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To each base (or other object) a number of tags can be attached. These can be used to label special bases or areas. If the alignment contains a line named "mask", the letter on a certain position in this line will be attached to all bases on this position as a tag. Attached tags can be changed using the object configuration dialog.

Tags can also be edited object by object,

or by adding tags from a list to the bases starting at a given position

The properties of objects such as color and font can be changed based on their tags, making it possible to e.g. use color coding to indicate the variability of different positions in a sequence as shown in the SSU rRNA model.

Peter De Rijk