A computational method is described which uses the process of cis-regulatory module evolution to identify conserved sequence patches which exhibit suppression of change by snp/indel occurrence, including determining sequence similarities significantly greater than random expectation on selected genome sequences from two or more species in sequences that lie outside of protein coding regions, sorting the similarities for conserved patches of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels). and selecting such patches to identify cis-regulatory modules. Further, the disclosed method is practiced in the absence of having to execute multiple interspecific sequence comparison analysis, where such identified cis-regulatory modules are used to produce libraries and arrays containing such cis-regulatory modules.