On the length and the position of the minimum sequence containing all runs of ones in a Markovian binary sequence

Let a sequence of binary (zero–one) trials which forms a nonhomogeneous/homogeneous Markov chain of first order with given initial probability distribution and one-step transition probability matrix. The trials are assumed to be ordered on a line. The statistics denoting the length and the position (starting, ending) of the shortest segment of the sequence containing all runs of ones, are considered. The study concerns with conditional probability distributions of the statistics given that there are at least two runs of ones in the sequence. Two application case studies related to learning experiments and DNA sequences are discussed. Illustrative numerics are presented.