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. (The new version 3.0 RNA rules are fixed at 37°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.

Isolated base pairs: A base pair is isolated if it is not adjacent to any other base pair. By default, base pairs that must be isolated are filtered out prior to computation.