Command line: [exonerate -m p2g --showtargetgff -q SPP00000034_1.0.fa -t SPP00000034_1.0.GL397492.1/GL397492.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete Target: GL397492.1:subseq(788612,138039) dna:supercontig supercontig:Nleu1.0:GL397492.1:1:1399117:1 REF:[revcomp] Model: protein2genome:local Raw score: 438 Query range: 291 -> 499 Target range: 53259 -> 46939 292 : GlyArgAspAlaCysThrArgLysIleGlyLeuGluThrValGlyValLysIleAsnGlu : 311 ||||||! ! !! !||||||!..:!:..!||||||! !!.!|||||| ! ! !!:! GlyArgValProAspThrArgSerLeuAsnLeuGluLysAlaGlyValAspThrSerPro 53259 : GGTCGAGTCCCAGACACCAGAAGTCTGAATTTGGAGAAGGCTGGGGTAGATACTAGCCCC : 53202 312 : LysThrGlyLysIleProValThrAspGluGluGlnThrAsnValProTyrIleTyrAla : 331 ! ||| !||||||! !||| !..!..!||| |||::!||||||:!!||||||||| AspThrGlnLysIleLeuValAspSerArgGluAlaThrSerValProHisIleTyrAla 53201 : GACACTCAGAAGATCCTGGTGGACTCCCGGGAAGCCACCTCTGTGCCCCACATCTATGCC : 53142 332 : IleGlyAspIleLeuGlu >>>> Target Intron 1 >>>> AspLysValGluL : 342 |||||||||:!::!!||| 2580 bp ! ::! !|||| IleGlyAspValValGlu++ ++GlyArgProGluL 53141 : ATTGGTGACGTGGTGGAGgt.........................agGGGCGGCCTGAGC : 50529 343 : euThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyrAlaGlySerT : 362 ||||||||..!||||||..!|||||||||||||||!.!|||||||||!:!!.! !!|||: euThrProThrAlaIleMetAlaGlyArgLeuLeuValGlnArgLeuPheGlyArgSerS 50528 : TGACACCCACAGCGATCATGGCCGGGAGGCTCCTGGTGCAGCGGCTTTTCGGCAGGTCCT : 50469 363 : hrValLysCysAspTyrGluAsn >>>> Target Intron 2 >>>> ValProTh : 372 !!! ! ! ||||||!!:||| 350 bp |||||||| erAspLeuMetAspTyrAspAsn++ ++ValProTh 50468 : CAGATCTGATGGACTACGACAATgt.........................agGTTCCCAC : 50089 373 : rThrValPheThrProLeuGluTyrGlyAlaCysGlyLeuSerGluGluLysAlaValGl : 392 ||||||||||||||||||||||||||||..! |||||||||||||||:!!||||||! rThrValPheThrProLeuGluTyrGlyCysValGlyLeuSerGluGluGluAlaValAl 50088 : GACTGTCTTCACCCCGCTGGAGTATGGCTGTGTGGGGCTGTCCGAGGAGGAGGCAGTGGC : 50029 393 : uLysPheGlyGluGluAsnIleGlu >>>> Target Intron 3 >>>> ValTyr : 402 ::: !|||:!!|||:!!:!!||| 1920 bp ||| ! aArgHisGlyGlnGluHisValGlu++ -+ValGln 50028 : TCGCCACGGGCAGGAGCATGTTGAGgt.........................ggGTGCAG : 48079 403 : HisSerTyrPheTrpProLeuGluTrpThrIleProSerArgAspAsnAsnLysCysTyr : 422 !.!!! ! ! ! ! ! !! !|||.!!! !! !.!.! !||| ! GlyGlyCysArgValAspThrThrGlnProProProGlyLeuValAlaGluMetCysGly 48078 : GGTGGATGCAGGGTGGACACAACCCAGCCCCCTCCTGGGCTGGTGGCTGAGATGTGCGGC : 48019 423 : AlaLysIleIleCysAsnThrLysAspAsnGluArgValValGlyPheHisValLeuGly : 442 !:!!!!::!:||| ! !:!! ! :!!! !|||:!!|||.!.||| !!|||||| PheGlnMetValCysLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGly 48018 : TTTCAGATGGTGTGCCTGAGGGAGCCCCCGCAGCTGGTGCTGGGCCTGCACTTCCTTGGC : 47959 443 : ProAsnAlaGlyGluValThrGlnGlyPheAlaAlaAlaLeu{Ly} >>>> Target : 457 ||||||||||||||||||||||||||||||||| !!.!:!!{||} 84 ProAsnAlaGlyGluValThrGlnGlyPheAlaLeuGlyIle{Ly}++ 47958 : CCCAACGCAGGCGAAGTTACTCAGGGATTTGCTCTGGGGATC{AA}gt............ : 47910 458 : Intron 4 >>>> {s}CysGlyLeuThrLysLysGlnLeuAspSerThrIleGlyIle : 471 6 bp {|}|||||| !:!! ! !|||:!! !!|||:!:|||||| ++{s}CysGlyAlaSerTyrValGlnValMetArgThrValGlyIle 47909 : .............ag{G}TGTGGGGCCTCCTATGTGCAGGTGATGCGGACCGTGGGTATC : 47026 472 : HisProValCysAlaGluValPheThrThrLeuSerValThrLysArgSerGlyAlaSer : 491 ||||||..!|||:!!|||! ! ! ..!! !||| !!|||:!!|||||||||||| !..! HisProThrCysSerGluGluValValLysLeuArgValSerLysArgSerGlyLeuAsp 47025 : CATCCCACATGCTCTGAGGAGGTAGTCAAGCTGCGCGTCTCCAAGCGCTCAGGCCTGGAC : 46966 492 : IleLeuGlnAlaGlyCysUnkGly : 499 ! ! !.!!|||||| ||| ProThrValThrGlyCys***Gly 46965 : CCCACGGTGACAGGCTGCTGAGGG : 46940 vulgar: SPP00000034_1.0 291 499 . GL397492.1:subseq(788612,138039) 53259 46939 - 438 M 46 138 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 1916 3 0 2 M 56 168 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(788612,138039) exonerate:protein2genome:local gene 46940 53259 438 - . gene_id 1 ; sequence SPP00000034_1.0 ; gene_orientation + GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 53122 53259 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 53122 53259 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 53120 53121 . - . intron_id 1 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 50542 53121 . - . intron_id 1 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 50542 50543 . - . intron_id 0 ; splice_site "AG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 50446 50541 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 50446 50541 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 50444 50445 . - . intron_id 2 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 50096 50445 . - . intron_id 2 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 50096 50097 . - . intron_id 1 ; splice_site "AG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 50003 50095 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 50003 50095 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 50001 50002 . - . intron_id 3 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 48083 50002 . - . intron_id 3 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 48083 48084 . - . intron_id 2 ; splice_site "GG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 47913 48082 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 47913 48082 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 47911 47912 . - . intron_id 4 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 47067 47912 . - . intron_id 4 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 47067 47068 . - . intron_id 3 ; splice_site "AG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 46940 47066 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 46940 47066 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local similarity 46940 53259 438 - . alignment_id 1 ; Query SPP00000034_1.0 ; Align 53260 292 138 ; Align 50542 338 96 ; Align 50096 370 93 ; Align 48083 401 168 ; Align 47066 458 126 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete Target: GL397492.1:subseq(788612,138039) dna:supercontig supercontig:Nleu1.0:GL397492.1:1:1399117:1 REF:[revcomp] Model: protein2genome:local Raw score: 351 Query range: 11 -> 123 Target range: 107436 -> 87177 12 : AspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLysGlu{ : 31 ||||||||||||:!::!:|||||||||||||||||||||||||||..!|||||||||{ AspTyrAspLeuLeuValIleGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGlu{ 107436 : GACTATGATCTCCTGGTGATCGGCGGGGGATCTGGCGGCCTGGCTTGTGCCAAGGAG{ : 107379 32 : A} >>>> Target Intron 1 >>>> {la}AlaGlnTyrGlyLysLysValMe : 39 !} 19283 bp {.!} !! !.! ! !! G}++ ++{ly}LysProProAlaValThr***Th 107378 : G}gt.........................ag{GG}AAGCCTCCAGCCGTCACCTGAAC : 88072 40 : tValLeuAspPheValThrProThrProLeuGlyThrArgTrpGlyLeuGlyGlyThr : 58 !:!!.!. ! !:!! !! ! !! !||||||||||||||||||||||||||| r***IleGlnValCysSerSerHisValProGlyThrArgTrpGlyLeuGlyGlyThr 88071 : ATAAATTCAAGTGTGCTCTTCCCACGTCCCAGGCACTCGGTGGGGCCTCGGCGGCACC : 88015 59 : CysValAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyG : 78 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CysValAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyG 88014 : TGTGTCAATGTGGGCTGCATCCCCAAGAAGCTGATGCACCAGGCGGCACTGCTGGGAG : 87955 79 : lnAlaLeuGlnAspSerArgAsnTyrGlyTrpLysValGluGluThrValLysHisAs : 97 !:!!||||||:!!! !:!!|||||||||:!!|||! :!! !!||| !||||| lyLeuIleGlnAspAlaProHisTyrGlyTrpGluValAlaGlnProValProHisAs 87954 : GCCTGATCCAAGATGCCCCTCACTATGGCTGGGAGGTGGCCCAGCCTGTGCCACATGA : 87898 98 : p{Tr} >>>> Target Intron 2 >>>> {p}AspArgMetIleGluAlaVal : 105 |{||} 640 bp {|} !:!||| !||||||||| p{Tr}++ ++{p}ArgLysMetAlaGluAlaVal 87897 : C{TG}gt.........................ag{G}AGGAAGATGGCAGAAGCTGTT : 87234 106 : GlnAsnHisIleGlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLys : 123 |||||||||:!: !|||||||||||||||:!!|||||| !|||!:!!!:!:! GlnAsnHisValLysSerLeuAsnTrpGlyHisArgValGlnLeuGlnAspArg 87233 : CAAAACCACGTGAAATCCCTGAACTGGGGCCACCGTGTCCAGCTTCAGGACAGG : 87178 vulgar: SPP00000034_1.0 11 123 . GL397492.1:subseq(788612,138039) 107436 87177 - 351 M 19 57 S 0 1 5 0 2 I 0 19279 3 0 2 S 1 2 M 66 198 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(788612,138039) exonerate:protein2genome:local gene 87178 107436 351 - . gene_id 2 ; sequence SPP00000034_1.0 ; gene_orientation + GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 107379 107436 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 107379 107436 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 107377 107378 . - . intron_id 1 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 88096 107378 . - . intron_id 1 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 88096 88097 . - . intron_id 0 ; splice_site "AG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 87894 88095 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 87894 88095 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 87892 87893 . - . intron_id 2 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 87254 87893 . - . intron_id 2 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 87254 87255 . - . intron_id 1 ; splice_site "AG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 87178 87253 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 87178 87253 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local similarity 87178 107436 351 - . alignment_id 2 ; Query SPP00000034_1.0 ; Align 107437 12 57 ; Align 88094 32 198 ; Align 87253 99 75 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete Target: GL397492.1:subseq(788612,138039) dna:supercontig supercontig:Nleu1.0:GL397492.1:1:1399117:1 REF:[revcomp] Model: protein2genome:local Raw score: 145 Query range: 170 -> 230 Target range: 104087 -> 68283 171 : ProGlyAspLysGluTyrCysIleSerSerAspAspLeu{P} >>>> Target In : 184 ||| !! |||||||||||||||||| ..!|||{ } 34829 ProArgProAlaGluTyrCysIleSerSerProSerLeu{G}-+ 104087 : CCACGCCCAGCTGAGTACTGTATTTCCAGTCCGAGTTTG{G}tt.............. : 104045 185 : tron 1 >>>> {he}SerLeuProTyrCysProGlyLysThrLeuValValGlyAl : 198 bp { !}:!!||| !! !||| !..!!!.! !|||||||||||||| +-{ly}AlaLeuSerLeuCysPheSerAsnArgLeuValValGlyAl 104044 : ...........ac{GT}GCTCTCTCTCTCTGTTTCTCTAACAGGTTGGTGGTCGGGGC : 69177 199 : aSer{T} >>>> Target Intron 2 >>>> {yr}ValAlaLeuGluCysAla : 206 ||||{|} 795 bp {||}|||||||||||||||||| aSer{T}++ ++{yr}ValAlaLeuGluCysAla 69176 : CAGC{T}gt.........................ag{AT}GTGGCCCTGGAGTGTGCT : 68358 207 : GlyPheLeuAlaGlyIleGlyLeuAspValThrValMetValArgSerIleLeuLeuA : 226 |||||||||.!!|||||||||||||||..!|||:!!|||:!!|||||||||! !|||| GlyPheLeuThrGlyIleGlyLeuAspThrThrIleMetMetArgSerIleProLeuA 68357 : GGCTTCCTCACTGGGATTGGGCTGGACACCACCATCATGATGCGCAGCATCCCCCTCC : 68298 227 : rgGlyPheAspGln : 230 |||||||||||||| rgGlyPheAspGln 68297 : GCGGCTTCGACCAG : 68284 vulgar: SPP00000034_1.0 170 230 . GL397492.1:subseq(788612,138039) 104087 68283 - 145 M 13 39 S 0 1 5 0 2 I 0 34825 3 0 2 S 1 2 M 15 45 S 0 1 5 0 2 I 0 791 3 0 2 S 1 2 M 30 90 # --- 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(788612,138039) exonerate:protein2genome:local gene 68284 104087 145 - . gene_id 3 ; sequence SPP00000034_1.0 ; gene_orientation + GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 104048 104087 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 104048 104087 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 104046 104047 . - . intron_id 1 ; splice_site "TT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 69219 104047 . - . intron_id 1 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 69219 69220 . - . intron_id 0 ; splice_site "AC" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 69171 69218 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 69171 69218 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice5 69169 69170 . - . intron_id 2 ; splice_site "GT" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local intron 68376 69170 . - . intron_id 2 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local splice3 68376 68377 . - . intron_id 1 ; splice_site "AG" GL397492.1:subseq(788612,138039) exonerate:protein2genome:local cds 68284 68375 . - . GL397492.1:subseq(788612,138039) exonerate:protein2genome:local exon 68284 68375 . - . insertions 0 ; deletions 0 GL397492.1:subseq(788612,138039) exonerate:protein2genome:local similarity 68284 104087 145 - . alignment_id 3 ; Query SPP00000034_1.0 ; Align 104088 171 39 ; Align 69217 185 45 ; Align 68374 201 90 # --- END OF GFF DUMP --- # -- completed exonerate analysis