Command line: [exonerate -m p2g --showtargetgff -q SELENON.fa.txt -t SELENON.subseq.txt] Hostname: [ws116044u] C4 Alignment: ------------ Query: SPP00000079_2.0 # Protein # Selenoprotein N (SELENON) # Human Target: JSZB01007029.1:subseq(106000,115000) Manis javanica isolate MP_PG03-UM SCAFFOLD8080, whole genome shotgun sequence Model: protein2genome:local Raw score: 2138 Query range: 132 -> 590 Target range: 54267 -> 63742 133 : LeuLeuArgSerThrProAlaAlaSerCysGluGluGluGluLeuProProAspProSer : 152 |||:!! !!|||! !|||||||||||| |||||||||||||||||||||||||||||| LeuIleGlySerIleProAlaAlaSer---GluGluGluGluLeuProProAspProSer 54268 : CTCATAGGGTCAATCCCTGCAGCCAGC---GAGGAGGAGGAGCTTCCGCCTGACCCTAGT : 54322 153 : GluGluThrLeuThrIleGluAlaArgPheGlnProLeuLeuProGluThrMetThrLys : 172 ||||||||||||!.!|||||||||||||||||||||||||||||||||:!!||||||||| GluGluThrLeuAsnIleGluAlaArgPheGlnProLeuLeuProGluSerMetThrLys 54323 : GAGGAGACGCTCAACATAGAAGCCcgattccagcctctgctcccggAGTCCATGACCAAG : 54382 173 : SerLysAspGlyPheLeuGly >>>> Target Intron 1 >>>> ValSerArgL : 183 ||||||||||||||||||||| 2678 bp |||||||||| SerLysAspGlyPheLeuGly++ ++ValSerArgL 54383 : AGCAAAGACGGGTTCCTGGGGgt.........................agGTCTCCCGCC : 57093 184 : euAlaLeuSerGlyLeuArgAsnTrpThrAlaAlaAlaSerProSerAlaValPheAlaT : 203 ||||||||!!!||||||||||||||||||.!!|||||||||||||||||||||||||||. euAlaLeuThrGlyLeuArgAsnTrpThrThrAlaAlaSerProSerAlaValPheAlaA 57094 : TGGCCTTGACCGGCCTCCGTAACTGGACGACTGCAGCTTCTCCGAGCGCAGTGTTTGCTG : 57153 204 : hrArgHisPheGlnProPheLeuProProProGlyGln<->GluLeuGlyGluProTrpT : 222 !!|||||||||!:!|||||||||||||||||||||!!. ||||||||||||||||||| laArgHisPheArgProPheLeuProProProGlyHisAlaGluLeuGlyGluProTrpT 57154 : CCCGCCACTTCCGGCCCTTCCTCCCACCTCCGGGCCACGCAGAGCTGGGCGAGCCCTGGT : 57213 223 : rpIleIleProSerGluLeuSerMetPheThrGlyTyrLeuSerAsnAsnArgPheTyrP : 242 |||||||||||.!!|||||||||:!:|||||||||||||||||||||||||||||||||| rpIleIleProGlyGluLeuSerValPheThrGlyTyrLeuSerAsnAsnArgPheTyrP 57214 : GGATCATCCCCGGCGAGCTGAGTGTCTTCACTGGCTACTTGTCCAACAACCGCTTCTACC : 57273 243 : roProProProLysGlyLysGlu >>>> Target Intron 2 >>>> ValIleIl : 252 ||||||||||||||||||||||| 222 bp |||||||| roProProProLysGlyLysGlu++ ++ValIleIl 57274 : CACCGCCACCCAAGGGCAAAGAAgt.........................agGTCATCAT : 57525 253 : eHisArgLeuLeuSerMetPheHisProArgProPheValLysThrArgPheAlaProGl : 272 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| eHisArgLeuLeuSerMetPheHisProArgProPheValLysThrArgPheAlaProGl 57526 : CCACCGGCTCCTGAGCATGTTCCACCCTCGGCCCTTTGTGAAGACCCGCTTTGCCCCCCA : 57585 273 : nGlyAlaValAlaCysLeuThrAlaIleSerAspPheTyrTyrThrValMetPhe{Ar} : 291 |||||||||||||||||||||||||||||||||||||||||||||||||:!!|||{||} nGlyAlaValAlaCysLeuThrAlaIleSerAspPheTyrTyrThrValLeuPhe{Ar}+ 57586 : GGGGGCCGTCGCCTGCCTGACCGCCATCAGCGACTTTTACTACACTGTGCTGTTC{CG}g : 57644 292 : >>>> Target Intron 3 >>>> {g}IleHisAlaGluPheGlnLeuSerGluPr : 301 558 bp {|}||||||||||||||||||||||||||||| + ++{g}IleHisAlaGluPheGlnLeuSerGluPr 57645 : t.........................ag{G}ATCCACGCTGAGTTCCAGCTCAGCGAACC : 58230 302 : oProAspPheProPheTrpPheSerProAlaGlnPheThrGlyHisIleIleLeuSerLy : 321 ||||||||||||||||||||||||||||!.!||||||||||||||||||||||||||||| oProAspPheProPheTrpPheSerProGlyGlnPheThrGlyHisIleIleLeuSerLy 58231 : GCCCGACTTCCCCTTCTGGTTCTCGCCCGGCCAGTTCACCGGCCACATCATCCTCTCCAA : 58290 322 : sAspAlaThrHisValArgAspPheArgLeuPheValProAsnHis{Ar} >>>> Tar : 337 |||||||||||||:!!||||||||||||||||||||||||||||||{||} sAspAlaThrHisIleArgAspPheArgLeuPheValProAsnHis{Ar}++ 58291 : AGATGCCACTCACATCCGCGACTTCCGGCTCTTTGTGCCCAACCAC{AG}gt........ : 58342 338 : get Intron 4 >>>> {g}SerLeuAsnValAspMetGluTrpLeuTyrGlyAlaSe : 350 1373 bp {|}|||||||||||||||||||||||||||||||||||||| ++{g}SerLeuAsnValAspMetGluTrpLeuTyrGlyAlaSe 58343 : .................ag{G}TCTCTGAATGTGGACATGGAGTGGCTGTACGGAGCCAG : 59750 351 : rGluSerSerAsnMetGluValAspIleGlyTyrIleProGln >>>> Target Int : 365 ||||||||||!:!|||||||||||||||||||||||||||||| 421 b rGluSerSerSerMetGluValAspIleGlyTyrIleProGln++ 59751 : TGAGAGCAGCAGCATGGAGGTGGACATTGGCTACATACCCCAGgt............... : 59797 366 : ron 5 >>>> MetGluLeuGluAlaThrGlyProSerValProSerValIleLeuAsp : 380 p |||||||||||||||||||||||||||||||||||||||||||||||| ++MetGluLeuGluAlaThrGlyProSerValProSerValIleLeuAsp 59798 : ..........agATGGAGCTGGAGGCCACAGGCCCCTCAGTGCCCTCTGTGATCCTGGAC : 60261 381 : GluAspGlySerMetIleAspSerHisLeuProSerGlyGluProLeuGlnPheValPhe : 400 |||||||||!:!|||||||||||||||||||||||||||||||||||||||||||||||| GluAspGlyAsnMetIleAspSerHisLeuProSerGlyGluProLeuGlnPheValPhe 60262 : GAGGATGGCAACATGATTGACAGCCACCTGCCCTCAGGGGAGCCCCTCCAGTTTGTGTTT : 60321 401 : GluGluIleLysTrpGlnGlnGluLeuSerTrpGluGluAlaAlaArgArgLeuGluVal : 420 |||||||||!!.|||||||||||||||!:!|||||||||||||||!:!|||||||||||| GluGluIleAsnTrpGlnGlnGluLeuAsnTrpGluGluAlaAlaGlnArgLeuGluVal 60322 : GAAGAGATCAATTGGCAGCAGGAGCTGAACTGGGAGGAAGCTGCCCAGCGCCTGGAGGTG : 60381 421 : AlaMetTyrProPheLysLys >>>> Target Intron 6 >>>> ValSerTyrL : 431 ||||||||||||||||||||| 293 bp |||!!!|||| AlaMetTyrProPheLysLys++ ++ValThrTyrL 60382 : GCTATGTACCCCTTCAAGAAGgt.........................agGTCACCTACC : 60707 432 : euProPheThrGluAlaPheAspArgAlaLysAlaGluAsnLysLeuValHisSerIleL : 451 ||||||||||||||||||||:!!!:!|||||||||:!!|||||||||||||||||||||| euProPheThrGluAlaPheAsnGlnAlaLysAlaLysAsnLysLeuValHisSerIleL 60708 : TGCCATTCACCGAGGCCTTCAACCAAGCCAAGGCCAAGAACAAGCTGGTGCACTCAATCC : 60767 452 : euLeuTrpGlyAlaLeuAspAspGlnSerCysUnk{G} >>>> Target Intron 7 : 463 |||||||||||||||||||||||||||||||| {|} 1110 bp euLeuTrpGlyAlaLeuAspAspGlnSerCys***{G}++ 60768 : TGTTGTGGGGGGCCCTGGACGACCAGTCCTGCTGA{G}gt.................... : 60806 464 : >>>> {ly}SerGlyArgThrLeuArgGluThrValLeuGluSerSerProIleLeuT : 480 {||}|||||||||||||||||||||||||||||||||||| !!|||||||||. ++{ly}SerGlyArgThrLeuArgGluThrValLeuGluSerProProIleLeuA 60807 : .....ag{GT}TCAGGGCGGACTCTCCGGGAGACGGTCCTGGAAAGTCCGCCCATTCTTG : 61964 481 : hrLeuLeuAsnGluSerPheIleSerThrTrpSerLeuValLysGluLeuGluGluLeuG : 500 !!|||||||||||||||||||||||||||||||||||||||!:!|||||||||!!:|||| laLeuLeuAsnGluSerPheIleSerThrTrpSerLeuValArgGluLeuGluAspLeuG 61965 : CCCTCCTCAACGAGAGCTTTATCAGCACCTGGTCCCTGGTGAGGGAGCTGGAGGACCTGC : 62024 501 : ln >>>> Target Intron 8 >>>> AsnAsnGlnGluAsnSerSerHisGlnLy : 510 || 93 bp |||||||||||||||:!!||||||||||| ln++ ++AsnAsnGlnGluAsnAlaSerHisGlnLy 62025 : AGgt.........................agAACAACCAGGAGAACGCCTCCCATCAGAA : 62147 511 : sLeuAlaGlyLeuHisLeuGluLysTyrSerPheProValGluMetMetIleCysLeuPr : 530 |||||||! !|||||||||||||||||||||||||||||||||||||||||||||||||| sLeuAlaAspLeuHisLeuGluLysTyrSerPheProValGluMetMetIleCysLeuPr 62148 : GCTGGCTGACCTGCACCTGGAGAAGTACAGCTTCCCCGTGGAGATGATGATCTGCCTGCC : 62207 531 : oAsnGlyThrVal >>>> Target Intron 9 >>>> ValHisHisIleAsnAla : 540 ||||||||||||| 1356 bp |||!!.|||||||||||| oAsnGlyThrVal++ ++ValGlnHisIleAsnAla 62208 : CAATGGCACTGTGgt.........................agGTCCAGCATATCAACGCC : 63593 541 : AsnTyrPheLeuAspIleThrSerValLysProGluGluIleGluSerAsnLeuPheSer : 560 ||||||||||||||||||||||||:!!|||||||||!!::!:||| !!.:!!|||||| AsnTyrPheLeuAspIleThrSerMetLysProGluAspValGlu---LysValPheSer 63594 : AACTACTTCCTGGACATCACCTCCATGAAGCCTGAGGACGTGGAA---AAGGTCTTCAGC : 63650 561 : PheSerSerThrPheGluAspProSerThrAlaThrTyrMetGlnPheLeuLysGluGly : 580 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| PheSerSerThrPheGluAspProSerThrAlaThrTyrMetGlnPheLeuLysGluGly 63651 : TTCTCGTCCACCTTCGAAGACCCATCTACAGCCACCTACATGCAGTTCCTGAAGGAGGGT : 63710 581 : LeuArgArgGlyLeuProLeuLeuGlnPro : 590 |||||||||||||||||||||||||||||| LeuArgArgGlyLeuProLeuLeuGlnPro 63711 : CTCCGGCGGGgcctgcccctcctccagccc : 63742 vulgar: SPP00000079_2.0 132 590 . JSZB01007029.1:subseq(106000,115000) 54267 63742 + 2138 M 9 27 G 1 0 M 37 111 5 0 2 I 0 2674 3 0 2 M 36 108 G 0 3 M 34 102 5 0 2 I 0 218 3 0 2 M 41 123 S 0 2 5 0 2 I 0 554 3 0 2 S 1 1 M 45 135 S 0 2 5 0 2 I 0 1369 3 0 2 S 1 1 M 27 81 5 0 2 I 0 417 3 0 2 M 63 189 5 0 2 I 0 289 3 0 2 M 35 105 S 0 1 5 0 2 I 0 1106 3 0 2 S 1 2 M 37 111 5 0 2 I 0 89 3 0 2 M 34 102 5 0 2 I 0 1352 3 0 2 M 21 63 G 1 0 M 34 102 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-22 ##type DNA # # # seqname source feature start end score strand frame attributes # JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local gene 54268 63742 2138 + . gene_id 1 ; sequence SPP00000079_2.0 ; gene_orientation + JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 54268 54405 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 54268 54405 . + . insertions 0 ; deletions 1 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 54406 54407 . + . intron_id 1 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 54406 57083 . + . intron_id 1 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 57082 57083 . + . intron_id 0 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 57084 57296 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 57084 57296 . + . insertions 3 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 57297 57298 . + . intron_id 2 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 57297 57518 . + . intron_id 2 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 57517 57518 . + . intron_id 1 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 57519 57643 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 57519 57643 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 57644 57645 . + . intron_id 3 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 57644 58201 . + . intron_id 3 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 58200 58201 . + . intron_id 2 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 58202 58339 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 58202 58339 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 58340 58341 . + . intron_id 4 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 58340 59712 . + . intron_id 4 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 59711 59712 . + . intron_id 3 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 59713 59794 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 59713 59794 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 59795 59796 . + . intron_id 5 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 59795 60215 . + . intron_id 5 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 60214 60215 . + . intron_id 4 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 60216 60404 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 60216 60404 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 60405 60406 . + . intron_id 6 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 60405 60697 . + . intron_id 6 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 60696 60697 . + . intron_id 5 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 60698 60803 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 60698 60803 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 60804 60805 . + . intron_id 7 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 60804 61913 . + . intron_id 7 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 61912 61913 . + . intron_id 6 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 61914 62026 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 61914 62026 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 62027 62028 . + . intron_id 8 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 62027 62119 . + . intron_id 8 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 62118 62119 . + . intron_id 7 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 62120 62221 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 62120 62221 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice5 62222 62223 . + . intron_id 9 ; splice_site "GT" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local intron 62222 63577 . + . intron_id 9 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local splice3 63576 63577 . + . intron_id 8 ; splice_site "AG" JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 63578 63742 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 63578 63742 . + . insertions 0 ; deletions 1 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local similarity 54268 63742 2138 + . alignment_id 1 ; Query SPP00000079_2.0 ; Align 54268 133 27 ; Align 54295 143 111 ; Align 57084 180 108 ; Align 57195 216 102 ; Align 57519 250 123 ; Align 58203 292 135 ; Align 59714 338 81 ; Align 60216 365 189 ; Align 60698 428 105 ; Align 61916 464 111 ; Align 62120 501 102 ; Align 63578 535 63 ; Align 63641 557 102 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000079_2.0 # Protein # Selenoprotein N (SELENON) # Human Target: JSZB01007029.1:subseq(106000,115000) Manis javanica isolate MP_PG03-UM SCAFFOLD8080, whole genome shotgun sequence Model: protein2genome:local Raw score: 189 Query range: 59 -> 104 Target range: 50953 -> 51088 60 : ArgGlnGluLeuAlaLeuLysThrLeuGlyThrAspGlyLeuPheLeuPheSerSerLeu : 79 :::|||||| !|||||||||.!!|||||||||!!:|||||||||||||||||||||||| LysGlnGluSerAlaLeuLysAlaLeuGlyThrGluGlyLeuPheLeuPheSerSerLeu 50954 : aagcaggagtcAGCACTAAAGGCCCTGGGGACAGAAggcctctttctcttttcctccttg : 51011 80 : AspThrAspGlyAspMetTyrIleSerProGluGluPheLysProIleAlaGluLysLeu : 99 ||||||||| !|||||||||||||||||||||||||||||||||||||||||||||||| AspThrAspGlnAspMetTyrIleSerProGluGluPheLysProIleAlaGluLysLeu 51012 : gaCACTGACCAGGATATGTACATCAGCCCTGAGGAGTTCAAGCCCATCGCTGAGAAGCTG : 51071 100 : ThrGlySerCysSer : 104 ||||||!!! ! ||| ThrGlyThrArgSer 51072 : ACAGGTACCAGGAGT : 51088 vulgar: SPP00000079_2.0 59 104 . JSZB01007029.1:subseq(106000,115000) 50953 51088 + 189 M 45 135 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-22 ##type DNA # # # seqname source feature start end score strand frame attributes # JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local gene 50954 51088 189 + . gene_id 2 ; sequence SPP00000079_2.0 ; gene_orientation . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local cds 50954 51088 . + . JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local exon 50954 51088 . + . insertions 0 ; deletions 0 JSZB01007029.1:subseq(106000,115000) exonerate:protein2genome:local similarity 50954 51088 189 + . alignment_id 2 ; Query SPP00000079_2.0 ; Align 50954 60 135 # --- END OF GFF DUMP --- # -- completed exonerate analysis