When you start Oligo and load a sequence file Oligo displays two windows: the top one represents a Tm graph, and the bottom window displays internal stability of oligos (DG of pentamers).
There is a third window (oligonucleotide frequency window) hidden under the Internal Stability window, but this will be explained later.
The Melting Temperature window displays a segment of the active DNA/RNA sequence file and a Tm plot of the oligonucleotides with a default length of 21 nt within the segment. The length of the segment displayed will vary, depending upon the monitor resolution. Each point (or bar) on the Tm plot represents the melting temperature of a 21-mer oligonucleotide. The underlined oligo, called the Current Oligo is available for analysis. To view a Tm plot of the entire file, you would need to select the "zoom" feature at the top of the Melting Temperature graph. The presentation of data displayed in the "Melting Temperature" window can be modified with the "Graph" and "Options" submenus next to "Zoom." You may select forward and reverse primers (called here "Upper" and "Lower") by clicking on the buttons in the lower left corner of the window. These primers can be analyzed by several Analysis options.
The horizontal line bisecting the Tm plot (solid blue line) represents the average Tm (or free energy or degeneracy or %GC) of all the 21-mer oligonucleotides in the sequence file. Below the Tm plot is the nucleotide sequence (both strands) in upper case letters. Corresponding amino acids appear in color below (color indicates the codon usage).
