Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/SELO.fa -t gi|397461378|gb|JH734123.1|subseq.fa]
Hostname: [ws101062]
C4 Alignment:
------------
Query: SPP00000081_2.0 # Protein # Selenoprotein O (SelO) # Human (Homo sapiens)
Target: gi|397461378|gb|JH734123.1|:subseq(1630000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-5035, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 2090
Query range: 103 -> 627
Target range: 70748 -> 50896
104 : AlaLeuLeuGlyLeuGlyAlaProProAlaArgGluAlaGluAlaGluAlaAlaLeuPhe : 123
||||||||||||||| !! !!||| !!!.! !||||||||| !||||||||||||! !
AlaLeuLeuGlyLeuArgProProAlaGlySerGluAlaGluAsnGluAlaAlaLeuCys
70748 : GCGCTGCTGGGGCTGCGGCCGCCGGCGGGGTCCGAGGCCGAGAACGAGGCCGCGCTGTGC : 70691
124 : PheSerGlyAsnAlaLeuLeuProGlyAlaGluProAlaAlaHisCysTyrCysGlyHis : 143
|||||||||||| !|||! !|||||||||||||||||||||||||||||||||||||||
PheSerGlyAsnArgLeuProProGlyAlaGluProAlaAlaHisCysTyrCysGlyHis
70690 : TTCAGCGGCAACCGCCTGCCGCCCGGCGCCGAGCCCGCCGCGCACTGCTACTGCGGCCAC : 70631
144 : GlnPheGlyGlnPheAlaGlyGlnLeuGlyAspGlyAlaAlaMetTyrLeuGlyGluVal : 163
|||||||||...||||||||||||||||||||||||||||||||||||||||||||||||
GlnPheGlySerPheAlaGlyGlnLeuGlyAspGlyAlaAlaMetTyrLeuGlyGluVal
70630 : CAGTTCGGCAGCTTCGCGGGCCAGCTGGGCGACGGCGCCGCCATGTACCTGGGCGAGGTG : 70571
164 : CysThrAlaThrGlyGluArgTrpGluLeuGlnLeuLysGlyAlaGlyProThrProPhe : 183
! !!.!!|||..!|||||||||:!!||||||||||||||||||! !|||||||||
LeuGlyProAlaGlyArgArgTrpGluValGlnLeuLysGlyAlaGlyLeuThrProPhe
70570 : CTGGGCCCGGCCGGGCGGCGCTGGGAGGTGCAGCTCAAGGGCGCCGGCCTCACGCCCTTC : 70511
184 : Ser{Ar} >>>> Target Intron 1 >>>> {g}GlnAlaAspGlyArgLysVal : 192
|||{||} 4704 bp {|}|||||||||||||||||||||
Ser{Ar}++ ++{g}GlnAlaAspGlyArgLysVal
70510 : TCC{CG}gt.........................ag{G}CAAGCTGATGGTCGTAAGGTC : 65780
193 : LeuArgSerSerIleArgGluPheLeuCysSerGluAlaMetPheHisLeuGlyValPro : 212
||||||||||||||||||||||||||||||||||||||||||||||||||||||:!!|||
LeuArgSerSerIleArgGluPheLeuCysSerGluAlaMetPheHisLeuGlyIlePro
65779 : CTGCGGTCAAGTATAAGAGAATTCCTGTGCAGTGAGGCTATGTTTCACCTTGGAATACCC : 65720
213 : ThrThrArgAlaGlyAlaCysValThrSerGluSerThrValValArgAspValPheTyr : 232
|||||||||||||||.!!||||||||||||!!:|||! !|||:!!|||||||||||||||
ThrThrArgAlaGlyThrCysValThrSerAspSerLysValIleArgAspValPheTyr
65719 : ACAACAAGGGCTGGAACATGTGTAACATCTGACTCGAAAGTTATTCGGGATGTATTCTAT : 65660
233 : AspGlyAsnProLysTyrGluGlnCysThrValValLeuArgValAlaSerThrPheIle : 252
|||||||||||||||:!!|||::!||||||||||||||||||:!!|||||||||||||||
AspGlyAsnProLysHisGluArgCysThrValValLeuArgIleAlaSerThrPheIle
65659 : GATGGAAATCCAAAACATGAAAGATGCACAGTTGTCCTGAGAATAGCTTCCACTTTTATA : 65600
253 : {Ar} >>>> Target Intron 2 >>>> {g}PheGlySerPheGluIlePheLys : 261
{||} 944 bp {|}||||||||||||||||||||||||
{Ar}++ ++{g}PheGlySerPheGluIlePheLys
65599 : {AG}gt.........................ag{G}TTTGGATCATTTGAGATTTTTAAA : 64629
262 : SerAlaAspGluHisThrGlyArgAlaGlyProSerValGlyArgAsnAspIleArgVal : 281
!! !|||||||||||||||||| !||||||||||||..!|||||||||||||||..!
ProMetAspGluHisThrGlyArgLysGlyProSerValAsnArgAsnAspIleArgThr
64628 : CCTATGGATGAACATACAGGACGGAAGGGTCCCAGTGTCAACCGAAATGATATTCGAACA : 64569
282 : GlnLeuLeuAspTyrValIleSerSerPheTyrProGluIleGlnAlaAlaHisAlaSer : 301
|||:!!|||:!!||||||||||||!!!|||||||||||||||||| !|||:!! !!..!
GlnMetLeuAsnTyrValIleSerThrPheTyrProGluIleGlnGlnAlaTyrProAsp
64568 : CAGATGCTTAACTACGTGATCAGTACTTTCTATCCAGAAATCCAGCAGGCTTATCCTGAC : 64509
302 : AspSerValGlnArgAsnAlaAlaPhePheArgGlu >>>> Target Intron 3 > : 314
:!!!!!:!!||||||||||||||||||||||||||| 6245 bp
AsnThrIleGlnArgAsnAlaAlaPhePheArgGlu++
64508 : AACACTATTCAGAGGAATGCTGCTTTCTTCAGAGAGgt...................... : 64468
315 : >>> ValThrArgArgThrAlaArgMetValAlaGluTrpGlnCysValGlyPheCysH : 332
:!!|||!:!||||||||||||:!!|||||||||||||||||||||||||||||||
++IleThrLysArgThrAlaArgLeuValAlaGluTrpGlnCysValGlyPheCysH
64467 : ...agATAACAAAGCGGACAGCAAGGTTGGTTGCTGAATGGCAGTGTGTTGGATTTTGCC : 58171
333 : isGlyValLeuAsnThrAspAsnMetSerIleLeuGlyLeuThrIleAspTyrGlyProP : 352
||||||||||||||||||||||||||||||||:!!|||||||||||||||||||||||||
isGlyValLeuAsnThrAspAsnMetSerIleValGlyLeuThrIleAspTyrGlyProP
58170 : ATGGTGTGCTGAACACAGATAATATGAGCATCGTAGGACTTACTATTGACTATGGCCCTT : 58111
353 : heGlyPheLeuAsp{Ar} >>>> Target Intron 4 >>>> {g}TyrAspProA : 361
||||||||:!!|||{||} 757 bp {|}|||||||||!
heGlyPheMetAsp{Ar}++ ++{g}TyrAspProG
58110 : TTGGGTTTATGGAC{AG}gt.........................ag{A}TATGACCCTG : 57327
362 : spHisValCysAsnAlaSerAspAsnThrGlyArgTyrAlaTyrSerLysGlnProGluV : 381
!:|||:!!||||||!.!|||||||||||||||||||||||||||!:!||||||||||||:
luHisIleCysAsnGlySerAspAsnThrGlyArgTyrAlaTyrAsnLysGlnProGluI
57326 : AACACATTTGCAATGGTTCTGATAATACAGGACGCTACGCTTATAACAAGCAGCCAGAAA : 57267
382 : alCysArgTrpAsnLeuArgLysLeuAlaGluAlaLeuGlnProGluLeuProLeuGluL : 401
!!|||!:!||||||||| !!|||||||||||||||||| ||||||||||||||||||:
leCysLysTrpAsnLeuGlyLysLeuAlaGluAlaLeuValProGluLeuProLeuGluI
57266 : TTTGCAAATGGAATCTAGGGAAGCTTGCTGAAGCTTTAGTCCCTGAATTGCCCTTGGAGA : 57207
402 : euGlyGluAlaIleLeuAlaGluGluPheAspAlaGluPheGlnArgHisTyrLeuGlnL : 421
!!.!!||| !||||||! !||||||!:!:!!!.!||||||:!!!:!|||||||||||||
leSerGluLeuIleLeuGluGluGluTyrAsnValGluPheGluLysHisTyrLeuGlnL
57206 : TCAGCGAACTCATTCTGGAAGAGGAGTACAATGTAGAATTTGAGAAGCATTATTTGCAGA : 57147
422 : ysMetArgArgLysLeuGlyLeuValGlnValGluLeuGluGluAspGlyAlaLeuValS : 441
||||||||!:!||||||||||||:!!|||:!!|||||||||||||||..! !|||||||
ysMetArgLysLysLeuGlyLeuIleGlnLeuGluLeuGluGluAspAsnLysLeuValS
57146 : AGATGAGAAAGAAGCTAGGACTCATTCAGCTGGAATTAGAAGAAGATAATAAATTGGTAT : 57087
442 : erLysLeuLeuGluThrMetHisLeuThr{G} >>>> Target Intron 5 >>>> : 451
||:!!||||||||||||||||||||||||{|} 227 bp
erGluLeuLeuGluThrMetHisLeuThr{G}++ +
57086 : CTGAACTCCTAGAAACTATGCATCTCACA{G}gt.........................a : 56831
452 : {ly}AlaAspPheThrAsnThrPheTyrLeuLeuSerSerPheProValGluLeuGluS : 470
{||}|||||||||||||||! !||| ||||||||||||||| !!|||!!:|||!!:!
+{ly}AlaAspPheThrAsnIlePheArgLeuLeuSerSerPheSerValAspLeuAspP
56830 : g{GT}GCAGACTTCACAAATATTTTCCGGTTGCTGAGTTCGTTCTCAGTAGATTTGGATT : 56773
471 : erProGlyLeuAlaGluPheLeuAlaArgLeuMetGluGlnCysAlaSerLeuGluGluL : 490
! ! !!!!! !|||||||||! !!:!:!! .!.||||||||||||:!!|||||||
heLeuLysPheGluGluPheLeuGluLysIleAlaAsnGlnCysAlaSerMetGluGluL
56772 : TTTTAAAATTTGAGGAATTTCTAGAAAAAATTGCCAATCAGTGTGCTTCCATGGAAGAAT : 56713
491 : euArgLeuAlaPheArgProGlnMetAspPro{Ar} >>>> Target Intron 6 > : 501
||!:!:!!||||||!:!|||||||||||||||{||} 2277 bp
euLysValAlaPheLysProGlnMetAspPro{Ar}++
56712 : TGAAAGTCGCTTTCAAGCCCCAGATGGATCCA{AG}gt...................... : 56676
502 : >>> {g}GlnLeuSerMetMetLeuMetLeuAlaGlnSerAsnProGlnLeuPheAlaL : 519
{|}||||||||||||||||||||||||||||||||||||||||||||||||||||
++{g}GlnLeuSerMetMetLeuMetLeuAlaGlnSerAsnProGlnLeuPheAlaL
56675 : ...ag{A}CAACTTTCCATGATGCTGATGTTGGCTCAATCTAATCCTCAACTGTTTGCTT : 54349
520 : euMetGlyThrArgAlaGlyIleAlaArgGluLeuGluArgValGluGlnGlnSerArgL : 539
||!!:||||||!:!|||..!||| !..!||||||||||||:!!|||||| ! |||!:!|
euIleGlyThrLysAlaAsnIleAsnGluGluLeuGluArgIleGluGlnTyrSerLysL
54348 : TAATTGGAACAAAAGCTAATATAAATGAAGAATTAGAACGCATAGAACAATATTCTAAAT : 54289
540 : euGluGlnLeuSerAlaAlaGluLeuGlnSerArgAsnGlnGlyHisTrpAlaAspTrpL : 559
||:!!||||||!!!||||||!!:|||! |||||||||.!. !!||||||.!!!!:||||
euGlnGlnLeuThrAlaAlaAspLeuLeuSerArgAsnAsnArgHisTrpThrGluTrpL
54288 : TGCAGCAGTTAACAGCAGCTGACCTACTCAGCAGAAATAACAGACATTGGACAGAATGGT : 54229
560 : euGlnAlaTyr{Ar} >>>> Target Intron 7 >>>> {g}AlaArgLeuAspL : 568
||:!! !|||{||} 2567 bp {|}|||||||||!!:|
euGluLysTyr{Ar}++ ++{g}AlaArgLeuGluL
54228 : TGGAGAAATAC{AG}gt.........................ag{A}GCCCGCTTAGAAA : 51635
569 : ysAspLeuGluGlyAlaGlyAspAlaAlaAlaTrpGlnAlaGluHisValArgValMetH : 588
||!!::!!|||..! !..!! !!.!! !.!!|||.!.||||||!.!|||!:!||||||:
ysGluIleGluAsnIleAsnAlaValAspThrTrpAsnAlaGluArgValLysValMetA
51634 : AAGAAATAGAAAACATTAATGCTGTTGATACTTGGAATGCTGAACGTGTGAAAGTTATGA : 51575
589 : isAlaAsnAsnProLysTyrValLeuArgAsnTyrIleAlaGlnAsnAlaIleGluAlaA : 608
!!:!!|||||||||||||||:!!|||||||||||||||||||||||||||||||||||||
snSerAsnAsnProLysTyrIleLeuArgAsnTyrIleAlaGlnAsnAlaIleGluAlaA
51574 : ATTCAAACAATCCAAAATATATTTTGAGAAACTACATCGCTCAAAATGCCATAGAAGCAG : 51515
609 : laGluArgGlyAspPheSerGlu >>>> Target Intron 8 >>>> ValArgAr : 618
|||||!.!|||||||||!!!||| 559 bp ||||||!:
laGluAsnGlyAspPheThrGlu++ ++ValArgLy
51514 : CTGAAAATGGTGACTTCACAGAGgt.........................agGTAAGAAA : 50926
619 : gValLeuLysLeuLeuGluThrProTyr : 627
!|||||||||||||||||| !|||!:!
sValLeuLysLeuLeuGluAspProPhe
50925 : GGTGTTGAAGCTGTTGGAGGATCCATTC : 50897
vulgar: SPP00000081_2.0 103 627 . gi|397461378|gb|JH734123.1|:subseq(1630000,100000) 70748 50896 - 2090 M 81 243 S 0 2 5 0 2 I 0 4700 3 0 2 S 1 1 M 67 201 S 0 2 5 0 2 I 0 940 3 0 2 S 1 1 M 60 180 5 0 2 I 0 6241 3 0 2 M 43 129 S 0 2 5 0 2 I 0 753 3 0 2 S 1 1 M 93 279 S 0 1 5 0 2 I 0 223 3 0 2 S 1 2 M 49 147 S 0 2 5 0 2 I 0 2273 3 0 2 S 1 1 M 61 183 S 0 2 5 0 2 I 0 2563 3 0 2 S 1 1 M 52 156 5 0 2 I 0 555 3 0 2 M 12 36
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local gene 50897 70748 2090 - . gene_id 1 ; sequence SPP00000081_2.0 ; gene_orientation +
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 70504 70748 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 70504 70748 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 70502 70503 . - . intron_id 1 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 65800 70503 . - . intron_id 1
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 65800 65801 . - . intron_id 0 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 65596 65799 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 65596 65799 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 65594 65595 . - . intron_id 2 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 64652 65595 . - . intron_id 2
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 64652 64653 . - . intron_id 1 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 64471 64651 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 64471 64651 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 64469 64470 . - . intron_id 3 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 58226 64470 . - . intron_id 3
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 58226 58227 . - . intron_id 2 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 58095 58225 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 58095 58225 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 58093 58094 . - . intron_id 4 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 57338 58094 . - . intron_id 4
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 57338 57339 . - . intron_id 3 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 57057 57337 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 57057 57337 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 57055 57056 . - . intron_id 5 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 56830 57056 . - . intron_id 5
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 56830 56831 . - . intron_id 4 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 56679 56829 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 56679 56829 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 56677 56678 . - . intron_id 6 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 54402 56678 . - . intron_id 6
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 54402 54403 . - . intron_id 5 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 54216 54401 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 54216 54401 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 54214 54215 . - . intron_id 7 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 51649 54215 . - . intron_id 7
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 51649 51650 . - . intron_id 6 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 51492 51648 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 51492 51648 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice5 51490 51491 . - . intron_id 8 ; splice_site "GT"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local intron 50933 51491 . - . intron_id 8
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local splice3 50933 50934 . - . intron_id 7 ; splice_site "AG"
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local cds 50897 50932 . - .
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local exon 50897 50932 . - . insertions 0 ; deletions 0
gi|397461378|gb|JH734123.1|:subseq(1630000,100000) exonerate:protein2genome:local similarity 50897 70748 2090 - . alignment_id 1 ; Query SPP00000081_2.0 ; Align 70749 104 243 ; Align 65799 186 201 ; Align 64651 254 180 ; Align 58226 314 129 ; Align 57337 358 279 ; Align 56828 452 147 ; Align 54401 502 183 ; Align 51648 564 156 ; Align 50933 616 36
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis