MegAlign Pro supports searching for positions where the same letter code does not occur in all sequences. This type of search looks only at IUPAC letter codes and ignores gaps. In other words, it will not look for positions in which one sequence has a letter code and the others have gaps, or vice versa.

By default, the search tools are hidden. To display them, click on the Search tool () in the upper right of most views. This causes the search tools to be displayed on the top left of that view.

  1. From the Find drop-down menu, choose Difference.

  1. Use the green right/left arrows to jump to the next/previous find.

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