Command line: [exonerate --showtargetgff --model protein2genome TR1.prot TR1_UCSC.fa] C4 Alignment display: Model: protein2genome Raw score: 2366 Aligned positions 0->499 of query Aligned positions 12889->49145 of target Query: TR1 Target: 12 dna:chromosome chromosome:CHIMP1A:12:105672694:106000000:1 1 : MetAsnGlyProGluAspLeuProLysSerTyrAspTyrAspLeuIleIleIleGlyGly : 19 ||||||||||||||||||||||||:!!||||||||||||||||||||||||||||||||| MetAsnGlyProGluAspLeuProGluSerTyrAspTyrAspLeuIleIleIleGlyGly 12890 : ATGAACGGCCCTGAAGATCTTCCCGAGTCCTATGACTATGACCTTATCATCATTGGAGGT : 12946 20 : GlySerGlyGlyLeuAlaAlaAlaLys >>>> Target Intron 1 >>>> GluA : 30 ||||||||||||||||||||||||||| 1852 bp |||| GlySerGlyGlyLeuAlaAlaAlaLys GluA 12947 : GGCTCAGGAGGTCTGGCAGCTGCTAAGgc.........................agGAGG : 14831 31 : laAlaGlnTyrGlyLysLysValMetValLeuAspPheValThrProThrProLeuGlyT : 50 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| laAlaGlnTyrGlyLysLysValMetValLeuAspPheValThrProThrProLeuGlyT 14832 : CAGCCCAATATGGCAAGAAGGTGATGGTCCTGGACTTTGTCACTCCCACCCCTCTTGGAA : 14891 51 : hrArgTrp{G} >>>> Target Intron 2 >>>> {ly}LeuGlyGlyThrCysV : 59 ||||||||{|} 2477 bp {||}|||||||||||||||| hrArgTrp{G} {ly}LeuGlyGlyThrCysV 14892 : CTAGATGG{G}gt.........................ag{GT}CTCGGAGGAACATGTG : 17395 60 : alAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaL : 79 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| alAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaL 17396 : TGAATGTGGGTTGCATACCTAAAAAACTGATGCATCAAGCAGCTTTGTTAGGACAAGCCC : 17455 80 : euGlnAspSerArgAsnTyrGlyTrpLysValGluGluThr{V} >>>> Target In : 93 |||||||||||||||||||||||||||||||||||||||||{|} 3016 euGlnAspSerArgAsnTyrGlyTrpLysValGluGluThr{V} 17456 : TGCAAGACTCTCGAAATTATGGATGGAAAGTCGAGGAGACA{G}gt.............. : 17500 94 : tron 3 >>>> {al}LysHisAspTrpAspArgMetIleGluAlaValGlnAsnHisI : 108 bp {||}||||||||||||||||||||||||||||||||||||||||||| {al}LysHisAspTrpAspArgMetIleGluAlaValGlnAsnHisI 17501 : ...........ag{TT}AAGCATGATTGGGACAGAATGATAGAAGCTGTACAGAATCACA : 20558 109 : leGlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluA : 128 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| leGlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluA 20559 : TTGGCTCTTTGAATTGGGGCTACCGAGTAGCTCTGCGGGAGAAAAAAGTCGTCTATGAGA : 20618 129 : snAlaTyrGlyGlnPheIleGlyProHisArgIleLys >>>> Target Intron 4 : 141 |||||||||||||||||||||||||||||||||||||| 436 bp snAlaTyrGlyGlnPheIleGlyProHisArgIleLys 20619 : ATGCTTACGGGCAATTTATTGGTCCTCACAGGATTAAGgt.................... : 20659 142 : >>>> AlaThrAsnAsnLysGlyLysGluLysIleTyrSerAlaGluSerPheLeuIl : 158 ||||||||||||||||||||||||||||||||||||||||||!!!|||||||| AlaThrAsnAsnLysGlyLysGluLysIleTyrSerAlaGluArgPheLeuIl 20660 : .....agGCAACAAATAATAAAGGCAAAGAAAAAATTTATTCAGCAGAGAGATTTCTCAT : 21144 159 : eAlaThrGlyGluArgProArgTyrLeuGlyIleProGlyAspLysGluTyrCysIleSe : 178 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| eAlaThrGlyGluArgProArgTyrLeuGlyIleProGlyAspLysGluTyrCysIleSe 21145 : TGCCACTGGTGAAAGACCACGTTACTTGGGCATCCCTGGTGACAAAGAATACTGCATCAG : 21204 179 : r{Se} >>>> Target Intron 5 >>>> {r}AspAspLeuPheSerLeuProTy : 187 |{||} 1506 bp {|}||||||||||||||||||||||| r{Se} {r}AspAspLeuPheSerLeuProTy 21205 : C{AG}gt.........................ag{T}GATGATCTTTTCTCCTTGCCTTA : 22737 188 : rCysProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPh : 207 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| rCysProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPh 22738 : CTGCCCGGGTAAGACCCTGGTTGTTGGAGCATCCTATGTCGCTTTGGAGTGCGCTGGATT : 22797 208 : eLeuAlaGlyIleGlyLeuGlyValThrValMetValArgSerIleLeuLeuArgGlyPh : 227 |||||||||||||||||||! !|||||||||||||||||||||||||||||||||||||| eLeuAlaGlyIleGlyLeuAspValThrValMetValArgSerIleLeuLeuArgGlyPh 22798 : TCTTGCTGGTATTGGTTTAGACGTCACTGTTATGGTTAGGTCCATTCTTCTTAGAGGATT : 22857 228 : eAspGlnAspMetAlaAsnLysIleGlyGluHisMetGluGluHisGlyIleLysPheIl : 247 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| eAspGlnAspMetAlaAsnLysIleGlyGluHisMetGluGluHisGlyIleLysPheIl 22858 : TGACCAGGACATGGCCAACAAAATTGGTGAACACATGGAAGAACATGGCATCAAGTTTAT : 22917 248 : eArgGlnPheValProIleLys >>>> Target Intron 6 >>>> ValGluGln : 257 |||||||||||||||||||||| 2960 bp ||||||||| eArgGlnPheValProIleLys ValGluGln 22918 : AAGACAGTTCGTACCAATTAAAgt.........................agGTTGAACAA : 25907 258 : IleGluAlaGlyThrProGlyArgLeuArgValValAlaGlnSerThrAsnSerGluGlu : 277 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| IleGluAlaGlyThrProGlyArgLeuArgValValAlaGlnSerThrAsnSerGluGlu 25908 : ATTGAAGCGGGGACACCAGGCCGACTCAGAGTAGTAGCTCAGTCCACCAATAGTGAGGAA : 25967 278 : IleIleGluGlyGluTyrAsnThr >>>> Target Intron 7 >>>> ValMetL : 288 |||||||||||||||||||||||| 915 bp |||:!!| IleIleGluGlyGluTyrAsnThr ValLeuL 25968 : ATCATTGAAGGAGAATATAATACGgt.........................agGTGTTGC : 26915 289 : euAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGluThrValGlyValLysI : 308 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| euAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGluThrValGlyValLysI 26916 : TGGCAATAGGAAGAGATGCTTGCACAAGAAAAATTGGCTTAGAAACCGTAGGGGTGAAGA : 26975 309 : leAsnGlu{Ly} >>>> Target Intron 8 >>>> {s}ThrGlyLysIleProV : 317 ||||||||{||} 1100 bp {|}|||||||||||||||| leAsnGlu{Ly} {s}ThrGlyLysIleProV 26976 : TAAATGAA{AA}gt.........................ag{G}ACTGGAAAAATACCTG : 28102 318 : alThrAspGluGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluA : 337 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| alThrAspGluGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluA 28103 : TCACAGATGAAGAACAGACCAATGTGCCTTACATCTATGCCATTGGCGATATATTGGAGG : 28162 338 : spLysValGluLeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuT : 357 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| spLysValGluLeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuT 28163 : ATAAGGTGGAGCTCACCCCAGTTGCAATCCAGGCAGGAAGATTGCTGGCTCAGAGGCTCT : 28222 358 : yrAlaGlySerThrValLys >>>> Target Intron 9 >>>> CysAspTyrGl : 367 |||||||||||||||||||| 3858 bp ||||||||||| yrAlaGlySerThrValLys CysAspTyrGl 28223 : ATGCAGGTTCCACTGTCAAGgt.........................agTGTGACTATGA : 32110 368 : uAsnValProThrThrValPheThrProLeuGluTyrGlyAlaCysGlyLeuSerGluGl : 387 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| uAsnValProThrThrValPheThrProLeuGluTyrGlyAlaCysGlyLeuSerGluGl 32111 : AAATGTTCCAACCACTGTATTTACTCCTTTGGAATATGGTGCTTGTGGCCTTTCTGAGGA : 32170 388 : uLysAlaValGluLysPheGlyGluGluAsnIleGlu >>>> Target Intron 10 : 400 ||||||||||||||||||||||||||||||||||||| 2593 bp uLysAlaValGluLysPheGlyGluGluAsnIleGlu 32171 : GAAAGCTGTGGAGAAGTTTGGGGAAGAAAATATTGAGgt..................... : 32211 401 : >>>> ValTyrHisSerTyrPheTrpProLeuGluTrpThrIleProSerArgAspAs : 417 ||||||||||||||||||||||||||||||||||||||||||||||||||||| ValTyrHisSerTyrPheTrpProLeuGluTrpThrIleProSerArgAspAs 32212 : .....agGTTTACCATAGTTACTTTTGGCCATTGGAATGGACGATTCCGTCAAGAGATAA : 34853 418 : nAsnLysCysTyrAlaLysIleIleCysAsnThrLysAspAsn >>>> Target Int : 432 ||||||||||||||||||||||||||||||||||||||||||| 4797 nAsnLysCysTyrAlaLysIleIleCysAsnThrLysAspAsn 34854 : CAACAAATGTTATGCAAAAATAATCTGTAATACTAAAGACAATgt............... : 34900 433 : ron 11 >>>> GluArgValValGlyPheHisValLeuGlyProAsnAlaGlyGluVa : 447 bp ||||||||||||||||||||||||||||||||||||||||||||||| GluArgValValGlyPheHisValLeuGlyProAsnAlaGlyGluVa 34901 : ...........agGAACGTGTTGTGGGCTTTCACGTACTGGGTCCAAATGCTGGAGAAGT : 39740 448 : lThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLysLysGlnLeuAspSerTh : 467 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLysLysGlnLeuAspSerTh 39741 : TACACAAGGCTTTGCAGCTGCGCTCAAATGTGGACTGACCAAAAAGCAGCTGGACAGCAC : 39800 468 : rIleGlyIleHisProValCysAlaGlu >>>> Target Intron 12 >>>> Va : 477 |||||||||||||||||||||||||||| 9249 bp || rIleGlyIleHisProValCysAlaGlu Va 39801 : AATTGGAATCCACCCTGTCTGTGCAGAGgt..........................agGT : 49079 478 : lPheThrThrLeuSerValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyCys** : 497 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lPheThrThrLeuSerValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyCys** 49080 : ATTCACAACATTGTCTGTGACCAAGCGCTCTGGGGCAAGCATCCTCCAGGCTGGCTGCTG : 49139 498 : *Gly : 499 |||| *Gly 49140 : AGGT : 49145 vulgar: TR1 0 499 . 12 12889 49145 + 2366 M 29 87 5 0 2 I 0 1848 3 0 2 M 24 72 S 0 1 5 0 2 I 0 2473 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 3012 3 0 2 S 1 2 M 47 141 5 0 2 I 0 432 3 0 2 M 38 114 S 0 2 5 0 2 I 0 1502 3 0 2 S 1 1 M 75 225 5 0 2 I 0 2956 3 0 2 M 31 93 5 0 2 I 0 911 3 0 2 M 25 75 S 0 2 5 0 2 I 0 1096 3 0 2 S 1 1 M 52 156 5 0 2 I 0 3854 3 0 2 M 36 108 5 0 2 I 0 2589 3 0 2 M 32 96 5 0 2 I 0 4793 3 0 2 M 45 135 5 0 2 I 0 9245 3 0 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome 0.8.2 ##date 2006-03-16 ##type DNA # # # seqname source feature start end score strand frame attributes # 12 exonerate:protein2genome gene 12890 49145 2366 + . gene_id 2 ; sequence TR1 ; gene_orientation + ; 12 exonerate:protein2genome exon 12890 12976 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 12977 12978 . + . intron_id 1 ; splice_site "GC" ; 12 exonerate:protein2genome intron 12977 14828 . + . intron_id 1 ; 12 exonerate:protein2genome splice3 14827 14828 . + . intron_id 0 ; splice_site "AG" ; 12 exonerate:protein2genome exon 14829 14901 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 14902 14903 . + . intron_id 2 ; splice_site "GT" ; 12 exonerate:protein2genome intron 14902 17378 . + . intron_id 2 ; 12 exonerate:protein2genome splice3 17377 17378 . + . intron_id 1 ; splice_site "AG" ; 12 exonerate:protein2genome exon 17381 17498 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 17499 17500 . + . intron_id 3 ; splice_site "GT" ; 12 exonerate:protein2genome intron 17499 20514 . + . intron_id 3 ; 12 exonerate:protein2genome splice3 20513 20514 . + . intron_id 2 ; splice_site "AG" ; 12 exonerate:protein2genome exon 20517 20657 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 20658 20659 . + . intron_id 4 ; splice_site "GT" ; 12 exonerate:protein2genome intron 20658 21093 . + . intron_id 4 ; 12 exonerate:protein2genome splice3 21092 21093 . + . intron_id 3 ; splice_site "AG" ; 12 exonerate:protein2genome exon 21094 21209 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 21210 21211 . + . intron_id 5 ; splice_site "GT" ; 12 exonerate:protein2genome intron 21210 22715 . + . intron_id 5 ; 12 exonerate:protein2genome splice3 22714 22715 . + . intron_id 4 ; splice_site "AG" ; 12 exonerate:protein2genome exon 22717 22941 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 22942 22943 . + . intron_id 6 ; splice_site "GT" ; 12 exonerate:protein2genome intron 22942 25901 . + . intron_id 6 ; 12 exonerate:protein2genome splice3 25900 25901 . + . intron_id 5 ; splice_site "AG" ; 12 exonerate:protein2genome exon 25902 25994 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 25995 25996 . + . intron_id 7 ; splice_site "GT" ; 12 exonerate:protein2genome intron 25995 26909 . + . intron_id 7 ; 12 exonerate:protein2genome splice3 26908 26909 . + . intron_id 6 ; splice_site "AG" ; 12 exonerate:protein2genome exon 26910 26986 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 26987 26988 . + . intron_id 8 ; splice_site "GT" ; 12 exonerate:protein2genome intron 26987 28086 . + . intron_id 8 ; 12 exonerate:protein2genome splice3 28085 28086 . + . intron_id 7 ; splice_site "AG" ; 12 exonerate:protein2genome exon 28088 28243 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 28244 28245 . + . intron_id 9 ; splice_site "GT" ; 12 exonerate:protein2genome intron 28244 32101 . + . intron_id 9 ; 12 exonerate:protein2genome splice3 32100 32101 . + . intron_id 8 ; splice_site "AG" ; 12 exonerate:protein2genome exon 32102 32209 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 32210 32211 . + . intron_id 10 ; splice_site "GT" ; 12 exonerate:protein2genome intron 32210 34802 . + . intron_id 10 ; 12 exonerate:protein2genome splice3 34801 34802 . + . intron_id 9 ; splice_site "AG" ; 12 exonerate:protein2genome exon 34803 34898 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 34899 34900 . + . intron_id 11 ; splice_site "GT" ; 12 exonerate:protein2genome intron 34899 39695 . + . intron_id 11 ; 12 exonerate:protein2genome splice3 39694 39695 . + . intron_id 10 ; splice_site "AG" ; 12 exonerate:protein2genome exon 39696 39830 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome splice5 39831 39832 . + . intron_id 12 ; splice_site "GT" ; 12 exonerate:protein2genome intron 39831 49079 . + . intron_id 12 ; 12 exonerate:protein2genome splice3 49078 49079 . + . intron_id 11 ; splice_site "AG" ; 12 exonerate:protein2genome exon 49080 49145 . + . insertions 0 ; deletions 0 ; 12 exonerate:protein2genome similarity 12890 49145 2366 + . alignment_id 2 ; Align 12890 1 87 ; Align 14829 30 72 ; Align 17381 55 117 ; Align 20517 95 141 ; Align 21094 142 114 ; Align 22717 181 225 ; Align 25902 256 93 ; Align 26910 287 75 ; Align 28088 313 156 ; Align 32102 365 108 ; Align 34803 401 96 ; Align 39696 433 135 ; Align 49080 478 66 ; # --- END OF GFF DUMP --- # -- completed exonerate analysis