# Find shortest prefix to generate original string by overlapping

Given a string $$S$$, I want to find the prefix string $$P$$ of shortest length, such that the original string $$S$$ can be generated by concatenating copies of $$P$$ (where overlapping is allowed).

For example, if $$S = atgatgatatgat$$, I want to find $$P = atgat$$; $$P$$ is the smallest prefix of $$S$$ that can be concatenated (in this case three times, starting at indices $$\{0,3,8\}$$ of $$S$$, where the first and second copies overlap but the second and third copies do not overlap) to equal $$S$$.

Obviously, there is an $$\mathcal{O}(n^2)$$ algorithm by checking each prefix of $$S$$, but a colleague mentioned it might be possible to do it in $$\mathcal{O}(n \log n)$$. I'm thinking of using suffix arrays for different prefixes of $$S$$ but haven't quite been able to proceed from there.

What you are looking for is called the quasiperiod of a string. If such a string has a quasiperiod of $$|S|$$ it is called superprimitive, and can not be covered by a substring.
A method for computing it in $$O(n)$$ time is given in "An On-Line String Superprimitivity Test" by Dany Breslauer. You might also be interested in "Of Periods, Quasiperiods, Repetitions and Covers" by Alberto Apostolico and Dany Breslauer.