Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: DgriCAF1    Primary Table: simpleRepeat    Row Count: 140,990   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom scaffold_1varchar(255) values
chromStart 0int(10) unsigned range
chromEnd 2759int(10) unsigned range
name TTTCAAAACTAATCGGvarchar(255) values
period 755int(10) unsigned range
copyNum 3.7float range
consensusSize 745int(10) unsigned range
perMatch 93int(10) unsigned range
perIndel 3int(10) unsigned range
score 4628int(10) unsigned range
A 31int(10) unsigned range
C 20int(10) unsigned range
G 17int(10) unsigned range
T 29int(10) unsigned range
entropy 1.96float range
sequence TTTCAAAACTAATCGGATTTTGTGCAA...longblob  

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585scaffold_102759TTTCAAAACTAATCGG7553.77459334628312017291.96TTTCAAAACTAATCGGATTTTGTGCAAAAGCAAGACGAGCGCTTCAGGAGGCACGGTGGGATCAAAAAGTGGTCATATACAAACTACATTTTTCGATTGTACAACAAAATCTAAATGTAAGTTACCAC ...
585scaffold_102759TTTCAAAACTAATCGG7533.77459334567312017291.96TTTCAAAACTAATCGGATTTTGTGCAAAAGCAAGACGAGCGCTTCAGGAGGCACGGTGGGATCAAAAAGTGGTCATATACAAACTACATTTTTCGATTGTACAACAAAATCTAAATGTAAGTTACCAC ...
585scaffold_1255324CA234.5210001384950001CA
585scaffold_19841075CA245.529101464650121.2CA
585scaffold_117391799CA23029301024848111.21CA
585scaffold_124922540CA2242950875047021.12CA
585scaffold_1002249TGTCTCTTTTATTTTT7283.17289433887301817321.95TGTCTCTTTTATTTTTAATTACTCATCTTTATGTTTTAGCTTGGAAAATGCGACAAGAGAAAACACGTATTTAAGAGAACATCACTATAAGCGGACATGGACATTTTCAAAACTAATCGGATTTTGTG ...
585scaffold_10347398CA225.52950934949011.12CA
585scaffold_1010751126CA225.52950934949011.12CA
585scaffold_1000350501AAAATTAAGATTCAAA592.5598832146657191.38AAAATTAAGATTCAAAAATATTAAAATTAAGAAAACCAAAAAAGGAAAAAAATAAACAA

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