If the underlying sequence in the Mesquite's matrix has been reverse-complemented relative to how it came out of Phrap originally, a panel on the left will show up in dark orange rather than gray: The default components of the chromatogram viewer are shown below: If you wish to change the behavior so that it opens up in a separate tab within the same window as the matrix, then touch on the View Chromatograms tool icon ( ) and a menu will appear with an "Open in new window" toggle, and you can uncheck that option. There are many options for the elements that are displayed, and how they are displayed. For example, you can choose to hide the overview panel, or the closeup panel, or show other panels not illustrated above. Some pre-built styles exist that set a number of options all at once these are available in the Styles submenu of the Chromatograms menu. There are various options changing the display of the chromatograms. Once you have set up the display to meet your needs, you may wish to choose "Save Current Settings as Defaults" from the Chromatograms menu, which will establish your display settings as those to be used for future chromatograms you will view.
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