Abstract

The case of ungapped alignment of two literal sequences under constrains is considered. The analysis lead to general formulas for probability mass function and cumulative distribution function for the general case of using an alphabet with a chosen number of letters in the expression of the literal sequences. Formulas for three statistics including mean, mode, and standard deviation were obtained. Distributions are depicted for three important particular cases: alignment on binary sequences, alignment of trinomial series, and alignment of genetic sequences. A particular case when sequences contain each letter of the alphabet at least once in both sequences has also been analyzed and some statistics for this restricted case are given