM--EGDRKHMLQALFITITLGVYFTLLQASEYYEA--PFTI-SDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAGAWYWHFVDVVWLFLYVSIYWWGS

‎Ref/CPS.ref

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>seq0001
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---RFQHAVERLKLKQPANATVT---AIEMAVEKAKEIGYPLVVRA-------AMEIVYDEADLRRYFQT--------AVLLDHFLDDAVEVDVDAICDG-EMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQV-RGLMNVQFAVK--NNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQG---------VTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGS
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>seq0002
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DRRRFDVAMKKIGLETARSGIAH---TMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGL
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>seq0003
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DKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKRG-------MRVVRGDAELAQSISMTRAEA--KMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQ--KVVEEAPAPGITPELRRYIGERCAKACVDIGY-RGAGTFEFLFE--NGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLS----------IKQEEVHV---------------------------------------------------

‎Ref/CUB.ref

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>seq0001
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LPRNT---NCGGILKEESGVIATYYGPKTNCVWTIQMPPEYHVRVSIQYLQLNCNKESLEIIDGLPGSPVLGKICEGSLMDYRSSGSIMTVKYIREPEHPASFYEVLYFQDPQA
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>seq0002
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-LDYH---ACGGRLTDDYGTIFTYKGPKTECVWTLQVDPKYKLLVSIPTLNLTCGKEYVEVLEGAPGSKSLGKFCEGLSILNRG-SSGMTVKYKRDSGHPASPYEIIFLRDSQG
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>seq0003
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-ARINGPDECGRVIKDTSGSISNTDRQKNLCTWTILMKPDQKVRMAIPYLNLACGKEYVEVFDGLLSGPSYGKLCAGAAIVFLSTANTMTIKYNRISGNSSSPFLIYFYGSSP-

‎Ref/Cu_nir.ref

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>seq0001
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ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG-
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>seq0002
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----DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGADALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPI
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>seq0003
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----DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM

‎Ref/Cys_Met_Meta_PP.ref

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>seq0001
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-------KLDTQLVNAGRS--KKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVKHLQP-NTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAAT-YLVGHSDAMIGTAVC-NARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQ---GEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV--
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>seq0002
4+
------RKQATIAVRSGLNDDEQY--GCVVPPIHLSSTYNFTGF--------NEPR-AHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALA-EKPKLVLVESPSNPLLRVVDIAKICHLAREV--GAVSVVDNTFLSPALQNPLALGADLVLHSCT-YLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDG--DEQTLRRFLGGLSLFTLAESLGGVESLISH-AATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG
5+
>seq0003
6+
KYASFLNSDGSVAIHAGERLGRGIVTDAITTPVVNTSAYFFNKTSELIDFKEKRRA-SFEYGRYGNPTTVVLEEKISALEGAESTLLMASGMCASTVMLLALVPAGGHIVTTTDCYRKTRIFIETILPKMGITATVIDPADVGALELALNQKKVNLFFTESPTNPFLRCVDIELVSKLCHEK--GALVCIDGTFATPLNQKALALGADLVLHSATKFLGGHNDVLAGCISG-PLKLVSEIRNLHHILGGALNPNAAYLIIRGMKTLHLRVQQQNSTALRMAEILEAHPKVRHVYYPGLQSHPEHHIAKKQMTGFGGAVSFEVDG--DLLTTAKFVDALKIPYIAPSFGGCESIVDQ-PAIMSYWDLSQSDRAKYGIMDNLVRFSFGVEDFDDLKADILQALDSI---

‎Ref/DAHP_synth_1.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
---------------------------------------------------EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFK-EVEFVFKSSFDKANRSSIHSFRGH--------------GLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFG------------------GAKEIYLTERGTTFGYNNLVVDFRSLPIMKQW-------AKVIYDATHSVQLPGGL-----GDKSGGMREFIFPLIRAAVAV------GCDGVFMETHPE-------PEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI---
3+
>seq0002
4+
-----------------------------------MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLG--IPYVFKASFDKANRSSIHSYRGP--------------GLEEGMKIFQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEG------------------GNEKVILCDRGANFGYDNLVVDMLGFSIMKKVSG----NSPVIFDVTHALQCRDPFGAASG-----GRRAQVAELARAGMAV------GLAGLFIEAHPD-------PEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK
5+
>seq0003
6+
DLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKG------NDDRLLVVIGPCSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTV--GWKGLINDPHMDNSFQINDGLRIARKLLLDINDS-GLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGK----EPNYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSK--------------QFKKQMDVCADVCQQIAGGEKAIIGVMVESHLVEGNQSLPLAYGKSITDACIGWEDTDALLRQLANAVKARR---------

‎Ref/DEAD.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
----------------TFRYRGP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALG-----RPALVLAPNKILAAQLAAEFRELFPENAVEYFISYYDYYQPEAYVPGKDLYIEKDASINPEIERLRHSTTRSLLTRRDVIVVASVSAIYGLGDPREYRARNLVG---------------------------------------------------------------------------FVLFPATHYLSPE-GLEEILKEIEKELWERVRYFEERGEVLYAQRLKERTLYDLEMLRVMGTCPGVENYARYFTGKAPGEPPYTLLDYFPEDFLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFVSATPGPFELAHSG-----RVVEQIIRP
3+
>seq0002
4+
--------------EGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVN-----KPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIFRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIEAEVDALTGKVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSP-----GVVEQIIRP
5+
>seq0003
6+
VEYNFNELNLSDNILNAIRNKGFEKPTDIQ-KVIPLFLN----DEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGG----------------------KAIYPQIKALK------NANIVVGTPGRIL------DHINR-------------------------------------------------------------------------------------------------------------------------------------------------------------------GTLNLKNVKYFILDEADELN--------GFIKDVEKILN--ACNK----------------DKRILLFSAT-PREILNLAKKYGDYSFIKAKI--

‎Ref/DHH.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
SKILVFGHQNPDSDAIGSS-AYAYLKRQL-GVDAQAVALGNPNEETAFVLDYFGIQAPPVVKSAQAEGAKQVILTDHNEFQQSIADIREVEVVEVVDHHRVANFETANPLY-RLEPVGSASSIVYRLYKENGVAIPKEIAGV-LSGLISDTLLLKSPTTHASDPAVAEDLAKIAGVDLQEYGLA-LKAG
3+
>seq0002
4+
SKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPRVITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLEEYGLAMLKAG
5+
>seq0003
6+
EKILIFGHQNPDTDTICSAIAYADLKNKL-GFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANE-VNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNK-YKENNVKIEKEIAGL-LSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLN-LKAG

‎Ref/DHOdehase.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAG-FDKHGEAVDGLYKMGFGFVEIGSVTPK--PQEGNPRPRVFRLPED--------QAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPL--ADYLVVNVSSPNTA---------GLGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTV-SRPA-----GLQGA----LRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHR-R
3+
>seq0002
4+
----------------------------------------------ISVEMAGLKFINPFGLASAAPTTSSSMIRRAFEAGWGFALTKTFSLDKDIVT-NVSPRIVRGTTSGPMYGPGQSSFLNIELISEKTAAYWCQSVTELKADFP-D----NIVIASIMCS----YNKNDWMELSRKAEASG-ADALELNLSCPHGMGERGMGLACGQDPELVRNICRWVRQAVQ-------IPFFAKLTPNVT--DIVSIARAAKEGGADGVTATNTVS-GLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPG-FPILATGGIDSAESGLQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIE-------------
5+
>seq0003
6+
---------------------------------------------MLNTTFANAKFANPFMNASGVHCMTIEDLEELKASQAGAYITKSSTLE--KREGNPLPRYVDLE----------LGSINSMGLPNLGFDYYLDYVLKNQKENAQE----GPIFFSIAGM-----SAAENIAMLKKIQESDFSGITELNLSCPNVP----GKPQLAYDFEATEKLLKEVFTFFT-------KPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFIDPEAESVVIKPK----DGFGGIGGAYIKPTALANVRAFYTRLKPEIQIIGTGGIETGQDAFEHLLCGATMLQIGTALHKEGPAIFDRIIKELEEIMNQKGYQSIADFHGKLKSL-

‎Ref/DUF170.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
----MQILFN----------DQAMQCAAGQTVHELLEQLD---------QRQAGAALAINQQIVPREQWAQHIVQDGDQILLFQVIAGG
3+
>seq0002
4+
----MIKVLFFAQVRELVGTDATEVAADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVS----FDHPLTDGDEVAFFPPVTGG
5+
>seq0003
6+
MVIGMKFTVITD------DGKKILESGAPRRIKDVLGELE---------IPIETVVVKKNGQIVI----DEEEIFDGDIIEVIRVIYGG

‎Ref/EFTU_2.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
-------------------TRDLEKPFLLPVESVYSIPGRGTVVTGTLERGILKKGDECEFLGH-SKNIRTVVTGIEMF----HKSLDRAEAGDNLGALVRGLKREDLRRGLVMAKPGSIQP---
3+
>seq0002
4+
PLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTK---GRKERVARLLRMHANHREEVEELKAGDLGAVVGLK----ETITGDTLVGEDAPRVILE
5+
>seq0003
6+
P------------------VRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMH----RKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITP---

‎Ref/EFTU_C.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
----HQKVEAQVYILTKEEGGRHKPFVSHFMPVMFSLTWDMACRIILPPGKELAMPGEDLKLTLILRQPMILEKGQRFTLRDGNRTIGTGLVTDTPAMTEEDKNIKW
3+
>seq0002
4+
TIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS----------
5+
>seq0003
6+
----HTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE----------

‎Ref/EGF_Lam.ref

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>seq0001
2+
CPCPG------GSSCAIVPKTKEVVCTHCPTGTAGKRCELCDDGYFGDPLGSNGPVRLCRP
3+
>seq0002
4+
CQCNDNIDPNAVGNCN--RLT--GECLKCIYNTAGFYCDRCKEGFFGNPLAPNPAD-KCKA
5+
>seq0003
6+
CACNPYGTVQQQSSCN--PVT--GQC-QCLPHVSGRDCGTCDPGYY-NLQSG----QGCER

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