MutaPrimer is a free desktop tool for Windows to design mutagenic primers for Stratagene's QuikChange® site directed mutagenesis kits. You can add the mutant information to the sequence and then design primers with a single click. The powerful search algorithm searches for all possible primers that meet the design criteria within the allowed length and positional boundaries. They are checked for all possible secondary structures such as dimers, hairpin, repeats and runs, and rejected if they fail to meet the specified criteria. It then reports the best mutagenic primers with upto fifty alternative designs.

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