Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: tupBel1    Primary Table: simpleRepeat    Row Count: 719,680   Data last updated: 2008-10-15
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 scaffold_0.1-13376varchar(255) Reference sequence chromosome or scaffold
chromStart 68int(10) unsigned Start position in chromosome
chromEnd 108int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 14int(10) unsigned Length of repeat unit
copyNum 2.8float Mean number of copies of repeat
consensusSize 14int(10) unsigned Length of consensus sequence
perMatch 88int(10) unsigned Percentage Match
perIndel 3int(10) unsigned Percentage Indel
score 53int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 70int(10) unsigned Percent of A's in repeat unit
C 2int(10) unsigned Percent of C's in repeat unit
G 2int(10) unsigned Percent of G's in repeat unit
T 25int(10) unsigned Percent of T's in repeat unit
entropy 1.13float Entropy
sequence TAAAATAAAAAAGTlongblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585scaffold_0.1-1337668108trf142.814883537022251.13TAAAATAAAAAAGT
585scaffold_0.1-1337612901341trf412.8410001027600230.79AAAT
585scaffold_0.1-1337639033933trf47.541000602600730.84TATT
585scaffold_1.1-51135586700trf502.350863149112640211.87GGGCTGCCCCATGGACGTTGGCAGGGGCTACTGCCCCATGGACGTTAGTG
585scaffold_1.1-51135586902trf1222.6123883438112441221.86GGGCTGCCCCATGGATGTTGGCGGGGGCTGCTGCCCGTGGACGTTAGTGGGGCTGCCCGATGGACGTTGGCAGGGGCTACTGCCTCATGGATGTTAGTGGGGCTGCGCCCATGGACATTAGCG
585scaffold_1.1-51135588643trf272.1268637492941201.82GCTGCCCCGTAGACGTTAGCGGGGCT
585scaffold_1.1-51135615843trf733.172825235102540231.87GCTGCCCCGTGGACGTTAGCGGGGCTGCCCCATGGATGTTGGCAGGGGCTACTGCCCATGGACATTAGTGGG
585scaffold_1.1-51135624999trf2415.324691397102242241.85TGGACGTTGGTGGGGGCTGTCCCA
585scaffold_1.1-511356851001trf496.547749204102243231.84GGGGCTGCCCCATGGACGTTAGTGGGGCTGCCCCGTGGATGTTGGCG
585scaffold_1.1-51135732989trf733.57583729492243231.83GGGGCTGCTGCCCGTGGACATTAGTGGGGCTGCCCGATGGATGTTGGCAGGGGCTGCTGCCTCGTGGACGTTAGT

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