Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: rn6    Primary Table: simpleRepeat    Row Count: 1,620,303   Data last updated: 2014-07-07
Format description: Describes the Simple Tandem Repeats
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 479int(10) unsigned Start position in chromosome
chromEnd 510int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 12int(10) unsigned Length of repeat unit
copyNum 2.6float Mean number of copies of repeat
consensusSize 12int(10) unsigned Length of consensus sequence
perMatch 94int(10) unsigned Percentage Match
perIndel 0int(10) unsigned Percentage Indel
score 53int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 48int(10) unsigned Percent of A's in repeat unit
C 25int(10) unsigned Percent of C's in repeat unit
G 6int(10) unsigned Percent of G's in repeat unit
T 19int(10) unsigned Percent of T's in repeat unit
entropy 1.72float Entropy
sequence ACATACATGCAAlongblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585chr1479510trf122.6129405348256191.72ACATACATGCAA
585chr132263251trf46.2410005002424521.48TGTC
585chr134993538trf162.5158415534653001ACACACACCACACAC
585chr135383599trf230.52866884944501.23AG
585chr157645815trf225.5210001025000491AT
585chr11240313313trf8410.884776634381818251.93TGTGGTAAAGCCTTTGCACATCATAGTCATCTCCAAAGACATAAAAGAATACATACTGGAGAGAAACTCTACGAATGTAATCAA
585chr11240313252trf3362.5336822992381818251.93TGTGGTAAAGCCTTTGCATCTCATAGTTATCTCCAAGTACATAAAAGAATACATACTGGAGAGAAGCTCTATGAATGTAAGCAATGTGGTAAAGCCTTTACATCTCATAATCATCTTCAAAGTCATGA ...
585chr12949929534trf181.918100070401125221.88AAGAATTCATAGCTGAGG
585chr13511535141trf122.212100052070920.39TTCTTTTTTTTT
585chr13569635740trf22222100088222227271.99TGTGAGGAGCTGTCCTCACATA

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 repeats) 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. PMID: 9862982; PMC: PMC148217