Command line: [exonerate -m p2g --showtargetgff -q ../Sel.tortu/SELP.fa -t gi|397460716|gb|JH734785.1|subseq.fa -E]
Hostname: [ws101145]
** (process:3330): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00002140_2.0 # Protein # Selenoprotein P (SelP) # Softshell turtle (Pelodiscus sinensis)
Target: gi|397460716|gb|JH734785.1|:subseq(44689,103000) Alligator mississippiensis unplaced genomic scaffold scaffold-6128, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 691
Query range: 14 -> 201
Target range: 52289 -> 17448
15 : ValAlaGluAsnLysThrArgIleCysGlnProAlaProGlnTrpAlaIleAsnGlyThr : 34
:!!|||||| !! !|||||||||||||||||||||! !||| !||||||||||||
LeuAlaGluValThrAspArgIleCysGlnProAlaProLeuTrpLysIleAsnGlyThr
52289 : CTGGCGGAAGTCACCGACCGCATCTGCCAGCCAGCTCCGCTGTGGAAGATCAATGGGACG : 52232
35 : AlaProMetLysArgGluLeuGlyArgValThrValValAlaLeuLeuLysAlaSerUnk : 54
!.!|||||| ! ..!! !||||||!:!||||||||||||||||||||||||||||||
ValProMetAspGluAlaLeuGlyGlnValThrValValAlaLeuLeuLysAlaSer***
52231 : GTCCCGATGGACGAGGCGCTGGGGCAGGTGACGGTGGTGGCGCTTTTGAAGGCCAGCTGA : 52172
55 : GlnPheCysLeuLysGlnAlaHis{Se} >>>> Target Intron 1 >>>> {r} : 63
|||||||||||||||||||||:!!{||} 119 bp {|}
GlnPheCysLeuLysGlnAlaAsn{Se}++ ++{r}
52171 : CAGTTCTGTCTCAAGCAAGCTAAC{AG}gt.........................ag{C} : 52024
64 : LeuGlyGlyLeuArgAlaLysLeuSerArgAspGlyLeuThrAspIleSerTyrMetIle : 83
|||||||||||||||! !||||||||||||.!.|||:!!.!!:!!:!!||||||||||||
LeuGlyGlyLeuArgGluLysLeuSerArgGlnGlyMetAlaAsnValSerTyrMetIle
52023 : CTTGGCGGCTTGCGCGAGAAGCTGTCCCGGCAAGGGATGGCCAACGTCAGCTACATGATC : 51966
84 : ValAsnGluLysAlaAlaLeuSerArgAlaMetTyrTrpGlnLeuLysArgGlnAlaPro : 103
||||||||||||||| !!|||||||||||||||||||||:!!||||||||||||||||||
ValAsnGluLysAlaProLeuSerArgAlaMetTyrTrpGluLeuLysArgGlnAlaPro
51965 : GTGAATGAGAAGGCGCCGCTGTCCCGGGCCATGTACTGGGAGCTGAAGCGCCAGGCCCCC : 51906
104 : LysGlyValProValTyrGlnGlnGluLeuLeuGluProAspValTrpGlnIleLeuAsp : 123
:!!|||||||||||||||||||||! !:!!|||!!:||||||||||||||||||||||||
GluGlyValProValTyrGlnGlnGlyIleLeuAspProAspValTrpGlnIleLeuAsp
51905 : GAGGGGGTGCCCGTGTACCAGCAGGGGATCCTGGACCCCGACGTCTGGCAGATCCTGGAT : 51846
124 : GlyAspLysAspAspPheLeuIleTyrAsp{Ar} >>>> Target Intron 2 >>> : 134
||||||||||||||||||||||||||||||{!:} 1676 bp
GlyAspLysAspAspPheLeuIleTyrAsp{Ly}++
51845 : GGGGATAAGGACGACTTCCTCATCTACGAC{AA}gt........................ : 51809
135 : > {g}CysGlyArgLeuAlaPheHisIleProLeuProTyrSerPheLeuHisLeuArg : 152
{!}||||||||||||!.!||||||||| !!|||||||||||||||||||||!!!! !
++{s}CysGlyArgLeuValPheHisIleSerLeuProTyrSerPheLeuHisPhePro
51808 : .ag{G}TGCGGCCGCTTGGTCTTCCACATCTCGCTGCCCTACAGCTTCCTGCACTTCCCC : 50083
153 : TyrValGluSerAlaValArgValThrHisAlaLysAspPheCysGlyAsnCysSerPhe : 172
||||||||||||||||||!.! !!|||:!!.!!||||||!:!||||||||||||! ! !
TyrValGluSerAlaValHisPheThrTyrThrLysAspTyrCysGlyAsnCysIleHis
50082 : TACGTGGAGTCCGCCGTGCACTTCACGTACACCAAGGATTACTGCGGGAACTGCATCCAC : 50023
173 : TyrSerAsnSerThrGlnGluVal >>>> Target Intron 3 >>>> ArgAsnH : 183
||||||||||||||||||:!!! ! 11488 bp ! ! |
TyrSerAsnSerThrGlnGlnGlu++ ++ProLeuH
50022 : TACTCCAACAGCACCCAGCAAGAGgt.........................agCCCCTGC : 38502
184 : isSerArgAlaArgAlaLeuThrValAlaSer{G} >>>> Target Intron 4 >> : 194
|| !!:!|||! !!.!! ! !:!!||||||{|} 20997 bp
isLeuGlnAlaProGlyGlnGluIleAlaSer{G}-+
38501 : ACCTGCAGGCACCAGGCCAGGAAATTGCTAGT{G}tt....................... : 38466
195 : >> {ly}CysAlaProArgIleThrArg : 201
{||}||| ! ! !:!:.!!|||
++{ly}CysGlnGluAlaValAlaArg
38465 : ..ag{GC}TGCCAGGAGGCAGTGGCAAGG : 17449
vulgar: SPP00002140_2.0 14 201 . gi|397460716|gb|JH734785.1|:subseq(44689,103000) 52289 17448 - 691 M 48 144 S 0 2 5 0 2 I 0 115 3 0 2 S 1 1 M 70 210 S 0 2 5 0 2 I 0 1672 3 0 2 S 1 1 M 46 138 5 0 2 I 0 11484 3 0 2 M 13 39 S 0 1 5 0 2 I 0 20993 3 0 2 S 1 2 M 7 21
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-20
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local gene 17449 52289 691 - . gene_id 1 ; sequence SPP00002140_2.0 ; gene_orientation +
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local cds 52144 52289 . - .
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local exon 52144 52289 . - . insertions 0 ; deletions 0
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice5 52142 52143 . - . intron_id 1 ; splice_site "GT"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local intron 52025 52143 . - . intron_id 1
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice3 52025 52026 . - . intron_id 0 ; splice_site "AG"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local cds 51812 52024 . - .
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local exon 51812 52024 . - . insertions 0 ; deletions 0
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice5 51810 51811 . - . intron_id 2 ; splice_site "GT"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local intron 50136 51811 . - . intron_id 2
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice3 50136 50137 . - . intron_id 1 ; splice_site "AG"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local cds 49997 50135 . - .
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local exon 49997 50135 . - . insertions 0 ; deletions 0
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice5 49995 49996 . - . intron_id 3 ; splice_site "GT"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local intron 38509 49996 . - . intron_id 3
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice3 38509 38510 . - . intron_id 2 ; splice_site "AG"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local cds 38469 38508 . - .
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local exon 38469 38508 . - . insertions 0 ; deletions 0
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice5 38467 38468 . - . intron_id 4 ; splice_site "TT"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local intron 17472 38468 . - . intron_id 4
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local splice3 17472 17473 . - . intron_id 3 ; splice_site "AG"
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local cds 17449 17471 . - .
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local exon 17449 17471 . - . insertions 0 ; deletions 0
gi|397460716|gb|JH734785.1|:subseq(44689,103000) exonerate:protein2genome:local similarity 17449 52289 691 - . alignment_id 1 ; Query SPP00002140_2.0 ; Align 52290 15 144 ; Align 52024 64 210 ; Align 50135 135 138 ; Align 38509 181 39 ; Align 17470 195 21
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis