Pairing Probabilities Plot
The numbering of the dot plot begins at the top left corner. Numbers on the axes of the dot plot correspond to the numbers of nucleotides in the sequence being depicted. Points on the plot represent individual base pairs. The bottom left triangle shows only the base pairs that are present in the MFE structure of the sequence under consideration (which may differ from the target structure). The top right triangle shows the base pairs predicted to form. The darker the point, the more likely the pair is to form. An "ideal" dot plot is a mirror image, reflected along the diagonal.
The dot plot can provide insight into the range of structures that a sequence could potentially form. Stacks appear as diagonal rows of dots. In an ideal dot plot, the bottom left triangle (desired pairings) and top right triangle (predicted pairings) are identical. A "good" dot plot does not guarantee successful folding. The calculations used to predict pairing probabilities are based on the free energy calculated for an RNA. Poor designs with extremely low in free energy, such as christmas trees, may appear to have "good" dot plots. Extremely messy dot plots, however, do reliably predict low synthesis scores.
Example 1: A Moderately "Messy" Dot Plot
|In this dot plot, the bottom left and top right triangles differ considerably. This suggests that the RNA in question can form multiple structures that are close in energy.
Example 2: A "clean" Dot Plot
In this dot plot, both triangles are very similar. This suggests that the minimum free energy structure of the RNA is not surrounded by many other structures of comparable energy.