msatcommander

If you're looking for a powerful tool to locate microsatellite repeats within fasta-formatted sequence or consensus files, look no further than msatcommander. This Python program is specifically designed to make finding SSR or VNTR repeats easy and efficient, with the ability to search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats. What's more, you can even customize your search by selecting fewer repeat types or combinations of repeat types.

One of msatcommander's biggest advantages is its ability to tag and design primers using primer3 as its primer design engine. This makes primer design a breeze, saving you time and effort. The program is also capable of searching for all mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats, and these repeats can be combined across user-specified distances in bp.

With msatcommander, you can be sure you're getting the best possible primers for your search, as the program tags and tests primers using m13R, CAG, or a custom tag, and reports the best primer to the user. If you're new to the world of SSR and VNTR repeats, you'll appreciate the convenient GUI that the program offers, making it easy to use for a majority of users.

Finally, msatcommander outputs its results in csv format, making it easy to import and analyze data in spreadsheet software. If you're looking for a software tool that streamlines the process of finding and designing primers for microsatellite repeats, msatcommander is definitely worth a closer look.