The color changes suggest the occurrence of a frame shift. The detection of the frame shift in the text report would be time-consuming because it would require looking through 800 pages of text. AV's use different colors for different frames makes this phenomenon stand out immediately. As can be seen in this figure, two regions labeled as A and B correspond to large concentrations of positive residue pair scores. Remember that a positive residue pair score corresponds to a strong match.
Biologists are interested in the identification of conserved regions in sequences.
Conserved regions are regions of a sequence that have been preserved over evolution, and are less likely to change due to mutation and selection. A region that is conserved through evolution may play an important role in the function of the sequence. The large concentration of positive scores suggest that the two regions labeled A and B are conserved. We also see in Figure 3 a region labeled C where negative residue pair scores are abundant. These negative pair scores suggest a region in which residues are weakly conserved, since there are more differences between the query sequence and the database sequences.