Hello,
Wenn I have a sequence with different annotation types, like primer_binding, mRNA, promoter, CDS, Fragment they have all their own row in the sequence zoom view and they are in alphabetical order. First capital letter A-Z, then lower case letter a-z. Thats why they are in the order CDS, Fragments, mRNA, primer_binding, promoter. Thats all fine. However, when I show now restriction enzyme cut sites for like 50 enzymes, the sequence zoom view becomes confusing, because the restriction enzymes are also included in the alphabetical order. At the top of the window I have CDS annotation, then some enzyme rows, then the Fragment row, then many enzyme annotation rows and finally the lowercase features.
So now I have to scroll up and down a lot, because I can't see the lowercase annotations and CDS at the same time. I find that very stressing and confusing.
What I tried is, I renamed annotations CDS to cds. The problem is now, that they don't confere to the genebank file format any more and are therefore saved as misc_features with ugene_name etc. in the genebank file. So this workaround is not good (because of compatibility with other programs).
My suggestion is to change the order in the sequence zoom view, so that at the top are the Autoannotations (first restriction enzymes then orfs) and below the normal annotations. In both two categories the annoation types would still be in alphabetical order, so there is a logic behind this.

Greetings,
Thomas