To find gaps or areas of disagreement in an alignment:

  • MegAlign – Use Edit > Find Disagreement and choose whether to search for a disagreement or a gap

    Or, to make facets of the alignment stand out in the Alignment Report, add one or more decorations to the Worktable using Options > New Decoration.


  • MegAlign Pro – Use the Style panel’s Pairwise Alignment or Multiple Alignment sections to specify how to display similarities or differences. See the MegAlign Pro User Guide topics Pairwise Alignment section and Multiple Alignment section for details.

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