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An MMSE per channel fractionally spaced equalizer is developed for an OFDM/OQAM system with a time varying channel, under the assumption of perfect channel knowledge at the receiver. The equalizer is analyzed for an example with a doubly dispersive channel with Jakes Doppler spectrum and an exponential delay profile, and where the transmitter and receiver filters are square root of cosine rolloff. The performance is measured in terms of ergodic channel capacity, which will be an upper bound for the throughput of the system, assuming perfect channel estimation and ideal channel coding. The results show that the channel capacity may be significantly increased by using an equalizer of finite length, instead of a one-tap equalizer. The channel capacity is for instance increased by 60% for Es/N0 = 20 dB in a channel with spreading factor 0.01.