How do I add custom colors to a DNA sequence?
Select a Sequence Region

Select the sequence region that will be labeled with a color.
Customize the Sequence Color

To customize the sequence color, click Edit → Set DNA Color... .

Alternatively, to customize the sequence color using the side toolbar, click the "Show colors" menu button from the side toolbar, then click "Set DNA Color..." .
Customize the Sequence Color

Choose the color and specify which strand(s), then click OK.
Switch Color Modes

Click Yes to show Custom DNA colors (note the icon change).

Alternatively, to show previously customized DNA colors, open the Options dialog by clicking View → Map & Sequence Options... . Click the "Show colors" menu button to select "Custom DNA Colors", then click OK.
View the Custom Sequence Colors

The customized sequence colors will now be shown in Map and Sequence views.