Command line: [exonerate -m p2g --showtargetgff -q SPP00000034_1.0.fa -t SPP00000034_1.0.GL397380.1/GL397380.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete Target: GL397380.1:subseq(4770525,133137) dna:supercontig supercontig:Nleu1.0:GL397380.1:1:5303870:1 REF:[revcomp] Model: protein2genome:local Raw score: 1007 Query range: 8 -> 256 Target range: 85331 -> 72064 9 : LysSerTyrAspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAla : 28 ..!:!!|||||||||||||||||||||||||||||||||||||||||||||:!!..!||| SerAlaTyrAspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuSerCysAla 85331 : TCGGCATATGATTATGATCTCATCATCATCGGTGGTGGTTCTGGAGGCCTTTCATGTGCG : 85274 29 : Lys >>>> Target Intron 1 >>>> GluAlaAlaGlnTyrGlyLysLysValM : 39 ||| 238 bp ||||||||| ! ||||||||||||| Lys++ ++GluAlaAlaIleLeuGlyLysLysValM 85273 : AAGgt.........................agGAAGCTGCCATTTTGGGAAAGAAAGTTA : 85003 40 : etValLeuAspPheValThrProThrProLeuGlyThrArgTrp{G} >>>> Target : 54 |||||||||||||||||..!|||:!!|||! !|||||| !|||{|} 18 etValLeuAspPheValValProSerProGlnGlyThrSerTrp{G}++ 85002 : TGGTGCTAGACTTTGTTGTCCCGTCACCTCAGGGCACATCCTGG{G}gt........... : 84955 55 : Intron 2 >>>> {ly}LeuGlyGlyThrCysValAsnValGlyCysIleProLysL : 68 21 bp {||}|||||||||||||||:!!|||||||||||||||||||||| ++{ly}LeuGlyGlyThrCysLeuAsnValGlyCysIleProLysL 84954 : ..............ag{GT}CTTGGTGGCACTTGTCTAAATGTAGGTTGTATTCCTAAGA : 83095 69 : ysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaLeuGlnAspSerArgAsnTyrGlyT : 88 |||||||||||||||||||||||||||||||||||||| |||||||||!!.!:!|||| ysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaLeuCysAspSerArgLysPheGlyT 83094 : AATTGATGCATCAGGCTGCCCTTTTGGGGCAGGCATTATGTGACTCAAGGAAATTTGGCT : 83035 89 : rpLysValGluGluThr{V} >>>> Target Intron 3 >>>> {al}LysHisA : 97 ||:!! !!!::!! !{|} 7605 bp {||}!:!|||: rpGluTyrAspGlnGln{V}++ ++{al}ArgHisA 83034 : GGGAGTATGATCAACAA{G}gt.........................ag{TG}AGGCACA : 75403 98 : spTrpAspArgMetIleGluAlaValGlnAsnHisIleGlySerLeuAsnTrpGlyTyrA : 117 !!|||!!:! !|||! !:!!|||:!!||||||||||||.!!||||||||||||||||||| snTrpGluThrMetThrLysAlaIleGlnAsnHisIleSerSerLeuAsnTrpGlyTyrA 75402 : ACTGGGAGACGATGACAAAAGCGATTCAGAACCACATCAGCTCTCTAAACTGGGGCTACA : 75343 118 : rgValAlaLeuArgGluLysLysValValTyrGluAsnAlaTyrGlyGlnPheIleGlyP : 137 ||:!!:!!|||||||||||| |||!.!|||! |||:!!||||||:!!|||:!!! !! rgLeuSerLeuArgGluLysAlaValAlaTyrValAsnSerTyrGlyGluPheValGluH 75342 : GGTTGTCTCTGAGGGAAAAGGCTGTGGCCTATGTCAATTCCTATGGAGAATTTGTTGAAC : 75283 138 : roHisArgIleLys >>>> Target Intron 4 >>>> AlaThrAsnAsnLysGl : 147 !|||!:!|||||| 2032 bp |||||||||!!.||||| isHisLysIleLys++ ++AlaThrAsnLysLysGl 75282 : ATCATAAAATAAAGgt.........................agGCAACCAATAAAAAAGG : 73221 148 : yLysGluLysIleTyrSerAlaGluArgPheLeuIleAlaThrGlyGluArgProArgTy : 167 |:!!|||! !|||!!!|||! !!:!|||:!!|||||||||||||||||||||||||| yGlnGluThrTyrTyrThrAlaAlaGlnPheValIleAlaThrGlyGluArgProArgTy 73220 : ACAGGAGACTTATTATACTGCTGCACAGTTTGTCATAGCAACGGGTGAAAGGCCACGGTA : 73161 168 : rLeuGlyIleProGlyAspLysGluTyrCysIleSer{Se} >>>> Target Intro : 180 ||||||||||! !|||||||||||||||||||||!!!{||} 827 bp rLeuGlyIleGlnGlyAspLysGluTyrCysIleThr{Se}++ 73160 : TTTAGGAATCCAAGGAGATAAAGAATACTGTATTACT{AG}gt................. : 73118 181 : n 5 >>>> {r}AspAspLeuPheSerLeuProTyrCysProGlyLysThrLeuValVa : 196 {|}||||||||||||||||||! !|||||||||||||||||||||||||| ++{r}AspAspLeuPheSerLeuHisTyrCysProGlyLysThrLeuValVa 73117 : ........ag{T}GATGACCTTTTTTCTCTGCATTATTGCCCTGGCAAAACATTAGTGGT : 72247 197 : lGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyIleGlyLeuAspVa : 216 ||||||||||||||||||||||||||||||||||||||||||||||.!!||||||||||| lGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyPheGlyLeuAspVa 72246 : GGGTGCCTCTTATGTCGCCCTGGAGTGTGCAGGGTTTCTGGCTGGCTTTGGCCTAGATGT : 72187 217 : lThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaAsnLysIl : 236 |||||||||||||||||||||||||||||||||||||||||||!!:||||||.!.|||:! lThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnGluMetAlaGluLysVa 72186 : CACAGTTATGGTACGCTCAATCCTTCTCCGTGGCTTCGACCAAGAAATGGCAGAAAAAGT : 72127 237 : eGlyGluHisMetGluGluHisGlyIleLysPheIleArgGlnPheValProIleLysVa : 256 :|||...:!!||||||:!!||||||:!:||||||:!!|||:!!|||:!!|||:!:! !|| lGlySerTyrMetGluGlnHisGlyValLysPheLeuArgLysPheIleProValMetVa 72126 : GGGTTCCTACATGGAGCAGCATGGTGTGAAGTTCCTACGGAAATTCATACCTGTGATGGT : 72067 257 : l : 256 | l 72066 : A : 72065 vulgar: SPP00000034_1.0 8 256 . GL397380.1:subseq(4770525,133137) 85331 72064 - 1007 M 21 63 5 0 2 I 0 234 3 0 2 M 24 72 S 0 1 5 0 2 I 0 1817 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 7601 3 0 2 S 1 2 M 47 141 5 0 2 I 0 2028 3 0 2 M 38 114 S 0 2 5 0 2 I 0 823 3 0 2 S 1 1 M 76 228 # --- 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 # GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local gene 72065 85331 1007 - . gene_id 1 ; sequence SPP00000034_1.0 ; gene_orientation + GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 85269 85331 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 85269 85331 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 85267 85268 . - . intron_id 1 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 85031 85268 . - . intron_id 1 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 85031 85032 . - . intron_id 0 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 84958 85030 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 84958 85030 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 84956 84957 . - . intron_id 2 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 83137 84957 . - . intron_id 2 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 83137 83138 . - . intron_id 1 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 83017 83136 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 83017 83136 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 83015 83016 . - . intron_id 3 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 75412 83016 . - . intron_id 3 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 75412 75413 . - . intron_id 2 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 75269 75411 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 75269 75411 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 75267 75268 . - . intron_id 4 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 73237 75268 . - . intron_id 4 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 73237 73238 . - . intron_id 3 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 73121 73236 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 73121 73236 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 73119 73120 . - . intron_id 5 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 72294 73120 . - . intron_id 5 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 72294 72295 . - . intron_id 4 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 72065 72293 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 72065 72293 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local similarity 72065 85331 1007 - . alignment_id 1 ; Query SPP00000034_1.0 ; Align 85332 9 63 ; Align 85031 30 72 ; Align 83135 55 117 ; Align 75410 95 141 ; Align 73237 142 114 ; Align 72293 181 228 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete Target: GL397380.1:subseq(4770525,133137) dna:supercontig supercontig:Nleu1.0:GL397380.1:1:5303870:1 REF:[revcomp] Model: protein2genome:local Raw score: 833 Query range: 286 -> 499 Target range: 63868 -> 49407 287 : ValMetLeuAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGluThrValGly : 306 |||:!!||||||||||||||||||:!!||||||||||||||||||||||||! !:!!||| ValLeuLeuAlaIleGlyArgAspSerCysThrArgLysIleGlyLeuGluLysIleGly 63868 : GTTTTGTTAGCTATTGGTCGTGACTCTTGTACAAGGAAAATAGGCTTGGAGAAGATTGGT : 63811 307 : ValLysIleAsnGlu{Ly} >>>> Target Intron 1 >>>> {s}ThrGlyLys : 315 |||||||||||||||{||} 556 bp {|}!:!|||||| ValLysIleAsnGlu{Ly}++ ++{s}SerGlyLys 63810 : GTCAAAATTAATGAG{AA}gt.........................ag{G}AGTGGAAAA : 63228 316 : IleProValThrAspGluGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIle : 335 |||||||||!.!|||! !|||||||||||||||||||||:!!||||||:!!||||||||| IleProValAsnAspValGluGlnThrAsnValProTyrValTyrAlaValGlyAspIle 63227 : ATACCTGTAAATGATGTGGAACAGACCAATGTGCCATATGTCTATGCTGTTGGGGATATT : 63168 336 : LeuGluAspLysValGluLeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGln : 355 |||||||||||| !||||||||||||||||||||||||:!!|||!:!|||||||||!:! LeuGluAspLysProGluLeuThrProValAlaIleGlnSerGlyLysLeuLeuAlaArg 63167 : TTGGAGGATAAGCCAGAGCTCACTCCTGTCGCCATACAGTCAGGCAAGCTGCTAGCTCGG : 63108 356 : ArgLeuTyrAlaGlySerThrValLys >>>> Target Intron 2 >>>> CysA : 366 ||||||!:!!.!!.!||| !! !||| 6120 bp |||| ArgLeuPheGlyAlaSerLeuGluLys++ ++CysA 63107 : AGACTTTTTGGGGCCTCTTTAGAAAAGgt.........................agTGTG : 56955 367 : spTyrGluAsnValProThrThrValPheThrProLeuGluTyrGlyAlaCysGlyLeuS : 386 ||||| |||||||||||||||||||||||||||||||||||||||..!|||||||||| spTyrIleAsnValProThrThrValPheThrProLeuGluTyrGlyCysCysGlyLeuS 56954 : ATTATATTAATGTTCCGACTACGGTCTTTACTCCTCTGGAGTATGGTTGCTGTGGATTAT : 56895 387 : erGluGluLysAlaValGluLysPheGlyGluGluAsnIleGlu >>>> Target In : 401 ||||||||||||||:!!||| !!:! !:!!||||||:!!||| 4168 erGluGluLysAlaIleGluValTyrLysLysGluAsnLeuGlu++ 56894 : CTGAAGAGAAAGCTATTGAAGTATATAAAAAAGAGAATCTAGAAgt.............. : 56848 402 : tron 3 >>>> ValTyrHisSerTyrPheTrpProLeuGluTrpThrIleProSerAr : 416 bp :!!||||||!!!! |||||||||||||||||||||:!! !!.!!|| ++IleTyrHisThrLeuPheTrpProLeuGluTrpThrValAlaGlyAr 56847 : ...........agATATATCATACTTTGTTCTGGCCTCTTGAATGGACAGTAGCTGGCAG : 52637 417 : gAspAsnAsnLysCysTyrAlaLysIleIleCysAsnThrLysAspAsn >>>> Targ : 433 |!!:||||||! ||||||||||||||||||||||||! ! |||:!! gGluAsnAsnThrCysTyrAlaLysIleIleCysAsnLysPheAspHis++ 52636 : AGAGAACAACACTTGTTATGCAAAGATAATCTGCAATAAATTCGACCATgt......... : 52584 434 : et Intron 4 >>>> GluArgValValGlyPheHisValLeuGlyProAsnAlaGly : 446 2449 bp !!:||||||:!!|||||||||:!!|||||||||||||||||| ++AspArgValIleGlyPheHisIleLeuGlyProAsnAlaGly 52583 : ................agGATCGGGTGATAGGATTTCATATTCTTGGACCAAACGCCGGT : 50098 447 : GluValThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLysLysGlnLeuAsp : 466 |||||||||||||||||||||||||||:!!||||||||||||||||||:!!! !|||||| GluValThrGlnGlyPheAlaAlaAlaMetLysCysGlyLeuThrLysGlnLeuLeuAsp 50097 : GAGGTTACCCAAGGATTTGCAGCTGCAATGAAATGTGGCCTCACAAAACAGCTACTTGAT : 50038 467 : SerThrIleGlyIleHisProValCysAlaGlu >>>> Target Intron 5 >>>> : 478 ..!||||||||||||||||||..!|||!.!||| 529 bp AspThrIleGlyIleHisProThrCysGlyGlu++ 50037 : GACACCATTGGAATTCACCCCACATGTGGGGAGgt......................... : 50000 479 : ValPheThrThrLeuSerValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyC : 497 |||||||||||||||..!:!!|||||| !|||||| !..!||| !||| !|||| ++ValPheThrThrLeuGluIleThrLysSerSerGlyLeuAspIleThrGlnLysGlyC 49999 : agGTGTTCACGACTTTGGAAATCACAAAGTCGTCTGGACTAGACATCACTCAGAAAGGCT : 49416 498 : ysUnkGly : 499 || ||| ys***Gly 49415 : GCTGAGGC : 49408 vulgar: SPP00000034_1.0 286 499 . GL397380.1:subseq(4770525,133137) 63868 49407 - 833 M 25 75 S 0 2 5 0 2 I 0 552 3 0 2 S 1 1 M 52 156 5 0 2 I 0 6116 3 0 2 M 36 108 5 0 2 I 0 4164 3 0 2 M 32 96 5 0 2 I 0 2445 3 0 2 M 45 135 5 0 2 I 0 525 3 0 2 M 22 66 # --- 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 # GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local gene 49408 63868 833 - . gene_id 2 ; sequence SPP00000034_1.0 ; gene_orientation + GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 63792 63868 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 63792 63868 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 63790 63791 . - . intron_id 1 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 63236 63791 . - . intron_id 1 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 63236 63237 . - . intron_id 0 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 63079 63235 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 63079 63235 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 63077 63078 . - . intron_id 2 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 56959 63078 . - . intron_id 2 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 56959 56960 . - . intron_id 1 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 56851 56958 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 56851 56958 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 56849 56850 . - . intron_id 3 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 52683 56850 . - . intron_id 3 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 52683 52684 . - . intron_id 2 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 52587 52682 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 52587 52682 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 52585 52586 . - . intron_id 4 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 50138 52586 . - . intron_id 4 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 50138 50139 . - . intron_id 3 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 50003 50137 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 50003 50137 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice5 50001 50002 . - . intron_id 5 ; splice_site "GT" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local intron 49474 50002 . - . intron_id 5 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local splice3 49474 49475 . - . intron_id 4 ; splice_site "AG" GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local cds 49408 49473 . - . GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local exon 49408 49473 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770525,133137) exonerate:protein2genome:local similarity 49408 63868 833 - . alignment_id 2 ; Query SPP00000034_1.0 ; Align 63869 287 75 ; Align 63235 313 156 ; Align 56959 365 108 ; Align 52683 401 96 ; Align 50138 433 135 ; Align 49474 478 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis