Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: mm39    Primary Table: simpleRepeat    Row Count: 1,641,063   Data last updated: 2020-07-27
Format description: Describes the Simple Tandem Repeats
fieldexampleSQL type description
bin 608smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 3054198int(10) unsigned Start position in chromosome
chromEnd 3054223int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 12int(10) unsigned Length of repeat unit
copyNum 2.1float Mean number of copies of repeat
consensusSize 12int(10) unsigned Length of consensus sequence
perMatch 100int(10) unsigned Percentage Match
perIndel 0int(10) unsigned Percentage Indel
score 50int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 24int(10) unsigned Percent of A's in repeat unit
C 16int(10) unsigned Percent of C's in repeat unit
G 0int(10) unsigned Percent of G's in repeat unit
T 60int(10) unsigned Percent of T's in repeat unit
entropy 1.36float Entropy
sequence TCTATATTCTATlongblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
608chr130541983054223trf122.11210005024160601.36TCTATATTCTAT
608chr130541983054253trf192.9198928521161601.45TCTATTTTCTATTCTATAT
608chr130548303054886trf228210001125050001AC
608chr130570453057070trf131.9131000508816681.38ACTTTGTTTTGTT
608chr130585543058617trf331.93390099301739121.87CTCAGCAGGAGGAATGGGGCAGCAGAAATTCAC
608chr130592873059356trf417.54783773016611.09AGGG
608chr130627293062771trf85.4888550142126381.91CTGTGATC
608chr130627293062774trf2322386063152026371.92CTGTGATCCTGAGATCCTGGATC
608chr130627373062775trf152.51683853152126361.93CTGTGATTCTGAGATC
608chr130633093063368trf2922987128610203661.36TCTTCCTTTCTATTTGTATTCTTTTCATT

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