Command line: [exonerate -m p2g --showtargetgff -q SecS/SecS_x.fa -t SecS/SUBSEQ/CM004420.1_4_subseq.txt --exhaustive] Hostname: [ws101084U] C4 Alignment: ------------ Query: SPP00000631_2.0 Protein Selenocysteine synthase (SecS) Zebrafish Target: CM004420.1:subseq(13642442,25131) Ictalurus punctatus breed USDA103 chromosome 7, whole genome shotgun sequence Model: protein2genome:local Raw score: 1949 Query range: 0 -> 447 Target range: 9816 -> 25131 1 : MetAsnSerGluAsnPheArgLeuSerGluLysLeuValSerAlaSerTyrValArgGln : 20 ||||||..!||||||||||||||||||||||||||||||||||||||||||||||||||| MetAsnAspGluAsnPheArgLeuSerGluLysLeuValSerAlaSerTyrValArgGln 9817 : ATGAATGACGAAAACTTCCGGCTGAGTGAGAAGCTGGTGTCCGCTTCCTATGTGCGGCAG : 9874 21 : GlyLeuAspAlaArgArgGlyHisGluGlnLeuIleArgArgLeuLeuAspGln >>>> : 39 |||:!!.!.|||||| !!||||||:!!||||||||||||! !||||||!!:||| GlyValGlnAlaArgCysGlyHisGlnGlnLeuIleArgThrLeuLeuGluGln++ 9875 : GGTGTCCAGGCTCGCTGCGGTCATCAGCAACTCATCAGGACTCTGCTAGAGCAGgt.... : 9933 40 : Target Intron 1 >>>> GlyLysCysProGluGluGlyTrpSerGluSerThrI : 51 2651 bp ||||||||||||||||||||||||!:!|||||||||| ++GlyLysCysProGluGluGlyTrpAsnGluSerThrI 9934 : .....................agGGCAAATGTCCAGAGGAGGGATGGAACGAAAGCACCA : 12618 52 : leGluLeuPheLeuAsnGluLeuAlaValMetAspSerAsnAsnPheLeuGlyAsnCysG : 71 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| leGluLeuPheLeuAsnGluLeuAlaValMetAspSerAsnAsnPheLeuGlyAsnCysG 12619 : TAGAGCTCTTTCTGAATGAGCTCGCAGTCATGGACAGTAATAATTTCTTGGGGAACTGTg : 12678 72 : lyValGlyGluArgGluGlyArgValAlaSerSerLeuValAlaArgArgHisTyr{Ar} : 90 ||||||||||||||||||||||||||||||||.!!|||||||||||||||||||||{||} lyValGlyGluArgGluGlyArgValAlaSerGlyLeuValAlaArgArgHisTyr{Ar} 12679 : gagttggagagagagagggccgAGTTGCCTCTGGCCTGGTGGCCCGAAGACATTAC{AG} : 12735 91 : >>>> Target Intron 2 >>>> {g}LeuIleHisGlyIleGlyArgSerGlyA : 100 1846 bp {|}|||||||||||||||||||||||||||| ++ ++{g}LeuIleHisGlyIleGlyArgSerGlyA 12736 : gt.........................ag{A}TTGATCCATGGCATCGGCCGCTCTGGTG : 14611 101 : spIleAlaAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS : 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| spIleAlaAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS 14612 : ATATTGCTGCTGTTCAGCCGAAGGCCGCTGGCTCCAGTCTCCTCAACAAGATCACCAATT : 14671 121 : erValValLeuAspValLeuLysLeuThr{G} >>>> Target Intron 3 >>>> : 130 ||||||||||||||||||||!:!!!!!:!{|} 81 bp erValValLeuAspValLeuArgPheSer{G}++ + 14672 : CAGTAGTGCTGGATGTTCTCAGATTTAGC{G}gt.........................a : 14781 131 : {ly}ValArgSerValSerSerCysPheValValProMetAlaThrGlyMetSerLeuT : 149 {||}||||||||||||||||||||||||||||||||||||||||||||||||||||||| +{ly}ValArgSerValSerSerCysPheValValProMetAlaThrGlyMetSerLeuT 14782 : g{GT}GTTAGAAGTGTGTCATCATGCTTTGTGGTGCCCATGGCAACTGGAATGAGCTTGA : 14839 150 : hrLeuCysPheLeuThrLeuArgHisArgArgProLysAlaArgTyrIleLeuTrpProA : 169 |||||||||||||||||||||||||||||||||||..!|||||||||||||||||||||| hrLeuCysPheLeuThrLeuArgHisArgArgProSerAlaArgTyrIleLeuTrpProA 14840 : CGTTGTGTTTCCTGACACTCCGACACAGGAGGCCATCAGCACGCTACATTCTTTGGCCTC : 14899 170 : rgIleAspGlnLysSerCysPheLysSerMetValThrAla{G} >>>> Target In : 183 |||||||||||||||||||||||||||||||||||||||||{|} 322 rgIleAspGlnLysSerCysPheLysSerMetValThrAla{G}++ 14900 : GCATTGACCAGAAGTCCTGTTTCAAATCGATGGTCACTGCC{G}gt.............. : 14944 184 : tron 4 >>>> {ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL : 198 bp {||}||||||||||||||||||||||||||||||||||||||||||| ++{ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL 14945 : ...........ag{GG}TTTGAGCCGGTGGTCATTGAGAATGTTCTGGAAGGAGATGAGT : 15308 199 : euArgThrAsnLeuGluGluValGluArgLysIleGluGluPheGlyAlaGluAsnIleL : 218 ||||||||:!!||||||! ||||||!:!|||:!!||||||.!!|||||||||||||||| euArgThrAspLeuGluAlaValGluLysLysValGluGluLeuGlyAlaGluAsnIleL 15309 : TGAGGACAGACCTGGAGGCTGTGGAGAAGAAGGTCGAGGAACTTGGAGCTGAGAATATTC : 15368 219 : euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar} >>>> Ta : 234 |||||||||||||||||||||||||||||||||||||||||||||||{||} euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar}+- 15369 : TGTGTGTTCATTccaccacttcctgttttgctCCTCGCGTCCCTGAC{AG}gc....... : 15420 235 : rget Intron 5 >>>> {g}LeuGluGluLeuSerValLeuCysAlaLysHisAspI : 247 1460 bp {|}||||||||||||||||||:!!|||||||||:!!:!!| ++{g}LeuGluGluLeuSerValMetCysAlaLysTyrAsnI 15421 : ..................ag{G}TTGGAAGAGCTCTCTGTTATGTGTGCCAAATATAACA : 16915 248 : leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG : 267 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG 16916 : TCCCTCATATAGTCAACAATGCCTACGGAGTGCAGTCATCCAAATGCATGCACCTCATAC : 16975 268 : lnGln >>>> Target Intron 6 >>>> GlyAlaArgValGlyArgIleAspAl : 277 ||||| 93 bp |||||||||||||||||||||||||| lnGln++ ++GlyAlaArgValGlyArgIleAspAl 16976 : AACAGgt.........................agGGTGCGCGAGTGGGCAGAATTGATGC : 17098 278 : aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl : 297 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl 17099 : CTTTGTTCAAAGCCTGGACAAAAATTTCATGGTTCCTGTTGGAGGTGCCATTATTGCAGG : 17158 298 : yPheAspGluAsnPheIleGlnGluIleSerLysIleTyrPro{G} >>>> Target : 312 ||||||||||:!!||||||:!!||||||||||||!!:||||||{|} 54 yPheAspGluAspPheIleLysGluIleSerLysMetTyrPro{G}++ 17159 : CTTTGATGAGGACTTCATTAAGGAGATCAGTAAAATGTACCCT{G}gt............ : 17206 313 : Intron 7 >>>> {ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe : 326 4 bp {||}||||||||||||||||||||||||||||||||||||||||| ++{ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe 17207 : .............ag{GT}CGTGCATCAGCTTCCCCCTCTCTGGACGTGCTTATCACTCT : 17789 327 : uLeuThrLeuGlyAlaAsnGlyTyrLysLysLeuLeuAlaAspArgLys >>>> Targ : 343 ||||!:!|||||||||!:!||||||||||||||||||:!!!!:|||||| uLeuSerLeuGlyAlaSerGlyTyrLysLysLeuLeuSerGluArgLys++ 17790 : GCTCAGTCTCGGGGCCAGTGGCTATAAAAAACTCCTGTCTGAGAGAAAGgt......... : 17842 344 : et Intron 8 >>>> GluLeuTyrGlyHisLeuAlaGlnGluLeuSerAlaLeuAla : 356 3551 bp ||||||||| !||||||!.!|||||||||!.! !|||||| ++GluLeuTyrThrHisLeuValGlnGluLeuLysIleLeuAla 17843 : ................agGAGCTGTACACCCACCTGGTTCAAGAGCTGAAGATACTGGCT : 21430 357 : AlaArgHisGlyGluArgLeuLeuLysThrProHisAsnProIleSerLeu{A} >>>> : 374 ! !!!!|||||||||||||||||| ! ||||||||||||||||||||||||{|} AspSerHisGlyGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A}++ 21431 : GATAGCCATGGAGAGAGACTGCTGCATACGCCACATAATCCCATATCACTG{G}gt.... : 21487 375 : Target Intron 9 >>>> {la}MetSerLeuAsnHisLeuGluAlaHisSerSer : 385 368 bp {||}|||||||||:!! !|||:!!|||:!!!!!..! ++{la}MetSerLeuAspAlaLeuGlnAlaAsnCysAsp 21488 : .....................ag{CT}ATGTCTCTGGATGCTCTTCAGGCTAACTGTGAT : 21885 386 : SerAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar} : 404 !.!|||:!!|||||||||||||||||||||||||||||||||||||||||||||{||} LysAlaIleThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++ 21886 : AAAGCCATTACCCAGCTGGGCTCTATGCTCTTCACCAGGCAGGTGTCGGGAGCC{AG}gt : 21944 405 : >>>> Target Intron 10 >>>> {g}ValValProLeuGlyValGlnGlnThrVa : 414 3058 bp {|}|||||||||||||||..!:!!|||||||| ++{g}ValValProLeuGlyThrGluGlnThrVa 21945 : ..........................ag{G}GTTGTGCCACTGGGAACCGAACAAACTGT : 25030 415 : lSerGlyHisThrPheSerGlyPheMetSerHisSerGluAlaTyrProCysProTyrLe : 434 |||||||||||||||| !!||||||||||||||||||!!:|||||||||||||||||||| lSerGlyHisThrPheArgGlyPheMetSerHisSerAspAlaTyrProCysProTyrLe 25031 : GAGCGGACACACGTTTCGTGGCTTCATGTCACATTCGGATGCCTACCCATGCCCATACCT : 25090 435 : uAsnAlaAlaSerAlaIleGlyIleThrLysGlyAspVal : 447 ||||||||||||||||||||||||||||!:! !|||||| uAsnAlaAlaSerAlaIleGlyIleThrArgLysAspVal 25091 : TAATGCTGCTTCTGCTATTGGCATCACCAGAAAAGACGTG : 25131 vulgar: SPP00000631_2.0 0 447 . CM004420.1:subseq(13642442,25131) 9816 25131 + 1949 M 38 114 5 0 2 I 0 2647 3 0 2 M 51 153 S 0 2 5 0 2 I 0 1842 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 77 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 318 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 1456 3 0 2 S 1 1 M 34 102 5 0 2 I 0 89 3 0 2 M 43 129 S 0 1 5 0 2 I 0 540 3 0 2 S 1 2 M 30 90 5 0 2 I 0 3547 3 0 2 M 31 93 S 0 1 5 0 2 I 0 364 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 3054 3 0 2 S 1 1 M 43 129 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local gene 9817 25131 1949 + . gene_id 1 ; sequence SPP00000631_2.0 ; gene_orientation + CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 9817 9930 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 9817 9930 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 9931 9932 . + . intron_id 1 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 9931 12581 . + . intron_id 1 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 12580 12581 . + . intron_id 0 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 12582 12736 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 12582 12736 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 12737 12738 . + . intron_id 2 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 12737 14582 . + . intron_id 2 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 14581 14582 . + . intron_id 1 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 14583 14701 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 14583 14701 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 14702 14703 . + . intron_id 3 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 14702 14782 . + . intron_id 3 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 14781 14782 . + . intron_id 2 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 14783 14941 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 14783 14941 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 14942 14943 . + . intron_id 4 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 14942 15263 . + . intron_id 4 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 15262 15263 . + . intron_id 3 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 15264 15417 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 15264 15417 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 15418 15419 . + . intron_id 5 ; splice_site "GC" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 15418 16877 . + . intron_id 5 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 16876 16877 . + . intron_id 4 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 16878 16980 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 16878 16980 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 16981 16982 . + . intron_id 6 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 16981 17073 . + . intron_id 6 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 17072 17073 . + . intron_id 5 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 17074 17203 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 17074 17203 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 17204 17205 . + . intron_id 7 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 17204 17747 . + . intron_id 7 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 17746 17747 . + . intron_id 6 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 17748 17839 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 17748 17839 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 17840 17841 . + . intron_id 8 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 17840 21390 . + . intron_id 8 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 21389 21390 . + . intron_id 7 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 21391 21484 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 21391 21484 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 21485 21486 . + . intron_id 9 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 21485 21852 . + . intron_id 9 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 21851 21852 . + . intron_id 8 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 21853 21943 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 21853 21943 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice5 21944 21945 . + . intron_id 10 ; splice_site "GT" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local intron 21944 25001 . + . intron_id 10 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local splice3 25000 25001 . + . intron_id 9 ; splice_site "AG" CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local cds 25002 25131 . + . CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local exon 25002 25131 . + . insertions 0 ; deletions 0 CM004420.1:subseq(13642442,25131) exonerate:protein2genome:local similarity 9817 25131 1949 + . alignment_id 1 ; Query SPP00000631_2.0 ; Align 9817 1 114 ; Align 12582 39 153 ; Align 14584 91 117 ; Align 14785 131 156 ; Align 15266 184 150 ; Align 16879 235 102 ; Align 17074 269 129 ; Align 17750 313 90 ; Align 21391 343 93 ; Align 21855 375 87 ; Align 25003 405 129 # --- END OF GFF DUMP --- # -- completed exonerate analysis