Command line: [exonerate -m p2g --showtargetgff -q SelV/SelV_U.fa -t SelV/SUBSEQ/KB228931.1_1_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SelV Target: KB228931.1:subseq(1036051,50077) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold54, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 100 Query range: 52 -> 260 Target range: 41280 -> 2598 53 : SerProAlaGlyThrSerProLeuValLeuThrProAlaProAlaGlnIleProThrLeu : 72 |||||||||||||||.!! !! ! ! ! !||| !||| !!! ! !||| !! ! SerProAlaGlyThrGlyValTrpProAlaArgProLeuProProProAlaProProAla 41280 : TCGCCGGCCGGGACCGGGGTCTGGCCTGCGCGCCCTCTTCCTCCGCCGGCCCCGCCAGCT : 41223 73 : ValProThrProAlaLeuAlaArgIleProArgLeuValProProProAlaProAlaTrp : 92 ! ! !||| !! ! !||| !|||||| ||||||||| ! ArgGlyArgProLeuProArgArgProProArgArgProProProProProAspLeuLeu 41222 : CGCGGGCGACCGCTGCCTCGCCGGCCTCCTcggcggccgccgccgccgccggacCTTCTC : 41163 93 : <->IleProThrProValProThrProValProValArgAsnProThrProValProThr : 111 !||| ! !!!.!||| !|||!.!|||!.! !..!! ! !||| !|||.!! ArgAlaProArgAlaAlaProGlyProAlaProAlaSerArgArgLeuProProProAla 41162 : CGGGCTCCGCGGGCCGCGCCGGGGCCGGCTCCCGCCTCCCGCCGCCTACCTCCGCCTGCC : 41103 112 : ProAlaArg{T} >>>> Target Intron 1 >>>> {hr}LeuThrProProVal : 120 ! !|||{ } 8383 bp { !} ||| ||| GlyArgArg{G}++ ++{ly}HisGlyProArgVal 41102 : GGACGTCGC{G}gt.........................ag{gt}catggtcccagggtc : 32693 121 : ArgValProAlaProAlaProAlaGlnLeuLeuAlaGlyIleArgAlaAlaLeuProVal : 140 :::|||||| ......||||||:::||| |||::: LeuGlySerSerProAlaSerGlySerLeuLeuSerGlyGluProAlaSerProSerPro 32692 : ctgggatcgagccctgcatcgggctccctgctcagcggggagcctgcttctccctctccc : 32633 141 : LeuAspSerTyrLeuAlaProAlaLeuProLeuAspProProPro{Gl} >>>> Targ : 156 ||| ...|||:::||| :::... {:!} ThrLeuSerAlaCysValProSerLeuThrValSerLeuSerVal{Ly}-+ 32632 : actctctctgcttgtgttccttctctcactgtgtctctctctgtc{aa}at......... : 32581 157 : et Intron 2 >>>> {u}ProAlaProGluLeuProLeuLeuProGluGluAspPro : 169 4428 bp {!}||||||||| ||| !!! !! ! ! ! ++{s}ProAlaProPheLeuAlaCysCysCysLeuIleTrpGlu 32580 : ................ag{A}CCTGCACCCTTCCTTGCCTGTTGCTGCCTCATCTGGGAA : 28118 170 : GluProAlaProSerLeu >>>> Target Intron 3 >>>> LysLeuIleProS : 180 ..!|||!.! !.!!:!! 14930 bp !!! !||| ArgProGlyArgGlyMet++ ++LeuPheCysProL 28117 : CGGCCGGGTAGGGGGATGgt.........................agCTTTTCTGTCCTC : 13155 181 : erValSerSerGluAlaGlyProAlaProGlyProLeuProThrArgThrProLeuAlaA : 200 !:!!..!!.! .!! ! ! ||| |||||||||..!! !!:!|||||| !| euLeuGlnLysThrThrThrAspIleProHisProLeuProValLeuSerProLeuAsnA 13154 : TCCTTCAGAAAACCACCACCGACAtcccacaccccctccctgtCCTTAGTCCTCTCAATG : 13095 201 : laAsnSerProGlyProThrLeuAspPheThrPheArgAlaAspProSerAlaIleGlyL : 220 ||!.!.!!||| !! !.!!! ! !.!...! !! !.!! ||| !!|||:!! !! laThrGlyProArgGluAlaSerIleIleValHisThrThrLeuProProAlaValProP 13094 : CCACCGGGCCTAGGGAGGCCTCGATTATAGTACACACCACCTTACCTCCGGCTGTCCCCC : 13035 221 : euAla >>>> Target Intron 4 >>>> AspProProIleProSerProVal{P : 230 !.!! 8917 bp !!:||| !:!: |||||| {! roThr++ ++GluProLysLeuAsnSerProPro{G 13034 : CAACCgt.........................agGAACCGAAATTGAAttctcctccc{c : 4088 231 : } >>>> Target Intron 5 >>>> {ro}SerProIleLeuGlyThrIleProSe : 239 } 1397 bp { !}:!! !! !||| !!..!:!! || }-+ +-{ln}AlaLysAsnLeuArgValValAspSe 4087 : }tt.........................ac{aG}GCTAAAAACCTTAGAGTTGTTGActc : 2664 240 : rAlaIleSerLeuGlnAsnCysThrGluThrPheProSerSerSerGluAsnPheAlaLe : 259 |::: ||| ...!.!|||||| !! !.!.|||!!! !|||..!|||!:! !|| rSerSerSerProHisThrCysThrProIleLeuProThrLeuSerSerAsnTyrIleLe 2663 : ctcttcctcaccccacACCTGTACCCCAATCCTGCCCACTCTTTCTTCAAATTATATCTT : 2604 260 : uAsp : 260 |:!! uAsn 2603 : AAAT : 2599 vulgar: 52 260 . KB228931.1:subseq(1036051,50077) 41280 2598 - 100 M 40 120 G 0 3 M 22 66 S 0 1 5 0 2 I 0 8379 3 0 2 S 1 2 M 40 120 S 0 2 5 0 2 I 0 4424 3 0 2 S 1 1 M 19 57 5 0 2 I 0 14926 3 0 2 M 46 138 5 0 2 I 0 8913 3 0 2 M 8 24 S 0 1 5 0 2 I 0 1393 3 0 2 S 1 2 M 30 90 # --- 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 # KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local gene 2599 41280 100 - . gene_id 1 ; sequence ; gene_orientation + KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local cds 41091 41280 . - . KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local exon 41091 41280 . - . insertions 3 ; deletions 0 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice5 41089 41090 . - . intron_id 1 ; splice_site "GT" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local intron 32708 41090 . - . intron_id 1 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice3 32708 32709 . - . intron_id 0 ; splice_site "ag" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local cds 32584 32707 . - . KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local exon 32584 32707 . - . insertions 0 ; deletions 0 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice5 32582 32583 . - . intron_id 2 ; splice_site "at" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local intron 28156 32583 . - . intron_id 2 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice3 28156 28157 . - . intron_id 1 ; splice_site "AG" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local cds 28098 28155 . - . KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local exon 28098 28155 . - . insertions 0 ; deletions 0 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice5 28096 28097 . - . intron_id 3 ; splice_site "GT" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local intron 13168 28097 . - . intron_id 3 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice3 13168 13169 . - . intron_id 2 ; splice_site "AG" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local cds 13030 13167 . - . KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local exon 13030 13167 . - . insertions 0 ; deletions 0 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice5 13028 13029 . - . intron_id 4 ; splice_site "GT" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local intron 4113 13029 . - . intron_id 4 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice3 4113 4114 . - . intron_id 3 ; splice_site "AG" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local cds 4088 4112 . - . KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local exon 4088 4112 . - . insertions 0 ; deletions 0 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice5 4086 4087 . - . intron_id 5 ; splice_site "tt" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local intron 2691 4087 . - . intron_id 5 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local splice3 2691 2692 . - . intron_id 4 ; splice_site "ac" KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local cds 2599 2690 . - . KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local exon 2599 2690 . - . insertions 0 ; deletions 0 KB228931.1:subseq(1036051,50077) exonerate:protein2genome:local similarity 2599 41280 100 - . alignment_id 1 ; Query ; Align 41281 53 120 ; Align 41158 93 66 ; Align 32706 116 120 ; Align 28155 157 57 ; Align 13168 176 138 ; Align 4113 222 24 ; Align 2689 231 90 # --- END OF GFF DUMP --- # -- completed exonerate analysis