Command line: [exonerate -m p2g --showtargetgff -q msra522/msra522_x.fa -t msra522/SUBSEQ/CM004422.1_1_subseq.txt --exhaustive] Hostname: [ws112615u] C4 Alignment: ------------ Query: SPP00000626_2.0 Protein Methionine sulfoxide reductase A (MsrA) Zebrafish Target: CM004422.1:subseq(24078979,25146) Ictalurus punctatus breed USDA103 chromosome 9, whole genome shotgun sequence Model: protein2genome:local Raw score: 625 Query range: 54 -> 227 Target range: 2 -> 25146 55 : ThrValProProPheProGluGlyLeuGlnMetValLeuPhe{G} >>>> Target I : 69 |||||| !|||||||||!!:||| !:!!|||:!!:!!|||{|} 383 ThrValGluProPheProAspGlyThrGluMetIleMetPhe{G}++ 3 : ACAGTCGAGCCATTTCCTGACGGGACAGAGATGATCATGTTT{G}gt............. : 48 70 : ntron 1 >>>> {ly}MetGlyCysPheTrpGlyAlaGluArgLysPheTrpArgGln : 83 bp {||}|||||||||||||||||||||||||||:::||||||! !! ++{ly}MetGlyCysPheTrpGlyAlaGluArgArgPheTrpThrLeu 49 : ............ag{GT}ATGGGCTGTTTTTGGGGTGCAGAGAGACGCTTCTGGACTCTT : 470 84 : LysGlyValTyrSerThrGlnValGlyTyrSerGlyGlyTyrThrProAsnProThrTyr : 103 ||||||!:!||||||||||||||||||:!!||||||!:!|||||||||||||||||| ProGlyValPheSerThrGlnValGlyTyrAlaGlyGlyPheThrProAsnProThrTyr 471 : CCTGGTGTGTTCTCTACTCAAGTGGGATATGCAGGTGGATTCACCCCCAACCCAACCTAC : 530 104 : GluGluValCysThr{G} >>>> Target Intron 2 >>>> {ly}LysThrGly : 112 :!!|||||||||:!!{|} 1839 bp {||} !|||||| LysGluValCysSer{G}++ ++{ly}LeuThrGly 531 : AAGGAGGTGTGTTCA{G}gt.........................ag{GT}CTAACGGGT : 2396 113 : HisThrGluValValArgValValPheGluProGlnLysIleLysPheSerGluLeuLeu : 132 ||||||||||||||||||||||||!:! |||:!! ! :!:!...!...!:!!|||||| HisThrGluValValArgValValTyrProProLysAspValSerLeuGluLysLeuLeu 2397 : CACACGGAGGTGGTGCGTGTGGTCTACCCTCCTAAAGATGTGAGCCTGGAGAAACTGCTG : 2456 133 : LysValPheTrpGluSerHisAsnProThrGln{G} >>>> Target Intron 3 > : 144 |||||||||||||||||||||:!!|||||||||{|} 15369 bp LysValPheTrpGluSerHisAspProThrGln{G}++ 2457 : AAGGTGTTCTGGGAGAGCCATGACCCCACTCaa{g}gt...................... : 2495 145 : >>> {ly}MetArgGlnGlyAsnAspValGlyThrThrTyrArgSerSerIleTyrThr : 161 {||}||| !|||||||||||| !|||||| !|||||||||:!!||||||||| ++{ly}MetAlaGlnGlyAsnAspLysGlyThrGlnTyrArgSerAlaIleTyrThr 2496 : ...ag{gt}atgGCTCAGGGGAATGATAAAGGTACACAGTATCGCTCTGCAATCTACACA : 17912 162 : AsnThrGlnGluGlnLeuGluGlnAlaLeuGlnSerArgGluGluTyrGlnLys >>>> : 180 !!!:!! !||||||! !|||||||||:!!::!!!!!:!||| ||||||::: TyrSerProGluGlnGlnGluGlnAlaMetArgThrLysGluThrTyrGlnGln++ 17913 : TACAGTCCAGAACAGCAGGAACAAGCCATGAGGACTAAAGAGACCTAccagcaggt.... : 17971 181 : Target Intron 4 >>>> ValLeuThrGluGluGlyPheGlyAlaIleThrThrG : 192 7034 bp ..!|||! !:!!:!!||| |||! !|||||||||| ++AlaLeuLysGlnLysGlyLysGlyGluIleThrThrG 17972 : .....................aggcTCTGAAGCAGAAAGGTAAGGGTGAGATCACCACAG : 25039 193 : luIleThrMetAlaLysGluPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerL : 212 |||||! !..!! !:!!! |||||||||||||||:!!|||||||||||||||||| !| luIleArgGlnAspGluValPheTyrTyrAlaGluAsnTyrHisGlnGlnTyrLeuHisL 25040 : AAATCAGACAGGACGAGGTCTTCTATTATGCTGAGAATTACCATCAGCAGTACCTGCACA : 25099 213 : ysAsnProAspGlyTyrCysGlyLeuGlyGlyThrGlyValSerCys : 227 || |||:!!||||||||||||||| !||||||||||||!!!||| ysValProAsnGlyTyrCysGlyLeuLysGlyThrGlyValThrCys 25100 : AGGTGCCTAATGGGTACTGCGGGTTAAAGGGCACCGGGGTCACCTGC : 25146 vulgar: SPP00000626_2.0 54 227 . CM004422.1:subseq(24078979,25146) 2 25146 + 625 M 14 42 S 0 1 5 0 2 I 0 379 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 1835 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 15365 3 0 2 S 1 2 M 35 105 5 0 2 I 0 7030 3 0 2 M 48 144 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-15 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local gene 3 25146 625 + . gene_id 1 ; sequence SPP00000626_2.0 ; gene_orientation + CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local cds 3 45 . + . CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local exon 3 45 . + . insertions 0 ; deletions 0 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice5 46 47 . + . intron_id 1 ; splice_site "GT" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local intron 46 428 . + . intron_id 1 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice3 427 428 . + . intron_id 0 ; splice_site "AG" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local cds 429 548 . + . CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local exon 429 548 . + . insertions 0 ; deletions 0 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice5 549 550 . + . intron_id 2 ; splice_site "GT" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local intron 549 2387 . + . intron_id 2 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice3 2386 2387 . + . intron_id 1 ; splice_site "AG" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local cds 2388 2492 . + . CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local exon 2388 2492 . + . insertions 0 ; deletions 0 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice5 2493 2494 . + . intron_id 3 ; splice_site "gt" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local intron 2493 17861 . + . intron_id 3 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice3 17860 17861 . + . intron_id 2 ; splice_site "ag" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local cds 17862 17968 . + . CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local exon 17862 17968 . + . insertions 0 ; deletions 0 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice5 17969 17970 . + . intron_id 4 ; splice_site "gt" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local intron 17969 25002 . + . intron_id 4 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local splice3 25001 25002 . + . intron_id 3 ; splice_site "ag" CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local cds 25003 25146 . + . CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local exon 25003 25146 . + . insertions 0 ; deletions 0 CM004422.1:subseq(24078979,25146) exonerate:protein2genome:local similarity 3 25146 625 + . alignment_id 1 ; Query SPP00000626_2.0 ; Align 3 55 42 ; Align 431 70 117 ; Align 2390 110 102 ; Align 17864 145 105 ; Align 25003 180 144 # --- END OF GFF DUMP --- # -- completed exonerate analysis