<p>
Gap open : 12 <br> Gap extend : 2
</p>
- <p>When you select the pairwise alignment option a new window will
- come up which will display the alignments in a text format as they
- are calculated. Also displayed is information about the alignment
- such as alignment score, length and percentage identity between the
- sequences.</p>
- <p> </p>
+ <p>When you select the pairwise alignment option, a new window will
+ come up which displays the alignments in a text format, for example:</p>
+ <p style="font-family:'Lucida Console', monospace">
+ <pre>
+ FER1_SPIOL/5-13 TTMMGMAT<br/>
+ |. .. ||<br/>
+ FER1_MESCR/5-15 TAALSGAT
+ </pre>shows the aligned sequences, where '|' links identical residues, and (for peptide) '.' links residues that have a positive PAM250 score.
+ <p>The window also shows information about the alignment such as alignment score, length and percentage identity between the sequences.</p>
+ <p>A button is also provided to allow you to view the sequences as an alignment.</p>
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