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: Q9UHJ4_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF167082_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 1222.34 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.
Q9UHJ4_HUMAN 1 MPSSGRALLDSPLDSGSLTSLDSSVFCSEGEGEPLALGDCFTVNVGGSR
MPSSGRALLDSPLDSGSLTSLDSSVFCSEGEGEPLALGDCFTVNVGGSR
MPSSGRALLDSPLDSGSLTSLDSSVFCSEGEGEPLALGDCFTVNVGGSR
AF167082_2 1 actagagccgtccgagtcatcgtagttagggggctgcggttagagggac
tccgggcttacctaggctcctacgttggagagactctgagtctatgggg
gtcccagggcgggccccgccgcttccccgtaggcggcgcccgccgcccc
Q9UHJ4_HUMAN 50 FVLSQQALSCFPHTRLGKLAVVVASYRRPGALAAVPSPLELCDDANPVD
FVLSQQALSCFPHTRLGKLAVVVASYRRPGALAAVPSPLELCDDANPVD
FVLSQQALSCFPHTRLGKLAVVVASYRRPGALAAVPSPLELCDDANPVD
AF167082_2 148 tgctccgctttccaccgacgggggttcccggcgggcaccgctgggacgg
tttcaactcgtcacgtgatctttccaggcgctcctcgctatgaacacta
cgcgggggcccgcgctcggcgggtcccccgcgccgcctggtcctcccgc
Q9UHJ4_HUMAN 99 NEYFFDRSSQAFRYVLHYYRTGRLHVMEQLCALSFLQEIQYWGIDELSI
NEYFFDRSSQAFRYVLHYYRTGRLHVMEQLCALSFLQEIQYWGIDELSI
NEYFFDRSSQAFRYVLHYYRTGRLHVMEQLCALSFLQEIQYWGIDELSI
AF167082_2 295 agtttgcatcgtctgccttcagcccgagcctgcttccgacttgaggcaa
aaattaggcactgattaaagcggtattaatgctcttaataaggtaatgt
cgccccccgggcatcgcccccccgtcggggcgcccgggcgcgcctgccc
Q9UHJ4_HUMAN 148 DSCCRDRYFRRKELSETLDFKKDTEDQESQHESEQDFSQGPCPTVRQKL
DSCCRDRYFRRKELSETLDFKKDTEDQESQHESEQDFSQGPCPTVRQKL
DSCCRDRYFRRKELSETLDFKKDTEDQESQHESEQDFSQGPCPTVRQKL
AF167082_2 442 gtttagattaaagcagatgtaagaggcgaccgagcgttcgctcagccac
acgggagatggaatgactataaacaaaagaaagaaatcagcgcctgaat
tcccgcaccagaggtataccggcaacgatatgtagcccaattcttcggc
Q9UHJ4_HUMAN 197 WNILEKPGSSTAARIFGVISIIFVVVSIINMALMSAELSWLDLQLLEIL
WNILEKPGSSTAARIFGVISIIFVVVSIINMALMSAELSWLDLQLLEIL
WNILEKPGSSTAARIFGVISIIFVVVSIINMALMSAELSWLDLQLLEIL
AF167082_2 589 taacgacgttaggcatggataatgggtaaaagcatggtatcgccccgac
gattaacgcccccgttgttcttttttcttatcttccatggtatattatt
gtcggatatcatctctcccctccgggcctcgcggatgacggcggggacg
Q9UHJ4_HUMAN 246 EYVCISWFTGEFVLRFLCVRDRCRFLRKVPNIIDLLAILPFYITLLVES
EYVCISWFTGEFVLRFLCVRDRCRFLRKVPNIIDLLAILPFYITLLVES
EYVCISWFTGEFVLRFLCVRDRCRFLRKVPNIIDLLAILPFYITLLVES
AF167082_2 736 gtgtaattaggtgcctctgcgatctcaagcaaagccgatcttaaccgga
aatgtggtcgatttgttgtgagggttgatcattattcttctatctttag
gtgctcgccggtccccgtggcgtccaaggaccacctccgccccttgagc
Q9UHJ4_HUMAN 295 LSGSQTTQELENVGRIVQVLRLLRALRMLKLGRHSTGLRSLGMTITQCY
LSGSQTTQELENVGRIVQVLRLLRALRMLKLGRHSTGLRSLGMTITQCY
LSGSQTTQELENVGRIVQVLRLLRALRMLKLGRHSTGLRSLGMTITQCY
AF167082_2 883 cagacaacgcgaggcagcgtaccagccacacgactagtctcgaaaactt
tgggaccaataatggttattgttgctgttatggaccgtgctgtctcaga
atgcgcgggggcggctcgggggcgtgcgaggcatcaaacctggaccgtc
Q9UHJ4_HUMAN 344 EEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTT
EEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTT
EEVGLLLLFLSVGISIFSTVEYFAEQSIPDTTFTSVPCAWWWATTSMTT
AF167082_2 1030 ggggcccctctggatattaggttggcaacgaataagctgtttgaataaa
aatgttttttctgtcttcctaatcaagtcacctcgtcgcgggcccctcc
aaccagcatacgactatataacttgacttcaccatcttagggccctgtt
Q9UHJ4_HUMAN 393 VGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLK
VGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLK
VGYGDIRPDTTTGKIVAFMCILSGILVLALPIAIINDRFSACYFTLKLK
AF167082_2 1177 ggtggaacgaaagaaggtatattgacgtgtcagaaagcttgtttataca
tgagatgcacccgattcttgttcgttttctctcttaagtccgatctata
gatgctaacccacacgccgtaagattcgcgtttttctccttccccgacg
Q9UHJ4_HUMAN 442 EAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERAST
EAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERAST
EAAVRQREALKKLTKNIATDSYISVNLRDVYARSIMEMLRLKGRERAST
AF167082_2 1324 ggggaccggcaacaaaagagttaagataggtgcaaagacccagagagaa
acctgagactaatcaatccacatgtatgatacggttattgtaggagcgc
aattagtacaggtcgtactcatcttcgatctcgtcggggagacaaaatt
Q9UHJ4_HUMAN 491 RSSGGDDFWF
RSSGGDDFWF
RSSGGDDFWF
AF167082_2 1471 aaaggggttt
gggggaatgt
gccgattcgt
//
cmbi.kun.nl), 30-Jun-2005