The "Supercluster Size:" and "Supercluster Window:" fields let you search for clusters of clusters. They are similar to the "Cluster Size:" and "Window Size:" fields. If you specify a supercluster size of 3 and a supercluster window of 1000, then, after finding clusters that match all of the other search criteria, Genome Enhancer will look for groups of 3 clusters that fall within a 1000-base window.