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+<p><strong>Pairwise alignment (Proteins only)</strong></p>\r
+<p>This calculation is performed on the selected sequences only. Java is not the \r
+ fastest language in the world and aligning more than a handful of sequences \r
+ will take a fair amount of time. <br>\r
+ For each pair of sequences the best global alignment is found using BLOSUM62 \r
+ as the scoring matrix. The scores reported are the raw scores. The sequences \r
+ are aligned using a dynamic programming technique and using the following gap \r
+ penalties : </p>\r
+<p>Gap open : 12 <br>\r
+ Gap extend : 2 </p>\r
+<p>When you select the pairwise alignment option a new window will come up which \r
+ will display the alignments in a text format as they are calculated. Also displayed \r
+ is information about the alignment such as alignment score, length and percentage \r
+ identity between the sequences.</p>\r
+<p> </p>\r
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