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Table 2.

Reduction of total cis-element search space for identification of conserved TF-binding site clusters by restriction to phylogenetically conserved sequence regions.

Gene		Number of TF binding sites in genomic sequences		Total number of TF binding sites of the two sequences (a)		TF binding sites in common within `BLASTZ` aligned regions (b)	% Reduction based on no. sharedcis-elements within `BLASTZ` -aligned sequence blocks (100—b/a%)
Gene		Human	Mouse
ADA	2225	1740	3965	798	80
APEX	1850	1721	3571	458	87
XRCC1	2276	2209	4485	469	90
ERCC2	1806	1051	2857	299	90
CD4	2609	2609	5218	910	83
PAX6	29398	27321	56719	12444	78
ATM	12653	8753	21406	4093	81
MYO7A	7492	5146	12638	3116	75

[i] Examples of genes in which cis-element matrix hits are reduced 75% to 90%.