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  Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: bosTau4    Primary Table: rmsk    Row Count: 5,430,738
Format description: RepeatMasker .out record
fieldexampleSQL type description
bin 585smallint unsigned Indexing field to speed chromosome range queries.
swScore 812int unsigned Smith Waterman alignment score
milliDiv 131int unsigned Base mismatches in parts per thousand
milliDel 0int unsigned Bases deleted in parts per thousand
milliIns 0int unsigned Bases inserted in parts per thousand
genoName chrXvarchar(255) Genomic sequence name
genoStart 0int unsigned Start in genomic sequence
genoEnd 130int unsigned End in genomic sequence
genoLeft -88516533int -#bases after match in genomic sequence
strand -char(1) Relative orientation + or -
repName Bov-tA2varchar(255) Name of repeat
repClass SINEvarchar(255) Class of repeat
repFamily BovAvarchar(255) Family of repeat
repStart -78int Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd 134int End in repeat sequence
repLeft 5int -#bases after match (if strand is +) or start (if strand is -) in repeat sequence
id 1char(1) First digit of id field in RepeatMasker .out file. Best ignored.

  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, 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. (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, srpRNA)
  • 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.


Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2007.

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

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6): 657-63.

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8.