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Read about the mutations file format
Read about the genomic elements file format

Indicate whether you want to concatenate or not the genomic regions of each of the elements under analysis:

Window of a given length (bp) where mutations are smoothed using the Tukey kernel function.
Window of a given length (bp) to search for adjacent clusters and merge them.
Number of simulations to be computed. The minimum number of simulations is 1,000.
Kmer-nucleotide context to calculate background mutational probabilities.
Window of a given length (bp) to randomly sample mutations according to the background model.

Whether to allow simulation windows to fall outside the regions or limit them to the regions under analysis: