--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta	Fri Mar 06 11:48:09 2015 -0500
@@ -0,0 +1,119 @@
+>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis
+MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE
+LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI
+KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD
+NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH
+TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN
+LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP
+QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF
+GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR
+>Streptococcus_suis|ORF2 length 385 aa, 1158 bp, from 1507..2664 of Streptococcus_suis
+IINKGESMIQFSINKNIFLQALSITKRAISTKNAIPILSTVKITVTSEGITLTGSNGQIS
+IEHFISIQDENAGLLISSPGSILLEAGFFINVVSSMPDLVLDFNEIEQKQIVLTSGKSEI
+TLKGKEAEQYPRLQEVPTSKPLVLETKVLKQTINETAFAASTQESRPILTGVHFVLTENK
+NLKTVATDSHRMSQRKLVLDTSGDDFNVVIPSRSLREFTAVFTDDIETVEVFFSNNQILF
+RSEHISFYTRLLEGTYPDTDRLIPTEFKTTAIFDTANLRHSMERARLLSNATQNGTVKLE
+IANNVVSAHVNSPEVGRVNEELDTVEVSGEDLVISFNPTYLIEALKATTSEQVKISFISS
+VRPFTLIPNNEGEDFIQLVTPVRTN
+>Streptococcus_suis|ORF291 length 760 aa, 2283 bp, from complement(184307..186589) of Streptococcus_suis
+KRGEFMRFNQFSFIKKETSVYLQELDTLGFQLIPDASSKTNLETFVRKCHFLTANTDFAL
+SNMIAEWDTDLLTFFQSDRELTDQIFYQVAFQLLGFVPGMDYTDVMDFVEKSNFPIVYGD
+IIDNLYQLLNTRTKSGNTLIDQLVSDDLIPEDNHYHFFNGKSMATFSTKNLIREVVYVET
+PVDTAGTGQTDIVKLSILRPHFDGKIPAVITNSPYHQGVNDVASDKALHKMEGELAEKQV
+GTIQVKQASITKLDLDQRNLPVSPATEKLGHITSYSLNDYFLARGFASLHVSGVGTLGST
+GYMTSGDYQQVEGYKAVIDWLNGRTKAYTDHTRSLEVKADWANGKVATTGLSYLGTMSNA
+LATTGVDGLEVIIAEAGISSWYDYYRENGLVTSPGGYPGEDLDSLTALTYSKSLQAGDFL
+RNKAAYEKGLAAERAALDRTSGDYNQYWHDRNYLLHADRVKCEVVFTHGSQDWNVKPIHV
+WNMFHALPSHIKKHLFFHNGAHVYMNNWQSIDFRESMNALLSQKLLGYENNYQLPTVIWQ
+DNSGEQTWTTLDTFGGENETVLPLGTGSQTVANQYTQEDFERYGKSYSAFHQDLYAGKAN
+QISIELPVTEGLLLNGQVTLKLRVASSVAKGLLSAQLLDKGNKKRLAPIPAPKARLSLDN
+GRYHAQENLVELPYVEMPQRLVTKGFMNLQNRTDLMTVEEVVPGQWMNLTWKLQPTIYQL
+KKGDVLELILYTTDFECTVRDNSQWQIHLDLSQSQLILPH
+>Streptococcus_suis|ORF292 length 216 aa, 651 bp, from 185183..185833 of Streptococcus_suis
+AVGKDHLTLDPISVEQIIAVMPVLIVVTAGAVQGSTLGSQSFFVGCFIAEEVTCLQTLGV
+GQGGQAVQIFAWIATRAGHQPVFTVVVIPRGNPCFCDDDFQSVHASCCQGIGHGTEIRQS
+RRRYLTIGPIGLDLKRASVVCVGLGATVQPVNHRFIALHLLVVARCHVARRAQRANTRHM
+EAGKAASEEVVIEGVRSNVPQFFSSRADRQVPLVQV
+>Streptococcus_suis|ORF583 length 391 aa, 1176 bp, from 397805..398980 of Streptococcus_suis
+RKKMKKQFELIATAAAGLEAVVGREIRNLGYECQVENGRVRFQGDVKSIIETNIWLRSAD
+RIKIIVGQFPAKTFEELFQGVFNLDWENYLPLGCKFPISKAKCVKSKLHNEPSVQAISKK
+AVVKKLQKHFSRPEGVPLQEMGAEFKIEVSILKDVATVMIDTTGSSLFKRGYRVEKGGAP
+IKENMAAAILQLSNWYPDKPLIDPTCGSGTFCIEAAMLAKNIAPGLKRSFAFEEWPWVED
+QLVVALRKEAQASIKTDLVLDITGSDIDARMIEIAKKNAFAAGVEQDIVFKQMRVQDLRT
+DKINGVIISNPPYGERLLDDEAIVTLYREMGETFEPLKTWSKFILTSDELFETRFGQQAD
+KKRKLYNGTLKVDLYQFFGQRVKRQVQEVQG
+>Streptococcus_suis|ORF584 length 487 aa, 1464 bp, from 398981..400444 of Streptococcus_suis
+EDIVGEKNSHHLPLDEEKVLDFEVAKDLTIEEAVKKHKEIEAGVTEDDGLLDRYIKQHRA
+EIESQKFETKINHLPLVEVADEEKNQGHESAEEVEANESSLTEVSEEIAPIVEELSVTPM
+ETLEETVIASTVAMEGLSSVADDSSLELEEDETEDLDHSEGADRDQKKKFYFWSAVGLSM
+IGVMATALVWMNSVNKSNTATSSSSTSTSQTSSTASSSTDANVTAFEQLYNSFFTDSSLT
+KLKNSEFGKLAELKVLLEKLDKNSDSYTKAKEQYDHLEKAIAAIQAINGQFDKEVVVNGE
+IDTTATVKSGESLSATTTGISAVDSLLASVVNFGRSQQEVASATVASEAAVTRNQGADET
+VSTGVPATTEVASTTVSGSTTDFGIAVPAGVVLQRDRSRVPYNQAMIDDVNNEAWNFNPG
+ILENIVTISQQRGYITGNQYILEKVNIINGNGYYNMFKPDGTYLFSINCKTGYFVGNGAG
+HSDALDY
+>Streptococcus_suis|ORF873 length 343 aa, 1032 bp, from 605439..606470 of Streptococcus_suis
+TLGEETMTNVFKGRHFLAEKDFTRAELEWLIDFSAHLKDLKKRNIPHRYLEGKNIALLFE
+KTSTRTRAAFTVASIDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQKM
+VEELAEFSGVPVWNGLTDAWHPTQMLADYLTVKENFGKLEGLTLVYCGDGRNNVANSLLV
+TGAILGVNVHIFSPKELFPEEEVVALAEGFAKESGARVLITDNADEAVKGADVLYTDVWV
+SMGEEDKFAERVALLKPYQVNMELVKKAENENLIFLHCLPAFHDTNTVYGKDVAEKFGVE
+EMEVTDEVFRSKYARHFDQAENRMHTIKAVMAATLGDPFVPRV
+>Streptococcus_suis|ORF874 length 113 aa, 342 bp, from complement(605625..605966) of Streptococcus_suis
+VSNIVTAITTVNQSQAFQLAKVFFDSQVVRQHLSWVPCICQTIPYWHTGEFCQFFHHFLT
+ETTEFNTVEHTSQNFSSIFCRFFLTKLDVICTKIFWMGTKVNRCYCEGSTSTC
+>Streptococcus_suis|ORF1165 length 105 aa, 318 bp, from 811613..811930 of Streptococcus_suis
+AYNESVKRKECHLMKQVNMSKIINYLTILGLLILLSAFFLDNWIRDWFFPSSWGNVATML
+ILPLLGALILILSIYYKKLWTGLISIFLIISFPLIFGIGYFIFGP
+>Streptococcus_suis|ORF1166 length 125 aa, 378 bp, from 811867..812244 of Streptococcus_suis
+YLLNNLISSDIRYWLLYIWPLEGVVMNLTLLKRLNLVLYGIAIFLFVMLFLPIGQWFDIV
+NVNFKLTFFIIPFFGLASLPTAIYTKNVRQILLSVLLVALYFILFSLITALSGLFHLNFY
+SFFFK
+>Streptococcus_suis|ORF1455 length 114 aa, 345 bp, from 1026973..1027317 of Streptococcus_suis
+SCKLSLHIRWESWMGQGFYCYRFKLIHLRTNSNPFSFFRHLNSHFQHLRNEWTVMLPDSV
+LDQDISTSHCRCHHKGTRFDTILHHLMFCASQFFYTSNRNRLCTCPLNFCPHFV
+>Streptococcus_suis|ORF1456 length 116 aa, 351 bp, from complement(1027944..1028294) of Streptococcus_suis
+YGNACNSRPPTCDKSYSCWETLIYMGLNLVQFHFLISWYNGNMVISILQFFSHILFIYLA
+HHLLVTTVDWSRWLKVTGDNQRKINLLILFLAIALGYLVSTFFLELLMMGRSFANM
+>Streptococcus_suis|ORF1747 length 335 aa, 1008 bp, from complement(1225218..1226225) of Streptococcus_suis
+RMLNTDDTVTIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARG
+LASKKTTTVGVVIPNIANAYFATLAKGIDDIADMYKYNIVLANSDENDEKEINVVNTLFS
+KQVDGIIFMGYHLTDKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYAAASVDAVNLLAK
+NNKKIAFVSGPLVDDINGKVRFAGYKQGLKDNGIEFNEGLVFESKYKYEEGYALAERILN
+AGATAAYVAEDEIAAGLLNGVSDMGIKVPEDFEIITSDDSLVTKFTRPNLTSINQPLYDI
+GAIAMRMLTKIMHKEELENREVVLNHGIKVRKSTK
+>Streptococcus_suis|ORF1748 length 377 aa, 1134 bp, from 1226384..1227517 of Streptococcus_suis
+TKISLFLPLHARKVSTMSKLHHVKSYLEANKMDLAIFSDPVSIYYLTGYHSDPHERHMML
+FVMPDHDSLLFLPALDVERAVATVDFPVAGYMDSENPWQIIKSKLPQKSFSAICAEFDNL
+NLTRYHGLQSIFSQPFSDITPLINTMKLIKSRDEIEKMLVAGEFADKAMQVGFNNISLDV
+TETDIIAQIEFEMKKQGISKMSFETMVLTGDNAANPHGIPSTNKIENNALLLFDLGVEAL
+GYTSDMTRTVAVGKPDQFKKDIYNLTLEAHMAAVNMIKPGVTAGEIDYAARSVIEKAGYG
+EYFNHRLGHGLGMSVHEFPSIMEGNDLVIEEGMCFSVEPGIYIPGKVGVRIEDCGYVTKN
+GFEVFTKTPKELLYFEG
+>Streptococcus_suis|ORF2037 length 234 aa, 705 bp, from complement(1422380..1423084) of Streptococcus_suis
+KSMTKTALITGVSSGIGLAQAGIFLENGWRVFGIDLASKPDLAGDFHFLQLDLTGDLSPV
+FSWCQSVDVLCNTAGILDDYRPHLDISEDELAQIFAVNFFAVTRLTRPYLQQMVDRQSGI
+IINMCSIASSLAGGGGSAYTASKHALAGFTKQLALDYAKDKVQIFGIAPGAVQTGMTQKD
+FEPGGLADWVADQTPIGRWTQPSEIAELTFMLATGKLASMQGQIITIDGGWSLK
+>Streptococcus_suis|ORF2038 length 112 aa, 339 bp, from 1422849..1423187 of Streptococcus_suis
+SSKMPAVLQRTSTDWHQEKTGDKSPVRSSCRKWKSPAKSGLLARSIPKTRQPFSKKIPAC
+ARPMPLETPVMRAVLVMDFYPVGRKDIARGRAPHGEAFTLAGHVDEEIGRRL
+>Streptococcus_suis|ORF2329 length 160 aa, 483 bp, from 1612284..1612766 of Streptococcus_suis
+LIETNWFHHLTGQEGLDVLFFHNLGFRITDQLYLEVRKFHLLQGLSQLLRRWSQESRVKG
+ARYIERNHPLDTCFLQQFNRLIHCSHLASDDDLGWCVVVGWGNNPRGNSRTDFFNQVDIC
+VENSNHLTSPCWRSQFHIFTTLSNQGNRIFKGQSSRCHQS
+>Streptococcus_suis|ORF2330 length 329 aa, 990 bp, from complement(1613050..1614039) of Streptococcus_suis
+ARKKDEGIMKTKITELLDIKYPIFQGGMAWVADGDLAGAVSNAGGLGIIGGGNAPKEVVK
+ANIDKVKSITDKPFGVNIMLLSPFADDIVDLVIEEGVKVVTTGAGNPGKYMERLHAAGIT
+VIPVVPSVALAKRMEKLGVDAVIAEGMEAGGHIGKLTTMTLVRQVVEAVSIPVIAAGGIA
+DGAGAAAAFMLGAEAVQVGTRFVVATESNAHQAYKEKVLKAKDIDTTVSASIVGHPVRAI
+KNKLSSAYAAAEKDFLAGKISADAIEELGAGALRNAVVDGDVTNGSVMAGQIAGLVSKEE
+SCEDILKDIYYGAAKVIREEASRWASVGE
+>Streptococcus_suis|ORF2619 length 107 aa, 324 bp, from 1802386..1802709 of Streptococcus_suis
+QLCVGSNPINSLFRRNFFVCCISSQSSCYVHTMWFVGIIVEIIVARYIIIAMGNFQCVCP
+CRRWSNVLNFRNDTIIQPHVFVLNIQTGVNDCNHHSATICLIFRTCF
+>Streptococcus_suis|ORF2620 length 192 aa, 579 bp, from complement(1803558..1804136) of Streptococcus_suis
+RLKIPCFQRKEVTMYDSFDKGWFVLQTYSGYENKVKENLLQRAHTYNMLENILRVEIPTQ
+TVQVEKNGEVKEVEENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLE
+EEIRQILVSMGQTVQEFDIDVKVGDTVRIIDGAFTDYTGKITEIDNNKVKMVISMFGNDT
+IAEVNLSQIAEL