By default, MacVector ignores gaps when calculating the consensus of a multiple sequence alignment. However, this can lead to some unexpected results. For example, consider this three sequence alignment where one sequence has a long insertion compared to the other two.
In this case it does not seem reasonable to believe that the “consensus” should contain that sequence as only one of the three sequences has those residues.It can look even worse if you look at the Picture tab and have the appropriate shading turned on.
The solution is to tell MacVector to treat gaps as valid characters. This can be done by clicking on the Prefs toolbar item and checking the appropriate checkbox in the resulting dialog;
Then the consensus will take gaps into account.
And the Picture tab will reflect those changes.
