To easily identify bases which do not match the consensus, turn on Highlighting in the consensus section of the sequence viewer options. Select the options Disagreements to Consensus (this is the default setting for nucleotide alignments). When this is on, any base in the sequences which matches the consensus at that position is grayed out and bases not matching are left colored.
With this on you can quickly jump to each disagreement by pressing Ctrl+D (command+D on Mac OS X) or by clicking the Next Disagreement button in the sequence viewer option panel to the right. Each disagreement can then be examined or resolved.
You can also use this feature if you have aligned to a reference sequence and you are interested in finding differences between each sequence and the reference (or SNPs).