Schema for Microsatellite - Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
  Database: ornAna1    Primary Table: microsat    Row Count: 9,136   Data last updated: 2015-05-22
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 Contig100008varchar(255) values Reference sequence chromosome or scaffold
chromStart 579int(10) unsigned range Start position in chromosome
chromEnd 610int(10) unsigned range End position in chromosome
name 15xGTvarchar(255) values Name of item

Sample Rows
 
binchromchromStartchromEndname
585Contig10000857961015xGT
585Contig100091377141117xGA
585Contig10015492596118xTG
585Contig10030255162555921xCA
585Contig100589887992418xCA
585Contig10058134661349916xCA
585Contig100666954698616xTA
585Contig1006911056109821xTG
586Contig100717138117141919xGT
585Contig10086126171264815xGT

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