Command line: [exonerate -m p2g --showtargetgff -q SecS.x.fa -t SecS.extraction.KV885014.1.fa] Hostname: [sitdoc] C4 Alignment: ------------ Query: SecS # Protein # Selenocysteine synthase (SecS) # Zebrafish Target: KV885014.1:subseq(270895,100000) Monopterus albus unplaced genomic scaffold scaffold326.1, whole genome shotgun sequence Model: protein2genome:local Raw score: 2027 Query range: 0 -> 466 Target range: 49999 -> 58155 1 : MetAsnSerGluAsnPheArgLeuSerGluLysLeuValSerAlaSerTyrValArgGln : 20 |||||||||||||||||| !|||||||||||||||||||||:!!||||||:!!|||||| MetAsnSerGluAsnPheAlaLeuSerGluLysLeuValSerSerSerTyrIleArgGln 50000 : ATGAACAGTGAGAACTTCGCCCTGAGTGAGAAGCTCGTGTCGTCCTCCTACATTCGACAG : 50057 21 : GlyLeuAspAlaArgArgGlyHisGluGlnLeuIleArgArgLeuLeuAspGln >>>> : 39 |||! !.!.|||||||||.!!||||||||||||||||||!.!||||||!!:||| GlySerGlnAlaArgArgSerHisGluGlnLeuIleArgHisLeuLeuGluGln++ 50058 : GGGTCTCAGGCACGACGCAGCCACGAGCAGCTCATTAGACACTTACTGGAGCAGgt.... : 50116 40 : Target Intron 1 >>>> GlyLysCysProGluGluGlyTrpSerGluSerThrI : 51 72 bp |||||||||||||||!!:||||||||||||||||||: ++GlyLysCysProGluAspGlyTrpSerGluSerThrV 50117 : .....................agGGTAAGTGTCCTGAGGACGGCTGGAGCGAGAGCACTG : 50222 52 : leGluLeuPheLeuAsnGluLeuAlaValMetAspSerAsnAsnPheLeuGlyAsnCysG : 71 !:||||||||||||||||||||||||||||||||||||||||||||||||.!!||||||| alGluLeuPheLeuAsnGluLeuAlaValMetAspSerAsnAsnPheLeuSerAsnCysG 50223 : TGGAGCTCTTCTTGAATGAGCTGGCTGTGATGGACAGCAATAACTTTCTCAGCAACTGTG : 50282 72 : lyValGlyGluArgGluGlyArgValAlaSerSerLeuValAlaArgArgHisTyr{Ar} : 90 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||{||} lyValGlyGluArgGluGlyArgValAlaSerSerLeuValAlaArgArgHisTyr{Ar} 50283 : GAGTCGGGGAGAGGGAGGGCCGGGTGGCCTCCAGCCTGGTGGCACGACGACACTAC{AG} : 50339 91 : >>>> Target Intron 2 >>>> {g}LeuIleHisGlyIleGlyArgSerGlyA : 100 422 bp {|}|||||||||||||||||||||||||||| ++ ++{g}LeuIleHisGlyIleGlyArgSerGlyA 50340 : gt.........................ag{G}TTGATCCATGGCATCGGTCGGTCCGGTG : 50791 101 : spIleAlaAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS : 120 ||||||||||||||||||||||||||||||||||||||||||||||||||:!:||||||| spIleAlaAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysLeuThrAsnS 50792 : ACATCGCTGCCGTTCAGCCCAAAGCTGCAGGCTCCAGTCTGCTTAACAAGCTGACCAACT : 50851 121 : erValValLeuAspValLeuLysLeuThr{G} >>>> Target Intron 3 >>>> : 130 ||||||||||||||:!!|||||||||.!!{|} 298 bp erValValLeuAspIleLeuLysLeuAla{G}++ + 50852 : CAGTTGTGTTAGACATCTTGAAACTTGCA{G}gt.........................a : 51178 131 : {ly}ValArgSerValSerSerCysPheValValProMetAlaThrGlyMetSerLeuT : 149 {||}||||||||||||:!!!!!||||||||||||||||||||||||||||||||||||| +{ly}ValArgSerValAlaThrCysPheValValProMetAlaThrGlyMetSerLeuT 51179 : g{GT}GTTCGGAGTGTGGCGACCTGCTTCGTCGTTCCCATGGCAACAGGGATGAGCTTGA : 51236 150 : hrLeuCysPheLeuThrLeuArgHisArgArgProLysAlaArgTyrIleLeuTrpProA : 169 ||||||||||||||||||||||||||||||||||||||||||||||||||:!!||||||| hrLeuCysPheLeuThrLeuArgHisArgArgProLysAlaArgTyrIleIleTrpProA 51237 : CTCTGTGCTTCCTGACCCTTCGTCATCGGAGACCCAAGGCTCGCTATATCATTTGGCCTC : 51296 170 : rgIleAspGlnLysSerCysPheLysSerMetValThrAla{G} >>>> Target In : 183 ||||||||||||||||||||||||||||||||:!!||||||{|} 282 rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G}++ 51297 : GCATCGATCAGAAGTCCTGTTTCAAATCCATGATCACAGCA{G}gt.............. : 51341 184 : tron 4 >>>> {ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL : 198 bp {||}|||||||||||||||:!:||||||!.!|||||||||||||||| ++{ly}PheGluProValValValGluAsnAlaLeuGluGlyAspGluL 51342 : ...........ag{GG}TTTGAACCGGTGGTGGTGGAGAACGCTCTTGAAGGAGATGAGC : 51665 199 : euArgThrAsnLeuGluGluValGluArgLysIleGluGluPheGlyAlaGluAsnIleL : 218 |||||||||||||||||! !|||||||||||||||||||||.!!|||||||||||||||| euArgThrAsnLeuGluAlaValGluArgLysIleGluGluLeuGlyAlaGluAsnIleL 51666 : TGCGGACAAACTTGGAAGCAGTCGAACGTAAGATAGAGGAGCTTGGAGCCGAGAACATCC : 51725 219 : euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar} >>>> Ta : 234 |||||||||||||||||||||||||||||||||||||||||||||||{||} euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar}++ 51726 : TGTGTGTTCATTCGACAACATCCTGCTTCGCCCCACGAGTCCCTGAC{AG}gt....... : 51777 235 : rget Intron 5 >>>> {g}LeuGluGluLeuSerValLeuCysAlaLysHisAspI : 247 124 bp {|}||||||||||||:!!!.!:!!|||||||||:!!:!!| ++{g}LeuGluGluLeuAlaAlaMetCysAlaLysTyrAsnI 51778 : ..................ag{G}CTTGAAGAGCTGGCTGCTATGTGTGCCAAATATAATA : 51936 248 : leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG : 267 ||||||||||||||||||||||||||||||||||||||!!!||||||||||||||||||| leProHisIleValAsnAsnAlaTyrGlyValGlnSerThrLysCysMetHisLeuIleG 51937 : TTCCCCACATAGTTAACAATGCATACGGAGTGCAGTCGACCAAATGCATGCACCTTATAC : 51996 268 : lnGln >>>> Target Intron 6 >>>> GlyAlaArgValGlyArgIleAspAl : 277 ||||| 243 bp |||||||||||||||||||||||||| lnGln++ ++GlyAlaArgValGlyArgIleAspAl 51997 : AACAGgt.........................agGGGGCCCGTGTGGGGAGAATTGATGC : 52269 278 : aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl : 297 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl 52270 : CTTTGTACAAAGCTTGGACAAGAACTTTATGGTCCCAGTAGGTGGCGCCATTATCGCAGG : 52329 298 : yPheAspGluAsnPheIleGlnGluIleSerLysIleTyrPro{G} >>>> Target : 312 ||||||||||::!||||||||||||||||||:!!!!:||||||{|} 111 yPheAspGluSerPheIleGlnGluIleSerGlnMetTyrPro{G}++ 52330 : CTTTGATGAGTCCTTCATACAGGAGATAAGCCAGATGTACCCA{G}gt............ : 52377 313 : Intron 7 >>>> {ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe : 326 7 bp {||}||||||||||||||||||||||||||||||||||||||||| ++{ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe 52378 : .............ag{GT}CGAGCATCGGCCTCACCCTCCCTCGACGTCCTCATTACGCT : 53533 327 : uLeuThrLeuGlyAlaAsnGlyTyrLysLysLeuLeuAlaAspArgLys >>>> Targ : 343 |||||||||||||||||||||||||||||||||||||:!!!!:|||||| uLeuThrLeuGlyAlaAsnGlyTyrLysLysLeuLeuSerGluArgLys++ 53534 : TCTCACTCTGGGAGCCAACGGCTACAAGAAACTCTTGTCAGAACGAAAGgt......... : 53586 344 : et Intron 8 >>>> GluLeuTyrGlyHisLeuAlaGlnGluLeuSerAlaLeuAla : 356 1951 bp |||:!!|||..! !|||||||||||||||!.!.!!|||||| ++GluIleTyrSerPheLeuAlaGlnGluLeuLysThrLeuAla 53587 : ................agGAGATTTATTCGTTCCTGGCTCAGGAGCTGAAGACTCTGGCC : 55574 357 : AlaArgHisGlyGluArgLeuLeuLysThrProHisAsnProIleSerLeu{A} >>>> : 374 :!! !|||||||||||||||||| ! ||||||||||||||||||||||||{|} SerAlaHisGlyGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A}++ 55575 : TCTGCACATGGGGAGAGATTGCTTCACACCCCACATAACCCCATTTCACTT{G}gt.... : 55631 375 : Target Intron 9 >>>> {la}MetSerLeuAsnHisLeuGluAlaHisSerSer : 385 158 bp {||}|||||||||:!! !|||:!!|||!!.|||..! ++{la}MetSerLeuAspGlyLeuGlnAlaGlnSerGlu 55632 : .....................ag{CC}ATGTCTCTGGATGGTCTCCAGGCCCAGAGTGAG : 55819 386 : SerAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar} : 404 !.!|||||||||||||||||||||||||||||||||||||||||||||||||||{||} LysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++ 55820 : AAGGCAGTGACACAGCTGGGCTCAATGCTGTTCACCCGGCAAGTGTCAGGAGCC{AG}gt : 55878 405 : >>>> Target Intron 10 >>>> {g}ValValProLeuGlyValGlnGlnThrVa : 414 2091 bp {|}||||||||||||||| !:!!|||..!:! ++{g}ValValProLeuGlyLysGluGlnValIl 55879 : ..........................ag{G}GTAGTGCCTCTGGGCAAGGAGCAGGTCAT : 57997 415 : lSerGlyHisThrPheSerGlyPheMetSerHisSerGluAlaTyrProCysProTyrLe : 434 !||||||:!!|||||| !||||||||||||||||||||||||||||||||||||||||| eSerGlyTyrThrPheHisGlyPheMetSerHisSerGluAlaTyrProCysProTyrLe 57998 : CAGCGGGTACACGTTCCACGGCTTCATGTCGCACTCTGAGGCGTACCCCTGCCCCTACCT : 58057 435 : uAsnAlaAlaSerAlaIleGlyIleThrLysGlyAspValThrValCysMetLysArgLe : 454 ||||.!!|||||||||:!:|||||||||::!! !|||||||||:!!|||||||||||||| uAsnThrAlaSerAlaValGlyIleThrArgGluAspValThrLeuCysMetLysArgLe 58058 : CAACACCGCCTCAGCTGTGGGCATCACTCGGGAAGACGTCACTCTGTGCATGAAACGGCT : 58117 455 : uGluLysCysLeuLysIleLeuLysLysGluLysSer : 466 |!!:||||||||||||! !||||||||||||:!!||| uAspLysCysLeuLysThrLeuLysLysGluGlnSer 58118 : CGACAAATGCTTGAAGACTCTGAAGAAAGAGCAAAGT : 58155 vulgar: SecS 0 466 . KV885014.1:subseq(270895,100000) 49999 58155 + 2027 M 38 114 5 0 2 I 0 68 3 0 2 M 51 153 S 0 2 5 0 2 I 0 418 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 294 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 278 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 120 3 0 2 S 1 1 M 34 102 5 0 2 I 0 239 3 0 2 M 43 129 S 0 1 5 0 2 I 0 1113 3 0 2 S 1 2 M 30 90 5 0 2 I 0 1947 3 0 2 M 31 93 S 0 1 5 0 2 I 0 154 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 2087 3 0 2 S 1 1 M 62 186 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-23 ##type DNA # # # seqname source feature start end score strand frame attributes # KV885014.1:subseq(270895,100000) exonerate:protein2genome:local gene 50000 58155 2027 + . gene_id 1 ; sequence SecS ; gene_orientation + KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 50000 50113 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 50000 50113 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 50114 50115 . + . intron_id 1 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 50114 50185 . + . intron_id 1 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 50184 50185 . + . intron_id 0 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 50186 50340 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 50186 50340 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 50341 50342 . + . intron_id 2 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 50341 50762 . + . intron_id 2 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 50761 50762 . + . intron_id 1 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 50763 50881 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 50763 50881 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 50882 50883 . + . intron_id 3 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 50882 51179 . + . intron_id 3 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 51178 51179 . + . intron_id 2 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 51180 51338 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 51180 51338 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 51339 51340 . + . intron_id 4 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 51339 51620 . + . intron_id 4 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 51619 51620 . + . intron_id 3 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 51621 51774 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 51621 51774 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 51775 51776 . + . intron_id 5 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 51775 51898 . + . intron_id 5 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 51897 51898 . + . intron_id 4 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 51899 52001 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 51899 52001 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 52002 52003 . + . intron_id 6 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 52002 52244 . + . intron_id 6 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 52243 52244 . + . intron_id 5 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 52245 52374 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 52245 52374 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 52375 52376 . + . intron_id 7 ; splice_site "gt" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 52375 53491 . + . intron_id 7 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 53490 53491 . + . intron_id 6 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 53492 53583 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 53492 53583 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 53584 53585 . + . intron_id 8 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 53584 55534 . + . intron_id 8 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 55533 55534 . + . intron_id 7 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 55535 55628 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 55535 55628 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 55629 55630 . + . intron_id 9 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 55629 55786 . + . intron_id 9 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 55785 55786 . + . intron_id 8 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 55787 55877 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 55787 55877 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice5 55878 55879 . + . intron_id 10 ; splice_site "GT" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local intron 55878 57968 . + . intron_id 10 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local splice3 57967 57968 . + . intron_id 9 ; splice_site "AG" KV885014.1:subseq(270895,100000) exonerate:protein2genome:local cds 57969 58155 . + . KV885014.1:subseq(270895,100000) exonerate:protein2genome:local exon 57969 58155 . + . insertions 0 ; deletions 0 KV885014.1:subseq(270895,100000) exonerate:protein2genome:local similarity 50000 58155 2027 + . alignment_id 1 ; Query SecS ; Align 50000 1 114 ; Align 50186 39 153 ; Align 50764 91 117 ; Align 51182 131 156 ; Align 51623 184 150 ; Align 51900 235 102 ; Align 52245 269 129 ; Align 53494 313 90 ; Align 55535 343 93 ; Align 55789 375 87 ; Align 57970 405 186 # --- END OF GFF DUMP --- # -- completed exonerate analysis