Description

This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence, as well as a modified version of the query sequence in which all the annotated repeats have been masked. RepeatMasker uses the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. "Repbase Update: a database and an electronic journal of repetitive elements". Trends Genet. 9:418-420 (2000).

In full display mode, this track displays nine different classes of repeats:

The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The lower the combined number of these, the darker the shading.

For a discussion of repeats in mammalian genomes, see:

Methods

UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet.

Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information.

Credits

We'd like to thank Arian Smit and GIRI for providing the tools and repeat libraries used to generate this track.