Command line: [exonerate -m p2g --showtargetgff -q msra2_zf.aa.fa.canviat -t genomemsra2_JXSJ01000913.1.fa] Hostname: [ws116078U] C4 Alignment: ------------ Query: SPP00000626_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Zebrafish Target: JXSJ01000913.1:subseq(19129,88681) Miichthys miiuy scaffold913, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 759 Query range: 0 -> 191 Target range: 67053 -> 49972 1 : MetValAlaArgThrSerValArgLeuIleTrpArgGlnPheIleGlnSerArgMetGly : 20 ||||||:!! !:!!!!!:!!||||||:!!||||||!!.|||!!:.!.|||||||||||| MetValSerSerSerArgLeuArgLeuValTrpArgHisPheMetAsnSerArgMetGly 67053 : atggtcTCCTCCTCCAGACTCCGTCTGGTCTGGCGTCATTTTATGAACAGTAGGATGGGA : 66996 21 : GluMetSerSerLysValGlnMetIleSerProGluGluAlaLeuProGlyArgGluGln : 40 !!:|||:!!|||! !!.!|||||| !!!|||||| !||||||||||||||| !.!. AspMetAlaSerThrAlaGlnMetProThrProGluThrAlaLeuProGlyArgProAsp 66995 : GACATGGCCTCTACAGCTCAGATGCCGACCCCAGAGACGGCGCTGCCCGGCCGGCCGGAC : 66936 41 : SerIleLysValSer{A} >>>> Target Intron 1 >>>> {la}LysHisAsp : 49 .!!||||||||||||{|} 12404 bp {||}||||||||| GlyIleLysValSer{A}++ ++{la}LysHisAsp 66935 : GGCATTAAAGTCTCC{G}gt.........................ag{CC}AAACATGAC : 54505 50 : ValAsnGlyAsnArgThrValProProPheProGluGlyLeuGlnMetValLeuPhe{G} : 69 ||||||||||||||||||||||||||||||||||||||| !:!!||||||:!!|||{|} ValAsnGlyAsnArgThrValProProPheProGluGlyThrGluMetValMetPhe{G} 54504 : GTGAACGGTAACAGGACGGTTCCACCTTTTCCAGAGGGGACAGAGATGGTCATGTTC{G} : 54445 70 : >>>> Target Intron 2 >>>> {ly}MetGlyCysPheTrpGlyAlaGluArg : 78 959 bp {||}||||||||||||||||||||||||||| ++ ++{ly}MetGlyCysPheTrpGlyAlaGluArg 54444 : gt.........................ag{GT}ATGGGCTGTTTCTGGGGAGCCGAGAGG : 53459 79 : LysPheTrpArgGlnLysGlyValTyrSerThrGlnValGlyTyrSerGlyGlyTyrThr : 98 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LysPheTrpArgGlnLysGlyValTyrSerThrGlnValGlyTyrSerGlyGlyTyrThr 53458 : AAGTTCTGGAGACAAAAAGGGGTTTATTCCACCCAAGTGGGCTACTCAGGAGGGTACACA : 53399 99 : ProAsnProThrTyrGluGluValCysThr{G} >>>> Target Intron 3 >>>> : 109 !!||||||!:!|||.!.||||||||||||{|} 2476 bp SerAsnProSerTyrAsnGluValCysThr{G}++ 53398 : TCCAACCCCAGCTACAATGAAGTCtgcaca{g}gt......................... : 53363 110 : {ly}LysThrGlyHisThrGluValValArgValValPheGluProGlnLysIleLys : 127 {||}::!|||||||||||||||||||||||||||||||||.!.|||:!!||||||!.. ++{ly}ArgThrGlyHisThrGluValValArgValValPheHisProGluLysIleSer 53362 : ag{GT}CGGACGGGACACACCGAGGTGGTGAGAGTTGTCTTCCATCCAGAGAAGATCAGC : 50836 128 : PheSerGluLeuLeuLysValPheTrpGluSerHisAsnProThrGln{G} >>>> Ta : 144 |||.!!:!!|||||||||||||||||||||||||||||||||||||||{|} PheGlyLysLeuLeuLysValPheTrpGluSerHisAsnProThrGln{G}++ 50835 : TTTGGCAAACTGCTCAAAGTTTTCTGGGAAAGCCACAATCCGACTCAA{G}gt....... : 50782 145 : rget Intron 4 >>>> {ly}MetArgGlnGlyAsnAspValGlyThrThrTyrArg : 156 669 bp {||}|||||||||||||||||||||||||||||||||||| ++{ly}MetArgGlnGlyAsnAspValGlyThrThrTyrArg 50781 : ..................ag{gG}ATGCGACAGGGGAACGATGTCGGGACGACGTACCGC : 50080 157 : SerSerIleTyrThrAsnThrGlnGluGlnLeuGluGlnAlaLeuGlnSerArgGluGlu : 176 |||:!!:!!|||||| !!|||:!!:!!!!.|||!!::!!|||||| |||!:!!!:||| SerAlaValTyrThrTyrThrLysGlnHisLeuAspGluAlaLeuAlaSerLysAspGlu 50079 : TCTGCCGTCTACACCTACACGAAGCAGCACCTCGACGAGGCTTTGGCCTCCAAAGATGAA : 50020 177 : TyrGlnLysValLeuThrGluGluGlyPheGlyAlaIleThrThr : 191 ||||||||||||! !||| !!:..!.!!..! ! !.!!||| TyrGlnLysValArgThrPheAspSerIleSerGlnTyrAlaThr 50019 : TACCAGAAGGTACGAACCTTTGACTCCATTTCCCAGTATGCAACT : 49973 vulgar: SPP00000626_2.0 0 191 . JXSJ01000913.1:subseq(19129,88681) 67053 49972 - 759 M 45 135 S 0 1 5 0 2 I 0 12400 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 955 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 2472 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 665 3 0 2 S 1 2 M 47 141 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-18 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local gene 49973 67053 759 - . gene_id 1 ; sequence SPP00000626_2.0 ; gene_orientation + JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local cds 66918 67053 . - . JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local exon 66918 67053 . - . insertions 0 ; deletions 0 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice5 66916 66917 . - . intron_id 1 ; splice_site "GT" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local intron 54514 66917 . - . intron_id 1 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice3 54514 54515 . - . intron_id 0 ; splice_site "AG" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local cds 54445 54513 . - . JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local exon 54445 54513 . - . insertions 0 ; deletions 0 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice5 54443 54444 . - . intron_id 2 ; splice_site "GT" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local intron 53486 54444 . - . intron_id 2 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice3 53486 53487 . - . intron_id 1 ; splice_site "AG" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local cds 53366 53485 . - . JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local exon 53366 53485 . - . insertions 0 ; deletions 0 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice5 53364 53365 . - . intron_id 3 ; splice_site "gt" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local intron 50890 53365 . - . intron_id 3 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice3 50890 50891 . - . intron_id 2 ; splice_site "aG" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local cds 50785 50889 . - . JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local exon 50785 50889 . - . insertions 0 ; deletions 0 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice5 50783 50784 . - . intron_id 4 ; splice_site "GT" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local intron 50116 50784 . - . intron_id 4 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local splice3 50116 50117 . - . intron_id 3 ; splice_site "ag" JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local cds 49973 50115 . - . JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local exon 49973 50115 . - . insertions 0 ; deletions 0 JXSJ01000913.1:subseq(19129,88681) exonerate:protein2genome:local similarity 49973 67053 759 - . alignment_id 1 ; Query SPP00000626_2.0 ; Align 67054 1 135 ; Align 54512 47 66 ; Align 53484 70 117 ; Align 50888 110 102 ; Align 50114 145 141 # --- END OF GFF DUMP --- # -- completed exonerate analysis