How to find the self aligned repeat region in human genome

Question

[Chen Sun]

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.

Answer 1

[Pierre Lindenbaum]

See http://hgdownload.cse.ucsc.edu/goldenPath/hg38/vsSelf/

This directory contains alignments of Human (hg38, Dec. 2013, GRC Build GRCh38) to itself,

[Chen Sun]

Thanks, that really helps

[Chen Sun]

Actually, the result of UCSC is not 100% report, I find lots of false negatives. And the tools they are using is blastz from Penn State University.

[serpalma.v]

Is there any similar data set for Bos taurus (UMD3.1)?. I've browsed UCSC and Ensembl corresponding directories.