Gene expression in eukaryotic organisms is regulated by complex interactions of enzymes, some of which directly bind to DNA. Although this binding is mostly nonspecific, one can still characterize and then search for motifs appearing with significant frequency and consistency, which are generally presumed to be target sites for transcription factors. We here report an algorithm for the identification of such motifs and subsequent genome-wide scans for their conglomerations at loci other than these provided as input sequences, for which we usually select promoter regions of coexpressed genes. The initial testing of the software implementing this method has been performed on human Hox gene clusters.