We have developed a program, Cluster Analyzer for Transcription Sites (CATS), which identifies clusters of transcription factor binding sites in any genome sequence. The program searches for clusters of the consensus sequence for DNA binding within a window (length of DNA). The window size and the cluster size (number of consensus sequences within a given window) can be varied. CATS can be used for single or multiple transcription factors for which consensus sequences have been deduced based on biochemical and mutational analysis, or by comparative genomics. The use of CATS for clusters of different transcription factor binding sites may facilitate the identification of genes that are co-regulated in a cell type-specific or developmental stage-specific manner. CATS is simple to install and use on computers running any Windows NT-platforms.