Clover: Cis-eLement OVERrepresentation
Clover is a program for identifying functional sites in DNA sequences. If you give it 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.
Martin C Frith, Yutao Fu, Liqun Yu, Jiang-Fan Chen, Ulla Hansen, Zhiping Weng
(2004). Detection of functional DNA motifs via statistical over-representation.
Acids Research 32(4):1372-81.
Here are the data sets studied in the paper.