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Table 1 Criteria for oligonucleotide probe selection

From: A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Oligo selection criterion probes satisfying the rule [%] Rule symbol
Oligonucleotide properties
Melting temperature = 70°C (+/- 8°C) 97.18% T
Nucleotide composition: oligonucleotide cannot have a contiguous single nucleotide base repeat longer than 8 bases AND probe GC content fits the 20-to-60% range AND each base cannot constitute more than 40% of the oligonucleotide sequence 85.33% C
Secondary structure
Stem of potential hairpin structure cannot be longer than 8 bases 99.20% H
Probe specificity
Minimum Hamming distance to non-target parts of genome > 25 99.45% D
Substring: not more than 20 contiguous bases common to other (non-target) parts of genome 99.02% S