Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: dm6    Primary Table: rmsk    Row Count: 61,686
fieldexampleSQL type info
bin 585smallint(5) unsigned range
swScore 778int(10) unsigned range
milliDiv 167int(10) unsigned range
milliDel 7int(10) unsigned range
milliIns 20int(10) unsigned range
genoName chr2Lvarchar(255) values
genoStart 1int(10) unsigned range
genoEnd 154int(10) unsigned range
genoLeft -23513558int(11) range
strand +char(1) values
repName HETRP_DMvarchar(255) values
repClass Satellitevarchar(255) values
repFamily Satellitevarchar(255) values
repStart 1519int(11) range
repEnd 1669int(11) range
repLeft -203int(11) range
id 1char(1) values

Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RepeatMasker (rmsk) Track 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 Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka, J. (2000) in the References section below.

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.


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.


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


Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-20. PMID: 10973072