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Base fingerprint and base bucket. (A) The fingerprint of a base is defined as a 5D vector composed of the types of the two SSEs, the angle (α) between their axial vectors, the midpoint-to-midpoint distance between their axes and their line distance. (B) A base bucket stores almost-congruent bases. The bases are stored in columns according to the protein they belong to. The paths shown in red, green, and magenta are examples for possible multiple base alignments.
