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Content-based copy detection (CBCD) is more and more important in the field of information security, assurance, copyright protection etc. The sequences matching, one of the key technologies in CBCD, is very critical for querying quickly and accurately. In this paper, we propose a novel fingerprint sequences matching algorithm based on the dynamic programming. This method is universal to all kinds of fingerprint sequences matching. We examined this method with experiments at last in this paper. The experimental results demonstrate it's effective in sequences matching.