This tab contains several options addressing the color/appearance of non-track elements in the image, as well as some other miscellaneous options.
Axis
The options for axis appearance are here. You can change the foreground and background colors to suit your needs. Changes to the colors will not appear dynamically, but will take place when the Preferences window is closed.
You can alter how the number scale appears to reflect your preference. Changing Number format to FULL shows the number with no separators and the unit 'kb'. COMMA shows the numbers with commas at every 10^3 (American style) and with no unit designations. This is the default appearance. ABBREV will show the numbers as abbreviated as is reasonable, with unit designations, i.e. zoomed all the way out, numbers are 10M 20M etc. Zoomed in a bit, numbers are shown as 19,500k, 20,500k. Zoomed all the way in, numbers are shown fully. Changes made here appear dynamically in your image.
ORF (Open Reading Frames) Analyzer
This set of preferences changes the color of the stop codons and the ORFs shown in the Sliced View tab. After setting new color options, uncheck and recheck the Analyze ORFs option in the Sliced View tab to show the new color scheme.
Change Residue Colors
IGB shows each residue with an individual color highlight at the fully zoomed in level. At less zoom, where the letter cannot be fully shown, IGB will still show the color for each residue. Zoomed out to the point where IGB cannot resolve individual bases, the sequence will appear as a gray bar. In this section, you can change what color represents each residue individually. If you do NOT wish for individual residue highlights, set the colors to white. Changes made in this section will be applied to the imageafter the Preferences window is closed.