Command line: [exonerate -m p2g --showtargetgff -q SARS2n/SARS2n_U.fa -t SARS2n/SUBSEQ/KB228931.1_1_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SARS2n Target: KB228931.1:subseq(1521883,25098) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold54, whole genome shotgun sequence Model: protein2genome:local Raw score: 1747 Query range: 0 -> 422 Target range: 16514 -> 25098 1 : MetAlaAlaSerMetAlaArgArgLeuTrpProLeuLeuThrArgArgGlyPheArgPro : 20 ||||||||||||||||||||||||||||||||||||:!!.!! !||||||.!!|||||| MetAlaAlaSerMetAlaArgArgLeuTrpProLeuValAlaAlaArgGlyLeuArgPro 16515 : ATGGCTGCGTCCATGGCGCGGCGCTTGTGGCCTTTGGTGGCTGCTCGGGGTCTTCGGCCC : 16572 21 : ArgGlyGlyCysIleSerAsnAspSerProArgArgSerPheThrThrGluLysArgAsn : 40 ||| !!.!!|||:!!!!!!:! !!|||||| !!|||!!!|||.!!|||||||||!:!..! ArgArgSerCysValCysSerHisSerProGlyArgThrPheAlaThrGluLysGlnGly 16573 : CGGAGAAGCTGTGTCTGCAGCCATAGCCCAGGGAGAACTTTTGCCACGGAGAAACAAGGC : 16632 41 : ArgAsnLeuLeuTyrGluTyrAlaArgGluGlyTyrSerAlaLeuProGlnLeuAspIle : 60 ||||||||||||||||||:!!||||||||||||||||||||||||||||||||||||!!: ArgAsnLeuLeuTyrGluHisAlaArgGluGlyTyrSerAlaLeuProGlnLeuAspMet 16633 : CGGAACCTCCTGTACGAGCACGCGCGCGAGGGCTACAGCGCGCTCCCTCAGCTGGACATG : 16692 61 : GluArgPheCysAlaCysProGluGluAlaAlaHisAlaLeuGluLeuArgLysGlyGlu : 80 ||| !.!.||||||||||||||||||||||||!.!||||||..!||||||||||||||| GluSerLeuCysAlaCysProGluGluAlaAlaArgAlaLeuArgLeuArgLysGlyGlu 16693 : GAGTCGCTGTGCGCATGCCCGGAAGAGGCCGCGCGCGCCCTGCGGCTCCGCAAGGGGGAG : 16752 81 : LeuArgSerAlaAspLeuProAlaIle >>>> Target Intron 1 >>>> IleS : 91 |||||| !!! !||||||||||||||| 2731 bp |||| LeuArgProGluAspLeuProAlaIle++ ++IleS 16753 : CTGCGGCCGGAAGACCTGCCCGCGATCgt.........................agATCT : 19516 92 : erThrTrpGlnGluLeuArgGlnLeuGlnGluGlnIleArgSerLeuGluGluGluLysA : 111 ||||||||||||||||||||||||||!:!|||||||||||||||||||||||||||||| erThrTrpGlnGluLeuArgGlnLeuArgGluGlnIleArgSerLeuGluGluGluLysG 19517 : CCACATGGCAGGAGCTGAGGCAGCTGCGGGAGCAGATCCGGAgtctggaggaggagaagg : 19576 112 : laAlaValThrGluAlaValArgAlaLeuLeu >>>> Target Intron 2 >>>> : 122 ||||||.!!||||||:!!|||||||||||| 1385 bp luAlaValAlaGluAlaIleArgAlaLeuLeu++ + 19577 : aggctgtGGCTGAGGCAATACGGGCCCTGCTGgt.........................a : 20992 123 : AlaAsnGlnAspSerGlyGluValGlnGlnValArgLeuAspProGly >>>> Targ : 138 !.!|||||||||!:!|||:!!||||||||||||! !! !! !! ! +ValAsnGlnAspAsnGlyGlnValGlnGlnValLeuGlnGlyValAsp+- 20993 : gGTAAACCAGGACAACGGTCAAGTACAGCAGGTACTACAGGGGGTTGATgc......... : 21044 139 : et Intron 3 >>>> AlaGlySerIlePheGlyProThrPheLeuProPheProGly : 151 113 bp |||||||||||||||||| !!.!!|||!!! !!||||||! ! ++AlaGlySerIlePheGlySerAlaPhePheSerPheProAsp 21045 : ................agGCTGGCTCCATATTTGGTTCTGCTTTCTTCTCGTTCCCAGAC : 21194 152 : GlnLeuSerLeuLeuVal >>>> Target Intron 4 >>>> GluAlaGlnLeuG : 162 |||||||||! !||| ! 404 bp |||.!!||||||| GlnLeuSerProLeuArg+- ++GluThrGlnLeuG 21195 : CAACTTTCTCCTCTTAGAga.........................agGAGACCCAGCTCG : 21631 163 : luGluGlnPheTyrLeuGlnAlaLeuLysLeuProAsnGlnThrHisProAspVal >> : 181 |||||||||||!:!||||||||||||!:!|||||||||!:!||||||||||||||| luGluGlnPhePheLeuGlnAlaLeuArgLeuProAsnArgThrHisProAspVal++ 21632 : AGGAGCAGTTCTTCCTGCAGGCGCTGAGGCTGCCCAACCGGACCCACCCGGACGTGgt.. : 21690 182 : >> Target Intron 5 >>>> ProValGlyAspGluSerGlnAlaArgValLeuHi : 192 82 bp |||:!!||||||||||||||||||||||||||||| ++ProIleGlyAspGluSerGlnAlaArgValLeuHi 21691 : .......................agCCCATTGGGGACGAGAGCCAGGCCCGAGTGCTGCA : 21803 193 : sMetValGlyAspLysPro{V} >>>> Target Intron 6 >>>> {al}PheSe : 201 |:!!|||||||||||||||{!} 488 bp {.!}||||| sValValGlyAspLysPro{A}++ ++{la}PheSe 21804 : CGTGGTCGGAGACAAGCCA{G}gt.........................ag{ct}ttctc : 22318 202 : rPheGlnProArgGlyHisLeuGluIleGlyGluLysLeuAspIleIleArgGln{Ly} : 220 |||| |||||||||||||||||||||!.!||||||||||||||||||||||||{||} rPheProProArgGlyHisLeuGluIleAlaGluLysLeuAspIleIleArgGln{Ly}+ 22319 : cttcccaccccgGGGCCACCTGGAAATCGCCGAGAAACTCGACATCATCCGTCAG{AA}g : 22377 221 : >>>> Target Intron 7 >>>> {s}ArgLeuSerHisValSerGlyHisArgSe : 230 200 bp {|}||||||||||||||||||||||||||||| + ++{s}ArgLeuSerHisValSerGlyHisArgSe 22378 : t.........................ag{G}CGCCTGTCCCACGTGTCCGGCCACCGCTC : 22605 231 : rTyrTyrLeuArgGlyAlaGlyAlaLeuLeuGlnHisGlyLeuValAsnPheThrPheAs : 250 ||||||||||||||||||||||||||||||||||||||||||||||!:!||||||.!!|| rTyrTyrLeuArgGlyAlaGlyAlaLeuLeuGlnHisGlyLeuValSerPheThrLeuAs 22606 : CTACTACCTCCGTGGGGCTGGGGCCCTCCTGCAGCACGGCCTGGTCAGCTTCACACTCAA : 22665 251 : nLysLeuLeuArgArg >>>> Target Intron 8 >>>> GlyPheThrProMet : 260 |||||||:!!|||||| 673 bp ||||||||||||||| nLysLeuValArgArg++ ++GlyPheThrProMet 22666 : CAAGCTCGTCCGCCGGgt.........................agGGCTTCACTCCCATG : 23368 261 : ThrValProAspLeuLeuArgGlyAlaValPhe >>>> Target Intron 9 >>>> : 272 ||||||||||||||||||||||||||||||||| 230 bp ThrValProAspLeuLeuArgGlyAlaValPhe++ 23369 : ACAGTGCCAGACCTTCTCCGAGGAGCTGTGTTTgt......................... : 23406 273 : GluGlyCysGlyMetThrProAsnAlaAsnProSerGlnIleTyrAsnIleAspProA : 291 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||: ++GluGlyCysGlyMetThrProAsnAlaAsnProSerGlnIleTyrAsnIleAspProS 23407 : agGAAGGCTGTGGGATGACACCAAATGCCAACCCATCCCAGATTTACAACATCGACCCCT : 23691 292 : laArgPheLysAspLeuAsnLeuAlaGlyThrAlaGluValGlyLeuAla{G} >>>> : 308 !!||||||:!!|||||||||||||||||||||||||||||||||||||||{|} erArgPheGluAspLeuAsnLeuAlaGlyThrAlaGluValGlyLeuAla{G}++ 23692 : CCCGCTTTGAAGACCTTAATCTGGCTGGGACAGCAGAGGTGGGGCTTGCA{G}gt..... : 23745 309 : Target Intron 10 >>>> {ly}TyrPheMetAspHisThrValAlaPheArgAsp : 319 297 bp {||}|||||||||||||||:!!||||||||||||||| ++{ly}TyrPheMetAspHisSerValAlaPheArgAsp 23746 : .....................ag{gc}tACTTCATGGACCACTCCGTGGCCTTCAGGGAC : 24072 320 : LeuProVal{Ar} >>>> Target Intron 11 >>>> {g}MetValCysSerSe : 328 ||||||:!!{||} 84 bp {|}|||||||||||||| LeuProIle{Ar}++ ++{g}MetValCysSerSe 24073 : CTGCCCATC{AG}gt..........................ag{g}ATGGTTTGTTCCAG : 24183 329 : rThrCysTyrArgAlaGluThrAsnThrGlyGlnGluProArgGlyLeuTyrArgValHi : 348 ||||||||||||||||||||||:!!||||||:!!|||||| !!||||||||||||||||| rThrCysTyrArgAlaGluThrAspThrGlyLysGluProTrpGlyLeuTyrArgValHi 24184 : TACCTGCTACCGGGCTGAGACAGACACAGGGAAGGAGCCATGGGGACTGTATCGAGTACA : 24243 349 : sHisPheThrLys >>>> Target Intron 12 >>>> ValGluMetPheGlyVa : 358 ||||||||||||| 82 bp ||||||||||||||||| sHisPheThrLys++ ++ValGluMetPheGlyVa 24244 : CCACTTCACCAAGgt..........................agGTGGAGATGTTTGGGGT : 24355 359 : lThrGlyProGlyLeuGluGlnSerSerGlnLeuLeuGluGluPheLeuSerLeuGlnMe : 378 |||||||||||||||||||||||||||||||||||||||||||||||||! !|||||||| lThrGlyProGlyLeuGluGlnSerSerGlnLeuLeuGluGluPheLeuPheLeuGlnMe 24356 : GACAGGCCCTGGGCTGGAGCAGAGCTCACAGCTGCTGGAGGAGTTCCTGTTCCTGCAGAT : 24415 379 : tGluIleLeuThrGluLeuGlyLeuHisPhe{Ar} >>>> Target Intron 13 > : 389 |||||||||||||||||||||||||||||||{||} 549 bp tGluIleLeuThrGluLeuGlyLeuHisPhe{Ar}++ 24416 : GGAGATCTTGACGGAGCTGGGCCTGCACTTC{CG}gt....................... : 24452 390 : >>> {g}ValLeuAspMetProThrGlnGluLeuGlyLeuProAlaTyrArgLysPheA : 407 {|}|||||||||||||||||||||||||||||||||||||||||||||||||||| ++{g}ValLeuAspMetProThrGlnGluLeuGlyLeuProAlaTyrArgLysPheA 24453 : ...ag{C}GTCCTGGACATGCCCACCCAGGAACTGGGCCTTCCCGCCTACCGCAAGTTTG : 25051 408 : spIleGluAlaTrpMetProGlyArgGlyArgPheGlyGluValThr : 422 ||||||||||||||||||||||||||||||||||||||||||||!:! spIleGluAlaTrpMetProGlyArgGlyArgPheGlyGluValSer 25052 : ATATCGAGGCCTGGATGCCAGGCCGCGGCCGCTTCGGTGAGGTGAGC : 25098 vulgar: SARS2n 0 422 . KB228931.1:subseq(1521883,25098) 16514 25098 + 1747 M 89 267 5 0 2 I 0 2727 3 0 2 M 32 96 5 0 2 I 0 1381 3 0 2 M 16 48 5 0 2 I 0 109 3 0 2 M 20 60 5 0 2 I 0 400 3 0 2 M 23 69 5 0 2 I 0 78 3 0 2 M 18 54 S 0 1 5 0 2 I 0 484 3 0 2 S 1 2 M 20 60 S 0 2 5 0 2 I 0 196 3 0 2 S 1 1 M 35 105 5 0 2 I 0 669 3 0 2 M 16 48 5 0 2 I 0 226 3 0 2 M 36 108 S 0 1 5 0 2 I 0 293 3 0 2 S 1 2 M 14 42 S 0 2 5 0 2 I 0 80 3 0 2 S 1 1 M 29 87 5 0 2 I 0 78 3 0 2 M 36 108 S 0 2 5 0 2 I 0 545 3 0 2 S 1 1 M 33 99 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local gene 16515 25098 1747 + . gene_id 1 ; sequence SARS2n ; gene_orientation + KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 16515 16781 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 16515 16781 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 16782 16783 . + . intron_id 1 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 16782 19512 . + . intron_id 1 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 19511 19512 . + . intron_id 0 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 19513 19608 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 19513 19608 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 19609 19610 . + . intron_id 2 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 19609 20993 . + . intron_id 2 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 20992 20993 . + . intron_id 1 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 20994 21041 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 20994 21041 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 21042 21043 . + . intron_id 3 ; splice_site "GC" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 21042 21154 . + . intron_id 3 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 21153 21154 . + . intron_id 2 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 21155 21214 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 21155 21214 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 21215 21216 . + . intron_id 4 ; splice_site "GA" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 21215 21618 . + . intron_id 4 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 21617 21618 . + . intron_id 3 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 21619 21687 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 21619 21687 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 21688 21689 . + . intron_id 5 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 21688 21769 . + . intron_id 5 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 21768 21769 . + . intron_id 4 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 21770 21824 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 21770 21824 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 21825 21826 . + . intron_id 6 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 21825 22312 . + . intron_id 6 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 22311 22312 . + . intron_id 5 ; splice_site "Ag" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 22313 22376 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 22313 22376 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 22377 22378 . + . intron_id 7 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 22377 22576 . + . intron_id 7 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 22575 22576 . + . intron_id 6 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 22577 22682 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 22577 22682 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 22683 22684 . + . intron_id 8 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 22683 23355 . + . intron_id 8 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 23354 23355 . + . intron_id 7 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 23356 23403 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 23356 23403 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 23404 23405 . + . intron_id 9 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 23404 23633 . + . intron_id 9 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 23632 23633 . + . intron_id 8 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 23634 23742 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 23634 23742 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 23743 23744 . + . intron_id 10 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 23743 24039 . + . intron_id 10 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 24038 24039 . + . intron_id 9 ; splice_site "ag" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 24040 24085 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 24040 24085 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 24086 24087 . + . intron_id 11 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 24086 24169 . + . intron_id 11 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 24168 24169 . + . intron_id 10 ; splice_site "ag" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 24170 24257 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 24170 24257 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 24258 24259 . + . intron_id 12 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 24258 24339 . + . intron_id 12 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 24338 24339 . + . intron_id 11 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 24340 24449 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 24340 24449 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice5 24450 24451 . + . intron_id 13 ; splice_site "GT" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local intron 24450 24998 . + . intron_id 13 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local splice3 24997 24998 . + . intron_id 12 ; splice_site "AG" KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local cds 24999 25098 . + . KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local exon 24999 25098 . + . insertions 0 ; deletions 0 KB228931.1:subseq(1521883,25098) exonerate:protein2genome:local similarity 16515 25098 1747 + . alignment_id 1 ; Query SARS2n ; Align 16515 1 267 ; Align 19513 90 96 ; Align 20994 122 48 ; Align 21155 138 60 ; Align 21619 158 69 ; Align 21770 181 54 ; Align 22315 200 60 ; Align 22578 221 105 ; Align 23356 256 48 ; Align 23634 272 108 ; Align 24042 309 42 ; Align 24171 324 87 ; Align 24340 353 108 ; Align 25000 390 99 # --- END OF GFF DUMP --- # -- completed exonerate analysis