Command line: [exonerate -m p2g --showtargetgff -q SPP00000035_1.0.fa -t SPP00000035_1.0.GL397326.1/GL397326.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397326.1:subseq(9230278,124652) dna:supercontig supercontig:Nleu1.0:GL397326.1:1:14093033:1 REF Model: protein2genome:local Raw score: 344 Query range: 38 -> 167 Target range: 45562 -> 53259 39 : AspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGluAla : 58 ||||||||||||:!!:!!:!!||||||||||||||||||||||||..!||||||! ! ! AspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLysAlaArg 45563 : GACTATGACCTTATCATCATTGGAGGTGGCTCAGGAGGCCTGGCAGCTGCTAAGGCAAGG : 45620 59 : AlaGlnLeuGlyArgLysValAlaValValAspTyrValGluProSerProGln{Gl} : 77 !! :!! ! !! ||| !||||||! ! :!! ! !!|||! ! !{||} LeuLeuValLeuCysValValTrpValValValArgIleLeuThrSerLeuThr{Gl}++ 45621 : CTCCTTGTGTTGTGTGTTGTCTGGGTGGTAGTTAGAATATTAACATCCCTGACA{GG}gt : 45679 78 : >>>> Target Intron 1 >>>> {y}ThrArgTrpGlyLeuGlyGlyThrCysVal : 87 4311 bp {|}..! ! ||||||||||||||||||||| +-{y}ValValValGlyLeuGlyGlyThrCysVal 45680 : .........................aa{T}GTTGTTGTAGGTCTTGGAGGAACATGTGTG : 50018 88 : AsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlyLeuIle : 107 ||||||||||||||||||||||||||||||||||||||||||||||||||| ! !:!: AsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaLeu 50019 : AATGTGGGTTGCATACCTAAAAAACTGATGCATCAAGCAGCTTTGTTAGGACAAGCCCTG : 50078 108 : GlnAspAlaProAsnTyrGlyTrpGluValAlaGlnPro{V} >>>> Target Intr : 121 ||||||:!!! !||||||||||||:!!|||! !:!! !!{|} 2999 bp GlnAspSerArgAsnTyrGlyTrpLysValGluGluThr{V}++ 50079 : CAAGACTCTCGAAACTATGGATGGAAAGTCGAGGAGACA{G}gt................ : 50123 122 : on 2 >>>> {al}ProHisAspTrpArgLysMetAlaGluAlaValGlnAsnHisVal : 136 {||} !||||||||| !!:!||| !||||||||||||||||||:!! ++{al}LysHisAspTrpAspArgMetIleGluAlaValGlnAsnHisIle 50124 : .........ag{TT}AAGCATGATTGGGACAGAATGATAGAAGCTGTACAGAATCACATT : 53164 137 : LysSerLeuAsnTrpGlyHisArgValGlnLeuGlnAspArgLysValLysTyrPheAsn : 156 |||||||||||||||:!!|||||| |||!:!!!:!:!|||||| ||| ||| GlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluAsn 53165 : GGCTCTTTGAATTGGGGCTACCGAGTAGCTCTGCGGGAGAAAAAAGTCGTCTATGAGAAT : 53224 157 : IleLysAlaSerPheValAspGluHisThrVal : 167 ! ! !.!..!|||:!!! ! |||! !:!! AlaTyrGlyGlnPheIleGlyProHisArgIle 53225 : GCTTACGGGCAATTTATTGGTCCTCATAGGATT : 53259 vulgar: SPP00000035_1.0 38 167 . GL397326.1:subseq(9230278,124652) 45562 53259 + 344 M 38 114 S 0 2 5 0 2 I 0 4307 3 0 2 S 1 1 M 43 129 S 0 1 5 0 2 I 0 2995 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 # GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local gene 45563 53259 344 + . gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation + GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 45563 45678 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 45563 45678 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice5 45679 45680 . + . intron_id 1 ; splice_site "GT" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local intron 45679 49989 . + . intron_id 1 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice3 49988 49989 . + . intron_id 0 ; splice_site "AA" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 49990 50120 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 49990 50120 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice5 50121 50122 . + . intron_id 2 ; splice_site "GT" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local intron 50121 53119 . + . intron_id 2 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice3 53118 53119 . + . intron_id 1 ; splice_site "AG" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 53120 53259 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 53120 53259 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local similarity 45563 53259 344 + . alignment_id 1 ; Query SPP00000035_1.0 ; Align 45563 39 114 ; Align 49991 78 129 ; Align 53122 122 138 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397326.1:subseq(9230278,124652) dna:supercontig supercontig:Nleu1.0:GL397326.1:1:14093033:1 REF Model: protein2genome:local Raw score: 286 Query range: 337 -> 426 Target range: 60303 -> 63914 338 : ThrGlnLysIleLeuValAspSerArgGluAlaThrSerValProHisIleTyrAlaIle : 357 ||| !||||||! !||| ..!..!||| !|||!:!||||||:!!|||||||||||| ThrGlyLysIleProValThrAspGluGluGlnThrAsnValProTyrIleTyrAlaIle 60304 : ACTGGAAAAATACCTGTCACAGATGAAGAACAGACCAATGTGCCTTACATTTATGCCATT : 60361 358 : GlyAspValValGluGlyArgProGluLeuThrProIleAlaIleMetAlaGlyArgLeu : 377 ||||||:!!:!!|||! !!:! !||||||||||||:!!||||||..!|||||||||||| GlyAspIleLeuGluAspLysValGluLeuThrProValAlaIleGlnAlaGlyArgLeu 60362 : GGCGATATACTGGAGGATAAGGTGGAGCTCACCCCAGTTGCAATCCAGGCAGGAAGATTG : 60421 378 : LeuValGlnArgLeuPheGlyGlySerSerAspLeu >>>> Target Intron 1 > : 390 |||!.!|||||||||!:!!.!||||||!!!! ! ! 3344 bp LeuAlaGlnArgLeuTyrAlaGlySerThrValLys++ 60422 : CTGGCTCAGAGGCTCTATGCAGGTTCCACTGTCAAGgt...................... : 60462 391 : >>> MetAspTyrAspAsnValProThrThrValPheThrProLeuGluTyrGlyCysV : 408 ||||||!!:|||||||||||||||||||||||||||||||||||||||..! ++CysAspTyrGluAsnValProThrThrValPheThrProLeuGluTyrGlyAlaC 60463 : ...agTGTGACTATGAAAATGTTCCAACCACTGTATTTACTCCTTTGGAATATGGTGCTT : 63858 409 : alGlyLeuSerGluGluGluAlaValAlaArgHisGlyGlnGluHisValGluVal : 426 !|||||||||||||||:!!||||||! !!:! !|||:!!|||:!!:!!|||||| ysGlyLeuSerGluGluLysAlaValGluLysPheGlyGluGluAsnIleGluVal 63859 : GTGGCCTTTCTGAGGAGAAAGCTGTGGAGAAGTTTGGGGAAGAAAATATTGAGGTA : 63914 vulgar: SPP00000035_1.0 337 426 . GL397326.1:subseq(9230278,124652) 60303 63914 + 286 M 52 156 5 0 2 I 0 3340 3 0 2 M 37 111 # --- 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 # GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local gene 60304 63914 286 + . gene_id 2 ; sequence SPP00000035_1.0 ; gene_orientation + GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 60304 60459 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 60304 60459 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice5 60460 60461 . + . intron_id 1 ; splice_site "GT" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local intron 60460 63803 . + . intron_id 1 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice3 63802 63803 . + . intron_id 0 ; splice_site "AG" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 63804 63914 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 63804 63914 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local similarity 60304 63914 286 + . alignment_id 2 ; Query SPP00000035_1.0 ; Align 60304 338 156 ; Align 63804 390 111 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397326.1:subseq(9230278,124652) dna:supercontig supercontig:Nleu1.0:GL397326.1:1:14093033:1 REF Model: protein2genome:local Raw score: 281 Query range: 201 -> 321 Target range: 54970 -> 73703 202 : LeuGluTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSerProGlyLysThr : 221 ||| !:! !.!! !!|||||||||:!!|||! ||| ! !!!|||||||||||| LeuProPhePhePheProSerAspAspLeuPheSerLeuProTyrCysProGlyLysThr 54971 : CTTCCTTTTTTTTTTCCCAGTGATGATCTTTTCTCCTTGCCTTACTGCCCGGGTAAGACT : 55028 222 : LeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuThrGlyIleGly : 241 ||||||||||||||||||||||||||||||||||||||||||||||||.!!||||||||| LeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyIleGly 55029 : CTGGTTGTTGGAGCATCCTATGTCGCCTTGGAGTGTGCTGGATTTCTTGCTGGTATTGGT : 55088 242 : LeuAspThrThrIleMetMetArgSerIleProLeuArgGlyPheAspGlnGlnMetSer : 261 ||||||..!|||:!!|||:!:|||||||||! !||||||||||||||||||.!.|||:!! LeuAspValThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAla 55089 : TTAGACGTCACTGTTATGGTTAGGTCCATTCTTCTTAGAGGATTTGACCAGGACATGGCC : 55148 262 : SerMetValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCysAlaPro : 281 !:!! :!! !|||||||||! !..!||||||! !!:!|||:!!||| !! !!.!||| AsnLysIleGlyGluHisMetGluGluHisGlyIleLysPheIleArgGlnPheValPro 55149 : AACAAAATTGGTGAACACATGGAAGAACATGGCATCAAGTTTATAAGACAGTTTGTACCA : 55208 282 : SerArgVal{A} >>>> Target Intron 1 >>>> {rg}ArgLeuProAspGly : 290 ! !!:!|||{|} 18373 bp {||} !! !! ! ! IleLysVal{A}++ ++{rg}SerGlnLeuLeuGln 55209 : ATTAAAGTA{A}gt.........................ag{GG}TCCCAGCTATTGCAA : 73608 291 : GlnLeuGlnValThrTrpGluAspSerThrThrGlyLysGluAspThrGlyThrPheAsp : 310 !:!!...||| ! !:!!.!.|||!.!||||||:::||||||||| ! !|||||| IleValSerValGluLeuLysGlnSerAsnThrGlyArgGluAspThrLeuHisPheAsp 73609 : ATAGTCTCTGTGGAGCTGAAACAATCAAATACAGGACGTGAGGACACCCTGCACTTTGAT : 73668 311 : ThrValLeuTrpAlaIleGlyArgValProAsp : 321 !.!:!!!!! ! !||| ! !:!! !||| AsnIlePheGlnAsnIleLeuValIleLysAsp 73669 : AATATTTTCCAGAACATTTTGGTGATTAAAGAC : 73703 vulgar: SPP00000035_1.0 201 321 . GL397326.1:subseq(9230278,124652) 54970 73703 + 281 M 83 249 S 0 1 5 0 2 I 0 18369 3 0 2 S 1 2 M 36 108 # --- 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 # GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local gene 54971 73703 281 + . gene_id 3 ; sequence SPP00000035_1.0 ; gene_orientation + GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 54971 55220 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 54971 55220 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice5 55221 55222 . + . intron_id 1 ; splice_site "GT" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local intron 55221 73593 . + . intron_id 1 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice3 73592 73593 . + . intron_id 0 ; splice_site "AG" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 73594 73703 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 73594 73703 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local similarity 54971 73703 281 + . alignment_id 3 ; Query SPP00000035_1.0 ; Align 54971 202 249 ; Align 73596 286 108 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: GL397326.1:subseq(9230278,124652) dna:supercontig supercontig:Nleu1.0:GL397326.1:1:14093033:1 REF Model: protein2genome:local Raw score: 191 Query range: 455 -> 524 Target range: 74511 -> 83778 456 : ProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGlyGluValThrGln : 475 ||| !:!!! !|||:!!|||!!!||| ! |||||||||||||||||||||||||||||| Pro***GluArgValValGlyPheHisValLeuGlyProAsnAlaGlyGluValThrGln 74512 : CCTTAGGAACGTGTTGTGGGCTTTCACGTACTGGGTCCAAATGCTGGAGAAGTTACACAA : 74569 476 : GlyPheAlaLeuGlyIleLysCysGlyAlaSerTyrAlaGlnValMetArgThrValGly : 495 ||||||||| !!.!:!!||||||||| !!!! ! !|||:!! !!!|||:!!||| GlyPheAlaAlaAlaLeuLysCysGlyLeuThrLysAsnGlnLeuAspSerThrIleGly 74570 : GGCTTCGCAGCTGCGCTCAAATGTGGACTGACCAAAAACCAGCTGGACAGCACAATTGGA : 74629 496 : IleHisProThrCysSerGlu >>>> Target Intron 1 >>>> GluValValL : 506 |||||||||..!|||:!!||| 9060 bp ! ! !!..!! IleHisProValCysAlaGlu++ ++ValPheThrT 74630 : ATCCACCCTGTCTGTGCAGAGgt.........................agGTATTCACAA : 83722 507 : ysLeuArgIleSerLysArgSerGlyLeuAspProThrValThrGlyCysUnkGly : 524 !||| !:!:!!!|||||||||||| !..! ! ! !.!!|||||| ||| hrLeuSerValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyCys***Gly 83723 : CATTGTCTGTGACCAAGCGCTCTGGGGCAAGCATCCTTCAGGCTGGCTGCTGAGGT : 83778 vulgar: SPP00000035_1.0 455 524 . GL397326.1:subseq(9230278,124652) 74511 83778 + 191 M 47 141 5 0 2 I 0 9056 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 # GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local gene 74512 83778 191 + . gene_id 4 ; sequence SPP00000035_1.0 ; gene_orientation + GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 74512 74652 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 74512 74652 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice5 74653 74654 . + . intron_id 1 ; splice_site "GT" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local intron 74653 83712 . + . intron_id 1 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local splice3 83711 83712 . + . intron_id 0 ; splice_site "AG" GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local cds 83713 83778 . + . GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local exon 83713 83778 . + . insertions 0 ; deletions 0 GL397326.1:subseq(9230278,124652) exonerate:protein2genome:local similarity 74512 83778 191 + . alignment_id 4 ; Query SPP00000035_1.0 ; Align 74512 456 141 ; Align 83713 503 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis