When designing primers for PCR, two types of secondary structures should be analyzed: dimers and hairpins. For dimers, both self- and hetero-dimers should be reviewed. In general, the ΔG value for dimer analysis should be between 0 to −9 kcal/mole for optimal design. Values more negative than this may adversely affect PCR reactions. For hairpins, the T<sub>m</sub> of the hairpin ... Detection Cloning Sequencing Primer_List Primer_Check. Select primer pairs to detect the given template sequence. Optionally targets and included/excluded regions can be specified.
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