The sequence colors shown in Map and Sequence views can be customized.
Select the sequence region that will be labeled with a 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..." .
Choose the color and specify which strand(s), then click OK.
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.
The customized sequence colors will now be shown in Map and Sequence views.