polydot compares all sequences in a set of sequences. It then draws a dotplot for each pair of sequences by marking where words (tuples) of a specified length have an exact match in both sequences and optionally reports all identical matches to feature files.
Here is a sample session with polydot:
% polydot globin.fasta -gtitle="Polydot of globin.fasta"
Mandatory qualifiers (bold if not always prompted):