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