This tool designs CAPS assays for up to 12 sequences. Two types of nucleotide inputs are accepted: fasta sequences and clustal alignment. It generates a list of polymorphic enzymes that cut the sequences into different length products.

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.