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: danio
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 471.13 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
danio 10 PKDFPELRNDTFLRAARGEEIEHIPVWCMRQAGRYLP
P+ FPEL+NDTFLRAA GEE ++ PVWCMRQAGRYLP
PQGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLP
HS307871 1749 ccgtcgcaagatccggtgggagtacgttaccggcttc
cagtcataaacttgccggaacaacctggtgacggatc
tgttggggtcacgaacgagaacctctgcgcgactcaa
danio 47 FRESRAGKDFFETCRSPEACCEL
FRE+RA +DFF TCRSPEACCEL
E:E[gag] FRETRAAQDFFSTCRSPEACCEL
HS307871 1860 GGTAAGAG Intron 1 CAGAGtagacggcgttaatctcggttgc
<1-----[1861 : 1975]-1> tgacgccaattgcggccacggat
tgacgtcgctccgtcttgcctag
danio 71 TLQ PLRRFPFDAAIIFSDILVVPQ
TLQ PLRRF +DAAIIFSDILVVPQ
TLQ PLRRFLLDAAIIFSDILVVPQ
HS307871 2047 accGTGAGGG Intron 2 CAGcccctccgggaattgacggcc
cta<0-----[2056 : 2131]-0>ctggtttacctttcattttca
tgg agtcctgttcctccccttacg
danio 95 AMGMEVQMCPGKGPTFPEPLKEPEDL
A+GMEV M PGKGP+FPEPL+E +DL
ALGMEVTMVPGKGPSFPEPLREEQDL
HS307871 2195 GTACCCA Intron 3 CAGgcgaggaagcgagcatcgctaggcgc
<0-----[2195 : 2433]-0>ctgtatcttcgagcgtcactgaaaat
agcgggcgatcaacccagaaaaggca
danio 121 QRLKTQVDVYSELDYVFKAITLTRHKIEGKVPLIGFTGAP
+RL+ V SEL YVF+AITLTR ++ G+VPLIGF GAP
ERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAP
HS307871 2512 gcccgcggggtgcgtgtcgaacaccccggcgccagtgggc
agtgacattccatgattactctcgagtcggtcttgtcgcc
acagtaagactgactgcaccctcaaagtatgggtctttca
danio 161 WTLMSYMIEGGGSATHSKAKRWLYRY
WTLM+YM+EGGGS+T ++AKRWLY+
WTLMTYMVEGGGSSTMAQAKRWLYQR
HS307871 2632 GTAATGT Intron 4 TAGtacaatagggggtaaagcgactctca
<0-----[2632 : 2748]-0>gcttcattagggcgctcacaggtaag
gcggacgtgttcaccgtgcgcgctga
danio 187 PEASHKLLSQLTDVIVEYLLGQVKAGAQ
P+ASH+LL LTD +V YL+GQV AGAQ
PQASHQLLRILTDALVPYLVGQVVAGAQ
HS307871 2827 ccgacccccacaggcgctcggcgggggcGTGAGTC Intron 5
cacgaattgttcacttcattgattcgca<0-----[2911 : 3278]
tgttcggtccctttgcatgaaaggttcg
danio 215 ALQVFESHTGCLGPVEFKEFSLPYLRDIARRVKDKIKESGLDNVPM
ALQ+FESH G LGP F +F+LPY+RD+A++VK +++E+GL VPM
ALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVPM
HS307871 3276 TAGgtcctgtcggccgccctaatgcctacgggacgagatcgggcgcgca
-0>ctattacacgatgcattaatctcatgatcaatacgtgacgtcctct
agggtgctagttcagcccgtagtccttgcgaggcggggacgaagcg
danio 261 IVFAKDGHYGLEDLSESAYEVVGLDW
I+FAKDGH+ LE+L+++ YEVVGLDW
IIFAKDGHFALEELAQAGYEVVGLDW
HS307871 3417 GTGAGGA Intron 6 TAGaatgaggctgcggcgcggtggggcgt
<0-----[3417 : 3575]-0>tttcaagatctaatcacgaattgtag
ccttgtgttcggggcatctggtgtcg
danio 287 TIDPRSA VRTGGKVSLQGNMDPC
T+ P+ A G V+LQGN+DPC
TVAPKKA R:R[cgg] ECVGKTVTLQGNLDPC
HS307871 3654 aggcaagCGGTAAGCC Intron 7 CAGGgtggaagatcgacgct
ctccaac <2-----[3677 : 3779]-2> agtgactctagatacg
agcagac gtgggggaggccgcct
danio 311 ALYGTK ESISEIVRRMLEGFGTKGYI
ALY ++ E I ++V++ML+ FG YI
ALYASE EEIGQLVKQMLDDFGPHRYI
HS307871 3829 gttgtgGTAACAG Intron 8 CAGggagctgacacggtgcccta
ctacca<0-----[3847 : 4178]-0>aatgattaattaatgcagat
cgtatg ggcggggggggtctaatcct
danio 337 ANLGHGLYPDMDPENVGAFVEAVHNHSRQL
ANLGHGLYPDMDPE+VGAFV+AVH HSR L
ANLGHGLYPDMDPEHVGAFVDAVHKHSRLL
HS307871 4239 gatgcgctcgagcgcgggtggggcactccc
catgagtacatacaatgcttactaaacgtt
ccgctgtttcgcaatgcctgttgtacatgt
//
Gene 1
Gene 1749 4328
Exon 1749 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 4328 phase 0
//
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