Command line: [exonerate -m p2g --showtargetgff -q ./SPP00000345_2.0.fa -t ./SPP00000345_2.0/fastasubseq/KV390105.1_fastasubseq.fa]
Hostname: [ws101072u]
C4 Alignment:
------------
Query: SPP00000345_2.0 # Protein # Selenocysteine synthase (SecS) # Marmoset
Target: KV390105.1:subseq(89394,100281) Cebus capucinus imitator isolate Cc_AM_T3 unplaced genomic scaffold Scaffold679, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 2443
Query range: 0 -> 493
Target range: 86588 -> 49999
1 : MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgGln : 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgGln
86588 : ATGAACCGCGAGAGCTTCGCGGCGGGCGAGCGACTGGTGTCGCCGGCTTACGTGAGGCAG : 86531
21 : GlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys >>>> : 39
||||||||||||||||||||||||||||||||||||||||||||||||||||||
GlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys++
86530 : GGCTGTGAGGCCCGCCGCTCGCATGAGCACCTCATACGGCTGCTTCTGGAGAAGgt.... : 86472
40 : Target Intron 1 >>>> GlyLysCysProGluAsnGlyTrpAspGluSerThrL : 51
1140 bp |||||||||||||||||||||||||||||||||||||
++GlyLysCysProGluAsnGlyTrpAspGluSerThrL
86471 : .....................aggGCAAGTGTCCAGAGAATGGCTGGGATGAAAGTACAC : 85298
52 : euGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGlyAsnCysG : 71
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
euGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGlyAsnCysG
85297 : TTGAACTCTTTTTACATGAACTTGCAATCATGGACAGCAACAATTTCTTAGGCAATTGTG : 85238
72 : lyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArgHisTyr{Ar} : 90
||||||||||||||||||||||||||||||||||||||||||||||||||||||||{||}
lyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArgHisTyr{Ar}
85237 : GtgtgggagaaagggaagggagagttGCATCCGCATTAGTTGCTCGTCGTCATTAC{AG} : 85181
91 : >>>> Target Intron 2 >>>> {g}LeuIleHisGlyIleGlyArgSerGlyA : 100
1658 bp {|}!!!|||||||||||||||||||||||||
++ ++{g}PheIleHisGlyIleGlyArgSerGlyA
85180 : gt.........................ag{G}TTCATTCATGGGATTGGACGATCGGGTG : 83493
101 : spIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnP : 120
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||!
spIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS
83492 : ATATTTCTGCTGTGCAACCAAAAGCTGCAGGCTCTAGCCTTTTGAACAAAATTACCAATT : 83433
121 : heLeuValLeuAspMetIleLysLeuAla{G} >>>> Target Intron 3 >>>> : 130
!||||||||||||!!:||||||||||||{|} 312 bp
erLeuValLeuAspIleIleLysLeuAla{G}++ +
83432 : CTTTGGTCCTGGACATTATCAAGCTGGCT{G}gt.........................a : 83092
131 : {ly}ValHisThrValAlaAsnCysPheValValProMetAlaThrGlyMetSerLeuT : 149
{||}|||||||||||||||||||||||||||||||||||||||||||||||||||||||
+{ly}ValHisThrValAlaAsnCysPheValValProMetAlaThrGlyMetSerLeuT
83091 : g{GT}GTCCATACAGTAGCCAACTGCTTTGTAGTTCCTATGGCAACTGGTATGAGTCTAA : 83034
150 : hrLeuCysPheLeuThrLeuArgHisLysArgProLysAlaLysTyrIleIleTrpProA : 169
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
hrLeuCysPheLeuThrLeuArgHisLysArgProLysAlaLysTyrIleIleTrpProA
83033 : CCCTATGTTTCTTAACATTACGACACAAAAGACCAAAGGCAAAGTATATTATATGGCCAC : 82974
170 : rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G} >>>> Target In : 183
|||||||||||||||||||||||||||||||||||||||||{|} 910
rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G}++
82973 : GAATAGACCAGAAGTCCTGCTTTAAATCCATGATCACTGCA{G}gt.............. : 82929
184 : tron 4 >>>> {ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL : 198
bp {||}|||||||||||||||||||||||||||||||||||||||||||
++{ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL
82928 : ...........ag{GT}TTTGAGCCTGTGGTgatagaaaatgttttggaagGTGACGAGC : 81977
199 : euArgThrAspLeuGlnAlaValLysAlaLysValGlnGluLeuGlyProAspAsnIleL : 218
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
euArgThrAspLeuGlnAlaValLysAlaLysValGlnGluLeuGlyProAspAsnIleL
81976 : TGCGTACAGACCTGCAAGCAGTAAAGGCTAAAGTCCAGGAACTTGGGCCTGATAACATTC : 81917
219 : euCysIleHisSerThrThrSerCysPheAlaProArgValProAsp{Ar} >>>> Ta : 234
|||||||||||||||||||||||||||||||||||||||||||||||{||}
euCysIleHisSerThrThrSerCysPheAlaProArgValProAsp{Ar}++
81916 : TGTGTATTCATTCTACTACATCCTGTTTTGCTCCGAGGGTGCCTGAT{AG}gt....... : 81865
235 : rget Intron 5 >>>> {g}LeuGluGluLeuAlaValIleCysAlaAsnPheAspI : 247
2899 bp {|}|||||||||||||||||||||||||||||||||! !|
++{g}LeuGluGluLeuAlaValIleCysAlaAsnPheGlyI
81864 : ..................ag{a}ctAGAAGAACTGGCTGTGATTTGTGCTAATTTTGGCA : 78931
248 : leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG : 267
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG
78930 : TTCCACATATAGTCAATAATGCTTATGGAGTGCAGTCTTCAAAGTGTATGCACCTCATTC : 78871
268 : lnGln >>>> Target Intron 6 >>>> GlyAlaArgValGlyArgIleAspAl : 277
||||| 6515 bp ||||||||||||||||||||||||||
lnGln++ ++GlyAlaArgValGlyArgIleAspAl
78870 : AGCAGgt.........................agGGGGCTCGAGTTGGTAGAATAGATGC : 72326
278 : aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl : 297
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl
72325 : TTTTGTTCAGAGCTTGGACAAAAATTTTATGGTTCCAGTAGGTGGCGCTATAATTGCTGG : 72266
298 : yPheAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G} >>>> Target : 312
|||||||||||||||||||||||||||||||||||||||||||{|} 13
yPheAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G}++
72265 : CTTTAATGATTCCTTCATTCAGGAAATCAGCAAGATGTATCCA{G}gt............ : 72218
313 : Intron 7 >>>> {ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe : 326
3 bp {||}|||||||||||||||||||||||||||||||||||||||||
++{ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe
72217 : .............ag{GA}AGAGCTTCAGCTTCACCTTCTTTAGATGTCCTTATTACTTT : 72046
327 : uLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys >>>> Targ : 343
|||||||||||||||||||||||||||||||||||||||||||||||||
uLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys++
72045 : ATTATCACTTGGATCAAATGGCTATaagaaactattaaaagaaagaaaggt......... : 71993
344 : et Intron 8 >>>> GluMetPheSerTyrLeuSerAsnGlnIleLysLysLeuSer : 356
18596 bp ||||||||||||||||||||||||||||||||||||||||||
++GluMetPheSerTyrLeuSerAsnGlnIleLysLysLeuSer
71992 : ................aggaaatgttttcatatttgtcCAACCAAATAAAGAAGTTGTCA : 53360
357 : GluAlaTyrAsnGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A} >>>> : 374
|||||||||||||||||||||||||||||||||||||||||||||||||||{|}
GluAlaTyrAsnGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A}++
53359 : GAAGCCTACAATGAAAGACTGTTGCATACACCTCACAATCCCATATCTTTA{G}gt.... : 53303
375 : Target Intron 9 >>>> {la}ValThrLeuLysThrLeuAspLysHisHisAsp : 385
1471 bp {||}|||||||||||||||||||||||||||||||||
++{la}ValThrLeuLysThrLeuAspLysHisHisAsp
53302 : .....................ag{ct}gtgACACTTAAAACATTAGATAAACACCATGAC : 51802
386 : LysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar} : 404
||||||||||||||||||||||||||||||||||||||||||||||||||||||{||}
LysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++
51801 : AAAGCTGTCACTCAGCTTGGCTCTATGCTTTTTACCAGACAGGTTTCTGGAGCC{AG}gt : 51743
405 : >>>> Target Intron 10 >>>> {g}ValValProLeuGlySerValGlnThrVa : 414
1476 bp {|}|||||||||||||||||||||||||||||
++{g}ValValProLeuGlySerValGlnThrVa
51742 : ..........................ag{G}GTTGTGCCTCTTGGGTCTGTGCAAACTGT : 50239
415 : lSerGlyTyrThrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLe : 434
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
lSerGlyTyrThrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLe
50238 : GAGTGGCTATACTTTCAGAGGCTTTATGTCACATACAAATAATTACCCTTGTGCTTACCT : 50179
435 : uAsnAlaAlaSerAlaIleGlyMetLysMetGlnAspValAspLeuPheIleLysArgLe : 454
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
uAsnAlaAlaSerAlaIleGlyMetLysMetGlnAspValAspLeuPheIleLysArgLe
50178 : CAATGCTGCATCAGCCATCGGAATGAAGATGCAGGATGTGGACCTGTTCATAAAGAGACT : 50119
455 : uAspArgCysLeuLysThrValArgLysGluGlnSerLysAspSerAspAspAsnTyrAs : 474
||||||||||||||||||||||||||||||||||||||||:::|||||||||||||||||
uAspArgCysLeuLysThrValArgLysGluGlnSerLysGluSerAspAspAsnTyrAs
50118 : TGACAGGTGTTTAAAGACagtaagaaaagaacaaagtaaagaGAGTGATGACAATTATGA : 50059
475 : pLysThrGluAspValAspIleGluGluMetAlaLeuLysLeuAspAsnValLeuLeu : 493
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
pLysThrGluAspValAspIleGluGluMetAlaLeuLysLeuAspAsnValLeuLeu
50058 : CAAAACTGAAGATGTGGATATTGAAGAAATGGCTTTAAAACTAGATAATGTACTTCTT : 50000
vulgar: SPP00000345_2.0 0 493 . KV390105.1:subseq(89394,100281) 86588 49999 - 2443 M 38 114 5 0 2 I 0 1136 3 0 2 M 51 153 S 0 2 5 0 2 I 0 1654 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 308 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 906 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 2895 3 0 2 S 1 1 M 34 102 5 0 2 I 0 6511 3 0 2 M 43 129 S 0 1 5 0 2 I 0 129 3 0 2 S 1 2 M 30 90 5 0 2 I 0 18592 3 0 2 M 31 93 S 0 1 5 0 2 I 0 1467 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 1472 3 0 2 S 1 1 M 89 267
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2016-11-17
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local gene 50000 86588 2443 - . gene_id 1 ; sequence SPP00000345_2.0 ; gene_orientation +
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 86475 86588 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 86475 86588 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 86473 86474 . - . intron_id 1 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 85335 86474 . - . intron_id 1
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 85335 85336 . - . intron_id 0 ; splice_site "ag"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 85180 85334 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 85180 85334 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 85178 85179 . - . intron_id 2 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 83522 85179 . - . intron_id 2
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 83522 83523 . - . intron_id 1 ; splice_site "AG"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 83403 83521 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 83403 83521 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 83401 83402 . - . intron_id 3 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 83091 83402 . - . intron_id 3
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 83091 83092 . - . intron_id 2 ; splice_site "AG"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 82932 83090 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 82932 83090 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 82930 82931 . - . intron_id 4 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 82022 82931 . - . intron_id 4
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 82022 82023 . - . intron_id 3 ; splice_site "AG"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 81868 82021 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 81868 82021 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 81866 81867 . - . intron_id 5 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 78969 81867 . - . intron_id 5
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 78969 78970 . - . intron_id 4 ; splice_site "ag"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 78866 78968 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 78866 78968 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 78864 78865 . - . intron_id 6 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 72351 78865 . - . intron_id 6
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 72351 72352 . - . intron_id 5 ; splice_site "AG"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 72221 72350 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 72221 72350 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 72219 72220 . - . intron_id 7 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 72088 72220 . - . intron_id 7
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 72088 72089 . - . intron_id 6 ; splice_site "AG"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 71996 72087 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 71996 72087 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 71994 71995 . - . intron_id 8 ; splice_site "gt"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 53400 71995 . - . intron_id 8
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 53400 53401 . - . intron_id 7 ; splice_site "ag"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 53306 53399 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 53306 53399 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 53304 53305 . - . intron_id 9 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 51835 53305 . - . intron_id 9
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 51835 51836 . - . intron_id 8 ; splice_site "ag"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 51744 51834 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 51744 51834 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice5 51742 51743 . - . intron_id 10 ; splice_site "GT"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local intron 50268 51743 . - . intron_id 10
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local splice3 50268 50269 . - . intron_id 9 ; splice_site "AG"
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local cds 50000 50267 . - .
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local exon 50000 50267 . - . insertions 0 ; deletions 0
KV390105.1:subseq(89394,100281) exonerate:protein2genome:local similarity 50000 86588 2443 - . alignment_id 1 ; Query SPP00000345_2.0 ; Align 86589 1 114 ; Align 85335 39 153 ; Align 83521 91 117 ; Align 83089 131 156 ; Align 82020 184 150 ; Align 78968 235 102 ; Align 72351 269 129 ; Align 72086 313 90 ; Align 53400 343 93 ; Align 51833 375 87 ; Align 50267 405 267
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis