seqmatchall does an all-against-all pairwise comparison of words (fragments of the sequences of a specified fixed size) in a set of sequences and finds regions of similarity within any two sequences.

Here is a sample session with seqmatchall. We use an increased word size to avoid accidental matches:

% seqmatchall
Does an all-against-all comparison of a set of sequences
Input sequence set: embl:eclac*
Word size [4]: 15
Output file [outfile.seqmatchall]:

Mandatory qualifiers:

[-sequence] (seqset)

Sequence set USA.

-wordsize (integer)

Word size.

[-outfile] (outfile)

Output filename.