This tool designes CAPS assays for two sequences. Two types of nucleotide inputs are accepted: fasta sequences and clustal aligment. It generates a list of polymorphic enzymes that cut the sequences into different length products. The user is allowed to input up to three sequences, however each time only two are analyzed.

1. Low quality nucleotides and "n"s at both ends of a sequence generate ambiguity. Please remove them from the input sequences.
2. Polymorphic digested fragments of too small sizes are hard to visualize on 1-4% agarose gel, thus not suitable for CAPS experiment. Please exclude some nucleotides (for example 20) at both ends to avoid the problem.