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An ultrafast tool for genome-wide survey of microsatellites and primer design
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Krait: Microsatellite investigation and primer design

Table of Contents


Krait is a robust and ultrafast tool with a user-friendly graphic interface for genome-wide investigation of microsatellites, which attempts to overcome the limitations of the currently available tools. Krait is written in Python and can be run as a standalone desktop application on Windows, Linux or Mac systems without dependencies. The microsatellite search engine is written in C and compiled as Python modules for import into Krait


  • Identification of perfect SSRs, imperfect SSRs (iSSRs), compound SSRs (cSSRs) and VNTRs from extremely large genome
  • Locating the SSRs in gene coding region
  • Design primer for microsatellite
  • Statistical analysis and plotting
  • Supporting gzip compressed fasta as input file
  • Supporting export FASTA, GFF3 or CSV
  • Downloading DNA sequence from NCBI database




Du L, Zhang C, Liu Q, Zhang X, Yue B (2018) Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics. 34(4):681-683. 10.1093/bioinformatics/btx665

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