An array-of-microarrays and the corresponding clusters. 48 subarrays are spotted to each glass each having the entire set of 40 anti-tags spotted in triplicates (left panel insert) thus constituting an array-of-arrays (left panel). The colors are artificially added according to signal intensity by the software. The two signals for each SNP are plotted together as cluster diagrams where the three clusters represent each of the three possible genotypes (right panel). Allelic fractions (AFs, x-axes) are calculated from the signal intensities as spot 1/(spot 1 + spot 2) and logarithm of the total signal is used for the y-axes. To investigate the variability between tag sequences, each allele-specific extension primer was designed with two alternative tag sequences. All combinations for each SNP gave similar clusters to the presented.