A flowchart for NEXT-peak algorithm. First, the program reads the mapped tags. Then, it selects regions based on the tag count with a user specified length of the window (default: 150) and a user specified minimum count (default: 15). If motif site locations are provided, it estimates σ and β using motif site locations. For an unknown motif, run the NEXT-peak program with default values (σ = 30 and β = 50), and identify the strongest motif from a motif search. For each region, the program estimates μ and ν. It computes the standard deviation estimates for these estimates. As a post-processing step, the program computes the region length and p-value cut-off recommendations to screen out potential spurious regions when the motif site information is available.