REPPER - Detecting regions with short gapless REPeats in protein sequences
It finds PERiodicities by Fourier Transform (FTwin) and internal homology analysis (REPwin). The exact locations of the periodic patterns are traced by a sliding window. The output is complemented by coiled coil prediction (COILS) and optionally by secondary structure prediction according to Jones (PSIPRED).
M.Gruber, J.Söding, and A.N.Lupas (2005) REPPER - repeats and their periodicities in fibrous proteins Nucl. Acids Res., 33(2), W239-43 FREE PDF