In a MIMO-OFDMA system, carrier interferometry multiplexed (CIM) signals with the discrete Fourier transform based channel estimation (CIM/DFT-CE) have been proposed. Using CIM/DFT-CE, high channel estimation accuracy is realized with a small number of symbols under ideal conditions. In this paper we indicate that the channel estimation accuracy of the sub-channel at the edge in the active band is significantly degraded under real conditions. To improve this degradation, we propose a new virtual sub-carrier allocation method, taking the periodic property of the CIM signals in the receiver into consideration. We use computer simulation to demonstrate that the channel estimation accuracy of the sub-channel at the edge is improved by the proposed method under real conditions.