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Probes are bound to the chip at the 3′ end; thus, the 5′ end of the probe is used for match/mismatch detection. Probes can be synthesized with a specific melting temperature and with a 3′ linker. For SNP detection and re-sequencing, four identical probes are synthesized, each having a different 5′ end (A, G, C, or T).
