COMIT: identification of noncoding motifs under selection in coding sequences

Table 1 Abridged table of mouse-human genome-wide codon conservation frequencies, as a function of each of the 20 × 20 pairs of aligned amino acids

For a given pair of amino acids, there are eight possible conservation patterns for the underlying nucleotides (000, 001, 010, 011, 100, 101, 110, 111), where 1 means a conserved base and 0 means a non-conserved base. These frequencies provide a null model for the expected conservation patterns at the nucleotide level, given the amino acid sequence. Here '#' indicates the number of instances in which amino acid 1 (AA1) is aligned to AA2 in the complete set of coding alignments between mouse and human.

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