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: KCNA4_MUSPF
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence MP06156_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 1613.64 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.
KCNA4_MUSPF 1 MEVAMVSAESSGCNSHMPYGYAAQARARERERLAHSRAAAAAAVAAATA
MEVAMVSAESSGCNSHMPYGYAAQARARERERLAHSRAAAAAAVAAATA
MEVAMVSAESSGCNSHMPYGYAAQARARERERLAHSRAAAAAAVAAATA
MP06156_2 1 agggagaggatgtaacactgtggcgcgcgcgacgctaggggggggggag
tatcttgcagcggagatcagaccacgcgagagtcacgcccccctccccc
ggtaggtggcagcctcgtttctcgcgcgggggctcggccgtccgaccat
KCNA4_MUSPF 50 AVEGSGGSGGGSHHHHQSRGACTSHDPQGGRGSRRRRRQRPEKKKAHHR
AVEGSGGSGGGSHHHHQSRGACTSHDPQGGRGSRRRRRQRPEKKKAHHR
AVEGSGGSGGGSHHHHQSRGACTSHDPQGGRGSRRRRRQRPEKKKAHHR
MP06156_2 148 ggggaggtgggtccccctcggtatcgccggcgacaaaccccgaaagccc
ctaggggcgggcaaaaacggcgccaacaggggggggggagcaaaacaag
tgaccgtcatctccccggtgcccctctgtcggtgaggcggtgggatcct
KCNA4_MUSPF 99 QSSFPHCSDLMPSGSEEKILRELSEEEEEEEDEEEEEEEGRFYYSEDDH
QSSFPHCSDLMPSGSEEKILRELSEEEEEEEDEEEEEEEGRFYYSEDDH
QSSFPHCSDLMPSGSEEKILRELSEEEEEEEDEEEEEEEGRFYYSEDDH
MP06156_2 295 caatccttgcacagtggaacagcaggggggggggggggggatttagggc
aggtcagcattcggcaaattgatgaaaaaaaaaaaaaaaggtaagaaaa
gcctttctcggctctgggcggggcgagaggacggggaggagtcttatct
KCNA4_MUSPF 148 GDECSYTDLLPQDDGGGGGYSSVRYSDCCERVVINVSGLRFETQMKTLA
GDECSYTDLLPQDDGGGGGYSSVRYSDCCERVVINVSGLRFETQMKTLA
GDECSYTDLLPQDDGGGGGYSSVRYSDCCERVVINVSGLRFETQMKTLA
MP06156_2 442 gggtttagccccgggggggtatgctagttgcggaagtgcctgacaaacg
gaagcacattcaaagggggagctgagaggagtttatcgtgtacatactc
ttatccgcggtgttgcttcttacccccctatggataacgctacgggtgc
KCNA4_MUSPF 197 QFPETLLGDPEKRTQYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLKRP
QFPETLLGDPEKRTQYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLKRP
QFPETLLGDPEKRTQYFDPLRNEYFFDRNRPSFDAILYYYQSGGRLKRP
MP06156_2 589 ctcgattggcgaaacttgctcagtttgaaacatggattttctggccaac
atcacttgacaagcaatactgaaattagagcgtacttaaaacgggtagc
gtagtggactgggtgctctgttgtttcgcgtcttccatttaaacccgga
KCNA4_MUSPF 246 VNVPFDIFTEEVKFYQLGEEALLKFREDEGFVREEEDRALPENEFKKQI
VNVPFDIFTEEVKFYQLGEEALLKFREDEGFVREEEDRALPENEFKKQI
VNVPFDIFTEEVKFYQLGEEALLKFREDEGFVREEEDRALPENEFKKQI
MP06156_2 736 gagctgatagggattctggggccatcggggtgaggggagtcgagtaaca
tatctattcaatataatgaacttatgaaagttgaaaagctcaaataaat
ctccttccgggggccggaagcgcgtggtgctgagggcgcgagtacaggt
KCNA4_MUSPF 295 WLLFEYPESSSPARGIAIVSVLVILISIVIFCLETLPEFRDDRDLIMAL
WLLFEYPESSSPARGIAIVSVLVILISIVIFCLETLPEFRDDRDLIMAL
WLLFEYPESSSPARGIAIVSVLVILISIVIFCLETLPEFRDDRDLIMAL
MP06156_2 883 tcctgtcgatacgagagagtgcgatatagattcgatcgtaggagcaagc
gtttaacagcgccggtcttcttttttcttttgtactcatgaagatttct
gtctgtggcccaagcacccccgccacctctccgatatgtgccgtccgag
KCNA4_MUSPF 344 SAGGHSGLLNDTSAPHLENSGHTIFNDPFFIVETVCIVWFSFEFVVRCF
SAGGHSGLLNDTSAPHLENSGHTIFNDPFFIVETVCIVWFSFEFVVRCF
SAGGHSGLLNDTSAPHLENSGHTIFNDPFFIVETVCIVWFSFEFVVRCF
MP06156_2 1030 agggcagttagatgcccgatgcaatagcttaggagtagttttgtggctt
gcggaggttaaccccataacgacttaacttttactgttgtctatttggt
taaactgggtctaaccagcagccacccccccggactttgtccgtgtcct
KCNA4_MUSPF 393 ACPSQALFFKNIMNIIDIVSILPYFITLGTDLAQQQGGGNGQQQQAMSF
ACPSQALFFKNIMNIIDIVSILPYFITLGTDLAQQQGGGNGQQQQAMSF
ACPSQALFFKNIMNIIDIVSILPYFITLGTDLAQQQGGGNGQQQQAMSF
MP06156_2 1177 gtcacgcttaaaaaaagagtatcttaacgagcgcccgggagccccgatt
cgcgactttaattattattcttcattctgcatcaaagggagaaaactct
ttccagcccaccgcctctcctgtcccggcttgcggggtccgggggcgct
KCNA4_MUSPF 442 AILRIIRLVRVFRIFKLSRHSKGLQILGHTLRASMRELGLLIFFLFIGV
AILRIIRLVRVFRIFKLSRHSKGLQILGHTLRASMRELGLLIFFLFIGV
AILRIIRLVRVFRIFKLSRHSKGLQILGHTLRASMRELGLLIFFLFIGV
MP06156_2 1324 gacaaaccgcgtcatactactagccacgcacagaacgcgccattctagg
cttgttgttgttgttatcgacagtattgactgcgtgatgttttttttgt
ctcgcttgcaacaccaccgccgcggcgtcccaccggggctgccccctgc
KCNA4_MUSPF 491 ILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYGDMKPITVGGK
ILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYGDMKPITVGGK
ILFSSAVYFAEADEPTTHFQSIPDAFWWAVVTMTTVGYGDMKPITVGGK
MP06156_2 1471 acttaggttgggggcaactcaacggtttgggaaaaggtggaacaaggga
tttcgctatcacaacccatagtcactggcttctcctgagatactctgga
cgtcctgtcgggtattctcaccgtatggtggcgatgctgcggcctggcg
KCNA4_MUSPF 540 IVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETENEEQTQLTQNAVSCP
IVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETENEEQTQLTQNAVSCP
IVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETENEEQTQLTQNAVSCP
MP06156_2 1618 aggtctgagggtaagtcgcgagtatatttcagagaggcaccacaggatc
ttgctgctcgttctctctctttcataataagacaaaaacatcaactggc
cggcgtctatgacttgagagtctctctcccagtatgagaggagtactca
KCNA4_MUSPF 589 YLPSNLLKKFRSSTSSSLGDKSEYLEMEEGVKESLCAKEGKCQGKGDDS
YLPSNLLKKFRSSTSSSLGDKSEYLEMEEGVKESLCAKEGKCQGKGDDS
YLPSNLLKKFRSSTSSSLGDKSEYLEMEEGVKESLCAKEGKCQGKGDDS
MP06156_2 1765 tcctatcaatcatatttcggatgtcgaggggagtctgaggatcgaggga
atccattaatggccccctgaacaatataagtaactgcaagagagagaag
cctttgggatgcttttcggcgagtaggaaatgatctaggggtgaggcct
KCNA4_MUSPF 638 ETDKNNCSNAKAVETDV
ETDKNNCSNAKAVETDV
ETDKNNCSNAKAVETDV
MP06156_2 1912 gagaaattagagggagg
acaaaagcacactacat
gatacctttagtggctg
//
cmbi.kun.nl), 28-Jun-2005