Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 2583–2585.

Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106 (3): 411-422

Version info: 

v2.1, 2020-08-25



Usage & parameter (6 steps):

1. Enter your email address: After submitting your query sequence the process is send to our server and results will be provided via mail.
2. Paste your sequence or upload FASTA file: Query sequence need to be in FASTA format
3. Enter project name (optional): If you wish to tag your results with a project name set this option.
4. Set SSR search parameters: Fill in the lengths of your desired motifs and a minimal repeat number, separated by a ‘-’, e.g.: 2-5 (dinucleotide microsatellite with at least 5 repetitions). Each pair of motif and repeat number is separated by a blank space, e.g.: 1-6 2-5 3-8
5. Set compound SSR search parameters: Set the maximum number of bases between two distinct SSRs in order to classify compound microsatellites.
6. Set output file parameter: If you prefer to receive the results in GFF3 format mark the box titled GFF otherwise results will be provided in .misa format (see output).