Update Alert

This is an old version of the database which is not maintained anymore. A newer version with more data and features is now available at https://data.ccmb.res.in/msdb. If you are not redirected to the new site in 10 seconds, click here.


MicroSatellite DataBase (MSDB) is a collection of simple sequence repeats (SSRs), also known as microsatellites. SSRs are short tandem repeats of 1 to 6 base long motifs present in all genomes, particularly in Eukaryotes. Many studies have pointed to the role of SSRs in gene regulation, and have shown that SSRs can act as transcription factor binding sites, enhancer-blockers, insulators etc., making them an interesting class of DNA elements to study. MSDB aims to be the go-to resource for both accessing as well as visualizing SSR-related information.

Currently, MSDB has information of 6,893 species belonging to various Kingdoms, as outlined below:

Kingdom or Group Number of species
Archaea 514
Bacteria 5732
Plants 74
Fungi 191
Protozoa 72
Invertebrates 112
Vertebrates 198

Quick links to commonly studied species

Species name Common name Genome Size Total number of SSRs Genome covered(%)
Homo sapiens Human 3236.34MB 4585519 2.13%
Mus musculus Mouse 2807.72MB 5194607 3.38%
Rattus norvegicus Rat 2616.42MB 4232429 2.88%
Gallus gallus Chicken 1230.26MB 1698863 2.17%
Danio rerio Zebrafish 1371.1MB 2937095 4.23%
Drosophila melanogaster Fruitfly 143.73MB 263465 2.58%
Caenorhabditis elegans Worm 100.29MB 100997 1.49%
Saccharomyces cerevisiae Yeast 12.16MB 12073 1.38%

Change Log


  • Added species summary tab in view.
  • Added quick links from home page to view for commonly studies species.
  • [0.2.1]

  • Bugfixes and changes in the explore tab.
  • Show genomic sequence when clicked on a repeat entry, in explore table.
  • [0.2.0]

  • Created microsatellite database version 2.0 with updated and new genomes.
  • View & Compare tab- Option to download the plot.
  • Option to merge plots based on repeat type on compare tab.
  • [0.1.3]

  • Downloads optimization, explore optimization and plot display changes.
  • Changed - Line and stacked plot merged in view & compare tabs.
  • Optimized - Downloads tab
  • Options to make the plots more interactive.
  • Column filters to explore tab.
  • Column hiding feature on explore tab.
  • Export as csv feature on explore tab.
  • Reset filter on explore tab.

  • [0.1.2]

  • Download tab- To direct download repeats data for specific organisms.
  • Compare tab- To compare plots among different organisms.
  • [0.1.1]

  • Created microsatellite database.
  • View tab- To visualise repeat data through different kinds of plots.
  • Explore tab- Tabular view of repeats data for an organism.

  • For queries or suggestions please contact: