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.

x	p plain weights	g free energy weights
3'cisx	1/((c - i) log(L - i))	|Gci|/((c - i) log(L-i))
3'transx	1/((c - ) log(L - ))	|Gci|/((c - ) log(L - ))
5'cisx	1/((i-c) log(i))	|Gic|/((i-c) log(i))
5'transx	1/(( - c)log())	|Gic|/(( - c) log())
cisx	5'cisx - 3'cisx
transx	3'transx - 5'transx
3'Cisx	Σ#3'cis 3'cisx
3'Transx	Σ#3'trans 3'transx
5'Cisx	Σ#5'cis 5'cisx
5'Transx	Σ#5'trans 5'transx
Cisx	5'Cisx - 3'Cisx
Transx	3'Transx - 5'Transx
where x ∈ {p,g}, y ∈ {3'Cis, 3'Trans, 5'Cis, 5'Trans, Cis, Trans}