Command line: [exonerate -m p2g --showtargetgff -q SELENOU2.fa -t genomic.fa] Hostname: [ws101074U] C4 Alignment: ------------ Query: SPP00000114_2.0 # Protein # Selenoprotein U2 (SELENOU2) # Human Target: CM004418.1:subseq(16770000,150000) Ictalurus punctatus breed USDA103 chromosome 5, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 495 Query range: 17 -> 186 Target range: 8815 -> 3823 18 : ValProAlaProSerGlyProAspSerGlyGlnProLeuAlaAlaAlaValAlaGluLeuPr : 38 |||||| !! !!|||..! !! |||!.! |||:!! |||! !|||! !!!:! !! ValProProThrSerSerAlaThrSerAlaValProIle---AlaGluValGluAspCysLe 8815 : GTACCTCCGACTTCTTCAGCCACATCTGCTGTTCCCATT---GCCGAGGTAGAGGATTGTCT : 8758 39 : oValLeuAspAlaArgGlyGlnArgValProPheGlyAlaLeuPheArgGluArgArgAlaV : 59 !:!!! !||| !!.!|||! |||:!! !!||| !::!|||!:!!:! !.!!:!|||: uIleTyrAspArgAsnGlyLeuArgLeuThrPheLysSerLeuTyrGlnThrHisLysAlaI 8757 : CATCTATGATCGAAACGGGCTTCGATTAACCTTTAAGAGCTTATATCAAACCCACAAAGCTA : 8695 60 : alValValPheValArg >>>> Target Intron 1 >>>> HisPheLeuCysTyrI : 70 !!:!!:!!||||||||| 4113 bp |||||||||||||||! leIleIlePheValArg++ ++HisPheLeuCysTyrT 8694 : TCATTATTTTTGTGAGGgt.........................agcatTTTTTGTGCTACA : 4549 71 : leCysLysGluTyrValGluAspLeuAlaLysIleProArgSerPheLeuGln >>>> Ta : 88 !|||:!!||||||||||||||||||::!|||||||||!:!..!.!.||| ! hrCysGlnGluTyrValGluAspLeuSerLysIleProGlnGluMetLeuLeu++ 4548 : CATGTCAGGAATATGTTGAAGACCTAAGCAAAATACCACAGGAAATGCTATTGgt....... : 4493 89 : rget Intron 2 >>>> GluAlaAsnValThrLeuIleValIleGlyGlnSerSerTyr : 101 100 bp !!:|||:!!||| !|||||||||||||||||||||.!!!:! ++AspAlaAspValArgLeuIleValIleGlyGlnSerGlyPhe 4492 : ..................agGATGCTGATGTCCGACTTATTGTCATTGGGCAATCAGGCTTT : 4356 102 : HisHisIleGlu >>>> Target Intron 3 >>>> ProPheCysLysLeuThrGly : 112 !||||||||| 88 bp !||||||..!||||||||| SerHisIleGlu++ ++AlaPheCysSerLeuThrGly 4355 : TCCCATATAGAGgt.........................aggcATTCTGCTCGCTGACAGGC : 4235 113 : TyrSerHisGluIleTyrValAspProGluArgGluIleTyrLysArgLeuGlyMetLysAr : 133 |||..!|||||||||||||||||||||||||||.!.|||||||||!:!|||||||||||||| TyrGlnHisGluIleTyrValAspProGluArgHisIleTyrLysLysLeuGlyMetLysAr 4234 : TATCAACATGAAATTTATGTTGATCCAGAGCGACATATTTATAAGAAACTAGGGATGAAAAG : 4172 134 : gGlyGluGluIle<->AlaSer{S} >>>> Target Intron 4 >>>> {er}GlyG : 142 ||||||| ! ! :::{:} 184 bp {!!}..!| gGlyGluIleTyrGluGluThr{A}++ ++{la}SerG 4171 : AGGGGAGATCTATGAGGaaaca{g}gt.........................ag{CC}TCTC : 3958 143 : lnSerProHisIleLysSerAsnLeuLeuSerGlySerLeuGlnSerLeuTrpArgAlaVal : 162 |||||||||||:!:||||||!:!:!!||| !||||||:!!:!!|||:!!|||||||||:!! lnSerProHisValLysSerSerMetLeuValGlySerIleLysSerMetTrpArgAlaMet 3957 : AAAGCCCACATGTGAAATCCAGCATGCTTGTTGGCAGTATAAAGAGCATGTGGCGTGCCATG : 3898 163 : ThrGlyProLeuPheAspPheGlnGlyAspProAlaGlnGlnGlyGlyThrLeuIleLeuGl : 183 |||.!!||| !||||||||||||||||||||| !||||||||||||.!!||||||:!!|| ThrSerProAlaPheAspPheGlnGlyAspProLeuGlnGlnGlyGlyAlaLeuIleIleGl 3897 : ACCAGTCCTGCCTTTGATTTTCAAGGAGATCCTCTCCAGCAAGGAGGAGCACTCATCATTGG : 3835 184 : yProGlyAsn : 186 |||||||:!! yProGlyAsp 3834 : CCCAGGTGAT : 3824 vulgar: SPP00000114_2.0 17 186 . CM004418.1:subseq(16770000,150000) 8815 3823 - 495 M 13 39 G 1 0 M 33 99 5 0 2 I 0 4109 3 0 2 M 23 69 5 0 2 I 0 96 3 0 2 M 18 54 5 0 2 I 0 84 3 0 2 M 32 96 G 0 3 M 2 6 S 0 1 5 0 2 I 0 180 3 0 2 S 1 2 M 46 138 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local gene 3824 8815 495 - . gene_id 1 ; sequence SPP00000114_2.0 ; gene_orientation + CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local cds 8678 8815 . - . CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local exon 8678 8815 . - . insertions 0 ; deletions 1 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice5 8676 8677 . - . intron_id 1 ; splice_site "GT" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local intron 4565 8677 . - . intron_id 1 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice3 4565 4566 . - . intron_id 0 ; splice_site "ag" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local cds 4496 4564 . - . CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local exon 4496 4564 . - . insertions 0 ; deletions 0 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice5 4494 4495 . - . intron_id 2 ; splice_site "GT" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local intron 4396 4495 . - . intron_id 2 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice3 4396 4397 . - . intron_id 1 ; splice_site "AG" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local cds 4342 4395 . - . CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local exon 4342 4395 . - . insertions 0 ; deletions 0 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice5 4340 4341 . - . intron_id 3 ; splice_site "GT" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local intron 4254 4341 . - . intron_id 3 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice3 4254 4255 . - . intron_id 2 ; splice_site "ag" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local cds 4148 4253 . - . CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local exon 4148 4253 . - . insertions 3 ; deletions 0 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice5 4146 4147 . - . intron_id 4 ; splice_site "gt" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local intron 3964 4147 . - . intron_id 4 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local splice3 3964 3965 . - . intron_id 3 ; splice_site "AG" CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local cds 3824 3963 . - . CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local exon 3824 3963 . - . insertions 0 ; deletions 0 CM004418.1:subseq(16770000,150000) exonerate:protein2genome:local similarity 3824 8815 495 - . alignment_id 1 ; Query SPP00000114_2.0 ; Align 8816 18 39 ; Align 8777 32 99 ; Align 4565 65 69 ; Align 4396 88 54 ; Align 4254 106 96 ; Align 4155 138 6 ; Align 3962 141 138 # --- END OF GFF DUMP --- # -- completed exonerate analysis