I need to sample starting positions in a DNA sequence of given length L.
These starting positions represent starting points of functional domains in DNA sequences. They have a length of d. The starting positions should be distributed uniformly and must have a minimal distance of d between them (functional domains should not overlap). Positions higher then L-d+1 are not possible because functional domains should be complete.
The approach of sampling iterativly a starting position i and procecede with sampling in uniformly in the interval [i+d, L-d+1] does not produce a uniform distribution.
Do you know of any solution to this?