Difference dot Plot of native and mutated secondary structure of a 3 GU mutation of the CXCR4 siRNA gene. The red part on the right hand side shows the base pairing probability of the 5' part of the micro RNA, which is 80% higher in the native structure. This is an alternative explanation for the missing function of the mutant. Because of the mutations, the stack a little to the left gets more stable, and the probability of binding of the 5' end of the siRNA is reduced significantly.The color of the dots encodes the difference of the pair probabilities in the two molecules such positive (red) squares denote pairs more more probable in the second molecule (see color bar). The area of the dots is proportional to the larger of the two pair probabilities.