For calculating the index of coincidence for each sequence
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.