Abstract: A visual interface that allows a user to designate intuitively a two-dimensional sequence suitable for a target sequence for a functional nucleic acid is provided. Secondary structure data of a target mRNA is displayed on a screen, and various information such as characteristic sequences to be effectively influenced by the functional nucleic acid, binding sites for protein motifs, and UTRs are displayed on the secondary structure. A target site of the functional nucleic acid is designated by the user with a pointing device, and the intuitive determination of a most suitable sequence is supported by repeating the design of the functional nucleic acid.