PAL2NAL outputPAL2NAL output
>AMPA_PSEA7
gaattccttgttaaaagcgtacgcccggaaaccctgaaaaccgccaccctggtgctcgcc
gtaggcgaaggccgcaagctcggcgccagcgccaaggcggtcgacgacgccaccggcggc
gccatcgcagtgctcaagcgtggcgacctggccggcaaggtcggccagaccctgctcctg
cagctgcccaatctcaaggccgagcgcgtgctgctggtcggcgccggcaaggagcgcgaa
ctgggcgaccgccagtaccgcaagctggcctccgccgtgctgtcgaccctcaagggcctg
gccggcgccgatgccctggccctcggcgatctcgcggtgaaaggccgcgatgcccacgcg
aaggcgcgtctgctggtggaaaccctggccgatggcctgtacgtgttcgatcgctacaag
agccagaaagccgagccgctgaaactgaagaagctgaccctgctcgccgacaaggccgac
agcgccgccgtcgagcaaggcagcaaggaagctcaggccatcgccaatggcatggccctg
acccgcgatctcggcaaccttccgccgaacgtctgccatccgacgttcctcggcgagcag
gccaagctggccaaggagttcaagggcctgaaggtcgaggtcgacgagaaactgcgcgag
ctgggcatgggctcgttcctcgccgtcgcccagggcagccagccgccgcggctgatcgtc
ctgcaatacaacggcgcgaagaaggaccaggccccgcacgtgctggtcggcaagggcatc
accttcgacaccggcggcatcagcctcaagccgggcctgggcatggacgagatgaagttc
gacatgtgcggcgccgccagcgtcttcggcaccttccgcgcggtgctcgaactgcagttg
ccgatcaacctggtcggcctgctggcctgcgccgagaacatgcccagcggcggagccacc
cgtccgggcgacatcgtcaccaccatgagcgggcagaccgtcgagatcctcaacaccgac
gccgaagggcgcctggtgctgtgcgatgcactgacctacgccgagcgcttcaagcctcag
tcggtggacatcgccaccctcaccggcgcctgcatcgtcgccctgggcagcaacacctcg
ggccttatgggcaacaacgaagcgctggtcaggcaactgctcaaggccggcgagttcgcc
gacgaccgcgcctggcaattgccgctgttcgacgaataccaggaacagctggacagcccg
ttcgccgacatcgccaacatcggcgggccgaaggccggcaccatcaccgccggctgcttc
ctctcgcgcttcgccaagaaataccactgggcgcacttggacatcgccggcaccgcctgg
atcagcggcaaggacaaaggcgccaccggccgcccggttccgttgttgacccagtacctg
ctggaacgggccaag
>AMPA_ECOLI
gagtttagtgtaaaaagcggtagcccggagaaacagcggagtgcctgcatcgtcgtgggc
gtcttcgaaccacgtcgcctttctccgattgcagaacagctcgataaaatcagcgatggg
tacatcgccctgctacgtcggggcgaactggaaggaaaaccggggcagacattgttgctg
cacgttccgaatgtactttccgagcgaattctccttattggttgcggcaaagaacgtgag
ctggatgagcgtcagtacaagcaggttattcagaaaaccattaatacgctgaatgatact
ggctcaatggaagcgtgctttctgactgagctgcacgttaaaggccgtaacaactactgg
aaagtgcgtcaggctgtcgagacggcaaaagagacgctctacagtttcgatcagctgaaa
acgaacaagagcgaaccgcgtcgtctgcgtaagatggtgttcgtgccgacccgccgtgaa
ctgaccagcggtgagcgcgcgatccagcacggtctggcgattgccgccgggattaaagca
gcaaaagatctcggcaatatgccgccgaatatctgtaacgccgcttacctcgcttcacaa
gcgcgcctggctgacagctacaagaatgtcatcacccgcgttggcgaacagatgaaagag
ctggggatgcattcctatctggcggtcggtcagggttcgaacgaatcgctgatgtcggtg
attgagtacaaaggcgcgtcggaagatgcacgcccaatcgtgctggtgggtaaaggttta
accttcgactccggcggtatctcgatcaagccttcagaaggcatggatgagatgaagtac
gatatgtgcggtgcggcagcggtttacggcgtgatgcggatggtcgcggagctacaactg
ccgattaacgttatcggcgtgttggcaggctgcgaaaacatgcctggcggacgagcctat
cgtccgggcgatgtgttaaccaccatgtccggtcaaaccgttgaagtgctgaacaccgac
gctgaaggccgcctggtactgtgcgacgtgttaacttacgttgagcgttttgagccggaa
gcggtggacgtggcgacgctgaccggtgcctgcgtgatcgcgctgggtcatcatattact
ggtctgatggcgaaccataatccgctggcccatgaactgattgccgcgtctgaacaatcc
ggtgaccgcgcatggcgcttaccgctgggtgacgagtatcaggaacaactggagtccaat
tttgccgatatggcgaacattggcggtcgtcctggtggggcgattaccgcaggttgcttc
ctgtcacgctttacccgtaagtacaactgggcgcacctggatatcgccggtaccgcctgg
cgttctggtaaagcaaaaggcgccaccggtcgtccggtagcgttgctggcacagttcctg
ttaaaccgcgctggg


Synonymous (KS) and non-synonymous (KA) substitution rates calcualted by 
      codeml in the PAML package:
      KS = 60.4277
      KA = 0.3476
      KA/KS = 0.0058
      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.