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To realize both the single and the dual transmit antenna modes in TDS-OFDM systems based on flexible frequency binary padding, a novel channel estimation and equalization algorithm has been proposed in this paper. A low complexity implementation architecture for this algorithm is also designed. The pipeline structure is used here to meet the real-time processing requirement and to increase the resource efficiency. The resource analysis shows that the proposed scheme significant reduces the implementation complexity while the simulation results from the FPGA test shows it has good bit error ratio (BER) performance.