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To apply an alignment highlighting mode, select it in the Highlighting context menu:

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     <img src="/wiki/download/attachments/16122233/Highlighting Alignment.png"/>
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or on the Highlighting tab of the Options Panel:

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     <img src="/wiki/download/attachments/16122233/Highlighting Alignment_1.png"/>
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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.
• Conservation level - highlights conservation level of symbols in a multiple alignment >= or <= treshhold. To select the conservation parameters use the Highlighting Options Panel tab.
• Transitions - highlights transitions.
• Transversions - highlights transversions.

To use dots instead of symbols which are not highlighted check the Use dots checkbox in the Options Panel or use the Highlighting->Use dots context menu item.

To select a reference sequence use the Set this sequence as reference context menu or Reference sequence field in the Highlighting tab of the Options Panel.

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

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     <img src="/wiki/download/attachments/7667818/Highlighting Alignment_2.png"/>
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Select file to export, exported area and click on the Export button. The task report will appear in the Notifications.