Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: danRer11    Primary Table: simpleRepeat    Row Count: 1,077,677   Data last updated: 2017-06-02
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 chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 6480int(10) unsigned Start position in chromosome
chromEnd 6509int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 3int(10) unsigned Length of repeat unit
copyNum 9.7float Mean number of copies of repeat
consensusSize 3int(10) unsigned Length of consensus sequence
perMatch 100int(10) unsigned Percentage Match
perIndel 0int(10) unsigned Percentage Indel
score 58int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 68int(10) unsigned Percent of A's in repeat unit
C 31int(10) unsigned Percent of C's in repeat unit
G 0int(10) unsigned Percent of G's in repeat unit
T 0int(10) unsigned Percent of T's in repeat unit
entropy 0.89float Entropy
sequence AAClongblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585chr164806509trf39.731000586831000.89AAC
585chr168116856trf222.521000905104801AG
585chr170067048trf22121000845050001CA
585chr175907709trf148.81481710233481601.52GCACACACACGCAC
585chr175917670trf419.849206836501201.41CACA
585chr175917719trf1012.8107969834481511.55CACACACGCA
585chr175937682trf185.11887410133501501.45CACACACACGCACGCACG
585chr176137699trf184.6186785529502001.49CACACACACGCGCACGCG
585chr176217682trf416.2480137626502201.49CACG
585chr179748033trf229.5210001180050491GT

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