The diagram shows a schematic representation of a DNA re-sequencing microarray experiment. The array is based on a reference sequence on length n bases (up to 30Kb), represented in a series of n overlapping ("tiled") oligonucleotide probes each of length 25. For each probe, three variant probes are included that vary the middle (13^th) base, one for each of the three alternative code letters. In the example, given a reference DNA sequence AGCC at positions 1, 2, 3, & 4, the four probes tiling position 1 are (top to bottom) TGCC, GGCC, CGCC, and AGCC. The same arrangement occurs for probes tiling positions 122-124: note that the order of the variant bases in each set of probes is constant (T, G, C, A = 1^st , 2^nd, 3^rd, 4^th).

    Consider an experimental DNA sequence that has a single nucleotide polymorphism (SNP) at position 4: AGCT. The complementary strand ~~~TCGA~~~ will match the middle position of only one of the four variant probe sequences at each tiling position: that probe will anneal preferentially to the experimental DNA, because the mismatch will interfere with annealing to the other oligos. The pattern of annealing on the chip is read by a computer (blue array). In this case, template annealing to the 4^th, 2^nd, 3^rd, and 1^st probes at positions 1,2,3, and  4 "re-sequences" this region, indicates that the original (complementary) sequence is AGCT.