Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/PSTK.fa -t gi|397460868|gb|JH734633.1|subseq.fa -E]
Hostname: [ws101067]
C4 Alignment:
------------
Query: SPP00000052_2.0 # Protein # Phosphoseryl-tRNA kinase (PSTK) # Human (Homo sapiens)
Target: gi|397460868|gb|JH734633.1|:subseq(120000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-5878, whole genome shotgun sequence
Model: protein2genome:local
Raw score: 725
Query range: 15 -> 336
Target range: 49708 -> 95000
16 : ArgLysArgGlyLeuCysValLeuCysGlyLeuProAlaAlaGlyLysSerThrPheAla : 35
||| ! !|||||||||||||||||||||||||||||||||||||||!!!|||.!..!!
ArgGlyLeuGlyLeuCysValLeuCysGlyLeuProAlaAlaGlyLysThrThrLeuThr
49709 : CGGGGCCTGGGTCTGTGCGTGTTGTGCGGGCTGCCCGCAGCGGGCAAGACCACGCTAACG : 49766
36 : ArgAlaLeuAlaHisArgLeuGlnGlnGluGlnGlyTrpAlaIleGlyValValAlaTyr : 55
!:! !||| !:!! !|||::!! !! !|||! ! ! ! !:!!:!!|||
GlnArgLeu------LysGlnGlnArgGlyTrpAspTrpAspCysPheArgLeuSerTyr
49767 : CAGCGCCTG------AAGCAGCAGAGAGGCTGGGACTGGGATTGCTTCCGCCTTTCCTAC : 49820
56 : AspAspValMetPro<->AspAlaPheLeuAlaGlyAlaArgAlaArgProAla >>>> : 73
||||||:!!!!:||| !!:|||||| ! !..!!.!! !!.! ! ! !
AspAspLeuIleProLeuGluAlaPheSerGlnSerValProGlyAlaGlyLeu+-
49821 : GATGACCTCATTCCGCTGGAGGCCTTCAGCCAATCAGTGCCGGGGGCGGGGCTTga.... : 49879
74 : Target Intron 1 >>>> ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuL : 85
1712 bp !|||!::||||||! !! !|||||||||||||||
++ValSerArgTrpLysSerTyrArgGlnGluLeuLeuV
49880 : .....................agGTGTCGCGCTGGAAATCATACCGGCAGGAACTGCTGG : 51625
86 : ysTyrLeuGluTyrPheLeuMetAlaValIleAsnGlyCysGlnMetSerValProProA : 105
!|||||||||:!!||||||..!|||:!!:!!|||||| !! :!!|||!.!||| !!!
alTyrLeuGluHisPheLeuGlnAlaLeuLeuAsnGlyAspProLeuSerAlaProAlaS
51626 : TATACCTTGAACATTTCCTGCAGGCTCTTCTTAATGGGGATCCCCTGTCTGCCCCAGCAA : 51685
106 : snArgThrGluAlaMetTrpGluAspPheIleThrCysLeuLysAspGlnAspLeuIleP : 125
:!||||||||||||! |||||| !|||:!!:!!|||!!!!:!!!:|||! ||||||!
erArgThrGluAlaThrTrpGluArgPheValSerCysPheArgGluGlnGlyLeuIleS
51686 : GCAGGACAGAAGCCACCTGGGAACGTTTTGTTTCCTGCTTCAGAGAACAAGGATTAATAT : 51745
126 : heSerAlaAlaPheGluAlaGlnSerCysTyrLeuLeuThrLysThrAlaValSerArgP : 145
!|||! !!.! !!!:|||:!!|||||| !! !:!!! !!!..!!.!!!.!|||||||
erSerAspValProAspAlaLysSerCysArgTyrValIleAsnAlaThrAlaSerArgP
51746 : CTTCAGACGTACCTGATGCTAAATCTTGTCGTTATGTGATCAATGCCACCGCTTCCAGAC : 51805
146 : roLeuPheLeuValLeuAspAspAsnPheTyrTyrGlnSerMetArgTyrGluValTyrG : 165
|||||! !!!!:!!||||||||||||||||||||||||||||||||||||||||||||||
roLeuCysPheIleLeuAspAspAsnPheTyrTyrGlnSerMetArgTyrGluValTyrG
51806 : CACTGTGTTTCATTTTGGATGACAACTTTTATTATCAAAGCATGAGATACGAAGTATACC : 51865
166 : lnLeuAlaArgLys{T} >>>> Target Intron 2 >>>> {yr}SerLeuGlyP : 174
||||||||||||||{|} 295 bp {||}||||||||||
lnLeuAlaArgLys{T}++ ++{yr}SerLeuGlyP
51866 : AGCTAGCTCGCAAA{T}gt.........................ag{AT}TCATTAGGCT : 52187
175 : heCysGlnLeuPheLeuAspCysProLeuGluThrCysLeuGlnArgAsnGlyGlnArgP : 194
|||||||||||||||||||||||||||||||| !||||||||||||||| !! !|||
heCysGlnLeuPheLeuAspCysProLeuGluCysCysLeuGlnArgAsnArgValArgS
52188 : TCTGCCAGTTATTTTTAGACTGTCCACTTGAATGCTGCTTACAGAGGAATCGCGTGAGAA : 52247
195 : roGlnAlaLeuProProGluThrIleHisLeuMetGlyArgLysLeuGluLysProAsnP : 214
!||| !!|||||| !|||! !||| !||||||!.!!:!|||:!!||| !||||||!
erGlnProLeuProAspGluIleIleCysLeuMetAlaLysLysIleGluAlaProAsnL
52248 : GTCAGCCCTTACCTGACGAGATCATATGTCTAATGGCAAAAAAGATAGAAGCACCAAATC : 52307
215 : roGluLysAsnAlaTrpGluHisAsnSerLeuThrIleProSerProAlaCysAlaSerG : 234
!!!:||||||.!!||||||!!.||||||||||||:!: !.!!! !! !! !.!!||||
euAspLysAsnThrTrpGluGlnAsnSerLeuThrLeuLysGlyLeuGluTyrThrSerG
52308 : TTGATAAAAATACCTGGGAACAAAATAGTCTCACTCTGAAAGGGCTTGAATACACTTCAG : 52367
235 : luAla{Se} >>>> Target Intron 3 >>>> {r}LeuGluValThrAspLeuL : 243
||! !{!:} 422 bp {!}|||:!!|||! !..!||||
luAsp{As}++ ++{n}LeuGlnValIleSerLeuL
52368 : AAGAT{AA}gt.........................ag{T}TTACAGGTAATCAGCCTGT : 52816
244 : euLeuThrAlaLeuGluAsnProValLysTyrAlaGluAspAsnMetGluGlnLys >> : 262
||:!!|||||||||:!!|||||||||||| ! !|||!!:|||!!:|||||||||
euValThrAlaLeuLysAsnProValLysGlnIleGluGluAsnIleGluGlnLys++
52817 : TGGTTACTGCTTTGAAAAATCCAGTGAAACAAATTGAAGAAAATATTGAGCAAAAGgt.. : 52875
263 : >> Target Intron 4 >>>> AspThrAspArgIleIleCysSerThrAsnIleLe : 273
564 bp ! .!!|||||| !||||||:!!.!!!:!|||||
++AlaAlaAspArgAlaIleCysAlaAlaSerIleLe
52876 : .......................agGCAGCAGATCGAGCAATCTGTGCAGCTAGTATCCT : 53470
274 : uHisLysThrAspGlnThrLeuArgArgIleValSerGlnThrMetLysGluAlaLys{G : 293
||||:!!.!!|||||||||!!!|||||||||:!!|||||||||||||||!!:||||||{|
uHisGlnAlaAspGlnThrPheArgArgIleIleSerGlnThrMetLysAspAlaLys{G
53471 : CCATCAAGCTGATCAGACTTTTAGACGAATTATTTCTCAAACAATGAAGGATGCAAAA{G : 53530
294 : } >>>> Target Intron 5 >>>> {ly}AsnGlnGluAla >>>> Target : 298
} 11254 bp {||}!!.|||||| ! 884
}++ ++{ly}LysGlnGluLys+-
53531 : }gt.........................ag{GT}AAGCAGGAAAAGga............ : 64801
299 : Intron 6 >>>> PheSerGluMetThrPheLysGlnArgTrpValArgAlaAsnHis : 312
3 bp !!!! ! ||||||...!!.!!! |||! ! !||||||
++LysThrValTyrThrPheSerHisSerLysValLeu***AsnHis
64802 : .............agAAGACAGTATATACATTTTCCCACAGCAAAGTACTGTAGAATCAT : 73684
313 : AlaAlaIle{T} >>>> Target Intron 7 >>>> {rp}ArgIleIleLeuGly : 321
:!! !:!:{|} 10503 bp {||}!.! ! ! !
SerTyrLeu{T}++ ++{rp}HisTrpCysAspGln
73685 : TCATACCTG{T}gt.........................ag{GG}CACTGGTGCGACCAG : 84214
322 : AsnGluHis{Il} >>>> Target Intron 8 >>>> {e}LysCysArgSerAla : 330
:::! |||{ } 10739 bp {!}|||||||||!!! !
SerGlyHis{Ar}++ ++{g}LysCysArgCysTyr
84215 : TCAGGCCAT{CG}gt.........................ag{C}AAATGCAGATGCTAC : 94980
331 : LysValGlyTrpLeuGln : 336
|||||| !||||||::!
LysValLeuTrpLeuArg
94981 : AAAGTCTTATGGCTCAGA : 95000
vulgar: SPP00000052_2.0 15 336 . gi|397460868|gb|JH734633.1|:subseq(120000,100000) 49708 95000 + 725 M 23 69 G 2 0 M 20 60 G 0 3 M 12 36 5 0 2 I 0 1708 3 0 2 M 97 291 S 0 1 5 0 2 I 0 291 3 0 2 S 1 2 M 65 195 S 0 2 5 0 2 I 0 418 3 0 2 S 1 1 M 25 75 5 0 2 I 0 560 3 0 2 M 31 93 S 0 1 5 0 2 I 0 11250 3 0 2 S 1 2 M 4 12 5 0 2 I 0 8839 3 0 2 M 18 54 S 0 1 5 0 2 I 0 10499 3 0 2 S 1 2 M 8 24 S 0 2 5 0 2 I 0 10735 3 0 2 S 1 1 M 11 33
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local gene 49709 95000 725 + . gene_id 1 ; sequence SPP00000052_2.0 ; gene_orientation +
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 49709 49876 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 49709 49876 . + . insertions 3 ; deletions 2
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 49877 49878 . + . intron_id 1 ; splice_site "GA"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 49877 51588 . + . intron_id 1
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 51587 51588 . + . intron_id 0 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 51589 51880 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 51589 51880 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 51881 51882 . + . intron_id 2 ; splice_site "GT"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 51881 52175 . + . intron_id 2
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 52174 52175 . + . intron_id 1 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 52176 52374 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 52176 52374 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 52375 52376 . + . intron_id 3 ; splice_site "GT"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 52375 52796 . + . intron_id 3
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 52795 52796 . + . intron_id 2 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 52797 52872 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 52797 52872 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 52873 52874 . + . intron_id 4 ; splice_site "GT"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 52873 53436 . + . intron_id 4
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 53435 53436 . + . intron_id 3 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 53437 53530 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 53437 53530 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 53531 53532 . + . intron_id 5 ; splice_site "GT"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 53531 64784 . + . intron_id 5
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 64783 64784 . + . intron_id 4 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 64785 64798 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 64785 64798 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 64799 64800 . + . intron_id 6 ; splice_site "GA"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 64799 73641 . + . intron_id 6
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 73640 73641 . + . intron_id 5 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 73642 73696 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 73642 73696 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 73697 73698 . + . intron_id 7 ; splice_site "GT"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 73697 84199 . + . intron_id 7
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 84198 84199 . + . intron_id 6 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 84200 84227 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 84200 84227 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice5 84228 84229 . + . intron_id 8 ; splice_site "GT"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local intron 84228 94966 . + . intron_id 8
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local splice3 94965 94966 . + . intron_id 7 ; splice_site "AG"
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local cds 94967 95000 . + .
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local exon 94967 95000 . + . insertions 0 ; deletions 0
gi|397460868|gb|JH734633.1|:subseq(120000,100000) exonerate:protein2genome:local similarity 49709 95000 725 + . alignment_id 1 ; Query SPP00000052_2.0 ; Align 49709 16 69 ; Align 49778 41 60 ; Align 49841 61 36 ; Align 51589 73 291 ; Align 52178 171 195 ; Align 52798 237 75 ; Align 53437 262 93 ; Align 64787 294 12 ; Align 73642 298 54 ; Align 84202 317 24 ; Align 94968 326 33
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis