SiteSifter finds highly conserved DNA motifs embedded within coding regions. Each instance of a motif is scored based on
the chance that its constituent codons are conserved over and above that required for amino acid conservation.
Forman J, Legesse-Miller A, Coller H (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proceedings of the National Academy of Sciences of the United States of America 105:39, 14879-14884. (Link)