Pairing mask

The second section of the data file is the pairing mask. This mask is only required when sequences contain some base-paired nucleotides (in that case the code should be RNA or MIXED). In the case of fully unpaired sequences - i.e., when the DNA code is used - the pairing mask must not be provided. The pairing mask is in the form of a mathematical expression consisting of round brackets. Corresponding brackets indicate that the bases at those positions in the sequence form a base-pair in the RNA secondary structure. Unpaired sites can be indicated with a dot ``.'' or a hyphen ``-''. For example a sequence ACCAGAUGGU with a pairing mask (((.(.)))) indicates that the sequence is made of the base-pairs AU-CG-CG-GU and unpaired sites A-A.