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: rattus
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 642.05 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
rattus 1 MEANGL LQNFPELKNDTFLRAAT
MEANGL Q FPELKNDTFLRAA
MEANGL G:G[gga] PQGFPELKNDTFLRAAW
HS307871 1107 aggagtGGGTGAGTT Intron 1 CAGAccgtcgcaagatccggt
tacagt <2-----[1127 : 1747]-2> cagtcataaacttgccg
gagtgg tgttggggtcacgaacg
rattus 25 GEETDYTPVWCMRQAGRYLP FRE
GEETDYTPVWCMRQAGRYLP FRE
GEETDYTPVWCMRQAGRYLP E:E[gag] FRE
HS307871 1800 gggagtacgttaccggcttcGGTAAGAG Intron 2 CAGAGtag
gaacaacctggtgacggatc <1-----[1861 : 1975]-1> tga
agaacctctgcgcgactcaa tga
rattus 49 TRAAQDFFSTCRSPEACCELTLQ PVR
TRAAQDFFSTCRSPEACCELTLQ P+R
TRAAQDFFSTCRSPEACCELTLQ PLR
HS307871 1987 acggcgttaatctcggttgcaccGTGAGGG Intron 3 CAGccc
cgccaattgcggccacggatcta<0-----[2056 : 2131]-0>ctg
cgtcgctccgtcttgcctagtgg agt
rattus 75 RFPLDAAIIFSDILVVPQ ALAMEVTM
RF LDAAIIFSDILVVPQ AL MEVTM
RFLLDAAIIFSDILVVPQ ALGMEVTM
HS307871 2141 ctccgggaattgacggccGTACCCA Intron 4 CAGgcgaggaa
gtttacctttcattttca<0-----[2195 : 2433]-0>ctgtatct
cctgttcctccccttacg agcgggcg
rattus 101 VPGKGPSFPEPLREERDLERLRDPAAVASELGYVFQAITLTRQRLAGRV
VPGKGPSFPEPLREE+DLERLRDP VASELGYVFQAITLTRQRLAGRV
VPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRV
HS307871 2458 gcgagcatcgctaggcgcgcccgcggggtgcgtgtcgaacaccccggcg
tcgagcgtcactgaaaatagtgacattccatgattactctcgagtcggt
atcaacccagaaaaggcaacagtaagactgactgcaccctcaaagtatg
rattus 150 PLIGFAGAP WTLMTYMVEGGSFKTMA
PLIGFAGAP WTLMTYMVEGG TMA
PLIGFAGAP WTLMTYMVEGGGSSTMA
HS307871 2605 ccagtgggcGTAATGT Intron 5 TAGtacaatagggggtaaag
cttgtcgcc<0-----[2632 : 2748]-0>gcttcattagggcgctc
ggtctttca gcggacgtgttcaccgt
rattus 176 QAKRWLYQKPVASHKLLGILTHALVPYLIGQVAAGAQ
QAKRWLYQ+P ASH+LL ILT ALVPYL+GQV AGAQ
QAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQ
HS307871 2800 cgactctcaccgacccccacaggcgctcggcgggggc
acaggtaagcacgaattgttcacttcattgattcgca
gcgcgctgatgttcggtccctttgcatgaaaggttcg
rattus 213 ALQLFESHAGHLGSELFSKFALPYIR
ALQLFESHAGHLG +LF+KFALPYIR
ALQLFESHAGHLGPQLFNKFALPYIR
HS307871 2911 GTGAGTC Intron 6 TAGgtcctgtcggccgccctaatgcctac
<0-----[2911 : 3278]-0>ctattacacgatgcattaatctcatg
agggtgctagttcagcccgtagtcct
rattus 239 DVAKRVKAGLQKAGLTRMPM IIFAKD
DVAK+VKA L++AGL +PM IIFAKD
DVAKQVKARLREAGLAPVPM IIFAKD
HS307871 3357 gggacgagatcgggcgcgcaGTGAGGA Intron 7 TAGaatgag
atcaatacgtgacgtcctct<0-----[3417 : 3575]-0>tttcaa
tgcgaggcggggacgaagcg ccttgt
rattus 265 GHFALEELAQAGYEVVGLDWTVAPKKA
GHFALEELAQAGYEVVGLDWTVAPKKA
GHFALEELAQAGYEVVGLDWTVAPKKA R:R[cgg]
HS307871 3594 gctgcggcgcggtggggcgtaggcaagCGGTAAGCC Intron 8
gatctaatcacgaattgtagctccaac <2-----[3677 : 3779]
gttcggggcatctggtgtcgagcagac
rattus 292 EPVGKTVTLQGELDPCALYASE
E VGKTVTLQG LDPCALYASE
ECVGKTVTLQGNLDPCALYASE
HS307871 3777 CAGGgtggaagatcgacgctgttgtgGTAACAG Intron 9 CAG
-2> agtgactctagatacgctacca<0-----[3847 : 4178]-0>
gtgggggaggccgcctcgtatg
rattus 315 EEIGRLVQQMLNDFGPQRYIANLGHGLYPDMDPEHVGAFLDAVHKHSRL
EEIG+LV+QML+DFGP RYIANLGHGLYPDMDPEHVGAF+DAVHKHSRL
EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSRL
HS307871 4179 ggagctgacacggtgccctagatgcgctcgagcgcgggtggggcactcc
aatgattaattaatgcagatcatgagtacatacaatgcttactaaacgt
ggcggggggggtctaatcctccgctgtttcgcaatgcctgttgtacatg
rattus 364 LRQN
LRQN
LRQN
HS307871 4326 ccca
tgaa
tagc
//
Gene 1
Gene 1107 4337
Exon 1107 1126 phase 0
Exon 1748 1860 phase 2
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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