transrate 0.1.0 → 0.2.0
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- checksums.yaml +4 -4
- data/.gitignore +16 -1
- data/.travis.yml +8 -0
- data/README.md +45 -43
- data/Rakefile +36 -0
- data/bin/transrate +98 -50
- data/deps/deps.yaml +55 -0
- data/lib/transrate.rb +19 -4
- data/lib/transrate/assembly.rb +93 -182
- data/lib/transrate/bowtie2.rb +37 -13
- data/lib/transrate/cmd.rb +19 -0
- data/lib/transrate/comparative_metrics.rb +239 -19
- data/lib/transrate/contig.rb +212 -0
- data/lib/transrate/contig_metrics.rb +76 -0
- data/lib/transrate/read_metrics.rb +83 -41
- data/lib/transrate/samtools.rb +73 -0
- data/lib/transrate/transrater.rb +31 -11
- data/lib/transrate/version.rb +1 -1
- data/test/data/150uncovered.l.fq +892 -0
- data/test/data/150uncovered.r.fq +892 -0
- data/test/data/Os.protein.2.fa +95 -0
- data/test/data/Os.protein.fa +199 -0
- data/test/data/assembly.2.fa +26 -0
- data/test/{assembly.fasta → data/assembly.fasta} +0 -0
- data/test/data/bridging_reads.l.fastq +20 -0
- data/test/data/bridging_reads.r.fastq +20 -0
- data/test/data/sorghum_transcript.fa +4 -0
- data/test/data/tiny.sam +4 -0
- data/test/helper.rb +33 -2
- data/test/test_bowtie.rb +54 -0
- data/test/test_cmd.rb +15 -0
- data/test/test_comp_metrics.rb +177 -0
- data/test/test_contig.rb +61 -0
- data/test/test_contig_metrics.rb +50 -0
- data/test/test_inline.rb +10 -9
- data/test/test_read_metrics.rb +68 -0
- data/test/test_samtools.rb +22 -0
- data/test/test_transrate.rb +40 -0
- data/test/test_transrater.rb +68 -0
- data/transrate.gemspec +16 -10
- metadata +232 -57
- data/lib/transrate/express.rb +0 -37
- data/lib/transrate/log.rb +0 -16
- data/lib/transrate/rb_hit.rb +0 -33
- data/lib/transrate/reciprocal_annotation.rb +0 -105
- data/lib/transrate/usearch.rb +0 -66
- data/test/test_test.rb +0 -41
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@@ -0,0 +1,95 @@
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1
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+
>LOC_Os03g60760.1|PACid:24121828
|
|
2
|
+
MEVEMGHGEEVAAAMEEEELQGWETPRREECRIPVVPPQCPAPPRKRPVALPELGKERREPPKGGYFQPPDLESLFVLAP
|
|
3
|
+
PRRQASSCA
|
|
4
|
+
>LOC_Os03g08270.3|PACid:24121831
|
|
5
|
+
MSIEERTLSLINKTTALNPNAQEFVPSSLRSINDVSNRSDTSRISVSGSSKDTIADQQDPVIPSNPDEEAHRYWQEQLPD
|
|
6
|
+
DITPDFKVLGQDEMPGPDNISLTGLSINDSIGASLFSPNQTSNLQHRASPFIRDTLSTRSKIEFPSPTYVEEQSRATIMS
|
|
7
|
+
PTASAMSPTAAPWVKTVRNGVQYNANRRDASHYNGDSSIGAPVQNLTDAYFGSRRSFSSTMDIMSQLENKVDGRFNQNLR
|
|
8
|
+
SLSFGHSSPPSPASYGQNGLANYNKEAFGLANNTYRSHSAVLADDILSPSAGREHISLDAPRGRYNTTNLPVSGLGSSRG
|
|
9
|
+
SQFMASSFNGNHDIVSNNTLQNIAGVQTGPAWLEADTAANMFLESKDEAHDFASLRHALLEQDRQVLLTGANPLAKELNI
|
|
10
|
+
KELYNLQSRLAQEKARDVYRQRFQMPEFQGLVQEQNTPIDLCGLHVSEAIHALNYELNNRRKIARSTGRRLQVIIISSTR
|
|
11
|
+
TPARLTAAVEQYLLEHGIQYTQAQPGLFRVLLQ
|
|
12
|
+
>LOC_Os10g39590.1|PACid:24095156
|
|
13
|
+
MSMITVKVKTLTGKEVEVSIEATETVARIKEQVEAAEGIPPPQQTLIYGGRQLADDMTAEMCDLRHGSELHLVLALRGGL
|
|
14
|
+
L*
|
|
15
|
+
>LOC_Os10g41970.1|PACid:24095158
|
|
16
|
+
MRGSRMNPGDRRTRSTMSIVIVMSLCCFFYILGAWQKSGTGRGDSIALRVTKETDCTILPNLHFETHHSLGGVNPLVMTD
|
|
17
|
+
KVFEPCHIRYSDYTPCQDQNRAMNFPRENMNYRERHCPTETKKLRCLIPAPKGYVTPFPWPKSRDYVPYANAPYKNLTVE
|
|
18
|
+
KAVQNWVQFEGDVFRFPGGGTMFPNGANAYIDELASVIPFTDGTIRTALDTGCGVASWGAYLMDRNVLTMSFAPRDSHEA
|
|
19
|
+
QVQFALERGVPAVIGVLGTIKLPYPSGSFDMAHCSRCLISWKSNDAMYMFEVDRVLRPGGYWILSGPPINWKTNHQAWKR
|
|
20
|
+
SKEDLEAEQNVIEKIAEMLCWGKIHEKGDTVIWRKKADSNECHNKDDHPSKMCKIQDADDVWYKKMEGCITPFPEEAQLR
|
|
21
|
+
KFPERLFAAPPRILQGRTPGVTEEIFEEDNKLWKKYVSTYKRINKLIGSLRYRNIMDMNAGLGSFAAIIDSPISWVMNVV
|
|
22
|
+
PTISEKNTLGIIYERGLIGIYHDWCEAFSTYPRTYDLIHANGLFSLYQNKCNMEDILLEMDRILRPEGAVILRDNVEVLN
|
|
23
|
+
KVRRTVMGMRWKSKLLDHEDGPHIPEKILVSVKKYWVGNEEENSS*
|
|
24
|
+
>LOC_Os09g38670.1|PACid:24136581
|
|
25
|
+
MPFASCLLASSSSTMMARPGAVKNIESWDEFTKHFVKSEDKLVVLVFMAPWSEPWKLMRPAVEKMASGLKSEEAEVCTIS
|
|
26
|
+
VDRFNTLGRLLRVEALPTFVLVKRHRAVARVVGVNRDDLHSSINKHLAPPSSSPQPINIS*
|
|
27
|
+
>LOC_Os09g26780.1|PACid:24136584
|
|
28
|
+
MAGRATATATAAGKDRSSFAVTCSLLSQFLKEKKGGGGGLQGLGLGLRPAPAAPPAAGAGGAFRPPPTTMNLLSGLDAPA
|
|
29
|
+
VEVEPNTAETAADELPLIKAPADQQSDESASEAAGEKAQQLTIFYGGKVVVFENFPSTKVKDLLQIVSTGDGVDKNTGTA
|
|
30
|
+
ATQSLPRPAHNSLPDLPIARRNSLHRFLEKRKGRMNANAPYQANCTAAPSKQANGDKSWLGFGQEMTIKQEI*
|
|
31
|
+
>LOC_Os12g21920.1|PACid:24147808
|
|
32
|
+
MPTPSTATRRPSTVTRFALCLSSPPSTPLPTPVAAAHADADAAAAVIGRPKGEGREWEERSRSQRTPSPPNSESPPKANW
|
|
33
|
+
GIASNNCYSRMIIASAALTSDRRMSNACDRMLAAVIPSPTAQPHAGHKGRDVCVLGYASPCPCPHLAGATAMNAT*
|
|
34
|
+
>LOC_Os12g24659.1|PACid:24147809
|
|
35
|
+
MADDKVISAIGPYFGKKLDLELIYGKKWQCSKEAALDSSTWQLNHQFMLI*
|
|
36
|
+
>LOC_Os01g36294.1|PACid:24116931
|
|
37
|
+
MAKVHELSTKGMAVDMTELFSTFSNDLICRLVSGKNFQGEGRNKLFRQLFKANSVLLAGFNLKDYYPGLARLKAVSMVMC
|
|
38
|
+
AKARNTRKLWDELLDEIIDERMSKQQCEHDEGNDQDEMNFVNVLLLQEQGITREHLKAILVDMYQAGTETSSVVLVFAMA
|
|
39
|
+
ELMQKPHLMAKLQAELRTTIPKQGHELITERDLTDMTYLKAVIKETLRLHPPTPLLLPHLAMADCNIDGYTVRSGTRVIV
|
|
40
|
+
NAWAIGRNSESWEAAEEFLPERFVDDGSAANVDFIGTDFQFLPFGAGRRICPGINFASASMEIILANLLYHFDWDVSAEA
|
|
41
|
+
AIDKDGIDMAEAFGLSVQLKEKLLLVPVDYKDGMQDSAVILL*
|
|
42
|
+
>LOC_Os01g36410.1|PACid:24116932
|
|
43
|
+
MAGVGGRLGTATARVVRRMMTRLKDGGAPWDYEEAYPVLYLGGGEGGAGDRQWEPGAVGLALSLRASALAGGGGYGLATA
|
|
44
|
+
AAVVGFAGGRHGGRGVCFADAGQWLSRRRQQRSGSSRLVAPGRGAASVGRGGCEGSAGRGRASGRGGAEASSALHSLAAR
|
|
45
|
+
FAGRGGMGGLGATTFGSHPMCSMKCLQGKRWERGERDGVLGHWQVGSRVLGPTDQRSTGIGEMRNISSQGFFFREG*
|
|
46
|
+
>LOC_Os12g22750.1|PACid:24148077
|
|
47
|
+
MSGVPPAAAGGDGTGGAPPGAGAGGGAPGAGAANNNINGGNSASQSSGGPFSRCILLLFPLLALSLYCHVRYVPVPDLHD
|
|
48
|
+
ASSMLLSYCNVSVPDIHDAHRKENGAFNTRKRRAFSAASLYVRPCSGMLRPPLSSELGGGGSEEEEGEPRGERE*
|
|
49
|
+
>LOC_Os12g22780.1|PACid:24148079
|
|
50
|
+
MEDLHDWECRFTPRKLASLNKWSSRAGLSPMELQSCAGEVTDKVTAIAWGGRIRYLHLAFGGSSCWRYVVGLREGNKNVG
|
|
51
|
+
AIVKGFHDGVAMGVFSLVDSREAAEAPTASHGDGLESQCGGSHAAVQGEHNLEPWAEACVCSIAF*
|
|
52
|
+
>LOC_Os02g55190.1|PACid:24133604
|
|
53
|
+
MAMERNAAPRVSASSSAAASPSTVGALLSKASVAAAPAREIPSPRSLLSRILHRSGGGGGFGCRLRLPRYCSSGAAAKED
|
|
54
|
+
AAAEYVEVEVEAEAAAPKVVGRQAVDRESPRSSLGKKAAEEVSPASLGLGASLMLLLSKSAAELNRMAELRAQMERLVLD
|
|
55
|
+
TKGEEEARSSNHPNASDDHADITKEEPTAFSGGALSRCSRTAAAPGNAGHHAAVPMDQMEAELEAELTLLQCATPRRDRQ
|
|
56
|
+
LEIGDDEEESTDTHAATFADADDDTDGADDEEEEEEESGAAAQGGVSARELERRLHELLQWRHEERIAELETALERARKR
|
|
57
|
+
LQEKEREVCWWRNTAKLVTRHKDDSRLR*
|
|
58
|
+
>LOC_Os02g56470.1|PACid:24133605
|
|
59
|
+
MVPQSGVGTKAVDYEVEQRDGGRVVKRKEAGLTRGSHGGVPVATSSVGRDMLAVSDIQAETPYAQLNAASVPGEAGRQGR
|
|
60
|
+
WGSLPTARTLCRPCLLAADLSDELALTPIHQLRRLTSCT*
|
|
61
|
+
>LOC_Os03g56500.1|PACid:24123297
|
|
62
|
+
MSGEAESREASRQRRRRERAAAVERFVGVPLADVVRENSLVHLPPAAAARLRVVHPSWASHMSSPLFAVAHAAAPRRVSG
|
|
63
|
+
VFVPSAGFLPFDGDDDAVPSPSLSFVPASSELVVLSSSRGVACCFSPADDAYAVCNPATASWTAVPSPPWRSWPRPAIVV
|
|
64
|
+
LFDTSAYNFRGDFTLVCPFESEPGSSGAYCFQVFTSGTGAWWVTDAMSPAEGLVAASGVAAGATAWWRTSIGTAVGYTPV
|
|
65
|
+
TGRVDLVTCPGDSDQWEIGLAAGMLHCAVIDGGDVVVFRLHEHGIWEVTTRVAVAEILQPSQPPPPARATTSTEIVASQQ
|
|
66
|
+
HDESGAEEEEGSRAVVAAANAPLRLDDGVRLLGFQGAEVEVVVLAGRRLVAFDARTRRRREVAVPDEVDAAWDGAEHAAH
|
|
67
|
+
INTLALIAPAALAAEPPLAKPPADP*
|
|
68
|
+
>LOC_Os03g30530.1|PACid:24123298
|
|
69
|
+
MPSRMMQAFAQEASDFDRQMGCMAGMFQIFDRRRLLTARQRGGARGTAPPGSHVLPNSNSNVSIQNPVASNNTLDKTFSK
|
|
70
|
+
SMTENSSLSMESSRASSSSSSCSSFSSTDINRPIQQELSYINKERFAGKPPRSSQTKSVKCSKTEAKTKDPHTGFRDIVK
|
|
71
|
+
ESINRETHGMTIKTSTKESRKGLHKDSPRPLLISKSTDGTYVIGIDRSTGVPGYVHESSRPPRFSCDDRQLLRSVEAQDS
|
|
72
|
+
KKPSAKLKELPRLSLDSRKESMNPCSRLKNSGYIRTDDNLLDVLKHQESPSHQRASSVVAKLMGLEGTTPDIHETARSPT
|
|
73
|
+
PVHGTQIDQPSHCQRIKNQDHSVPVQKNHSPVLKTNPSPRIIPEAAPWRQNERAVTGRAAEVKPRTASIYADIQRRLRGL
|
|
74
|
+
ELSECNKELRALRILSTLHKKDGPSQSDNNPELTAIQKKASEQIVDSENFQSPIVIMKPARCITKPDASDTLVAPLSRPK
|
|
75
|
+
GIRRLRHEETSFTRKNENSDSKRNHSPNESAHSSGEEPVNSARSPRLSSSLSPRLAQKKADSERRSRPPVLPTSPGKKSK
|
|
76
|
+
ETVSPRGRLRSRHSQTKSNSDNDNVLHIPETKINLAKQIDVGVVDHPNPLNANSPYIHQSKIASTPNREEMPTILPADKK
|
|
77
|
+
>LOC_Os03g56724.1|PACid:24125111
|
|
78
|
+
MSCEKLSRQSLHLVLNEGRGLFSLRHMDVSKLFYPSTAEALEAEAKAKKKKNGTNKIGSIGRLPTPSIHYQPYTWSASNP
|
|
79
|
+
YSSLCALALFGERSKNKILCTDMAGHTSIYNPELRSFMRMPDLNSPKRYNSCVAVSIPGASAHAMSNFDIDTDHSLYIMD
|
|
80
|
+
IDPTYWCSSEVLAYDPVEECWCWGPLPQPPFFQDREYKVPLKPRFMVVDSTKICVSTTTATYSFDMVTRDWNKVGDWVLP
|
|
81
|
+
FNAEYVPELGHCLGMSDGGPFDLCILDNLSTAAGSPPPVVRHVGMEFELPENWSQVYRDLVNLGSLRFCIVNGYTIENER
|
|
82
|
+
YECDFNPVTVFTGVEVLPTSSEQGLLMIKHKSKCIMTYIMFVL*
|
|
83
|
+
>LOC_Os03g49850.1|PACid:24125112
|
|
84
|
+
MTPGLEGVDPAVLDSGAADSPLLTSVTSTMRMTVVARATATIATSHARVDLAAPDSGAADPPPPSSAMMMTIMTTRARMT
|
|
85
|
+
TMTMASRARADPSGAELGRGRFANVGLRSCGDCCGDRVP*
|
|
86
|
+
>LOC_Os01g11360.1|PACid:24119702
|
|
87
|
+
MAARGSRSCAWPCGLGMAGGGQEGSGNRQGVGDGVPPDGGRDSEARRKMVTALGGYGSPRGCGVPRQWQSEHCESDKVEA
|
|
88
|
+
DPIEQIQRGFSIYRANTEGKGVVDGGFTCFAMGIGRVVSAGTAAASAESRLRRLLEMLLVVVSNIGTYQTRGILVKDLLK
|
|
89
|
+
*
|
|
90
|
+
>LOC_Os01g44140.1|PACid:24119703
|
|
91
|
+
MTVAAAAAAAADDAGRPGAAAARLRVMWRVVRAAEALALAVLLSRSLPLLPVAAGAAGAVLRVGASFLLHPCSVFLLANG
|
|
92
|
+
IVVLLVALSRRDRPSSSSSSSSSSSCSDDHDDVHDQFLSFAGAHLPPLPAAITGAAAADQEEGAVFEDKQAVHVTPARAA
|
|
93
|
+
PRRSRSEKVGRGRRPTRAASPELRRSESERCRRRRRSLSSSSASLADWGMEEDDGGEKEEEEFRRAVEAFIAKQQTRFHR
|
|
94
|
+
EESFVLVAGAGAGDETSAAAAAVEVK*
|
|
95
|
+
|
|
@@ -0,0 +1,199 @@
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|
|
1
|
+
>ChrUn.fgenesh.mRNA.8|PACid:24093257
|
|
2
|
+
MSHSSGASDASSTSDEEPVPAPSTSVLQTVNIRSHVPVVLDLDVSNYSQWRCSFESVLGKFGLEAHVQEPPALDLRTAEW
|
|
3
|
+
RRADHCVVNWLHNSIAKNVFDVVYKPRASAFTVWSDIEGVFRDNAVQRSVYLETEFRSINQGDMTITQYTAKLKQLADGL
|
|
4
|
+
RDINMPVSEPSQVLNLLRGLNTKFRSLRASIADRNPPHTFMTARSYLLLAELQMQHDAKAEAGEALYAGTGSSSGTSDTT
|
|
5
|
+
GQPRPKGRGKRRGRGGGAPPGGAPSTPGGGAGAGHDGQPRPPAPWGYNPWTGFVQAWPFPFRAPGAGVLGPRPPFQAQQA
|
|
6
|
+
MTAQHLLPALPPASPGVQSTGAWDNSALYSALQSAGVATTTPPSAADWFLISSSHVRLLHLPRRLPHLLVVQAADDRLEA
|
|
7
|
+
TIAYCDNISSVYMSKNPVHHKRTKHIELDIHFVREKVALGELRVLPIPSAHQFADVFTKGLPSSMFNEFRASLCVDRRST
|
|
8
|
+
AGSGALTSSTTEYSPTMLSISEFRYGSLASVARLIDRSSCTCTYLVLGNAPMALESSKVFAKAAVFAMCMIVALTSPSNH
|
|
9
|
+
FCPSQELSSAVTDVLTCAYAVLLSALRRSWSRDNWRTNRHCPQCDNIPHPLAHSYARSGGISNNVEVGEVMGPSESVRSA
|
|
10
|
+
RGEVAVVARLALWLRRDKKKHARPRGKRIGASTIKGTSSSADARFDTQIPGSSTHKYQRGVCGDFINLKIYRSNLSEVSI
|
|
11
|
+
GPFRGWALDFTGQIYPSSSKGHWFVLVAMDYFTKWAEAVPPENITCTEANG*
|
|
12
|
+
>ChrUn.fgenesh.mRNA.7|PACid:24093258
|
|
13
|
+
MDRRSRHWRDGGRGRTGGGSAGVIEVEDGLTPGGGGAMEVDGRSAESRGGAVEAEGGAAEVHGGCGKAESAWWRRKAEAP
|
|
14
|
+
WKRRRCIGGGRRRRRDRAQRNAMGRGGAAFVACGLVGGRYHVSVMVKTTNGSRDSNNASGSEEQINGPRASGASDNSPSP
|
|
15
|
+
PHENPTIDQVLDNQTQMMTMMMQQMQQQYHQVLQQSKLLKFLRVKPPTFSGTTNPIEANDWLHAIEKKLNLLQCNDQEKV
|
|
16
|
+
AFATHQLQGPVSVWWDNYMVTRPAGTEVTWSEFCQSFNKAQVPEGIVAQKKREFRSLQQGTKTVIEYLHEFNRLARYAPE
|
|
17
|
+
DVRTDAERQEKFLSGLDDELINQLISRDYEDFEKLHCPYHPGSFNKNYNSGSHSNKEAQSAPEVILGTFPINWTPAVILF
|
|
18
|
+
DSGATHSFISKRFAGAHGLSLVKLKIPMRVHTPGGGMTTTHYCPSVTVEIQGLIFLANLILLESKDLDVILGMDWLTRHR
|
|
19
|
+
GATGEEQEVVVEKTTKKLEDITIVREYPEVFPDDLTTMPPKRDIEFRIDLAPGTAPIHKRPYRMGANELAEVKKQVDEQL
|
|
20
|
+
QKGYIRSSTSPWGAPLRIREEDIPKTAFITRYGLFECTIMSFGLTNAPAFFMNLMNKVFMEFLDKFVVVFINDILIYSKF
|
|
21
|
+
EEEHEQHLRLVLEKLKEHQLYAKFSKCDFWLKKVQFLGHVISAQGVAVDPANVESVTKWTPPRTVTQGLRCVLMQDGKVV
|
|
22
|
+
AYASRKLRPHEGNYLTHDLELATVVHALKIWRHYLIGNRCERRWLELIKDYDMGIHYHPGKANVVADALSRKSYCNVAWV
|
|
23
|
+
EELCCEAQPTLVEQVRIAQASDPEIAKLKKNMRVGKARGFTEDEHETIWMGERLCVPENKELKDLILIEAHQTQYSIHPG
|
|
24
|
+
STKMYQDLKEKFWWVSMRREIAEFIALCGVCQRVKAEHQRPAGLLQPLQIPEWKWEEIGMDFITGLPRTSSGHNSIWVVI
|
|
25
|
+
DRLTKVAHFIPVHTTYSGKRLAELYLARIMCLHGVVGNFL*
|
|
26
|
+
>ChrUn.fgenesh.mRNA.71|PACid:24093259
|
|
27
|
+
MAVRRRGSVAGDSNQAAREVAAHGAKGGGVGQRRLRTRERRVRGGGPHQRAWRPAQRMKAAVTTGDAEARTADGDT*
|
|
28
|
+
>ChrUn.fgenesh.mRNA.11|PACid:24093260
|
|
29
|
+
MTWRKFRTDRAGKAVMAIEEVQALRKEFDAQQASNYQQPVHKKVRKDLYYAFHGRSSHTTEQCRNIRQRGNVQDPRPQQG
|
|
30
|
+
ATVEAPREAVQEQAPPAEQRQDAQRRVIQVITRADPPSQLSKRQKKMQIRTVHSITSAGEGAPQYLNQLISFGPEDAEGV
|
|
31
|
+
MFPHQDPLVILAEIAGFEVRRILVDGGSSADVIFAEAYAKMGLPTQALTPAPASLRRFGGEAVEVLGQALLLIAFGSGEN
|
|
32
|
+
RREVQLQRHLRPCNPEQVRSHFPPQLSQAQDARPDRSDSARITGGDMGEEEAESILEVLKKNIDIFAWSPDEVGGVSTDL
|
|
33
|
+
IIHHLAVKPDGKPRKQKLRKMSADRQEVAKAEVQKLLRAGVIQESNHPEWLANPMLVRKSNDKWRMCVDFTDLNKACPKD
|
|
34
|
+
DFPLPRIDQLVDSIAGCELMSFLDAYSGYHQIHMNPPDIPKTAFITPFGTFCHLRMPFGLRNAGATFARQVYKVLCKQLG
|
|
35
|
+
RNVEAYVDDIVVKSRKAFDHTSDLQETFDNLRAADIKLNPEKCVFGIRAGKLLGFLVSERGIEANPEKIDAILQMKPPSS
|
|
36
|
+
VHEIQKLAGRIAALSQFLSKAAERGLPFFKTLRGAGKFNWTPECQAVFDELKQYLQSPPALISPAPGSELLQYLAASPVA
|
|
37
|
+
ISAVLIQETEFGQKPVYFVSEALQGVKTRYIEMEKLAYALVMASRKLKHYFQAHKVIVPSQYSLGEILRGKEVTSRLSKW
|
|
38
|
+
AAELSPFDLHFVARTAVKSQVLADFVAEWTPVFAPEPEPVEQLWVMCSDGSWSHKGAGIAAVLISPNGVPIRYAARLQFD
|
|
39
|
+
TTNNTAEYEAILLGLRKAKVLGVRRFLIQTDSKLVAGHVDKSFEAKEEGMKRYLEAVRSMEKCFTGITVEHLPRGQNEEA
|
|
40
|
+
DALAKSAACGGPHSPGILFEVLHAPSVPMDSLEVMAIDQVKLGEDPYDWRIPFVKHLETGWLLEDEAEAKRLQLRATKYK
|
|
41
|
+
MVSGQLYRSGVLQPLLRCISFAEGEEMAKEIHQGLCGAHQAARTVASKVFRQGVYWPTVLKVCVEQIKKCESCQRHGRTQ
|
|
42
|
+
TAPQYDLQPIAPIWPFARWGLDIIGPFPVARNGYKFAIVAVEYFSRWIEAEPLGAITSAAVQKFVWKNIVCRFGVPKEFI
|
|
43
|
+
TDNGKQFDSDKFREMCEGLNLEIRFASVAHP*
|
|
44
|
+
>ChrUn.fgenesh.mRNA.52|PACid:24093261
|
|
45
|
+
MDGRDRTGPRRLTGEGLDDASDDVTDDGGGSAEETARTAHARRRTAARGRKRRTPGRSGQHGEHTDDQSDGGGGTNDDGD
|
|
46
|
+
EERAAATFGLSTATMLRRVPTAAKGRTRTATTWRPRRRSSRATATTGATAELGWSGGGDGEARAHGARTIPATRGKGEGC
|
|
47
|
+
DNYGTYTCPDGEESATLMHAVHMLSAMDAVSVERDKAAHDRENWNGGKICKLESKVYRLQKELAELKGETPPPAPKLRLT
|
|
48
|
+
ARKRTCPPPRLQLASKIRVIGEAVPDRAEPMVNTRTGSGSGSGSGATNNEGDPTLAQILAQQTQLINLLVQQAQNQQANN
|
|
49
|
+
QNQNPPPPPQNKLADFLHLHGPAAEWWDHFRQGRAEGEPITWQEFTAAFKKTHIPTGVVALKKREFRALNQGSRSVTEYL
|
|
50
|
+
HDFNRLARYAPEDVRSDEERQEKFLEGLNDELSYALMSTDFRDFQQLVDKAIRQEDKYNRMEQKKRRAAQFKAQQGSNQR
|
|
51
|
+
PCLVTGPQAPSYPQGGSSSVVRPQRQFYNNNTGNRGNDNRNMVARPAATPAQNQPVRKEQGSKPVVCFNCGDPGHYADKC
|
|
52
|
+
PKPRRVKNAPASNNSNVPAPKARVNHVAAAEAQNAPDVVLGTFPVNSIPATVLFDSGATHSFLSKSFASNHGMEVISLGR
|
|
53
|
+
PLLVNTPGNQVFSTQYCLSVTIEIEEVPFPSSLILLESKDLDVILGMDWLSRHRGVIDCANRKVTLTNSNGETISFFASS
|
|
54
|
+
LKSHGVILNQVVLQEIPIVQDYPDVFPEDLPGMPPKRDIEFRIDLVPGTNPIHKRPYRMAANELAEVKRQVDDLLQKGYI
|
|
55
|
+
RPNTSPWGAPVIFVEKKDHTQRMCVDYRALNEVTIKNKYPLPRIDDLFDQLEGATVFSKIDLRSGYHQLRIREEDIPKTA
|
|
56
|
+
FTTRYGLFECTVMSFGLTNAPAFFMNLMNKVFMEYLDKFVVVFIDDILIYSKTKEEHEEHLRLALEKLREHQLYAKFSKC
|
|
57
|
+
EFWLSEVKFLCHVISSGGVAVDPSNVESVLSWKQPKTVSEIRSFLGLAGYYRRFIENFSKIARPMTRLLQKEVKYKWTED
|
|
58
|
+
CERSFQELKKRLVTAPVLILPDSRKGFQVYCDASRLGLGCVLMQEGKVVAYASRQLRPHENNYPTHDLELAAVVHALKIW
|
|
59
|
+
RHYLFGNRTEIYTDHKSLKYIFTQPDLNMRQRRWLELIKDYDMEIHYHPGKANVVADALSRKSYCNMSEGRRLPWELCQE
|
|
60
|
+
FERLNLGIVSKGFVAALEAKPTLFD*
|
|
61
|
+
>ChrUn.fgenesh.mRNA.61|PACid:24093262
|
|
62
|
+
MKEMRVTKDDTDYAPADEIGLSQLADAPEATKPSQSPRQIN*
|
|
63
|
+
>ChrUn.fgenesh.mRNA.67|PACid:24093263
|
|
64
|
+
MTTASLVHPSASSSSSSTRAEVEVVGGVFVCSDSCSGDIVRNLIVDYGSGKITLTAACIQFCVPCTRPQPLLPPLCHSGP
|
|
65
|
+
INTCFATADDRGRSRFRHYH*
|
|
66
|
+
>ChrUn.fgenesh.mRNA.75|PACid:24093264
|
|
67
|
+
MSSKVTFQIVHGEGNIRFGPDGVDLSDFVMTSKGIDRPAERTFQSIYSWLLRGFRIDQEVYTMSVSVVVSRAIEGYFWEL
|
|
68
|
+
MPMDSTTAWRRYVEMAFERSWPLVIFVSVQEKDTNVSMRTEDVEGPSNAGDVVGPSMENEENQPREEQAMGMADEGERVG
|
|
69
|
+
IIVDEMEREDSDNEQAEDDASSDEEGDVMATDWANEDFSGLVISEGDHVPWEYKENEVIEGARYAHKDEMKEAVKHWAVS
|
|
70
|
+
LQREFRVVKHIENKFKYTISYAKAWRAKQKIIEMRYGTFEASYDNLPRLLATIAQRNNNTYYDLHTFTSVDDRTKSVLQR
|
|
71
|
+
AFFSLGACINAFVHCRPVLCIDGTFMTGKYRGQILTAIGCDGNNQVLPMAFAFVESENTESWYWFLERVHIAVVRMRPNV
|
|
72
|
+
CLIHDRHAGMLRAIDYLQNGWDEKGLPAKWPDVRSRWCMRHMGANFYKQFKNKHLMDLFKRLCAQNQEKKFNELWDKLDE
|
|
73
|
+
LTTKQTDEQSRRPQVEGEEPPIPLGALHDDPPTMRRRSGSSIRNFSQWIENEPKEKWSLLFDTDGSRYGIMTTNLAEVYN
|
|
74
|
+
WVMRGVRVLPLVAIVEFILHGTQAYFRDRYKKIGPSMADNNIVFGNVVTKYMEDKIKKARRHRVVAQGTQVRRYEIMCVD
|
|
75
|
+
RSRRGIYRKQAIQECVLKADGGCTCSCMKPKLRHLPCSHVLAAAGDCGISPNVYVSNYFRKEAIFHTWSEEIYGFGISGS
|
|
76
|
+
YTTLSAQVFYIPDPSKLRVKKGRRQTRRIRNDMDESEAGGRTLRCSKCDLRGHTYKKCPKNAEVPSGADASPSGQASDGM
|
|
77
|
+
AYDTPALLNRGIDRNHRSFLSAVEGAQLGTFRPRTSREWLRVDPRHVPWLRAAGLLPLCRLVEAAADDRDPAKRWDADRS
|
|
78
|
+
LLAALVDRWRPETHTFHLPCGEMAPTLQDVSYLLGLPLAGAPVGPVAGVVGWKEDITARFEQVMRLPHLGPTNTLPPYST
|
|
79
|
+
VGPSKAWLLQFTADLLHPDADDYSVRRSLEAYLLWLFGWVMFTSTHGHAVDFRLVHYARSIADAQPQDVPQWSWGSAVLA
|
|
80
|
+
ATYRALCEACTKTDAGAIIAGCPMLLQLWAAERFAIGRPVVDSAPYGVGRSAQWPEDGPTMGTYWCRRGRRYAHVQVRRG
|
|
81
|
+
YPDFVFEFDRLQPSDVIWEPYTEEVVAARAPLGLSSLCTRDQAYWLTILPMVFDIFVEPHCPQRVMRQFGLRQVFPGNVQ
|
|
82
|
+
PTVPPADHSLTRRGQLAGALWAPRVQQYVDDWVLATEEVINELFPHTEENYRDYLRWYLPRTRARVTFTPDAPEPHVAAV
|
|
83
|
+
TDAYPTHRDRDYFVAADAARDISADITAVQVRLNRGLHLTDVEQRATFDRMQEKMRAVMRVFSCRSAVDVVPPAGPDLVC
|
|
84
|
+
LRARSQARPGASASSAGAFATSSGAFASSSSHGASIPRPHAGYAAGIFGTGASSSHAGRTGPTSQFYDDDLHGADHQDVL
|
|
85
|
+
GSSQLGGAPEAHTQEQPEVTPVQAGRVGRAVPPDRLTYSQGHIRAQGRRDRVIFIHMVLEQLMLTTTHFRRFTVVPYPVA
|
|
86
|
+
RTVHNSTHEKRQLELSLSTFGVAC*
|
|
87
|
+
>ChrUn.fgenesh.mRNA.32|PACid:24093265
|
|
88
|
+
MEFCSKIFKSYYKYEGIVRHYTVPHKPQQNGVAERFPKQFWAEAVSTACYLINQSPIYTIDKKTHFEVWSSSPANYSDLR
|
|
89
|
+
VFGCTAYAHIDNGKLKPRAIKCIFHGYLSGVKGYKLWCPETKKIQVATVEQSPKCSIAKDKPKGNTKPPQRYIEETNIIA
|
|
90
|
+
YALSVVEEIEEQMDVKTAFLHGGLEEDIYMEQPEGFVVPRKDNLVCRLKKSLYGLKQSPRQWYMRFDSFMIPQKFRRSNF
|
|
91
|
+
YSCVYLKVVDGSAIYLFLYVNDMLIAAKDKSKIAKLKAQLSSEFEMKDLGAAKQILVSTPLAAHFRLSSNLYPQSDYDIE
|
|
92
|
+
FIPRVPYSSAVGSLMYAIVYSRPNLSHALSVVSRYMANPGKEHWKAVQWIFIYLHGTSSGCLQFGGSRDGLVGCKDLDFA
|
|
93
|
+
GDLDRRRSLTGYVFTIGGCAVSWKASLQAAIALSTTEAEYMAISKACNEAIWFRALYTQLCEVTSCINIFCDSQSAICLI
|
|
94
|
+
KYQMFHERTKYIDVRYHFIRGVNA*
|
|
95
|
+
>ChrUn.fgenesh.mRNA.29|PACid:24093266
|
|
96
|
+
MAEGIVGLLITKLSAVLARDATTLLGASQLLKEVSALRGLFSEIHDVKEELESMQAFLQGAELFRDTDKTTSVFVKKIRD
|
|
97
|
+
LAFEIEDVVDEFTYKLDDKHGGFVDRVKKRIKHVKTWHRLAHKLQEIKRRLEAADRRNVRYGMRGIQMKGGCSDAHSKSA
|
|
98
|
+
GQTSYFAREEDLVGIKENKEKLIQWLTGDRELGSKITTIWGMGGVGKTTLVQHVYNTIKVEFDAAAWIAVSKSYDVEDLM
|
|
99
|
+
KKMAKDFGLRIDIVNMENRSLIEMMHRYLQGKRYIVIMDDVWGVDVWFKVRHVFPTNCISRFIITSRIHEVALLATRNSV
|
|
100
|
+
IQLEPLHEHHSWELFCKEAFWNNDNKTCPLELKYLAQKFVEKCNGLPIAIACIGRLLSCKQLTYSEWENMYKQLEIQLTN
|
|
101
|
+
NAIFDVSNILKLSLEDLPYNLKNCLMYCTIFPEDYLIHRRKIIRHWITAGFIQEIGNKTLEQVAEGYLNELVNRSLLQVV
|
|
102
|
+
RRNEFGRLRQCQMHDIIHLLALNKSNEERFCQIYNGSRKVLVAGTRRLSIQNENVEQLDRSGATYLRALHVFKSHINIDL
|
|
103
|
+
LRPILKSSNMLSTLDLENVQINMLPNEVFDLFNLRYLGLHNTNIETLPESLGRLQNLEVLDAFETNLSYLPKHVVKLEKL
|
|
104
|
+
RYLYAGTFFRDHEIIGAFGGIEMPNGLRHLTGLQALQCVKASSEILHEVGALRELRTLGVANVKSEYSADLCAAITKLSH
|
|
105
|
+
LIHLEITAPGEMEVLHLEGLHLPMTVSWLGIEGILEKTSMPQVLSSWSHVSTLTRLRLAFCRLDEDSFSSLLVLHGLYCL
|
|
106
|
+
EISTKGFIGKRLKFSAGSFPNLRTLIVGGAPELNQVDIENGAMQSLDYLLFIECPNLRDLPHGIEHLTVLEKLCLLEASE
|
|
107
|
+
ELIQRLRKMRDSDECDEDLMKISHIRNVTVGQIQKQIWERIR*
|
|
108
|
+
>ChrUn.fgenesh.mRNA.15|PACid:24093267
|
|
109
|
+
MSWHRAGVLLLGAQSCLPVPGVPAVGGIGSVLLSMARMGWKLCHVFRPYTVVMAGSVTRRGLDMTGFVLELRGMCVVLGY
|
|
110
|
+
PHGVDYQARPLPEQEGDDAEPHAAWEVTAVILAGSPERTSLAVTAGGDSFPAACQNAALLAIGTLHQRYPDELQHSPYRY
|
|
111
|
+
HPRRGGARDYATFRDASSEDDATIVHLARMVEVYDAARIDFHQMVRRGMVENNLKILELRQENLQLKKDLDAVEAQLHQL
|
|
112
|
+
KIAQGEVCRPKRRRVCRSQKITARKSTSRPELVRQSLAWTCFVETPRAEPAPVVPQEGEASGFGSTEDALLLTFRPGPSQ
|
|
113
|
+
RRNAATGDGNQPEGSNHNHQGNPPPPPPPPPPPPPDTNAILTQILAQQANMMTAFLYHLQNPPQHNAPPPPPQHSKLAEF
|
|
114
|
+
LRIRPPTFSSSNNPVDALDWLHAVGKKLDTVQCSDEEKVIFAAHQLQGPASLWWDHFQATQPEGQPITWARFTAAFRRTH
|
|
115
|
+
VPAGVVALKKREFRELKQGNRSVMEYLHEFNNLARYASEDVREDEEKQEKFLAGMDPELSVRLVSGDYPDFQRLVDKSIR
|
|
116
|
+
LEAKHKELESHKRRLANFRNQQGANQRVRYTNPYPGGSSSQQQQQQQQPRSTPRPQFVVRVPQPQQQQSQQGTRAPRPPT
|
|
117
|
+
PTVQPGQGRRDAQGPQRLCFNCFEPGHFADKCPKPRRQQGQAPPRSNNGGKDVIRGRVNHVTAEDVLTTPDVIVGTFLIH
|
|
118
|
+
SIPATILFDSGASHSFISVPFVGRNQLGVERLRNPLLITTPGGVMTAKYYSPAVPIEIQGIPFPSDLILLDTKNLDVILG
|
|
119
|
+
MNWLAQFQGVVDCARRTVTLYRGPEQPVLFFAPPTSVSSSELHQIGLSEISIVREFGDVFPEELPGMPPKREIEFRIDLA
|
|
120
|
+
PGTTPLYKRPYRMAANELAEVKKQLEELKEKGYIRPSTSPWGAPVIFVEKKDKTKRMCVDYRALNEVTIKNKYPLPRIDD
|
|
121
|
+
LFDQLKGATVFSKIDLRSGYHQLRIREEDIPKTAFTTRYGLYEFTVMSFGLTNAPAFFMNLMNKVFMEYLDKFVVVFIDD
|
|
122
|
+
ILIYSQSEEDHQHHLRLVLGKLREHQLYAKLSKCEFWLSEVKFLGHVISVKGVAVDPETVTAVTDWKQPKTVTQVRSFLG
|
|
123
|
+
LAGYYRRFIENFSKIARPMTQLLKKEEKFVWSPQCEKAFQTLKEKLVSLPVLILPDTRKDFMVYCDASRQGLGCVLMQDG
|
|
124
|
+
HVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHKSLKYIFTQSDLNLRQRRWLELIKDYDVGIH
|
|
125
|
+
YHPGKANVVADALSRKSHCNTLNVRGIPPEFNQQMEALNLSIVGRGFLAALEAKPTLLDQIREAQKNDPDMHGLLKNMKQ
|
|
126
|
+
GKAAGFTEDEHGTLWNGNRVCVPDNRELKQLILQEAHESPYSIHPGSTKMYLDLKEKYWWVSMKREIAEFVALCDVCQRV
|
|
127
|
+
KAEHQRPAGLLQPLQVPEWKWDEIGMDFITGLPKTQGGYDSIWVVVDRLTKVARFIPVKTTYGGNKLAELYFARIVSLHG
|
|
128
|
+
IPKKIVSDRGSQFTSHFWKKLQEELGTRLNFSTAYHPQTDGQTERLNQILEDMLRACVLDFGKTWDKSLPYAEFSYNNSW
|
|
129
|
+
HFMKRCMGANAGHRYCGTKLGKAKFQTKGKLAPRFVGPFRIIARRGEVAYQLELPASLGNVHDVFHVSQLKKCLRVPSEQ
|
|
130
|
+
ADSEHIEVREDLTYVERPVKILDTMERRTRNRVIRFCKVQWSNHAEEEATWEREDELKAAHPDLFASSSESRGRDSV*
|
|
131
|
+
>ChrUn.fgenesh.mRNA.65|PACid:24093268
|
|
132
|
+
MATWRRGTGREADGTGPRRRDVGGDGQRQRAARERRWNVMVTAARGGATARGGDSSAGREAAAAERGDGDGDGPRRRGAR
|
|
133
|
+
GRLGAVWQRRGKG*
|
|
134
|
+
>ChrUn.fgenesh.mRNA.80|PACid:24093269
|
|
135
|
+
MRLEEEVEREDDRRQDSRPLDQTAAVLGTARSRVLLLRPPSSPLLWPDLGGREGGEESVAGCCAVLRAAGYCVVFHAARS
|
|
136
|
+
PPGLHAPPRRRLLWPLPPPSMSLAGSKRRGEEVKGEGRGRDEGCYERTNKCNNYEELRNWDFYKSTLVQKKKARQVVVLF
|
|
137
|
+
RMSYPSSELNFEAAIVIRASWLKGSRRYLITEGMSAFIVYFGEGEILENESGVDLSNFRQCTLHHPNPDTLTMPEVWRRG
|
|
138
|
+
YEYVMLVQACQGRVPTESAAGQSSNREELGSSSHEEDEVVAPHRGGDVGPDIQNLSIQGDEVVNHHPTGEADEGEDIPAI
|
|
139
|
+
VEEIERVDRHAIEDEENLAAEENDDEDEQQVEEVPMPASWNQEDPGYIAENSCHDSIWFYGDGQINLGAMFRDKTGLQDV
|
|
140
|
+
VKSWSFKTQRQFRVVKSNKTEYTVVCETEGCTFRLHGHVPKYESYWIVSKLHEHSCLIRNTRESHRNLTAAYVANKYYKE
|
|
141
|
+
IIEGDDLPVRHIIKLVEKACIHAFQCPRPVLCVDGTFLTGKYRGQILTAVGADANNQIIPVAFAFVESENYESWLWFLQH
|
|
142
|
+
LKWGVVQKRTSICIIHDRNAGLLKAIKELQEDGDGAYYWPDMHSRWCMRHMGANFFKQFNSRRLMNMFKWLCKANQSTKF
|
|
143
|
+
DELWKQLDEATRTHTRSKQTNSNPKDVHVPQALEPMDDLIPSNGKKRRSSKNIKCFTHWIECKPNDKWALLHDTNGARHG
|
|
144
|
+
IMTTNLAEAYNAVLCKLRPLSLTAIVEGIMHRTTMWMRTRRAAALQQMSNAQTPFCKKMAEYLQEKANKARFHTVITTGN
|
|
145
|
+
VRRRWEVTCRTKGGFGSSTGVITHEVTLGHESDNTCSCSCNKPKLLHKPCSHVLAACAKIKLDSTSYVSTFYLKDRVLNA
|
|
146
|
+
WSAEILGWRSLQHLVETGGDNRIYVPDLDLLKAGKGRRQTRRLRNDMDASEAGGPVRRCEECLQYGHRTRDCKNNKEGTS
|
|
147
|
+
SPVEPRQQRARRNRRGSQDIEEEWPYPLLSKEIDARHRAKKIYDGNSCSSLAVLIPRTAGLLSAAGLLTFVQMTQARMHY
|
|
148
|
+
DAREPKQKLMGAHSKRRQNIDKSLLMALVDRWRPETHTFHLPCGEMTITLQDVSMLTGLPLAGQAIVLPDPPEDWRDDIV
|
|
149
|
+
SRYACILSRYAIGDTDDDEDKIFFSEKETHGPTLKWLSQFEVRYMPDDVQEYQLTLYLEAYLLWLFGWVLFTGSHGNTVD
|
|
150
|
+
ARLIPLARQIAEGNISPSAQFSWGSAILAATYRGFCDACIKTGQREAIFTGCPLLVMLWSYERFSFGRPYMSVVVAHKDD
|
|
151
|
+
YTDAVDDRPTFGTRWCYGPPQWARIQVHNVYEYFTEAFESLRENEVRWTPYTNEEAILRAPHGVSILCYRDEAYWMTRKM
|
|
152
|
+
LVYDIFVEGQNRQADNRYRRSMHSRMTPWIEAWSQALNDVVHETRAYDHNTYKQYMAWYTSQTRIRLLAPEDPDERGPPT
|
|
153
|
+
IDQIYDMQLAPPAHLTTDIAGELVKEAKTLWEKLRDGMAGTNQEVMAAVDSLRRKGKRIMRLASCRHSSDIYNPATSRRT
|
|
154
|
+
FEPMRERPSTSSRPSTSSRPSASARRSSDGRVGVRSTSFREPPTIPTIPEITEISERLGGFGSTQEGTRMVRPVPHMPPA
|
|
155
|
+
RPQMIRQMAPDVPTSHWQGGFAPFAGPTQPVPLHAPTYGTNPWQGQSMDYGGTSFGGGVQGYMDLLQQGDWLFGQYSSHP
|
|
156
|
+
NEIRYMQAPSTGSFRPELMSGFRPYTTSYGDMSSFGGGSSSVPNELRTSQTDDAPQVTQPTQPEVGEGNDNDPRRSNRER
|
|
157
|
+
HEPNRLSLSGPRHAARQRKKTTKKRGGTSTTTTDHDDDDEYN*
|
|
158
|
+
>ChrUn.fgenesh.mRNA.70|PACid:24093270
|
|
159
|
+
MSSKVTFQIVHGEGNIRFGPDGVDLSDFVMTSKGIDRPAERTFQSIYSWLLRGFRIDQEVYTMSVSVVVSRAIEGYFWEL
|
|
160
|
+
MPMDSTTAWRRYVEMAFERSWPLVIFVSVQEKDTNVSMRTEDVEGPSNAGDVVGPSMENEENQPREEQAMGMADEGERVG
|
|
161
|
+
IIVDEMEREDSDNEQAEDDASSDEEGDVMATDWANEDFSGLVISEGDHVPWEYKENEVIEGARYAHKDEMKEAVKHWAVS
|
|
162
|
+
LQREFRVVKHIENKFKYTISYAKAWRAKQKIIEMRYGTFEASYDNLPRLLATIAQRNNNTYYDLHTFTSVDDRTKSVLQR
|
|
163
|
+
AFFSLGACINAFVHCRPVLCIDGTFMTGKYRGQILTAIGCDGNNQVLPMAFAFVESENTESWYWFLERVHIAVVRMRPNV
|
|
164
|
+
CLIHDRHAGMLRAIDYLQNGWDEKGLPAKWPDVRSRWCMRHMGANFYKQFKNKHLMDLFKRLCAQNQEKKFNELWDKLDE
|
|
165
|
+
LTTKQTDEQSRRPQVEGEEPPIPLGALHDDPPTMRRRSKVEARHRCPLSVTGTNFRPD*
|
|
166
|
+
>ChrUn.fgenesh.mRNA.17|PACid:24093271
|
|
167
|
+
MWDALETKFGVSNAGNELYVMEQFYDYKMVDDRSVVEQAHEIQILAKELENNSSKLPDKFVAGGIIAKLPHSWSDFVTSL
|
|
168
|
+
KHKRRRRQRTTTTKRSREVLAPIWCRRRTLMHLITITRRSNQMPNPRQQLILRRKGKERQMTTALCAVGRGSSLLMGNGL
|
|
169
|
+
LVVVHGVGTVTLEFTSRKIAQLKNM*
|
|
170
|
+
>ChrUn.fgenesh.mRNA.68|PACid:24093272
|
|
171
|
+
MGSCCCMGCNDDDGGSGGGDGGLDPKGFLLALMIALVLFMICHRPQPRRNNYVVYRCY*
|
|
172
|
+
>ChrUn.fgenesh.mRNA.47|PACid:24093273
|
|
173
|
+
MVNTRASGSGNNNNEGNPTLAQVLAQQTQLMNMMIQQMQNQLNQGNNNAPPAQNKLADFLRVRPPTFSSTTNPVEAGDWL
|
|
174
|
+
HTIEMKLELLQCTDQEKVVFASHQLQGPASEWWDHFWMNRAEGQPITWADFTEAFKKTHIPTGVVSLKKREFRALKQKDQ
|
|
175
|
+
TVAEYLHEFNRLARYAPEDVRTDEERQEKFLEGLKDELSVTLISHDYADFQQLVDKAIRLEDKKNRMDNRKRKMTVFQEA
|
|
176
|
+
QGSSQRQRIEPLQIGESFSAGQGQSQQLNIGGEIKLETNENTEVNIEQANQPVPVQQDQSQENNNSGRKQQVCFNCYKPG
|
|
177
|
+
HFARECPKPKHQQQQGQVNNIVVTGANAVPVASSRVVSSSVTAQPPVSKQQ*
|
|
178
|
+
>ChrUn.fgenesh.mRNA.56|PACid:24093274
|
|
179
|
+
MAPIATPSRSHIAGPTEHHKLQSSLAPPDCRRYAGPPIIATAIEVRSSPDPGLDTPDLDPEGQIRPFPILHHRRRPAFRV
|
|
180
|
+
GTRGKPRSSPTHSPHSRCRRAPQSPDPTGDTLDLDLGRSDPVVPLAACPREGGGHWRRTWRRRNQAQAQCLPRSLKPGEE
|
|
181
|
+
EREEGERKREGEKREGEEEEEEAAPPLPACGGVAGGSEAGEAQRGWS*
|
|
182
|
+
>ChrUn.fgenesh.mRNA.72|PACid:24093275
|
|
183
|
+
MTTASLVHPSASSSSSSTRAEVEVVGGVFVCSDSCSGDIVRNLIVDYGSGKITLTAACIQFCVPCTRPQPLLPPLCHSGP
|
|
184
|
+
INTCFATADDRGRSRFRHYH*
|
|
185
|
+
>ChrUn.fgenesh.mRNA.81|PACid:24093276
|
|
186
|
+
MAALTGEWRGVGSGSGIRRKRGGRGGPYDGKRGGVVGAARRGG*
|
|
187
|
+
>ChrUn.fgenesh.mRNA.62|PACid:24093277
|
|
188
|
+
MGTYLVIMLISNMAPLYSGSYFYVLAQEATIAAKGNFNHYHVQMQEMSDWILLFKRYCIYVNERYVISPAFSRRVGFVLL
|
|
189
|
+
DIYGVISMYGENDSLEQYLLHVAPNQKMMLYKTFMMSNSILRRNVVHDINSAKVSYFATHQSTGPNENYYGLRATMDVYG
|
|
190
|
+
HELKPGQLSGGALWVSHFGDDGKLSSYNAVSAGWHIDPQRYGDSRPHFYTSWTRDGYATTGCYNMDCPGFERANGAAVGP
|
|
191
|
+
GASIDPVSDDKSLQSITVEVPLDRTSGDWWVYYGFNSVPTGVGSYPKSLFTNMAEKANAIAFGGYVVTRRALPTPPMGSG
|
|
192
|
+
SHPHTNKSRAASLTNLGVINQDGNTNPINADLPTYMGNEQCYSITPVAQAECFYGGPGGCMP*
|
|
193
|
+
>ChrUn.fgenesh.mRNA.45|PACid:24093278
|
|
194
|
+
MAWPTGSGDDRRSERETATNWGRGRLFLRVLLLLVLLVGLTFHGARFDVAATAAKGSDLLLLLLYSLPTLPLPRTHNWKR
|
|
195
|
+
GREGQKNWTIEIESPPCPSPKMDRQWMYADQRSKEFIEGVHYFLRVAEANRQRGFICCPCNKCKNQKEYSASRTIHFHLF
|
|
196
|
+
ESGFMPSYNCWTSHGEQGVEMEEDEVEDDNIPDFAQYVGFEGNQTGEEEIAADGNDVADDLGQMLQDAREVCKSEKEAHK
|
|
197
|
+
LDKMLEDHRTSLYPGCEQGHKKLDTTLELLQWKAKNGVSDKAFGNLLKLVKNILPGGNKLPETTYEAKKIVCPLGLEVHK
|
|
198
|
+
IHACPNDCILYRGEEYENLEACPVCKALRYKIRRDDPGEVDGQLTKKRIPAKVMWYFPIIARLRRLFRNKGNARMLRWHA
|
|
199
|
+
EERQQDGMLRHPADGSQWRNIDRKFKEFGKDALSRPEFLSKIPNAYMCVKPSSRNQPRHTMTI*
|
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
>scaf_Os03g60760.1
|
|
2
|
+
ATGGAGGTGGAGATGGGGCACGGAGAGGAGGTGGCGGCGGCGATGGAGGAGGAGGAGCTGCAGGGGTGGGAGACGCCGAGGAGGGAGGAGTGCCGCATCCCGGTGGTGCCGCCGCAGTGCCCGGCGCCGCCGAGGAAGAGGCCGGTGGCGCTGCCGGAGCTGGGGAAGGAGCGGCGGGAGCCGCCCAAGGGCGGGTACTTCCAGCCGCCGGACCTCGAGTCGCTCTTCGTGCTCGCGCCGCCGCGGAGGC
|
|
3
|
+
>scaf_Os03g60760.2
|
|
4
|
+
ATCGAGGTGGAGATGCACGGAGAGGAGGTGGCGGCGGCGATGGAGGAGGAGGAGCTGCAGGGGTGGGAGACGCCGAGGAGGGAGGAGTGCCGCATCCCGGTGGTGCCGCCGCAGTGCCCGGCGCCGCCGAGGAAGAGGCCGGTGGCGCTGCGGGAAGGAGCGGCGGGAGCCGCCCAAGGGCGGGTACTTCCAGCCCGCGCGGCCGGACCTCGAGTCGCTCTTCGTGCTCGCGCCGCGGTGGC
|
|
5
|
+
>scaf_Os10g39590.1
|
|
6
|
+
ATGAGCATGATAACGGTGAAGGTGAAGACGCTGACGGGGAAGGAGGTGGAGGTGAGCATCGAGGCGACGGAGACGGTGGCGAGGATCAAGGAGCAGGTGGAGGCGGCGGAGGGGATCCCGCCGCCGCAGCAGACGCTGATCTACGGCGGCAGGCAGCTCGCCGACGACATGACCGCCGAGATGTGCGACCTCAGGCATGGCT
|
|
7
|
+
>scaf_Os10g39590.2
|
|
8
|
+
CATCGAGGCGACGGAGACGGTGGCGAGGATCAAGGAGCAGGTGGAGGCGGCGGAGGGGATCCCGCCGCCGCAGCAGACGCTGATCTACGGCGGCAGGCAGCTCGCCGACGACATGACCGCCGAGATGTGCGACCTCAGGCATGGCTCCGAGCTGCACCTCGTTCTTGCTCTCAGGGGTGGACTACTTTGA
|
|
9
|
+
>scaf_Os09g38670.1
|
|
10
|
+
CCGCAAGGAATTGCAGTCCTGCAGATAAGAGATGCCATTTGCTAGTTGCCTCCTTGCATCTTCGAGCTCTACCATGATGGCAAGGCCCGGCGCTGTGAAGAATATTGAAAGCTGGGACGAGTTTACAAAGCATTTTGTGAAATCAGAGGACAAGCTGGTGGTGCTGGTATTCATGGCGCCGTGGTCGGAGCCGTGGAAGCTGATGAGGCCGGCGGTGGAGAAGATGGCGTCGGGGCTGAAGAGCGAGGAGGCCGAGGTGTGCACGATCAGCGTCGACCGGTTCAACACGCTGGGGCGGCTGCTGCGGGTGGAGGCGCTGCCGACGTTCGTGCTGGTGAAGAGGCACCGGGCGGTGGCTCGCGTCGTCGGCGTCAACCGGGACGATCTTCACAGCAGCATCAACAAGCACCTCGCACCACCCTCTTCTTCTCCACAACCCATTAATATTTCTTAGTGCTGTTGATGATTCTTGGTTGATTGCATGATATAATCGAGTAATGCCATGCGTCTTAATTATGAGTTGTAATTGTTTATCACATACTGTATTTGAGACATATTCAACCTTGTTTCGAGAAAAAAAAATGGAGATGAAAAAAAAATCTATTCATACTTATAGATTTTCTTTGAAGAA
|
|
11
|
+
>scaf_Os12g21920.1
|
|
12
|
+
ATGCCGACGCCCTCCACCGCCACGCGCCGCCCATCGACCGTCACACGCTTCGCTCTCTGCCTGTCGTCGCCGCCGTCGACGCCGCTGCCGACACCCGTCGCTGCCGCCCACGCCGATGCCGACGCTGCCGCTGCTGTTATCGGGAGGCCGAAAGGGGAGGGGAGAGAATGGGAGGAGAGGAGTCGTTCCCAACGAACACCATCACCACCCAACTCAGAGTCGCCGCCAAAAGCCAACTGGGGTATTGCCAGCAACAACTGCTACTCAAGAATGATCATTGCGTCGGCTGCCTTAACAAGCGATCGCCGAATGAGTAATGCCTGCGACCGCATGCTCGCGGCGGTCATACCCTCGCCCACGGCGCAACCACATGCTGGCCATAAAGGACGGGATGTTTGCGTCCTTGGTTACGCCTCACCCTGCCCTTGCCCACACCTCGCCGGCGCCACGGCCATGAATGCCACATAG
|
|
13
|
+
>scaf_Os01g36294.1
|
|
14
|
+
GTTGCACTGCAACTCTGCAAGTAGCCATGGAACAAGCAGCTGGACTAGTGTACCAACTCTTCCAACACGAAATGTTTCCCTGGACCTTCTCTGTCCTAGCCTTGTTCCCTTTCCTTCTCCTAGTGCTGCACTACTTGGCAACAAATCATAGAACACCAACAACCTGCAAGGAAACGAAGAATCATCATCCTCCCCCACCTTCACCTCCGAGGCTGCCCATCATAGGGCACCTGCACCTCATCGGTGGCCTCCTGCACGTCTCTCTTCGTGAGCTCGCTCATCGGTACGGCCCCGACCTCATGCTCCTCCACCTCGGCCAAGTCCCGAACCTCATTGTCTCCTCCCCGCGCGCCGCAGAGGCTGTCTTGCGCACGCACGACCTTGTCTTCGCGTCACGGCCATACTCCTTGATCGCCGACATACTCCTTTACGGCCCGTCTGATGTCGGGCTTTCGCCTTACGGCGAGTAGTGGCGGAGGAGGATCATCACAACGCACCTGCTGACCAACAAGAAGGTGCGGTCGTACCGTGTAGCACGAGAAGAGGAGGTGCATAAGGTAATGGCCAAAGTCCATGAGTTATCCACCAAGGGTATGGCAGTGGATATGACTGAGCTCTTCAGCACCTTCTCAAATGACCTCATATGCCGCCTTGTGTCGGGGAAGAACTTCCAAGGGGAAGGTCGAAACAAGCTGTTCCGTCAACTGTTCAAAGCAAATTCTGTACTCCTCGCAGGGTTTAACCTCAAGGACTACTACCCAGGCTTGGCAAGGCTCAAAGCTGTCTCAATGGTGATGTGTGCCAAGGCCAGGAACACGAGGAAGTTGTGGGATGAATTGCTCGACGAGATTATCGATGAGCGTATGAGCAAACAACAATGTGAGCATGATGAAGGCAATGATCAAGATGAGATGAACTTCGTAAATGTTTTGCTCCTTCAAGAGCAGGGCATCACCAGAGAACACCTTAAAGCAATTCTAGTTGACATGTATCAAGCCGGCACGGAGACGTCATCAGTGGTCTTAGTATTTGCCATGGCCGAGCTTATGCAGAAGCCACATCTCATGGCCAAGTTGCAAGCCGAACTAAGAACAACCATACCCAAGCAGGGACACGAATTGATTACTGAACGTGATCTTACCGACATGACCTACCTCAAGGCTGTCATCAAGGAGACGCTTCGGTTGCATCCACCAAC
|
|
15
|
+
>scaf_Os12g22750.1
|
|
16
|
+
ATGTCTGGAGTTCCCCCCGCCGCTGCTGGAGGAGATGGCACAGGTGGTGCGCCGCCAGGAGCTGGAGCCGGCGGTGGTGCGCCAGGAGCCGGTGCCGCGAACAACAACATCAACGGAGGCAATTCTGCCTCACAATCCAGTGGAGGGCCATTCTCGAGGTGTATCCTTCTTCTGTTCCCTTTGTTAGCGCTATCGCTTTACTGTCATGTGCGCTATGTTCCTGTTCCTGACCTTCATGATGCCTCAAGCATGTTATTGAGTTACTGTAATGTTTCTGTTCCTGACATTCATGATGCGCATAGAAAGGAAAATGGCGCCTTCAACACGCGGAAGCGGCGAGCCTTCTCGGCGGCGTCCTTGTACGTGCGCCCGTGCTCCGGCATGCTTCGGCCGCCGTTGTCGTCGGAGCTTGGAGGCGGCGGGAGTGAGGAAGAAGAGGGAGAGCCGAGAGGGGAGAGGGAATGA
|
|
17
|
+
>scaf_Os02g55190.1
|
|
18
|
+
TGGGCCACAAAATTTCTCCAAATTTTGAATTCCAGAGGCGACCAGTCCGGCTCGAAATCCCCGCCTTATAAATTACGCACGCCGACACGATACGCCCCCATCGAATTCAGGCGCAAAAACCTCCAAAACCTTTGCAATATTCCTCGTAAATCGTAATTCCCCCTCGCGATCGAGCTCGCGACGCCCATGGCGATGGAGAGAAACGCGGCGCCGCGCGTCTCGGCCTCGTCGTCGGCGGCGGCGTCGCCCTCCACCGTCGGTGCGCTCCTCTCGAAGGCCTCGGTGGCTGCCGCTCCCGCACGCGAGATCCCCTCGCCGCGGTCGCTGCTGTCGCGCATCCTCCATAGGAGTGGCGGCGGCGGCGGCTTCGGGTGTCGCCTTCGCCTCCCCCGATACTGCTCCAGCGGCGCGGCCGCCAAGGAGGACGCCGCCGCCGAGTACGTGGAGGTTGAGGTTGAGGCGGAGGCTGCGGCGCCGAAGGTGGTGGGCCGCCAAGCGGTTGATCGCGAGTCGCCTCGGAGCTCGCTCGGGAAGAAGGCGGCGGAGGAGGTGTCGCCGGCGAGCCTGGGGCTGGGCGCGAGCCTCATGCTGCTGCTCTCCAAGAGCGCGGCGGAGCTGAACAGGATGGCGGAGCTCCGCGCCCAGATGGAGCGGCTGGTGCTCGACACCAAGGGGGAGGAGGAGGCGCGGAGCAGCAACCACCCCAACGCGTCCGACGATCACGCCGACATCACCAAGGAGGAGCCCACCGCCTTCTCCGGCGGCGCATTATCCCGCTGCTCACGCACGGCCGCCGCCCCGGGAAACGCAGGGCACCACGCCGCCGTTCCAATGGACCAGATGGAAGCGGAGCTCGAGGCGGAGCTGACGCTCCTGCAATGCGCGACTCCTCGTCGGGATCGTCAACTCGAGATCGGCGACGACGAGGAGGAGTCCACGGACACCCACGCGGCCACCTTCGCCGACGCCGACGATGACACGGACGGTGCTGACGACGAGGAGGAGGAGGAGGAGGAGAGCGGGGCGGCGGCGCAGGGCGGCGTGTCGGCGAGGGAGCTGGAGAGGAGGCTGCACGAGCTGCTCCAGTGGCGGCACGAGGAGCGGATCGCGGAGCTGGAGACGGCGCTGGAGCGCGCCAGGAAGAGGCTGCAGGAGAAGGAGCGCGAGGTTTGCTGGTGGCGCAACACCGCCAAGCTCGTCACCCGCCACAAGGACGACTCCCGCCTCAGATAGCAAGAATTAATCCGCCATGAGATGAGATCAAACAAGAACAAGATCAAGATCGATCATCTCGCCTCGCAGTGATCCGTTTTGTACTCTGGTGATCATGCTGCAACTAGACTAGAAGAACAAATTCCAACCAGAAAACATTGATTGCATAAACTAACTGGGATCACAGATTCACAGGATTCGGTTGCTGCAGCCTATCAACATTTGGAGCAGATGGTAAGGTGTTTTTTACCTATCTAGTCTACGGATTGATTCCAAGATGATTGTGTTTCGGCCTTTCATTCGACCTCCAAACGTGACTAAATTAAGATGCATGGAATGACGCACAATCTCTTA
|
|
19
|
+
>scaf_Os03g56500.1
|
|
20
|
+
ATCAAGCCGTCCACTTCCCCCACGACCACCAGCGTCCGAGCGGGTCGAGGAGGCCATGTCCGGCGAAGCAGAGTCCCGCGAGGCGTCGCGGCAGCGGCGGCGGCGGGAGCGGGCTGCGGCGGTCGAGCGATTCGTCGGGGTGCCGCTCGCCGACGTGGTCAGGGAGAACTCGCTCGTGCACCTCCCGCCGGCGGCGGCGGCGCGCCTCCGCGTCGTGCACCCGTCGTGGGCGAGCCACATGTCGTCCCCGCTCTTCGCCGTCGCGCACGCGGCCGCCCCGAGGCGGGTCTCCGGGGTGTTCGTCCCATCAGCGGGGTTCCTCCCCTTCGACGGCGACGACGACGCCGTGCCGTCCCCGTCGCTCTCGTTCGTGCCGGCCTCGTCGGAGCTCGTCGTGCTGTCGTCGTCGCGCGGGGTCGCCTGCTGCTTCTCCCCCGCCGACGACGCGTACGCCGTGTGCAACCCGGCTACGGCGTCGTGGACGGCCGTCCCGTCCCCGCCGTGGCGGTCCTGGCCGCGCCCGGCGATCGTCGTCCTCTTCGACACGAGCGCCTACAACTTCCGCGGCGACTTCACGCTCGTCTGCCCCTTCGAGTCGGAGCCGGGTTCTTCCGGCGCCTACTGCTTCCAGGTGTTCACGTCCGGGACCGGCGCGTGGTGGGTCACCGACGCGATGTCGCCAGCCGAAGGGCTCGTCGCCGCGTCGGGCGTGGCGGCCGGCGCCACGGCGTGGTGGCGGACGAGCATCGGCACCGCGGTGGGGTACACCCCTGTCACGGGGCGCGTCGACCTCGTGACCTGCCCCGGCGACAGTGACCAGTGGGAGATCGGATTGGCCGCGGGCATGCTCCACTGCGCCGTGATCGACGGCGGCGACGTGGTGGTGTTCCGGCTGCACGAGCACGGAATCTGGGAGGTGACCACCAGGGTCGCCGTCGCAGAGATACTGCAACCATCTCAGCCGCCGCCGCCGGCAAGGGCGACGACGTCCACGGAGATCGTGGCGTCCCAGCAGCACGACGAGTCCGGCGCGGAGGAGGAGGAGGGCTCGCGCGCTGTTGTCGCCGCGGCGAATGCACCACTCCGGCTGGACGACGGGGTGCGGCTGCTGGGTTTCCAGGGCGCGGAGGTGGAGGTGGTGGTGCTGGCAGGGAGGCGCCTGGTGGCGTTCGACGCGCGGACGCGGCGGCGGCGCGAGGTCGCCGTGCCGGACGAGGTCGACGCGGCATGGGACGGCGCGGAGCACGCTGCGCACATCAACACCCTCGCGCTGATCGCGCCCGCCGCTCTCGCGGCCGAGCCGCCGCTCGCGAAGCCGCCGGCTGATCCATGAAGTGGCAATGGCATCGTCATCTTAGCGAATCTTACTGCAATGCATGGCGATCAATCACTCGATCTAAGAGTAAGTTTGTGGATGTGAAGTTCCATTTTGAGAAATTTAACTCGCAAGCTGCAATAAATTGTGTATATTAATCATCAGATGAGCTTTTTCCCCAGTTCAATATATGTTTTTCAAATAGTTTTTGGGTGAGGTACTTGCCAGTTGAGTTGATCTATACTTTAACAGTGGGAGAATGAATAGCTACTTTGTCACTTTTTTTTCTTTGTTTTTGGGTGTGTTAGTTGACGTCAAAATTTAAAGTTTGATTGAAATTGAAACAATGTGACGTTCAATGGAACGATGTGACGCAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAAGGTTTAGAACTTAA
|
|
21
|
+
>scaf_Os03g56500.2
|
|
22
|
+
ATCAAGCCGTCCACTTCCCCCACGACCACCAGCGTCCGAGCGGGTCGAGGAGGCCATGTCCGGCGAAGCAGAGTCCCGCGAGGCGTCGCGGCAGCGGCGGCGGCGGGAGCGGGCTGCGGCGGTCGAGCGATTCGTCGGGGTGCCGCTCGCCGACGTGGTCAGGGAGAACTCGCTCGTGCACCTCCCGCCGGCGGCGGCGGCGCGCCTCCGCGTCGTGCACCCGTCGTGGGCGAGCCACATGTCGTCCCCGCTCTTCGCCGTCGCGCACGCGGCCGCCCCGAGGCGGGTCTCCGGGGTGTTCGTCCCATCAGCGGGGTTCCTCCCCTTCGACGGCGACGACGACGCCGTGCCGTCCCCGTCGCTCTCGTTCGTGCCGGCCTCGTCGGAGCTCGTCGTGCTGTCGTCGTCGCGCGGGGTCGCCTGCTGCTTCTCCCCCGCCGACGACGCGTACGCCGTGTGCAACCCGGCTACGGCGTCGTGGACGGCCGTCCCGTCCCCGCCGTGGCGGTCCTGGCCGCGCCCGGCGATCGTCGTCCTCTTCGACACGAGCGCCTACAACTTCCGCGGCGACTTCACGCTCGTCTGCCCCTTCGAGTCGGAGCCGGGTTCTTCCGGCGCCTACTGCTTCCAGGTGTTCACGTCCGGGACCGGCGCGTGGTGGGTCACCGACGCGATGTCGCCAGCCGAAGGGCTCGTCGCCGCGTCGGGCGTGGCGGCCGGCGCCACGGCGTGGTGGCGGACGAGCATCGGCACCGCGGTGGGGTACACCCCTGTCACGGGGCGCGTCGACCTCGTGACCTGCCCCGGCGACAGTGACCAGTGGGAGATCGGATTGGCCGCGGGCATGCTCCACTGCGCCGTGATCGACGGCGGCGACGTGGTGGTGTTCCGGCTGCACGAGCACGGAATCTGGGAGGTGACCACCAGGGTCGCCGTCGCAGAGATACTGCAACCATCTCAGCCGCCGCCGCCGGCAAGGGCGACGACGTCCACGGAGATCGTGGCGTCCCAGCAGCACGACGAGTCCGGCGCGGAGGAGGAGGAGGGCTCGCGCGCTGTTGTCGCCGCGGCGAATGCACCACTCCGGCTGGACGACGGGGTGCGGCTGCTGGGTTTCCAGGGCGCGGAGGTGGAGGTGGTGGTGCTGGCAGGGAGGCGCCTGGTGGCGTTCGACGCGCGGACGCGGCGGCGGCGCGAGGTCGCCGTGCCGGACGAGGTCGACGCGGCATGGGACGGCGCGGAGCACGCTGCGCACATCAACACCCTCGCGCTGATCGCGCCCGCCGCTCTCGCGGCCGAGCCGCCGCTCGCGAAGCCGCCGGCTGATCCATGAAGTGGCAATGGCATCGTCATCTTAGCGAATCTTACTGCAATGCATGGCGATCAATCACTCGATCTAAGAGTAAGTTTGTGGATGTGAAGTTCCATTTTGAGAAATTTAACTCGCAAGCTGCAATAAATTGTGTATATTAATCATCAGATGAGCTTTTTCCCCAGTTCAATATATGTTTTTCAAATAGTTTTTGGGTGAGGTACTTGCCAGTTGAGTTGATCTATACTTTAACAGTGGGAGAATGAATAGCTACTTTGTCACTTTTTTTTCTTTGTTTTTGGGTGTGTTAGTTGACGTCAAAATTTAAAGTTTGATTGAAATTGAAACAATGTGACGTTCAATGGAACGATGTGACGGAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAAGGTTTAGAACTTAA
|
|
23
|
+
>scaf_Os03g56724.1
|
|
24
|
+
ATGAGCTGCGAGAAGTTGAGCCGTCAGTCTCTGCATTTGGTGTTGAACGAGGGTCGCGGCTTGTTCTCGCTAAGGCACATGGACGTATCAAAGCTCTTCTACCCATCAACGGCAGAAGCACTGGAAGCAGAGGCTAAAGCTAAGAAGAAGAAGAATGGCACCAACAAAATTGGGAGCATCGGCCGTTTGCCAACACCGAGCATACACTACCAGCCATATACGTGGTCTGCGTCTAATCCCTACAGTTCACTGTGTGCACTTGCTCTCTTTGGTGAGAGGAGCAAGAACAAGATCCTCTGCACGGACATGGCAGGCCACACCAGCATCTACAACCCCGAGTTGCGCTCATTCATGAGAATGCCTGATCTGAATTCGCCCAAGAGATACAATAGTTGTGTGGCTGTCTCCATCCCAGGTGCTTCTGCCCATGCCATGTCCAACTTTGACATCGACACAGACCACAGCCTGTACATCATGGATATCGATCCTACCTACTGGTGTAGTTCTGAGGTGCTTGCCTATGATCCTGTGGAGGAGTGTTGGTGCTGGGGGCCACTCCCGCAGCCGCCATTCTTTCAGGACCGAGAGTATAAGGTCCCCCTTAAGCCTCGCTTCATGGTGGTCGATAGCACCAAGATATGCGTGTCTACCACCACGGCGACCTACTCCTTTGACATGGTGACGAGAGATTGGAATAAGGTGGGTGATTGGGTGCTGCCCTTCAATGCCGAGTATGTCCCTGAGCTGGGCCACTGCCTCGGCATGTCGGATGGCGGCCCCTTTGACCTGTGCATCTTGGACAACCTCTCCACCGCCGCAGGCTCTCCTCCGCCGGTGGTGCGGCATGTCGGGATGGAGTTTGAGCTGCCGGAGAACTGGTCTCAGGTGTACCGTGACCTGGTGAACCTTGGATCACTGAGGTTTTGCATTGTCAATGGCTACACCATTGAAAACGAGCGGTACGAGTGTGACTTTAACCCAGTGACTGTCTTCACCGGCGTGGAGGTGTTGCCAACAAGCAGTGAACAGGGGCTCCTTATGATCAAGCACAAGTCCAAATGTATCATGACTTACATCATGTTCGTGCTCTGA
|
|
25
|
+
>scaf_Os01g11360.1
|
|
26
|
+
ATGGCGGCCAGAGGCAGCCGGTCCTGCGCCTGGCCGTGTGGGTTGGGGATGGCTGGAGGTGGTCAGGAGGGCAGCGGGAACCGGCAAGGAGTCGGCGATGGAGTCCCTCCGGACGGCGGTAGGGACAGCGAAGCACGGCGGAAGATGGTGACGGCGCTCGGCGGCTACGGCAGCCCTAGGGGCTGCGGCGTCCCAAGACAGTGGCAGTCTGAGCACTGTGAATCCGATAAAGTGGAAGCTGATCCCATCGAGCAAATACAGAGGGGATTTTCGATCTACAGAGCCAATACAGAGGGGAAAGGAGTGGTGGATGGGGGTTTTACCTGCTTTGCTATGGGCATCGGCAGGGTGGTCTCAGCAGGGACGGCGGCGGCCTCAGCAGAGAGTAGACTAAGGAGGCTGTTGGAGATGCTCTTAGTAGTAGTATCGAACATCGGGACATACCAAACGAGAGGGATTTTGGTCAAGGATTTACTAAAGTAG
|
|
File without changes
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
@read1:1
|
|
2
|
+
AAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGGGG
|
|
3
|
+
+
|
|
4
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
5
|
+
@read2:1
|
|
6
|
+
CACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCA
|
|
7
|
+
+
|
|
8
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
9
|
+
@read3:1
|
|
10
|
+
CACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCA
|
|
11
|
+
+
|
|
12
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
13
|
+
@read4:1
|
|
14
|
+
CTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGG
|
|
15
|
+
+
|
|
16
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
17
|
+
@read5:1
|
|
18
|
+
ACGACGCGCACCACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGC
|
|
19
|
+
+
|
|
20
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
@read1:2
|
|
2
|
+
AGGCCGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGC
|
|
3
|
+
+
|
|
4
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
5
|
+
@read2:2
|
|
6
|
+
GGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGT
|
|
7
|
+
+
|
|
8
|
+
ggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
9
|
+
@read3:2
|
|
10
|
+
CGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTAT
|
|
11
|
+
+
|
|
12
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
13
|
+
@read4:2
|
|
14
|
+
ACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGCTAAG
|
|
15
|
+
+
|
|
16
|
+
ggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
17
|
+
@read5:2
|
|
18
|
+
GGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGC
|
|
19
|
+
+
|
|
20
|
+
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
|
|
@@ -0,0 +1,4 @@
|
|
|
1
|
+
>Sb02g000720.1a
|
|
2
|
+
CCCCAACCCTCCTCTTCTCCCTCCCCTGACTGGAGAGAGAGAACCTGAACCTTCCCGAGAGGATAGATAGGGGGGACGGAAGGCACCCGCATCGAGGAAACCAAAAGAGAGGCAATCTCTAGAACCCTCTCTTCCACCTCCCTCTCTCCCTCCCGCGCCGATCCATTCCATTCCATTCCAACTCAATCCCCCCCCACCCAGCCCAAACAATGGCGTCGGACGGGAGCGGCGTGGTGACGGTGTACGGGAACAACGGCGCAGCCCTTCTGGAACCCTCAAAGCAGCCCAAGTCGGCGACTTTCTCCGTCAAGGTCGGCCTCGCGCAGATGCTCCGTGGCGGGGTCATCATGGACGTCGTCACCCCGGAACAAGCCCGCATCGCGGAGGAAGCCGGCGCCTGCGCCGTCATGGCGCTGGAGCGCGTCCCCGCCGACATCCGCTCGCAGGGCGGCGTGGCGCGGATGTCCGACCCGGGCCTCATCCGCGACATCAAGCGCGCCGTCACCATCCCCGTCATGGCCAAAGCGCGCATCGGCCACTTCGTCGAGGCGCAGATCCTCGAGGCCGTCGGCGTCGACTACGTCGACGAGAGCGAGGTCCTCACACCCGCCGACGACGCGCACCACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGGGG
|
|
3
|
+
>Sb02g000720.1b
|
|
4
|
+
AGGCCGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGCTAAGCGCATCGCCGCGCCGTATGATTTGGTGATGCAGACCAAGCAGCTGGGCCGCCTCCCTGTTGTGCAGTTCGCGGCCGGGGGTGTGGCCACGCCTGCTGATGCCGCGCTCATGATGCAGCTTGGGTGCGACGGCGTCTTCGTCGGCTCGGGAATCTTCAAGAGTGGCGACCCTGCTCGCCGCGCGCGTGCCATCGTTCAGGCTGTCACCCACTACAGCGACCCTACCATCCTCGCCGACGTCAGCGCCGGACTCGGGGAGGCCATGGTCGGCATCAACCTCAACGACCCTAAGGTCGAGCGATACGCCGCCAGATCCGAGTGAACAACCCTATCCGCTCCACCATCGTCATCTTCTCTCATATATTTGTATCACCCATCCATCCATCTGCCTTCGATATGCATCTCCACTCCGCCGGCTTCATCCTTCTCTTCTTAATAATTTTTGCATTACAAACAGTAGCTTATTTTGTCTCATGTCTCTCCATCAGTAATAACGGGACTGAATCAATGGTAAGAAATCAAAGCGTATGGTACTATGCAGAACCTCTTTATTTTTGTGTCCTCTTATTAGCTACTGTATTAAGTTAGACTAGGCTCCCCTGGTTTATCATGTACTCAATCAAATGTTGAACGGTTTGTATGTCTGTCGCTCTGCCAGCCCTGCTTATGGCTTATGAATGATGAATCAATGAATGAATCACATGTTCTTCATCC
|
data/test/data/tiny.sam
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
1
|
+
@HD VN:1.0 SO:unsorted
|
|
2
|
+
@SQ SN:NM_014620 LN:2300
|
|
3
|
+
@PG ID:bowtie2 PN:bowtie2 VN:2.2.3 CL:"/Users/rds45/.rvm/gems/ruby-2.0.0-p247/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -p 8 -X 350 --quiet --seed 1337 -x transcripts --passthrough -1 /Users/rds45/code/eXpress/sample_data/reads_1.fastq -2 /Users/rds45/code/eXpress/sample_data/reads_2.fastq"
|
|
4
|
+
2:NM_014620:1094:172 99 NM_014620 1095 1 50M = 1217 172 ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP
|
data/test/helper.rb
CHANGED
|
@@ -7,10 +7,41 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
|
|
|
7
7
|
]
|
|
8
8
|
SimpleCov.start
|
|
9
9
|
|
|
10
|
-
require '
|
|
10
|
+
require 'minitest/autorun'
|
|
11
11
|
begin; require 'turn/autorun'; rescue LoadError; end
|
|
12
|
-
require 'shoulda
|
|
12
|
+
require 'shoulda/context'
|
|
13
13
|
require 'transrate'
|
|
14
14
|
|
|
15
15
|
Turn.config.format = :pretty
|
|
16
16
|
Turn.config.trace = 5
|
|
17
|
+
|
|
18
|
+
# fake CRBBlast class
|
|
19
|
+
class CRBHelper
|
|
20
|
+
|
|
21
|
+
attr_accessor :target_is_prot, :hash
|
|
22
|
+
def initialize t
|
|
23
|
+
@target_is_prot = t
|
|
24
|
+
end
|
|
25
|
+
|
|
26
|
+
def reciprocals
|
|
27
|
+
return @hash
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
end
|
|
31
|
+
|
|
32
|
+
# rake Hit class
|
|
33
|
+
class HitHelper
|
|
34
|
+
|
|
35
|
+
attr_accessor :query, :target, :qstart, :qend, :tstart, :tend, :qlen, :tlen
|
|
36
|
+
def initialize query, target, qstart, qend, tstart, tend, qlen, tlen
|
|
37
|
+
@query = query
|
|
38
|
+
@target = target
|
|
39
|
+
@qstart = qstart
|
|
40
|
+
@tstart = tstart
|
|
41
|
+
@tend = tend
|
|
42
|
+
@qend = qend
|
|
43
|
+
@qlen = qlen
|
|
44
|
+
@tlen = tlen
|
|
45
|
+
end
|
|
46
|
+
|
|
47
|
+
end
|
data/test/test_bowtie.rb
ADDED
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
|
|
3
|
+
require 'helper'
|
|
4
|
+
require 'tmpdir'
|
|
5
|
+
|
|
6
|
+
class TestBowtie < Test::Unit::TestCase
|
|
7
|
+
|
|
8
|
+
context "bowtie" do
|
|
9
|
+
|
|
10
|
+
setup do
|
|
11
|
+
@reference = File.join(File.dirname(__FILE__), 'data',
|
|
12
|
+
'sorghum_transcript.fa')
|
|
13
|
+
@left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
|
|
14
|
+
@right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
|
|
15
|
+
@mapper = Transrate::Bowtie2.new
|
|
16
|
+
end
|
|
17
|
+
|
|
18
|
+
should "build index" do
|
|
19
|
+
Dir.mktmpdir do |tmpdir|
|
|
20
|
+
Dir.chdir tmpdir do
|
|
21
|
+
@mapper.build_index @reference
|
|
22
|
+
assert File.exist?("sorghum_transcript.1.bt2")
|
|
23
|
+
end
|
|
24
|
+
end
|
|
25
|
+
end
|
|
26
|
+
|
|
27
|
+
should "build index and map reads" do
|
|
28
|
+
Dir.mktmpdir do |tmpdir|
|
|
29
|
+
Dir.chdir tmpdir do
|
|
30
|
+
@mapper.build_index @reference
|
|
31
|
+
left = File.basename(@left)
|
|
32
|
+
right = File.basename(@right)
|
|
33
|
+
index = File.basename(@mapper.index_name)
|
|
34
|
+
@mapper.map_reads(@reference, @left, @right)
|
|
35
|
+
sam = @mapper.sam
|
|
36
|
+
assert File.exist?("#{sam}"), "sam file doesn't exist"
|
|
37
|
+
cmd = "grep -v \"^@\" #{sam} | wc -l "
|
|
38
|
+
line_in_sam_file = `#{cmd}`.chomp.to_i
|
|
39
|
+
assert_equal 424, line_in_sam_file
|
|
40
|
+
end
|
|
41
|
+
end
|
|
42
|
+
end
|
|
43
|
+
|
|
44
|
+
should "raise error when no index built" do
|
|
45
|
+
Dir.mktmpdir do |tmpdir|
|
|
46
|
+
Dir.chdir tmpdir do
|
|
47
|
+
assert_raise Transrate::Bowtie2Error do
|
|
48
|
+
@mapper.map_reads(@reference, @left, @right)
|
|
49
|
+
end
|
|
50
|
+
end
|
|
51
|
+
end
|
|
52
|
+
end
|
|
53
|
+
end
|
|
54
|
+
end
|