The problem with this task - e.g. common substrings problem, is that is a high complexity so that it requires a lot of difficult heuristic tricks to get it below O(n^2) otherwise it is too slow or uses too much memory. I have not seen any tools to do this. It would work with pictures or videos or audio as well - to find matching image sections, video subclips, etc. But really, it would be quite useful. I am quite certain we are talking an NP-hard problem please see:
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https://en.wikipedia.org/wiki/Longest_common_substring_problem
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Although this problem is less complex, you did not specify only the longest common substring but all common substrings. Yes the suffix tree and other tricks can solve this one faster.
And there are proofs I believe that shortest common substring is NP-hard.
See for example
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https://docs.lib.purdue.edu/cgi/viewcontent.cgi?httpsredir=1&article=2225&context=cstech
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