Transcription regulation is controlled by coordinated binding of one or more 
transcription factors in the promoter regions of genes. In many species, 
especially higher eukaryotes, transcription factor binding sites tend to occur 
as homotypic or heterotypic clusters, also known as cis-regulatory modules. The 
number of sites and distances between the sites, however, vary greatly in a 
module. We propose a statistical model to describe the underlying cluster 
structure as well as individual motif conservation and develop a Monte Carlo 
motif screening strategy for predicting novel regulatory modules in upstream 
sequences of coregulated genes. We demonstrate the power of the method with 
examples ranging from bacterial to insect and human genomes.