NUCmer has a function turned on by default, called the "simplify" function. The manual supplied explanation is not very clear to me:
--[no]simplify Simplify alignments by removing shadowed clusters. Turn this option off if aligning a sequence to itself to look for repeats (default --simplify)
I understand that this function is supposed to be turned off when doing a self-reflecting comparison. I still don't understand what is meant with "shadowed clusters" though. Also why wouldn't it be good to have this function turned off when doing a normal comparison (two different samples)
I hope somebody could clear this up for me.