Command line: [exonerate -m p2g --showtargetgff -q TR2/TR2_U.fa -t TR2/SUBSEQ/KB229706.1_15_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: TR2 Target: KB229706.1:subseq(803937,50230) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold829, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 993 Query range: 120 -> 524 Target range: 50227 -> 17472 121 : ValProHisAspTrpArgLysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsn : 140 ||| !|||||||||!.!||||||.!!||||||||||||||||||:!! ||||||||| ValLysHisAspTrpAsnLysMetThrGluAlaValGlnAsnHisIleGlySerLeuAsn 50227 : GTTAAACATGACTGGAATAAAATGACAGAAGCCGTACAGAACCACATTGGTTCTCTGAAC : 50170 141 : TrpGlyHisArgValGlnLeuGlnAspArgLysValLysTyrPheAsnIleLysAlaSer : 160 ||||||:!!|||||| |||!:!!!:!:!||||||! ||| ||| ! !.!..! TrpGlyTyrArgValAlaLeuArgGluLysLysValThrTyrGluAsnAlaPheGlyGln 50169 : TGGGGCTACCGGGTAGCTCTGCGGGAGAAGAAAGTCACCTATGAGAATGCATTTGGGCAG : 50110 161 : PheValAspGluHisThrValCys >>>> Target Intron 1 >>>> GlyValA : 171 ||||||! ! |||! !:!! 361 bp !.!..! PheValGlyProHisArgIleLys++ ++AlaThrA 50109 : TTTGTGGGTCCTCATAGGATTAAGgt.........................agGCAACAA : 49716 172 : laLysGlyGlyLysGluIleLeuLeuSerAlaAspHisIleIleIleAlaThrGlyGlyA : 191 ... ||||||||| ::: ||||||!!:....!!:!!||||||||||||! !| snAsnLysGlyLysGluLysIleTyrSerAlaGluArgPheLeuIleAlaThrGlyGluA 49715 : ataacaaaggcaaagaaaaaatttattcgGCAGAGAGATTTCTCATTGCTACTGGTGAGA : 49656 192 : rgProArgTyrProThrHisIleGluGlyAlaLeuGluTyrGlyIleThr{Se} >>>> : 208 ||||||||||| ! !||| |||! ! !|||||| !!|||!:!{||} rgProArgTyr---LeuGlyIleProGlyAspArgGluTyrCysIleSer{Se}++ 49655 : GGCCACGTTAC---TTGGGCATCCCTGGTGACAGAGAGTACTGCATCAGC{AG}gt.... : 49604 209 : Target Intron 2 >>>> {r}AspAspIlePheTrpLeuLysGluSerProGlyL : 220 1323 bp {|}||||||:!!|||! ||| ! !!!||||||| ++{r}AspAspLeuPheSerLeuProTyrCysProGlyL 49603 : .....................ag{t}gATGATCTTTTCTCCTTACCTTATTGCCCGGGTA : 48249 221 : ysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuThrGlyI : 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||.!!|||| ysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyI 48248 : AGACGCTGGTGGTTGGAGCATCCTATGTTGCCCTTGAATGTGCTGGATTTCTTGCTGGCA : 48189 241 : leGlyLeuAspThrThrIleMetMetArgSerIleProLeuArgGlyPheAspGlnGlnM : 260 |||||||||||..!|||:!!|||:!:|||||||||! !||||||||||||||||||.!.| leGlyLeuAspValThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspM 48188 : TTGGCTTAGATGTTACTGTTATGGTACGATCCATTCTCCTTAGAGGATTTGACCAGGACA : 48129 261 : etSerSerMetValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCysA : 280 ||:!!!:!! :!! !|||||||||! !..!||||||..!!:!|||:!!!:! !! ! etAlaAsnLysIleGlyGluHisMetGluGluHisGlyValLysPheIleLysGlnPheI 48128 : TGGCCAACAAAATTGGTGAACATATGGAAGAACATGGTGTCAAGTTTATAAAACAGTTTA : 48069 281 : laProSerArg >>>> Target Intron 3 >>>> ValArgArgLeuProAspGl : 290 !|||! !!:! 4583 bp :!!..! ! ! !! || leProIleLys++ +-IleGluAlaGlyThrProGl 48068 : TACCAATAAAAgt.........................aaATTGAAGCAGGGACACCAGG : 43456 291 : yGlnLeuGlnValThrTrpGluAspSerThrThrGlyLysGluAspThrGlyThrPheAs : 310 |!:!|||::!|||! ! :!!..!!!!!:!!:!! !:!! ! !||| !!:!:! yArgLeuArgValIleAlaLysSerThrSerSerAspGluIleIleGluGlyGluTyrAs 43455 : CCGACTCAGGGTGATAGCTAAGTCCACCAGTAGTGATGAAATTATCGAAGGAGAGTATAA : 43396 311 : pThr >>>> Target Intron 4 >>>> ValLeuTrpAlaIleGlyArgValPro : 320 !||| 554 bp |||||| !||||||||||||! ! !! nThr++ ++ValLeuLeuAlaIleGlyArgAspAla 43395 : TACGgt.........................agGTATTGCTGGCAATAGGAAGAGATGCT : 42812 321 : AspThrArgSerLeuAsnLeuGluLysAlaGlyValAspThrSerPro{As} >>>> T : 337 !||||||!.!:!!..!||||||! !.!|||||| ::: { !} CysThrArgLysIleGlyLeuGluThrValGlyValLysIleAsnGlu{Ly}++ 42811 : TGCACAAGAAAAATTGGCTTAGAAACCGTGGGggtaaagataaatgaa{aa}gt...... : 42757 338 : arget Intron 5 >>>> {p}ThrGlnLysIleLeuValAspSerArgGluAlaThr : 349 2394 bp { }||| !||||||! !||| ..!..!||| !||| ++{s}ThrGlyLysIleProValThrAspGluGluGlnThr 42756 : ...................ag{G}ACTGGAAAAATACCTGTCACAGATGAAGAGCAGACC : 40331 350 : SerValProHisIleTyrAlaIleGlyAspValValGluGlyArgProGluLeuThrPro : 369 !:!||||||:!!||||||||||||||||||:!!:!!||||||!:!! !|||||||||||| AsnValProTyrIleTyrAlaIleGlyAspIleLeuGluGlyLysLeuGluLeuThrPro 40330 : AATGTGCCTTACATCTATGCCATTGGCGATATATTAGAGGGGAAGCTGGAGCTTACCCCA : 40271 370 : IleAlaIleMetAlaGlyArgLeuLeuValGlnArgLeuPheGlyGlySerSerAspLeu : 389 :!!||||||..!|||||||||||||||!.!|||||||||!:!!.!||||||!:!! ! ValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyrAlaGlySerAsnValLys 40270 : GTAGCAATCCAGGCAGGAAGACTGCTGGCTCAGAGGCTTTATGCTGGCTCCAATGTGAAG : 40211 390 : >>>> Target Intron 6 >>>> MetAspTyrAspAsnValProThrThrValP : 400 4895 bp ||||||!!:||||||||||||||||||| ++ ++CysAspTyrGluAsnValProThrThrValP 40210 : gt.........................agTGTGACTATGAGAATGTTCCAACGACTGTGT : 35283 401 : heThrProLeuGluTyrGlyCysValGlyLeuSerGluGluGluAlaValAlaArgHisG : 420 ||||||||||||||||||||..! !|||||||||||||||..!||||||! ! | heThrProLeuGluTyrGlyAlaCysGlyLeuSerGluGluArgAlaValGluThrPheG 35282 : TTACTCCTTTGGAATATGGTGCCTGTGGTCTTTCTGAGGAGAGAGCTGTGGAGacatttg : 35223 421 : lyGlnGluHisValGlu >>>> Target Intron 7 >>>> ValTyrHisAlaHi : 430 ||:::|||::::::||| 2412 bp |||||||||::!:! lyGluGluAsnIleGlu++ ++ValTyrHisSerTy 35222 : gggaagaaaatattgaggt.........................agGTTTACCATAGTTA : 32781 431 : sTyrLysProLeuGluPheThrValAlaGlyArgAspAlaSerGlnCysTyrValLysMe : 450 !!:! !|||||||||!::|||:!! !!..!|||||| !!:!:!!||||||!.!|||:! rPheTrpProLeuGluTrpThrIleProSerArgAspAsnAsnLysCysTyrAlaLysVa 32780 : CTTTTGGCCGCTGGAGTGGACGATTCCATCAAGAGATAACAACAAATGTTATGCAAAAGT : 32721 451 : tValCysLeuArgGluProPro >>>> Target Intron 8 >>>> GlnLeuVal : 460 ::!!||| !! !:!! ! ! 3556 bp :!!! !||| lIleCysAsnIleLysAspAsn++ ++GluArgVal 32720 : AATCTGTAATATCAAAGACAACgt.........................agGAACGTGTT : 29135 461 : LeuGlyLeuHisPheLeuGlyProAsnAlaGlyGluValThrGlnGlyPheAlaLeuGly : 480 :!!|||!!!||| ! ||||||||||||||||||||||||||||||||||||||| !!.! ValGlyPheHisValLeuGlyProAsnAlaGlyGluValThrGlnGlyPheAlaAlaAla 29134 : GTGGGCTTCCACGTACTGGGTCCAAATGCTGGAGAAGTGACACAAGGCTTTGCAGCTGCC : 29075 481 : IleLysCysGlyAlaSerTyrAlaGlnValMetArgThrValGlyIleHisProThrCys : 500 :!!||||||||| !!!! ! !|||:!! !!!|||:!!||||||||||||..!||| LeuLysCysGlyLeuThrLysLysGlnLeuAspSerThrIleGlyIleHisProValCys 29074 : CTCAAGTGTGGACTGACCAAAAAGCAGCTGGACAGTACCATTGGAATCCACCCCGTCTGT : 29015 501 : SerGlu >>>> Target Intron 9 >>>> GluValValLysLeuArgIleSerL : 511 :!!||| 11468 bp ! ! !!..!! ||| !:!:!!!| AlaGlu++ ++ValPheThrThrLeuSerValThrL 29014 : GCAGAGgt.........................agGTATTCACGACTCTGTCGGTGACCA : 17514 512 : ysArgSerGlyLeuAspProThrValThrGlyCysUnkGly : 524 ||||||||||| !..! ! ! !.!!|||||| ||| ysArgSerGlyGlySerIleLeuGlnAlaGlyCys***Gly 17513 : AGCGCTCTGGGGGAAGCATCCTCCAGGCCGGCTGCTGAGGT : 17473 vulgar: 120 524 . KB229706.1:subseq(803937,50230) 50227 17472 - 993 M 48 144 5 0 2 I 0 357 3 0 2 M 26 78 G 1 0 M 12 36 S 0 2 5 0 2 I 0 1319 3 0 2 S 1 1 M 75 225 5 0 2 I 0 4579 3 0 2 M 28 84 5 0 2 I 0 550 3 0 2 M 25 75 S 0 2 5 0 2 I 0 2390 3 0 2 S 1 1 M 52 156 5 0 2 I 0 4891 3 0 2 M 36 108 5 0 2 I 0 2408 3 0 2 M 32 96 5 0 2 I 0 3552 3 0 2 M 45 135 5 0 2 I 0 11464 3 0 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-26 ##type DNA # # # seqname source feature start end score strand frame attributes # KB229706.1:subseq(803937,50230) exonerate:protein2genome:local gene 17473 50227 993 - . gene_id 1 ; sequence ; gene_orientation + KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 50084 50227 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 50084 50227 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 50082 50083 . - . intron_id 1 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 49723 50083 . - . intron_id 1 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 49723 49724 . - . intron_id 0 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 49607 49722 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 49607 49722 . - . insertions 0 ; deletions 1 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 49605 49606 . - . intron_id 2 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 48284 49606 . - . intron_id 2 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 48284 48285 . - . intron_id 1 ; splice_site "ag" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 48058 48283 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 48058 48283 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 48056 48057 . - . intron_id 3 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 43475 48057 . - . intron_id 3 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 43475 43476 . - . intron_id 2 ; splice_site "AA" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 43391 43474 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 43391 43474 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 43389 43390 . - . intron_id 4 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 42837 43390 . - . intron_id 4 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 42837 42838 . - . intron_id 3 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 42760 42836 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 42760 42836 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 42758 42759 . - . intron_id 5 ; splice_site "gt" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 40366 42759 . - . intron_id 5 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 40366 40367 . - . intron_id 4 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 40209 40365 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 40209 40365 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 40207 40208 . - . intron_id 6 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 35314 40208 . - . intron_id 6 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 35314 35315 . - . intron_id 5 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 35206 35313 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 35206 35313 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 35204 35205 . - . intron_id 7 ; splice_site "gt" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 32794 35205 . - . intron_id 7 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 32794 32795 . - . intron_id 6 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 32698 32793 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 32698 32793 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 32696 32697 . - . intron_id 8 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 29142 32697 . - . intron_id 8 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 29142 29143 . - . intron_id 7 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 29007 29141 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 29007 29141 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice5 29005 29006 . - . intron_id 9 ; splice_site "GT" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local intron 17539 29006 . - . intron_id 9 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local splice3 17539 17540 . - . intron_id 8 ; splice_site "AG" KB229706.1:subseq(803937,50230) exonerate:protein2genome:local cds 17473 17538 . - . KB229706.1:subseq(803937,50230) exonerate:protein2genome:local exon 17473 17538 . - . insertions 0 ; deletions 0 KB229706.1:subseq(803937,50230) exonerate:protein2genome:local similarity 17473 50227 993 - . alignment_id 1 ; Query ; Align 50228 121 144 ; Align 49723 169 78 ; Align 49645 196 36 ; Align 48283 209 225 ; Align 43475 284 84 ; Align 42837 312 75 ; Align 40365 338 156 ; Align 35314 390 108 ; Align 32794 426 96 ; Align 29142 458 135 ; Align 17539 503 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis