We present a DNA sequence analyzing system for a cellular slime mold called Dictyostelium discoideum. The upstream sequences may include cis-elements which are involved in the temporal and spatial regulation of transcription. Our goal is to identify the cis-elements with statistic methods. For this purpose, we have developed a distributed system. Its main components are an alignment program based on dynamic programming which estimates candidates for cis-elements on upstream sequences, and a statistical analyzer which checks if the candidate elements have a statistical property. The system supports SOAP and the components can be deployed and collaborate on the web. In this paper, we mainly discuss the system architecture and evaluate its efficiency.