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Biological sequence alignment is an extremely important task in the field of computational biology. This paper presents an FPGA based solution which exploits the multiple granularities of hardware parallelism available in a high- performance reconfigurable computer system. Thus, multiple cores are implemented per chip and system level parallelism is achieved via message passing. The design was developed in VHDL, with the message passing interface (MPI) providing for system level parallelism and implemented on both the Cray XD1 and SRC systems. The results will show order of magnitude speed up when compared with modern microprocessors. The study is also used to provide some insight into the architectural issues associated with modern high-performance reconfigurable computers.