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			Considering gaps when calculating the consensus of a multiple alignment When calculating the consensus of a multiple sequence alignment, gaps are ignored by default. For example, in an alignment of three sequences where two sequences contain a gap at a particular position, then the third sequence is classed as having 100% identity to the consensus position which is based on the sequence without the gap. e.g. Note that wherever there is a gap, then the consensus uses the other sequences, unless the "Treat gaps as valid characters" option is selected. Ensuring gaps are considered when calculating the consensus of a multiple alignment. Use the "Treat gaps as valid characters" option to ensure that gaps are considered in the calculation of the consensus sequence. This option can be enabled as follows: Removing gaps from the consensus of a multiple alignment Use the No gaps in consensus option in conjunction with the Treat gaps as valid characters option to exclude gaps from the consensus. This option is enabled as follows:

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