Command line: [exonerate -m p2g --showtargetgff -q TXNRD1.fa -t genomic.fa] Hostname: [ws101125u] C4 Alignment: ------------ Query: SPP00000129_2.0 # Protein # Thioredoxin reductase 1 (TXNRD1) # Human Target: CM004424.1:subseq(16780000,150000) Ictalurus punctatus breed USDA103 chromosome 11, whole genome shotgun sequence Model: protein2genome:local Raw score: 1931 Query range: 159 -> 649 Target range: 3735 -> 10814 160 : SerTyrAspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLys : 179 :!!||||||||||||||||||:!:|||||||||||||||||||||||||||..!:!!||| AlaTyrAspTyrAspLeuIleValIleGlyGlyGlySerGlyGlyLeuAlaCysSerLys 3736 : GCGTATGACTATGACCTCATTGTGATAGGGGGTGGCTCTGGAGGTCTGGCTTGCTCAAAG : 3793 180 : >>>> Target Intron 1 >>>> GluAlaAlaGlnTyrGlyLysLysValMetV : 190 603 bp ||||||||| ! ||||||!:!||||||| ++ ++GluAlaAlaAlaLeuGlyLysArgValMetV 3794 : gt.........................agGAAGCAGCTGCCTTGGGGAAGAGGGTCATGG : 4429 191 : alLeuAspPheValThrProThrProLeuGlyThrArgTrp{G} >>>> Target In : 204 ||||||||!:!|||..!||||||||||||||||||! !|||{|} 103 alLeuAspTyrValValProThrProLeuGlyThrThrTrp{G}++ 4430 : TTTTAGATTATGTTGTTCCCACACCTTTGGGCACAACTTGG{G}gt.............. : 4474 205 : tron 2 >>>> {ly}LeuGlyGlyThrCysValAsnValGlyCysIleProLysLysL : 219 bp {||}||||||||||||||||||||||||||||||||||||||||||| ++{ly}LeuGlyGlyThrCysValAsnValGlyCysIleProLysLysL 4475 : ...........ag{GT}CTGGGTGGCACATGTGTGAACGTGGGTTGTATTCCTAAGAAGC : 4619 220 : euMetHisGlnAlaAlaLeuLeuGlyGlnAlaLeuGlnAspSerArgAsnTyrGlyTrpL : 239 |||||||||||.!!||||||||| ! ||||||:!!|||:!!|||!!.!:!||||||: euMetHisGlnThrAlaLeuLeuHisThrAlaLeuGluAspAlaArgLysPheGlyTrpG 4620 : TGATGCATCAGACTGCCCTGCTGCACACTGCTCTGGAGGATGCCCGAAAATTTGGTTGGG : 4679 240 : ysValGluGluThr{V} >>>> Target Intron 3 >>>> {al}LysHisAspT : 248 !! !!...|||.!!{|} 506 bp {||}!..|||:!!| luPheSerGluAla{V}++ ++{al}SerHisAsnT 4680 : AGTTCAGTGAGGCA{G}gt.........................ag{TA}AGTCATAACT : 5212 249 : rpAspArgMetIleGluAlaValGlnAsnHisIleGlySerLeuAsnTrpGlyTyrArgV : 268 ||!!:! !|||! ||||||.!.|||:!!|||||||||||||||||||||||||||| rpGluThrMetLysThrAlaValAsnAsnTyrIleGlySerLeuAsnTrpGlyTyrArgV 5213 : GGGAAACAATGAAGACTGCCGTGAATAACTACATCGGCTCTTTGAACTGGGGCTACAGAG : 5272 269 : alAlaLeuArgGluLysLysValValTyrGluAsnAlaTyrGlyGlnPheIleGlyProH : 288 ||:!!||||||!!:|||!..|||! !||| !|||||||||!.!:!!|||:!:! !|||| alSerLeuArgAspLysSerValGluTyrThrAsnAlaTyrAlaGluPheValGluProH 5273 : TGTCTTTACGTGACAAGAGCGTTGAATATACGAATGCTTATGCAGAGTTTGTGGAGccac : 5332 289 : isArgIleLys >>>> Target Intron 4 >>>> AlaThrAsnAsnLysGlyLy : 298 ||:::|||||| 215 bp |||||||||!!.::!||||| isLysIleLys++ ++AlaThrAsnLysArgGlyLy 5333 : acaaaatcaaggt.........................agGCGACAAACAAGCGAGGCAA : 5577 299 : sGluLysIleTyrSerAlaGluArgPheLeuIleAlaThrGlyGluArgProArgTyrLe : 318 ||||! !.!!|||!!!|||! !:!|||:!!:!:|||||||||||||||||||||||||| sGluThrPheTyrThrAlaAlaLysPheValLeuAlaThrGlyGluArgProArgTyrLe 5578 : AGAGACGTTCTACACTGCAGCCAAGTTTGTGCTGGCAACAGGAGAGCGGCCGCGCTACCT : 5637 319 : uGlyIleProGlyAspLysGluTyrCysIleSer{Se} >>>> Target Intron 5 : 330 |||||||||||||||||||||||||||||||!!!{||} 1529 bp uGlyIleProGlyAspLysGluTyrCysIleThr{Se}++ 5638 : GGGCATCCCTGGAGACAAAGAATACTGCATCACC{AG}gt.................... : 5677 331 : >>>> {r}AspAspLeuPheSerLeuProTyrCysProGlyLysThrLeuValValGl : 347 {|}||||||||||||! !||| !!||||||||||||||||||||||||:!!|| ++{r}AspAspLeuPheTyrLeuSerTyrCysProGlyLysThrLeuValIleGl 5678 : .....ag{T}GATGATCTGTTCTACTTGTCCTACTGTCCTGGTAAAACGCTGGTGATCGG : 7253 348 : yAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyIleGlyLeuAspValTh : 367 |||||||||||||||||||||||||!.!|||||||||||||||:!:|||||||||||||| yAlaSerTyrValAlaLeuGluCysGlyGlyPheLeuAlaGlyLeuGlyLeuAspValTh 7254 : AGCATCGTACGTGGCTCTGGAGTGCGGTGGATTCCTGGCAGGTCTGGGACTTGATGTCAC : 7313 368 : rValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaAsnLysIleGl : 387 |:!!||||||||||||||||||||||||||||||||||||||||||||||||::: !|| rIleMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaAsnArgAlaGl 7314 : CATAATGGTGCGCTCCATTCTGCTGAGAGGCTTTGACCAGGACATGGCCAACCGTGCAGG : 7373 388 : yGluHisMetGluGluHisGlyIleLysPheIleArgGlnPheValProIleLys >>> : 406 |!!:||||||||| !||||||:!!||||||:!!||||||||||||||||||||| yAspHisMetGluThrHisGlyValLysPheLeuArgGlnPheValProIleLys++ 7374 : GGACCATATGGAGACACACGGGGTCAAATTTCTCAGGCAGTTTGTCCCGATTAaggt... : 7432 407 : > Target Intron 6 >>>> ValGluGlnIleGluAlaGlyThrProGlyArgLeu : 417 173 bp |||||||||:!!|||||||||||||||||||||||| ++ValGluGlnLeuGluAlaGlyThrProGlyArgLeu 7433 : ......................aggtagAGCAGCTTGAGGCTGGTACTCCAGGCAGATTG : 7636 418 : ArgValValAlaGlnSerThrAsnSerGluGluIleIleGluGlyGluTyrAsnThr > : 437 !:!|||..!|||:!!||||||.!.!!!!!:|||:!!.!!|||||||||||||||||| LysValThrAlaLysSerThrGluThrAspGluLeuPheGluGlyGluTyrAsnThr++ 7637 : AAAGTGACTGCCAAGTCTACAGAAACTGATGAGCTCTTTGAAGGAGAGTACAACACTgt. : 7698 438 : >>> Target Intron 7 >>>> ValMetLeuAlaIleGlyArgAspAlaCysThrA : 448 89 bp |||:!!:!!|||:!:|||||||||||||||||| ++ValLeuIleAlaValGlyArgAspAlaCysThrG 7699 : ........................agGTACTGATAGCTGTGGGTCGTGATGCTTGTACAG : 7818 449 : rgLysIleGlyLeuGluThrValGlyValLysIleAsnGlu{Ly} >>>> Target I : 462 !!...|||||||||!!:! !!.!|||||||||:!!|||..!{||} 1082 lySerIleGlyLeuAspLysAlaGlyValLysValAsnSer{Ly}++ 7819 : GATCTATAGGTCTAGACAAGGCTGGGGTGAAGGTCAACTCA{AA}gt............. : 7864 463 : ntron 8 >>>> {s}ThrGlyLysIleProValThrAspGluGluGlnThrAsnValP : 477 bp {|}!.!||||||:!!||||||!.!|||||||||||||||||||||| ++{s}AsnGlyLysValProValAsnAspGluGluGlnThrAsnValP 7865 : ............ag{G}AATGGGAAGGTCCCAGTGAATGACGAAGAGCAGACCAACGTTC : 8987 478 : roTyrIleTyrAlaIleGlyAspIleLeuGluAspLysValGluLeuThrProValAlaI : 497 ||:!!|||||||||||||||||||||||||||! !||| !||||||||||||||||||| roHisIleTyrAlaIleGlyAspIleLeuGluGlyLysTrpGluLeuThrProValAlaI 8988 : CACACATCTACGCTATCGGGGACATCCTGGAGGGCAAGTGGGAGCTGACTCCTGTGGCCA : 9047 498 : leGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyrAlaGlySerThrValLys >>>> : 515 |||||||||||!:!|||||||||!::||||||!:!|||||||||:!!|||||| leGlnAlaGlyLysLeuLeuAlaArgArgLeuPheAlaGlySerSerValLys++ 9048 : TTCAGGCTGGAAAACTGCTGGCTCGTAGACTGTTTGCAGGTTCCTCTGTGAAGgt..... : 9103 516 : Target Intron 9 >>>> CysAspTyrGluAsnValProThrThrValPheThrPr : 527 560 bp |||||||||! !|||||||||||||||||||||||||| ++CysAspTyrValAsnValProThrThrValPheThrPr 9104 : ....................agtGTGACTATGTGAATGTTCCTACTACTGTGTTCACACC : 9697 528 : oLeuGluTyrGlyAlaCysGlyLeuSerGluGluLysAlaValGluLysPheGlyGluGl : 547 |||||||||||||::!||||||||||||||||||||||||:!!||| ! !|||||||| oLeuGluTyrGlySerCysGlyLeuSerGluGluLysAlaIleGluTyrHisGlyGluGl 9698 : TCTGGAGTATGGCAGTTGTGGTCTTTCTGAAGAAAAGGCCATAGAGTATCATGGAGAGGA : 9757 548 : uAsnIleGlu >>>> Target Intron 10 >>>> ValTyrHisSerTyrPheTr : 557 ||||:!:||| 79 bp :!!!:!|||||| ||||| uAsnLeuGlu++ ++IlePheHisSerLeuPheTr 9758 : AAACCTGGAGgt..........................agATTTTTCACAGTCTGTTTTG : 9866 558 : pProLeuGluTrpThrIleProSerArgAspAsnAsnLysCysTyrAlaLysIleIleCy : 577 ||||||||||!::|||||||||.!!||||||||||||!:!|||||||||||||||||||| pProLeuGluPheThrIleProGlyArgAspAsnAsnArgCysTyrAlaLysIleIleCy 9867 : GCCTCTGGAGTTCACCATACCTGGCAGGGACAACAACAGGTGCTACGCCAAGATCATTTG : 9926 578 : sAsnThrLysAspAsn >>>> Target Intron 11 >>>> GluArgValValGl : 587 ||||! ! !|||!:! 551 bp :!:||||||:!!|| sAsnLysLeuAspSer++ ++AspArgValIleGl 9927 : CAACAAGTTGGACAGTgt..........................aggACCGTGTCATTGG : 10507 588 : yPheHisValLeuGlyProAsnAlaGlyGluValThrGlnGlyPheAlaAlaAlaLeuLy : 607 ||||||| !||||||||||||||||||||||||||||||||||||!.!||||||:!!|| yPheHisTyrLeuGlyProAsnAlaGlyGluValThrGlnGlyPheGlyAlaAlaMetLy 10508 : TTTTCACTACCTGGGCCCTAACGCTGGTGAGGTGACTCAGGGCTTTGGTGCTGCCATGAA : 10567 608 : sCysGlyLeuThrLysLysGlnLeuAspSerThrIleGlyIleHisProValCysAlaGl : 627 |||||||:!!||||||:!!|||||||||!:!||||||||||||||||||..!|||||||| sCysGlyValThrLysGluGlnLeuAspAsnThrIleGlyIleHisProThrCysAlaGl 10568 : GTGTGGGGTCACAAAGGAGCAGTTAGACAACACCATTGGAATACACCCTACCTGTGCtga : 10627 628 : u >>>> Target Intron 12 >>>> ValPheThrThrLeuSerValThrLysAr : 637 | 119 bp :!!|||||||||:!!..!||||||||||| u++ ++IlePheThrThrMetGluValThrLysAr 10628 : ggt..........................agATATTCACCACAATGGAAGTGACTAAGAG : 10776 638 : gSerGlyAlaSerIleLeuGlnAlaGlyCysUnkGly : 649 |||||||!.!..!||| !|||:!!|||||| ||| gSerGlyGlyAspIleLysGlnSerGlyCys***Gly 10777 : GTCAGGTGGCGACATCAAACAGTCTGGCTGCTGAGGT : 10814 vulgar: SPP00000129_2.0 159 649 . CM004424.1:subseq(16780000,150000) 3735 10814 + 1931 M 20 60 5 0 2 I 0 599 3 0 2 M 24 72 S 0 1 5 0 2 I 0 99 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 502 3 0 2 S 1 2 M 47 141 5 0 2 I 0 211 3 0 2 M 38 114 S 0 2 5 0 2 I 0 1525 3 0 2 S 1 1 M 75 225 5 0 2 I 0 169 3 0 2 M 31 93 5 0 2 I 0 85 3 0 2 M 25 75 S 0 2 5 0 2 I 0 1078 3 0 2 S 1 1 M 52 156 5 0 2 I 0 556 3 0 2 M 36 108 5 0 2 I 0 75 3 0 2 M 32 96 5 0 2 I 0 547 3 0 2 M 45 135 5 0 2 I 0 115 3 0 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-12-05 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local gene 3736 10814 1931 + . gene_id 1 ; sequence SPP00000129_2.0 ; gene_orientation + CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 3736 3795 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 3736 3795 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 3796 3797 . + . intron_id 1 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 3796 4398 . + . intron_id 1 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 4397 4398 . + . intron_id 0 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 4399 4471 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 4399 4471 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 4472 4473 . + . intron_id 2 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 4472 4574 . + . intron_id 2 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 4573 4574 . + . intron_id 1 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 4575 4694 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 4575 4694 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 4695 4696 . + . intron_id 3 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 4695 5200 . + . intron_id 3 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 5199 5200 . + . intron_id 2 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 5201 5343 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 5201 5343 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 5344 5345 . + . intron_id 4 ; splice_site "gt" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 5344 5558 . + . intron_id 4 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 5557 5558 . + . intron_id 3 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 5559 5674 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 5559 5674 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 5675 5676 . + . intron_id 5 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 5675 7203 . + . intron_id 5 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 7202 7203 . + . intron_id 4 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 7204 7429 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 7204 7429 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 7430 7431 . + . intron_id 6 ; splice_site "gt" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 7430 7602 . + . intron_id 6 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 7601 7602 . + . intron_id 5 ; splice_site "ag" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 7603 7695 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 7603 7695 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 7696 7697 . + . intron_id 7 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 7696 7784 . + . intron_id 7 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 7783 7784 . + . intron_id 6 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 7785 7861 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 7785 7861 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 7862 7863 . + . intron_id 8 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 7862 8943 . + . intron_id 8 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 8942 8943 . + . intron_id 7 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 8944 9100 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 8944 9100 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 9101 9102 . + . intron_id 9 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 9101 9660 . + . intron_id 9 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 9659 9660 . + . intron_id 8 ; splice_site "ag" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 9661 9768 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 9661 9768 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 9769 9770 . + . intron_id 10 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 9769 9847 . + . intron_id 10 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 9846 9847 . + . intron_id 9 ; splice_site "AG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 9848 9943 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 9848 9943 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 9944 9945 . + . intron_id 11 ; splice_site "GT" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 9944 10494 . + . intron_id 11 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 10493 10494 . + . intron_id 10 ; splice_site "ag" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 10495 10629 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 10495 10629 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice5 10630 10631 . + . intron_id 12 ; splice_site "gt" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local intron 10630 10748 . + . intron_id 12 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local splice3 10747 10748 . + . intron_id 11 ; splice_site "aG" CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local cds 10749 10814 . + . CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local exon 10749 10814 . + . insertions 0 ; deletions 0 CM004424.1:subseq(16780000,150000) exonerate:protein2genome:local similarity 3736 10814 1931 + . alignment_id 1 ; Query SPP00000129_2.0 ; Align 3736 160 60 ; Align 4399 180 72 ; Align 4577 205 117 ; Align 5203 245 141 ; Align 5559 292 114 ; Align 7205 331 225 ; Align 7603 406 93 ; Align 7785 437 75 ; Align 8945 463 156 ; Align 9661 515 108 ; Align 9848 551 96 ; Align 10495 583 135 ; Align 10749 628 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis