Command line: [exonerate -m p2g --showtargetgff -q SPP00000005_1.0.fa -t SPP00000005_1.0.GL397342.1/GL397342.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000005_1.0 # Protein # Glutathione peroxidase 2 (GPx2) # Homo sapiens # Complete Target: GL397342.1:subseq(5664896,131442) dna:supercontig supercontig:Nleu1.0:GL397342.1:1:10140663:1 REF Model: protein2genome:local Raw score: 297 Query range: 57 -> 187 Target range: 79094 -> 81442 58 : ProArgArgLeuValValLeuGlyPheProCysAsnGlnPheGlyHisGlnGluAsnCys : 77 ||| ! !!|||||||||||||||||||||||||||||||||||| ! |||||| ! ProTyrGlyLeuValValLeuGlyPheProCysAsnGlnPheGlyLysGlnGluProGly 79095 : CCCTATGGTCTAGTTGTGCTGGGCTTTCCCTGCAACCAATTTGGAAAGCAAGAACCAGGA : 79152 78 : GlnAsnGluGluIleLeuAsnSerLeu{Ly} >>>> Target Intron 1 >>>> : 87 .!.|||:!!||||||||| !.!!|||{||} 427 bp AspAsnLysGluIleLeuProGlyLeu{Ly}++ ++ 79153 : GATAACAAAGAGATTCTTCCTGGGCTC{AA}gt.........................ag : 79609 88 : {s}TyrValArgProGlyGlyGlyTyrGlnProThrPheThrLeuValGlnLysCysGlu : 106 {|}|||||||||||||||||||||!:! !|||!.!||| !||| !!:!!||| !!!!: {s}TyrValArgProGlyGlyGlyPheValProAsnPheGlnLeuPheGluLysGlyAsp 79610 : {G}TATGTCCGTCCAGGGGGAGGATTTGTACCTAATTTCCAGCTTTTTGAGAAAGGTGAT : 79666 107 : ValAsnGlyGlnAsnGluHisProValPheAlaTyrLeuLys >>>> Target Intr : 121 |||||||||:!!!!.|||!!. !||||||::!!:!|||||| 1531 bp ValAsnGlyGluLysGluGlnLysValPheSerPheLeuLys++ 79667 : GTGAATGGTGAAAAAGAACAGAAAGTCTTCAGCTTCTTGAAGgt................ : 79713 122 : on 2 >>>> AspLysLeuProTyrProTyrAspAspProPheSerLeuMetThrAspP : 137 ..! !||| !:!! !!! ! ! !!|||! !..!:!!:!! ! --SerLeuLeu***HisSerCysProHisProSerGluIleLeuGlyThrP 79714 : .........tcTCTCTGCTTTAGCACTCCTGTCCTCATCCCTCTGAGATTTTGGGCACAT : 81290 138 : roLysLeuIleIleTrpSerProValArgArgSerAspValAlaTrpAsnPheGluLysP : 157 !|||! !||| !|||..!||||||!:! ! !|||:!! !|||||||||||||||| heLysSerIleSerTrpAspProValLysValHisAspIleArgTrpAsnPheGluLysP 81291 : TCAAATCTATATCCTGGGACCCTGTAAAGGTCCATGACATCCGTTGGAACTTTGAAAAGT : 81350 158 : heLeuIleGlyProGluGlyGluProPheArgArgTyrSerArgThrPheProThrIleA : 177 |||||:!:||||||!!:||| ||| !!! !|||!::|||!.! ! ! !!..!! !: heLeuValGlyProAspGlyIleProValMetArgTrpSerHisArgAlaThrValSerS 81351 : TCCTGGTGGGGCCTGATGGAATCCCTGTCATGCGCTGGTCCCACCGGGCTACGGTCAGCT : 81410 178 : snIleGluProAspIleLysArgLeuLeuLys : 187 :::!::!! !!|||||| ! !! !|||||| erValLysThrAspIleLeuAlaTyrLeuLys 81411 : CAGTGAAGACAGACATCCTGGCGTACTTGAAG : 81442 vulgar: SPP00000005_1.0 57 187 . GL397342.1:subseq(5664896,131442) 79094 81442 + 297 M 29 87 S 0 2 5 0 2 I 0 423 3 0 2 S 1 1 M 33 99 5 0 2 I 0 1527 3 0 2 M 67 201 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-29 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local gene 79095 81442 297 + . gene_id 1 ; sequence SPP00000005_1.0 ; gene_orientation + GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local cds 79095 79183 . + . GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local exon 79095 79183 . + . insertions 0 ; deletions 0 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice5 79184 79185 . + . intron_id 1 ; splice_site "GT" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local intron 79184 79610 . + . intron_id 1 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice3 79609 79610 . + . intron_id 0 ; splice_site "AG" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local cds 79611 79710 . + . GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local exon 79611 79710 . + . insertions 0 ; deletions 0 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice5 79711 79712 . + . intron_id 2 ; splice_site "GT" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local intron 79711 81241 . + . intron_id 2 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice3 81240 81241 . + . intron_id 1 ; splice_site "TC" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local cds 81242 81442 . + . GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local exon 81242 81442 . + . insertions 0 ; deletions 0 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local similarity 79095 81442 297 + . alignment_id 1 ; Query SPP00000005_1.0 ; Align 79095 58 87 ; Align 79612 88 99 ; Align 81242 121 201 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000005_1.0 # Protein # Glutathione peroxidase 2 (GPx2) # Homo sapiens # Complete Target: GL397342.1:subseq(5664896,131442) dna:supercontig supercontig:Nleu1.0:GL397342.1:1:10140663:1 REF:[revcomp] Model: protein2genome:local Raw score: 256 Query range: 60 -> 187 Target range: 54857 -> 49999 61 : LeuValValLeuGlyPheProCysAsnGlnPheGlyHisGlnGluAsnCysGlnAsnGlu : 80 :!!:!!||||||!.!||||||||||||||||||||| ! |||||| !|||..! ValIleValLeuAlaPheProCysAsnGlnPheGlyLysGlnGluProGluThrAsnSer 54857 : GTCATTGTGTTGGCCTTTCCCTGCAACCAGTTTGGAAAACAAGAACCAGAAACAAACTCA : 54800 81 : GluIleLeuAsnSerLeu{Ly} >>>> Target Intron 1 >>>> {s}TyrVal : 89 ||||||||| !.!!|||{||} 500 bp {|}|||||| GluIleLeuLeuGlyLeu{Ly}++ ++{s}TyrVal 54799 : GAAATACTTCTTGGTCTC{AA}gt.........................ag{G}TATGTG : 54273 90 : ArgProGlyGlyGlyTyrGlnProThrPheThrLeuValGlnLysCysGluValAsnGly : 109 |||||||||.!!|||!:! |||!.!||| !||| !!:!!||| ! !!:||||||||| ArgProGlySerGlyPheValProAsnPheGlnLeuPheGluLysGlyAspValAsnGly 54272 : CGTCCAGGTAGTGGCTTTGTCCCCAATTTCCAGCTCTTTGAGAAAGGGGATGTGAATGGA : 54213 110 : GlnAsnGluHisProValPheAlaTyrLeuLys >>>> Target Intron 2 >>>> : 121 :!!!!.|||!!. !||||||.!!! !|||||| 3977 bp GluLysGluGlnLysValPheThrCysLeuLys++ 54212 : GAAAAAGAACAGAAGGTCTTTACTTGCCTGAAGgt......................... : 54175 122 : AspLysLeuProTyrProTyrAspAspProPheSerLeuMetThrAspProLysLeuI : 140 ..! !|||! ! !! !!! ! ! !!! !..!|||:!! !... !!!..! !: --SerLeuLeuGlnAsnSerCysProProThrSerAspLeuLeuGlySerSerSer***L 54174 : taTCTCTGCTCCAGAACTCCTGCCCTCCGACCTCTGATCTTTTGGGCTCATCAAGCTAAC : 50143 141 : leIleTrpSerProValArgArgSerAspValAlaTrpAsnPheGluLysPheLeuIleG : 160 !!.!!|||..!|||:!!!:! ! !|||:!! !|||||||||||||||||||||:!:| euPheTrpGluProMetLysValHisAspIleArgTrpAsnPheGluLysPheLeuValG 50142 : TCTTCTGGGAGCCCATGAAGGTTCATGATATCCGCTGGAACTTTGAGAAATTTCTGGTGG : 50083 161 : lyProGluGlyGluProPheArgArgTyrSerArgThrPheProThrIleAsnIleGluP : 180 |||||!!:|||! ||| !!! !!.!!::!!!!.! ! !|||..!! !!..:!!:!! lyProAspGlyValProValMetHisTrpCysHisGlnAlaProValSerThrValLysS 50082 : GGCCCGATGGAGTCCCTGTCATGCACTGGTGCCACCAGGCTCCAGTCAGCACAGTCAAGT : 50023 181 : roAspIleLysArgLeuLeuLys : 187 !!|||||| !..!! !|||||| erAspIleLeuGluTyrLeuLys 50022 : CAGACATCCTGGAGTACCTAAAG : 50000 vulgar: SPP00000005_1.0 60 187 . GL397342.1:subseq(5664896,131442) 54857 49999 - 256 M 26 78 S 0 2 5 0 2 I 0 496 3 0 2 S 1 1 M 33 99 5 0 2 I 0 3973 3 0 2 M 67 201 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-29 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local gene 50000 54857 256 - . gene_id 1 ; sequence SPP00000005_1.0 ; gene_orientation + GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local cds 54778 54857 . - . GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local exon 54778 54857 . - . insertions 0 ; deletions 0 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice5 54776 54777 . - . intron_id 1 ; splice_site "GT" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local intron 54278 54777 . - . intron_id 1 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice3 54278 54279 . - . intron_id 0 ; splice_site "AG" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local cds 54178 54277 . - . GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local exon 54178 54277 . - . insertions 0 ; deletions 0 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice5 54176 54177 . - . intron_id 2 ; splice_site "GT" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local intron 50201 54177 . - . intron_id 2 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local splice3 50201 50202 . - . intron_id 1 ; splice_site "TA" GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local cds 50000 50200 . - . GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local exon 50000 50200 . - . insertions 0 ; deletions 0 GL397342.1:subseq(5664896,131442) exonerate:protein2genome:local similarity 50000 54857 256 - . alignment_id 1 ; Query SPP00000005_1.0 ; Align 54858 61 78 ; Align 54277 88 99 ; Align 50201 121 201 # --- END OF GFF DUMP --- # -- completed exonerate analysis