Command line: [exonerate -m p2g --showtargetgff -q SPP00000035_1.0.fa -t SPP00000035_1.0.GL397380.1/GL397380.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397380.1:subseq(4770528,133134) dna:supercontig supercontig:Nleu1.0:GL397380.1:1:5303870:1 REF:[revcomp] Model: protein2genome:local Raw score: 490 Query range: 339 -> 502 Target range: 63225 -> 49999 340 : LysIleLeuValAspSerArgGluAlaThrSerValProHisIleTyrAlaIleGlyAsp : 359 ||||||! !|||:!!..! !||| !|||!:!||||||:!!:!!||||||:!!|||||| LysIleProValAsnAspValGluGlnThrAsnValProTyrValTyrAlaValGlyAsp 63225 : AAAATACCTGTAAATGATGTGGAACAGACCAATGTGCCATATGTCTATGCTGTTGGGGAT : 63168 360 : ValValGluGlyArgProGluLeuThrProIleAlaIleMetAlaGlyArgLeuLeuVal : 379 :!!:!!|||! !!:!|||||||||||||||:!!||||||..!:!!|||!:!||||||!.! IleLeuGluAspLysProGluLeuThrProValAlaIleGlnSerGlyLysLeuLeuAla 63167 : ATTTTGGAGGATAAGCCAGAGCTCACTCCTGTCGCCATACAGTCAGGCAAGCTGCTAGCT : 63108 380 : GlnArgLeuPheGlyGlySerSerAspLeu >>>> Target Intron 1 >>>> M : 390 !:!||||||||||||!.!|||! !!!: ! 6120 bp ArgArgLeuPheGlyAlaSerLeuGluLys++ ++C 63107 : CGGAGACTTTTTGGGGCCTCTTTAGAAAAGgt.........................agT : 56955 391 : etAspTyrAspAsnValProThrThrValPheThrProLeuGluTyrGlyCysValGlyL : 410 |||||| !|||||||||||||||||||||||||||||||||||||||||| !|||| ysAspTyrIleAsnValProThrThrValPheThrProLeuGluTyrGlyCysCysGlyL 56954 : GTGATTATATTAATGTTCCGACTACGGTCTTTACTCCTCTGGAGTATGGTTGCTGTGGAT : 56895 411 : euSerGluGluGluAlaValAlaArgHisGlyGlnGluHisValGlu >>>> Target : 426 |||||||||||:!!|||:!!! ! !:!! !:!!|||:!!:!!||| 41 euSerGluGluLysAlaIleGluValTyrLysLysGluAsnLeuGlu++ 56894 : TATCTGAAGAGAAAGCTATTGAAGTATATAAAAAAGAGAATCTAGAAgt........... : 56845 427 : Intron 2 >>>> ValTyrHisAlaHisTyrLysProLeuGluPheThrValAlaGl : 440 68 bp :!!||||||.!! !:! !|||||||||!::||||||||||| ++IleTyrHisThrLeuPheTrpProLeuGluTrpThrValAlaGl 56844 : ..............agATATATCATACTTTGTTCTGGCCTCTTGAATGGACAGTAGCTGG : 52637 441 : yArgAspAlaSerGlnCysTyrValLysMetValCysLeuArgGluProPro >>>> T : 458 ||||!!: !!:! ||||||!.!|||!!::!!||| !!:! !! ! yArgGluAsnAsnThrCysTyrAlaLysIleIleCysAsnLysPheAspHis++ 52636 : CAGAGAGAACAACACTTGTTATGCAAAGATAATCTGCAATAAATTCGACCATgt...... : 52581 459 : arget Intron 3 >>>> GlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAla : 470 2449 bp .!.! !|||:!!|||!!!|||.!!||||||||||||||| ++AspArgValIleGlyPheHisIleLeuGlyProAsnAla 52580 : ...................agGATCGGGTGATAGGATTTCATATTCTTGGACCAAACGCC : 50098 471 : GlyGluValThrGlnGlyPheAlaLeuGlyIleLysCysGlyAlaSerTyrAlaGlnVal : 490 |||||||||||||||||||||||| !!.!!!:||||||||| !!!! ! !! !:!! GlyGluValThrGlnGlyPheAlaAlaAlaMetLysCysGlyLeuThrLysGlnLeuLeu 50097 : GGTGAGGTTACCCAAGGATTTGCAGCTGCAATGAAATGTGGCCTCACAAAACAGCTACTT : 50038 491 : MetArgThrValGlyIleHisProThrCysSerGlu : 502 !|||:!!||||||||||||||||||.!!||| AspAspThrIleGlyIleHisProThrCysGlyGlu 50037 : GATGACACCATTGGAATTCACCCCACATGTGGGGAG : 50000 vulgar: SPP00000035_1.0 339 502 . GL397380.1:subseq(4770528,133134) 63225 49999 - 490 M 50 150 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 # --- 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(4770528,133134) exonerate:protein2genome:local gene 50000 63225 490 - . gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation + GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 63076 63225 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 63076 63225 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice5 63074 63075 . - . intron_id 1 ; splice_site "GT" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local intron 56956 63075 . - . intron_id 1 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice3 56956 56957 . - . intron_id 0 ; splice_site "AG" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 56848 56955 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 56848 56955 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice5 56846 56847 . - . intron_id 2 ; splice_site "GT" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local intron 52680 56847 . - . intron_id 2 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice3 52680 52681 . - . intron_id 1 ; splice_site "AG" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 52584 52679 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 52584 52679 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice5 52582 52583 . - . intron_id 3 ; splice_site "GT" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local intron 50135 52583 . - . intron_id 3 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice3 50135 50136 . - . intron_id 2 ; splice_site "AG" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 50000 50134 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 50000 50134 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local similarity 50000 63225 490 - . alignment_id 1 ; Query SPP00000035_1.0 ; Align 63226 340 150 ; Align 56956 390 108 ; Align 52680 426 96 ; Align 50135 458 135 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397380.1:subseq(4770528,133134) dna:supercontig supercontig:Nleu1.0:GL397380.1:1:5303870:1 REF:[revcomp] Model: protein2genome:local Raw score: 454 Query range: 38 -> 167 Target range: 85319 -> 75268 39 : AspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCysAlaLys >>>> : 57 ||||||||||||:!!:!!:!!|||||||||||||||||||||:!!||||||||| AspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuSerCysAlaLys++ 85319 : GATTATGATCTCATCATCATCGGTGGTGGTTCTGGAGGCCTTTCATGTGCGAAGgt.... : 85263 58 : Target Intron 1 >>>> GluAlaAlaGlnLeuGlyArgLysValAlaValValA : 69 238 bp ||||||||| ||||||!:!|||||| !|||:!!| ++GluAlaAlaIleLeuGlyLysLysValMetValLeuA 85262 : .....................agGAAGCTGCCATTTTGGGAAAGAAAGTTATGGTGCTAG : 84991 70 : spTyrValGluProSerProGlnGlyThrArgTrp{G} >>>> Target Intron 2 : 81 ||!:!|||! |||||||||||||||||| !|||{|} 1821 bp spPheValValProSerProGlnGlyThrSerTrp{G}++ 84990 : ACTTTGTTGTCCCGTCACCTCAGGGCACATCCTGG{G}gt.................... : 84952 82 : >>>> {ly}LeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetH : 98 {||}|||||||||||||||:!!||||||||||||||||||||||||||||||| ++{ly}LeuGlyGlyThrCysLeuAsnValGlyCysIleProLysLysLeuMetH 84951 : .....ag{GT}CTTGGTGGCACTTGTCTAAATGTAGGTTGTATTCCTAAGAAATTGATGC : 83083 99 : isGlnAlaAlaLeuLeuGlyGlyLeuIleGlnAspAlaProAsnTyrGlyTrpGluValA : 118 |||||||||||||||||||| ! !:!! |||:!! !!!.!:!||||||||| !! isGlnAlaAlaLeuLeuGlyGlnAlaLeuCysAspSerArgLysPheGlyTrpGluTyrA 83082 : ATCAGGCTGCCCTTTTGGGGCAGGCATTATGTGACTCAAGGAAATTTGGCTGGGAGTATG : 83023 119 : laGlnPro{V} >>>> Target Intron 3 >>>> {al}ProHisAspTrpArgL : 127 !|||! !{|} 7605 bp {||} !|||:!!|||..!! spGlnGln{V}++ ++{al}ArgHisAsnTrpGluT 83022 : ATCAACAA{G}gt.........................ag{TG}AGGCACAACTGGGAGA : 75391 128 : ysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnTrpGlyHisArgValGlnL : 147 !|||.!!:!!|||:!!|||||||||:!!!..|||||||||||||||:!!|||:!!...| hrMetThrLysAlaIleGlnAsnHisIleSerSerLeuAsnTrpGlyTyrArgLeuSerL 75390 : CGATGACAAAAGCGATTCAGAACCACATCAGCTCTCTAAACTGGGGCTACAGGTTGTCTC : 75331 148 : euGlnAspArgLysValLysTyrPheAsnIleLysAlaSerPheValAspGluHisThrV : 167 ||::!!!:!:! ||| ||| !!||| ! ! !.!..!||||||!!:.!.|||! !: euArgGluLysAlaValAlaTyrValAsnSerTyrGlyGluPheValGluHisHisLysI 75330 : TGAGGGAAAAGGCTGTGGCCTATGTCAATTCCTATGGAGAATTTGTTGAACATCATAAAA : 75271 168 : al : 167 !! le 75270 : TA : 75269 vulgar: SPP00000035_1.0 38 167 . GL397380.1:subseq(4770528,133134) 85319 75268 - 454 M 18 54 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 46 138 # --- 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(4770528,133134) exonerate:protein2genome:local gene 75269 85319 454 - . gene_id 2 ; sequence SPP00000035_1.0 ; gene_orientation + GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 85266 85319 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 85266 85319 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice5 85264 85265 . - . intron_id 1 ; splice_site "GT" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local intron 85028 85265 . - . intron_id 1 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice3 85028 85029 . - . intron_id 0 ; splice_site "AG" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 84955 85027 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 84955 85027 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice5 84953 84954 . - . intron_id 2 ; splice_site "GT" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local intron 83134 84954 . - . intron_id 2 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice3 83134 83135 . - . intron_id 1 ; splice_site "AG" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 83014 83133 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 83014 83133 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice5 83012 83013 . - . intron_id 3 ; splice_site "GT" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local intron 75409 83013 . - . intron_id 3 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local splice3 75409 75410 . - . intron_id 2 ; splice_site "AG" GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 75269 75408 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 75269 75408 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local similarity 75269 85319 454 - . alignment_id 2 ; Query SPP00000035_1.0 ; Align 85320 39 54 ; Align 85028 57 72 ; Align 83132 82 117 ; Align 75407 122 138 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397380.1:subseq(4770528,133134) dna:supercontig supercontig:Nleu1.0:GL397380.1:1:5303870:1 REF:[revcomp] Model: protein2genome:local Raw score: 253 Query range: 207 -> 285 Target range: 72292 -> 72058 208 : SerAspAspIlePheTrpLeuLysGluSerProGlyLysThrLeuValValGlyAlaSer : 227 |||||||||:!!|||! ||| ! ! !!!|||||||||||||||||||||||||||||| SerAspAspLeuPheSerLeuHisTyrCysProGlyLysThrLeuValValGlyAlaSer 72292 : AGTGATGACCTTTTTTCTCTGCATTATTGCCCTGGCAAAACATTAGTGGTGGGTGCCTCT : 72235 228 : TyrValAlaLeuGluCysAlaGlyPheLeuThrGlyIleGlyLeuAspThrThrIleMet : 247 ||||||||||||||||||||||||||||||.!!|||.!!|||||||||..!|||:!!||| TyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyPheGlyLeuAspValThrValMet 72234 : TATGTCGCCCTGGAGTGTGCAGGGTTTCTGGCTGGCTTTGGCCTAGATGTCACAGTTATG : 72175 248 : MetArgSerIleProLeuArgGlyPheAspGlnGlnMetSerSerMetValIleGluHis : 267 :!:|||||||||! !||||||||||||||||||:!!|||:!!..!! ||| !...:!! ValArgSerIleLeuLeuArgGlyPheAspGlnGluMetAlaGluLysValGlySerTyr 72174 : GTACGCTCAATCCTTCTCCGTGGCTTCGACCAAGAAATGGCAGAAAAAGTGGGTTCCTAC : 72115 268 : MetAlaSerHisGlyThrArgPheLeuArgGlyCysAlaProSerArgValArg : 285 |||! !..!||||||..!!:!||||||||| !! ! !||| !! !|||||| MetGluGlnHisGlyValLysPheLeuArgLysPheIleProValMetValArg 72114 : ATGGAGCAGCATGGTGTGAAGTTCCTACGGAAATTCATACCTGTGATGGTAAGG : 72059 vulgar: SPP00000035_1.0 207 285 . GL397380.1:subseq(4770528,133134) 72292 72058 - 253 M 78 234 # --- 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(4770528,133134) exonerate:protein2genome:local gene 72059 72292 253 - . gene_id 3 ; sequence SPP00000035_1.0 ; gene_orientation . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local cds 72059 72292 . - . GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local exon 72059 72292 . - . insertions 0 ; deletions 0 GL397380.1:subseq(4770528,133134) exonerate:protein2genome:local similarity 72059 72292 253 - . alignment_id 3 ; Query SPP00000035_1.0 ; Align 72293 208 234 # --- END OF GFF DUMP --- # -- completed exonerate analysis