You can see a breakdown of the percentage similarity and identity percentages for each sequence pair with the Calculate Similarity Matrix and Calculate Identity Matrix commands under the Sequence>Alignment menu. The output is a new window containing the table of the percentages. If there are selections in the Sequence Window, the pairwise similarity for the selected portion of the sequence is reported in the upper-right part of the table reports and the similarity for the full sequence is reported in the lower-left.