

This directory contains a sequence file, mcp112-20.seq, with
the twenty sequences with a hidden embedded motif (similar to
the LD-motif problem proposed by Pevzner et. al.).

To find the motif use:
../../src/gemoda-s -l 11 -g 7 -k 20 -p 20 -m dna_idmat -i mcp112-20seq

The calculation of motif signifigances will take a long time
for this example.  To expedite this, try '-s1000', which will
sample every 1000th point in the similarity matrix.  We've 
found that sampling almost never changes the relative signifigance
of motifs.
