PAL2NAL output

>P0A6V8
atgacaaagtatgcattagtcggtgatgtgggcggcaccaacgcacgtcttgctctgtgt
gatattgccagtggtgaaatctcgcaggctaagacctattcagggcttgattaccccagc
ctcgaagcggtcattcgcgtttatcttgaagaacataaggtcgaggtgaaagacggctgt
attgccatcgcttgcccaattaccggtgactgggtggcgatgaccaaccatacctgggcg
ttctcaattgccgaaatgaaaaagaatctcggttttagccatctggaaattattaacgat
tttaccgctgtatcgatggcgatcccgatgctgaaaaaagagcatctgattcagtttggt
ggcgcagaaccggtcgaaggtaagcctattgcggtttacggtgccggaacggggcttggg
gttgcgcatctggtccatgtcgataagcgttgggtaagcttgccaggcgaaggcggtcac
gttgattttgcgccgaatagtgaagaagaggccattatcctcgaaatattgcgtgcggaa
attggtcatgtttcggcggagcgcgtgctttctggccctgggctggtgaatttgtatcgc
gcaattgtgaaagctgacaaccgcctgccagaaaatctcaagccaaaagatattaccgaa
cgcgcgctggctgacagctgcaccgattgccgccgcgcattgtcgctgttttgcgtcatt
atgggccgttttggcggcaatctggcgctcaatctcgggacatttggcggcgtgtttatt
gcgggcggtatcgtgccgcgcttccttgagttcttcaaagcctccggtttccgtgccgca
tttgaagataaagggcgctttaaagaatatgtccatgatattccggtgtatctcatcgtc
catgacaatccgggccttctcggttccggtgcacatttacgccagaccttaggtcacatt
ctg
>Q1C5Z1
atgacgacttatgccctggtgggtgacgttggcggtacgaatgcccggttggcgctttgc
gctgttgcaacgggcgagatattgcaagcaaagacatattcagggttggaatatgaaagt
ttagaggatgtaatcaaacaatatctatcagagcatcaagccaaggtcaccgatgcttgt
atcgcgattgcctgcccgattaccggggattgggtcgcaatgaccaatcatacttgggca
ttttctattgccgccatgcaacagaatctgggtctggaccatttggaagtgatcaatgac
ttcaccgcagtctccatggctatccccgtgttacctgcccaagatgttctgcaatttggt
ggcacacagccacagcctggcaaaccggtggcagtgtatggcgcaggtactgggctgggg
gtagcacatttagtgaatgttgatcgccgttggattagtttagcgggagagggcgggcat
gttgatttcgcgcctaatagtgaagaagaagaccagattctggccgtattgcgccaggag
ttggggcatgtttccgctgagcgggtgctatctgggccgggcttagtcaatttatatcgg
gcaattgtgatttctgatgcgcgcctaccagagaaactggcaccgaaagatattaccgca
cgggcgctggcggatagctgtaccgattgtcgccgggcattatcactattttgcgtaatt
atgggccgctttgggggcaatttagcccttaacctcagtacgtttggtggcgtttatatt
gcggggggcatcgtgccgcgctttatggagttctttaaagcctctggttttcgcgctgcg
tttgaagataaaggccgttttaaagatttcttacaagatattccggtgtatatgattact
catccacaacccggtttactgggggctggtgcctatttacgccaaaaattggggtatgag
ttg
Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by codeml in the PAML package:
KS = 6.6905
KA = 0.1297
KA/KS = 0.0194
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.