Command line: [exonerate -m p2g --showtargetgff -q TR3/TR3_U.fa -t TR3/SUBSEQ/KB228921.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: TR3 Target: KB228921.1:subseq(5659763,50209) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold44, whole genome shotgun sequence Model: protein2genome:local Raw score: 1805 Query range: 27 -> 455 Target range: 3044 -> 50209 28 : ProSer{G} >>>> Target Intron 1 >>>> {ly}ProValProAlaProGln : 36 |||!!!{|} 14942 bp {||} !! !!|||||||||||| ProThr{G}++ ++{ly}SerPheProAlaProGln 3045 : CCCACA{G}gt.........................ag{GC}TCATTCCCGGCGCCGCAG : 18011 37 : ProProAlaPheArgPheValSerArgProGlyArgAlaArgSerGluSerGluThrLeu : 56 ||||||! !|||! !:!!!:! !!||||||!:!|||||||||!!:!!!! .!!||| ---ProAlaSerArgSerLeuAsnCysProGlyGlnAlaArgSerAspThrAlaAlaLeu 18012 : ---CCCGCCTCTAGGTCCCTGAACTGCCCCGGCCAGGCCCGGAGCGATACCGCCGCCCTG : 18068 57 : GluArgSerProPro<-><-><-><-><-><-><->GlnSerProGlyProGlyLysAla : 69 ! !!:! !!|||||| !||||||||||||! !||| ! AlaGlnProProProProProProProGlnAlaGlnThrSerProGlyProValLysMet 18069 : GCACAGCCACCGCCACCACCGCCGCCGCAGGCGCAGACATCGCCGGGGCCGGTGAAGATG : 18128 70 : GlyAspAlaProAsnArgArgSerGlyHisValArgGlyAlaArgValLeuSerProPro : 89 |||! !.!|||||||||||| !||| !|||||||||!.!! !:!!! !||||||||| GlyAlaValProAsnArgArgLeuGlySerValArgGlyValProMetSerSerProPro 18129 : GGGGCGGTCCCCAACCGCCGCCTGGGTAGTGTCCGCGGCGTGCCCATGTCTTCGCCGCCA : 18188 90 : GlyArgArgAlaArgLeuSerSerProGlyProSerArg<->SerSerGluAlaArgGlu : 108 |||||||||||||||||||||||||||||| !!.!!||| |||||||||||||||||| GlyArgArgAlaArgLeuSerSerProGlyThrGlyArgSerSerSerGluAlaArgGlu 18189 : GGGCGCCGGGCCCGCCTGTCGTCCCCCGGCACCGGCCGCTCGTCCTCCGAGGCCCGCGAG : 18248 109 : GluLeuArgArgHisLeuValGlyLeuIleGluArgSerArgValValIlePheSerLys : 128 ||||||||||||!.!|||:!!||||||||||||!!!!:!||||||:!!|||||||||||| GluLeuArgArgArgLeuLeuGlyLeuIleGluSerAsnArgValMetIlePheSerLys 18249 : GAGCTGCGGCGCCGCCTCCTGGGCCTCATCGAGAGCAACCGAGTGATGATCTTCAGCAAG : 18308 129 : SerTyrCysProHisSerThrArg >>>> Target Intron 2 >>>> ValLysG : 139 ||||||||||||||||||.!!||| 11750 bp ||||||| SerTyrCysProHisSerAlaArg++ ++ValLysG 18309 : AGTTACTGCCCGCACAGCGCGCGGgt.........................agGTTAAag : 30091 140 : luLeuPheSerSerLeuGlyValGluCysAsnValLeuGluLeuAspGlnVal{A} >> : 157 ||||||||||||||||||||||||||||||||:!!||||||||||||!:!|||{|} luLeuPheSerSerLeuGlyValGluCysAsnIleLeuGluLeuAspArgVal{A}++ 30092 : aactgttttcttctttgggaGTTGAATGTAATATCTTGGAACTTGATCGAGTT{G}gt.. : 30148 158 : >> Target Intron 3 >>>> {sp}AspGlyAlaArgValGlnGluValLeuSerG : 168 1055 bp {||}|||||||||!.!||||||||||||||||||| ++{sp}AspGlyAlaAsnValGlnGluValLeuSerG 30149 : .......................ag{AT}GATGGGGCCAATGTCCAAGAAGTGCTGTCAG : 31233 169 : luIleThrAsnGlnLysThrValProAsnIlePheValAsnLysValHisValGlyGlyC : 188 ||||||||||||||||||||||||||||||||||||||||||||||||||:!!||||||| luIleThrAsnGlnLysThrValProAsnIlePheValAsnLysValHisMetGlyGlyC 31234 : AGATCACTAATCAGAAAACCGTGCCcaatatttttgtgaataaagtgcATATGGGTGGAT : 31293 189 : ysAspGlnThrPheGln >>>> Target Intron 4 >>>> AlaTyrGlnSerGl : 198 |||||!:!||||||||| 1584 bp |||:!!|||!!!|| ysAspArgThrPheGln++ ++AlaHisGlnCysGl 31294 : GTGATCGAACTTTCCAGgt.........................agGCCCATCAGTGTGG : 32907 199 : yLeuLeuGlnLysLeuLeuGlnGluAspLeuAlaTyrAspTyrAspLeuIleIleIleGl : 218 |||||||||||||||||||||||||||| !|||!:!!!:||||||||||||:!!||||| yLeuLeuGlnLysLeuLeuGlnGluAspAlaAlaPheGluTyrAspLeuIleValIleGl 32908 : CTTATTACAGAAGCTCCTTCAGGAAGATGCAGCATTCGAATATGACCTCATTGTCATTGG : 32967 219 : yGlyGlySerGlyGlyLeuSerCysAlaLys >>>> Target Intron 5 >>>> : 229 |||||||||||||||||||:!!||||||:!! 224 bp yGlyGlySerGlyGlyLeuAlaCysAlaGln++ ++ 32968 : GGGAGGTTCTGGTGGCCTTGCATGTGCGCAGgt.........................ag : 33222 230 : GluAlaAlaIleLeuGlyLysLysValMetValLeuAspPheValValProSerProGln : 248 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GluAlaAlaIleLeuGlyLysLysValMetValLeuAspPheValValProSerProGln 33223 : GAAGCCGCCATCTTGGGAAAGAAAGTTATGGTGCTAGACTTTGTGGTCCCGTCACCTCAG : 33281 249 : GlyThrSerTrp{G} >>>> Target Intron 6 >>>> {ly}LeuGlyGlyThr : 257 ||||||||||||{|} 1859 bp {||}|||||||||||| GlyThrSerTrp{G}++ ++{ly}LeuGlyGlyThr 33282 : GGCACGTCCTGG{G}gt.........................ag{gT}CTTGGCGGGACT : 35167 258 : CysValAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGln : 277 ||||||||||||||||||:!!||||||||||||||||||||||||||||||||||||||| CysValAsnValGlyCysValProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGln 35168 : TGTGTAAATGTGGGCTGTGTTCCTAAGAAACTGATGCATCAAGCTGCCCTTTTGGGGCAG : 35227 278 : AlaLeuCysAspSerArgLysPheGlyTrpGluTyrAsnGlnGln{V} >>>> Targe : 293 |||||| !!|||:!!|||||||||||||||||||||!:!||||||{|} 1 AlaLeuSerAspAlaArgLysPheGlyTrpGluTyrSerGlnGln{V}++ 35228 : GCATTAAGTGACGCCAGGAAGTTTGGCTGGGAGTACAGTCAACAA{G}gt.......... : 35278 294 : t Intron 7 >>>> {al}ArgHisAsnTrpGluThrMetThrLysAlaIleGlnAsn : 306 2815 bp {||}!:!|||||||||||||||||||||:!!|||||||||||| ++{al}LysHisAsnTrpGluThrMetThrGluAlaIleGlnAsn 35279 : ...............ag{TG}AAGCACAACTGGGAGACGATGACAGAAGCGATTCAAAAT : 48129 307 : HisIleSerSerLeuAsnTrpGlyTyrArgLeuSerLeuArgGluLysAlaValAlaTyr : 326 ||||||.!!||||||||||||||||||||||||||||||||||||||||||||||||||| HisIleGlySerLeuAsnTrpGlyTyrArgLeuSerLeuArgGluLysAlaValAlaTyr 48130 : CACATCGGCTCTCTAAACTGGGGCTACAGATTGTCCTTGAGGGAGAAGGCCGTGGCCTAT : 48189 327 : ValAsnSerTyrGlyGluPheValGluHisHisLysIleLys >>>> Target Intr : 341 |||||||||||||||||||||||||||||||||||||||||| 734 bp ValAsnSerTyrGlyGluPheValGluHisHisLysIleLys++ 48190 : GTCAATTCCTATGGAGAATTTGTTGAACATCATAAAATAAAGgt................ : 48236 342 : on 8 >>>> AlaThrAsnLysLysGlyGlnGluThrTyrTyrThrAlaAlaGlnPheV : 357 |||||||||!:!||||||||||||||||||||||||||||||:!!|||| ++AlaThrAsnArgLysGlyGlnGluThrTyrTyrThrAlaAlaLysPheV 48237 : .........aggCAACCAATAGAAAAGGACAGGAAACTTACTATACTGCTGCAAAATTTG : 49016 358 : alIleAlaThrGlyGluArgProArgTyrLeuGlyIleGlnGlyAspLysGluTyrCysI : 377 ||:!!||||||||||||||||||||||||||||||||||||||||||||||||||||||| alLeuAlaThrGlyGluArgProArgTyrLeuGlyIleGlnGlyAspLysGluTyrCysI 49017 : TCCTAGCGACAGGCGAAAGGCCCCGCTATTTAGGAATCCAAGGAGATAAAGAGTACTGTA : 49076 378 : leThr{Se} >>>> Target Intron 9 >>>> {r}AspAspLeuPheSerLeuP : 386 |||||{||} 897 bp {|}||||||||||||||||||| leThr{Se}++ ++{r}AspAspLeuPheSerLeuP 49077 : TTACT{AG}gt.........................ag{t}gacgACCTGTTTTCTTTGC : 50000 387 : roTyrCysProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaG : 406 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| roTyrCysProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaG 50001 : CTTATTGCCCTGGCAAAACATTAGTGGTGGGGGCATCTTACGTCGCTCTGGAATGTGCAG : 50060 407 : lyPheLeuAlaGlyPheGlyLeuAspValThrValMetValArgSerIleLeuLeuArgG : 426 ||||||||||||||.!!||||||||||||||||||||||||||||||:!!|||||||||| lyPheLeuAlaGlyIleGlyLeuAspValThrValMetValArgSerValLeuLeuArgG 50061 : GGTTTCTTGCTGGCATTGGCTTAGATGTCACAGTTATGGTGCGCTCGGTCCTTCTTCGTG : 50120 427 : lyPheAspGlnGluMetAlaGluLysValGlySerTyrMetGluGlnHisGlyValLysP : 446 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lyPheAspGlnGluMetAlaGluLysValGlySerTyrMetGluGlnHisGlyValLysP 50121 : GCTTTGATCAAGAAATGGCAGAGAAAGTGGGTTCCTACATGGAGCAACATGGTGTTAAGT : 50180 447 : heLeuArgLysPheIleProValMetVal : 455 ||||||||||||||:!!|||||||||||| heLeuArgLysPheValProValMetVal 50181 : TCTTAAGAAAATTTGTACCTGTGATGGTA : 50209 vulgar: 27 455 . KB228921.1:subseq(5659763,50209) 3044 50209 + 1805 M 2 6 S 0 1 5 0 2 I 0 14938 3 0 2 S 1 2 M 6 18 G 1 0 M 24 72 G 0 21 M 41 123 G 0 3 M 34 102 5 0 2 I 0 11746 3 0 2 M 20 60 S 0 1 5 0 2 I 0 1051 3 0 2 S 1 2 M 36 108 5 0 2 I 0 1580 3 0 2 M 35 105 5 0 2 I 0 220 3 0 2 M 24 72 S 0 1 5 0 2 I 0 1855 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 12811 3 0 2 S 1 2 M 47 141 5 0 2 I 0 730 3 0 2 M 38 114 S 0 2 5 0 2 I 0 893 3 0 2 S 1 1 M 76 228 # --- 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 # KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local gene 3045 50209 1805 + . gene_id 1 ; sequence ; gene_orientation + KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 3045 3051 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 3045 3051 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 3052 3053 . + . intron_id 1 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 3052 17993 . + . intron_id 1 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 17992 17993 . + . intron_id 0 ; splice_site "AG" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 17994 18334 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 17994 18334 . + . insertions 24 ; deletions 1 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 18335 18336 . + . intron_id 2 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 18335 30084 . + . intron_id 2 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 30083 30084 . + . intron_id 1 ; splice_site "AG" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 30085 30145 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 30085 30145 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 30146 30147 . + . intron_id 3 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 30146 31200 . + . intron_id 3 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 31199 31200 . + . intron_id 2 ; splice_site "AG" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 31201 31310 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 31201 31310 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 31311 31312 . + . intron_id 4 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 31311 32894 . + . intron_id 4 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 32893 32894 . + . intron_id 3 ; splice_site "AG" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 32895 32999 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 32895 32999 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 33000 33001 . + . intron_id 5 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 33000 33223 . + . intron_id 5 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 33222 33223 . + . intron_id 4 ; splice_site "aG" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 33224 33296 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 33224 33296 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 33297 33298 . + . intron_id 6 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 33297 35155 . + . intron_id 6 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 35154 35155 . + . intron_id 5 ; splice_site "ag" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 35156 35275 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 35156 35275 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 35276 35277 . + . intron_id 7 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 35276 48090 . + . intron_id 7 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 48089 48090 . + . intron_id 6 ; splice_site "AG" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 48091 48233 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 48091 48233 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 48234 48235 . + . intron_id 8 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 48234 48967 . + . intron_id 8 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 48966 48967 . + . intron_id 7 ; splice_site "ag" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 48968 49083 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 48968 49083 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice5 49084 49085 . + . intron_id 9 ; splice_site "GT" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local intron 49084 49980 . + . intron_id 9 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local splice3 49979 49980 . + . intron_id 8 ; splice_site "ag" KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local cds 49981 50209 . + . KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local exon 49981 50209 . + . insertions 0 ; deletions 0 KB228921.1:subseq(5659763,50209) exonerate:protein2genome:local similarity 3045 50209 1805 + . alignment_id 1 ; Query ; Align 3045 28 6 ; Align 17996 31 18 ; Align 18014 38 72 ; Align 18107 62 123 ; Align 18233 103 102 ; Align 30085 137 60 ; Align 31203 158 108 ; Align 32895 194 105 ; Align 33224 229 72 ; Align 35158 254 117 ; Align 48093 294 141 ; Align 48968 341 114 ; Align 49982 380 228 # --- END OF GFF DUMP --- # -- completed exonerate analysis