Clustering analysis of sequences from DNase and random libraries. (A) The total number of clusters was determined for 15 different window sizes. For window sizes <5000 bp, there are larger numbers of clusters for the DNase library. For very large window sizes (100,000 bp), the majority of the DNase and random libraries cluster within only a few regions of the genome. (B) Example of how unique tags cluster into different sizes. The greatest spread between DNase and random libraries occurs at a 500-bp window. (C) Within this optimal window size, there are twice as many DNase clusters of two compared with random. Clusters of three or more are rarely found in random libraries.
