It has been observed by many researchers that the protein coding regions of DNA exhibit a period-3 behavior due to the codon structure. The period-3 property is not present outside coding regions, and can be exploited to locate coding regions. For eukaryotes (cells with nucleus) this periodicity has mostly been observed within the exons and not within the introns. Previously binary indicator sequence and electron-ion interaction pseudo potentials (EIIP) indicator sequence has been used for the identification of the coding regions. In this paper we observed that complex indicator sequence provides strong spectral component compared to EIIP indicator sequence. We also observed that windowed DFT taking complex indicator sequence provides better exon prediction compared to windowed DFT taking EIIP indicator sequence and digital filters methods. Computational overhead is reduced by 75% in complex indicator sequence compared to binary indicator sequence. There is maximum discrimination between coding and non coding regions in complex indicator sequence.