If TRUE then indels are allowed. In that case max.mismatch is interpreted as the maximum "edit distance" allowed between the pattern and a match. Note that in order to avoid pollution by redundant matches, only the "best local matches" are returned. Roughly speaking, a "best local match" is a match that is locally both the closest (to the pattern P) and the shortest. More precisely, a substring S' of the subject S is a "best local match" iff: