Abstract: A method for estimating the affinity ? of a first DNA strand, or “probe”, to be hybridized with a second DNA strand, or “target”, to form a hybrid of length Lbp, the method comprising: in each division of a set of M divisions of the hybrid, counting the number of times in which each hybrid of a set of P DNA strand hybrids is present in the division, the hybrids being of length k less than the length Lbp, or “k-hybrids”; for each combination of mismatches of a set of L combinations of mismatches in a hybrid of length Lbp, determining whether the pair of mismatches is present in the hybrid; and calculating the affinity ? according to the relation: ? = ? m = 1 M ? ? p = 1 P ? x m , p · ? ^ m , p + ? .

Abstract: A method for estimating the affinity ? of a first DNA strand, or “probe”, to be hybridized with a second DNA strand, or “target”, to form a hybrid of length Lbp, the method comprising: in each division of a set of M divisions of the hybrid, counting the number of times in which each hybrid of a set of P DNA strand hybrids is present in the division, the hybrids being of length k less than the length Lbp, or “k-hybrids”; for each combination of mismatches of a set of L combinations of mismatches in a hybrid of length Lbp, determining whether the pair of mismatches is present in the hybrid; and calculating the affinity ? according to the relation: ? = ? m = 1 M ? ? p = 1 P ? x m , p · ? ^ m , p + ?