Krait - online tool for microsatellite identification

Select a genome

Kingdom

Group

Subgroup

Species

Or input your DNA sequenceexample

Only support for fasta formatted sequence (size < 2.5M)

Or upload fasta file

Choose file Support for gzipped fasta file (size < 100M)

Or provide a URL for fasta formatted fileexample

Support for gzipped fasta

Search for

Perfect SSRs

Compound SSRs

Imperfect SSRs

Perfect and Compound: (Minimum tandem repeats)

Mono

Tri

Tetra

Penta

Hexa

Max distance allowed between two SSRs

Imperfect:

Min seed repeats

Min seed length

Max consecutive edits

Mismatch penalty

Gap penalty

Min score

Flanking sequence length Motif standardization

Input
Mode
Parameters

Email Message for task completed (optional)

The offline version with a user-friendly GUI can be downloaded from https://github.com/lmdu/krait

Reference

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