The biologists have proven that the function of transcription factor is to control gene expression and also gene sequence mutation. In several well-known DNA regulatory sequences, most of them have characteristic of consensus sequence; therefore, searching for motif interests biologists evermore. A great deal of numerous methods to predict motif patterns were published in the past, and among all the factors, the length of motif is absolutely critical in motif prediction. The purpose of this thesis is to predict possible motif lengths based on the method of Fast Fourier Transform (FFT). Simulation and known oncogene sequences are both used to verify the effectiveness of the proposed method. The results show that our method would improve the performance and accuracy of motif prediction algorithm significantly.