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: KCNQ1_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence RNU92655_2
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 511.65 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.
Warning: mismatch(es) found
KCNQ1_RAT 134 LVCLIFSVLSTIEQYAALATGTLFWMEIVLVVFFGTEYVVRLWSAGCRS
LVCLIFSVLSTIEQYAALATGTLFWMEIVLVVFFGT+YVVRLWSAGCR+
LVCLIFSVLSTIEQYAALATGTLFWMEIVLVVFFGTKYVVRLWSAGCRT
RNU92655_2 1 cgtcatagctaagctggcgagacttagagcggttgaatggccttggtca
ttgtttgttcctaaacctccgcttgtatttttttgcaattgtgccgggc
gccccctcgcttggtctgccgcccggatctggctgagtgctcgtacccc
*** ! !
KCNQ1_RAT 183 KYVGIWGRLRFARKPISIIDLIVVVASMVVLCVGSKGQVFATSAIRGIR
KY+GIWGRLRFARKPISIIDLIVVVASMVVLCVGSKGQVFATSAIRGIR
KYLGIWGRLRFARKPISIIDLIVVVASMVVLCVGSKGQVFATSAIRGIR
RNU92655_2 148 attgatgccctgcacataagcaggggtaggctggtagcgtgatgaagac
aatgtgggtgtcgactcttatttttccttttgtgcagattcccctggtg
gcgccgcgactcggctccccccgtactgtcctgtcagagccaatcgtcc
*** !
KCNQ1_RAT 232 FLQILRMLHVDRQGGTWRLLGSVVFIHRQELITTLYIGFLGLIFSSYFV
FLQILRMLHVDRQGGTWRLLGSV-FIHRQELITTLYIGFLGLIFSSYFV
FLQILRMLHVDRQGGTWRLLGSVFFIHRQELITTLYIGFLGLIFSSYFV
RNU92655_2 295 tccaccaccggccggataccgtgttacccgcaaactagtcgcatttttg
ttattgttatagaggcggttgcttttagaattcctatgttgtttccatt
ctacggggtttcgatcggcgctacctccgggcccgctctgtcccccctc
*** !
KCNQ1_RAT 281 YLAEKDAVNESGRIEFGSYADALWWGVVTVTTIGYGDKVPQTWVGKTIA
YLAEKDAVNESGRIEFGSYADALWWGVVTVTTIGYGDKVP-TWVGKTIA
YLAEKDAVNESGRIEFGSYADALWWGVVTVTTIGYGDKVP!TWVGKTIA
RNU92655_2 442 tcggagggagtgcagtgatgggcttgggagaaagtggagc2atggaaag
atcaaactaacggtatggacactgggttctcctgagaatc cgtgactc
cgtgatagtgccccgtcccattgggagcaccctccgtgac agtggccc
*** !
KCNQ1_RAT 330 SCFSVFAISFFALPAGILGSGFAL
SCFSVFAISFFALPAGILGSGFAL
SCFSVFAISFFALPAGILGSGFAL
RNU92655_2 588 ttttgtgatttgccggacgtgtgc
cgtcttctcttctccgttgcgtct
ctctcccacctacagcatctgtag
//
cmbi.kun.nl), 28-Jun-2005