2. The method of claim 1 , wherein the elements sometimes represent pauses, instead of pitches, further including forward propagating at least pitches, for scoring purposes, from cells included in the partial alignments into cells having pauses.
2. The method of claim 1 , wherein the elements sometimes represent pauses, instead of pitches, further including forward propagating at least pitches, for scoring purposes, from cells included in the partial alignments into cells having pauses. 3. The method of claim 2 , wherein the scoring of a potential inclusion transition into cell (i,j) as having a pitch difference of zero if elements i and j of the query and target sequences both include pauses.