Command line: [exonerate -m p2g --showtargetgff -q SPP00000037_1.0.fa -t SPP00000037_1.0.GL397332.1/GL397332.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000037_1.0 # Protein # SECIS binding protein 2 (SBP2) # Homo sapiens # Complete Target: GL397332.1:subseq(9281299,101732) dna:supercontig supercontig:Nleu1.0:GL397332.1:1:12460697:1 REF:[revcomp] Model: protein2genome:local Raw score: 138 Query range: 65 -> 232 Target range: 51732 -> 50917 66 : ThrGluAspMetAlaPheGlyAlaSerThrPheProProGlnTyrLeuSerSerGluIle : 85 |||||||||||||||!!.|||||||||! !||| !!|||||| ! ||||||! !:!!||| ThrGluAspMetAlaLeuGlyAlaSerArgPheSerProGlnLysLeuSerPheLysIle 51732 : ACTGAAGATATGGCGTTAGGAGCGTCAAGGTTTTCCCCTCAGAAGTTGTCTTTCAAGATA : 51675 86 : ThrLeuHisProTyrAlaTyrSerProTyrThrLeuAspSerThrGlnAsnValTyrSer : 105 ||| ||| ! !! ! !! ! !! ! ! ! ! !:!!|||!! ||| Thr------ProProLeuCysLeuLeuLeuArgThrArgValTyrIleHisVal***Ser 51674 : ACT------CCACCCCTATGCCTACTTCTTAGAACCCGGGTCTATATACATGTTTAATCA : 51621 106 : ValProGlySerGlnTyrLeuTyrAsnGlnProSerCysTyrArgGlyPheGlnThrVal : 125 ||||||!.!|||!!. ! ! !|||||||||||||||!! !:!! !||||||! !||| ValProAlaSerHisSerAspArgAsnGlnProSerCys***GlnAspPheGlnMetVal 51620 : GTGCCCGCCTCCCACAGTGATCGTAACCAACCTAGCTGTTAGCAAGACTTTCAAATGGTA : 51561 126 : LysHisArgAsnGluAsnThrCysProLeuProGlnGluMetLysAlaLeuPheLysLys : 145 |||! !|||||||||:!! !! ! !!! ! !!::!.!....! !:!!||| ! LysProArgAsnGluHisLeuSerSerHisThrArgAsnGlnThrLeuIlePhePheLeu 51560 : AAGCCCCGAAATGAGCACTTGTCCTCTCACACAAGAAATCAAACTCTGATTTTTTTTTTG : 51501 146 : {Ly} >>>> Target Intron 1 >>>> {s}ThrTyrAspGluLysLysThrTyr : 154 {||} 319 bp {|}! ! !:!!|||!.!||| {Ly}++ +-{s}LysArg******GluLysAsnTyr 51500 : {AA}gt.........................aa{A}AAAAGATGATGAGAAAAAAACTAT : 51155 155 : AspGlnGlnLysPheAspSerGluArgAlaAspGlyThrIleSerSerGluIleLysSer : 174 |||:!!|||||| !|||!!!|||! !.!!!!: ! ! !..!..! !!!...! AspGluGlnLysAlaAspArgGluLeuThrGlu---CysCysHisGlnArg***AsnGln 51154 : GATGAGCAAAAGGCTGACAGAGAGCTGACAGAA---TGCTGCCATCAGAGATGAAATCAG : 51098 175 : AlaArgGlySerHisHisLeuSerIleTyrAlaGluAsnSerLeuLysSerAspGlyTyr : 194 !! !!.! ! ! !! ! !!:!! !!|||:!!!..!:!||||||! !||||||:!! GlnMetAlaHisIleValCysProLeuAspAlaLysArgAsnLeuLysLeuAspGlyHis 51097 : CAAATGGCTCACATCGTTTGTCCACTTGATGCTAAGAGGAATTTGAAATTGGATGGGCAT : 51038 195 : HisLysArgThrAsp----ArgLysSerArgIleIleAlaLysAsnValSerThrSerLy : 213 !!.! |||! !!!:####!:!:!!!!!!:!! ! !!.!|||!:!! !||||||||||| GlnIleArgMetGlu####GlnGluThrGlnAsnHisGlyLysSerGlySerThrSerLy 51037 : CAGATCAGAATGGAACAGACAAGAAACCCAGAATCATGGAAAAAGTGGCTCTACCTCCAA : 50977 214 : sProGluPheGluPheThrThrLeuAspPheProGluLeuGlnGlyAlaGluAsnAsn : 232 ||||! !!!.||||||||||||||||||.!!|||:!!|||:!! ! !!||||||||| sProGlyLeuGluPheThrThrLeuAspLeuProLysLeuLysHisProGluAsnAsn 50976 : ACCTGGGTTGGAATTTACCACGCTGGATCTTCCTAAACTTAAGCATCCAGAGAACAAT : 50918 vulgar: SPP00000037_1.0 65 232 . GL397332.1:subseq(9281299,101732) 51732 50917 - 138 M 21 63 G 2 0 M 57 171 S 0 2 5 0 2 I 0 315 3 0 2 S 1 1 M 19 57 G 1 0 M 33 99 F 0 4 M 33 99 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-27 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local gene 50918 51732 138 - . gene_id 1 ; sequence SPP00000037_1.0 ; gene_orientation + GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local cds 51497 51732 . - . GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local exon 51497 51732 . - . insertions 0 ; deletions 2 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local splice5 51495 51496 . - . intron_id 1 ; splice_site "GT" GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local intron 51178 51496 . - . intron_id 1 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local splice3 51178 51179 . - . intron_id 0 ; splice_site "AA" GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local cds 50918 51177 . - . GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local exon 50918 51177 . - . insertions 0 ; deletions 1 ; frameshifts 4 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local similarity 50918 51732 138 - . alignment_id 1 ; Query SPP00000037_1.0 ; Align 51733 66 63 ; Align 51670 89 171 ; Align 51177 147 57 ; Align 51120 167 99 ; Align 51017 200 99 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000037_1.0 # Protein # SECIS binding protein 2 (SBP2) # Homo sapiens # Complete Target: GL397332.1:subseq(9281299,101732) dna:supercontig supercontig:Nleu1.0:GL397332.1:1:12460697:1 REF:[revcomp] Model: protein2genome:local Raw score: 136 Query range: 313 -> 453 Target range: 50127 -> 49503 314 : AlaAlaProLysAsnValThrSerMetIleAsnLeuLysThrIleAlaSerSerAlaAsp : 333 .!!||||||||||||||||||! !|||! !!..|||||||||:!!||||||||||||||| ThrAlaProLysAsnValThrPheMetThrArgLeuLysThrValAlaSerSerAlaAsp 50127 : ACTGCCCCTAAAAATGTTACTTTCATGACAAGACTAAAGACGGTTGCTTCATCAGCAGAT : 50070 334 : ProLysAsnValSerIle--ProSerSerGluAlaLeuSerSerAspProSerTyrAsnL : 353 |||||| :!!|||:!:## !!|||||||||!.!! !|||! !|||||||||||||||| ProLys---IleSerVal##SerSerSerGluValSerSerLeuAspProSerTyrAsnL 50069 : CCTAAA---ATTTCAGTGGATCATCCTCTGAAGTTTCATCTTTGGATCCTTCCTACAACA : 50011 354 : ysGluLysHisIleIleHisProThrGlnLysSerLysAlaSerGlnGlySerAspLeuG : 373 ||||||||||| ! ! !! ! !.!.!.. !!||| ! !:!! !! !| ysGluLysHisSerSerIleLeuLeuAsnSerProLysHisHisLys---ValValThrG 50010 : AAGAGAAACACTCATCCATCCTACTAAACAGCCCCAAGCATCACAAG---GTGGTGACTG : 49954 374 : luGlnAsnGluAlaSerArgLysAsnLysLysLysLysGluLysSerThrSer-LysTyr : 392 |||||:!!|||||||||..!|||||| :!!|||:!!!!..!! !!|||#||| luGlnAspGluAlaSerGluLysAsn------GluLysGlnAsnGlyProSer#LysIle 49953 : AGCAAGATGAAGCCTCAGAAAAGAAT------GAGAAACAGAACGGTCCAAGTGAAAATA : 49902 393 : GluValLeuThrValGlnGluProProArgIleGluAspAlaGluGluPheProAsnLeu : 412 !:!!|||||||||!!.||||||! !|||||||||:!! !! ! ! ! !..!! ! ***IleLeuThrValHisGluProLeuArgIleGluAsnLysAlaGlyArgSerGlySer 49901 : TGAATCCTGACTGTTCATGAGCCACTAAGAATTGAAAATAAGGCTGGGCGCAGTGGCTCA : 49842 413 : AlaValAlaSerGluArg >>>> Target Intron 1 >>>> ArgAspArgIleG : 423 ..!:!! !|||:!!!.! 213 bp ! !!!:||| . CysLeu***SerGlnHis-+ ++ProGluArgGlnS 49841 : TGCCTGTAATCCCAACACtt.........................agCCTGAGCGACAGA : 49596 424 : luThrProLysPheGlnSerLysGlnGlnProGlnAspAsnPheLysAsnAsnValLysL : 443 ..! ! !! ! :!!!.!|||:!!:!! !:!!:!!|||||| !|||! !! !|||| erLysThrLeuProLysLysLysLysLysIleLysAsnAsnPheLeuAsnIleGlyLysL 49595 : GCAAGACCCTGCCAAAAAAAAAAAAAAAAATTAAGAATAATTTTTTAAATATTGGGAAGA : 49536 444 : ysSerGlnLeuProValGlnLeuAspLeuGly : 453 ||||||||:!!! !:!!||||||||||||||| ysSerGlnIleLeuLeuGlnLeuAspLeuGly 49535 : AGAGCCAGATTCTGCTGCAGTTGGATTTGGGG : 49504 vulgar: SPP00000037_1.0 313 453 . GL397332.1:subseq(9281299,101732) 50127 49503 - 136 M 22 66 G 1 0 M 3 9 F 0 2 M 29 87 G 1 0 M 12 36 G 2 0 M 7 21 F 0 1 M 28 84 5 0 2 I 0 209 3 0 2 M 35 105 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-27 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local gene 49504 50127 136 - . gene_id 2 ; sequence SPP00000037_1.0 ; gene_orientation + GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local cds 49822 50127 . - . GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local exon 49822 50127 . - . insertions 0 ; deletions 4 ; frameshifts 3 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local splice5 49820 49821 . - . intron_id 1 ; splice_site "TT" GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local intron 49609 49821 . - . intron_id 1 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local splice3 49609 49610 . - . intron_id 0 ; splice_site "AG" GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local cds 49504 49608 . - . GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local exon 49504 49608 . - . insertions 0 ; deletions 0 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local similarity 49504 50127 136 - . alignment_id 2 ; Query SPP00000037_1.0 ; Align 50128 314 66 ; Align 50062 337 9 ; Align 50051 340 87 ; Align 49964 370 36 ; Align 49928 384 21 ; Align 49906 391 84 ; Align 49609 419 105 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000037_1.0 # Protein # SECIS binding protein 2 (SBP2) # Homo sapiens # Complete Target: GL397332.1:subseq(9281299,101732) dna:supercontig supercontig:Nleu1.0:GL397332.1:1:12460697:1 REF:[revcomp] Model: protein2genome:local Raw score: 121 Query range: 253 -> 412 Target range: 50271 -> 21049 254 : LeuLeuArgGluValValLysProAlaAlaValLeuSerLysGlyGluIleValValLys : 273 ||||||||||||! !|||||||||||| ! !||||||||||||||||||||||||||| LeuLeuArgGluGluValLysProAlaArgArgLeuSerLysGlyGluIleValValLys 50271 : CTTCTAAGAGAAGAGGTAAAACCAGCTAGAAGGTTATCAAAAGGTGAAATCGTGGTGAAA : 50214 274 : <->AsnAsnProAsnGluSerValThrAlaAsnAlaAlaThrAsnSerProSerCysThr : 292 |||||||||! !||||||||| !!||||||.!!||||||:!!||||||! ! ! AsnAsnAsnProIleGluSerValProAlaAsnThrAlaThrAspSerProTyrValTrp 50213 : AATAATAATCCAATTGAGTCTGTGCCTGCTAACACTGCTACCGACTCCCCTTACGTATGG : 50154 293 : ArgGluLeuSerTrpThrProMetGlyTyrValValArgGlnThrLeuSerThrGluLeu : 312 ..!...! !!.! ||| ! ! ! ! !!.! |||!!!! !|||..!||| GluSerTyrLysProThrGlyTyrThrAlaProLysAsnValThrPheMetThrArgLeu 50153 : GAGAGTTATAAACCAACGGGTTACACTGCCCCTAAAAATGTTACTTTCATGACAAGACTA : 50094 313 : SerAlaAlaProLysAsnValThrSerMetIleAsnLeu-----LysThrIleAlaSerS : 331 !.!.!!!.! !!..!:::!.! ! !!! |||::::!!#####...:!! !!.!|||| LysThrValAlaSerSerAlaAspProLysIleSerVal#####SerSerGluValSerS 50093 : AAGACGGTTGCTTCATCAGCAGATCCTAAAATTTCAGTGGATCATCCTCTGAAGTTTCAT : 50032 332 : erAlaAspProLysAsnValSerIleProSerSerGluAlaLeuSerSerAspProSerT : 351 || !||||||... !! !!.! ! !|||... !||| !!:!..!|||!.!: erLeuAspProSerTyrAsnLysGluLysHisSerSerIleLeuLeuAsnSerProLysH 50031 : CTTTGGATCCTTCCTACAACAAAGAGAAACACTCATCCATCCTACTAAACAGCCCCAAGC : 49972 352 : yrAsnLys<->GluLysHisIleIleHisProThrGlnLysSerLysAlaSerGlnGlyS : 370 !!:!!||| ! !! .!. ! !.!. !!:!!:!!|||!:!:!! !..!.!.||| isHisLysValValThrGluGlnAspGluAlaSerGluLysAsnGluLysGlnAsnGlyP 49971 : ATCACAAGGTGGTGACTGAGCAAGATGAAGCCTCAGAAAAGAATGAGAAACAGAACGGTC : 49912 371 : er{A} >>>> Target Intron 1 >>>> {sp}LeuGluGlnAsnGluAlaSerA : 379 !!{ } 28734 bp { !} !|||::!.!...!! !|||! ro{T}++ ++{hr}ArgGluArgGluArgAspSerL 49911 : CA{A}gt.........................ag{CC}AGAGAAAGAGAGCGAGACTCTC : 21151 380 : rgLysAsnLysLysLysLysGluLysSerThrSerLysTyrGluValLeuThrValGlnG : 399 !|||!!.||||||||||||:!!|||!!!! !!.!!:! !!! !..!:!!.!! !!!.! euLysLysLysLysLysLysLysLysArgLysLysArgAsnValThrMetAlaArgHisG 21150 : TCAAAAAAAAAAAAAAAAAGAAAAAAAGAAAGAAAAGAAACGTAACTATGGCCAGGCACG : 21091 400 : luProProArgIleGluAspAlaGluGluPheProAsnLeu : 412 ! !!|||:!: !!..!!.! !..!||| !|||||| lyGlySerArgLeu***SerValProArgPheAsnAsnLeu 21090 : GTGGCTCACGCCTGTAATCTGTGCCAAGGTTTAACAATTTA : 21050 vulgar: SPP00000037_1.0 253 412 . GL397332.1:subseq(9281299,101732) 50271 21049 - 121 M 20 60 G 0 3 M 52 156 F 0 5 M 28 84 G 0 3 M 17 51 S 0 1 5 0 2 I 0 28730 3 0 2 S 1 2 M 41 123 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-27 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local gene 21050 50271 121 - . gene_id 3 ; sequence SPP00000037_1.0 ; gene_orientation + GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local cds 49909 50271 . - . GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local exon 49909 50271 . - . insertions 6 ; deletions 0 ; frameshifts 5 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local splice5 49907 49908 . - . intron_id 1 ; splice_site "GT" GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local intron 21175 49908 . - . intron_id 1 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local splice3 21175 21176 . - . intron_id 0 ; splice_site "AG" GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local cds 21050 21174 . - . GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local exon 21050 21174 . - . insertions 0 ; deletions 0 GL397332.1:subseq(9281299,101732) exonerate:protein2genome:local similarity 21050 50271 121 - . alignment_id 3 ; Query SPP00000037_1.0 ; Align 50272 254 60 ; Align 50209 274 156 ; Align 50048 326 84 ; Align 49961 354 51 ; Align 21173 372 123 # --- END OF GFF DUMP --- # -- completed exonerate analysis