Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/SECS.fa -t gi|397463559|gb|JH731942.1|subseq.fa -E]
Hostname: [ws101066]
** (process:3698): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00000065_2.0 # Protein # Selenocysteine synthase (SecS) # Human (Homo sapiens)
Target: gi|397463559|gb|JH731942.1|:subseq(600000,155000) Alligator mississippiensis unplaced genomic scaffold scaffold-1514, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 2006
Query range: 0 -> 470
Target range: 115575 -> 66275
1 : MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgG : 20
|||||| !!|||!:!|||!.!|||.!!||||||||||||:!! !!|||||||||||||
MetAsnGlyGluAsnPheGlyAlaSerGluArgLeuValAlaAlaAlaTyrValArgG
115575 : ATGAACGGCGAGAACTTCGGTGCCAGCGAGAGGCTGGTGGCTGCGGCCTACGTGCGGC : 115518
21 : lnGlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys : 39
|||||...:!!!.!||||||:!!||||||! !! !:!:||| !|||||||||:!!
lnGlyAlaGlnGlyArgArgAlaHisGluLeuArgLeuArgAlaLeuLeuGluGln++
115517 : AGGGGGCGCAGGGCCGCCGCGCGCACGAGCTCCGCCTGCGGGCGCTGCTAGAGCAGgt : 115461
40 : >>>> Target Intron 1 >>>> GlyLysCysProGluAsnGlyTrpAspGluS : 49
6776 bp |||||||||||||||:!!|||||||||||||
++GlyLysCysProGluAspGlyTrpAspGluS
115460 : .........................agGGTAAGTGTCCCGAAGATGGATGGGATGAAA : 108655
50 : erThrLeuGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGl : 68
|||||:!!||||||||||||||||||||||||||||||||||||||||||||||||||
erThrIleGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGl
108654 : GTACCATTGAACTCTTTCTTCATGAACTTGCCATTATGGATAGCAACAATTTTCTGGG : 108598
69 : yAsnCysGlyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArg : 87
||||||||||||||||||||||||||||||||||||||||!.!|||||||||||||||
yAsnCysGlyValGlyGluArgGluGlyArgValAlaSerGlyLeuValAlaArgArg
108597 : GAATTGTGGTGTGGGTGAGAGGGAAGGAAGAGTGGCATCAGGACTTGTTGCCCGTCGG : 108541
88 : HisTyr{Ar} >>>> Target Intron 2 >>>> {g}PheIleHisGlyIleG : 96
||||||{||} 3953 bp {|}!!.|||||||||||||
HisTyr{Ar}++ ++{g}LeuIleHisGlyIleG
108540 : CATTAC{AG}gt.........................ag{G}TTGATCCATGGAATCG : 104561
97 : lyArgSerGlyAspIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAs : 115
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
lyArgSerGlyAspIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAs
104560 : GAAGGTCAGGTGATATTTCTGCTGTCCAGCCTAAAGCAGCAGGTTCTAGCCTTTTGAA : 104504
116 : nLysIleThrAsnSerLeuValLeuAspIleIleLysLeuAla{G} >>>> Targe : 130
||||:!!||||||! !:!!||||||||||||||||||||||||{|}
nLysLeuThrAsnLeuIleValLeuAspIleIleLysLeuAla{G}++
104503 : CAAACTTACTAATTTGATAGTTCTGGACATTATAAAGCTGGCT{G}gt.......... : 104456
131 : t Intron 3 >>>> {ly}ValHisThrValAlaAsnCysPheValValProMetA : 143
94 bp {||}|||!..||||||.!!!:!|||||||||||||||||||
++{ly}ValArgThrValThrSerCysPheValValProMetA
104455 : ...............ag{GT}GTCCGGACAGTGACCAGTTGTTTTGTGGTTCCTATGG : 104326
144 : laThrGlyMetSerLeuThrLeuCysPheLeuThrLeuArgHisLysArgProLysAl : 162
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
laThrGlyMetSerLeuThrLeuCysPheLeuThrLeuArgHisLysArgProLysAl
104325 : CAACCGGCATGAGTCTAACCCTTTGTTTCTTAACACTACGGCACAAGAGACCAAAGGC : 104269
163 : aLysTyrIleIleTrpProArgIleAspGlnLysSerCysPheLysSerMetIleThr : 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
aLysTyrIleIleTrpProArgIleAspGlnLysSerCysPheLysSerMetIleThr
104268 : AAAATATATTATTTGGCCACGTATAGACCAGAAATCTTGCTTTAAATCTATGATAACT : 104212
182 : Ala{G} >>>> Target Intron 4 >>>> {ly}PheGluProValValIleG : 190
|||{|} 5835 bp {||}|||||||||||||||||||
Ala{G}++ ++{ly}PheGluProValValIleG
104211 : GCA{G}gt.........................ag{GT}TTTGAGCCTGTGGTGATAG : 98350
191 : luAsnValLeuGluGlyAspGluLeuArgThrAspLeuLysAlaValGluAlaLysVa : 209
|||||:!!||||||..!|||||||||||||||||||||:!!!.!||||||||||||:!
luAsnIleLeuGluAsnAspGluLeuArgThrAspLeuGlnGlyValGluAlaLysIl
98349 : AGAATATATTAGAAAATGATGAGCTGCGCACAGACCTCCAGGGTGTGGAAGCTAAAAT : 98293
210 : lGlnGluLeuGlyProAspCysIleLeuCysIleHisSerThrThrSerCysPheAla : 228
!|||||||||||| !!!!: !:!!||||||:!!||||||||||||||||||||||||
eGlnGluLeuGlyAlaGluAsnValLeuCysValHisSerThrThrSerCysPheAla
98292 : CCAGGAGCTTGGGGCTGAAAATGTCCTTTGTGTTCATTCTACAACTTCCTGCTTTGCC : 98236
229 : ProArgValProAsp{Ar} >>>> Target Intron 5 >>>> {g}LeuGluG : 237
|||||||||||||||{||} 6036 bp {|}|||||||
ProArgValProAsp{Ar}++ ++{g}LeuGluG
98235 : CCAAGGGTACCTGAC{AG}gt.........................ag{A}CTGGAAG : 92173
238 : luLeuAlaValIleCysAlaAsnTyrAspIleProHisIleValAsnAsnAlaTyrGl : 256
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
luLeuAlaValIleCysAlaAsnTyrAspIleProHisIleValAsnAsnAlaTyrGl
92172 : AACTGGCTGTGATTTGTGCTAATTATGACATTCCCCATATTGTCAACAATGCATATGG : 92116
257 : yValGlnSerSerLysCysMetHisLeuIleGlnGln >>>> Target Intron : 269
||||||||||||||||||||||||||||||||||||| 3161 bp
yValGlnSerSerLysCysMetHisLeuIleGlnGln++
92115 : AGTTCAGTCTTCAAAATGTATGCATCTCATCCAGCAGgt................... : 92075
270 : 6 >>>> GlyAlaArgValGlyArgIleAspAlaPheValGlnSerLeuAspLysAs : 285
||||||||||||||||||||||||||||||:!!|||||||||||||||||
++GlyAlaArgValGlyArgIleAspAlaPheIleGlnSerLeuAspLysAs
92074 : ......agGGTGCTCGAGTAGGTAGAATAGATGCTTTCATCCAGAGCCTGGACAAAAA : 88868
286 : nPheMetValProValGlyGlyAlaIleIleAlaGlyPheAsnAspSerPheIleGln : 304
|||||||||||||||||||||||||||||||||||||||||||||||||||||||:!!
nPheMetValProValGlyGlyAlaIleIleAlaGlyPheAsnAspSerPheIleLys
88867 : TTTTATGGTTCCAGTAGGTGGAGCTATCATTGCTGGCTTCAATGATTCCTTCATAAAG : 88811
305 : GluIleSerLysMetTyrPro{G} >>>> Target Intron 7 >>>> {ly}A : 313
|||||||||||||||||||||{|} 126 bp {||}|
GluIleSerLysMetTyrPro{G}++ ++{ly}A
88810 : GAGATCAGTAAAATGTATCCA{G}gt.........................ag{GA}A : 88658
314 : rgAlaSerAlaSerProSerLeuAspValLeuIleThrLeuLeuSerLeuGlySerAs : 332
|||||||||||||||||||||||||||||!!!|||||||||||||||||||||:!!||
rgAlaSerAlaSerProSerLeuAspValPheIleThrLeuLeuSerLeuGlyAlaAs
88657 : GAGCATCAGCATCTCCTTCCTTAGATGTCTTTATTACTCTACTGTCACTAGGTGCAAA : 88601
333 : nGlyTyrLysLysLeuLeuLysGluArgLys >>>> Target Intron 8 >>>> : 343
|||||||::!:!!|||||||||:!!|||||| 19806 bp
nGlyTyrArgGlnLeuLeuLysGlnArgLys++
88600 : TGGCTACCGACAGCTACTAAAACAAAGAAAGgt......................... : 88566
344 : GluMetPheSerTyrLeuSerAsnGlnIleLysLysLeuSerGluAlaTyrAsnGl : 361
||||||||||||||||||!!!!:!:!!:!:|||||||||:!!||| !:!!|||||
++GluMetPheSerTyrLeuThrSerGluLeuLysLysLeuAlaGluIleHisAsnGl
88565 : agGAAATGTTTTCGTATCTTACAAGCGAGCTGAAGAAGTTGGCAGAAATCCACAATGA : 68708
362 : uArgLeuLeuHisThrProHisAsnProIleSerLeu{A} >>>> Target Intr : 374
|||||||||| !!||||||||||||||||||||||||{|} 617 bp
uArgLeuLeuAspThrProHisAsnProIleSerLeu{A}++
68707 : GAGACTCTTGGATACACCACACAACCCTATTTCATTA{G}gt................ : 68666
375 : on 9 >>>> {la}MetThrLeuLysThrLeuAspGluHisArgAspLysAlaValT : 389
{||}|||:!!||||||!.!||||||||||||!!!|||! |||||||
++{la}MetSerLeuLysAsnLeuAspGluHisSerAspThrAlaValT
68665 : .........ag{CC}ATGTCGCTAAAGAACCTAGATGAACACAGTGACACTGCTGTTA : 68007
390 : hrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar} >>>> Tar : 404
||||||||||||||||||||||||||||||||||||||||||||{||}
hrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++
68006 : CACAACTTGGATCTATGCTTTTTACAAGACAAGTTTCTGGAGCT{AG}gt........ : 67958
405 : get Intron 10 >>>> {g}ValValProLeuGlySerMetGlnThrValSerGl : 416
1486 bp {|}|||||||||! !..!! !..!|||||||||!:!..
++{g}ValValProArgAsnPheGlnGlnThrValAsnAs
67957 : ..................ag{G}GTGGTTCCCCGAAATTTTCAGCAAACAGTGAATAA : 66440
417 : yTyrThrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLeuAsn : 435
!|||||||||!:!|||||||||||||||.!!|||||||||||||||||||||||||||
nTyrThrPheLysGlyPheMetSerHisAlaAsnAsnTyrProCysAlaTyrLeuAsn
66439 : CTATACATTCAAAGGCTTTATGTCTCATGCAAATAACTACCCCTGTGCTTACCTCAAT : 66383
436 : AlaAlaSerAlaIleGlyMetLysMetGlnAspValAspLeuPheIleLysArgLeuA : 455
||||||||||||||||||||||||! !||||||||||||:!!|||:!!|||||||||:
AlaAlaSerAlaIleGlyMetLysLysGlnAspValAspMetPheLeuLysArgLeuA
66382 : GCTGCTTCAGCAATTGGCATGAAAAAGCAAGATGTGGACATGTTCCTTAAAAGACTCA : 66323
456 : spArgCysLeuLysAlaValArgLysGluArgSerLysGluSerAsp : 470
!!!:!|||||||||.!! !! !!||||||! !!:!|||! !!.!|||
snLysCysLeuLysThrPheGlyLysGluThrAsnLysGlyLysAsp
66322 : ATAAGTGTTTGAAGACTTTTGGAAAAGAAACAAACAAAGGAAAAGAC : 66276
vulgar: SPP00000065_2.0 0 470 . gi|397463559|gb|JH731942.1|:subseq(600000,155000) 115575 66275 - 2006 M 38 114 5 0 2 I 0 6772 3 0 2 M 51 153 S 0 2 5 0 2 I 0 3949 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 90 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 5831 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 6032 3 0 2 S 1 1 M 34 102 5 0 2 I 0 3157 3 0 2 M 43 129 S 0 1 5 0 2 I 0 122 3 0 2 S 1 2 M 30 90 5 0 2 I 0 19802 3 0 2 M 31 93 S 0 1 5 0 2 I 0 613 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 1482 3 0 2 S 1 1 M 66 198
# --- 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|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local gene 66276 115575 2006 - . gene_id 1 ; sequence SPP00000065_2.0 ; gene_orientation +
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 115462 115575 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 115462 115575 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 115460 115461 . - . intron_id 1 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 108686 115461 . - . intron_id 1
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 108686 108687 . - . intron_id 0 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 108531 108685 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 108531 108685 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 108529 108530 . - . intron_id 2 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 104578 108530 . - . intron_id 2
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 104578 104579 . - . intron_id 1 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 104459 104577 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 104459 104577 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 104457 104458 . - . intron_id 3 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 104365 104458 . - . intron_id 3
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 104365 104366 . - . intron_id 2 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 104206 104364 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 104206 104364 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 104204 104205 . - . intron_id 4 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 98371 104205 . - . intron_id 4
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 98371 98372 . - . intron_id 3 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 98217 98370 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 98217 98370 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 98215 98216 . - . intron_id 5 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 92181 98216 . - . intron_id 5
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 92181 92182 . - . intron_id 4 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 92078 92180 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 92078 92180 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 92076 92077 . - . intron_id 6 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 88917 92077 . - . intron_id 6
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 88917 88918 . - . intron_id 5 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 88787 88916 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 88787 88916 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 88785 88786 . - . intron_id 7 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 88661 88786 . - . intron_id 7
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 88661 88662 . - . intron_id 6 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 88569 88660 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 88569 88660 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 88567 88568 . - . intron_id 8 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 68763 88568 . - . intron_id 8
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 68763 68764 . - . intron_id 7 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 68669 68762 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 68669 68762 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 68667 68668 . - . intron_id 9 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 68052 68668 . - . intron_id 9
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 68052 68053 . - . intron_id 8 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 67961 68051 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 67961 68051 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice5 67959 67960 . - . intron_id 10 ; splice_site "GT"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local intron 66475 67960 . - . intron_id 10
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local splice3 66475 66476 . - . intron_id 9 ; splice_site "AG"
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local cds 66276 66474 . - .
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local exon 66276 66474 . - . insertions 0 ; deletions 0
gi|397463559|gb|JH731942.1|:subseq(600000,155000) exonerate:protein2genome:local similarity 66276 115575 2006 - . alignment_id 1 ; Query SPP00000065_2.0 ; Align 115576 1 114 ; Align 108686 39 153 ; Align 104577 91 117 ; Align 104363 131 156 ; Align 98369 184 150 ; Align 92180 235 102 ; Align 88917 269 129 ; Align 88659 313 90 ; Align 68763 343 93 ; Align 68050 375 87 ; Align 66474 405 198
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis