Schema for Microsatellite - Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
  Database: cavPor3    Primary Table: microsat    Row Count: 71,414   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_0varchar(255) values Reference sequence chromosome or scaffold
chromStart 87914int(10) unsigned range Start position in chromosome
chromEnd 87956int(10) unsigned range End position in chromosome
name 21xTGvarchar(255) values Name of item

Sample Rows
 
binchromchromStartchromEndname
585scaffold_0879148795621xTG
585scaffold_010745510749419xAC
585scaffold_012467512471319xCA
586scaffold_016876416881425xAC
586scaffold_017505117509120xAT
586scaffold_021591921596824xTC
586scaffold_024082724086720xAT
586scaffold_024361924364915xAT
587scaffold_027964027967417xAT
587scaffold_028206528210922xGT

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