G-test:16	$\text{GT}(i,j)=2{\sum }_{a,b}{\text{Obs}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}\text{log}\frac{{\text{Obs}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}}{{\text{Exp}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}},$
Pearson’s chi-square:	$\text{CHI}(i,j)={\sum }_{a,b}{\frac{({\text{Obs}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}-{\text{Exp}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}})}{{\text{Exp}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}}}^2,$
Mutual information (MI):27;28	$\text{MI}(i,j)={\sum }_{a,b}{P}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}\text{log}\frac{P_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}}{p_i^a{p}_j^b},$
MI normalized:29	$\text{MIr}(i,j)=\frac{\text{MI}(i,j)}{H(i,j)}=\frac{\text{MI}(i,j)}{-{\sum }_{a,b}{P}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}\text{log}{P}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}},$
MI with gap penalty:10	$\text{MIg}(i,j)=\text{MI}(i,j)-\frac{N_{\mathit{\text{ij}}}^G}{N},$
Obs-Minus-Exp-Squared:30	$\text{OMES}(i,j)={\sum }_{a,b}\frac{{({\text{Obs}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}}-{\text{Exp}}_{\mathit{\text{ij}}}^{\mathit{\text{ab}}})}^2}{N_{\mathit{\text{ij}}}},$
RNAalifold (RAF):31	$\text{RAF}(i,j)={\mathrm{B}}_{i,j},$
RNAalifold Stacking (RAFS):10	$\text{RAFS}(i,j)=\frac{1}{4}({\mathrm{B}}_{i-1,j+1}+2{\mathrm{B}}_{i,j}+{\mathrm{B}}_{i+1,j-1}),$