“…. x i,k ] responsible for this witness are then said to satisfy pattern k. This formulation follows the logic in the previous works [20,6,21,16,2,7] that, for each pattern, a legal occurrence on each sequence is chosen to support the feasibility of a constrained alignment, while those occurrences not chosen are treated as normal characters. Unlike the previous studies, we do not specify how the characters in the substrings S i [x i,k .…”