Command line: [exonerate -m p2g --showtargetgff -q ../SECp43-human.fa -t SECp43-NIVO01076485.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000284_2.0 # Protein # tRNA Sec 1 associated protein 1 (SECp43) # Cow Target: NIVO01076485.1:subseq(810170,121033) Ammotragus lervia isolate NAZ scaffold2_len1858434_cov72, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1446 Query range: 0 -> 277 Target range: 71033 -> 49999 1 : SerAlaLeuValPheThrGlnLeuGluProTyrMetAspGluAsnPheIleSerArgAla : 20 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SerAlaLeuValPheThrGlnLeuGluProTyrMetAspGluAsnPheIleSerArgAla 71033 : TCTGCTCTTGTGTTTACGCAGCTGGAGCCCTACATGGATGAGAACTTCATCTCCAGAGCC : 70976 21 : PheAlaThrMetGlyGluThrValMetSerValLysIleIleArgAsnArgLeuThr{Gl : 40 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||{|| PheAlaThrMetGlyGluThrValMetSerValLysIleIleArgAsnArgLeuThr{Gl 70975 : TTTGCTACCATGGGGGAGACAGTGATGAGCGTCAAAATTATCCGAAACCGCCTCACT{GG : 70916 41 : } >>>> Target Intron 1 >>>> {y}IleProAlaGlyTyrCysPheValGlu : 49 } 5971 bp {|}||||||||||||||||||||||||||| }++ ++{y}IleProAlaGlyTyrCysPheValGlu 70915 : }gt.........................ag{G}ATCCCGGCTGGCTACTGCTTTGTAGAA : 64918 50 : PheAlaAspLeuAlaThrAlaGluLysCysLeuHisLysIleAsnGlyLysProLeuPro : 69 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| PheAlaAspLeuAlaThrAlaGluLysCysLeuHisLysIleAsnGlyLysProLeuPro 64917 : TTCGCAGATTTGGCCACAGCTGAGAAGTGTTTGCATAAAATCAACGGGAAACCCCTTCCA : 64858 70 : GlyAlaThrPro >>>> Target Intron 2 >>>> AlaLysArgPheLysLeuA : 80 |||||||||||| 611 bp ||||||||||||||||||| GlyAlaThrPro++ ++AlaLysArgPheLysLeuA 64857 : GGAGCCACACCTgt.........................aggcaAAGCGTTTTAAACTGA : 64214 81 : snTyrAlaThrTyrGlyLysGlnProAspAsn{Se} >>>> Target Intron 3 > : 91 ||||||||||||||||||||||||||||||||{||} 2262 bp snTyrAlaThrTyrGlyLysGlnProAspAsn{Se}++ 64213 : ATTACGCCACTTATGGGAAACAGCCAGATAAC{AG}gt...................... : 64177 92 : >>> {r}ProGluTyrSerLeuPheValGlyAspLeuThrProAspValAspAspGlyM : 109 {|}|||||||||||||||||||||||||||||||||||||||||||||||||||| ++{r}ProGluTyrSerLeuPheValGlyAspLeuThrProAspValAspAspGlyM 64176 : ...ag{C}CCTGAATACTCCCTCTTTGTGGGGGATCTGACCCCAGATGTGGACGATGGCA : 61865 110 : etLeuTyrGluPhePheValLysValTyrProSerCysArgGlyGlyLysValValLeuA : 129 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| etLeuTyrGluPhePheValLysValTyrProSerCysArgGlyGlyLysValValLeuA 61864 : TGCTGTATGAGTTCTTCGTCAAAGTCTACCCCTCCTGCCGGGGAGGCAAGGTGGTTTTGG : 61805 130 : spGlnThrGlyValSer{Ly} >>>> Target Intron 4 >>>> {s}GlyTyrG : 138 |||||||||||||||||{||} 1511 bp {|}||||||| spGlnThrGlyValSer{Ly}++ ++{s}GlyTyrG 61804 : ACCAGACAGGCGTGTCT{AA}gt.........................ag{G}GGTTATG : 60267 139 : lyPheValLysPheThrAspGluLeuGluGlnLysArgAlaLeuThrGluCysGlnGlyA : 158 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lyPheValLysPheThrAspGluLeuGluGlnLysArgAlaLeuThrGluCysGlnGlyA 60266 : GTTTTGTGAAATTCACAGATGAGCTGGAACAGAAGCGAGCCCTGACAGAGTGCCAGGGAG : 60207 159 : laIleGlyLeuGlySerLysProValArgLeuSerValAlaIleProLys{Al} >>>> : 175 ||||||||||||||||||||||||||||||||||||||||||||||||||{||} laIleGlyLeuGlySerLysProValArgLeuSerValAlaIleProLys{Al}++ 60206 : CCATAGGACTGGGGTCTAAACCAGTGCGGCTGAGCGTGGCCATCCCCAAA{GC}gt.... : 60152 176 : Target Intron 5 >>>> {a}SerArgValLysProValGluTyrSerGlnMetT : 187 2902 bp {|}|||||||||||||||||||||||||||||||||| ++{a}SerArgValLysProValGluTyrSerGlnMetT 60151 : .....................ag{G}AGCCGTGTGAAGCCAGTGGAATATAGTCAAATGT : 57218 188 : yrSerTyrSerTyrAsnGlnTyrTyrGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpGlyT : 207 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| yrSerTyrSerTyrAsnGlnTyrTyrGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpGlyT 57217 : ACAGTTACAGCTACAACCAGTATTACCAGCAGTACCAGAACTACTACGCCCAGTGGGGCT : 57158 208 : yrAspGlnAsnThrGlySerTyrSerTyrSerTyrProGlnTyrGlyTyrThrGlnSerT : 227 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| yrAspGlnAsnThrGlySerTyrSerTyrSerTyrProGlnTyrGlyTyrThrGlnSerT 57157 : ATGACCAGAACACAGGCAGCTACAGCTACAGCTATCCCCAGTACGGCTACACCCAGAGCA : 57098 228 : hrMetGln >>>> Target Intron 6 >>>> ThrTyrGluGluValGlyAspAs : 237 |||||||| 205 bp ||||||||||||||||||||||| hrMetGln++ ++ThrTyrGluGluValGlyAspAs 57097 : CCATGCAGgt.........................agACGTATGAAGAAGTCGGAGATGA : 56863 238 : pAlaLeuGlu{A} >>>> Target Intron 7 >>>> {sp}ProMetProGlnLe : 246 ||||||||||{|} 6741 bp {||}|||||||||||||| pAlaLeuGlu{A}++ ++{sp}ProMetProGlnLe 56862 : TGCATTGGAA{G}gt.........................ag{AC}CCCATGCCGCAGCT : 50095 247 : uAspValThrGluAlaAsnLysGluPheMetGluGlnSerGluGluLeuTyrAspAlaLe : 266 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| uAspValThrGluAlaAsnLysGluPheMetGluGlnSerGluGluLeuTyrAspAlaLe 50094 : GGATGTGACCGAGGCCAACAAGGAGTTCATGGAGCAGAGCGAGGAGCTGTACGATGCGCT : 50035 267 : uMetAspCysHisTrpGlnProLeuAspThrVal : 277 |||||||||||||||||||||||||||||||||| uMetAspCysHisTrpGlnProLeuAspThrVal 50034 : GATGGACTGTCATTGGCAGCCTCTGGACACAGTG : 50000 vulgar: SPP00000284_2.0 0 277 . NIVO01076485.1:subseq(810170,121033) 71033 49999 - 1446 M 39 117 S 0 2 5 0 2 I 0 5967 3 0 2 S 1 1 M 33 99 5 0 2 I 0 607 3 0 2 M 17 51 S 0 2 5 0 2 I 0 2258 3 0 2 S 1 1 M 43 129 S 0 2 5 0 2 I 0 1507 3 0 2 S 1 1 M 39 117 S 0 2 5 0 2 I 0 2898 3 0 2 S 1 1 M 54 162 5 0 2 I 0 201 3 0 2 M 11 33 S 0 1 5 0 2 I 0 6737 3 0 2 S 1 2 M 36 108 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-24 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local gene 50000 71033 1446 - . gene_id 1 ; sequence SPP00000284_2.0 ; gene_orientation + NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 70915 71033 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 70915 71033 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 70913 70914 . - . intron_id 1 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 64944 70914 . - . intron_id 1 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 64944 64945 . - . intron_id 0 ; splice_site "ag" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 64844 64943 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 64844 64943 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 64842 64843 . - . intron_id 2 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 64233 64843 . - . intron_id 2 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 64233 64234 . - . intron_id 1 ; splice_site "ag" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 64180 64232 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 64180 64232 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 64178 64179 . - . intron_id 3 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 61918 64179 . - . intron_id 3 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 61918 61919 . - . intron_id 2 ; splice_site "AG" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 61786 61917 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 61786 61917 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 61784 61785 . - . intron_id 4 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 60275 61785 . - . intron_id 4 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 60275 60276 . - . intron_id 3 ; splice_site "AG" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 60155 60274 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 60155 60274 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 60153 60154 . - . intron_id 5 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 57253 60154 . - . intron_id 5 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 57253 57254 . - . intron_id 4 ; splice_site "ag" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 57090 57252 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 57090 57252 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 57088 57089 . - . intron_id 6 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 56885 57089 . - . intron_id 6 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 56885 56886 . - . intron_id 5 ; splice_site "AG" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 56851 56884 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 56851 56884 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice5 56849 56850 . - . intron_id 7 ; splice_site "GT" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local intron 50110 56850 . - . intron_id 7 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local splice3 50110 50111 . - . intron_id 6 ; splice_site "AG" NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local cds 50000 50109 . - . NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local exon 50000 50109 . - . insertions 0 ; deletions 0 NIVO01076485.1:subseq(810170,121033) exonerate:protein2genome:local similarity 50000 71033 1446 - . alignment_id 1 ; Query SPP00000284_2.0 ; Align 71034 1 117 ; Align 64943 41 99 ; Align 64233 74 51 ; Align 61917 92 129 ; Align 60274 136 117 ; Align 57252 176 162 ; Align 56885 230 33 ; Align 50108 242 108 # --- END OF GFF DUMP --- # -- completed exonerate analysis