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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.
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.