How do I analyze the base composition of a sequence.

When a DNA sequence is the active window, one or more property profiles can be calculated for the sequence.

Choose Analyze | Base Composition.
Select one or more check boxes in the List panel to generate a text listing of the required mono-, di- and trinucleotide frequencies and temperature information.
Select the Base composition check box to generate percentage composition plots.
Specify the required composition plots by selecting Options in the Plot panel.
Select the temperature profile check box to generate a running average of the sequence Tm or Td.
Specify temperature profile parameters in the Temperature parameters panel as follows:
choose Tm or Td from the Calculate drop-down menu
choose the duplex type from the adjacent drop-down menu
- enter a value in the nucleic acid conc. text box
- enter a value in the cation conc. text box.
Type a value in the window size text box for the number of residues over which properties are calculated.
Select the required check boxes in the Histograms panel to generate histograms for di- and trinucleotide repeats along the sequence.
Specify the required Nucleotide frequency histograms by selecting Options to the right of each check box.
If required, you can restrict the analysis to a portion of the sequence, by typing in the sequence numbers that bracket the region in the Region text boxes. Alternatively, select a region from the features table drop-down menu to the right of the text boxes.
Select OK