Figure 11.1:
Options for highlighting disagreements in an alignment
To easily identify bases which do not match the consensus or reference sequence, turn on Highlighting in the consensus section of the sequence viewer options (see figure 11.1 ). Select the options Disagreements to Consensus or Reference depending on your needs. When this is on, matching bases are 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.