Command line: [exonerate -m p2g --showtargetgff -q sel15.fa -t genomic.fa] Hostname: [ws116052u] C4 Alignment: ------------ Query: sp|Q802F3|SEP15_DANRE 15 kDa selenoprotein OS=Danio rerio GN=sep15 PE=2 SV=2 Target: CM004430.1:subseq(6320000,150000) Ictalurus punctatus breed USDA103 chromosome 17, whole genome shotgun sequence Model: protein2genome:local Raw score: 671 Query range: 0 -> 153 Target range: 2382 -> 4701 1 : MetAlaGlyGluValTyrLeuLeuTrpLeuLeuProLeuLeuGlnGly >>>> Target : 17 ||||||!.!||||||||||||||||||||||||||||||||||||..! 105 MetAlaAlaGluValTyrLeuLeuTrpLeuLeuProLeuLeuGlnSer++ 2383 : ATGGCTGCGGAGGTGTATTTACTTTGGCTGTTGCCATTGCTTCAGTCGgt............ : 2433 18 : Intron 1 >>>> LeuAlaSerTyrGlyAlaGluLeuSerSerGluAlaCysArgGluLe : 32 9 bp ||||||:!!!:!||||||||||||||||||||||||||||||||||| ++LeuAlaAlaPheGlyAlaGluLeuSerSerGluAlaCysArgGluLe 2434 : .............agCTAGCAGCGTTCGGAGCCGAGCTGTCGTCGGAGGCGTGCAGGGAGCT : 3535 33 : uGlyPheSerSerAsnLeuLeuCysSerSerCysGluLeuLeuGlyGlnPheSerLeuAsnG : 53 ||||||||||||||||||||||||||||||||||!!:|||||||||||||||||||||:::! uGlyPheSerSerAsnLeuLeuCysSerSerCysAspLeuLeuGlyGlnPheSerLeuSerP 3536 : CGGCTTCTCCAGTAACCTGCTGTGCAGCTCGTGTGATTTGCTGGGCCAGTTCAGCCTGTCGC : 3598 54 : lnLeuAspLeuProCysArgGlnCysCysGlnGluGluAlaGlnLeuGluAsnArgLys > : 73 !:!!!!:! ! !||||||||||||||||||||||||||||||||||||::!|||||| roIleGluProPheCysArgGlnCysCysGlnGluGluAlaGlnLeuGluSerArgLys++ 3599 : CGATTGAGCCCTTCTGCAGGCAGTGCTGCCAGGAGGAGGCTCAGCTCGAGTCCAGGAAGgt. : 3660 74 : >>> Target Intron 2 >>>> LeuTyrProGlyAlaIleLeuGluValCysGlyUnk : 84 85 bp ||||||||||||||||||||||||||||||||| ++LeuTyrProGlyAlaIleLeuGluValCysGly*** 3661 : ........................agCTCTACCCCGGAGCCATCCTTGAGGTCTGTGGATGA : 3776 85 : LysLeuGlyArgPheProGlnValGln{A} >>>> Target Intron 3 >>>> {la : 94 |||||||||||||||||||||||||||{|} 542 bp {|| LysLeuGlyArgPheProGlnValGln{A}++ ++{la 3777 : AAACTGGGGAGGTTCCCTCAAGTCCAA{G}gt.........................ag{CT : 4349 95 : }PheValArgSerAspLysProLysLeuPheArgGlyLeuGlnIleLys >>>> Target : 111 }||||||||||||||||||||||||:!!|||!:!||||||||||||||| 1 }PheValArgSerAspLysProLysMetPheLysGlyLeuGlnIleLys++ 4350 : }TTCGTCAGGAGCGACAAGCCGAAGATGTTCAAGGGCCTTCAGATTAAGgt........... : 4401 112 : Intron 4 >>>> TyrValArgGlySerAspProValLeuLysLeuLeuAspAspAsnG : 126 74 bp |||||||||||||||||||||||||||||||||||||||||||||| ++TyrValArgGlySerAspProValLeuLysLeuLeuAspAspAsnG 4402 : ..............agTATGTGCGAGGCTCGGATCCTGTACTGAAGCTGCTGGACGATAACG : 4618 127 : lyAsnIleAlaGluGluLeuSerIleLeuLysTrpAsnThrAspSerValGluGluPheLeu : 146 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lyAsnIleAlaGluGluLeuSerIleLeuLysTrpAsnThrAspSerValGluGluPheLeu 4619 : GGAACATTGCTGAAGAACTCAGCATCCTCAAGTGGAACACGGACAGCGTGGAGGAATTCCTC : 4678 147 : SerGluLysLeuGluArgIle : 153 ||||||||||||!!:|||||| SerGluLysLeuAspArgIle 4679 : AGTGAAAAACTCGACCGCATT : 4701 vulgar: sp|Q802F3|SEP15_DANRE 0 153 . CM004430.1:subseq(6320000,150000) 2382 4701 + 671 M 16 48 5 0 2 I 0 1055 3 0 2 M 56 168 5 0 2 I 0 81 3 0 2 M 21 63 S 0 1 5 0 2 I 0 538 3 0 2 S 1 2 M 16 48 5 0 2 I 0 170 3 0 2 M 43 129 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-22 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local gene 2383 4701 671 + . gene_id 1 ; sequence sp|Q802F3|SEP15_DANRE ; gene_orientation + CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local cds 2383 2430 . + . CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local exon 2383 2430 . + . insertions 0 ; deletions 0 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice5 2431 2432 . + . intron_id 1 ; splice_site "GT" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local intron 2431 3489 . + . intron_id 1 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice3 3488 3489 . + . intron_id 0 ; splice_site "AG" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local cds 3490 3657 . + . CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local exon 3490 3657 . + . insertions 0 ; deletions 0 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice5 3658 3659 . + . intron_id 2 ; splice_site "GT" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local intron 3658 3742 . + . intron_id 2 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice3 3741 3742 . + . intron_id 1 ; splice_site "AG" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local cds 3743 3806 . + . CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local exon 3743 3806 . + . insertions 0 ; deletions 0 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice5 3807 3808 . + . intron_id 3 ; splice_site "GT" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local intron 3807 4348 . + . intron_id 3 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice3 4347 4348 . + . intron_id 2 ; splice_site "AG" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local cds 4349 4398 . + . CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local exon 4349 4398 . + . insertions 0 ; deletions 0 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice5 4399 4400 . + . intron_id 4 ; splice_site "GT" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local intron 4399 4572 . + . intron_id 4 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local splice3 4571 4572 . + . intron_id 3 ; splice_site "AG" CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local cds 4573 4701 . + . CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local exon 4573 4701 . + . insertions 0 ; deletions 0 CM004430.1:subseq(6320000,150000) exonerate:protein2genome:local similarity 2383 4701 671 + . alignment_id 1 ; Query sp|Q802F3|SEP15_DANRE ; Align 2383 1 48 ; Align 3490 17 168 ; Align 3743 73 63 ; Align 4351 95 48 ; Align 4573 111 129 # --- END OF GFF DUMP --- # -- completed exonerate analysis