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This work examines the concept of S-permutation matrices, namely $n^2 \times n^2n \times n$ subsquare (block). The article suggests a formula for counting mutually disjoint pairs of S-permutation matrices in the general case by restricting this task to the problem of finding some numerical characteristics of the elements of specially defined for this purpose factor-set of the set of binary matrices. The paper describe an algorithm that solves the main problem. To do that, every binary matrix is represented uniquely as a n-tuple of integers.

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