Command line: [exonerate -m p2g --showtargetgff -q SelN/SelN_U.fa -t SelN/SUBSEQ/KB228911.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SelN Target: KB228911.1:subseq(3317894,25215) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold34, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1960 Query range: 179 -> 590 Target range: 25215 -> 18468 180 : ValSerArgLeuAlaLeuSerGlyLeuArgAsnTrpThrAlaAlaAlaSerProSerAla : 199 |||||||||||||||||||||||||||||||||||||||.!!|||||||||||||||||| ValSerArgLeuAlaLeuSerGlyLeuArgAsnTrpThrThrAlaAlaSerProSerAla 25215 : gtctCCCGCCTGGCCCTGTCCGGCCTCCGCAACTGGACAACGGCAGCCTCGCCAAGTGCG : 25158 200 : ValPheAlaThrArgHisPheGlnProPheLeuProProProGlyGln<->GluLeuGly : 218 |||||||||.!!|||||||||:::||||||||||||||| |||!:! ||||||||| ValPheAlaAlaArgHisPheArgProPheLeuProProArgGlyArgValGluLeuGly 25157 : GTGTTCGCTGCCCGCCACTTCcggcccttccttcctcctcggGGCCGGGTGGAGCTGGGC : 25098 219 : GluProTrpTrpIleIleProSerGluLeuSerMetPheThrGlyTyrLeuSerAsnAsn : 238 |||||||||||||||||||||||||||||||||:!:|||||||||||||||||||||||| GluProTrpTrpIleIleProSerGluLeuSerValPheThrGlyTyrLeuSerAsnAsn 25097 : GAGCCCTGGTGGATCATCCCCAGTGAGCTGAGCGTCTTCACCGGCTATCTGTCCAACAAC : 25038 239 : ArgPheTyrProProProProLysGlyLysGlu >>>> Target Intron 1 >>>> : 250 ||||||||||||||||||||||||||||||||| 176 bp ArgPheTyrProProProProLysGlyLysGlu++ 25037 : CGCTTCTACCCACCACCACCCAAGGGCAAAGAGgt......................... : 25000 251 : ValIleIleHisArgLeuLeuSerMetPheHisProArgProPheValLysThrArgP : 269 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ++ValIleIleHisArgLeuLeuSerMetPheHisProArgProPheValLysThrArgP 24999 : agGTCATCATCCACCGGCTCCTGAGCATGTTCCACCCTCGGCCCTTCGTGAAGACCCGCT : 24769 270 : heAlaProGlnGlyAlaValAlaCysLeuThrAlaIleSerAspPheTyrTyrThrValM : 289 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| heAlaProGlnGlyAlaValAlaCysLeuThrAlaIleSerAspPheTyrTyrThrValM 24768 : TTGCCCCTCAGGGGGCTGTCGCCTGCCTGACGGCCATCAGCGATTTCTACTACACTGTGA : 24709 290 : etPhe{Ar} >>>> Target Intron 2 >>>> {g}IleHisAlaGluPheGlnL : 298 |||||{||} 564 bp {|}||||||||||||||||||| etPhe{Ar}++ ++{g}IleHisAlaGluPheGlnL 24708 : TGTTC{CG}gt.........................ag{G}ATCCACGCCGAGTTCCAGC : 24118 299 : euSerGluProProAspPheProPheTrpPheSerProAlaGlnPheThrGlyHisIleI : 318 ||||||||||||||||||||||||||||||||||||||!.!||||||||||||||||||| euSerGluProProAspPheProPheTrpPheSerProGlyGlnPheThrGlyHisIleI 24117 : TCAGCGAGCCGCCTGACTTCCCCTTCTGGTTCTCACCTGGCCAGTTCACCGGCCACATCA : 24058 319 : leLeuSerLysAspAlaThrHisValArgAspPheArgLeuPheValProAsnHis{Ar} : 337 |||||||||||||||||||||||:!!||||||||||||||||||||||||||||||{||} leLeuSerLysAspAlaThrHisIleArgAspPheArgLeuPheValProAsnHis{Ar} 24057 : TCCTCTCCAAAGATGCCACTCACATCCGAGACTTCCGGCTCTTCGTGCCCAACCAC{AG} : 24001 338 : >>>> Target Intron 3 >>>> {g}SerLeuAsnValAspMetGluTrpLeuT : 347 1504 bp {|}|||||||||||||||||||||||||||| ++ ++{g}SerLeuAsnValAspMetGluTrpLeuT 24000 : gt.........................ag{G}TCTCTGAACGTGGACATGGAGTGGCTGT : 22467 348 : yrGlyAlaSerGluSerSerAsnMetGluValAspIleGlyTyrIleProGln >>>> : 365 ||||||||.!!|||||||||||||||||||||||||||||||||||||||||| yrGlyAlaGlyGluSerSerAsnMetGluValAspIleGlyTyrIleProGln++ 22466 : ACGGGGCTGGTGAGAGCAGCAACATGGAGGTGGACATTGGCTACATCCCCCAGgt..... : 22411 366 : Target Intron 4 >>>> MetGluLeuGluAlaThrGlyProSerValProSerVa : 377 373 bp ||||||||||||||| !||||||||||||||||||:! ++MetGluLeuGluAlaLeuGlyProSerValProSerMe 22410 : ....................agATGGAGCTGGAGGCCCTGGGCCCATCGGTCCCCTCCAT : 22004 378 : lIleLeuAspGluAspGlySerMetIleAspSerHisLeuProSerGlyGluProLeuGl : 397 !||||||||||||||||||!:!||||||:!!|||!.!! !|||||||||||||||||||| tIleLeuAspGluAspGlyAsnMetIleAsnSerArgProProSerGlyGluProLeuGl 22003 : GATCCTGGATGAGGATGGCAACATGATCAACAGCCGTCCGCCCTCAGGGGAGCCCCTCCA : 21944 398 : nPheValPheGluGluIleLysTrpGlnGlnGluLeuSerTrpGluGluAlaAlaArgAr : 417 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| nPheValPheGluGluIleLysTrpGlnGlnGluLeuSerTrpGluGluAlaAlaArgAr 21943 : GTTTGTGTTTGAGGAGATCAAGTGGCAGCAGGAGCTGAGCTGGGAGGAGGCCGCCCGGCG : 21884 418 : gLeuGluValAlaMetTyrProPheLysLys >>>> Target Intron 5 >>>> : 428 ||||||||||||||||||||||||||||||| 349 bp gLeuGluValAlaMetTyrProPheLysLys++ ++ 21883 : CCTGGAGGTGGCCATGTACCCCTTCAAGAAGgt.........................ag : 21504 429 : ValSerTyrLeuProPheThrGluAlaPheAspArgAlaLysAlaGluAsnLysLeuVal : 447 |||!!!||||||||||||! !||||||||||||!.!|||||||||:!!|||||||||||| ValThrTyrLeuProPheIleGluAlaPheAspHisAlaLysAlaLysAsnLysLeuVal 21503 : GTCACCTATCTGCCATTCATCGAGGCCTTCGACCACGCCAAGGCCAAGAACAAGCTGGTG : 21445 448 : HisSerIleLeuLeuTrpGlyAlaLeuAspAspGlnSerCysUnk{G} >>>> Targe : 463 |||||||||||||||||||||||||||||||||||||||||| {|} 1 HisSerIleLeuLeuTrpGlyAlaLeuAspAspGlnSerCys***{G}++ 21444 : CACTCAATTCTGCTGTGGGGGGCCCTGGATGACCAGTCCTGCTGA{G}gt.......... : 21394 464 : t Intron 6 >>>> {ly}SerGlyArgThrLeuArgGluThrValLeuGluSerSer : 476 205 bp {||}||||||||||||||||||||||||||||||||||||||| ++{ly}SerGlyArgThrLeuArgGluThrValLeuGluSerSer 21393 : ...............ag{GT}TCGGGGCGGACTCTCCGGGAGACTGTCCTGGAAAGTTCG : 20153 477 : ProIleLeuThrLeuLeuAsnGluSerPheIleSerThrTrpSerLeuValLysGluLeu : 496 ||||||:!!.!!|||||||||||||||||||||||||||||||||||||||!:!|||||| ProIleIleAlaLeuLeuAsnGluSerPheIleSerThrTrpSerLeuValArgGluLeu 20152 : CCCATCATCGCCCTCCTCAATGAGAGCTTCATCAGCACTTGGTCCCTGGTGAGGGAGCTG : 20093 497 : GluGluLeuGln >>>> Target Intron 7 >>>> AsnAsnGlnGluAsnSerS : 507 |||!!:|||||| 86 bp |||:!!||||||||| !!| GluAspLeuGln++ ++AsnAspGlnGluAsnProS 20092 : GAAGACCTGCAGgt.........................agAATGACCAGGAGAACCCGT : 19974 508 : erHisGlnLysLeuAlaGlyLeuHisLeuGluLysTyrSerPheProValGluMetMetI : 527 |||||:!!|||||||||! !|||||||||||||||||||||||||||||||||||||||| erHisLysLysLeuAlaAspLeuHisLeuGluLysTyrSerPheProValGluMetMetI 19973 : CCCACAAGAAGCTAGCTGACCTGCACCTGGAGAAGTACAGCTTCCCCGTGGAGATGATGA : 19914 528 : leCysLeuProAsnGlyThrVal >>>> Target Intron 8 >>>> ValHisHi : 537 ||||||||||||||||||||||| 1254 bp |||||||| leCysLeuProAsnGlyThrVal++ ++ValHisHi 19913 : TTTGTCTGCCCAACGGCACTGTGgt.........................agGTCCACCA : 18630 538 : sIleAsnAlaAsnTyrPheLeuAspIleThrSerValLysProGluGluIleGluSerAs : 557 |||||||||||||:!!||||||||||||||||||:!!|||||||||!!:||||||!:!|| sIleAsnAlaAsnHisPheLeuAspIleThrSerMetLysProGluAspIleGluAsnAs 18629 : CATCAACGCCAACCACTTCTTGGATATCACCTCCATGAAGCCCGAGGATATTGAGAACAA : 18570 558 : nLeuPheSerPheSerSerThrPheGluAspProSerThrAlaThrTyrMetGlnPheLe : 577 |:!!|||||||||||||||||||||||||||||||||||||||||||||||||||||||| nValPheSerPheSerSerThrPheGluAspProSerThrAlaThrTyrMetGlnPheLe 18569 : TGTCTTCAGCTTCTCATCCACCTTTGAAGACCCGTCCACGGCCACGTATATGCAGTTCCT : 18510 578 : uLysGluGlyLeuArgArgGlyLeuProLeuLeuGlnPro : 590 |||||||||||||||||||||||||||||||||||||||| uLysGluGlyLeuArgArgGlyLeuProLeuLeuGlnPro 18509 : GAAGGAGGGCCTTCGGCGtggcctgcccctcctccagccc : 18469 vulgar: 179 590 . KB228911.1:subseq(3317894,25215) 25215 18468 - 1960 M 36 108 G 0 3 M 34 102 5 0 2 I 0 172 3 0 2 M 41 123 S 0 2 5 0 2 I 0 560 3 0 2 S 1 1 M 45 135 S 0 2 5 0 2 I 0 1500 3 0 2 S 1 1 M 27 81 5 0 2 I 0 369 3 0 2 M 63 189 5 0 2 I 0 345 3 0 2 M 35 105 S 0 1 5 0 2 I 0 1201 3 0 2 S 1 2 M 37 111 5 0 2 I 0 82 3 0 2 M 34 102 5 0 2 I 0 1250 3 0 2 M 56 168 # --- 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 # KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local gene 18469 25215 1960 - . gene_id 1 ; sequence ; gene_orientation + KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 25003 25215 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 25003 25215 . - . insertions 3 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 25001 25002 . - . intron_id 1 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 24827 25002 . - . intron_id 1 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 24827 24828 . - . intron_id 0 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 24702 24826 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 24702 24826 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 24700 24701 . - . intron_id 2 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 24138 24701 . - . intron_id 2 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 24138 24139 . - . intron_id 1 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 24000 24137 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 24000 24137 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 23998 23999 . - . intron_id 3 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 22496 23999 . - . intron_id 3 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 22496 22497 . - . intron_id 2 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 22414 22495 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 22414 22495 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 22412 22413 . - . intron_id 4 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 22041 22413 . - . intron_id 4 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 22041 22042 . - . intron_id 3 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 21852 22040 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 21852 22040 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 21850 21851 . - . intron_id 5 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 21503 21851 . - . intron_id 5 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 21503 21504 . - . intron_id 4 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 21397 21502 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 21397 21502 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 21395 21396 . - . intron_id 6 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 20192 21396 . - . intron_id 6 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 20192 20193 . - . intron_id 5 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 20079 20191 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 20079 20191 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 20077 20078 . - . intron_id 7 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 19993 20078 . - . intron_id 7 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 19993 19994 . - . intron_id 6 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 19891 19992 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 19891 19992 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice5 19889 19890 . - . intron_id 8 ; splice_site "GT" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local intron 18637 19890 . - . intron_id 8 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local splice3 18637 18638 . - . intron_id 7 ; splice_site "AG" KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local cds 18469 18636 . - . KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local exon 18469 18636 . - . insertions 0 ; deletions 0 KB228911.1:subseq(3317894,25215) exonerate:protein2genome:local similarity 18469 25215 1960 - . alignment_id 1 ; Query ; Align 25216 180 108 ; Align 25105 216 102 ; Align 24827 250 123 ; Align 24137 292 135 ; Align 22495 338 81 ; Align 22041 365 189 ; Align 21503 428 105 ; Align 20190 464 111 ; Align 19993 501 102 ; Align 18637 535 168 # --- END OF GFF DUMP --- # -- completed exonerate analysis