I want to determine the begining and end of each interval formed only by Ns (masked region). Then I would like to split the chromosome into smaller intervals to keep the regions that are not masked.
I would like to get three intervals from this sequence: AGGTCGTT -> from 1 to 8 AACTG -> from 13 to 17 AGTC -> from 20 to 23
Is there a tool I could use to do the task? I have been searching, but I cannot find the right one.