The tall letters represent the highly conserved bases in DNA binding sites of several prokaryotic repressors and activators. Conservation is strongest where major grooves of the double helical DNA (represented by crests of a cosine wave) face the protein. This shows that conservation analysis alone can be used to predict the face of DNA that contacts the proteins.
Papp.Schneider1993 P. P. Papp D. K. Chattoraj, and T. D. Schneider. J. Mol. Biol. 233:219-230, 1993.