The "Window Size:" field lets you indicate how close together a group of motifs must be located in order to constitute a cluster. If you specify a cluster size of 3 and a window size of 1000, then Genome Enhancer will find places 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 window size, using commas. If you enter "100, 500, 1000" here, for example, then you will see the count of clusters that exist within a 100-base window, a 500-base window, or a 1000-base window. Detailed information on each cluster is not available when more than one window size is given.