Hi, I used to use Bioedit to check compare if my DNA sequence is the same as template. They'll match regions of high consensus and for base pairs where the program thinks that there is a mismatched or missing base pair, it will highlight that base pair and continue to match the rest of the sequence.

However, with UGene, the sequences are aligned very strictly meaning that possible missing base pairs are not ignored so a large majority of the sequence ends up wrong.

Any help on this? Thanks.

Thanks a lot for the report!

I think don't quite understand the problem. A small particular example (screenshots, sample sequences or step-by-step description) would help.

What kind of UGENE aligner do you use? A multiple sequence aligner? Find pattern? Smith-Waterman?