The "Cluster Size:" field lets you indicate how many motifs constitute a cluster. If you specify a cluster size of 3 and a window size of 1000, then Genome Enhancer will find places in the genome where at least 3 motifs (matching any of the sequences you specified) fall within a 1000-base window.

It is possible to specify more than one cluster size, using commas. If you enter "2, 3, 4" here, for example, then you will see the count of clusters of at least 2 motifs, at least 3 motifs, and at least 4 motifs within your given window size. Detailed information on each cluster is not available when more than one cluster size is given.