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Domain boundaries of superlattices formed on the highly oriented pyrolytic graphite surface are studied by scanning tunneling microscopy. Twist and glide boundaries are identified with help of theoretical simulations. The apparent vertical corrugation difference of the superlattices with the same lattice periodicity is explained in terms of overlayer attenuation. Our study reveals that the intra-layer strain has important effect on the electronic structure of the graphite surface. [Copyright &y& Elsevier]