We present a combinatorial method for discovering cis-regulatory modules in promoter sequences. Our approach combines "sliding window" approaches with a scoring function based on the so-called Tanimoto score. This allows to identify sets of binding sites that tend to occur preferentially in the vicin ity of each other in a given set of promoter sequences belonging to co-expressed or orthologous genes. We bench- mark our method on a data set derived from muscle-specific gen es, demonstrating that our approach is capable of identifying modules that were identified as functional in previous studies.