Command line: [exonerate -m p2g --showtargetgff -q eEFsec558/eEFsec558_x.fa -t eEFsec558/SUBSEQ/CM004424.1_1_subseq.txt --exhaustive] Hostname: [ws101070u] C4 Alignment: ------------ Query: SPP00000662_2.0 Protein Eukaryotic elongation factor (eEFsec) Zebrafish Target: CM004424.1:subseq(14554118,25278) Ictalurus punctatus breed USDA103 chromosome 11, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 2395 Query range: 3 -> 576 Target range: 25278 -> 18473 4 : PheProLysThrLeuAsnPheAsnValGlyValLeuGlyHisValAspSerGlyLysThr : 23 .!!|||!:!! !||||||||||||:!!||||||||||||||||||||||||||||||||| LeuProArgIleLeuAsnPheAsnLeuGlyValLeuGlyHisValAspSerGlyLysThr 25278 : CTCCCCAGAATTCTGAACTTTAACCTGGGCGTGCTGGGACATGTGGACAGCGGAAAGACG : 25221 24 : SerLeuAlaArgAlaLeuSerSerThrAlaSerThrAlaAlaPheAspLysAsnProGln : 43 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SerLeuAlaArgAlaLeuSerSerThrAlaSerThrAlaAlaPheAspLysAsnProGln 25220 : TCTCTGGCTCGAGCCCTGAGCAGCACCGCGTCCACGGCGGCCTTCGACAAGAACCCACAG : 25161 44 : SerLysGluArgGlyIleThrLeuAspLeuGlyPheSerAlaPheThrValProLeuPro : 63 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SerLysGluArgGlyIleThrLeuAspLeuGlyPheSerAlaPheThrValProLeuPro 25160 : TCCAAAGAGCGCGGCATTACATTGGACCTGGGATTCAGCGCCTTCACTGTTCCCCTGCCT : 25101 64 : GluHisLeuArgGluSerCysGlyGluLysGlnTyrAspSerLeuGlnPheThrLeuVal : 83 ||||||:!!|||:!!|||||||||||| ||||||||||||||||||||||||||| GluHisMetArgGlnSerCysGlyGlu------TyrAspSerLeuGlnPheThrLeuVal 25100 : GAGCACATGAGGCAGAGCTGTGGGGAA------TACGACAGTCTGCAGTTCACGCTGGTG : 25047 84 : AspCysProGlyHisAlaSerLeuIleArgThrIleIleGly{G} >>>> Target I : 98 ||||||||||||||||||||||||||||||||||||||||||{|} 703 AspCysProGlyHisAlaSerLeuIleArgThrIleIleGly{G}++ 25046 : GACTGTCCAGGACATGCCTCCCTCATTCGCACCATCATTGGC{G}gt............. : 24999 99 : ntron 1 >>>> {ly}AlaGlnIleIleAspLeuMetMetLeuValValAspValVal : 112 bp {||}|||||||||||||||||||||:!!|||||||||||||||||| ++{ly}AlaGlnIleIleAspLeuMetLeuLeuValValAspValVal 24998 : ............ag{gG}GCTCAGATCATTGACCTGATGTTGTTAGTGGTCGACGTTGTG : 24257 113 : LysGlyMetGlnThrGlnThrAlaGluCysLeuLeuIleGlyGlnLeuThrCysSerArg : 132 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||!.! LysGlyMetGlnThrGlnThrAlaGluCysLeuLeuIleGlyGlnLeuThrCysSerHis 24256 : AAAGGTATGCAGACGCAAACAGCAGAGTGcctcctgattggtcagctcACCTGTTCACAC : 24197 133 : MetValValIleLeuAsnLysThrAspLeuLeuProSerAspLysArgGlnValAlaIle : 152 |||:!!||||||||||||||||||||||||||||||||||||||||||||| !|||||| MetIleValIleLeuAsnLysThrAspLeuLeuProSerAspLysArgGlnSerAlaIle 24196 : ATGATCGTCATCCTCAATAAAACGGACCTGTTGCCCAGTGACAAGAGACAGAGTGCCATT : 24137 153 : AspLysMetThrLysArgMetHisLysThrLeuGluAsnThr{Ar} >>>> Target : 167 !!:|||||||||||||||||||||||||||||||||||||||{||} 20 GluLysMetThrLysArgMetHisLysThrLeuGluAsnThr{Ar}++ 24136 : GAGAAGATGACCAAGAGGATGCACAAAACCTTGGAAAACACT{AG}gt............ : 24088 168 : Intron 2 >>>> {g}PheLysAspCysProIleIleAlaValAlaAlaLysProGly : 181 3 bp {|}||||||! !||||||:!!|||||||||||||||||||||||| ++{g}PheLysGlyCysProValIleAlaValAlaAlaLysProGly 24087 : .............ag{A}TTTAAAGGTTGCCCGGTCATTGCCGTGGCAGCAAAGCCAGGG : 23847 182 : GlyProGluAlaProAspThrAspGluProGlnGlyIleThrGluLeuIleAsp >>>> : 200 |||||||||||||||||||||! !||| !!|||||||||||||||||||||!!: GlyProGluAlaProAspThrAlaGluAlaGlnGlyIleThrGluLeuIleGlu++ 23846 : GGACCTGAGGCTCCAGACACAGCTGAAGCACAGGGAATCACTGAGCTCATAGAGgt.... : 23788 201 : Target Intron 3 >>>> LeuLeuLysAlaGlnSerPheLeuProHisArgAspP : 212 804 bp |||||||||:!!|||:!!|||||||||!!.||||||| ++LeuLeuLysSerGlnAlaPheLeuProGlnArgAspP 23787 : .....................agCTGCTAAAATCCCAGGCGTTCCTACCTCAGAGAGACC : 22950 213 : roSerGlySerLeuLeuMetAlaValAspHisCysPheSerIleArgGlyGlnGlyThrV : 232 |||||||||||||||||:!!|||||||||||||||||||||||||||||||||||||||| roSerGlySerLeuLeuLeuAlaValAspHisCysPheSerIleArgGlyGlnGlyThrV 22949 : CATCTGGTTCTCTGCTACTGGCAGTGGATCACTGTTTCTCCATCCGTGGCCAGGGAACAG : 22890 233 : alIleThrGlyThrIleLeuGlnGlySerLeuSerValAsnAspAsnValGluIleProA : 252 ||||||||||||||||||||||||||:!!||| !!|||||||||!..:!!|||||||||| alIleThrGlyThrIleLeuGlnGlyAlaLeuArgValAsnAspThrLeuGluIleProA 22889 : TCATTACAGGCACTATCCTGCAGGGGGCACTGCGTGTCAATGACACACTAGAGATACCTG : 22830 253 : laLeuLys >>>> Target Intron 4 >>>> ValThrArgLysValLysSerVa : 262 |||||||| 865 bp |||||||||||||||||||||:! laLeuLys++ ++ValThrArgLysValLysSerIl 22829 : CACTCAaggt.........................agGTGACTCGTAAGGTGAAGTCGAT : 21935 263 : lGlnMetPheArgLysProValAlaSerAlaMetGlnGlyAspArgValGlyValCysVa : 282 !||||||||||||||||||||| !!||||||!!:|||||||||||||||||||||||||| eGlnMetPheArgLysProValProSerAlaIleGlnGlyAspArgValGlyValCysVa 21934 : CCAGATGTTCCGTAAGCCAGTTCCTAGTGCGATACAAGGAGATCGGGTCGGCGTGTGTGT : 21875 283 : lThrGlnPheAspProLysLeuLeuGluArgGlyValValCysThrProGlySerLeuGl : 302 |||||||||||||||||||:!!||||||||||||||||||||||||||||||||||||!! lThrGlnPheAspProLysMetLeuGluArgGlyValValCysThrProGlySerLeuHi 21874 : CACACAGTTTGACCCAAAGATGTTGGAGAGAGGGGTGGTGTGTACACCTGGTTCACTGCA : 21815 303 : nThrLeuTyrAlaAlaIleIleSerValGlnLysIleGluTyrTyrArgGlyAlaLeuAs : 322 .|||:!!:!!|||||||||||||||||| !|||||||||||||||||||||||||||!: sThrIleHisAlaAlaIleIleSerValTrpLysIleGluTyrTyrArgGlyAlaLeuSe 21814 : TACCATTCATGCCGCCATTATTTCTGTATGGAAGATCGAGTACTACCGTGGTGCACTTAG : 21755 323 : nSerArgAlaLysPheHisIleThrValGlyHisGluThrValMetAlaArgIleSerPh : 342 !|||||||||||||||||||||||||||||||||||||||||||||||||||:!:! !|| rSerArgAlaLysPheHisIleThrValGlyHisGluThrValMetAlaArgValLeuPh 21754 : CAGCCGAGCAAAATTCCACATCACCGTTGGACATGAAACAGTCATGGCACGCGTGTTATT : 21695 343 : ePheAsnArgValLeuProAlaAsnGluAsnGlyAspSerLysProThrSerGlnGluGl : 362 ||||!:!|||!.!! !! !::! !!!::::|||! :!!...|||||| ||||| ePheSerArgAlaSerLeuSerAlaAspSerGlyAlaAlaSerProThr------GluGl 21694 : CTTCAGCCGGGCTTCTCTAAGTGCTGACTCAGGAGCAGCGTCTCCTACA------GAACA : 21641 363 : nSerAlaAsnSerPheSerPheAspTrpGluPheHisHisLeuAspGluHisLeuThrSe : 382 |||||||.!.:!!||||||||||||||||||||| !|||! !!!:|||:!!||||||.! nSerAlaGluAlaPheSerPheAspTrpGluPheCysHisGlnGluGluTyrLeuThrGl 21640 : GAGCGCAGAGGCTTTCTCATTTGACTGGGAGTTTTGCCACCAGGAGGAGTATTTGACTGG : 21581 383 : rGlnAlaGluGlyGlyLysGlyGluProGlnGlnTrpAlaLeuLeuGluPheGluArgPr : 402 !|||!.!||| !! ! ! !! ! ||| !||||||||||||||||||||||||||||| yGlnGlyGluProGluGlyArgTyrProAlaGlnTrpAlaLeuLeuGluPheGluArgPr 21580 : CCAGGGAGAACCCGAAGGGAGGTATCCAGCGCAGTGGGCATTATTAGAGTTTGAACGGCC : 21521 403 : oValThrCysProProLeuCysLeuValIleGlySerArgLeuAspSerAspIleHisGl : 422 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.! oValThrCysProProLeuCysLeuValIleGlySerArgLeuAspSerAspIleHisSe 21520 : TGTCACATGTCCACCACTCTGTTTGGTGATTGGCTCACGGTTGGACTCTGATATCCACAG : 21461 423 : yAsnThrCysArgLeuAlaPheHisGlyLysLeuLeuGluGlyPheGluAspLysAsnTy : 442 !||||||||||||||||||||||||||||||||||||!!:|||||||||||||||||||| rAsnThrCysArgLeuAlaPheHisGlyLysLeuLeuAspGlyPheGluAspLysAsnTy 21460 : CAACACATGCAGACTTGCTTTCCACGGAAAGCTGTTGGACGGCTTCGAGGACAAAAATTA : 21401 443 : rThrGluThrAlaLeuProArgLeuLysIleSerLysAspLysGlnLysGluGlyAlaVa : 462 |..!!!:!:!|||||||||||||||||||||||||||||||||!!.|||||||||||||| rValAspSerAlaLeuProArgLeuLysIleSerLysAspLysHisLysGluGlyAlaVa 21400 : TGTGGACAGCGCGTTGCCCAGGCTCAAAATCAGTAAAGACAAGCACAAAGAAGGAGCAGT : 21341 463 : lGluArg >>>> Target Intron 5 >>>> ValThrAspAspTyrThrValIle : 472 ||||||| 1172 bp |||||||||||||||||||||||| lGluArg++ ++ValThrAspAspTyrThrValIle 21340 : GGAACGGgt.........................agGTGACAGACGACTACACTGTGATT : 20139 473 : GlyArgAsnLeuPheLysLysGluThrAsnLeuGlnLeuPheValGlyLeuLysValThr : 492 |||!:!|||||||||||||||||||||||||||||||||||||||||||||||||||||| GlyLysAsnLeuPheLysLysGluThrAsnLeuGlnLeuPheValGlyLeuLysValThr 20138 : GGTAAAAACCTGTTCAAGAAAGAGACCAACCTTCAGCTGTTTGTGGGGTTAAAGGTCACA : 20079 493 : LeuSerThrGlyGluAlaGlySerIleGluGlyGlyPheGlyGlnSerGlyLysIleLys : 512 ||||||:!!||||||.!!||| !|||||||||.!!|||||||||||||||||||||||| LeuSerSerGlyGluThrGlyValIleGluGlySerPheGlyGlnSerGlyLysIleLys 20078 : CTTTCTTCAGGAGAGACAGGGGTCATTGAAGGCAGCTTTGGACAGAGTGGCAAAATCAAA : 20019 513 : IleArgIlePro{G} >>>> Target Intron 6 >>>> {lu}GlyLeuLysGlu : 521 ||||||||||||{|} 1351 bp {||}|||||||||||| IleArgIlePro{G}++ ++{lu}GlyLeuLysGlu 20018 : ATTAGAATTCCA{G}gt.........................ag{AG}GGACTGAAAGAA : 18641 522 : GluThrLysGlnLeuLeuSerSerSerSerLysLysLysGlyLysGlyGlySerLysAsn : 541 |||||||||||| ...|||||||||||||||||||||||||||||||||:!!|||||| GluThrLysGlnHisPheSerSerSerSerLysLysLysGlyLysGlyGlyAlaLysAsn 18640 : GAAACAAAGCAAcacttctcttcctcctccaagAAAAAGGGAAAGGGCGGGGCTAAAAAT : 18581 542 : GluSerProLysLeuGluGluAlaLysProAspAlaGlnProValThrIleHisLeuAsn : 561 ||| !!|||||| !|||!!:.!!||| !|||:!!||||||:!!||||||||||||||| GluProProLysGluGluAspThrLysValAspSerGlnProIleThrIleHisLeuAsn 18580 : GAACCGCCTAAAGAGGAGGACACCAAAGTGGACTCACAGCCCATAACCATTCATCTGAAT : 18521 562 : PheLysArgTyrIleTyrAspProHisLysLysMetValGlnSer : 576 ||||||||||||:::|||||||||||||||||||||||||||||| PheLysArgTyrValTyrAspProHisLysLysMetValGlnSer 18520 : TttaaaagatatgtttatgaCCCCCATAAAAAGATGGTGCAGTCG : 18474 vulgar: SPP00000662_2.0 3 576 . CM004424.1:subseq(14554118,25278) 25278 18473 - 2395 M 69 207 G 2 0 M 23 69 S 0 1 5 0 2 I 0 699 3 0 2 S 1 2 M 68 204 S 0 2 5 0 2 I 0 199 3 0 2 S 1 1 M 32 96 5 0 2 I 0 800 3 0 2 M 55 165 5 0 2 I 0 861 3 0 2 M 104 312 G 2 0 M 104 312 5 0 2 I 0 1168 3 0 2 M 52 156 S 0 1 5 0 2 I 0 1347 3 0 2 S 1 2 M 59 177 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-14 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local gene 18474 25278 2395 - . gene_id 1 ; sequence SPP00000662_2.0 ; gene_orientation + CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 25002 25278 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 25002 25278 . - . insertions 0 ; deletions 2 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice5 25000 25001 . - . intron_id 1 ; splice_site "GT" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local intron 24299 25001 . - . intron_id 1 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice3 24299 24300 . - . intron_id 0 ; splice_site "ag" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 24091 24298 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 24091 24298 . - . insertions 0 ; deletions 0 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice5 24089 24090 . - . intron_id 2 ; splice_site "GT" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local intron 23888 24090 . - . intron_id 2 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice3 23888 23889 . - . intron_id 1 ; splice_site "AG" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 23791 23887 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 23791 23887 . - . insertions 0 ; deletions 0 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice5 23789 23790 . - . intron_id 3 ; splice_site "GT" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local intron 22987 23790 . - . intron_id 3 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice3 22987 22988 . - . intron_id 2 ; splice_site "ag" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 22822 22986 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 22822 22986 . - . insertions 0 ; deletions 0 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice5 22820 22821 . - . intron_id 4 ; splice_site "gt" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local intron 21957 22821 . - . intron_id 4 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice3 21957 21958 . - . intron_id 3 ; splice_site "AG" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 21333 21956 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 21333 21956 . - . insertions 0 ; deletions 2 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice5 21331 21332 . - . intron_id 5 ; splice_site "GT" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local intron 20161 21332 . - . intron_id 5 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice3 20161 20162 . - . intron_id 4 ; splice_site "AG" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 20004 20160 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 20004 20160 . - . insertions 0 ; deletions 0 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice5 20002 20003 . - . intron_id 6 ; splice_site "Gt" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local intron 18653 20003 . - . intron_id 6 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local splice3 18653 18654 . - . intron_id 5 ; splice_site "AG" CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local cds 18474 18652 . - . CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local exon 18474 18652 . - . insertions 0 ; deletions 0 CM004424.1:subseq(14554118,25278) exonerate:protein2genome:local similarity 18474 25278 2395 - . alignment_id 1 ; Query SPP00000662_2.0 ; Align 25279 4 207 ; Align 25072 75 69 ; Align 24297 99 204 ; Align 23887 168 96 ; Align 22987 200 165 ; Align 21957 255 312 ; Align 21645 361 312 ; Align 20161 465 156 ; Align 18651 518 177 # --- END OF GFF DUMP --- # -- completed exonerate analysis