The Kruskal and Sankoff version of the local alignment is implemented
[Sankoff & Kruskal, 1983]; this is very similar to the [Smith & Waterman, 1981] method.
All the routines for the local alignment are exactly the same as the
routines for the global alignment except that during the construction
of matrix 
the alignment is restarted each time the score becomes
higher than a cutoff. The second difference is that the backtracking
starts from the lowest element in the matrix, wherever it is.