Command line: [exonerate -m p2g --showtargetgff -q TXNRD2.fa -t genomic.fa] Hostname: [ws101074u] C4 Alignment: ------------ Query: SPP00000137_2.0 # Protein # Thioredoxin reductase 2 (TXNRD2) # Human Target: CM004435.1:subseq(2200000,150000) Ictalurus punctatus breed USDA103 chromosome 22, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1537 Query range: 4 -> 494 Target range: 61180 -> 44359 5 : AlaGlyGlnArgAspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCys : 24 .!!|||..! !||||||||||||:!!|||:!!||||||||||||||||||||||||||| ThrGlySerPheAspTyrAspLeuValValIleGlyGlyGlySerGlyGlyLeuAlaCys 61180 : ACAGGATCGTTTGATTATGACCTGGTGGTTATCGGTGGTGGATCTGGAGGTTTGGCGTGT : 61123 25 : AlaLysGlu{A} >>>> Target Intron 1 >>>> {la}AlaGlnLeuGlyArg : 33 :!!||||||{|} 276 bp {||}||||||||||||!:! SerLysGlu{A}++ ++{la}AlaGlnLeuGlyGln 61122 : TCCAAAGAA{G}gt.........................ag{CG}GCTCAGTTGGGGCAG : 60820 34 : LysValAlaValValAspTyrValGluProSerProGln{G} >>>> Target Intr : 47 !!.|||||||||:!!|||||||||||||||||| !::!{|} 133 bp AsnValAlaValLeuAspTyrValGluProSerValArg{G}++ 60819 : AACGTGGCTGTTCTGGATTATGTCGAACCTTCAGTGAGG{G}gt................ : 60775 48 : on 2 >>>> {ly}ThrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIle : 62 {||}|||!:!||||||:!!|||||||||||||||||||||||||||||| ++{ly}ThrLysTrpGlyIleGlyGlyThrCysValAsnValGlyCysIle 60774 : .........ag{gt}acTAAATGGGGTATCGGCGGAACGTGCGTAAATGTCGGCTGCATT : 60600 63 : ProLysLysLeuMetHisGlnAlaAlaLeuLeuGly<->GlyLeuIleGlnAspAlaPro : 81 |||||||||||||||||||||||||||! !|||||| !.!|||! !.!.|||:!! ! ProLysLysLeuMetHisGlnAlaAlaGlnLeuGlyThrAlaLeuLysAsnAspSerLys 60599 : CCTAAGAAGCTCATGCACCAGGCCGCTCAGCTCGGCACGGCGCTCAAAAACGACTCGAAG : 60540 82 : AsnTyrGlyTrpGluValAlaGlnProValProHisAsp{Tr} >>>> Target Int : 95 !!.|||||||||..!:!!||| |||||| !!||||||{||} 1710 b LysTyrGlyTrpArgIleAlaGlyProValSerHisAsp{Tr}++ 60539 : AAATACGGCTGGCGGATCGCCGGTCCTGTGTCTCACGAC{TG}gt............... : 60494 96 : ron 3 >>>> {p}ArgLysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsn : 110 p {|} !! ||||||! !:!!|||||||||:!!||||||||||||||| ++{p}AlaThrMetAlaGlySerValGlnAsnTyrValLysSerLeuAsn 60493 : ..........ag{g}gcGACCATGGCAGGATCTGTGCAGAATTATGTGAAATCTCTGAAT : 58743 111 : TrpGlyHisArgValGlnLeuGlnAspArgLysValLysTyrPheAsnIleLysAlaSer : 130 |||||||||||||||||||||||||||!:! !|||:!!:!! !..:!!||| ! ! TrpGlyHisArgValGlnLeuGlnAspLys***ValGlnHis---ThrValLysIleLeu 58742 : TGGGGTCACCGAGTTCAGCTGCAGGACAAGTGAGTGCAACAC---ACAGTTAAAATACTT : 58686 131 : PheValAspGluHisThrValCysGlyValAlaLysGlyGlyLysGlu >>>> Targe : 147 ! ! ... ::: |||::: ..!|||:::! ProHisArgAsnSerGlyIleArgGlyIleAsnProSerGlyArgAla++ 58685 : CCCCACAGGAacagtggtataagaggaataaacccgTCAGGACGCGCTgt.......... : 58633 148 : t Intron 4 >>>> IleLeuLeuSerAlaAspHisIleIleIleAlaThrGlyGlyA : 161 473 bp !:!!!!!||| :!!|||:!:|||||||||||||||| ++AlaThrValThrAlaArgAsnIleValIleAlaThrGlyGlyA 58632 : ...............agGCGACTGTGACGGCCAGGAACATAGTGATCGCGACCGGCGGGC : 58120 162 : rgProArgTyrProThrHis >>>> Target Intron 5 >>>> IleGluGlyAl : 171 |||||!:!|||||||||||| 222 bp :!! !||||| rgProLysTyrProThrHis++ ++ValProGlyAl 58119 : GTCCAAAATACCCCACGCATgt.........................agGTCCCGGGAGC : 57868 172 : aLeuGluTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSerProGlyLysTh : 191 | !||||||||||||||||||||||||:!!||||||||||||||||||||||||||||| aArgGluTyrGlyIleThrSerAspAspLeuPheTrpLeuLysGluSerProGlyLysTh 57867 : GAGAGAGTACGGCATCACCAGCGACGATCTCTTCTGGCTGAAAGAGTCTCCGGGAAAAAC : 57808 192 : rLeu >>>> Target Intron 6 >>>> ValValGlyAlaSerTyrValAlaLeu : 201 |! ! 5131 bp ! !|||..!..! !!||||||||| r***++ -+SerProGlyCysGluAspValAlaLeu 57807 : GTGAgt.........................tgAGCCCGGGGTGCGAAGACGTGGCTTTG : 52647 202 : GluCysAlaGlyPheLeuThrGlyIleGlyLeuAspThrThrIleMetMetArgSerIle : 221 ||||||||||||||||||||||||:!!|||||||||.!!|||:!:|||:!!||||||||| GluCysAlaGlyPheLeuThrGlyValGlyLeuAspAlaThrValMetValArgSerIle 52646 : GAGTGCGCTGGTTTTCTGACCGGCGTCGGACTGGACGCCACCGTGATGGTGCGTAGCATC : 52587 222 : ProLeuArgGlyPheAspGln >>>> Target Intron 7 >>>> GlnMetSerS : 232 !!|||||||||||||||||| 1436 bp ||||||:!! AlaLeuArgGlyPheAspGln++ ++GlnMetAlaA 52586 : GCCCTCCGCGGATTTGATCAGgt.........................agCAAATGGCTC : 51118 233 : erMetValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCysAlaProS : 252 !!:!!|||! !!!:||||||! !:!!||||||||||||||| ! !!.!!|||!.!|||! rgLeuValThrAspHisMetGluAlaHisGlyThrArgPheSerTrpSerCysValProL 51117 : GTTTGGTGACTGATCACATGGAGGCTCACGGAACTCGTTTCAGCTGGAGCTGCGTTCCTA : 51058 253 : erArgValArgArgLeuProAspGlyGlnLeuGlnValThrTrpGluAspSerThrThrG : 272 .!!:!|||..!!:!||||||...|||! ||||||||||||||| |||!!! !!:! ysLysValGluLysLeuProSerGlyLeuLeuGlnValThrTrpThrAspThrGlnSerG 51057 : AGAAGGTGGAGAAACTTCCGTCAGGACTTCTACAGGTCACCTGGACCGATACACAGAGCC : 50998 273 : lyLysGluAspThrGlyThrPheAspThrValLeuTrpAlaIle{G} >>>> Target : 287 !:!!||| !! !! !||||||..!:!!||||||||||||:!!{|} 36 lnGlnGluHisGlnAspThrPheSerSerValLeuTrpAlaVal{G}++ 50997 : AGCAGGAACATCAGGACACGTTCAGCTCAGTGCTGTGGGCTGTA{G}gt........... : 50950 288 : Intron 8 >>>> {ly}ArgValProAspThrArgSerLeuAsnLeuGluLysAlaG : 301 56 bp {||}|||!.!|||!!:!:! !!!!!|||||||||:!! ! !.!| ++{ly}ArgAlaProGluSerGlyThrLeuAsnLeuGlnHisValG 50949 : ..............ag{GT}CGAGCTCCTGAAAGCGGAACACTGAACTTGCAGCACGTCG : 47255 302 : lyValAspThrSerProAspThrGlnLysIleLeuValAspSerArgGluAlaThrSerV : 321 |||||!!: !!:! !!:!!||| ||||||:!!|||! !..! !||| !||||||| lyValGluLeuAsnThrAsnThrGlyLysIleIleValAlaAspAspGluArgThrSerV 47254 : GCGTTGAGCTCAACACAAACACGGGCAAAATCATCGTAGCTGATGATGAGCGAACATCCG : 47195 322 : alProHisIleTyrAlaIleGlyAspValValGlu >>>> Target Intron 9 >> : 333 |||||:!!:!!|||||||||||||||:!!!.!:!! 748 bp alProAsnValTyrAlaIleGlyAspIleAlaGln++ 47194 : TGCCTAATGTTTACGCCATCGGAGACATCGCACAGgt....................... : 47157 334 : >> GlyArgProGluLeuThrProIleAlaIleMetAlaGlyArgLeuLeuValGlnAr : 351 |||||||||||||||||||||! ||||||! ||||||!:!||||||!.!||||| ++GlyArgProGluLeuThrProThrAlaIleLysAlaGlyLysLeuLeuAlaGlnAr 47156 : ..agggtcgTCCTGAGCTCACCCCGACGGCCATCAAAGCGGGTAAACTCCTGGCTCAGCG : 46357 352 : gLeuPheGlyGlySerSerAspLeuMetAspTyrAspAsn >>>> Target Intron : 365 |||| !||| !|||!:!.!.||||||:!!||||||||| 94 bp gLeuAlaGlyHisSerAsnGlnLeuMetAsnTyrAspAsn++ 46356 : ATTAGCCGGTCACTCCAACCAGCTCATGAACTACGACAACgt.................. : 46313 366 : 10 >>>> ValProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSe : 381 |||||||||||||||||||||||||||||||||||||||||||||||||| ++ValProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSe 46312 : ........aggtgccCACCACAGTGTTCACTCCTCTGGAGTACGGATGTGTCGGTTTATC : 46173 382 : rGluGluGluAlaValAlaArgHisGlyGlnGluHisValGlu >>>> Target Int : 396 |||||||||||||! ! !|||:!!|||...!!::!!:!!||| 927 b rGluGluGluAlaGluArgArgTyrGlySerAspAsnIleGlu++ 46172 : CGAAGAAGAGGCCGAGAGGAGATACGGCAGTGACAATATAGAGgt............... : 46126 397 : ron 11 >>>> ValTyrHisAlaHisTyrLysProLeuGluPheThrValAlaGlyAr : 411 p |||||||||||| !||||||||||||||||||:!!||||||! !|| ++ValTyrHisAlaPheTyrLysProLeuGluPheSerValAlaGluAr 46125 : ...........agGTGTATCACGCCTTTTACAAACCTCTGGAGTTCTCCGTAGCCGAGAG : 45156 412 : gAspAlaSerGlnCysTyrValLys >>>> Target Intron 12 >>>> MetVa : 421 |||||||||||||||||||:!!||| 77 bp :!!|| gAspAlaSerGlnCysTyrIleLys++ ++ValVa 45155 : AGACGCCAGTCAGTGCTACATCAAGgt..........................agGTGGT : 45049 422 : lCysLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGl : 441 |||| !|||||| !||||||! !|||||||||||||||||| !|||||||||||||| lCysGluArgGluGluProGlnArgValLeuGlyLeuHisPheThrGlyProAsnAlaGl 45048 : GTGTGAGCGGGAAGAACCGCAGCGAGTGTTAGGGCTTCACTTTACCGGCCCCAACGCTGG : 44989 442 : yGluValThrGlnGlyPheAlaLeuGlyIle{Ly} >>>> Target Intron 13 > : 452 ||||||||||||||||||||||||||||.!!{:!} 468 bp yGluValThrGlnGlyPheAlaLeuGlyPhe{Gl}++ 44988 : AGAAGTGACCCAAGGCTTTGCGCTCGGCTTC{CA}gt....................... : 44952 453 : >>> {s}CysGlyAlaSerTyrAlaGlnValMetArgThrValGlyIleHisProThrC : 470 {!}! !||| !!!!|||:!!|||:!! !|||||||||||||||||||||| ++{n}PheGlyPheThrTyrSerGlnLeuArgAspThrValGlyIleHisProThrC 44951 : ...ag{G}TTCGGGTTCACGTACTCTCAGCTACGCGATACGGTCGGTATCCACCCTACGT : 44434 471 : ysSerGluGluValValLysLeuArgIleSerLysArgSerGlyLeuAspProThrValT : 490 ||:!!||||||:!!..!!!.|||!.!|||!!!|||||||||||||||||| !!||||||| ysAlaGluGluLeuThrAsnLeuHisIleThrLysArgSerGlyLeuAspAlaThrValT 44433 : GCGCCGAGGAGCTCACCAATCTCCACATCACCAAGCGTTCCGGTCTGGACGCCACGGTGA : 44374 491 : hrGlyCysUnkGly : 494 |||||||| ||| hrGlyCys***Gly 44373 : CTGGCTGCTGAGGT : 44360 vulgar: SPP00000137_2.0 4 494 . CM004435.1:subseq(2200000,150000) 61180 44359 - 1537 M 23 69 S 0 1 5 0 2 I 0 272 3 0 2 S 1 2 M 18 54 S 0 1 5 0 2 I 0 129 3 0 2 S 1 2 M 27 81 G 0 3 M 20 60 S 0 2 5 0 2 I 0 1706 3 0 2 S 1 1 M 29 87 G 1 0 M 21 63 5 0 2 I 0 469 3 0 2 M 21 63 5 0 2 I 0 218 3 0 2 M 25 75 5 0 2 I 0 5127 3 0 2 M 36 108 5 0 2 I 0 1432 3 0 2 M 58 174 S 0 1 5 0 2 I 0 3652 3 0 2 S 1 2 M 45 135 5 0 2 I 0 744 3 0 2 M 32 96 5 0 2 I 0 90 3 0 2 M 31 93 5 0 2 I 0 923 3 0 2 M 24 72 5 0 2 I 0 73 3 0 2 M 32 96 S 0 2 5 0 2 I 0 464 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 2016-11-23 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local gene 44360 61180 1537 - . gene_id 1 ; sequence SPP00000137_2.0 ; gene_orientation + CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 61111 61180 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 61111 61180 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 61109 61110 . - . intron_id 1 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 60835 61110 . - . intron_id 1 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 60835 60836 . - . intron_id 0 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 60778 60834 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 60778 60834 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 60776 60777 . - . intron_id 2 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 60645 60777 . - . intron_id 2 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 60645 60646 . - . intron_id 1 ; splice_site "ag" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 60497 60644 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 60497 60644 . - . insertions 3 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 60495 60496 . - . intron_id 3 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 58787 60496 . - . intron_id 3 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 58787 58788 . - . intron_id 2 ; splice_site "ag" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 58636 58786 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 58636 58786 . - . insertions 0 ; deletions 1 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 58634 58635 . - . intron_id 4 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 58163 58635 . - . intron_id 4 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 58163 58164 . - . intron_id 3 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 58100 58162 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 58100 58162 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 58098 58099 . - . intron_id 5 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 57878 58099 . - . intron_id 5 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 57878 57879 . - . intron_id 4 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 57803 57877 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 57803 57877 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 57801 57802 . - . intron_id 6 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 52672 57802 . - . intron_id 6 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 52672 52673 . - . intron_id 5 ; splice_site "TG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 52564 52671 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 52564 52671 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 52562 52563 . - . intron_id 7 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 51128 52563 . - . intron_id 7 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 51128 51129 . - . intron_id 6 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 50953 51127 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 50953 51127 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 50951 50952 . - . intron_id 8 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 47297 50952 . - . intron_id 8 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 47297 47298 . - . intron_id 7 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 47160 47296 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 47160 47296 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 47158 47159 . - . intron_id 9 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 46412 47159 . - . intron_id 9 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 46412 46413 . - . intron_id 8 ; splice_site "ag" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 46316 46411 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 46316 46411 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 46314 46315 . - . intron_id 10 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 46222 46315 . - . intron_id 10 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 46222 46223 . - . intron_id 9 ; splice_site "ag" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 46129 46221 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 46129 46221 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 46127 46128 . - . intron_id 11 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 45202 46128 . - . intron_id 11 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 45202 45203 . - . intron_id 10 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 45130 45201 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 45130 45201 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 45128 45129 . - . intron_id 12 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 45053 45129 . - . intron_id 12 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 45053 45054 . - . intron_id 11 ; splice_site "AG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 44955 45052 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 44955 45052 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice5 44953 44954 . - . intron_id 13 ; splice_site "GT" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local intron 44487 44954 . - . intron_id 13 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local splice3 44487 44488 . - . intron_id 12 ; splice_site "aG" CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local cds 44360 44486 . - . CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local exon 44360 44486 . - . insertions 0 ; deletions 0 CM004435.1:subseq(2200000,150000) exonerate:protein2genome:local similarity 44360 61180 1537 - . alignment_id 1 ; Query SPP00000137_2.0 ; Align 61181 5 69 ; Align 60833 29 54 ; Align 60643 48 81 ; Align 60559 75 60 ; Align 58786 96 87 ; Align 58699 126 63 ; Align 58163 147 63 ; Align 57878 168 75 ; Align 52672 193 108 ; Align 51128 229 174 ; Align 47295 288 135 ; Align 46412 333 96 ; Align 46222 365 93 ; Align 45202 396 72 ; Align 45053 420 96 ; Align 44486 453 126 # --- END OF GFF DUMP --- # -- completed exonerate analysis