Command line: [exonerate -m p2g --showtargetgff -q SELENOT1/SELENOT1_x.fa -t SELENOT1/SUBSEQ/CM004420.1_5_subseq.txt --exhaustive] Hostname: [ws112615u] C4 Alignment: ------------ Query: SPP00000649_2.0 Protein Selenoprotein T1 (SELENOT1) Zebrafish Target: CM004420.1:subseq(8986316,50131) Ictalurus punctatus breed USDA103 chromosome 7, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 763 Query range: 1 -> 178 Target range: 26378 -> 23246 2 : GlyLysMetArgTrpLeuProPheSerAlaLeuLeuLeuTrpAlaLeuCysLeuHisSer : 21 |||||||||||||||!!!|||.!!|||!.!||||||||| !|||! !! |||:!! !! GlyLysMetArgTrpPheProLeuSerValLeuLeuLeuLeuAlaCysSerLeuTyrArg 26378 : GGGAAGATGCGCTGGTTTCCGCTCTCTGTGTTACTATTACTGGCCTGCTCGCTTTATCGC : 26321 22 : AlaSerAlaAspAsnAsnGlyValLysLysMetLysMetGlnPheAlaThrGlyProLeu : 41 |||.!!!.! !!||||||||||||!:!|||! !|||||||||||||||.!!||||||||| AlaGlyGlyHisAsnAsnGlyValArgLysThrLysMetGlnPheAlaAlaGlyProLeu 26320 : GCCGGTGGCCATAACAACGGCGTCAGGAAAACGAAAATGCAGTTTGCAGCCGGTCCGCTT : 26261 42 : LeuLysPheGlnIle{Cy} >>>> Target Intron 1 >>>> {s}ValSerUnk : 50 |||||||||||||||{||} 1130 bp {|}:!!||| LeuLysPheGlnIle{Cy}++ ++{s}IleSer*** 26260 : CTTAAATTTCAAATC{TG}gt.........................ag{T}ATCTCCTGA : 25104 51 : GlyTyrLysArgValPheGluGluTyrThrGlnAlaLeuTyrGlnArgTyrProAspIle : 70 |||||||||||||||||||||||||||||||||||||||! !|||||||||||||||||| GlyTyrLysArgValPheGluGluTyrThrGlnAlaLeuSerGlnArgTyrProAspIle 25103 : GGGTACAAGCGGGTGTTTGAGGAGTACACGCAGGCCTTATCCCAGCGGTACCCAGACATC : 25044 71 : ArgIleGluGlyGluAsnTyrLeuProLeuProLeuTyr{Ar} >>>> Target Int : 84 |||||||||||||||||||||||||||||||||:!!|||{||} 750 b ArgIleGluGlyGluAsnTyrLeuProLeuProIleTyr{Ar}++ 25043 : CGCATTGAGGGGGAGAATTATCTCCCGCTGCCTATTTAC{AG}gt............... : 24998 85 : ron 2 >>>> {g}HisIleAlaSerPheLeuSerMetPheLysLeuLeuLeuIleGly : 99 p {|}|||:!!|||||||||||||||!!:|||||||||!!!||||||||| ++{g}HisValAlaSerPheLeuSerIlePheLysLeuPheLeuIleGly 24997 : ..........ag{g}cacgTCGCTTCCTTTCTGTCCATTTTCAAACTGTTCCTGATTGGG : 24207 100 : ValIleIleLeuGlyLysAspProPheAlaLeuCysGlyMetGlnAlaProGlyIleTrp : 119 :!!|||:!!:!!|||||||||||||||||||||! !||||||:!! !!||| !!:!!||| LeuIleValValGlyLysAspProPheAlaLeuPheGlyMetGluProProArgLeuTrp 24206 : CTGATCGTCGTAGGCAAGGATCCGTTTGCGCTTTTCGGCATGGAGCCACCACGACTTTGG : 24147 120 : ValTrpSerGlnGluAsnLys >>>> Target Intron 3 >>>> IleTyrAlaC : 130 ..!|||||||||||||||||| 424 bp |||||||||| ThrTrpSerGlnGluAsnLys++ ++IleTyrAlaC 24146 : ACTTGGAGTCAAGAGAACAAGgt.........................agATCTACGCCT : 23690 131 : ysMetMetValPhePhePheSerAsnMetIleGluAsnGlnCysMetSerThrGlyAlaP : 150 |||||||||||||||||||||||||||||:!!|||||||||||||||||||||||||||| ysMetMetValPhePhePheSerAsnMetLeuGluAsnGlnCysMetSerThrGlyAlaP 23689 : GCATGATGGTGTTCTTCTTCAGCAACATGCTTGAAAACCAGTGCATGTCGACGGGGGCAT : 23630 151 : heGluIleThrLeuAsn{A} >>>> Target Intron 4 >>>> {sp}ValProV : 159 |||||||||||!!!|||{|} 297 bp {||}||||||| heGluIleThrPheAsn{A}++ ++{sp}ValProV 23629 : TTGAAATCACGTTCAAC{G}gt.........................ag{AT}GTTCCCG : 23306 160 : alTrpSerLysLeuGluSerGlyHisLeuProSerMetGlnGlnLeuValGlnIleLeu : 178 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| alTrpSerLysLeuGluSerGlyHisLeuProSerMetGlnGlnLeuValGlnIleLeu 23305 : TGTGGTCAAAGCTGGAGTCAGGCCACCTTCCCTCCATGCAGCAGCTGGTGCAGATTCTG : 23247 vulgar: SPP00000649_2.0 1 178 . CM004420.1:subseq(8986316,50131) 26378 23246 - 763 M 45 135 S 0 2 5 0 2 I 0 1126 3 0 2 S 1 1 M 36 108 S 0 2 5 0 2 I 0 746 3 0 2 S 1 1 M 42 126 5 0 2 I 0 420 3 0 2 M 29 87 S 0 1 5 0 2 I 0 293 3 0 2 S 1 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-15 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local gene 23247 26378 763 - . gene_id 1 ; sequence SPP00000649_2.0 ; gene_orientation + CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local cds 26242 26378 . - . CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local exon 26242 26378 . - . insertions 0 ; deletions 0 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice5 26240 26241 . - . intron_id 1 ; splice_site "GT" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local intron 25112 26241 . - . intron_id 1 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice3 25112 25113 . - . intron_id 0 ; splice_site "AG" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local cds 25001 25111 . - . CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local exon 25001 25111 . - . insertions 0 ; deletions 0 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice5 24999 25000 . - . intron_id 2 ; splice_site "GT" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local intron 24251 25000 . - . intron_id 2 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice3 24251 24252 . - . intron_id 1 ; splice_site "ag" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local cds 24124 24250 . - . CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local exon 24124 24250 . - . insertions 0 ; deletions 0 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice5 24122 24123 . - . intron_id 3 ; splice_site "GT" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local intron 23700 24123 . - . intron_id 3 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice3 23700 23701 . - . intron_id 2 ; splice_site "AG" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local cds 23612 23699 . - . CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local exon 23612 23699 . - . insertions 0 ; deletions 0 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice5 23610 23611 . - . intron_id 4 ; splice_site "GT" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local intron 23315 23611 . - . intron_id 4 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local splice3 23315 23316 . - . intron_id 3 ; splice_site "AG" CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local cds 23247 23314 . - . CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local exon 23247 23314 . - . insertions 0 ; deletions 0 CM004420.1:subseq(8986316,50131) exonerate:protein2genome:local similarity 23247 26378 763 - . alignment_id 1 ; Query SPP00000649_2.0 ; Align 26379 2 135 ; Align 25111 48 108 ; Align 24250 85 126 ; Align 23700 127 87 ; Align 23313 157 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis