Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: wuhCor1    Primary Table: simpleRepeat    Row Count: 1   Data last updated: 2020-01-29
Format description: Describes the Simple Tandem Repeats
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom NC_045512v2varchar(255) values Reference sequence chromosome or scaffold
chromStart 29870int(10) unsigned range Start position in chromosome
chromEnd 29903int(10) unsigned range End position in chromosome
name trfvarchar(255) values Simple Repeats tag name
period 1int(10) unsigned range Length of repeat unit
copyNum 33float range Mean number of copies of repeat
consensusSize 1int(10) unsigned range Length of consensus sequence
perMatch 100int(10) unsigned range Percentage Match
perIndel 0int(10) unsigned range Percentage Indel
score 66int(10) unsigned range Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 100int(10) unsigned range Percent of A's in repeat unit
C 0int(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 0float range Entropy
sequence Alongblob   Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585NC_045512v22987029903trf13311000661000000A

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