Comparison between the experimentally observed fluorescent signals and the calculated affinities. Symbols: feature block 1, blue upward-pointing triangles; feature block 2, cyan circles; feature block 3, green downward-pointing triangles; feature block 4, magenta squares; average of the feature block signals, solid black line; prediction, solid red line. a) The predicted and experimentally obtained hybridization signals as a function of loop length for one specific loop position. PM signal is set to 1. b) The dependence of the theoretical and experimental hybridization signals on loop position for one specific loop length. PM signal is set to 1. The figures to the right in a) and b) show the experimental average (black) with 95% confidence intervals and the predicted signals (red). The experimentally observed hybridization signals are reproduced well by our theory.