reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active

1. Ensure 'add secondary structure annotation' is enabled and Import PDB structure 3W5V (also in examples directory).
2. Copy and paste a segment of one of the chains into a new alignment - e.g.
>3W5V|B/42-92
GSCSSCAGKVVSGSVDQSDQSYLDDGQICDGWVLTCHAYPTSDVVIETHKE
3. Delete the sequence associated annotation tracks, and then select the whole sequence, right click and select "Add reference annotation" for the selection.

The newly added annotation tracks will not be aligned correctly to the sequence.