Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: rn4    Primary Table: simpleRepeat    Row Count: 1,028,946   Data last updated: 2006-01-30
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 3874int(10) unsigned Start position in chromosome
chromEnd 3925int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 2int(10) unsigned Length of repeat unit
copyNum 25.5float Mean number of copies of repeat
consensusSize 2int(10) unsigned Length of consensus sequence
perMatch 83int(10) unsigned Percentage Match
perIndel 0int(10) unsigned Percentage Indel
score 66int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 45int(10) unsigned Percent of A's in repeat unit
C 1int(10) unsigned Percent of C's in repeat unit
G 5int(10) unsigned Percent of G's in repeat unit
T 47int(10) unsigned Percent of T's in repeat unit
entropy 1.38float Entropy
sequence ATlongblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585chr138743925trf225.52830664515471.38AT
585chr161936231trf142.714870583955501.48TATATATTATTACA
585chr186668751trf242.529501525247001AC
585chr11213812207trf234.52765684440501.42TG
585chr11460614673trf233.52765644440501.43TG
585chr13125031376trf661.966910207131818501.79TGTTTTCCTGGAATTCTTTCAGGGATTTTTGCGACTCCTCTCTATAGGCTTCTACTTGTTTATTTA
585chr14822448301trf612.568257349180321.48TATACA
585chr14826948312trf221.52850594842441.36AT
585chr16359163626trf311.731000700031680.9TTG
585chr17576175808trf223.52820584426461.4AT

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