The pairwise alignment has been generated with the "genewise" program of the Wise2 package. The output shows the protein sequence on the first line, followed by a line indicating the similarity level of the match, followed by 4 lines representing the DNA sequence; The DNA sequence descending in triplets, each triplet being a codon. The translation of each codon is shown above it.
Between the two protein sequences a line indicating the similarity of the match is printed. "+" indicates a conservative mismatch while "- "indicates a dramatic one. Mismatches are indicated by "***" in the left column in addition to "!" at the relevant position(s).
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: Q5FWS9_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence BC089219_3
Strand: forward
Start/End (protein) default
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 974.92 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.
Q5FWS9_RAT 1 MQVSIACTEHNLKSRNGEDRLLSKQSSTAPNVVNAARAKFRTVAIIARS
MQVSIACTEHNLKSRNGEDRLLSKQSSTAPNVVNAARAKFRTVAIIARS
MQVSIACTEHNLKSRNGEDRLLSKQSSTAPNVVNAARAKFRTVAIIARS
BC089219_3 1 acgtagtagcataacagggcccaacatagcaggaggcgatcaggaagca
tatctcgcaaataggagaagttgaagccccattaccgcatgctcttcgg
gaccaccagctggtattgcatgcggccccctggcacgcacctctcctcc
Q5FWS9_RAT 50 LGTFTPQHHISLKESTAKQTGMKYRNLGKSGLRVSCLGLGTWVTFGGQI
LGTFTPQHHISLKESTAKQTGMKYRNLGKSGLRVSCLGLGTWVTFGGQI
LGTFTPQHHISLKESTAKQTGMKYRNLGKSGLRVSCLGLGTWVTFGGQI
BC089219_3 148 cgataccccatcagtagacagaataacgatgcagtttgcgatgatggca
tgctccaaatctaacccaacgtaagatgacgtgtcgtgtgcgtctggat
ggccctgtcttcagctaggtcgatgttgaaacatgcgttaaggacatat
Q5FWS9_RAT 99 SDEVAERLMTIAYESGVNLFDTAEVYAAGKAEVILGSIIKKKGWRRSSL
SDEVAERLMTIAYESGVNLFDTAEVYAAGKAEVILGSIIKKKGWRRSSL
SDEVAERLMTIAYESGVNLFDTAEVYAAGKAEVILGSIIKKKGWRRSSL
BC089219_3 295 tgggggccaaagtgaggactgagggtgggagggacgaaaaaagtaatat
caatcagttctcaaggtattaccataccgacatttggttaaaggggcgt
atgttagggatctgtattccctaactttggtggtggcccggacgggacg
Q5FWS9_RAT 148 VITTKLYWGGKAETERGLSRKHIIEGLKGSLQRLQLEYVDVVFANRPDS
VITTKLYWGGKAETERGLSRKHIIEGLKGSLQRLQLEYVDVVFANRPDS
VITTKLYWGGKAETERGLSRKHIIEGLKGSLQRLQLEYVDVVFANRPDS
BC089219_3 442 gaaaacttggaggagagttaacaaggcagtccacccgtggggtgaccga
ttccatagggacacaggtcgaattagtagctagtataatatttcagcag
ccacaccgtaacaaaaagaagcctaagacccgggagatgcgctatcacc
Q5FWS9_RAT 197 NTPMEEIVRAMTHVINQGMAMYWGTSRWSAMEIMEAYSVARQFNMIPPV
NTPMEEIVRAMTHVINQGMAMYWGTSRWSAMEIMEAYSVARQFNMIPPV
NTPMEEIVRAMTHVINQGMAMYWGTSRWSAMEIMEAYSVARQFNMIPPV
BC089219_3 589 aacaggagcgaacgaacgagattgatatagagaaggttggcctaaaccg
acctaattgctcattaagtctaggccgggctattacactcgatattcct
cccgaactacggcgccacgagcgccgggcgggcgacctcgggccgcgtc
Q5FWS9_RAT 246 CEQAEYHLFQREKVEVQLPELYHKIGVGAMTWSPLACGIISGKYGNGVP
CEQAEYHLFQREKVEVQLPELYHKIGVGAMTWSPLACGIISGKYGNGVP
CEQAEYHLFQREKVEVQLPELYHKIGVGAMTWSPLACGIISGKYGNGVP
BC089219_3 736 tgcggtcctcagagggcccgctcaaggggaattccgtgaatgatgaggc
gaacaaattagaatatatcataaatgtgctcgcctcggttcgaagagtc
tgatgtttcgaagggcggagcctaagttagagtatttattaaatatgga
Q5FWS9_RAT 295 ESSRASLKCYQWLKERIVSEEGRKQQNKLKDLSPIAERLGCTLPQLAVA
ESSRASLKCYQWLKERIVSEEGRKQQNKLKDLSPIAERLGCTLPQLAVA
ESSRASLKCYQWLKERIVSEEGRKQQNKLKDLSPIAERLGCTLPQLAVA
BC089219_3 883 gatagtcattcttagaagagggaaccaacagctcaggccgtaccccggg
agcgcctagaagtaagttgaaggaaaaataatcctcagtggctcatctc
attataggccggggagtataagaagacggacctattacgacaatggtga
Q5FWS9_RAT 344 WCLRNEGVSSVLLGSSTPEQLIENLGAIQVLPKMTSHVVNEIDNILRNK
WCLRNEGVSSVLLGSSTPEQLIENLGAIQVLPKMTSHVVNEIDNILRNK
WCLRNEGVSSVLLGSSTPEQLIENLGAIQVLPKMTSHVVNEIDNILRNK
BC089219_3 1030 ttcaagggatgccgttacgccagacggacgccaaatcggagagaatcaa
ggtgaagtgctttgccccaattaatgctattcatccattaataattgaa
gcgacgtgctgggaacttaactacttctgcctggaatgatgttcagccg
Q5FWS9_RAT 393 PYSKKDYRS
PYSKKDYRS
PYSKKDYRS
BC089219_3 1177 ctaaagtat
cagaaaagc
cccagctac
//
cmbi.kun.nl), 18-Jul-2005