Command line: [exonerate -m p2g --showtargetgff -q MSRB2/MSRB2_x.fa -t MSRB2/SUBSEQ/CM004436.1_2_subseq.txt --exhaustive] Hostname: [ws116049u] C4 Alignment: ------------ Query: SPP00000646_2.0 Protein Methionine-R-sufoxide reductase 2 (MSRB2) Zebrafish Target: CM004436.1:subseq(2377721,25137) Ictalurus punctatus breed USDA103 chromosome 23, whole genome shotgun sequence Model: protein2genome:local Raw score: 716 Query range: 0 -> 179 Target range: 18825 -> 25137 1 : MetSerArgPheLeuValArgLeuSerThrValValSerLysGlyAlaThrGlyLysSer : 20 |||:!!|||.!!|||||||||||||||:!!!.!:!! !!!.||||||:!! !:!!||| MetAlaArgLeuLeuValArgLeuSerSerAlaLeuHisAsnGlyAlaSerThrGlnSer 18826 : ATGGCACGCCTCCTGGTGCGACTTTCTTCTGCACTTCACAATGGAGCTTCCACACAATCG : 18883 21 : ValLeuProGlnLysArgIlePheAlaGlyIleArgLeuIleSerSerSerThr{G} > : 39 |||||| ...!:!!!! ! !||| !||||||! !:!!|||!!!!!!|||{!} ValLeu---SerArgSerTrpSerAlaLeuIleArgProLeuSerThrThrThr{A}++ 18884 : GTTTTG---TCTAGGAGTTGGTCTGCGCTAATCCGACCACTAAGCACAACAACA{G}gt. : 18940 40 : >>> Target Intron 1 >>>> {ly}LeuGlnSerLeuThrArgTyrAspGlnSer : 49 3248 bp { !}||| ||||||||||||||||||:!! !! ++{sp}LeuLeuSerLeuThrArgTyrAspGluArg 18941 : ........................ag{at}cttctttCTTTGACACGTTATGATGAGCGT : 22215 50 : ThrAspTrpGlnArgLysLeuSerProGluGlnTyrValValThrArgGluLysGlyThr : 69 ..!||||||:!!!:!||||||!!!|||||||||||||||||||||||||||||||||||| ValAspTrpLysLysLysLeuThrProGluGlnTyrValValThrArgGluLysGlyThr 22216 : GTGGACTGGAAGAAGAAACTAACTCCAGAACAGTACGTAGTCACTCGAGAGAAAGGCACT : 22275 70 : GluVal >>>> Target Intron 2 >>>> ProPheSerGlyIleTyrLeuAsnH : 80 |||||| 153 bp |||||||||||||||||||||||| GluVal++ ++ProPheSerGlyIleTyrLeuAsnC 22276 : GAGGTGgt.........................agCCGTTCAGTGGAATCTATCTGAACT : 22461 81 : isAsnGluValGlyMetTyrHisCysValCysCysAspSerProLeuPhe{Se} >>>> : 97 !|||!!:||||||||||||||||||||||||||||||!!!|||||||||{||} ysAsnAspValGlyMetTyrHisCysValCysCysAspThrProLeuPhe{Se}++ 22462 : GTAATGATGTGGGCATGTACCACTGTGTGTGCTGCGATACACCACTCTTC{AG}gt.... : 22516 98 : Target Intron 3 >>>> {r}SerGluAlaLysTyrAspAlaGlyAlaGlyTrpP : 109 1138 bp {|}||||||:!!|||||||||:!!|||.!!||||||| ++{r}SerGluSerLysTyrAspSerGlyThrGlyTrpP 22517 : .....................ag{C}TCTGAATCAAAATACGACTCTGGAACAGGGTGGC : 23686 110 : roSerPheCysGluAlaHisGlyThrTrpGluLysAspGluSerHisAlaAsnIleValA : 129 ||||||||! !|||||||||||||||||||||!:!|||||||||||||||||||||:!!| roSerPhePheGluAlaHisGlyThrTrpGluArgAspGluSerHisAlaAsnIleIleA 23687 : CATCTTTCTTTGAGGCTCATGGGACGTGGGAGAGAGACGAGAGTCATGCCAACATTATCC : 23746 130 : rgArgProAspAsnSerLeuGlySerThrGlyThrGluValIleCysLysHis >>>> : 147 |||||||||||||||||||||||||| !!|||||||||||||||||||||!!. rgArgProAspAsnSerLeuGlySerProGlyThrGluValIleCysLysGln+- 23747 : GCAGACCCGATAACTCGTTAGGAAGCCCGGGAACAGAAGTCATCTGCAAACAGgc..... : 23802 148 : Target Intron 4 >>>> CysAspAlaHisLeuGlyHisValPheGluAspGlyPr : 159 1239 bp ||||||!.!||||||||||||||||||!!:|||||||| ++CysAspGlyHisLeuGlyHisValPheAspAspGlyPr 23803 : ....................agTGTGATGGCCATCTCGGCCATGTGTTCGATGATGGCCC : 25075 160 : oAspProThrGlyGlnArgPheCysIleAsnSerValAlaLeuAsnPheLysProArgGl : 179 ||||||||||||||||||||||||||||||||||!.!||||||||||||||||||||||| oAspProThrGlyGlnArgPheCysIleAsnSerAlaAlaLeuAsnPheLysProArgGl 25076 : GGATCCAACAGGCCAGAGATTCTGTATAAACAGTGCAGCTCTGAACTTCAAGCCTAGAGA : 25135 180 : u : 179 | u 25136 : A : 25137 vulgar: SPP00000646_2.0 0 179 . CM004436.1:subseq(2377721,25137) 18825 25137 + 716 M 22 66 G 1 0 M 15 45 S 0 1 5 0 2 I 0 3244 3 0 2 S 1 2 M 32 96 5 0 2 I 0 149 3 0 2 M 25 75 S 0 2 5 0 2 I 0 1134 3 0 2 S 1 1 M 49 147 5 0 2 I 0 1235 3 0 2 M 33 99 # --- 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 # CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local gene 18826 25137 716 + . gene_id 1 ; sequence SPP00000646_2.0 ; gene_orientation + CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local cds 18826 18937 . + . CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local exon 18826 18937 . + . insertions 0 ; deletions 1 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice5 18938 18939 . + . intron_id 1 ; splice_site "GT" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local intron 18938 22185 . + . intron_id 1 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice3 22184 22185 . + . intron_id 0 ; splice_site "ag" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local cds 22186 22283 . + . CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local exon 22186 22283 . + . insertions 0 ; deletions 0 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice5 22284 22285 . + . intron_id 2 ; splice_site "GT" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local intron 22284 22436 . + . intron_id 2 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice3 22435 22436 . + . intron_id 1 ; splice_site "AG" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local cds 22437 22513 . + . CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local exon 22437 22513 . + . insertions 0 ; deletions 0 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice5 22514 22515 . + . intron_id 3 ; splice_site "GT" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local intron 22514 23651 . + . intron_id 3 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice3 23650 23651 . + . intron_id 2 ; splice_site "AG" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local cds 23652 23799 . + . CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local exon 23652 23799 . + . insertions 0 ; deletions 0 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice5 23800 23801 . + . intron_id 4 ; splice_site "GC" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local intron 23800 25038 . + . intron_id 4 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local splice3 25037 25038 . + . intron_id 3 ; splice_site "AG" CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local cds 25039 25137 . + . CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local exon 25039 25137 . + . insertions 0 ; deletions 0 CM004436.1:subseq(2377721,25137) exonerate:protein2genome:local similarity 18826 25137 716 + . alignment_id 1 ; Query SPP00000646_2.0 ; Align 18826 1 66 ; Align 18892 24 45 ; Align 22188 40 96 ; Align 22437 72 75 ; Align 23653 98 147 ; Align 25039 147 99 # --- END OF GFF DUMP --- # -- completed exonerate analysis