Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP00000033_1.0.fa -t ./exonerate/SPP00000033_1.0_6_genomic.fa_exonerate.fa] Hostname: [luke] C4 Alignment: ------------ Query: SPP00000033_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Homo sapiens # Complete Target: gi|357434208|gb|JH378155.1|:subseq(1196959,301160) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00051, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 738 Query range: 250 -> 435 Target range: 150554 -> 149999 251 : ThrLysProLeuGlyThrGlnValAlaValAsnAlaHisGlnTrpLeuAspAsnProG : 270 .!!||||||||||||||||||||||||||||||||||||||||||||||||||||||| AlaLysProLeuGlyThrGlnValAlaValAsnAlaHisGlnTrpLeuAspAsnProG 150554 : GCTAAACCCTTAGGAACCCAAGTTGCTGTCAATGCACACCAATGGCTGGATAATCCTG : 150497 271 : luArgTrpAsnLysValLysMetValValSerArgGluGluValGluLeuAlaTyrGl : 289 ||||| !!!!.:!!||||||:!!||||||||| !!||| !!||||||||||||||||| luArgGlyLysGluValLysLeuValValSerGlyGlu***ValGluLeuAlaTyrGl 150496 : AAAGAGGGAAGGAGGTGAAGTTGGTGGTCTCTGGAGAATAGGTAGAGCTGGCCTATCA : 150440 290 : nGluAlaMetPheAsnMetAlaThrLeuAsnArgThrAlaAlaGlyLeuMetHisThr : 308 ||||||||||!!.|||||||||||||||! !!:!|||||||||||||||||||||||| nGluAlaMetLeuAsnMetAlaThrLeuIleGlnThrAlaAlaGlyLeuMetHisThr 150439 : GGAAGCCATGTTAAATATGGCCACCCTCATCCAAACTGCTGCTGGATTAATGCACACA : 150383 309 : PheAsnAlaHisAlaAlaThrAspIleThrGlyPheGlyIleLeuGlyHisSerGlnA : 328 !!||||||||||||||||||! !||||||||||||||||||! !||||||||||||| ValAsnAlaHisAlaAlaThrGlyIleThrGlyPheGlyIleProGlyHisSerGlnA 150382 : GTCAATGCCCATGCGGCCACAGGTATCACAGGCTTTGGTATTCCAGGACACTCTCAGA : 150323 329 : snLeuAlaLysGlnGlnArgAsnGluValSerPheValIleHisAsnLeuProIleIl : 347 |||||||||||||||||||||||!!:||||||||||||! !||||||||||||:!!|| snLeuAlaLysGlnGlnArgAsnAspValSerPheValThrHisAsnLeuProValIl 150322 : ATCTTGCAAAACAGCAAAGAAATGATGTGTCCTTTGTCACTCATAATCTGCCAGTCAT : 150266 348 : eAlaLysMetAlaAlaValSerLysAlaSerGlyArgPheGlyLeuLeuGlnGlyThr : 366 ||||||||||||||||:!!||||||.!!||||||!:!||| !!||||||||||||||| eAlaLysMetAlaAlaIleSerLysThrSerGlyGlnPhe***LeuLeuGlnGlyThr 150265 : TGCCAAGATGGCTGCCATCAGCAAGACCAGTGGGCAGTTTTGACTTCTTCAGGGAACC : 150209 367 : SerAlaGluThrSerGlyGlyLeuLeuIleCysLeuProArgGluGlnAlaAlaArgP : 386 ||||||||||||||| !!|||||||||||||||||||||!:!||| !!!.!! !!.!| SerAlaGluThrSerArgGlyLeuLeuIleCysLeuProLysGlu***ValAspHisP 150208 : TCAGCTGAAACCTCAAGAGGATTATTGATTTGTCTTCCAAAAGAATAGGTGGATCACT : 150149 387 : heCysSerGluIleLysSerSerLysTyrGlyGluGlyHisGlnAlaTrpIleValGl : 405 ||||||||||||||!:!|||||||||||| !!||||||||||||!.!||||||!.!|| heCysSerGluIleArgSerSerLysTyrArgGluGlyHisGlnGlyTrpIleAlaGl 150148 : TTTGTTCTGAAATCAGATCTTCCAAGTATAGAGAGGGTCACCAAGGGTGGATCGCTGG : 150092 406 : yIleValGluLysGlyAsnArgThrAlaArgIleIleAspLysProArgValIleGlu : 424 |||||||||||||||||||!:!|||||| !!:!!|||||||||||| !!||||||||| yIleValGluLysGlyAsnGlnThrAlaTrpValIleAspLysProGlyValIleGlu 150091 : CATTGTGGAAAAGGGAAACCAGACAGCCTGGGTCATTGACAAGCCTGGAGTTATTGAG : 150035 425 : ValLeuProArgGlyAlaThrAlaAlaValLeu : 435 |||||||||!.!! !||||||||||||!.!||| ValLeuProHisValAlaThrAlaAlaAlaLeu 150034 : GTCCTACCTCATGTGGCCACTGCCGCTGCTCTT : 150000 vulgar: SPP00000033_1.0 250 435 . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) 150554 149999 - 738 M 185 555 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-14 ##type DNA # # # seqname source feature start end score strand frame attributes # gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local gene 150000 150554 738 - . gene_id 1 ; sequence SPP00000033_1.0 ; gene_orientation . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local cds 150000 150554 . - . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local exon 150000 150554 . - . insertions 0 ; deletions 0 gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local similarity 150000 150554 738 - . alignment_id 1 ; Query SPP00000033_1.0 ; Align 150555 251 555 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000033_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Homo sapiens # Complete Target: gi|357434208|gb|JH378155.1|:subseq(1196959,301160) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00051, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 224 Query range: 104 -> 169 Target range: 150959 -> 150764 105 : GlyAlaGlyProSerProThrPheProAlaLeuGlyIleGlyMetAspSerCysValI : 124 |||!.!||||||!!!|||!:! ! !!|||! !||||||||||||||||||||||||| GlyGlyGlyProTrpProSerProSerAlaGlnGlyIleGlyMetAspSerCysValI 150959 : GGGGGTGGGCCCTGGCCCAGCCCTTCCGCTCAGGGCATTGGGATGGACTCTTGCGTCA : 150902 125 : leProLeuArgHisGlyGlyLeuSerLeuValGlnThrThrAspPhePheTyrProLe : 143 ||||||||||||||! !! !||||||! !|||||||||||||||||||||||| !!|| leProLeuArgHisGluAspLeuSerGlnValGlnThrThrAspPhePheTyrSerLe 150901 : TTCCCCTGAGACATGAGGACCTGTCACAGGTGCAGACCACAGACTTCTTCTACTCCTT : 150845 144 : uValGluAspProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeu : 162 |:!!|||||| !!|||||||||||| !!! !|||||||||!!.||||||!!!|||||| uMetGluAspSerTyrMetMetGlyCysThrAlaCysAlaLysValLeuArgAspLeu 150844 : GATGGAGGATTCCTACATGATGGGGTGCACAGCTTGTGCCAAAGTGCTAAGGGACCTC : 150788 163 : TyrAlaMetGlyIleThrGlu : 169 !::||||||! !|||.!!||| TrpAlaMetValIleAlaGlu 150787 : TGGGCCATGGTCATTGCTGAG : 150765 vulgar: SPP00000033_1.0 104 169 . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) 150959 150764 - 224 M 65 195 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-14 ##type DNA # # # seqname source feature start end score strand frame attributes # gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local gene 150765 150959 224 - . gene_id 2 ; sequence SPP00000033_1.0 ; gene_orientation . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local cds 150765 150959 . - . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local exon 150765 150959 . - . insertions 0 ; deletions 0 gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local similarity 150765 150959 224 - . alignment_id 2 ; Query SPP00000033_1.0 ; Align 150960 105 195 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000033_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Homo sapiens # Complete Target: gi|357434208|gb|JH378155.1|:subseq(1196959,301160) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00051, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 165 Query range: 176 -> 258 Target range: 150754 -> 145503 177 : LeuSerValSerGlnSerMetSerGluGluGluArgGluLysValThrProLeuMetV : 196 :!!..!||||||||||||||||||||||||||||||||||||:!!! !|||||||||: ValAspValSerGlnSerMetSerGluGluGluArgGluLysIleMetProLeuMetI 150754 : GTTGATGTTAGCCAGAGTATGAGTGAGGAGGAACGGGAAAAGATAATGCCACTCATGA : 150697 197 : alLysGlyPheArgAsp-AlaAlaGluGluGlyGlyThrAlaValThrGlyGlyGlnT : 215 !!||||||||| !!|||#|||:!!||||||! !||||||.!!|||||||||||||||| leLysGlyPheTrpAsp#AlaSerGluGluGluGlyThrThrValThrGlyGlyGlnT 150696 : TCAAAGGCTTTTGGGACAGCTTCTGAGGAGGAAGGAACTACAGTGACAGGTGGACAAA : 150639 216 : hrValValAsnProTrpIleIleIleGlyGlyValAlaThrValValCysGlnProAs : 234 ||||||||!.! !!||| :!!|||||||||||| !!||||||!.! ! !! ! hrValValThrSerTrp---LeuIleGlyGlyValProThrValAlaThr***CysLe 150638 : CGGTGGTCACCTCTTGG---CTTATCGGTGGGGTTCCCACTGTGGCAACTTAATGCTT : 150585 235 : nGluPheIleMet >>>> Target Intron 1 >>>> ProAspSerAlaValV : 244 !.!. !:!! 5007 bp !...|||||||||: uIleMetProLeu-+ ++SerSerSerAlaValL 150584 : AATAATGCCACTGtt.........................agAGCTCAAGTGCTGTGC : 145548 245 : alGlyAspValLeuValLeuThrLysProLeuGlyThrGlnVal : 258 !!||||||:!!|||:!!! !:!!:!!||| !|||! !.!.:!! euGlyAspLeuLeuLeuSerSerGluProAlaGlyArgAsnIle 145547 : TGGGAGATCTGCTGCTCTCTTCAGAGCCAGCAGGCAGGAATATT : 145504 vulgar: SPP00000033_1.0 176 258 . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) 150754 145503 - 165 M 25 75 F 0 1 M 19 57 G 1 0 M 17 51 5 0 2 I 0 5003 3 0 2 M 20 60 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-14 ##type DNA # # # seqname source feature start end score strand frame attributes # gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local gene 145504 150754 165 - . gene_id 3 ; sequence SPP00000033_1.0 ; gene_orientation + gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local cds 150571 150754 . - . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local exon 150571 150754 . - . insertions 0 ; deletions 1 ; frameshifts 1 gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local splice5 150569 150570 . - . intron_id 1 ; splice_site "TT" gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local intron 145564 150570 . - . intron_id 1 gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local splice3 145564 145565 . - . intron_id 0 ; splice_site "AG" gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local cds 145504 145563 . - . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local exon 145504 145563 . - . insertions 0 ; deletions 0 gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local similarity 145504 150754 165 - . alignment_id 3 ; Query SPP00000033_1.0 ; Align 150755 177 75 ; Align 150679 202 57 ; Align 150622 222 51 ; Align 145564 239 60 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000033_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Homo sapiens # Complete Target: gi|357434208|gb|JH378155.1|:subseq(1196959,301160) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00051, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 118 Query range: 21 -> 79 Target range: 151175 -> 151002 22 : GlyProAlaGlyLeuThrLeuGlyArgSerPheSerAsnTyrArgProPheGluProG : 41 ||| !!|||!.!! !:!!|||||||||:!!||||||!:!! !!:! !!|||:!!|||| GlySerAlaAlaSerSerLeuGlyArgAlaPheSerSerSerGlnSerPheGlnProG 151175 : GGCTCCGCGGCCTCGTCTCTGGGTCGGGCCTTCTCGAGCTCCCAGTCCTTCCAGCCCC : 151118 42 : lnAlaLeuGlyLeuSerProSerTrpArgLeu--ThrGlyPheSerGlyMetLysGly : 59 |||||! !|||||||||! !|||||| !!|||## ||| !!||||||! !|||! ! lnAlaTrpGlyLeuSerLeuSerTrp***Leu##---GlyValSerGlyArgLysAsp 151117 : AGGCATGGGGCCTCAGCCTGAGCTGGTGACTGAC---GGCGTCTCTGGCAGGAAGGAC : 151065 60 : UnkGlyCysLysValProGlnGluAlaLeuLeuLysLeuLeuAlaGlyLeuThrArgP : 79 |||||||||! !! !||||||||||||! !|||!!!||||||||||||||||||| ***GlyCysLysAspLeuGlnGluAlaLeuProLysPheLeuAlaGlyLeuThrArgP 151064 : TGAGGCTGCAAGGACCTGCAGGAGGCACTACCCAAATTCCTGGCGGGCCTGACACGGC : 151005 80 : ro : 79 || ro 151004 : CC : 151003 vulgar: SPP00000033_1.0 21 79 . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) 151175 151002 - 118 M 30 90 F 0 2 G 1 0 M 27 81 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-14 ##type DNA # # # seqname source feature start end score strand frame attributes # gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local gene 151003 151175 118 - . gene_id 4 ; sequence SPP00000033_1.0 ; gene_orientation . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local cds 151003 151175 . - . gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local exon 151003 151175 . - . insertions 0 ; deletions 1 ; frameshifts 2 gi|357434208|gb|JH378155.1|:subseq(1196959,301160) exonerate:protein2genome:local similarity 151003 151175 118 - . alignment_id 4 ; Query SPP00000033_1.0 ; Align 151176 22 90 ; Align 151084 53 81 # --- END OF GFF DUMP --- # -- completed exonerate analysis