genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright
Query protein: ovis
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End local
Target Sequence HS307871
Strand: forward
Start/End (protein) local
Gene Paras: human.gf
Codon Table: codon.table
Subs error: 1e-05
Indel error: 1e-05
Model splice? model
Model codon bias? flat
Model intron bias? tied
Null model syn
Algorithm 623
genewise output
Score 694.80 bits over entire alignment
Scores as bits over a synchronous coding model
Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info
ovis 6 SRPQGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLP
+RPQGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLP
ARPQGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLP
HS307871 1743 gaccgtcgcaagatccggtgggagtacgttaccggcttc
cgcagtcataaacttgccggaacaacctggtgacggatc
catgttggggtcacgaacgagaacctctgcgcgactcaa
ovis 45 FRETRAAQDFFSTCRSPEACCEL
FRETRAAQDFFSTCRSPEACCEL
E:E[gag] FRETRAAQDFFSTCRSPEACCEL
HS307871 1860 GGTAAGAG Intron 1 CAGAGtagacggcgttaatctcggttgc
<1-----[1861 : 1975]-1> tgacgccaattgcggccacggat
tgacgtcgctccgtcttgcctag
ovis 69 TLQ PLRRFPLDAAIIFSDILVVPQ
TLQ PLRRF LDAAIIFSDILVVPQ
TLQ PLRRFLLDAAIIFSDILVVPQ
HS307871 2047 accGTGAGGG Intron 2 CAGcccctccgggaattgacggcc
cta<0-----[2056 : 2131]-0>ctggtttacctttcattttca
tgg agtcctgttcctccccttacg
ovis 93 ALGMEVTMVPGKGPSFPEPLREERDL
ALGMEVTMVPGKGPSFPEPLREE+DL
ALGMEVTMVPGKGPSFPEPLREEQDL
HS307871 2195 GTACCCA Intron 3 CAGgcgaggaagcgagcatcgctaggcgc
<0-----[2195 : 2433]-0>ctgtatcttcgagcgtcactgaaaat
agcgggcgatcaacccagaaaaggca
ovis 119 ERLRDPATVASELGYVFQAITLTRQQLAGRVPLIGFAGAP
ERLRDP VASELGYVFQAITLTRQ+LAGRVPLIGFAGAP
ERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAP
HS307871 2512 gcccgcggggtgcgtgtcgaacaccccggcgccagtgggc
agtgacattccatgattactctcgagtcggtcttgtcgcc
acagtaagactgactgcaccctcaaagtatgggtctttca
ovis 159 WTLMTYMVEGGGSSTMSQAKRWLYQR
WTLMTYMVEGGGSSTM+QAKRWLYQR
WTLMTYMVEGGGSSTMAQAKRWLYQR
HS307871 2632 GTAATGT Intron 4 TAGtacaatagggggtaaagcgactctca
<0-----[2632 : 2748]-0>gcttcattagggcgctcacaggtaag
gcggacgtgttcaccgtgcgcgctga
ovis 185 PQASHQLLRILTDALVPYLVGQVAAGAQ
PQASHQLLRILTDALVPYLVGQV AGAQ
PQASHQLLRILTDALVPYLVGQVVAGAQ
HS307871 2827 ccgacccccacaggcgctcggcgggggcGTGAGTC Intron 5
cacgaattgttcacttcattgattcgca<0-----[2911 : 3278]
tgttcggtccctttgcatgaaaggttcg
ovis 213 ALQLFESHAGHLGPQLFSKFALPYIRDVSKRVKAGLQEAGLAPVPM
ALQLFESHAGHLGPQLF+KFALPYIRDV+K+VKA L+EAGLAPVPM
ALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVPM
HS307871 3276 TAGgtcctgtcggccgccctaatgcctacgggacgagatcgggcgcgca
-0>ctattacacgatgcattaatctcatgatcaatacgtgacgtcctct
agggtgctagttcagcccgtagtccttgcgaggcggggacgaagcg
ovis 259 IIFAKDGHFALEELAQAGYEVVGLDW
IIFAKDGHFALEELAQAGYEVVGLDW
IIFAKDGHFALEELAQAGYEVVGLDW
HS307871 3417 GTGAGGA Intron 6 TAGaatgaggctgcggcgcggtggggcgt
<0-----[3417 : 3575]-0>tttcaagatctaatcacgaattgtag
ccttgtgttcggggcatctggtgtcg
ovis 285 TVAPEKA ERVGKTVTLQGNLDPC
TVAP+KA E VGKTVTLQGNLDPC
TVAPKKA R:R[cgg] ECVGKTVTLQGNLDPC
HS307871 3654 aggcaagCGGTAAGCC Intron 7 CAGGgtggaagatcgacgct
ctccaac <2-----[3677 : 3779]-2> agtgactctagatacg
agcagac gtgggggaggccgcct
ovis 309 ALYASE EEIGKLVQQMLNDFGPQRYI
ALYASE EEIG+LV+QML+DFGP RYI
ALYASE EEIGQLVKQMLDDFGPHRYI
HS307871 3829 gttgtgGTAACAG Intron 8 CAGggagctgacacggtgcccta
ctacca<0-----[3847 : 4178]-0>aatgattaattaatgcagat
cgtatg ggcggggggggtctaatcct
ovis 335 ANLGHGLYPDMDPEHVGAFVDAVHKHSRLLRQN
ANLGHGLYPDMDPEHVGAFVDAVHKHSRLLRQN
ANLGHGLYPDMDPEHVGAFVDAVHKHSRLLRQN
HS307871 4239 gatgcgctcgagcgcgggtggggcactccccca
catgagtacatacaatgcttactaaacgttgaa
ccgctgtttcgcaatgcctgttgtacatgtagc
//
Gene 1
Gene 1743 4337
Exon 1743 1860 phase 0
Exon 1976 2055 phase 1
Exon 2132 2194 phase 0
Exon 2434 2631 phase 0
Exon 2749 2910 phase 0
Exon 3279 3416 phase 0
Exon 3576 3676 phase 0
Exon 3780 3846 phase 2
Exon 4179 4337 phase 0
//
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