PAL2NAL output

CLUSTAL W multiple sequence alignment

Hemn            atgtctgtacagcaaatcgactgggatctggccctgatccagaaatataactattccggg
Q1C239_YERPA    atgtctgagcacgctatagtttgggatctatccctgattcaaaaatataattattcaggg

Hemn            ccacgatacacctcgtacccgaccgcgctggagttttcagaagacttcggcgaacaggcg
Q1C239_YERPA    ccgcgttatacctcgtatccaacggctcttgagtttagtgaagattacaatgagtctgct

Hemn            tttttacaagccgtggcgcgctatcctgagcgtccattatctctctacgtacatatcccg
Q1C239_YERPA    ttccagcaggcggtgaaacgttatccgcaacggccattgtcgctgtatgtgcatattccg

Hemn            ttctgccataagctttgttacttctgcggttgcaataagattgttactcgccagcagcac
Q1C239_YERPA    ttttgccacaaactttgctacttctgtggctgcaataaactggtgacgcgtcagcaacat

Hemn            aaggccgatcagtatctggacgcgctggagcaagaaatcgtccatcgtgcaccgctgttc
Q1C239_YERPA    aaagctgatgaatatctggtggtgttggaaaaagagatccgccagcgggccgccttgttt

Hemn            gccgggcgtcacgtcagccaattgcactggggcggcggaacgccgacgtatctgaataaa
Q1C239_YERPA    accgggcgtcaggtcagccagatgcactggggggggggtacgccaacctatctgaataaa

Hemn            gcgcaaatcagccgcctgatgaagctgctgcgcgaaaacttccagttcaatgccgatgcg
Q1C239_YERPA    acgcaaatcagccatttaatgacggtgctgcgtgaacactttgattttctgcccgatgcg

Hemn            gagatttcgatcgaagtcgatccgcgggaaatcgaactggatgtactcgatcatttacgc
Q1C239_YERPA    gagcagtcaatcgaagttgacccccgtgaaattgaattagatgtgcttgatcacctgcgt

Hemn            gccgaaggctttaatcgcctgagcatgggcgtgcaggacttcaacaaagaagtgcaacgt
Q1C239_YERPA    gctgaagggtttaatcgcctgagcatgggggtgcaggatttcaataaagaggtgcagcgg

Hemn            ctggttaaccgcgagcaggatgaagagttcatctttgcactgcttaaccatgcgcgtgag
Q1C239_YERPA    ctggttaaccgcgagcaagatgaagattttatcttcgctttaattgcccgagctaaagcg

Hemn            attggttttacctccaccaacatcgacctgatttacggcctgccgaaacagacgccggag
Q1C239_YERPA    cttggatttaactcaaccaatattgatttgatttatggcttgcccaagcagacaccagaa

Hemn            agtttcgcctttaccctgaaacgtgtggcggagctgaaccccgatcgtctgagtgtcttt
Q1C239_YERPA    agttttgctttcaccttaaaacgggttgctgagctgaacccagatcgcttaagcgtgttt

Hemn            aactacgcgcatctgccgaccatttttgctgctcagcgcaaaatcaaagatgctgacctg
Q1C239_YERPA    aattacgcccatctgccaagcctgtttgccgcccaacgtaaaatcaaagacgctgatctg

Hemn            ccgagtccgcagcaaaaactcgatatcctgcaggaaaccatcgccttcctgacgcaatcg
Q1C239_YERPA    ccaacggcggagcaacggttggatattttgcagcacaccatccgtttcttaacggagtct

Hemn            ggctatcagtttatcggtatggatcactttgcccgtccggatgacgagctggcggtggcc
Q1C239_YERPA    ggctatcaattcattgggatggatcattttgcgcgtccggatgatgaactggcaattgct

Hemn            cagcgtgaaggcgtgctgcatcgtaacttccagggctacaccactcagggcgataccgat
Q1C239_YERPA    cagcaggaaggaacattacaccgcaactttcaagggtataccacgcagggtgagagcgat

Hemn            ctgctggggatgggcgtttccgccatcagcatgattggcgactgctacgcgcagaaccag
Q1C239_YERPA    ctccttgggttgggggtttctgctatcagcatgttaggtgacagctacgctcagaatgaa

Hemn            aaagagttgaagcagtactatcagcaagtggatgaacaaggcaatgcgctgtggcgtggt
Q1C239_YERPA    aaagatctggaaacatattacgcctgtgtagagcaacggggtaatgcgttgtggcgcggc

Hemn            attgcgctaacgcgtgatgactgtattcgccgcgatgtgattaagtcgctcatctgcaac
Q1C239_YERPA    ctgactatgaccgaagacgattgtttacgccgagatgtgattaaaacgctgatttgtcat

Hemn            ttccgtctggattacgcccctattgagaaacagtgggatttgcacttcgctgattacttt
Q1C239_YERPA    ttccaactcagttaccagccgattgagcagcgttatggtattcggtttgccgattatttt

Hemn            gcggaagatctcaagctgctcgccccgttagcaaaagatgggctggtggatgtggatgag
Q1C239_YERPA    gccgaagattttgagctgcttgcaccttttgaacaggatgggctggtggagcgaaatgaa

Hemn            aagggaatacaggtgacggcgaaaggtcgcttgctgatccgcaacatttgcatgtgcttt
Q1C239_YERPA    acagggcttcgcgtgaccccccgtgggcgcttactcattcgtaatatttgtatgtgtttc

Hemn            gatacctatctgcgccagaaagcgcggatgcagcagttctctcgggtgatt
Q1C239_YERPA    gatatctatttacgtaaacaggcgcgcaagcagcaattctcacgtgtaatc

Synonymous (K_S) and non-synonymous (K_A) substitution rates calcualted by codeml in the PAML package:
	K_S = 4.0109
	K_A = 0.1285
	K_A/K_S = 0.0320
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.