This section outlines the functions obtained from the Comparison menu. All produce graphical and textual output. Using a score matrix, the "Find similar spans" function compares every segment of one sequence with all those of the other and reports those that reach a user defined score. The segments are of a fixed length (span) set by the user. To look for short matching segments of any length, and allowing gaps, a local dynamic programming routine can be used. The fastest routine for locating segments of similarity (and generally only suitable for DNA sequences) finds all identical subsequences (or words). For a quick global comparison of sequences using a combination of the Matching Words and Matching Spans algorithms the "Find best diagonals" algorithm can be used. Global alignments can be produced and plotted using a dynamic programming algorithm.