We focus here on the distribution of the random count N of a regular expression in a multi-state random sequence generated by a heterogenous Markov source. We first briefly recall how classical Markov chain embedding techniques allow reducing the problem to the count of specific transitions in a (heterogenous) order 1 Markov chain over a deterministic finite automaton state space. From this result we derive the expression of both the mgf/pgf of N as well as the factorial and non-factorial moments of N. We then introduce the notion of evidence-based constraints in this context. Following the classical forward/backward algorithm in hidden Markov models, we provide explicit recursions allowing to compute the mgf/pgf of N under the evidence constraint. All the results presented are illustrated with a toy example.