The joint distribution of patterns in random sequences with application to the RC-measure for expressivity

A method previously developed for computation of pattern probabilitiesin random sequences under Markov chain models. We extend thismethod to the calculation of the joint distribution for twopatterns. An application yields the distribution of the rightchoice measure for expressivity and how significance boundsdepend on sequence length. These bounds are used to show thatthe choice of pyrimidine in codon position 3 of Escherichiacoli genes deviates considerably from a general Markov processmodel for coding regions. We also derive some statistical evidencethat this significant deviation is limited to codon position3.