The consensus calculation can be tuned by changing the threshhold at which a particular base type is considered to have the 'majority'; a dash (-) is displayed when the majority is not sufficiently high. See the staden package manual for precise details on this.
An additiona quality cutoff can be applied to each base. This determines the
contribution that each base makes to the consensus calculation and also the
colour used when displaying bases on the screen. Bases with a quality lower
than the cutoff are displayed in
colours, as defined in the configuration Options listed above.