Command line: [exonerate -m p2g --showtargetgff -q SelU1a/SelU1a_x.fa -t SelU1a/SUBSEQ/CM004416.1_1_subseq.txt --exhaustive] Hostname: [ws101122u] C4 Alignment: ------------ Query: SPP00000652_2.0 Protein Selenoprotein X1a (SELENOX1a) Zebrafish Target: CM004416.1:subseq(21009595,25185) Ictalurus punctatus breed USDA103 chromosome 3, whole genome shotgun sequence Model: protein2genome:local Raw score: 751 Query range: 11 -> 201 Target range: 22199 -> 25185 12 : ThrLeuAlaMetGlyMetTrpSerLeuGlyLeuGlyAlaValGlyAlaAlaIleAlaGly : 31 ||| ! !|||.!!||||||||||||.!!|||||||||:!!||||||!.!||||||||| ThrThrPheMetSerMetTrpSerLeuSerLeuGlyAlaMetGlyAlaValIleAlaGly 22200 : ACAACCTTCATGAGCATGTGGTCACTCAGCCTTGGAGCTATGGGTGCTGTCATTGCTGGC : 22257 32 : LeuIleLeuAlaAsnThrAspPheLeuLeuThrLysSerAlaProAlaThrValAspTyr : 51 :!!|||||||||||||||||||||!!!||||||||||||! ! !||||||:!!.!.||| IleIleLeuAlaAsnThrAspPhePheLeuThrLysSerAspPheAlaThrLeuGlnTyr 22258 : ATAATTCTGGCTAACACAGATTTTTTCCTGACCAAGTCTGATTTTGCTACTCTACAGTAT : 22317 52 : LeuAlaAsnAlaAspLeuLysThrIleAspGly{A} >>>> Target Intron 1 > : 63 |||! !:!!|||||||||||||||! !|||!.!{|} 1920 bp LeuGluAspAlaAspLeuLysThrThrAspAla{A}++ 22318 : CTGGAAGATGCTGACCTCAAAACCACTGACGCA{G}gt...................... : 22356 64 : >>> {sp}GluArgSerLeuLysAlaLysAlaLeuTrpGluLysSerGlyAlaValIle : 80 {||}|||::! !!!!||||||!:!.!!|||||||||! ||||||||||||||| ++{sp}GluLysValPheLysAlaArgThrLeuTrpGluThrSerGlyAlaValIle 22357 : ...ag{at}gagaAGGTATTTAAAGCTAGAACTCTTTGGGAGACTTCTGGAGCAGTGATC : 24324 81 : MetAlaValArgArgProGlyUnkPheLeuCysArgGlu >>>> Target Intron : 94 ||||||||||||||||||||| ||||||||||||||| 88 bp MetAlaValArgArgProGly***PheLeuCysArgGlu++ 24325 : ATGGCTGTACGGCGGCCTGGATGATTTTTGTGTAGAGAGgt................... : 24368 95 : 2 >>>> GluAlaSerGluLeuSerSerLeuLysProGlnLeuAspGluLeuGlyValP : 111 ||||||:!!||||||||||||||||||||||||||||||:!!|||||||||| ++GluAlaAlaGluLeuSerSerLeuLysProGlnLeuAspLysLeuGlyValP 24369 : ......agGAAGCCGCTGAGCTATCCTCTCTGAAGCCCCAACTGGACAAGCTTGGGGTTC : 24505 112 : roLeuTyrAlaValValLysGluAsnValGlyThrGluIleGlnAspPheArgProHisP : 131 ||||||||||||||||||||||||||:!!! !||||||:!!!!.||||||!:!||||||| roLeuTyrAlaValValLysGluAsnIleAspThrGluValHisAspPheLysProHisP 24506 : CTTTGTACGCTGTGGTCAAAGAGAACATTGATACAGAGGTTCACGATTTCAAACCACACT : 24565 132 : heAlaGlyGluIlePheLeuAspGluLys >>>> Target Intron 3 >>>> Gl : 141 ||||||||!!::!!||||||||||||||| 408 bp || heAlaGlyAspValPheLeuAspGluLys++ ++Gl 24566 : TTGCTGGAGATGTCTTCCTGGATGAGAAGgt.........................agCA : 25003 142 : nAlaPheTyrGlyProGlnGlnArgLysMetGlyGlyLeuGlyPheIleArgLeuGlyVa : 161 | !|||||||||||| ! !|||||||||||||||||||||||||||||||||||||| nLeuPheTyrGlyProThrLeuArgLysMetGlyGlyLeuGlyPheIleArgLeuGlyVa 25004 : ATTGTTCTATGGTCCCACCCTGAGGAAAATGGGAGGTCTTGGCTTCATTCGTCTGGGAGT : 25063 162 : lTrpGlnAsnPheValArgAlaTrpArgAlaGlyTyrGlnGlyAsnMetAsnGlyGluGl : 181 ||||||||||||||||||||||||||||:!!||||||||||||||||||!!.|||||||| lTrpGlnAsnPheValArgAlaTrpArgSerGlyTyrGlnGlyAsnMetLysGlyGluGl 25064 : TTGGCAGAACTTCGTAAGGGCCTGGAGGTCAGGTTACCAGGGAAACATGAAAGGAGAGGG : 25123 182 : yPheIleLeuGlyGlyValPheValMetGlySerGlyGlyGlnGlyValLeuLeuGluHi : 201 |||||||||||||||||||||||||!!:||||||||| !|||! !..!||||||...|| yPheIleLeuGlyGlyValPheValIleGlySerGlyLysGlnValThrLeuLeuArgHi 25124 : CTTCATCCTGGGTGGAGTGTTTGTCATTGGATCTGGCAAGCAGGTGACATTATTAAgaca : 25183 202 : s : 201 | s 25184 : t : 25185 vulgar: SPP00000652_2.0 11 201 . CM004416.1:subseq(21009595,25185) 22199 25185 + 751 M 51 153 S 0 1 5 0 2 I 0 1916 3 0 2 S 1 2 M 30 90 5 0 2 I 0 84 3 0 2 M 47 141 5 0 2 I 0 404 3 0 2 M 61 183 # --- 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 # CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local gene 22200 25185 751 + . gene_id 1 ; sequence SPP00000652_2.0 ; gene_orientation + CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local cds 22200 22353 . + . CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local exon 22200 22353 . + . insertions 0 ; deletions 0 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local splice5 22354 22355 . + . intron_id 1 ; splice_site "GT" CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local intron 22354 24273 . + . intron_id 1 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local splice3 24272 24273 . + . intron_id 0 ; splice_site "ag" CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local cds 24274 24365 . + . CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local exon 24274 24365 . + . insertions 0 ; deletions 0 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local splice5 24366 24367 . + . intron_id 2 ; splice_site "GT" CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local intron 24366 24453 . + . intron_id 2 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local splice3 24452 24453 . + . intron_id 1 ; splice_site "AG" CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local cds 24454 24594 . + . CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local exon 24454 24594 . + . insertions 0 ; deletions 0 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local splice5 24595 24596 . + . intron_id 3 ; splice_site "GT" CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local intron 24595 25002 . + . intron_id 3 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local splice3 25001 25002 . + . intron_id 2 ; splice_site "AG" CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local cds 25003 25185 . + . CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local exon 25003 25185 . + . insertions 0 ; deletions 0 CM004416.1:subseq(21009595,25185) exonerate:protein2genome:local similarity 22200 25185 751 + . alignment_id 1 ; Query SPP00000652_2.0 ; Align 22200 12 153 ; Align 24276 64 90 ; Align 24454 94 141 ; Align 25003 141 183 # --- END OF GFF DUMP --- # -- completed exonerate analysis