dottup looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of these words.
Here is a sample session with dottup:
% dottup embl:eclac embl:eclaci -wordsize=6 -gtitle="eclaci vs eclac"
Mandatory qualifiers (bold if not always prompted):
Optional qualifiers (bold if not always prompted):