An exemplary object of the present invention is to provide method, predictor and predicting program for predicting secondary structure of nucleic acid sequence capable of evaluating not only overall similarity and but also localized similarity of secondary structure of nucleic acid sequence. A method according to an exemplary aspect of the present invention includes the steps of: extracting a structural element of the secondary structure from the secondary structure of the nucleic acid sequence; and evaluating a similarity of each structural element of the nucleic acid sequence as a subject, based on a feature vector of the structural element.