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: IRK15_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AY028455_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 984.82 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.
IRK15_RAT 1 MVARWVKGSEDAPLALQKIPDLQSGPRSLRMEAIHIGMSSAPLVKHSNG
MVARWVKGSEDAPLALQKIPDLQSGPRSLRMEAIHIGMSSAPLVKHSNG
MVARWVKGSEDAPLALQKIPDLQSGPRSLRMEAIHIGMSSAPLVKHSNG
AY028455_2 1 aggatgagagggccgccaacgccagcaacaaggacagatagccgacaag
ttcggtaggaacctctaatcataggcggtgtactatgtcgccttaagag
gacgggggcgcgatcgggttcagttagcggggctctcgctcagggcctg
IRK15_RAT 50 VGLKAHRPRVMSKSGHSNVRIDKVDGIYLLYLQDLWTTVIDMKWRYKLT
VGLKAHRPRVMSKSGHSNVRIDKVDGIYLLYLQDLWTTVIDMKWRYKLT
VGLKAHRPRVMSKSGHSNVRIDKVDGIYLLYLQDLWTTVIDMKWRYKLT
AY028455_2 148 ggcagcaccgataagcaagaagagggattctccgttaagagaatataca
tgtacagcgttcaggagatgtaatagtattataatgccttataggaatc
tacaccgcacgggtacctgatcgactctgcccgcgggacccgggatgcc
IRK15_RAT 99 LFAATFVMTWFLFGVVYYAIAFIHGDLELGESNSNHTPCIMKVDSLTGA
LFAATFVMTWFLFGVVYYAIAFIHGDLELGESNSNHTPCIMKVDSLTGA
LFAATFVMTWFLFGVVYYAIAFIHGDLELGESNSNHTPCIMKVDSLTGA
AY028455_2 295 ctggatgaattctgggttgagtacggtgcggtatacactaaaggtcagg
ttccctttcgtttgttaactcttagatatgacacaaccgttatactcgc
gttcctggcgtttggcctcattttctaacgatttccgcctgagtccaga
IRK15_RAT 148 FLFSLESQTTIGYGVRSITEECPHAIFLLVAQLVITTLIEIFITGTFLA
FLFSLESQTTIGYGVRSITEECPHAIFLLVAQLVITTLIEIFITGTFLA
FLFSLESQTTIGYGVRSITEECPHAIFLLVAQLVITTLIEIFITGTFLA
AY028455_2 442 tctttgtcaaagtggctaaggtccgatctggccgaaatagataagatcg
tttctacacctgagtgctcaagcactttttcatttccttatttcgcttc
cctcggtgactctgctccaggtcctcccgtcagccccgtaccttaccgc
IRK15_RAT 197 KIARPKKRAETIKFSHCAVISKQNGKLCLVIQVANMRKSLLIQCQLSGK
KIARPKKRAETIKFSHCAVISKQNGKLCLVIQVANMRKSLLIQCQLSGK
KIARPKKRAETIKFSHCAVISKQNGKLCLVIQVANMRKSLLIQCQLSGK
AY028455_2 589 aagacaacggaaatactggaaacagactcgacggaaaaactactcctga
atcgcaagcactatgagcttgaaagatgtttatcatgagtttagatcga
gtaacagacgctgccccccccggtggacgccggtcgggtcgtgcgtcaa
IRK15_RAT 246 LLQTHVTKEGERILLNQATVKFHVDSSSESPFLILPMTFYHVLDETSPL
LLQTHVTKEGERILLNQATVKFHVDSSSESPFLILPMTFYHVLDETSPL
LLQTHVTKEGERILLNQATVKFHVDSSSESPFLILPMTFYHVLDETSPL
AY028455_2 736 cccacgaagggcaccacgagatcggtttgactcaccaattcgtggaacc
ttacatcaagagtttaacctatatacccagcttttctctaattaacgct
ccgattcagagctcccgttcaccgcctcgtctccgtgccctggtggccg
IRK15_RAT 295 RDLTPQNLKEKEFELVVLLNATVESTSAVCQSRTSYIPEEIYWGFEFVP
RDLTPQNLKEKEFELVVLLNATVESTSAVCQSRTSYIPEEIYWGFEFVP
RDLTPQNLKEKEFELVVLLNATVESTSAVCQSRTSYIPEEIYWGFEFVP
AY028455_2 883 cgcaccacagagtgtggccagaggtaaggtcacattacggattgtgtgc
gatccaataaaatatttttacctaccgctgaggccatcaataggtattc
gccacgcagaggtagggtctccgacccaccgcagtccaggccgctgtgt
IRK15_RAT 344 VVSLSKNGKYVADFSQFEQIRKSPDCTFYCADSEKQKLEEQYRQEDQRE
VVSLSKNGKYVADFSQFEQIRKSPDCTFYCADSEKQKLEEQYRQEDQRE
VVSLSKNGKYVADFSQFEQIRKSPDCTFYCADSEKQKLEEQYRQEDQRE
AY028455_2 1030 ggtctaagatgggtactgcacaacgtatttggtgacacggctacggcag
ttctcaagaatcatgataatgagcagctagcacaaaataaaagaaaaga
gttccatagtgttctatggcggcgttccctgttgaggtaggcgggcgga
IRK15_RAT 393 RELRSLLLQQSNV
RELRSLLLQQSNV
RELRSLLLQQSNV
AY028455_2 1177 cgcaacccccaag
gatggtttaagat
tgggctagggccc
//
cmbi.kun.nl), 28-Jun-2005