

This is a simple example using an alphabet drawn from
the English alphabet rather than nucleotides or amino
acid sequences.  To run the example use the command:

../../src/gemoda-s -i letters.seq  -k2 -l3 -g1 -m identity_aa


With this command, we're looking for motifs with support
of at least 2 and length of at least 3 in which each
window has a similarity score of 1 (of 3 possible) using
an identity matrix.  (Note that this is different than
the identity matrix used for nucleotide sequences.) This
should return three maximal motifs:


 ABCDEFG
 ABCEDFG


 BCDEF
 CEDFG


 CDEFG
 BCEDF

Notice that, with the low threshold (1/3), the final two
motifs are "held together" by only a one character match.

