Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/SELT.fa -t gi|397463993|gb|JH731508.1|subseq.fa -E]
Hostname: [ws101060]
** (process:3136): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW
C4 Alignment:
------------
Query: SPP00000106_2.0 # Protein # Selenoprotein T (SelT) # Human (Homo sapiens)
Target: gi|397463993|gb|JH731508.1|:subseq(490000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-851, whole genome shotgun sequence:[revcomp]
Model: protein2genome:local
Raw score: 869
Query range: 0 -> 195
Target range: 62322 -> 54266
1 : MetArgLeuLeuLeuLeuLeuLeuValAlaAlaSerAlaMetValArgSerGluAlaSer : 20
:!! !||||||||||||||| !|||||||||:!!||| :!!!!!:!!! !|||:!!
LeuAlaLeuLeuLeuLeuLeuAlaValAlaAlaAlaAlaGlyLeuSerAlaAlaAlaAla
62322 : CTGGCGCTGCTGCTGCTGCTCGCGGTGGCGGCGGCGGCCGGTCTGAGCGCGGCGGCGGCG : 62265
21 : AlaAsnLeuGlyGlyValProSerLysArgLeuLysMetGlnTyrAlaThrGlyProLeu : 40
!.!.!.! !||||||:!!|||:!!|||!:!|||:::||| ||||||||||||||||||
GlyGluProGlyGlyLeuProAlaLysLysLeuArgMetAlaTyrAlaThrGlyProLeu
62264 : GGCGAGCCGGGCGGGCTGCCGGCCAAGAAGCTGCGCATGGCCTACGCCACCGGGCCGCTG : 62205
41 : LeuLysPheGlnIle{Cy} >>>> Target Intron 1 >>>> {s}ValSerUnk : 49
|||||||||||||||{||} 3899 bp {|}||||||
LeuLysPheGlnIle{Cy}++ ++{s}ValSer***
62204 : CTCAAGTTCCAGATC{TG}gt.........................ag{T}GTTTCCTGA : 58279
50 : GlyTyrArgArgValPheGluGluTyrMetArgValIleSerGlnArgTyrProAspIle : 69
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GlyTyrArgArgValPheGluGluTyrMetArgValIleSerGlnArgTyrProAspIle
58278 : GGCTACAGGCGGGTGTTTGAGGAGTACATGCGGGTTATTAGCCAGCGGTACCCAGACATC : 58219
70 : ArgIleGluGlyGluAsnTyrLeuProGlnProIleTyr{Ar} >>>> Target Int : 83
|||||||||||||||||||||||||||||||||||||||{||} 939 b
ArgIleGluGlyGluAsnTyrLeuProGlnProIleTyr{Ar}++
58218 : CGCATTGAAGGAGAGAACTACCTTCCCCAACCTATATAT{AG}gt............... : 58173
84 : ron 2 >>>> {g}HisIleAlaSerPheLeuSerValPheLysLeuValLeuIleGly : 98
p {|}|||||||||||||||||||||:!!|||||||||||||||||||||
++{g}HisIleAlaSerPheLeuSerIlePheLysLeuValLeuIleGly
58172 : ..........ag{A}CACATAGCATCCTTCCTGTCAATCTTCAAACTAGTATTAATAGGC : 57193
99 : LeuIleIleValGlyLysAspProPheAlaPhePheGlyMetGlnAlaProSerIleTrp : 118
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LeuIleIleValGlyLysAspProPheAlaPhePheGlyMetGlnAlaProSerIleTrp
57192 : TTAATTATTGTTGGCAAGGATCCCTTCGCTTTCTTTGGCATGCAAGCTCCAAGTATCTGG : 57133
119 : GlnTrpGlyGlnGluAsnLys >>>> Target Intron 3 >>>> ValTyrAlaC : 129
||||||||||||||||||||| 1986 bp ||||||||||
GlnTrpGlyGlnGluAsnLys++ ++ValTyrAlaC
57132 : CAGTGGGGCCAAGAAAATAAGgt.........................agGTCTATGCTT : 55114
130 : ysMetMetValPhePheLeuSerAsnMetIleGluAsnGlnCysMetSerThrGlyAlaP : 149
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ysMetMetValPhePheLeuSerAsnMetIleGluAsnGlnCysMetSerThrGlyAlaP
55113 : GTATGATGGTTTTCTTTCTGAGCAACATGATTGAGAATCAGTGTATGTCAACAGGTGCAT : 55054
150 : heGluIleThrLeuAsn{A} >>>> Target Intron 4 >>>> {sp}ValProV : 158
|||||||||||||||||{|} 647 bp {||}|||||||
heGluIleThrLeuAsn{A}++ ++{sp}ValProV
55053 : TTGAGATAACTTTGAAT{G}gt.........................ag{AT}GTTCCAG : 54380
159 : alTrpSerLysLeuGluSerGlyHisLeuProSerMetGlnGlnLeuValGlnIleLeuA : 178
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
alTrpSerLysLeuGluSerGlyHisLeuProSerMetGlnGlnLeuValGlnIleLeuA
54379 : TGTGGTCTAAGCTGGAGTCTGGTCACCTTCCTTCCATGCAGCAACTTGTCCAAATTCTTG : 54320
179 : spAsnGluMetLysLeuAsnValHisMetAspSerIleProHisHisArgSer : 195
|||||||||||||||||||||||||||||!!:|||!!:|||||||||||||||
spAsnGluMetLysLeuAsnValHisMetGluSerMetProHisHisArgSer
54319 : ATAATGAAATGAAACTCAATGTGCACATGGAGTCAATGCCCCATCATCGATCA : 54267
vulgar: SPP00000106_2.0 0 195 . gi|397463993|gb|JH731508.1|:subseq(490000,100000) 62322 54266 - 869 M 45 135 S 0 2 5 0 2 I 0 3895 3 0 2 S 1 1 M 36 108 S 0 2 5 0 2 I 0 935 3 0 2 S 1 1 M 42 126 5 0 2 I 0 1982 3 0 2 M 29 87 S 0 1 5 0 2 I 0 643 3 0 2 S 1 2 M 40 120
# --- 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|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local gene 54267 62322 869 - . gene_id 1 ; sequence SPP00000106_2.0 ; gene_orientation +
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local cds 62186 62322 . - .
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local exon 62186 62322 . - . insertions 0 ; deletions 0
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice5 62184 62185 . - . intron_id 1 ; splice_site "GT"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local intron 58287 62185 . - . intron_id 1
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice3 58287 58288 . - . intron_id 0 ; splice_site "AG"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local cds 58176 58286 . - .
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local exon 58176 58286 . - . insertions 0 ; deletions 0
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice5 58174 58175 . - . intron_id 2 ; splice_site "GT"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local intron 57237 58175 . - . intron_id 2
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice3 57237 57238 . - . intron_id 1 ; splice_site "AG"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local cds 57110 57236 . - .
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local exon 57110 57236 . - . insertions 0 ; deletions 0
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice5 57108 57109 . - . intron_id 3 ; splice_site "GT"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local intron 55124 57109 . - . intron_id 3
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice3 55124 55125 . - . intron_id 2 ; splice_site "AG"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local cds 55036 55123 . - .
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local exon 55036 55123 . - . insertions 0 ; deletions 0
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice5 55034 55035 . - . intron_id 4 ; splice_site "GT"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local intron 54389 55035 . - . intron_id 4
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local splice3 54389 54390 . - . intron_id 3 ; splice_site "AG"
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local cds 54267 54388 . - .
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local exon 54267 54388 . - . insertions 0 ; deletions 0
gi|397463993|gb|JH731508.1|:subseq(490000,100000) exonerate:protein2genome:local similarity 54267 62322 869 - . alignment_id 1 ; Query SPP00000106_2.0 ; Align 62323 1 135 ; Align 58286 47 108 ; Align 57236 84 126 ; Align 55124 126 87 ; Align 54387 156 120
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis