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As explained on the link you posted, the Vigenere cipher with a key on length $n$ encrypts every $n$-th symbol with the same key under the Caesar cipher. So to calculate the IC you should take all the $n$ sub-sequences separately: $\{1, 1+n, \dots, 1+kn, \dots\}$, $\{2, 2+n, \dots, 2+kn, \dots\}$ and so on and compute the IC for every sub-sequence.

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