Repeat Masker track constructed with the HMMER alignment engine and Dfam_1.2 database.
1734398971 bases of 3209286105 (54.043%) in intersection
With the following profile of item counts in these classes of repeats:
1884179 SINE
1702529 LINE
805427 LTR
636906 Simple_repeat
565171 DNA
95480 Low_complexity
11861 Retroposon
10852 Satellite
9181 LTR?
6783 scRNA
4582 DNA?
3914 Unknown
2059 RC
1517 srpRNA
1484 RNA
970 SINE?
806 RC?
464 rRNA
5744165 total
In full display mode, this track displays up to ten different classes of repeats:
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.
A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed.
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, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track.
Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. https://www.repeatmasker.org/. 1996-2010.
Repbase Update is described in:
Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072
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. PMID: 10607616
Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846