PAL2NAL output

CLUSTAL W multiple sequence alignment

swissprot|P60906|SYH_ECOLI    gtggcaaaaaacattcaagccattcgcggcatgaacgattacctgcctggcgaaacggcc
swissprot|Q02RV6|SYH_PSEAB    gtgagcaagtccctgcaagccattcgtggcatgaacgacatcctgccggagcagactccg

swissprot|P60906|SYH_ECOLI    atctggcagcgcattgaaggcacactgaaaaacgtgctcggcagctacggttacagtgaa
swissprot|Q02RV6|SYH_PSEAB    gcctggcgctatctggaacgcaccttcgccggcctgctggacggctacggctacagcgag

swissprot|P60906|SYH_ECOLI    atccgcttgccgattgtagagcagaccccgctattcaaacgtgcgattggtgaagtcacc
swissprot|Q02RV6|SYH_PSEAB    atccgcctgcccatcctcgagttcaccgaactcttcgcccgcggcatcggcgaaggtacc

swissprot|P60906|SYH_ECOLI    gacgtggttgaaaaagagatgtacacctttgaggatcgcaatggcgacagcctgactctg
swissprot|Q02RV6|SYH_PSEAB    gacgtggtcgacaaggagatgtacaccttcctcgaccgcaacggcgaatccctgaccatg

swissprot|P60906|SYH_ECOLI    cgccctgaagggacggcgggctgtgtacgcgccggcatcgagcatggtcttctgtacaat
swissprot|Q02RV6|SYH_PSEAB    cgtccggaaggtaccgccggttgcgtgcgcgccgtgctggagcacggcctgagcggtggc

swissprot|P60906|SYH_ECOLI    caggaacagcgtctgtggtatatcgggccgatgttccgtcacgagcgtccgcagaaaggg
swissprot|Q02RV6|SYH_PSEAB    caggtgcagaagctctggtacaccgggccgatgttccgttacgagaaaccgcagaaaggt

swissprot|P60906|SYH_ECOLI    cgttatcgtcagttccatcagttgggctgcgaagttttcggtctgcaaggtccggatatc
swissprot|Q02RV6|SYH_PSEAB    cgctaccggcagttccaccagatcggcgtggaagtcttcaacctgcccggtccggacatc

swissprot|P60906|SYH_ECOLI    gacgctgaactgattatgctcactgcccgctggtggcgcgcgctgggtatttccgagcac
swissprot|Q02RV6|SYH_PSEAB    gacgccgagttgatcatcctcacctggcgcctgtggcagaagctcggcatggccgacgcg

swissprot|P60906|SYH_ECOLI    gtaactcttgagctgaactctatcggttcgctggaagcacgcgccaattaccgcgatgcg
swissprot|Q02RV6|SYH_PSEAB    gtgaccctgcagctcaacaccctcggttccagcgaggcccgcgcacgctatcgcgaggcc

swissprot|P60906|SYH_ECOLI    ctggtggcattccttgagcagcataaagaaaagctggacgaagactgcaaacgccgcatg
swissprot|Q02RV6|SYH_PSEAB    ctggtggcctatctgcaggagcgcttcgagcaactcgacgaagacagccagcggcgcatg

swissprot|P60906|SYH_ECOLI    tacactaacccgctgcgcgtgctggattcaaaaaatccggaagtgcaggcgcttctcaac
swissprot|Q02RV6|SYH_PSEAB    accaccaatccgctgcgaatcctcgacagcaaggtggagagcacccaggcgttgctggtc

swissprot|P60906|SYH_ECOLI    gacgctccggcattaggtgactatctggacgaggaatctcgtgagcattttgccggtctg
swissprot|Q02RV6|SYH_PSEAB    ggcgcgccgaccctgcacgactatctcgacgaagaatcgatcgcccacttcgagggtctc

swissprot|P60906|SYH_ECOLI    tgcaaactgctggagagcgcggggatcgcttacaccgtaaaccagcgtctggtgcgtggt
swissprot|Q02RV6|SYH_PSEAB    aaggcccgcctggatgctgtcggactgcgctacgaaatcaaccagaagctggtgcgcggc

swissprot|P60906|SYH_ECOLI    ctggattactacaaccgtaccgttttcgagtgggtgactaacagtctcggctcccagggc
swissprot|Q02RV6|SYH_PSEAB    ctggactattactgccgcacggctttcgagtgggtcaccgacaagcttggcgcccagggc

swissprot|P60906|SYH_ECOLI    accgtgtgtgcaggcggtcgttatgacggtcttgtggaacaactgggcggtcgtgcaaca
swissprot|Q02RV6|SYH_PSEAB    accgtttgcggcggtggccgctacgacgggctggtcagccagttcggcggcaagccgacc

swissprot|P60906|SYH_ECOLI    ccggctgtcggttttgctatgggcctcgaacgtcttgtattgttagtacaggccgttaat
swissprot|Q02RV6|SYH_PSEAB    ccgggcgtcggtttcgccatgggcgtggaacgcctggtgctgctgctggaaggggtgatc

swissprot|P60906|SYH_ECOLI    ccggaatttaaagccgatcctgtcgatatatacctggtggcttcaggtgctgatacacaa
swissprot|Q02RV6|SYH_PSEAB    cccgccgaactgaaccgtccggccgacctctacgtctgcgccttcggcgaaccggccgag

swissprot|P60906|SYH_ECOLI    tctgcggctatggcattagctgagcgtctgcgtgatgaattaccgggcgtgaaattgatg
swissprot|Q02RV6|SYH_PSEAB    ctggccgccctgaccctggccgaacagttgcgcagcgccattcccggcatacgcttgctg

swissprot|P60906|SYH_ECOLI    accaaccacggcggcggcaactttaagaaacagtttgcccgtgctgataaatggggtgcc
swissprot|Q02RV6|SYH_PSEAB    gtcaacgccggcgccggtagcttcaagagccagttcaagaaggccgacaagagcggcgcg

swissprot|P60906|SYH_ECOLI    cgcgttgctgtggtgctgggtgagtctgaagtggctaacggcacagcagtagtgaaggat
swissprot|Q02RV6|SYH_PSEAB    cgctttgccctgatcctcggggaggacgaggtggccaatcgcgtggtaggtttcaagccc

swissprot|P60906|SYH_ECOLI    ttgcgctctggtgagcaaacggcagttgcgcaggatagcgtagccgcgcatttgcgcacg
swissprot|Q02RV6|SYH_PSEAB    ctgcgtgagggcgagcaacaaagcattgcctgggatgctctgcccgagcacctggcagcc

swissprot|P60906|SYH_ECOLI    ttactgggt
swissprot|Q02RV6|SYH_PSEAB    tgtctggca



Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 53.7633
KA = 0.3014
KA/KS = 0.0056
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.