The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis-regulatory modules (CRMs). We present an expressive and easily comprehensible CRM representation which is capable of capturing several aspects of a CRMs structure and distinguishing between DNA sequences which do or do not contain it. We also present a learning algorithm tailored for this domain, and a novel method to avoid overfitting by controlling the expressivity of the model.