Command line: [exonerate -m p2g --showtargetgff -q MSRB3/MSRB3_x.fa -t MSRB3/SUBSEQ/CM004432.1_0_subseq.txt --exhaustive] Hostname: [ws116049u] C4 Alignment: ------------ Query: SPP00000647_2.0 Protein Methionine-R-sufoxide reductase 3 (MSRB3) Zebrafish Target: CM004432.1:subseq(15146578,25404) Ictalurus punctatus breed USDA103 chromosome 19, whole genome shotgun sequence Model: protein2genome:local Raw score: 777 Query range: 0 -> 186 Target range: 16508 -> 25404 1 : MetSerGlyPheAsnLeuLeuHisLeuValSerGlnGlyGlnProValLysLeuLysAla : 20 ||||||||||||||||||||||||||||||!!!:!!.!!||||||||||||||||||||| MetSerGlyPheAsnLeuLeuHisLeuValThrLysSerGlnProValLysLeuLysAla 16509 : ATGTCTGGGTTCAATCTTCTGCATTTGGTGACCAAAAGCCAACCTGTTAAACTCAAGGCC : 16566 21 : CysGlyLeuProSer{G} >>>> Target Intron 1 >>>> {ly}ThrCysArg : 29 |||||||||||||||{|} 1928 bp {||}||||||!.! CysGlyLeuProSer{G}++ ++{ly}ThrCysHis 16567 : TGCGGGCTTCCCTCA{G}gt.........................ag{GG}ACATGCCAC : 18521 30 : SerLysLysThrTrpProLysThrPheProGluGluGluLeuArgLysArgLeuThrPro : 49 !!!||||||||||||||||||!:!||| !! !||||||||||||||||||||||||||| ThrLysLysThrTrpProLysSerPheSerProGluGluLeuArgLysArgLeuThrPro 18522 : ACCAAGAAGACCTGGCCCAAAAGCTTCTCTCCGGAAGAACTGAGGAAGCGCTTGACACCT : 18581 50 : MetGlnTyrHisValThrGlnGlnLysGlyThrGlu{Se} >>>> Target Intron : 62 |||||||||||||||||||||:!!||||||||||||{||} 2466 bp MetGlnTyrHisValThrGlnGluLysGlyThrGlu{Se}++ 18582 : ATGCAGTACCATGTTACTCAGGAAAAGGGCACAGAG{AG}gt.................. : 18624 63 : 2 >>>> {r}AlaPheThrGlyLysTyrValAspAsnLysGluGluGlyThrTyrHis : 78 {|}||||||! !|||:!!|||..!|||:!!||||||||||||||||||... ++{r}AlaPheArgGlyGluTyrThrAspHisLysGluGluGlyThrTyrArg 18625 : .......ag{T}GCTTTCAGGGGAGAATATACAGACCACAAGGAGGAGGGGACATACAGG : 21134 79 : CysValValCysGlyAlaProLeuPhe{Me} >>>> Target Intron 3 >>>> : 88 |||||||||||||||||||||||||||{||} 762 bp CysValValCysGlyAlaProLeuPhe{Me}++ ++ 21135 : TGTGTTGTCTGCGGCGCCCCTCTGTTT{AT}gt.........................ag : 21926 89 : {t}SerGluLysLysPheAspSerGlySer{G} >>>> Target Intron 4 >>>> : 98 {|}|||!!:|||||||||||||||||||||{|} 3044 bp {t}SerAspLysLysPheAspSerGlySer{G}++ 21927 : {g}tcaGACAAGAAATTTGATTCTGGCTCA{G}gt......................... : 21959 99 : {ly}TrpProSerPhePheAspLeuIleAsnLysAspAlaIleAlaGlnThrAspAsp : 116 {||}||||||||||||||||||||||||!!.:!!!!::!!|||.!!! !||||||||| ++{ly}TrpProSerPhePheAspLeuIleLysGluGluSerIleThrLeuThrAspAsp 21960 : ag{ga}tgGCCATCCTTTTTTGATCTGATCAAAGAAGAATCAATAACACTGACAGATGAT : 25054 117 : PheSerTyrGlyMetHisArgValGluThrThrCysSerGln >>>> Target Intr : 131 ||||||||||||||||||||||||||||||!:!||||||||| 138 bp PheSerTyrGlyMetHisArgValGluThrSerCysSerGln++ 25055 : TTCTCTTATGGCATGCACAGAGTGGAGACTAGCTGCAGTCAGgt................ : 25101 132 : on 5 >>>> CysGlyAlaHisLeuGlyHisLeuPheAspAspGlyProArgProThrL : 147 |||||||||||||||||||||||||||||||||||||||!:!|||||| ++CysGlyAlaHisLeuGlyHisLeuPheAspAspGlyProGlnProThrG 25102 : .........agtgtggtgCTCACCTTGGACACCTCTTTGATGACGGCCCCCAGCCCACTG : 25285 148 : ysLysArgTyrCysIleAsnSerAlaSerLeuSerPheGlnProLysAsnSerAlaThrG : 167 !||||||!:!|||||||||||||||||||||!:!||||||||||||||| !||| !!| lyLysArgPheCysIleAsnSerAlaSerLeuAsnPheGlnProLysAsnValAlaProG 25286 : GGAAGCGCTTCTGCATAAACTCCGCCTCACTCAACTTTCAGCCAAAAAACGTTGCTCCTG : 25345 168 : luGluValGluAlaSerGlyAlaAlaGlyGlnSerSerThrSerLysAsnGluGluLeu : 186 ||! !!.!||| !!|||||||||.!!||||||||||||:!!|||!..!!....|||||| luGlyAlaGluProSerGlyAlaThrGlyGlnSerSerSerSerSerLysSerGluLeu 25346 : AAGGGGCAGAACCAAGTGGTGCCACAGGCCAATCGTCATCTTCTAGTAAGAGTGAGCTT : 25404 vulgar: SPP00000647_2.0 0 186 . CM004432.1:subseq(15146578,25404) 16508 25404 + 777 M 25 75 S 0 1 5 0 2 I 0 1924 3 0 2 S 1 2 M 35 105 S 0 2 5 0 2 I 0 2462 3 0 2 S 1 1 M 25 75 S 0 2 5 0 2 I 0 758 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 3040 3 0 2 S 1 2 M 32 96 5 0 2 I 0 134 3 0 2 M 56 168 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-16 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local gene 16509 25404 777 + . gene_id 1 ; sequence SPP00000647_2.0 ; gene_orientation + CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local cds 16509 16584 . + . CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local exon 16509 16584 . + . insertions 0 ; deletions 0 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice5 16585 16586 . + . intron_id 1 ; splice_site "GT" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local intron 16585 18512 . + . intron_id 1 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice3 18511 18512 . + . intron_id 0 ; splice_site "AG" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local cds 18513 18621 . + . CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local exon 18513 18621 . + . insertions 0 ; deletions 0 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice5 18622 18623 . + . intron_id 2 ; splice_site "GT" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local intron 18622 21087 . + . intron_id 2 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice3 21086 21087 . + . intron_id 1 ; splice_site "AG" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local cds 21088 21165 . + . CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local exon 21088 21165 . + . insertions 0 ; deletions 0 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice5 21166 21167 . + . intron_id 3 ; splice_site "gt" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local intron 21166 21927 . + . intron_id 3 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice3 21926 21927 . + . intron_id 2 ; splice_site "ag" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local cds 21928 21956 . + . CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local exon 21928 21956 . + . insertions 0 ; deletions 0 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice5 21957 21958 . + . intron_id 4 ; splice_site "GT" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local intron 21957 25000 . + . intron_id 4 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice3 24999 25000 . + . intron_id 3 ; splice_site "ag" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local cds 25001 25098 . + . CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local exon 25001 25098 . + . insertions 0 ; deletions 0 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice5 25099 25100 . + . intron_id 5 ; splice_site "GT" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local intron 25099 25236 . + . intron_id 5 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local splice3 25235 25236 . + . intron_id 4 ; splice_site "ag" CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local cds 25237 25404 . + . CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local exon 25237 25404 . + . insertions 0 ; deletions 0 CM004432.1:subseq(15146578,25404) exonerate:protein2genome:local similarity 16509 25404 777 + . alignment_id 1 ; Query SPP00000647_2.0 ; Align 16509 1 75 ; Align 18515 27 105 ; Align 21089 63 75 ; Align 21929 89 27 ; Align 25003 99 96 ; Align 25237 131 168 # --- END OF GFF DUMP --- # -- completed exonerate analysis