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The concept of S-permutation matrix is considered in this paper. It defines when two binary matrices are disjoint. For an arbitrary S-permutation matrix, a lower band of the number of all disjoint with it S-permutation matrices is found. A formula for counting a lower band of the number of all disjoint pairs of S-permutation matrices is formulated and proven. As a consequence, a lower band of the probability of two randomly generated S-permutation matrices to be disjoint is found. In particular, a different proof of a known assertion is obtained in the work. The cases when and are discussed in detail.

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