Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: galVar1    Primary Table: simpleRepeat    Row Count: 854,441   Data last updated: 2016-03-02
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 NW_007726111v1varchar(255) Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned Start position in chromosome
chromEnd 1953int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 32int(10) unsigned Length of repeat unit
copyNum 61.1float Mean number of copies of repeat
consensusSize 32int(10) unsigned Length of consensus sequence
perMatch 79int(10) unsigned Percentage Match
perIndel 2int(10) unsigned Percentage Indel
score 1879int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 38int(10) unsigned Percent of A's in repeat unit
C 26int(10) unsigned Percent of C's in repeat unit
G 12int(10) unsigned Percent of G's in repeat unit
T 22int(10) unsigned Percent of T's in repeat unit
entropy 1.9float Entropy
sequence CTCATCGATCTAAGTAAACTCATCAGA...longblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585NW_007726111v101953trf3261.1327921879382612221.9CTCATCGATCTAAGTAAACTCATCAGACCAAG
585NW_007726111v1531621trf302.930853108412612201.87CATCAGACCAAGCACATAGATCTAAGTACA
585NW_007726111v154245755trf3210.332755222392312231.9GCTCATCGATCAAAGTAAACTCATCAGACCAA
585NW_007726111v154245642trf962.396844262412312221.88GCTCATAGATCTAAGTAAACTCATCAGAGCAAGCAAATCCATCAAAGTAAACTCATCAGACCAAGATCATAAATCAAAGTAAACTCATCAGAACAA
585NW_007726111v154315755trf645.164728255402312231.89GATCTAAGTAAACTCATCAGACAAAGCTCATCGATCTAAGTAAACTCATCAGACCAAGCTAATA
585NW_007726111v172688022trf3223.632804749442313191.86GGAAAACTAATCAGACCAAGCTAATCGATCTA
585NW_007726111v11026010296trf182188910560160830.65CTTTCTTTCTTTTTTTTT
585NW_007726111v11207112110trf172.218904620217790.84TTTTGTTTGTGTGTTTTC
585NW_007726111v11891218973trf154.1158208626319501.63TGATTAGTATAGTTT
585NW_007726111v11982319856trf132.61390450909000.44AAAAACAAAAAAA

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