Command line: [exonerate -m p2g --showtargetgff -q SPP00000036_1.0.fa -t SPP00000036_1.0.GL397492.1/GL397492.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000036_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Homo sapiens # Complete Target: GL397492.1:subseq(826651,61961) dna:supercontig supercontig:Nleu1.0:GL397492.1:1:1399117:1 REF:[revcomp] Model: protein2genome:local Raw score: 549 Query range: 542 -> 754 Target range: 15232 -> 8900 543 : LeuLeuAlaIleGlyArgAspSerCysThrArgLysIleGlyLeuGluLysIleGlyVal : 562 |||!!! !! !||||||! ! !! !||||||!..:!:..!||||||||| !|||||| LeuPheProSerGlyArgValProAspThrArgSerLeuAsnLeuGluLysAlaGlyVal 15232 : CTGTTTCCTTCAGGTCGAGTCCCAGACACCAGAAGTCTGAATTTGGAGAAGGCTGGGGTA : 15175 563 : LysIleAsnGluLysSerGlyLysIleProValAsnAspValGluGlnThrAsnValPro : 582 ! ! !!:! ! !!! !||||||! !|||:!!..! !||| |||::!|||||| AspThrSerProAspThrGlnLysIleLeuValAspSerArgGluAlaThrSerValPro 15174 : GATACTAGCCCCGACACTCAGAAGATCCTGGTGGACTCCCGGGAAGCCACCTCTGTGCCC : 15115 583 : TyrValTyrAlaValGlyAspIleLeuGlu >>>> Target Intron 1 >>>> A : 593 :!!:!!||||||:!!||||||:!::!!||| 2580 bp ! HisIleTyrAlaIleGlyAspValValGlu++ ++G 15114 : CACATCTATGCCATTGGTGACGTGGTGGAGgt.........................agG : 12502 594 : spLysProGluLeuThrProValAlaIleGlnSerGlyLysLeuLeuAlaGlnArgLeuP : 613 ::!|||||||||||||||..!||||||..!:!!|||!:!||||||!.!|||||||||| lyArgProGluLeuThrProThrAlaIleMetAlaGlyArgLeuLeuValGlnArgLeuP 12501 : GGCGGCCTGAGCTGACACCCACAGCGATCATGGCCGGGAGGCTCCTGGTGCAGCGGCTTT : 12442 614 : heGlyAlaSerLeuGluLysCysAspTyrIleAsn >>>> Target Intron 2 >> : 625 ||||| !|||! !!!: ! |||||| !||| 350 bp heGlyArgSerSerAspLeuMetAspTyrAspAsn++ 12441 : TCGGCAGGTCCTCAGATCTGATGGACTACGACAATgt....................... : 12404 626 : >> ValProThrThrValPheThrProLeuGluTyrGlyCysCysGlyLeuSerGluGl : 643 ||||||||||||||||||||||||||||||||||||||| |||||||||||||| ++ValProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSerGluGl 12403 : ..agGTTCCCACGACTGTCTTCACCCCGCTGGAGTATGGCTGTGTGGGGCTGTCCGAGGA : 12002 644 : uLysAlaIleGluValTyrLysLysGluAsnLeuGlu >>>> Target Intron 3 : 656 |:!!|||:!:! !:!! !:!!|||:!!:!!||| 1742 bp uGluAlaValAlaArgHisGlyGlnGluHisValGlu++ 12001 : GGAGGCAGTGGCTCGCCACGGGCAGGAGCATGTTGAGgt..................... : 11961 657 : >>>> IleTyrHisThrLeuPheTrpProLeuGluTrpThrValAlaGlyArgGluAsn : 673 :!!||||||.!!! !!:! |||||||||!::|||||||||||||||!!: ++ValTyrHisAlaHisTyrLysProLeuGluPheThrValAlaGlyArgAspAla 11960 : ....agGTCTATCACGCCCATTATAAACCACTGGAGTTCACGGTGGCTGGACGGGATGCA : 10170 674 : AsnThrCysTyrAlaLys >>>> Target Intron 4 >>>> IleIleCysAsnL : 684 ::! !||||||!.!||| 178 bp !!::!:||| ! SerGlnCysTyrValLys++ ++MetValCysLeuA 10169 : TCCCAGTGTTATGTAAAGgt.........................agATGGTGTGCCTGA : 9959 685 : ysPheAspHisAspArgValIleGlyPheHisIleLeuGlyProAsnAlaGlyGluValT : 704 :! !! .!.! !|||:!:|||.!.|||.!!||||||||||||||||||||||||| rgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGlyGluValT 9958 : GGGAGCCCCCGCAGCTGGTGCTGGGCCTGCACTTCCTTGGCCCCAACGCAGGCGAAGTTA : 9899 705 : hrGlnGlyPheAlaAlaAlaMet{Ly} >>>> Target Intron 5 >>>> {s}C : 713 |||||||||||||| !!.!!!:{||} 846 bp {|}| hrGlnGlyPheAlaLeuGlyIle{Ly}++ ++{s}C 9898 : CTCAGGGATTTGCTCTGGGGATC{AA}gt.........................ag{G}T : 9026 714 : ysGlyLeuThrLysGlnLeuLeuAspAspThrIleGlyIleHisProThrCysGlyGluV : 733 ||||| !:!! ! !! !:!! |||:!:||||||||||||||||||..!|||! ysGlyAlaSerTyrValGlnValMetArgThrValGlyIleHisProThrCysSerGluG 9025 : GTGGGGCCTCCTATGTGCAGGTGATGCGGACCGTGGGTATCCATCCCACATGCTCTGAGG : 8966 734 : alPheThrThrLeuGluIleThrLysSerSerGlyLeuAspIleThrGlnLysGlyCysU : 753 ! ! ..!! !|||...:!!:!!||| !!|||||||||||| !||| !! !|||||| luValValLysLeuArgValSerLysArgSerGlyLeuAspProThrValThrGlyCys* 8965 : AGGTAGTCAAGCTGCGCGTCTCCAAGCGCTCAGGCCTGGACCCCACGGTGACAGGCTGCT : 8906 754 : nkGly : 754 ||| **Gly 8905 : GAGGG : 8901 vulgar: SPP00000036_1.0 542 754 . GL397492.1:subseq(826651,61961) 15232 8900 - 549 M 50 150 5 0 2 I 0 2576 3 0 2 M 32 96 5 0 2 I 0 346 3 0 2 M 31 93 5 0 2 I 0 1738 3 0 2 M 24 72 5 0 2 I 0 174 3 0 2 M 32 96 S 0 2 5 0 2 I 0 842 3 0 2 S 1 1 M 42 126 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-12-04 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397492.1:subseq(826651,61961) exonerate:protein2genome:local gene 8901 15232 549 - . gene_id 1 ; sequence SPP00000036_1.0 ; gene_orientation + GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 15083 15232 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 15083 15232 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 15081 15082 . - . intron_id 1 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 12503 15082 . - . intron_id 1 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 12503 12504 . - . intron_id 0 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 12407 12502 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 12407 12502 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 12405 12406 . - . intron_id 2 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 12057 12406 . - . intron_id 2 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 12057 12058 . - . intron_id 1 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 11964 12056 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 11964 12056 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 11962 11963 . - . intron_id 3 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 10222 11963 . - . intron_id 3 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 10222 10223 . - . intron_id 2 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 10150 10221 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 10150 10221 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 10148 10149 . - . intron_id 4 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 9972 10149 . - . intron_id 4 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 9972 9973 . - . intron_id 3 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 9874 9971 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 9874 9971 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 9872 9873 . - . intron_id 5 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 9028 9873 . - . intron_id 5 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 9028 9029 . - . intron_id 4 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 8901 9027 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 8901 9027 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local similarity 8901 15232 549 - . alignment_id 1 ; Query SPP00000036_1.0 ; Align 15233 543 150 ; Align 12503 593 96 ; Align 12057 625 93 ; Align 10222 656 72 ; Align 9972 680 96 ; Align 9027 713 126 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000036_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Homo sapiens # Complete Target: GL397492.1:subseq(826651,61961) dna:supercontig supercontig:Nleu1.0:GL397492.1:1:1399117:1 REF:[revcomp] Model: protein2genome:local Raw score: 278 Query range: 304 -> 378 Target range: 50000 -> 49138 305 : GlyThrSerTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeu : 324 |||||| !!||||||||||||||||||||||||||||||||||||||||||||||||||| GlyThrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeu 50000 : GGCACTCGGTGGGGCCTCGGCGGCACCTGTGTCAATGTGGGCTGCATCCCCAAGAAGCTG : 49943 325 : MetHisGlnAlaAlaLeuLeuGlyGlnAlaLeuCysAspSerArgLysPheGlyTrpGlu : 344 |||||||||||||||||||||||| !:!! |||:!!! ! ! !:!||||||||| MetHisGlnAlaAlaLeuLeuGlyGlyLeuIleGlnAspAlaProHisTyrGlyTrpGlu 49942 : ATGCACCAGGCGGCACTGCTGGGAGGCCTGATCCAAGATGCCCCTCACTATGGCTGGGAG : 49883 345 : TyrAsnGlnGlnValArgHisAsn{Tr} >>>> Target Intron 1 >>>> {p} : 353 !|||! |||! !|||:!!{||} 640 bp {|} ValAlaGlnProValProHisAsp{Tr}++ ++{p} 49882 : GTGGCCCAGCCTGTGCCACATGAC{TG}gt.........................ag{G} : 49214 354 : GluThrMetThrLysAlaIleGlnAsnHisIleSerSerLeuAsnTrpGlyTyrArgLeu : 373 ..!! !|||.!!:!!|||:!!|||||||||:!:!.!|||||||||||||||:!!|||:!! ArgLysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnTrpGlyHisArgVal 49213 : AGGAAGATGGCAGAAGCTGTTCAAAACCACGTGAAATCCCTGAACTGGGGCCACCGTGTC : 49156 374 : SerLeuArgGluLys : 378 ..!|||!:!!!:!:! GlnLeuGlnAspArg 49155 : CAGCTTCAGGACAGG : 49139 vulgar: SPP00000036_1.0 304 378 . GL397492.1:subseq(826651,61961) 50000 49138 - 278 M 48 144 S 0 2 5 0 2 I 0 636 3 0 2 S 1 1 M 25 75 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-12-04 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397492.1:subseq(826651,61961) exonerate:protein2genome:local gene 49139 50000 278 - . gene_id 2 ; sequence SPP00000036_1.0 ; gene_orientation + GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 49855 50000 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 49855 50000 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 49853 49854 . - . intron_id 1 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 49215 49854 . - . intron_id 1 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 49215 49216 . - . intron_id 0 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 49139 49214 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 49139 49214 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local similarity 49139 50000 278 - . alignment_id 2 ; Query SPP00000036_1.0 ; Align 50001 305 144 ; Align 49214 354 75 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000036_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Homo sapiens # Complete Target: GL397492.1:subseq(826651,61961) dna:supercontig supercontig:Nleu1.0:GL397492.1:1:1399117:1 REF:[revcomp] Model: protein2genome:local Raw score: 198 Query range: 424 -> 489 Target range: 42398 -> 30232 425 : IleGlnGlyAspLysGluTyrCysIleThrSerAspAspLeuPheSerLeuProTyrCys : 444 |||:!!|||! ! !|||||| ! |||||||||||||||:!!|||!!!||| ! ! ! ! IleGluGlyAlaLeuGluTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSer 42398 : ATCGAAGGTGCCTTGGAATATGGAATCACAAGTGATGACATCTTCTGGCTGAAGGAATCC : 42341 445 : ProGlyLys{Th} >>>> Target Intron 1 >>>> {r}LeuValValGlyAla : 453 |||||||||{||} 11176 bp {|}||||||||||||||| ProGlyLys{Th}++ ++{r}LeuValValGlyAla 42340 : CCTGGAAAA{AC}gt.........................ag{G}TTGGTGGTCGGGGCC : 31138 454 : Ser{T} >>>> Target Intron 2 >>>> {yr}ValAlaLeuGluCysAlaGly : 462 |||{|} 795 bp {||}||||||||||||||||||||| Ser{T}++ ++{yr}ValAlaLeuGluCysAlaGly 31137 : AGC{T}gt.........................ag{AT}GTGGCCCTGGAGTGTGCTGGC : 30316 463 : PheLeuAlaGlyPheGlyLeuAspValThrValMetValArgSerIleLeuLeuArgGly : 482 ||||||.!!|||.!!|||||||||..!|||:!!|||:!!|||||||||! !||||||||| PheLeuThrGlyIleGlyLeuAspThrThrIleMetMetArgSerIleProLeuArgGly 30315 : TTCCTCACTGGGATTGGGCTGGACACCACCATCATGATGCGCAGCATCCCCCTCCGCGGC : 30256 483 : PheAspGlnGluMetAlaGlu : 489 |||||||||! ! ! !||| PheAspGlnValAlaLeuGlu 30255 : TTCGACCAGGTAGCGCTGGAG : 30233 vulgar: SPP00000036_1.0 424 489 . GL397492.1:subseq(826651,61961) 42398 30232 - 198 M 23 69 S 0 2 5 0 2 I 0 11172 3 0 2 S 1 1 M 6 18 S 0 1 5 0 2 I 0 791 3 0 2 S 1 2 M 34 102 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-12-04 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397492.1:subseq(826651,61961) exonerate:protein2genome:local gene 30233 42398 198 - . gene_id 3 ; sequence SPP00000036_1.0 ; gene_orientation + GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 42328 42398 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 42328 42398 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 42326 42327 . - . intron_id 1 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 31152 42327 . - . intron_id 1 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 31152 31153 . - . intron_id 0 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 31132 31151 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 31132 31151 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice5 31130 31131 . - . intron_id 2 ; splice_site "GT" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local intron 30337 31131 . - . intron_id 2 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local splice3 30337 30338 . - . intron_id 1 ; splice_site "AG" GL397492.1:subseq(826651,61961) exonerate:protein2genome:local cds 30233 30336 . - . GL397492.1:subseq(826651,61961) exonerate:protein2genome:local exon 30233 30336 . - . insertions 0 ; deletions 0 GL397492.1:subseq(826651,61961) exonerate:protein2genome:local similarity 30233 42398 198 - . alignment_id 3 ; Query SPP00000036_1.0 ; Align 42399 425 69 ; Align 31151 449 18 ; Align 30335 456 102 # --- END OF GFF DUMP --- # -- completed exonerate analysis