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