Command line: [exonerate -m p2g --showtargetgff -q ../SecS-human.fa -t SecS-NIVO01007502.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000254_2.0 # Protein # Selenocysteine synthase (SecS) # Cow Target: NIVO01007502.1:subseq(1628487,134741) Ammotragus lervia isolate NAZ scaffold1331_len2273840_cov70, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 2464 Query range: 0 -> 503 Target range: 84741 -> 49999 1 : MetAsnArgGluPhePheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgGln : 20 ||||||||||||.!!||||||||||||||||||||||||||||||||||||||||||||| MetAsnArgGluLeuPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgGln 84741 : ATGAACCGCGAGCTCTTCGCGGCGGGCGAGCGGCTGGTGTCGCCGGCTTACGTGCGGCAG : 84684 21 : GlyCysGluAlaArgArgSerHisGluHisLeuMetArgLeuLeuLeuGluLys >>>> : 39 |||||||||||||||||||||||||||||||||||||||||||||||||||||| GlyCysGluAlaArgArgSerHisGluHisLeuMetArgLeuLeuLeuGluLys++ 84683 : GGCTGTGAGGCCCGCCGCTCGCACGAGCACCTCATGCGGCTACTTCTGGAGAAGgt.... : 84625 40 : Target Intron 1 >>>> GlyLysCysProGluAspGlyTrpAspGluSerThrL : 51 1370 bp ||||||||||||||||||||||||||||||||||||| ++GlyLysCysProGluAspGlyTrpAspGluSerThrL 84624 : .....................agGGCAAGTGTCCAGAGGATGGTTGGGATGAAAGTACGC : 83221 52 : euGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGlyAsnCysG : 71 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| euGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGlyAsnCysG 83220 : TTGAACTCTTTTTACATGAACTTGCAATTATGGACAGCAACAATTTCCTGGGCAATTGTG : 83161 72 : lyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArgHisTyr{Ar} : 90 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||{||} lyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArgHisTyr{Ar} 83160 : GtgtgggagaaagggaaggaagagtgGCATCTGCATTAGTTGCTCGGCGACATTAC{AG} : 83104 91 : >>>> Target Intron 2 >>>> {g}PheIleHisGlyIleGlyArgSerGlyA : 100 1732 bp {|}|||||||||||||||||||||||||||| ++ ++{g}PheIleHisGlyIleGlyArgSerGlyA 83103 : gt.........................ag{G}TTCATTCATGGAATTGGACGATCAGGTG : 81342 101 : spIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS : 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| spIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS 81341 : ATATTTCGGCTGTGCAACCCAAAGCTGCAGGTTCTAGCCTTTTGAACAAAATTACCAATT : 81282 121 : erLeuValLeuAspIleIleLysLeuAla{G} >>>> Target Intron 3 >>>> : 130 |||||||||||||||||||||||||||||{|} 312 bp erLeuValLeuAspIleIleLysLeuAla{G}++ + 81281 : CTTTGGTCCTGGACATCATAAAATTGGCT{G}gt.........................a : 80941 131 : {ly}ValHisThrValThrSerCysPheValValProMetAlaThrGlyMetSerLeuT : 149 {||}||||||||||||||||||||||||||||||||||||||||||||||||||||||| +{ly}ValHisThrValThrSerCysPheValValProMetAlaThrGlyMetSerLeuT 80940 : g{GT}GTCCATACAGTGACCAGCTGCTTTGTAGTTCCAATGGCAACTGGTATGAGTCTAA : 80883 150 : hrLeuCysPheLeuThrLeuArgHisArgArgProLysAlaLysTyrIleIleTrpProA : 169 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| hrLeuCysPheLeuThrLeuArgHisArgArgProLysAlaLysTyrIleIleTrpProA 80882 : CCCTGTGTTTCTTAACATTGCGACACAGAAGACCAAAGGCAAAGTATATTATATGGCCAC : 80823 170 : rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G} >>>> Target In : 183 |||||||||||||||||||||||||||||||||||||||||{|} 2471 rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G}++ 80822 : GAATAGACCAGAAGTCTTGCTTTAAATCCATGATCACTGCa{g}gt.............. : 80778 184 : tron 4 >>>> {ly}PheGluProValValIleGluAsnIleLeuGluGlyAspGluL : 198 bp {||}||||||||||||||||||||||||||||||||||||||||||| ++{ly}PheGluProValValIleGluAsnIleLeuGluGlyAspGluL 80777 : ...........ag{GT}TTTGAGCCTGTGGTGATAGAGAACATTTTAGAAGGTGATGAGC : 78265 199 : euArgThrAspLeuLysAlaValGluAlaLysValGlnGluLeuGlyProAspHisValL : 218 ||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||||| euArgThrAspLeuGluAlaValGluAlaLysValGlnGluLeuGlyProAspHisValL 78264 : TGCGCACAGACCTGGAAGCAGTGGAGGCTAAAGTCCAGGAACTTGGGCCTGATCACGTTC : 78205 219 : euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar} >>>> Ta : 234 |||||||||||||||||||||||||||||||||||||||||||||||{||} euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar}++ 78204 : TGTGTGTTCATTCTACCACGTCCTGTTTTGCTCCAAGAGTGCCTGAT{AG}gt....... : 78153 235 : rget Intron 5 >>>> {g}LeuGluGluLeuAlaValIleCysAlaAsnTyrGlyI : 247 4051 bp {|}||||||||||||||||||||||||||||||||||||| ++{g}LeuGluGluLeuAlaValIleCysAlaAsnTyrGlyI 78152 : ..................ag{G}TTAGAAGAACTGGCTGTGATTTGTGCTAATTATGGCA : 74067 248 : leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG : 267 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG 74066 : TTCCACATATAGTCAACAATGCTTATGGAGTGCAATCTTCAAAGTGCATGCACCTCATTC : 74007 268 : lnGln >>>> Target Intron 6 >>>> GlyAlaArgValGlyArgIleAspAl : 277 ||||| 8183 bp ||||||||||||||||||:!!||||| lnGln++ ++GlyAlaArgValGlyArgValAspAl 74006 : AGCAGgt.........................agGGAGCTCGTGTTGGTAGAGTAGATGC : 65794 278 : aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl : 297 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl 65793 : TTTCGTTCAGAGCTTGGACAAAAATTTTATGGTTCCAGTAGGTGGTGCTATAATTGCTGG : 65734 298 : yPheAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G} >>>> Target : 312 |||||||||||||||||||||||||||||||||||||||||||{|} 12 yPheAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G}++ 65733 : CTTTAATGATTCCTTCATTCAGGAAATCAGCAAGATGTATCCA{G}gt............ : 65686 313 : Intron 7 >>>> {ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe : 326 5 bp {||}||||||||||||||||||||||||||||||||||||||||| ++{ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe 65685 : .............ag{ga}agagcttcagcttcaccttcTTTAGATGTCCTTATTACTTT : 65522 327 : uLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys >>>> Targ : 343 ||||||||||||||||||||||||||||||||||||||||||||||||| uLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys++ 65521 : ATTATCACTTGGATCAAATGGCTACAAGAagctattaaaagaaagaaaggt......... : 65469 344 : et Intron 8 >>>> GluMetPheSerTyrLeuSerAsnGlnLeuLysLysLeuSer : 356 11927 bp |||||||||||||||||||||||||||||||||||||||||| ++GluMetPheSerTyrLeuSerAsnGlnLeuLysLysLeuSer 65468 : ................agGAAATGTTTTCCTATTTGTCCAACCAACTAAAGAAGCTGTCA : 53505 357 : GluAlaTyrAsnGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A} >>>> : 374 |||||||||!:!|||||||||||||||||||||||||||||||||||||||{|} GluAlaTyrSerGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A}++ 53504 : GAAGCCTACAGTGAAAGACTGTTGCATACACCTCACAATCCCATATcttta{g}gt.... : 53448 375 : Target Intron 9 >>>> {la}MetThrLeuArgThrLeuAspLysHisCysSer : 385 1736 bp {||}|||||||||!:!||||||||||||||||||||| ++{la}MetThrLeuLysThrLeuAspLysHisCysSer 53447 : .....................ag{CT}ATGACACTTAAAACCCTAGATAAACACTGTAGC : 51682 386 : ArgAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar} : 404 !:!|||||||||||||||||||||||||||||||||||||||||||||||||||{||} LysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++ 51681 : AAAGCTGTCACTCAGCTTGGCTCCATGCTTTTTACAAGACAGGTTTCTGGAGCC{AG}gt : 51623 405 : >>>> Target Intron 10 >>>> {g}ValValProLeuGlySerMetGlnThrVa : 414 1326 bp {|}||||||||||||||||||||||||||||| ++{g}ValValProLeuGlySerMetGlnThrVa 51622 : ..........................ag{G}GTTGTTCCTCTTGGGTCTATGCAGACTGT : 50269 415 : lSerGlyTyrThrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLe : 434 ||||||||||||||||||||||||||||||||||:!!||||||||||||||||||||||| lSerGlyTyrThrPheArgGlyPheMetSerHisSerAsnAsnTyrProCysAlaTyrLe 50268 : GAGTGGCTACACTTTCAGAGGCTTTATGTCACATTCAAATAATTACCCTTGTGCTTACCT : 50209 435 : uAsnAlaAlaSerAlaIleGlyMetLysThrGlnAspValAspLeuPheIleLysArgLe : 454 |||||||||||||||||||||||||||||||||||||||||||||||||:!!|||||||| uAsnAlaAlaSerAlaIleGlyMetLysThrGlnAspValAspLeuPheValLysArgLe 50208 : CAATGCTGCGTCAGCCATTGGAATGAAGACACAGGATGTGGACTTGTTCGTAAAGAGACT : 50149 455 : uAspLysCysLeuLysThrValArgLysGluGlnAsnLysGluSerAspIleSerGlyVa : 474 |||||||||||||||||||||||||||||||||||||||||||||||||:!!|||! !|| uAspLysCysLeuLysThrValArgLysGluGlnAsnLysGluSerAspValSerGluVa 50148 : TGACAAGTGTTTAAAGACAGtcagaaaggaacaaaataaagagAGTGATGTATCTGAAGT : 50089 475 : lAspAsnAsnAspLysThrGluAspValAspIleGluGluMetAlaLeuLysLeuAspAs : 494 ||||||||||||||||||||||||||||:!!|||||||||:!!|||||||||||||||!. lAspAsnAsnAspLysThrGluAspValAsnIleGluGluValAlaLeuLysLeuAspTh 50088 : TGACAATAATGACAAAACTGAAGATGTGAATATAGAAGAAGTGGCTTTAAAACTAGATAC : 50029 495 : nValCysLeuAspThrCysGlnAspSer : 503 !||| !!||||||||||||||||||||| rValArgLeuAspThrCysGlnAspSer 50028 : TGTACGTCTTGACACATGCCAGGATTCT : 50000 vulgar: SPP00000254_2.0 0 503 . NIVO01007502.1:subseq(1628487,134741) 84741 49999 - 2464 M 38 114 5 0 2 I 0 1366 3 0 2 M 51 153 S 0 2 5 0 2 I 0 1728 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 308 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 2467 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 4047 3 0 2 S 1 1 M 34 102 5 0 2 I 0 8179 3 0 2 M 43 129 S 0 1 5 0 2 I 0 121 3 0 2 S 1 2 M 30 90 5 0 2 I 0 11923 3 0 2 M 31 93 S 0 1 5 0 2 I 0 1732 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 1322 3 0 2 S 1 1 M 99 297 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-24 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local gene 50000 84741 2464 - . gene_id 1 ; sequence SPP00000254_2.0 ; gene_orientation + NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 84628 84741 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 84628 84741 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 84626 84627 . - . intron_id 1 ; splice_site "GT" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 83258 84627 . - . intron_id 1 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 83258 83259 . - . intron_id 0 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 83103 83257 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 83103 83257 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 83101 83102 . - . intron_id 2 ; splice_site "Gt" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 81371 83102 . - . intron_id 2 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 81371 81372 . - . intron_id 1 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 81252 81370 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 81252 81370 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 81250 81251 . - . intron_id 3 ; splice_site "GT" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 80940 81251 . - . intron_id 3 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 80940 80941 . - . intron_id 2 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 80781 80939 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 80781 80939 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 80779 80780 . - . intron_id 4 ; splice_site "gt" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 78310 80780 . - . intron_id 4 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 78310 78311 . - . intron_id 3 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 78156 78309 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 78156 78309 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 78154 78155 . - . intron_id 5 ; splice_site "GT" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 74105 78155 . - . intron_id 5 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 74105 74106 . - . intron_id 4 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 74002 74104 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 74002 74104 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 74000 74001 . - . intron_id 6 ; splice_site "GT" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 65819 74001 . - . intron_id 6 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 65819 65820 . - . intron_id 5 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 65689 65818 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 65689 65818 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 65687 65688 . - . intron_id 7 ; splice_site "GT" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 65564 65688 . - . intron_id 7 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 65564 65565 . - . intron_id 6 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 65472 65563 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 65472 65563 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 65470 65471 . - . intron_id 8 ; splice_site "gt" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 53545 65471 . - . intron_id 8 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 53545 53546 . - . intron_id 7 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 53451 53544 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 53451 53544 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 53449 53450 . - . intron_id 9 ; splice_site "gt" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 51715 53450 . - . intron_id 9 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 51715 51716 . - . intron_id 8 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 51624 51714 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 51624 51714 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice5 51622 51623 . - . intron_id 10 ; splice_site "GT" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local intron 50298 51623 . - . intron_id 10 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local splice3 50298 50299 . - . intron_id 9 ; splice_site "AG" NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local cds 50000 50297 . - . NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local exon 50000 50297 . - . insertions 0 ; deletions 0 NIVO01007502.1:subseq(1628487,134741) exonerate:protein2genome:local similarity 50000 84741 2464 - . alignment_id 1 ; Query SPP00000254_2.0 ; Align 84742 1 114 ; Align 83258 39 153 ; Align 81370 91 117 ; Align 80938 131 156 ; Align 78308 184 150 ; Align 74104 235 102 ; Align 65819 269 129 ; Align 65562 313 90 ; Align 53545 343 93 ; Align 51713 375 87 ; Align 50297 405 297 # --- END OF GFF DUMP --- # -- completed exonerate analysis