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  Schema for Interrupted Rpts - Fragments of Interrupted Repeats Joined by RepeatMasker ID
  Database: bosTau4    Primary Table: nestedRepeats    Row Count: 499,257
Format description: BED12+ describing joined (by ID) fragments of repeats from RepeatMasker.
fieldexampleSQL type info description
bin 585smallint range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Chromosome (or contig, scaffold, etc.)
chromStart 9235int unsigned range Start position in chromosome
chromEnd 10107int unsigned range End position in chromosome
name L1MD2varchar(255) values Name of item
score 406int unsigned range Average of fragment identity scores, transformed into 0..1000 range for shading.
strand +char(1) values +, -, or . for mixed (some fragments +, some -)
thickStart 9235int unsigned range for BED compatibility -- same as chromStart
thickEnd 10107int unsigned range for BED compatibility -- same as chromEnd
reserved 0int unsigned range for BED compatibility
blockCount 2int range Number of blocks
blockSizes 390,215,longblob   Comma separated list of block (fragment) sizes
chromStarts 0,657,longblob   Start positions relative to chromStart
blockStrands +,+,longblob   Strand of each fragment.
id 141621int unsigned range RepeatMasker-assigned ID used to join fragments.
repClass LINEvarchar(255) values Class of repeat
repFamily L1varchar(255) values Family of repeat

  Sample Rows

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

  Interrupted Rpts (nestedRepeats) Track Description


This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences using 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 detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output.

Display Conventions and Configuration

In pack or full mode, each interrupted repeat is displayed as boxes (fragments) joined by horizontal lines, labeled with the repeat name. If all fragments are on the same strand, then arrows are added to the horizontal line to indicate strand. In dense or squish mode, labels and arrows are omitted, and in dense mode, all items are collapsed to fit on a single row.

Items are shaded according to the average identity score of their fragments. Usually, the shade of an item is similar to the shades of its fragments, unless some fragments are much more diverged than others. The score displayed above is the average identity score, clipped to a range of 50% - 100%, and then mapped to the range 0 - 1000 for shading in the browser.


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. See the FAQ for more information.


Thanks to Arian Smit, Robert Hubley 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.