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-<head><title>Above PID Colours</title>
+<head>
+<title>Above PID Colours</title>
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-<p> <em>Colouring above a percentage identity threshold</em></p>
-<p> Selecting this option causes the colour scheme to be applied to only those
- residues that occur in that column more than a certain percentage of the time.
- For instance selecting the threshold to be 100 will only colour those columns
- with 100 % identity. This threshold option can be applied to the Zappo, Taylor,
- Hydrophobicity and User colour schemes. </p>
+ <p>
+ <strong>Colouring above a percentage identity threshold</strong>
+ </p>
+ <p>Selecting this option causes the colour scheme to be applied to
+ only those residues that occur in that column at least a certain
+ percentage of the time. For instance, selecting the threshold to be
+ 100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column.</p>
+ <p>The percentage calculation may include or exclude gaps in the column, depending on the option selected for the <a href="../calculations/consensus.html">consensus calculation</a>.</p>
+ <p>With a threshold of 0, colouring is unchanged.</p>
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