3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Alignment RNA Structure Conservation Annotation</title></head>
20 <body><p><strong>Alignment RNA Structure Conservation Annotation</strong></p>
21 <p>This is an automatically calculated quantitative alignment
22 annotation which measures the number of conserved base pairs in
23 relation to a secondary structure. The canonical Watson-Crick base
24 pairings (A-T/U, G-C) and the wobble base pair (G-T/U) are regarded as
26 The amount of valid base pairs is indicated by the profile in the Alignment Annotation row.