Is there a database for the self aligned repeat region. What I mean is to mark the region that are duplicated inside the chromosome or genome itself. Usually these regions are hard to find exact read mapping, because reads from these region can be mapped to multi repeat locations.

I look at repeatmasker's database(http://www.repeatmasker.org/species/hg.html), they only report 1. low complexity region, 2. region similar with reported repeat sequences such as Alu.