The goal of motif finding is the detection of novel, unknown signals in a set of sequences [1]. For example you might want to detect transcription factor binding sites in a genome, but do not know how they look like.
However, one can be quite certain, that such motifs are never conserved exactly but only approximately. This fact makes the problem difficult.
The first steps of the PROJECTION algorithm by Tompa (see also [1]) should be implemented in this project.