Final answer:
The 'footprint' left at the donor DNA site after a transposon uses the cut-and-paste mechanism is a sequence of DNA that is missing from the site.
Step-by-step explanation:
After a transposon moves from a donor DNA site to a new site using the "cut-and-paste" mechanism, it leaves a "footprint" at the donor site. This "footprint" is a sequence of DNA that is missing from the donor site, meaning the correct answer to the student's question is 1) A sequence of DNA that is missing from the donor site. The cut-and-paste mechanism involves the transposon being excised completely and the donor site being repaired, often imperfectly, which can lead to small insertions or deletions, thus producing the "footprint." In contrast, replicative transposition would leave a copy of the original transposon in place while inserting a new copy elsewhere.