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 Update library of repeats from the
Information Research Institute (GIRI). Repbase Update is described in
Jurka (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, arrows are added to the
horizontal line to indicate the 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, Green P.
Repbase Update is described in:
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:
Interspersed repeats and other mementos of transposable elements in mammalian genomes.
Curr Opin Genet Dev. 1999 Dec;9(6):657-63.
The origin of interspersed repeats in the human genome.
Curr Opin Genet Dev. 1996 Dec;6(6):743-8.