Figure 3

The detailed interface. This demonstrates that pknots was used to compute an MFE of -23.7 kcal/mol for the 100 bases following the AAAAAU slippery site at position 1653 of the EST2 gene. When randomized 100 times using Fisher-Yates shuffling, a mean MFE of -17.4 kcal/mol was computed for a normal distribution of correlation coefficient 0.9627. The MFE distribution of the randomized sequences is on the right; with the idealized normal distribution in red. The black vertical line marks the mean MFE of the randomized sequences, and the green vertical line marks the MFE of the native sequence. This secondary structure is significantly more stable than random (z score = -2.10). The predicted mRNA secondary structure of this sequence is shown below using both bracket notation, and using a Feynman diagram.