Colouring above a percentage identity threshold
Selecting this option causes the colour scheme to be applied to only those residues that occur in that column at least a certain percentage of the time. For instance, selecting the threshold to be 100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column.
The percentage calculation may include or exclude gaps in the column, depending on the option selected for the consensus calculation.
With a threshold of 0, colouring is unchanged.