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Total least square linear prediction has been successfully applied to frequency estimation for closely spaced sinusoids. In low signal to noise ratio, the resolving ability of TLS is degraded and extraneous roots of the predictor are close to unit circle. Hence the performance of total least square is severely degraded in low SNR. In this paper, a generalized total least squares method with a new root selection criterion, which is based on the envelope of the signal spectrum, is presented. An optimum procedure is introduced to provide a TLS solution that can perform closer to Cramer-Rao bound, particularly in low SNR.