Clover is a program for identifying functional sites in DNA sequences. For a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set.
module load clover clover
clover -t 0.05 mymotifs myseqs.fa background1.fa background2.fa