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 The following modes are available:

• Agreements — . highlights symbols that coincide with the reference sequence. 

• Disagreements — highlights nucleotides that differ from the reference sequence.

• Gaps - highlights gaps.
• Transitions - highlights transitions.
• Transversions - highlights transversions.

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Also you can export highlighting with a help of the Export button in the Options PanelPanel or by the Export->Export highlighted context menu item. The following dialog will appear:

<center>
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     <img src="/wiki/download/attachments/7667818/Highlighting Alignment_2.png"/>
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</center>

Select file to export, exported area and click on the Export button.