First, thank you to everyone involved with this software. It is fantastic! I have a feature request for alignments. It would be great if one could set up manual alignments, where you can actually drag and drop individual bases, or whole sections of sequence. If you're familiar with Bioedit, it would basically be all of bioedits type features, meshed with ugene, so that you could import your results into the annotation editor. Thanks for your considerations

It would be very cool if you could keep your annotations in the alignment editor. However, I do realize that once you start manually editing an alignment, the annotations would not really "signify" what they did before. Essentially, this is what I'm picturing... What if you have a sequence of a gene that you're working with, and you want to manually create your own set of primers with mutations, or maybe with your own restriction sites built into the ends. You can't really do this with just the primer 3 function. So, lets say one could use primer 3 to find very suitable primers for a certain region. Then, if you could have those primers existing as editable sequences within the sequence view, then you could add a few bases to the end of each primer, to be your restriction sites, and you could still have them lined up, and aligned visually, next to your main sequence. Or, you could take the primers which were given by primer 3, and change a single base for a mutation, and then you could see your new, edited primer next to (ie above or below) the main sequence, and you could see how it differs from the original sequence. I hope that I'm explaining this well. Thanks!!