Command line: [exonerate -m p2g --showtargetgff -q Secp43/Secp43_x.fa -t Secp43/SUBSEQ/CM004433.1_2_subseq.txt --exhaustive] Hostname: [ws101066u] C4 Alignment: ------------ Query: SPP00000664_2.0 Protein tRNA Sec 1 associated protein 1 (SECp43) Zebrafish Target: CM004433.1:subseq(7418435,25125) Ictalurus punctatus breed USDA103 chromosome 20, whole genome shotgun sequence Model: protein2genome:local Raw score: 342 Query range: 0 -> 135 Target range: 20542 -> 25125 1 : MetAsnSerLeuTrpMetGlyAsn >>>> Target Intron 1 >>>> LeuGluP : 11 |||!..|||||||||||||||:!! 1498 bp |||!!:| MetThrSerLeuTrpMetGlyAsp++ ++LeuAspP 20543 : ATGACAAGTCTGTGGATGGGCGATgt.........................agTTAGACC : 22071 12 : roTyrMetAspGluAspPheIleCysArgAlaPheAlaGlnMetGlyGluThrValValL : 31 ||||||||||||||:!!|||||| !:!||||||::! ||||||||||||!.! ! roTyrMetAspGluAsnPheIleLysGlnAlaPheSerThrMetGlyGluThrAlaTyrG 22072 : CATACATGGATGAAAATTTCATCAAACAAGCTTTCAGCACTATGGGGGAGACGGCATACG : 22131 32 : ysIleArgLeuIleArgAspLysIleThr{Gl} >>>> Target Intron 2 >>>> : 41 !:!:!:!:!!|||! ! !!::!:!!|||{||} 92 bp lyValLysIleIleThrHisArgValThr{Gl}++ 22132 : GGGTGAAAATTATAACACACCGGGTAACA{GG}gt......................... : 22165 42 : {y}LysAsnAlaGlyTyrGlyPheValGluLeuAlaAspAspThrAlaValGluArgC : 60 {|} ::!||||||||| !!||||||||||||||||||!!:.!!::!|||!!:|||| ++{y}GlySerAlaGlyTyrCysPheValGluLeuAlaAspGluAlaSerValAspArgC 22166 : ag{A}GGCTCTGCGGGATATTGTTTTGTAGAATTGGCAGATGAAGCCAGTGTTGACCGGT : 22310 61 : ysLeuArgLysValAsnGlyLysProLeuProGlyAlaThrPro >>>> Target In : 75 ||:!!!:!!:!:!!|||||||||! !:!!||||||:!!!.!||| 2485 ysValGlnArgLeuAsnGlyLysLeuValProGlySerAsnPro++ 22311 : GTGTCCAGAGGCTCAATGGCAAGCTTGTTCCAGGATCAAATCCTgt.............. : 22357 76 : tron 3 >>>> ProLysArgPheLysLeuSerArgSerAsnTyrGlyLysGlnGlyGl : 90 bp |||!:!!:!|||||||||!:! !:!!!..|||||||||::! !|| ++ProArgLysPheLysLeuAsnTyrAlaThrTyrGlyLysArgProGl 22358 : ...........agCCCAGAAAGTTCAAGCTGAATTATGCAACATATGGGAAAAGGCCTGA : 24885 91 : u<->{Se} >>>> Target Intron 4 >>>> {r}SerThrPheSerLeuPheVa : 98 | {.!} 100 bp {!} !! !||||||:!!||||| uPro{Gl}++ ++{y}ProGluPheSerValPheVa 24886 : GCCT{GG}gt.........................ag{G}CCTGAATTTTCTGTCTTTGT : 25012 99 : lSerAspLeuThrProAspValAspAspGlyMetLeuTyrGluPhePheHisTyrHisPh : 118 |.!!||||||||||||!!:||||||||| !..!|||:!!:!!||||||! ! ! !: lGlyAspLeuThrProGluValAspAspTyrGlnLeuHisGlnPhePheLeuLysLysTy 25013 : TGGAGACCTGACGCCAGAAGTCGATGATTATCAGCTACATCAGTTCTTTCTGAAAAAATA : 25072 119 : eSerSerCysCysSerGlyLysIleValLeuAspAlaAsnGlyHisSerLys : 135 ! !!|||||| .!!!.!|||:!!||| !||| !! !!|||:!!|||||| rProSerCysLysGlyAlaLysValValThrAspProTyrGlyAsnSerLys 25073 : CCCTTCATGCAAAGGAGCCAAAGTTGTCACTGATCCCTATGGAAATTCAAAG : 25125 vulgar: SPP00000664_2.0 0 135 . CM004433.1:subseq(7418435,25125) 20542 25125 + 342 M 8 24 5 0 2 I 0 1494 3 0 2 M 32 96 S 0 2 5 0 2 I 0 88 3 0 2 S 1 1 M 33 99 5 0 2 I 0 2481 3 0 2 M 16 48 G 0 3 S 0 2 5 0 2 I 0 96 3 0 2 S 1 1 M 44 132 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-21 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local gene 20543 25125 342 + . gene_id 1 ; sequence SPP00000664_2.0 ; gene_orientation + CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local cds 20543 20566 . + . CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local exon 20543 20566 . + . insertions 0 ; deletions 0 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice5 20567 20568 . + . intron_id 1 ; splice_site "GT" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local intron 20567 22064 . + . intron_id 1 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice3 22063 22064 . + . intron_id 0 ; splice_site "AG" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local cds 22065 22162 . + . CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local exon 22065 22162 . + . insertions 0 ; deletions 0 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice5 22163 22164 . + . intron_id 2 ; splice_site "gt" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local intron 22163 22254 . + . intron_id 2 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice3 22253 22254 . + . intron_id 1 ; splice_site "AG" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local cds 22255 22354 . + . CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local exon 22255 22354 . + . insertions 0 ; deletions 0 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice5 22355 22356 . + . intron_id 3 ; splice_site "GT" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local intron 22355 24839 . + . intron_id 3 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice3 24838 24839 . + . intron_id 2 ; splice_site "AG" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local cds 24840 24892 . + . CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local exon 24840 24892 . + . insertions 3 ; deletions 0 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice5 24893 24894 . + . intron_id 4 ; splice_site "GT" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local intron 24893 24992 . + . intron_id 4 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local splice3 24991 24992 . + . intron_id 3 ; splice_site "AG" CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local cds 24993 25125 . + . CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local exon 24993 25125 . + . insertions 0 ; deletions 0 CM004433.1:subseq(7418435,25125) exonerate:protein2genome:local similarity 20543 25125 342 + . alignment_id 1 ; Query SPP00000664_2.0 ; Align 20543 1 24 ; Align 22065 9 96 ; Align 22256 42 99 ; Align 24840 75 48 ; Align 24994 92 132 # --- END OF GFF DUMP --- # -- completed exonerate analysis