To edit the background and highlighting colors in the Pile-up pane display
In the Sample Previewer sub-pane, you specify the colors to use for background/highlighting and the nucleotides in the Pile-up pane display for the Mito Alignment viewer. If you edit the display colors, then the Sample Viewer Previewer sub-pane is dynamically updated with your settings.
1. On the Application Settings dialog box, ensure that the Sample Previewer sub-pane is visible.
2. Edit the background/highlighting colors and/or the nucleotide colors, noting the following:
• If Variants is selected (the default value), then all nucleotides other than variant nucleotides are displayed in color on a white background. Conversely, variant nucleotides are displayed in white on a colored background (referred to as a highlighted variant).
• If Blocks is selected, then all nucleotides are displayed in white on a colored background.
 | You can select both Variants and Blocks for the display. In this case, all nucleotides are still displayed in white on a colored background; however, all nucleotides other than variant nucleotides are dimmed and all variant nucleotides are highlighted to visually differentiate them from non-variant nucleotides. |
3. Do one of the following:
• If you are done specifying your settings, then click Save to close the Application Settings dialog box and return to the GeneMarkerHTS main window.
• Continue to edit other application settings as needed.