We develop an application for the analysis and management of data generated by Quadruple 9-mer-based Protein Binding Microarray (Q9-PBM) technology. It consists of three major modules such as those to store and to analyze Q9-PBM data and one to present the analyzed data in a web application. The data is integrated in a PostgreSQL DBMS. The analysis program for a web-based application consists of three parts; overall consensus logo, k-mer analysis and position mutation effect analysis. The overall consensus logo is implemented with the highest 9mer_based group probe sequences whose median were higher than cutoff intensity. The overall consensus logo was obtained by multiple alignments of the significant sequences with ClustalW and visualized with SeqLogo program. The k-mer analyses provide all possible sequence variants of k-mer data. It visualizes the number of, intensity mean and sequence logo of each k-mer data. The position mutation effect analysis shows the mutational effect on the binding intensities in the consensus binding motif and graphical position effect chart of DNA motif. The application is implemented as a web-based and includes a function to detect position mutation effect in real-time so that a user get the result instantaneously.