"what one wants to make in a ligation reaction isn't the only thing that gets made"
Well, there's this new thing called DNA sequencing. You pick a single colony that has clones of a single plasmid, and then sequence the DNA. You also look at the gel if there's only the expected band(s). So, yes, ligation creates different products but the plasmid you purify is usually analysed before *working with it*, leave alone releaseing it
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