Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: cerSim1    Primary Table: simpleRepeat    Row Count: 414,296   Data last updated: 2012-08-28
Format description: Describes the Simple Tandem Repeats
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom AKZM01053786varchar(255) values Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned range Start position in chromosome
chromEnd 35int(10) unsigned range End position in chromosome
name trfvarchar(255) values Simple Repeats tag name
period 2int(10) unsigned range Length of repeat unit
copyNum 17.5float range Mean number of copies of repeat
consensusSize 2int(10) unsigned range Length of consensus sequence
perMatch 100int(10) unsigned range Percentage Match
perIndel 0int(10) unsigned range Percentage Indel
score 70int(10) unsigned range Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 48int(10) unsigned range Percent of A's in repeat unit
C 51int(10) unsigned range Percent of C's in repeat unit
G 0int(10) unsigned range Percent of G's in repeat unit
T 0int(10) unsigned range Percent of T's in repeat unit
entropy 1float range Entropy
sequence CAlongblob   Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585AKZM01053786035trf217.521000704851001CA
585AKZM0105378615331567trf4948712547300260.83AATA
585AKZM0105378615341563trf142.1141000587200270.85ATAAATAAATAAAT
585AKZM0105378679548007trf252.125100010630227391.82TTTTGCTACAGCAACTATTACATCA
585AKZM010537861457714627trf222.2238210594622501.24TAATTTCTAAAATAAATTAATAT
585AKZM010537861500815046trf201.9208410516022341.24TATTATAAATAACAAATAAG
585AKZM010537861573315803trf342.134100014028273581.86GCAGGTCACATCCCAGAGAGCAGATGGAGCGGCA
585AKZM010537865085250878trf122.21210005230307301.85TTACATACCAGC
585AKZM010537866342063454trf103.698514501102850.71TTTTTTATT
585AKZM010541281227412299trf131.9131000502000800.72TTTATTTTATTTA

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