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  Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: bosTau4    Primary Table: simpleRepeat    Row Count: 441,972
Format description: Describes the Simple Tandem Repeats
fieldexampleSQL type info description
bin 585smallint unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 1978int unsigned range Start position in chromosome
chromEnd 2009int unsigned range End position in chromosome
name trfvarchar(255) values Simple Repeats tag name
period 2int unsigned range Length of repeat unit
copyNum 15.5float range Mean number of copies of repeat
consensusSize 2int unsigned range Length of consensus sequence
perMatch 100int unsigned range Percentage Match
perIndel 0int unsigned range Percentage Indel
score 62int unsigned range Score between and . Best is .
A 48int unsigned range Percent of A's in repeat unit
C 51int unsigned range Percent of C's in repeat unit
G 0int unsigned range Percent of G's in repeat unit
T 0int unsigned range Percent of T's in repeat unit
entropy 1float range Entropy
sequence CAlongblob   Sequence of repeat unit element

  Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585chr119782009trf215.521000624851001CA
585chr196259885trf1431.8144812326242429211.99GGAGAAGGAAATGGCAACCCACTCCAGTACTCTTGCCTAGAAAATCCCAGGGACGGAGGAGCCTAGAAGGCTGCAGTCCATGGGGTCACACAGAGTCGGACACAACTGAAGTGACTTCACTTTCACTT ...
585chr11344213558trf442.6449702145679261.59TTCAAGAAAAGTAAACATTTAAATTGATAACAAAATATAAGAAA
585chr11429714875trf5115.8567201914531491.25ATATT
585chr11429714914trf2344265252534631491.26AT
585chr11430114896trf784.4769172404631491.25TATATTA
585chr11436214896trf876.5826720794631491.25TATATTATATATATATATTATATATAATATACAATATATTTACATATTATTATATATATTATATATAATATATAATAATATA
585chr11641416956trf2292265201964322511.28AT
585chr11641616515trf372.7368091124623481.29ATATATAATATATTATATTAATATATTATGATATTA
585chr11654116869trf873.78977112794122541.24ATATATAATTATATATTTTATATATCATATATTTATTATATATTATATATTTATATATATATATATTTATATATTTAAATTATATATTT

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


  Simple Repeats (simpleRepeat) Track Description
 

Description

This track displays simple tandem repeats (possibly imperfect) located by Tandem Repeats Finder (TRF), which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases.

Methods

For more information about the TRF program, see Benson (1999).

Credits

TRF was written by Gary Benson.

References

Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80.