Wouldn't some of the new timeseries motif searching approaches work in this domain (you could assume each codon is a quantized enumerated value). Something lik

Wouldn't some of the new timeseries motif searching approaches work in this domain (you could assume each codon is a quantized enumerated value). Something like iSax (http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html) or Dynamic Time Warping (for motifs that are noisy) - http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf