2005, NucleaRDB.
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: STF1_MACEU
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF401742_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 1179.03 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.
STF1_MACEU 1 MDYSYDEDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTC
MDYSYDEDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTC
MDYSYDEDLDELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTC
AF401742_2 1 agtttgggcggctcgtggagtgtctgccatgatagttacagcaaactat
taacaaaataatgctggaatcgaaagttcgaggagttagctaaaaaacg
gctgccgcgcgacggcacagcacctggcccgctggctgcgagtcaccgc
STF1_MACEU 50 TESQNCKIDKTQRKRCPYCRFQKCLTVGMRLEAVRADRMRGGRNKFGPM
TESQNCKIDKTQRKRCPYCRFQKCLTVGMRLEAVRADRMRGGRNKFGPM
TESQNCKIDKTQRKRCPYCRFQKCLTVGMRLEAVRADRMRGGRNKFGPM
AF401742_2 148 agacataagaaccactcttctcatcaggaccgggcggcacggaaatgca
cagaagataacagaggcaggtaagtctgtgtactgcagtggggaatgct
cgcgccgtcgagtaaccccccggcgtgggggattgacaggtaacgttcg
STF1_MACEU 99 YKRDRALKQQKKALIRANGFKLETGPSMGPPPQTDYPLAPALHPGAKGL
YKRDRALKQQKKALIRANGFKLETGPSMGPPPQTDYPLAPALHPGAKGL
YKRDRALKQQKKALIRANGFKLETGPSMGPPPQTDYPLAPALHPGAKGL
AF401742_2 295 taagcgtaccaagcacgagtacgagctagccccagtctgcgcccggagt
aagagctaaaaacttgcagtatacgcctgcccacaactccctacgcagt
cgactcaaggggcgcactacgtggtacgattaatcccgtacccagcgcg
STF1_MACEU 148 APAPPAGPPGDYERGPYGPPGVPMAVPTHGPLAGYLYPAFPGRAIKSEY
APAPPAGPPGDYERGPYGPPGVPMAVPTHGPLAGYLYPAFPGRAIKSEY
APAPPAGPPGDYERGPYGPPGVPMAVPTHGPLAGYLYPAFPGRAIKSEY
AF401742_2 442 gcgccggccggtgcgctgccggcaggcacgctggtctcgtcgcgaatgt
ccccccgccgaaaggcagccgtctctccagctcgatacctcggctacaa
ataatagttactggctttaatatgggcctcagtctcctcttctccgagt
STF1_MACEU 197 PEPYASPHEPAPPYGYPEPYPSGPGLPGVPELILKLLQLEPDEGQLKAR
PEPYASPHEPAPPYGYPEPYPSGPGLPGVPELILKLLQLEPDEGQLKAR
PEPYASPHEPAPPYGYPEPYPSGPGLPGVPELILKLLQLEPDEGQLKAR
AF401742_2 589 cgctgaccgcgcctgtcgctcagcgccggcgcacaccccgcgggccagc
cacacgcaaccccagacacacggcgtcgtcatttattatacaagatacg
agcttcctgacactccagctttctcgagcagcccagggagttacgcgca
STF1_MACEU 246 ILACLQEPSKGRPDRPTPFGLMCKMADQTLFSIVEWARSCVVFKELEVA
ILACLQEPSKGRPDRPTPFGLMCKMADQTLFSIVEWARSCVVFKELEVA
ILACLQEPSKGRPDRPTPFGLMCKMADQTLFSIVEWARSCVVFKELEVA
AF401742_2 736 acgtccgctagccgccactgcataaggcacttaggtgcatggtagcggg
ttcgtaaccaggcagccctgttgatcaacttcttagcgggtttaatatc
agccaggtcgcgttgcatttcgcggttggccattagtgttgccgagggt
STF1_MACEU 295 DQMKLLQNCWSELLVFDHIYRQIQHGKEGSILLVTGQEVDLSTVAAQAG
DQMKLLQNCWSELLVFDHIYRQIQHGKEGSILLVTGQEVDLSTVAAQAG
DQMKLLQNCWSELLVFDHIYRQIQHGKEGSILLVTGQEVDLSTVAAQAG
AF401742_2 883 gcaactcattagccgtgcatacaccgaggaatcgagcgggttagggcgg
aatattaagggattttaatagataagaaggttttcgaatatcctccacg
cggatggtcgcggtctccccagcatggggctggctcggacaaagacgaa
STF1_MACEU 344 SLLHSLVLRAQDLVQQLHSLQVDRQEFVCLKFLILFSLDVKFLENHGLA
SLLHSLVLRAQDLVQQLHSLQVDRQEFVCLKFLILFSLDVKFLENHGLA
SLLHSLVLRAQDLVQQLHSLQVDRQEFVCLKFLILFSLDVKFLENHGLA
AF401742_2 1030 tcccacgccgcgcgcccctccggacgtgttatcactacggatcgacgcg
cttagtttgcaattaatactatagaattgtatttttgtatattaaagtc
ttcccagggcgctaaggctagtcggatccggccccccttggcggtctgc
STF1_MACEU 393 KDAQEKANSALLEYTMCHYPHCGDKFRQLLLRLAEVRSLSMQAEEYLYH
KDAQEKANSALLEYTMCHYPHCGDKFRQLLLRLAEVRSLSMQAEEYLYH
KDAQEKANSALLEYTMCHYPHCGDKFRQLLLRLAEVRSLSMQAEEYLYH
AF401742_2 1177 aggcgagatgccgtaatctcctggatcccccccgggctcaacgggtctc
aacaaacaccttaactgaacaggaatgatttgtcatgctgtacaaataa
gttaggccacgggccgctctctccgcgggcgcgtggctccggcggcgcc
STF1_MACEU 442 KHLGGEVPCNNLLIEMLHAKRT
KHLGGEVPCNNLLIEMLHAKRT
KHLGGEVPCNNLLIEMLHAKRT
AF401742_2 1324 accggggctaaccagaccgaca
aatggatcgaatttattacagc
gcgtgggccccgttgggtcggt
//
cmbi.kun.nl), 18-Feb-2005