FindMotif, by running MEME[1], takes as input a group of DNA or protein sequences and outputs as many motifs as requested.
Restrictions: At most 100 sequences per submission.
References:
[1] Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37:W202-W208.
[1] Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37:W202-W208.