Support annotations for multiple alignments

There was a feedback:

Also, I would expect to have sequences aligned on my plasmid with annotations kept. At the moment I see a bunch of nucleotides without annotations, which is completely useless.

There could be different solutions to this problem, for example:
1) Support annotations in the Alignment Editor, i.e. merge the Sequence View and the Alignment Editor into a single view as in Geneious.
2) Support synchronization between sequences in the Alignment Editor and the Sequence View so that one could work with the same sequences in both views. This must be made cozy enough so that it will be possible to work with several sequences at once.