Precise analysis of the genetic network, gene function and transcription regulation requires accurate prediction of transcription factor (TF) bindability on DNA. For calculating the matching score between an input sequence and a set of known TF binding sites, we use positional weight matrices (PWMs) and Buchers calculating method (Bucher, J. Mol. Biol., 212, 563-578, 1990). Since estimating TF binding sites requires cut-off values, we propose a robust cut-off value determining algorithm.