Sanger's PCR chain-termination sequencing, by its theory, is a simple method to sequence DNA from organisms. But what will happen if there are 2 allelic DNA with same primer binding site, but variations in some-other part?
My question is; 1. Is such overlap practically happens? 2. If it happens, then what problem it creates? (or does it create any problem at all); and 3. if it is problematic, then what techniques used to avoid or reduce such noise?