PAL2NAL output

CLUSTAL W multiple sequence alignment

ECOLI         atgtgtggaattgttggcgcgatcgcgcaacgtgatgtagcagaaatccttcttgaaggt
VIBCH         atgtgtggaattgttggtgcggttgcacaacgcgatgttgctgaaattttagtacaaggc

ECOLI         ttacgtcgtctggaataccgcggatatgactctgccggtctggccgttgttgatgcagaa
VIBCH         ctacgccgtcttgaataccgcggctatgactctgcgggcgtagctgttgtggatagcgat

ECOLI         ggtcatatgacccgcctgcgtcgcctcggtaaagtccagatgctggcacaggcagcggaa
VIBCH         aagcagctcacgcgtttacgccgtttgggtaaagtacaagagttggcggatgcggttgaa

ECOLI         gaacatcctctgcatggcggcactggtattgctcacactcgctgggcgacccacggtgaa
VIBCH         gcggcgcaagtcgcgggcggtacaggtatcgcgcatacccgttgggcaacgcatggtgag

ECOLI         ccttcagaagtgaatgcgcatccgcatgtttctgaacacattgtggtggtgcataacggc
VIBCH         ccttctgagatcaatgctcacccccatatttctggtgacattacggtggtacacaacggc

ECOLI         atcatcgaaaaccatgaaccgctgcgtgaagagctaaaagcgcgtggctataccttcgtt
VIBCH         attatcgaaaaccatgaaatgctgcgtactatgctgcaagatcgtggttatgtgtttact

ECOLI         tctgaaaccgacaccgaagtgattgcccatctggtgaactgggagctgaaacaaggcggg
VIBCH         tcacaaacggatactgaagtcattgctcatttagtggagtgggaattgcgcagtgcttcc

ECOLI         actctgcgtgaggccgttctgcgtgctatcccgcagctgcgtggtgcgtacggtacagtg
VIBCH         tctttattagaagcggtacaaaccaccgttaaacagcttacaggagcttacggcactgtg

ECOLI         atcatggactcccgtcacccggataccctgctggcggcacgttctggtagtccgctggtg
VIBCH         gtgatggatcgtaacgacccttcgcgcttagtggtcgctcgctcaggtagcccaattgtg

ECOLI         attggcctggggatgggcgaaaactttatcgcttctgaccagctggcgctgttgccggtg
VIBCH         attggttttggtatcggtgaaaacttccttgcgtcagaccaactcgcgctacttaacgtc

ECOLI         acccgtcgctttatcttccttgaagagggcgatattgcggaaatcactcgccgttcggta
VIBCH         acacgccgctttatgtatctggaagagggggatgtagcggaaatgactcgtcgtgatgtg

ECOLI         aacatcttcgataaaactggcgcggaagtaaaacgtcaggatatcgaatccaatctgcaa
VIBCH         cgcgtatttgatgctctggggcaacccgtacaacgtgaaatcagcgaatccaatctagaa

ECOLI         tatgacgcgggcgataaaggcatttaccgtcactacatgcagaaagagatctacgaacag
VIBCH         catgatgctgcggacaaaggtcactaccgccactacatgcaaaaagagattttcgagcag

ECOLI         ccgaacgcgatcaaaaacacccttaccggacgcatcagccacggtcaggttgatttaagc
VIBCH         ccaaaggcgctgatcaataccatggaagggcgtattacccatgactgcgtggtggtggaa

ECOLI         gagctgggaccgaacgccgacgaactgctgtcgaaggttgagcatattcagatcctcgcc
VIBCH         agcattggtgtgcacgcggcagagattctggcaaaagtggaacatgtacagatcgtcgcc

ECOLI         tgtggtacttcttataactccggtatggtttcccgctactggtttgaatcgctagcaggt
VIBCH         tgcggtacttcttataatgcagggatgacggcacgttactggtttgaatcgttagcgggt

ECOLI         attccgtgcgacgtcgaaatcgcctctgaattccgctatcgcaaatctgccgtgcgtcgt
VIBCH         gtgagctgtgatgtcgaaatcgcgtctgaattccgctatcgcaaatttgtcacgcgcccc

ECOLI         aacagcctgatgatcaccttgtcacagtctggcgaaaccgcggataccctggctggcctg
VIBCH         aatagcctactgatcactctatctcagtctggtgaaacggcagataccttagccgcgcta

ECOLI         cgtctgtcgaaagagctgggttaccttggttcactggcaatctgtaacgttccgggttct
VIBCH         cgtttagcgaaagagaaaggctatatggcggcgatgacgatttgtaacgttgcgggttct

ECOLI         tctctggtgcgcgaatccgatctggcgctaatgaccaacgcgggtacagaaatcggcgtg
VIBCH         tctctcgtgcgtgaatcggatttcgcctttatgactcgcgcaggtactgagattggtgtg

ECOLI         gcatccactaaagcattcaccactcagttaactgtgctgttgatgctggtggcgaacgtg
VIBCH         gcttcaaccaaagcctttaccactcagctagtcacattgttgatgctggtgactgcactt

ECOLI         tctcgcctgaaaggtctggatgcctccattgaacatgacatcgtgcatggtctgcaggcg
VIBCH         ggtaagcagcaacagattggtcgcgagttagaagctgagatcgtacatgcattgcatcaa

ECOLI         ctgccgagccgtattgagcagatgctgtctcaggacaaacgcattgaagcgctggcagaa
VIBCH         ctgccgaagcagattgaaaccgcattgtcgtttgaaaaacagatcgaaacgctcgcggaa

ECOLI         gatttctctgacaaacatcacgcgctgttcctgggccgtggcgatcagtacccaatcgcg
VIBCH         gattttgctgataagcatcataccctcttcttggggcgcggtgagtactacccgattgcg

ECOLI         ctggaaggcgcattgaagttgaaagagatctcttacattcacgctgaagcctacgctgct
VIBCH         gtagaagcgtctcttaaactgaaagagatctcttacatccacgcagaagcctatgcagcg

ECOLI         ggcgaactgaaacacggtccgctggcgctaattgatgccgatatgccggttattgttgtt
VIBCH         ggcgagctaaagcatggcccattggcgttaattgatgcggatatgccagtggttgtggtt

ECOLI         gcaccgaacaacgaattgctggaaaaactgaaatccaacattgaagaagttcgcgcgcgt
VIBCH         gcaccaagcaatgaactgttagaaaagcttaaatccaatattgaagaagtgcgtgcgcgc

ECOLI         ggcggtcagttgtatgtcttcgccgatcaggatgcgggttttgtaagtagcgataacatg
VIBCH         ggtggtttattgtacgtatttgccgatgaagtggcgggctttgaagcggatgagacgatg

ECOLI         cacatcatcgagatgccgcatgtggaagaggtgattgcaccgatcttctacaccgttccg
VIBCH         aaaatcattgcgatgccgcatgttagcgagattgtggctccgatttattacaccatccca

ECOLI         ctgcagctgctggcttaccatgtcgcgctgatcaaaggcaccgacgttgaccagccgcgt
VIBCH         atgcaactgctctcttaccatgtggctttaatcaaaggtaccgatgttgaccagcctcgt

ECOLI         aacctggcaaaatcggttacggttgag
VIBCH         aaccttgctaaagcggtaactgtcgag
Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 2.6722
KA = 0.2108
KA/KS = 0.0789
You can see the parameters used in codeml to calculate these values.
If you use these values, please cite the following peper:
  • Goldman, N. and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11:725-736.