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23 <title>T-COFFEE Annotation Scores</title>
27 <strong>Loading and viewing T-COFFEE Annotation Scores</strong>
30 T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can
31 be displayed on the alignment using the <strong><em>Colours→T-COFFEE
32 Scores</em></strong> or <strong><em>Colour → <a
33 href="../colourSchemes/annotationColouring.html">Colour
34 by Annotation</a></em></strong> options.
36 <img src="../colourSchemes/colbytcoffee.png" />
38 <strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br />
39 T-COFFEE score files like the one below can be dropped directly onto
40 the corresponding alignment to visualize alignment confidence
44 T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
61 1PHT 999999999999999999999999998762112222543211112134
62 1BB9 99999999999999999999999999987-------4322----2234
63 1UHC 99999999999999999999999999987-------5321----2246
64 1YCS 99999999999999999999999999986-------4321----1-35
65 1OOT 999999999999999999999999999861-------3------1135
66 1ABO 99999999999999999999999999986-------422-------34
67 1FYN 99999999999999999999999999985-------32--------35
68 1QCF 99999999999999999999999999974-------2---------24
69 cons 999999999999999999999999999851000110321100001134
72 1PHT ----------5666642367889999999999889
73 1BB9 1111111111676653-355679999999999889
74 1UHC ----------788774--66789999999999889
75 1YCS ----------78777--356789999999999889
76 1OOT ----------78877--356789999999997-67
77 1ABO ----------687774--56779999999999889
78 1FYN ----------6888842356789999999999889
79 1QCF ----------6878742356789999999999889
80 cons 00100000006877641356789999999999889
83 <tr><th>Score</th><th>0</th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th></tr>
86 <td bgcolor="#6666FF">102, 102, 255</td>
87 <td bgcolor="#00FF00">0, 255, 0</td>
88 <td bgcolor="#66FF00">102, 255, 0</td>
89 <td bgcolor="#CCFF00">204, 255, 0</td>
90 <td bgcolor="#FFFF00">255, 255, 0</td>
91 <td bgcolor="#FFCC00">255, 204, 0</td>
92 <td bgcolor="#FF9900">255, 153, 0</td>
93 <td bgcolor="#FF6600">255, 102, 0</td>
94 <td bgcolor="#FF3300">255, 51, 0</td>
95 <td bgcolor="#FF2000">255, 34, 0</td></tr>