Present DNA sequence alignment algorithms based on dynamic programming have a high time complexity. This paper introduce a global alignment system to address this problem.The system aligns sequences in FPGA and store sequences and aligning results in PC memory. The system also send commands to FPGA.The experiment results show compared to Needleman algorithm, the aligning time decreases by 58 when the sequences have a low similarity,and by 94 when the sequences have a high similarity.