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This paper took advantage of phylogenetic footprinting and statistical analysis to identify putative cis-regulatory elements in the promoters of human genes. Three organisms were investigated including human, mouse and drosophila melanogaster. 124 putative regulatory elements of length 8 were yielded from this research and they were grouped into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters revealed that SP1, EGR and NRF-1 were the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene ontology (GO) analysis revealed that many of GO categories of transcription factors binding to these elements matched the GO categories of genes whose promoters contain these elements.