Command line: [exonerate -m p2g --showtargetgff -q SPP00000001_1.0.fa -t SPP00000001_1.0.GL397352.1/GL397352.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000001_1.0 # Protein # Iodothyronine deiodinase 1 (DI1) # Homo sapiens # Complete Target: GL397352.1:subseq(7433105,117055) dna:supercontig supercontig:Nleu1.0:GL397352.1:1:7985188:1 REF:[revcomp] Model: protein2genome:local Raw score: 1239 Query range: 0 -> 249 Target range: 67055 -> 49999 1 : MetGlyLeuProGlnProGlyLeuTrpLeuLysArgLeuTrpValLeuLeuGluValAla : 20 ||||||||||||||| !!|||||||||||||||||||||||||||||||||||||||||| MetGlyLeuProGlnAlaGlyLeuTrpLeuLysArgLeuTrpValLeuLeuGluValAla 67055 : ATGGGGCTGCCCCAGGCAGGGCTGTGGCTGAAGAGGCTCTGGGTGCTCTTGGAGGTGGCT : 66998 21 : ValHisValValValGlyLysValLeuLeuIleLeuPheProAspArgValLysArgAsn : 40 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ValHisValValValGlyLysValLeuLeuIleLeuPheProAspArgValLysArgAsn 66997 : GTGCATGTGGTCGTGGGTAAAGTGCTTCTGATATTGTTTCCAGACAGAGTCAAGCGGAAC : 66938 41 : IleLeuAlaMetGlyGluLysThrGlyMetThrArgAsnProHisPheSerHisAspAsn : 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| IleLeuAlaMetGlyGluLysThrGlyMetThrArgAsnProHisPheSerHisAspAsn 66937 : ATCCTGGCCATGGGCGAGAAGACGGGTATGACCAGGAACCCCCATTTCAGCCACGACAAC : 66878 61 : TrpIleProThrPhePheSerThrGlnTyrPheTrpPheValLeuLysValArgTrpGln : 80 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| TrpIleProThrPhePheSerThrGlnTyrPheTrpPheValLeuLysValArgTrpGln 66877 : TGGATCCCGACCTTTTTCAGCACCCAGTATTTCTGGTTCGTCTTGAAGGTCCGTTGGCAG : 66818 81 : ArgLeuGluAspThrThrGluLeuGlyGlyLeuAlaProAsnCysProValValArgLeu : 100 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ArgLeuGluAspThrThrGluLeuGlyGlyLeuAlaProAsnCysProValValArgLeu 66817 : CGACTAGAGGACACAACTGAGCTAGGGGGTCTGGCCCCAAACTGCCCGGTGGTCCGCCTC : 66758 101 : SerGlyGlnArgCysAsnIleTrpGluPheMetGln{G} >>>> Target Intron : 113 |||||||||! !||||||||||||||||||||||||{!} 11494 bp SerGlyGlnThrCysAsnIleTrpGluPheMetGln{U}++ 66757 : TCAGGACAGACGTGCAACATTTGGGAGTTTATGCAA{G}gt................... : 66716 114 : 1 >>>> {ly}AsnArgProLeuValLeuAsnPheGlySerCysThrUnkProSerPhe : 129 { } !!|||||||||||||||||||||||| ||||||||| --{nk}UnkUnkUnkUnkValLeuAsnPheGlySerCysThr***ProSerPhe 66715 : ......nn{NN}NNNNNNNNNNTGGTGCTGAATTTTGGAAGTTGTACCTGACCTTCATTT : 55177 130 : MetPheLysPheAspGlnPheLysArgLeuIleGluAspPheSerSerIleAlaAspPhe : 149 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MetPheLysPheAspGlnPheLysArgLeuIleGluAspPheSerSerIleAlaAspPhe 55176 : ATGTTCAAATTTGACCAATTCAAGAGGCTTATTGAAGACTTTAGTTCCATAGCAGATTTT : 55117 150 : LeuValIleTyrIleGluGluAlaHisAlaSer{A} >>>> Target Intron 2 > : 161 |||||||||||||||||||||||||||||||||{|} 1287 bp LeuValIleTyrIleGluGluAlaHisAlaSer{A}++ 55116 : CTTGTCATTTACATTGAAGAAGCACATGCATCA{G}gt...................... : 55078 162 : >>> {sp}GlyTrpAlaPheLysAsnAsnMetAspIleArgAsnHisGlnAsnLeuGln : 178 {||}||||||||||||||||||||||||||||||||||||||||||||||||||| ++{sp}GlyTrpAlaPheLysAsnAsnMetAspIleArgAsnHisGlnAsnLeuGln 55077 : ...ag{AT}GGCTGGGCTTTTAAGAACAACATGGACATCAGAAATCACCAGAACCTTCAG : 53743 179 : AspArgLeuGlnAlaAlaHisLeuLeuLeuAlaArgSerProGlnCysProValValVal : 198 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AspArgLeuGlnAlaAlaHisLeuLeuLeuAlaArgSerProGlnCysProValValVal 53742 : GACCGCCTGCAGGCAGCCCACCTACTGCTGGCCAGGAGCCCCCAGTGCCCTGTGGTGGTG : 53683 199 : AspThrMetGlnAsnGlnSerSerGlnLeuTyrAlaAlaLeuProGluArgLeuTyrIle : 218 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||:!! AspThrMetGlnAsnGlnSerSerGlnLeuTyrAlaAlaLeuProGluArgLeuTyrVal 53682 : GACACCATGCAGAACCAGAGCAGCCAGCTCTACGCAGCACTGCCTGAGAGGCTCTACGTA : 53623 219 : IleGlnGluGlyArgIleLeuTyrLys >>>> Target Intron 3 >>>> GlyL : 229 ||||||||||||||||||||||||||| 3528 bp |||| IleGlnGluGlyArgIleLeuTyrLys++ ++GlyL 53622 : ATCCAGGAGGGCAGGATTCTCTACAAGgt.........................agGGTA : 50062 230 : ysSerGlyProTrpAsnTyrAsnProGluGluValArgAlaValLeuGluLysLeuHisS : 249 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ysSerGlyProTrpAsnTyrAsnProGluGluValArgAlaValLeuGluLysLeuHisS 50061 : AATCTGGCCCTTGGAACTACAACCCAGAGGAAGTTCGTGCTGTTCTGGAAAAGCTCCACA : 50002 250 : er : 249 || er 50001 : GT : 50000 vulgar: SPP00000001_1.0 0 249 . GL397352.1:subseq(7433105,117055) 67055 49999 - 1239 M 112 336 S 0 1 5 0 2 I 0 11490 3 0 2 S 1 2 M 47 141 S 0 1 5 0 2 I 0 1283 3 0 2 S 1 2 M 66 198 5 0 2 I 0 3524 3 0 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-27 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local gene 50000 67055 1239 - . gene_id 1 ; sequence SPP00000001_1.0 ; gene_orientation + GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local cds 66719 67055 . - . GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local exon 66719 67055 . - . insertions 0 ; deletions 0 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local splice5 66717 66718 . - . intron_id 1 ; splice_site "GT" GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local intron 55225 66718 . - . intron_id 1 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local splice3 55225 55226 . - . intron_id 0 ; splice_site "NN" GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local cds 55081 55224 . - . GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local exon 55081 55224 . - . insertions 0 ; deletions 0 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local splice5 55079 55080 . - . intron_id 2 ; splice_site "GT" GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local intron 53794 55080 . - . intron_id 2 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local splice3 53794 53795 . - . intron_id 1 ; splice_site "AG" GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local cds 53594 53793 . - . GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local exon 53594 53793 . - . insertions 0 ; deletions 0 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local splice5 53592 53593 . - . intron_id 3 ; splice_site "GT" GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local intron 50066 53593 . - . intron_id 3 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local splice3 50066 50067 . - . intron_id 2 ; splice_site "AG" GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local cds 50000 50065 . - . GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local exon 50000 50065 . - . insertions 0 ; deletions 0 GL397352.1:subseq(7433105,117055) exonerate:protein2genome:local similarity 50000 67055 1239 - . alignment_id 1 ; Query SPP00000001_1.0 ; Align 67056 1 336 ; Align 55223 114 141 ; Align 53792 162 198 ; Align 50066 228 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis