Schema for Microsatellite - Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
  Database: tupBel1    Primary Table: microsat    Row Count: 74,985   Data last updated: 2015-05-23
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom scaffold_100.1-123220varchar(255) values Reference sequence chromosome or scaffold
chromStart 64287int(10) unsigned range Start position in chromosome
chromEnd 64324int(10) unsigned range End position in chromosome
name 18xTGvarchar(255) values Name of item

Sample Rows
 
binchromchromStartchromEndname
585scaffold_100.1-123220642876432418xTG
585scaffold_100.1-123220962899632819xAC
585scaffold_10000.1-92493789337897722xGT
585scaffold_100000.1-43693188322719xAG
585scaffold_100006.1-12978119861202720xGT
585scaffold_10001.1-144433566255665917xGA
586scaffold_10001.1-14443314332714336519xGA
585scaffold_100010.1-181275465549515xCA
585scaffold_100010.1-18127100261006218xTG
585scaffold_10002.1-132336898538989420xTA

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Microsatellite (microsat) Track Description
 

Description

This track displays regions that are likely to be useful as microsatellite markers. These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats and tend to be highly polymorphic in the population.

Methods

The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. The Simple Repeats track is created using the Tandem Repeats Finder. For more information about this program, see Benson (1999).

Credits

Tandem Repeats Finder 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