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On standard 3′IVT, arrays such as the HGU133plus2 chip, each gene is typically targeted by a single probeset placed at the 3′ end of the transcript. These probesets consist of 11 Perfect Match spots and 11 paired Mis-Match spots in which the middle residue has been changed. Exon arrays have probesets placed against each exon along the length of the gene. Exon array probesets have no paired Mis-Match spots and four probes per probeset.
