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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.

From: Co-transcriptional folding is encoded within RNA genes

x p plain weights g free energy weights
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}