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 (13th) 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 = 1st , 2nd, 3rd, 4th).
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 mismtach will interfere with annealling 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 4th, 2nd, 3rd, and 1st probes at positions 1,2,3, and 4 "re-sequences" this region, indicates that the original (complementary) sequence is AGCT.