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: IRK13_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence RNO6129_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 897.32 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.
IRK13_RAT 1 MDSRNCKVNAPLLSQRYRRMVTKDGHSTLQMDGAQRGLVYLRDAWGILM
MDSRNCKVNAPLLSQRYRRMVTKDGHSTLQMDGAQRGLVYLRDAWGILM
MDSRNCKVNAPLLSQRYRRMVTKDGHSTLQMDGAQRGLVYLRDAWGILM
RNO6129_2 1 agaaatagagcccacatcaagaaggcaaccagggcagcgtccggtgaca
taggagataccttgagaggttcaagagctatagcaggttatgacggttt
gccgttattttcataacgggcaatcccatagtttaattgttgtagacag
IRK13_RAT 50 DMRWRWMMLVFSASFVVHWLVFAVLWYAVAEMNGDLEIDHDVPPENHTI
DMRWRWMMLVFSASFVVHWLVFAVLWYAVAEMNGDLEIDHDVPPENHTI
DMRWRWMMLVFSASFVVHWLVFAVLWYAVAEMNGDLEIDHDVPPENHTI
RNO6129_2 148 gactctaacgttgttggctcgtggcttggggaaggcgagcggccgacaa
atggggtttttccctttagtttcttgactcatagatataaatccaaact
cgcgcggggcttttctccgtttaccgttatggtttgaaccccgtacctc
IRK13_RAT 99 CVKHITSFTAAFSFSLETQLTIGYGTMFPSGDCPSAIALLAIQMLLGLM
CVKHITSFTAAFSFSLETQLTIGYGTMFPSGDCPSAIALLAIQMLLGLM
CVKHITSFTAAFSFSLETQLTIGYGTMFPSGDCPSAIALLAIQMLLGLM
RNO6129_2 295 tgacaaataggttttcgaccaagtgaatcaggtcagagtcgacaccgca
gtaatcgtccctctctacatctgagcttcggagcgctcttctatttgtt
tggccctcatgccctggaatacctccgcctgctataccatcaagcaccg
IRK13_RAT 148 LEAFITGAFVAKIARPKNRAFSIRFTDLAVVAHKDGKPNLIFQVANTRP
LEAFITGAFVAKIARPKNRAFSIRFTDLAVVAHKDGKPNLIFQVANTRP
LEAFITGAFVAKIARPKNRAFSIRFTDLAVVAHKDGKPNLIFQVANTRP
RNO6129_2 442 cggtaaggtggaagccaaagttactagtggggcaggacacatcggaacc
tacttcgcttcatcgcaagctctgtcatcttcaaagacatttatcacgc
agctcatctgggtagaatatcacacacaatatcatcatttccagcccgc
IRK13_RAT 197 SPLTSVRVSAVLYQERENGELYQTSVDFHLDGISSEECPFFIFPLTYYH
SPLTSVRVSAVLYQERENGELYQTSVDFHLDGISSEECPFFIFPLTYYH
SPLTSVRVSAVLYQERENGELYQTSVDFHLDGISSEECPFFIFPLTYYH
RNO6129_2 589 accaagcgtggctcgagaggctcaaggtccggaatggtcttatccattc
gctcgtgtccttaaagaagataacgtatatagtgcaagcttttctcaaa
ctgcctgcttactgaaattaccgctgcccttccttgataccccgacttt
IRK13_RAT 246 TITPSSPLATLLQHETPSHFELVVFLSAMQEGTGEICQRRTSYLPSEIM
TITPSSPLATLLQHETPSHFELVVFLSAMQEGTGEICQRRTSYLPSEIM
TITPSSPLATLLQHETPSHFELVVFLSAMQEGTGEICQRRTSYLPSEIM
RNO6129_2 736 aaactaccgaccccgactctgtggtctgacggaggatcaaattcctgaa
ctcccgctccttaaacccatatttttcctaagcgatgaggccatccatt
tcaaattatcgcgtgttactaatgccaagaactgaccaggaccattgcg
IRK13_RAT 295 LHHRFAALMTRGSKGEYQVKMENFDKTVPEHPTPVVSKSPHRTDLDIHI
LHHRFAALMTRGSKGEYQVKMENFDKTVPEHPTPVVSKSPHRTDLDIHI
LHHRFAALMTRGSKGEYQVKMENFDKTVPEHPTPVVSKSPHRTDLDIHI
RNO6129_2 883 tccctggcaacgtaggtcgaagatgaagcgccacggtaaccaagcgaca
taagtccttcggcagaaatataataactcaacccttcagcagcatatat
atcatatagtatcatgtacgggttcgtttatattgctgtatgtcatttc
IRK13_RAT 344 NGQSIDNFQIAETGLTE
NGQSIDNFQIAETGLTE
NGQSIDNFQIAETGLTE
RNO6129_2 1030 agcaagatcaggagcag
agagtaatatcacgtca
taactcttgttaaggaa
//
cmbi.kun.nl), 28-Jun-2005