ArrayIndexOutOfBoundsException for RNA Base Pair Logo

Loading RF00162 into the Jalview GSOC2011 build and enabling the base pair conservation results in an exception and failure to redraw the window correctly. Exception is:

Stack trace:
Building ws menu again Thread[Thread-31,6,main]
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 51
at jalview.analysis.StructureFrequency.extractProfile(StructureFrequency.java:439)
at jalview.gui.AnnotationPanel.getProfileFor(AnnotationPanel.java:1680)
at jalview.gui.AnnotationPanel.drawBarGraph(AnnotationPanel.java:1555)
at jalview.gui.AnnotationPanel.drawComponent(AnnotationPanel.java:1212)
at jalview.gui.AnnotationPanel.paintComponent(AnnotationPanel.java:752)
at javax.swing.JComponent.paint(JComponent.java:1029)
at javax.swing.JComponent.paintChildren(JComponent.java:862)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JViewport.paint(JViewport.java:795)
at javax.swing.JComponent.paintChildren(JComponent.java:862)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:862)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:862)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent._paintImmediately(JComponent.java:5098)
at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:812)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:694)
at javax.swing.RepaintManager.access$700(RepaintManager.java:41)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1672)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:643)
at java.awt.EventQueue$1.run(EventQueue.java:641)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)