As I reread his question, you may be correct. The problem is that his output does not match his stated conditions. According to his stated conditions, in the example he gives, he wants subsequences of length 2. However, his output includes a subsequence of length 3. For this reason, I am assuming that he misstated his conditions and means to say "I'd like to find common continuous subsequences of AT LEAST length n." If I am correct, then the time to solve an input of 1000's of sequences of 1000's of numbers would be prohibitively long, especially if n is small. If I am not correct, then you are closer to the actual runtime.
Very good solution.
davidj
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