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As a primary way of data transmission in a large variety of cognitive radio systems, Non-Contiguous Orthogonal Frequency Division Multiplexing (NC- OFDM) is a specialized OFDM with non-contiguous sub-carriers. In general, an OFDM system is required to be strictly synchronized. However, one of the huge challenges is the synchronization for NC-OFDM because of the non-contiguous and unevenly distributed sub-carriers of uncertain number in the NC- OFDM. In this paper, we proposed an adaptive synchronization algorithm for NC-OFDM system. In the new scheme, the training sequence is produced adaptively from detected available sub-carriers, and timing metric for synchronization is determined by PN-modulation of the training sequence. The algorithm compensates the frequency offset due to the multi-path channel effect, and yields a single peak on timing metric. A satisfactory performance with regard to estimation on the timing and frequency offset, and to the bit error rate (BER) is shown by simulation.