Analysis of Tm and Internal Stability
The Melting Temperature and Internal Stability windows are the main graphic windows of Oligo Software. The values can be displayed as bars or dots, depending on user's choice.
The Current Oligo - the oligonucleotide sequence surrounded by a rectangle within the active sequence - can be analyzed by various criteria. The Upper (forward) and/or Lower (reverse) Primer, when selected and located within the "Melting Temperature" window subsequence. The Upper Primer is displayed in red one line above the positive strand of the active sequence and includes a primer extension arrow. It is displayed in upper case letters except for nucleotides within the Upper Primer mismatched to the active sequence. These are displayed in lower case letters. The Lower Primer is displayed in blue one line below the negative strand of the active sequence and has the same characteristics as the Upper Primer.