## 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 (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000) in the References section below.

The RepBase version used on this mouse assembly was RepBase Update 8.4, RM database version 20030619 and RepeatMasker script version 20030623.

## Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats:

- Short interspersed nuclear elements (SINE), which include ALUs
- Long interspersed nuclear elements (LINE)
- Long terminal repeat elements (LTR), which include retroposons
- DNA repeat elements (DNA)
- Simple repeats (micro-satellites)
- Low complexity repeats
- Satellite repeats
- RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA)
- Other repeats, which includes class RC (Rolling Circle)
- Unknown

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 higher the combined number of these, the lighter the shading.

## 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

Thanks to Arian Smit and GIRI for providing the tools and repeat libraries used to generate this track.

## References

RepBase is described in Jurka, J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16(9), 418-420 (2000).

For a discussion of repeats in mammalian genomes, see:

Smit, A.F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9(6), 657-63 (1999).

Smit, A.F. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 6(6), 743-8 (1996).