Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: canFam3    Primary Table: simpleRepeat    Row Count: 984,325   Data last updated: 2012-01-06
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 100int(10) unsigned Start position in chromosome
chromEnd 11540int(10) unsigned End position in chromosome
name trfvarchar(255) Simple Repeats tag name
period 1474int(10) unsigned Length of repeat unit
copyNum 7.8float Mean number of copies of repeat
consensusSize 1475int(10) unsigned Length of consensus sequence
perMatch 90int(10) unsigned Percentage Match
perIndel 2int(10) unsigned Percentage Indel
score 15661int(10) unsigned Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A 24int(10) unsigned Percent of A's in repeat unit
C 25int(10) unsigned Percent of C's in repeat unit
G 24int(10) unsigned Percent of G's in repeat unit
T 25int(10) unsigned Percent of T's in repeat unit
entropy 2float Entropy
sequence TATGTGAGAAGGTAGCTGAACGCCTTG...longblob Sequence of repeat unit element

Sample Rows
 
binchromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
585chr110011540trf14747.8147590215661242524252TATGTGAGAAGGTAGCTGAACGCCTTGTCCAAAATCATCTTACTGCTGAGAGTTGAGCTCACCCTCAGTCCCTCACAGTTCCACACTGCCTGCAGAGTGAGTTTCCCACGTCTTCACCAGAGACGTTT ...
585chr110311541trf73815.573891115574242524252GTGAGAAGGTAGTTGAACGCCTTGTCCAAAATCATCTTACTTCTGAGAGTTGAGCTCACCCTCAGTCCCTCACAGTTCCACACTGCCTGCAGAGTGAGTTTCGCACGTCTTCACCAGAGACGTTTGCC ...
585chr11163611663trf213.521000544805101GA
585chr11350113532trf74.47910538312300.75AAAAACA
585chr11368413762trf272.82882988125714151.65CCCCCATGTCCCCTCCCACCCAGGCTGA
585chr11468414791trf273.92870127821592151.49CCCCACACCATCCCCCTCACACCATCAC
585chr11471314791trf145.61377106624572151.51CCACACCATCCCC
585chr11750717544trf152.515864581800810.7ATTTATTTTATTTTT
585chr11750817544trf103.89927541600830.65TTTATTTTT
585chr12001620294trf2511.225832319213719201.94CCTCCTTACAGATGAGGACCCCCGT

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