...
These preferences affect colors used to indicate 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 colors residues highlights each residue in a different color when zoomed in. In this section, you can change color settings for residues. By default, IGB uses cool colors for A and T residues and warmer colors for G and C residues. Other refers to residues that are either 'N', 'X' or '-' (missing) and can be set to a bright color if you are looking for deletions in short read sequences; otherwise you may wish to leave it as the neutral gray. Changes made in this section will be are immediately applied to the image after the Preferences window is closed.
Tip: Reset residue colors to whatever the Axis backround color to avoid coloring bases. showing your current colors to the current background color of the If you do NOT wish for individual residue highlightsresidues to be highlighted, set the colors to white or a light grey. Another great color scheme, if you are looking for CpG islands, is to set A and T to a neutral white . or grey, make C a bright red and then G a moderate blue - this makes it easy for the eye to pick out the CG combination when skimming across genomic DNA.
Miscellaneous Options
IGB warns you when you are about to exit the program, before you delete a file or files, and before you attempt to load alignments data (BAM files) for very large regions. Each of these warnings has the option Do not show again. To turn off these warnings or reset your previous choice, check (or uncheck) Ask before exiting, Confirm before delete and/or Confirm before load.
...