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I was tempted to ask this in academia stack, but I thought the question too technically specific.

For an assignment which specifies that students create websites, how do you detect if an online service (like Wix, simvoly or website.com) has been used to create these sites? Or is there a specific instruction that one could give that would be able to distinguish handwritten from template?

I have thought about asking that a specific comment be inserted in markup, but if it's possible for these services to output html there's nothing stopping someone from adding a comment like this after the fact. While really specific markup or code can be searched online to detect plagiarism, if the code is really generic this becomes quite difficult.

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It depends on the service. Some services create specific files or directories, but in general html code generation is really good nowadays, so it is not easy to detect.

You could check the href attribute to see if there are some external files excluded the students forgot to download.