Table 1 Definitions of the different statistics. Definitions of the different statistics used. i and denote the sequence positions of a base-pair in the known structure, c is an alternative pairing partner for i (but according to the base-pairing rules therefore not for ), L is the length of the RNA sequence, N is the number of sequences in the data set and the index x indicates the type of weight used. Please refer to the text for a description of how alternative pairing partners are calculated.

3'cis _x

1/((c - i) log(L - i))

|G _ci |/((c - i) log(L-i))

3'trans _x

1/((c - ) log(L - ))

|G _ci |/((c - ) log(L - ))

5'cis _x

1/((i-c) log(i))

|G _ic |/((i-c) log(i))

5'trans _x

1/(( - c)log())

|G _ic |/(( - c) log())

cis _x

5'cis _x - 3'cis _x

trans _x

3'trans _x - 5'trans _x

3'Cis _x

Σ_#3'cis3'cis _x

3'Trans _x

Σ_#3'trans3'trans _x

5'Cis _x

Σ_#5'cis5'cis _x

5'Trans _x

Σ_#5'trans5'trans _x

Cis _x

5'Cis _x - 3'Cis _x

Trans _x

3'Trans _x - 5'Trans _x

where x ∈ {p,g}, y ∈ {3'Cis, 3'Trans, 5'Cis, 5'Trans, Cis, Trans}