Currently the program will recognize upper and lower case A G C T U with or without spaces. Characters other than A G C T U are converted to N and treated as an unknown base (and as a mismatch in the base pairing rules).

Each line of text is followed by a hard return. Additional hard returns are ignored.

Note that varying sodium ion concentration and/or CT will affect the estimated Tm value. A higher monovalent salt concentration value will result in a higher Tm prediction.

Note that varying sodium ion concentration and/or CT will affect the estimated Tm value. A higher total strand concentration value will result in a higher Tm prediction.

The temperature at which ΔG is calculated can be varied depending on the intended use of the sequences. For example, one might set ΔG Temperature to a higher value than the 37°C default when screening PCR primers where the temperature may never fall below 50 °C.

A score value is determined by combining the number of Watson-Crick base pairs (+1) with mismatches (-1). Gaps and "N" nucleotides are not included in the score calculation since the program is intended to screen short DNA oligomers.

If the Score is set to 7 then all predicted interactions of Score 7 and higher will be returned. Setting the Score to a lower value such as 4 will typically result in more interactions being returned.