Definition of the statistics. Pictorial definitions of the four configurations 3'cis, 3'trans, 5'cis and 5'trans which correspond to the four statistics used to measure the directedness of RNA folding. Sequence positions i and form a base-pair within the known secondary structure. Sequence position c is an alternative base-pairing partner for i (but according to the base-pairing rules therefore not for ) within a competing, alternative helix of a minimum length minstem. See the text for more explanation.
Meyer and Miklós BMC Molecular Biology 2004 5:10 doi:10.1186/1471-2199-5-10