help-twostate-fold

Sequences: Enter one or more sequences, in 5'-to-3' order, separated by semicolons. The letters 'A', 'C', 'G', 'T' and 'U' are recognized as the corresponding nucleotides. (Us are converted to Ts for DNA and vice versa for RNA.) All other letters are treated as unknown nucleotides; such unknowns are not permitted to form base pairs. All non-alphabetic characters are stripped out prior to processing.

Energy Rules: Choose whether to interpret sequences as DNA (the default) or RNA. Enter a hybridization temperature in °C. For DNA rules only, enter the concentrations of Sodium and Magnesium ions. (Salt conditions for RNA are fixed at [Na+] = 1 M and [Mg++] = 0 M.) Oligomer mode is the default; if polymer mode is chosen, [Mg++] is ignored.

Sequence Type: Choose whether the molecules are linear or circular. (Linear molecules and circular molecules may not be folded in the same job.)