Command line: [exonerate -m p2g --showtargetgff -q ELAVL1n/ELAVL1n_U.fa -t ELAVL1n/SUBSEQ/KB228974.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SPP00002928_2.0 # Protein # ELAV like RNA binding protein 1 (ELAVL1) # Human (Homo sapiens) Target: KB228974.1:subseq(3413217,25344) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold97, whole genome shotgun sequence Model: protein2genome:local Raw score: 1446 Query range: 0 -> 326 Target range: 24371 -> 25344 1 : MetSerAsnGlyTyrGluAspHisMetAlaGluAspCysArgGlyAspIleGlyArgThr : 20 :::|||||||||||||||||||||||||||||||||||||||! !! !|||||||||||| IleSerAsnGlyTyrGluAspHisMetAlaGluAspCysArgAspGlyIleGlyArgThr 24372 : atatctaaTGGTTATGAAGACCACATGGCCGAAGACTGCAGGGATGGTATCGGGAGAACG : 24429 21 : AsnLeuIleValAsnTyrLeuProGlnAsnMetThrGlnAspGluLeuArgSerLeuPhe : 40 ||||||||||||||||||||||||||||||||||||||||||||||||!:!||||||||| AsnLeuIleValAsnTyrLeuProGlnAsnMetThrGlnAspGluLeuGlnSerLeuPhe 24430 : AATTTAATTGTCAACTACCTCCCTCAGAACATGACCCAGGATGAGTTGCAGAGTCTGTTC : 24489 41 : SerSerIleGlyGluValGluSerAlaLysLeuIleArgAspLysValAlaGlyHisSer : 60 ||||||:!! !!|||||||||||||||||||||||||||||||||||||||||||||||| SerSerValArgGluValGluSerAlaLysLeuIleArgAspLysValAlaGlyHisSer 24490 : AGCAGTGTCCGTGAAGTTGAATCTGCAAAACTCATTCGGGATAAAGTAGCAGGGCACAGC : 24549 61 : LeuGlyTyrGlyPheValAsnTyrValThrAlaLysAspAlaGluArgAlaIleAsnThr : 80 ||||||||||||||||||||||||||||||||||||||||||||||||||||||:!!||| LeuGlyTyrGlyPheValAsnTyrValThrAlaLysAspAlaGluArgAlaIleAspThr 24550 : TTGGGCTACGGCTTTGTGAACTACGTGACTGCCAAGGATGCGGAGAGAGCGATCGACACC : 24609 81 : LeuAsnGlyLeuArgLeuGlnSerLysThrIleLysValSerTyrAlaArgProSerSer : 100 |||||||||||||||||||||||||||||||||||||||||||||||| !!||||||||| LeuAsnGlyLeuArgLeuGlnSerLysThrIleLysValSerTyrAlaCysProSerSer 24610 : CTGAATGGCCTGCGGCTCCAGTCAAAAACCATTAAGGTGTCGTACGCTTGCCCAAGCTCA : 24669 101 : GluValIleLysAspAlaAsnLeuTyrIleSerGlyLeuProArgThrMetThr--GlnL : 120 ||||||||||||||||||||||||||||||||||||||||||||| ##|||| GluValIleLysAspAlaAsnLeuTyrIleSerGlyLeuProArg---------##GlnL 24670 : GAGGTCATCAAAGACGCCAACCTGTACATCAGCGGGCTCCCGCGG---------ACCAGA : 24722 121 : ysAspValGluAspMetPheSerArgPheGlyArgIleIleAsnSerArgValLeuValA : 140 ||||||||||| !!||||||||||||||||||||| |||||||||||||||||||||| ysAspValGluHisMetPheSerArgPheGlyArg---IleAsnSerArgValLeuValA 24723 : AGGACGTGGAGCACATGTTCTCTCGGTTCGGGCGA---ATCAACTCCCGGGTCCTTGTGG : 24779 141 : spGlnThrThrGlyLeuSerArgGlyValAlaPheIleArgPheAspLysArgSerGluA : 160 |||||||||||||||||||||||||||||!.!|||||||||||||||||||||||||||| spGlnThrThrGlyLeuSerArgGlyValValPheIleArgPheAspLysArgSerGluA 24780 : ATCAGACCACAGGTTTGTCCAGAGGGGTTGTGTTTATCCGGTTTGACAAACGGTCGGAGG : 24839 161 : laGluGluAlaIleThrSerPheAsnGlyHisLysProProGlySerSerGluProIleT : 180 |||||||||||||||||||||||||||||!.!|||||||||||||||||||||||||||| laGluGluAlaIleThrSerPheAsnGlyArgLysProProGlySerSerGluProIleT 24840 : CAGAAGAGGCAATTACCAGTTTCAATGGTCGTAAACCCCCAGGTTCCTCCGAGCCCATTA : 24899 181 : hrValLysPheAlaAlaAsnProAsnGlnAsnLysAsnValAlaLeuLeuSerGlnLeuT : 200 |||||||||||||||||||||||||||||||||||||||||||||||||||||!!.|||| hrValLysPheAlaAlaAsnProAsnGlnAsnLysAsnValAlaLeuLeuSerHisLeuT 24900 : CAGTGAAGTTTGCAGCCAACCCCAACCAGAACAAAAACGTGGCGCTGCTCTCCCACCTGT : 24959 201 : yrHisSerProAlaArgArgPheGlyGlyProVal-----HisHisGlnAlaGlnArgPh : 218 ||||||||||||||||||||||| !!|||||||||#####||||||||||||:!!||||| yrHisSerProAlaArgArgPheArgGlyProVal#####HisHisGlnAlaLysArgPh 24960 : ACCACTCGCCCGCCAGACGGTTCAGAGGCCCCGTTCACCACACCACCAGGCGAAGAGATT : 25018 219 : eArgPheSerProMetGlyValAspHisMetSerGlyLeuSerGlyValAsnValProGl : 238 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| eArgPheSerProMetGlyValAspHisMetSerGlyLeuSerGlyValAsnValProGl 25019 : CAGGTTCTCCCCTATGGGTGTAGATCACATGAGTGGGCTTTCTGGTGTCAATGTCCCGGG : 25078 239 : yAsnAlaSerSerGlyTrpCysIlePheIleTyrAsnLeuGlyGlnAspAlaAspGluGl : 258 |||||||! !||||||!! |||||||||||||||||||||||||||||||||:!!||||| yAsnAlaTyrSerGlyCysCysIlePheIleTyrAsnLeuGlyGlnAspAlaAsnGluGl 25079 : CAACGCGTATTCGGGGTGCTGCATCTTCATCTACAACCTCGGGCAGGACGCCAATGAGGG : 25138 259 : yIleLeuTrpGlnMetPheGlyProPheGlyAlaValThrAsnValLysValIleArgAs : 278 |||||||||||||||||||||||||||||||||||||||||||||||||||||||!.!:! yIleLeuTrpGlnMetPheGlyProPheGlyAlaValThrAsnValLysValIleHisAs 25139 : GATCCTCTGGCAGATGTTTGGCCCCTTTGGGGCAGTCACCAATGTGAAAGTAATTCACAA : 25198 279 : pPheAsnThrAsnLysCysLysGlyPheGlyPheValThrMetThrAsnTyrGluGluAl : 298 !||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| nPheAsnThrAsnLysCysLysGlyPheGlyPheValThrMetThrAsnTyrGluGluAl 25199 : CTTCAACACCAACAAGTGCAAAGGCTTTGGCTTTGTGACCATGACAAACTATGAAGAAGC : 25258 299 : aAlaMetAlaIleAlaSerLeuAsnGlyTyrArgLeuGlyAspLysIleLeuGlnValSe : 318 |||||||||||||||||||:!!|||||||||!.!|||||||||||||||||||||||||| aAlaMetAlaIleAlaSerMetAsnGlyTyrHisLeuGlyAspLysIleLeuGlnValSe 25259 : CGCCATGGCCATAGCGAGTATGAACGGCTACCACCTGGGGGACAAAATCTTACAGGTTTC : 25318 319 : rPheLysThrAsnLysSerHisLys : 326 ||||||||||||||||||||||||| rPheLysThrAsnLysSerHisLys 25319 : CTTCAAAACCAATAAGTCCCACAAA : 25344 vulgar: SPP00002928_2.0 0 326 . KB228974.1:subseq(3413217,25344) 24371 25344 + 1446 M 115 345 G 3 0 F 0 2 M 13 39 G 1 0 M 79 237 F 0 5 M 115 345 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local gene 24372 25344 1446 + . gene_id 1 ; sequence SPP00002928_2.0 ; gene_orientation . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local cds 24372 25344 . + . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local exon 24372 25344 . + . insertions 0 ; deletions 4 ; frameshifts 7 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local similarity 24372 25344 1446 + . alignment_id 1 ; Query SPP00002928_2.0 ; Align 24372 1 345 ; Align 24719 119 39 ; Align 24758 133 237 ; Align 25000 212 345 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00002928_2.0 # Protein # ELAV like RNA binding protein 1 (ELAVL1) # Human (Homo sapiens) Target: KB228974.1:subseq(3413217,25344) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold97, whole genome shotgun sequence Model: protein2genome:local Raw score: 108 Query range: 95 -> 169 Target range: 24398 -> 24620 96 : AlaArgProSerSerGluValIleLysAspAlaAsnLeuTyrIleSerGlyLeuProArg : 115 |||..! !!!!!!!!!:! !||| ! .!!|||||| !:!!!:! !||||||!:! AlaGluAspCysArgAspGlyIleGlyArgThrAsnLeuIleValAsnTyrLeuProGln 24399 : GCCGAAGACTGCAGGGATGGTATCGGGAGAACGAATTTAATTGTCAACTACCTCCCTCAG : 24456 116 : ThrMetThrGlnLysAspValGluAspMetPheSerArgPheGlyArgIleIleAsnSer : 135 !.!||||||||| ! !!::!!:!!..!:!!||||||!!! !! !!..!:!! !::!:!! AsnMetThrGlnAspGluLeuGlnSerLeuPheSerSerValArgGluValGluSerAla 24457 : AACATGACCCAGGATGAGTTGCAGAGTCTGTTCAGCAGTGTCCGTGAAGTTGAATCTGCA : 24516 136 : ArgValLeuValAspGlnThrThrGlyLeuSerArgGlyValAlaPheIleArgPheAsp : 155 !:!:!!:!! !|||:!!..!.!!|||! !||| !||| !!.!|||:!:!.!!:!! LysLeuIleArgAspLysValAlaGlyHisSerLeuGlyTyrGlyPheValAsnTyrVal 24517 : AAACTCATTCGGGATAAAGTAGCAGGGCACAGCTTGGGCTACGGCTTTGTGAACTACGTG : 24576 156 : LysArgSerGluAlaGluGluAlaIleThrSerPheAsnGly : 169 ! !!.!!!:||||||..!|||||| !!!!.!.|||||| ThrAlaLysAspAlaGluArgAlaIleAspThrLeuAsnGly 24577 : ACTGCCAAGGATGCGGAGAGAGCGATCGACACCCTGAATGGC : 24620 vulgar: SPP00002928_2.0 95 169 . KB228974.1:subseq(3413217,25344) 24398 24620 + 108 M 74 222 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local gene 24399 24620 108 + . gene_id 2 ; sequence SPP00002928_2.0 ; gene_orientation . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local cds 24399 24620 . + . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local exon 24399 24620 . + . insertions 0 ; deletions 0 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local similarity 24399 24620 108 + . alignment_id 2 ; Query SPP00002928_2.0 ; Align 24399 96 222 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00002928_2.0 # Protein # ELAV like RNA binding protein 1 (ELAVL1) # Human (Homo sapiens) Target: KB228974.1:subseq(3413217,25344) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold97, whole genome shotgun sequence Model: protein2genome:local Raw score: 105 Query range: 32 -> 170 Target range: 24718 -> 25290 33 : GlnAspGluLeuArgSerLeuPheSerSerIleGlyGluValGluSerAlaLysLeuIle : 52 ||| ! !!::!!..! !:!!|||||| !!.!!|||..!:!!.!.||| ! |||:!: GlnLysAspValGluHisMetPheSerArgPheGlyArgIleAsnSerArgValLeuVal 24719 : CAGAAGGACGTGGAGCACATGTTCTCTCGGTTCGGGCGAATCAACTCCCGGGTCCTTGTG : 24776 53 : ArgAspLysValAlaGlyHisSerLeuGlyTyrGlyPheValAsnTyrValThrAlaLys : 72 |||:!!..!.!!||| ||| !||| !! !|||:!!...!:!! !! ! !..! ---AspGlnThrThrGlyLeuSerArgGlyValValPheIleArgPheAspLysArgSer 24777 : ---GATCAGACCACAGGTTTGTCCAGAGGGGTTGTGTTTATCCGGTTTGACAAACGGTCG : 24833 73 : AspAlaGluArgAlaIleAsnThrLeuAsnGlyLeuArgLeuGln{S} >>>> Targe : 88 !!:||||||..!||||||!.!!:!!!!||||||! !!:!! !! !{.} GluAlaGluGluAlaIleThrSerPheAsnGlyArgLysProPro{A}++ 24834 : GAGGCAGAAGAGGCAATTACCAGTTTCAATGGTCGTAAACCCCCA{G}gt.......... : 24884 89 : t Intron 1 >>>> {er}LysThrIleLysValSerTyrAlaArgProSerSerGlu : 101 161 bp {.!} ! ! !! ! !:!!||| !!.!!.! ! !!.!!.!. ++{sp}HisMetSerGlyLeuSerGlyValAsnValProGlyAsn 24885 : ...............ag{AT}CACATGAGTGGGCTTTCTGGTGTCAATGTCCCGGGCAAC : 25081 102 : ValIleLysAspAlaAsnLeuTyrIleSerGlyLeuProArgThrMetThrGlnLysAsp : 121 !.! !..!! ..! !:!!!:!|||! !..!||| !!:! ! !.!:!! ! ! AlaTyrSerGlyCysCysIlePheIleTyrAsnLeuGlyGlnAspAlaAsnGluGlyIle 25082 : GCGTATTCGGGGTGCTGCATCTTCATCTACAACCTCGGGCAGGACGCCAATGAGGGGATC : 25141 122 : ValGluAspMetPheSerArgPheGlyArgIleIleAsnSerArgValLeuValAspGln : 141 :!! !.!.||||||.!!! !|||||| !:!!! !||| !!:!|||:!! !:!! LeuTrpGlnMetPheGlyProPheGlyAlaValThrAsnValLysValIleHisAsnPhe 25142 : CTCTGGCAGATGTTTGGCCCCTTTGGGGCAGTCACCAATGTGAAAGTAATTCACAACTTC : 25201 142 : ThrThrGlyLeuSerArgGlyValAlaPheIleArgPheAspLysArgSerGluAlaGlu : 161 !.!|||..! !!!!!:!||| !!!.!|||:!:! !.!. !!. !..!||||||! AsnThrAsnLysCysLysGlyPheGlyPheValThrMetThrAsnTyrGluGluAlaAla 25202 : AACACCAACAAGTGCAAAGGCTTTGGCTTTGTGACCATGACAAACTATGAAGAAGCCGCC : 25261 162 : GluAlaIleThrSerPheAsnGlyHis : 170 !||||||.!!|||.!.||||||:!! MetAlaIleAlaSerMetAsnGlyTyr 25262 : ATGGCCATAGCGAGTATGAACGGCTAC : 25290 vulgar: SPP00002928_2.0 32 170 . KB228974.1:subseq(3413217,25344) 24718 25290 + 105 M 20 60 G 1 0 M 34 102 S 0 1 5 0 2 I 0 157 3 0 2 S 1 2 M 82 246 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local gene 24719 25290 105 + . gene_id 3 ; sequence SPP00002928_2.0 ; gene_orientation + KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local cds 24719 24881 . + . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local exon 24719 24881 . + . insertions 0 ; deletions 1 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local splice5 24882 24883 . + . intron_id 1 ; splice_site "GT" KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local intron 24882 25042 . + . intron_id 1 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local splice3 25041 25042 . + . intron_id 0 ; splice_site "AG" KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local cds 25043 25290 . + . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local exon 25043 25290 . + . insertions 0 ; deletions 0 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local similarity 24719 25290 105 + . alignment_id 3 ; Query SPP00002928_2.0 ; Align 24719 33 60 ; Align 24779 54 102 ; Align 25045 89 246 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00002928_2.0 # Protein # ELAV like RNA binding protein 1 (ELAVL1) # Human (Homo sapiens) Target: KB228974.1:subseq(3413217,25344) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold97, whole genome shotgun sequence Model: protein2genome:local Raw score: 104 Query range: 243 -> 319 Target range: 10546 -> 24656 244 : TrpCysIlePheIleTyrAsnLeuGlyGln >>>> Target Intron 1 >>>> A : 254 :::|||||||||||| !|||:!!..! 13882 bp : TyrCysIlePheIleSerAsnValAsnThr++ ++A 10547 : tattgcatatttatatCCAATGTAAATActgt.........................agA : 24459 255 : spAlaAspGluGlyIleLeuTrpGlnMetPheGlyProPheGlyAlaValThrAsnValL : 274 !! ! !:!!! ! ||| !...:!!|||.!! ! !! !!! !||| !::!!.!| snMetThrGlnAspGluLeuGlnSerLeuPheSerSerValArgGluValGluSerAlaL 24460 : ACATGACCCAGGATGAGTTGCAGAGTCTGTTCAGCAGTGTCCGTGAAGTTGAATCTGCAA : 24519 275 : ysValIleArgAspPheAsnThrAsnLysCysLysGlyPheGlyPheValThrMetThrA : 294 ||:!!||||||||| .!!... ! !! !|||!:!|||||||||!.! ..!! ysLeuIleArgAspLysValAlaGlyHisSerLeuGlyTyrGlyPheValAsnTyrValT 24520 : AACTCATTCGGGATAAAGTAGCAGGGCACAGCTTGGGCTACGGCTTTGTGAACTACGTGA : 24579 295 : snTyrGluGluAlaAlaMetAlaIleAlaSerLeuAsnGlyTyrArgLeuGlyAspLysI : 314 .! !:!!!!:|||! !! ||||||! !!!!||||||||| |||||| !...|||! hrAlaLysAspAlaGluArgAlaIleAspThrLeuAsnGlyLeuArgLeuGlnSerLysT 24580 : CTGCCAAGGATGCGGAGAGAGCGATCGACACCCTGAATGGCCTGCGGCTCCAGTCAAAAA : 24639 315 : leLeuGlnValSerPhe : 319 !:!!:!!||||||!:! hrIleLysValSerTyr 24640 : CCATTAAGGTGTCGTAC : 24656 vulgar: SPP00002928_2.0 243 319 . KB228974.1:subseq(3413217,25344) 10546 24656 + 104 M 10 30 5 0 2 I 0 13878 3 0 2 M 66 198 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local gene 10547 24656 104 + . gene_id 4 ; sequence SPP00002928_2.0 ; gene_orientation + KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local cds 10547 10576 . + . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local exon 10547 10576 . + . insertions 0 ; deletions 0 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local splice5 10577 10578 . + . intron_id 1 ; splice_site "gt" KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local intron 10577 24458 . + . intron_id 1 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local splice3 24457 24458 . + . intron_id 0 ; splice_site "AG" KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local cds 24459 24656 . + . KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local exon 24459 24656 . + . insertions 0 ; deletions 0 KB228974.1:subseq(3413217,25344) exonerate:protein2genome:local similarity 10547 24656 104 + . alignment_id 4 ; Query SPP00002928_2.0 ; Align 10547 244 30 ; Align 24459 254 198 # --- END OF GFF DUMP --- # -- completed exonerate analysis