Use Primer Hairpin Risk when you need to heuristic primer-hairpin screen that looks for non-overlapping reverse-complementary stems of at least four bases separated by a loop of at least three bases. Enter Sequence using the definitions and units below so the result can be reproduced.

Sequence

A sequence, category, or text value.

The published tool contract uses this rule: Heuristic primer-hairpin screen that looks for non-overlapping reverse-complementary stems of at least four bases separated by a loop of at least three bases.

Hairpin risk

Whether hairpin risk is true.

Longest complementary match

The calculated longest complementary match.

The calculation does not propagate measurement uncertainty, sampling error, or biological and chemical variability.

Retain the original Sequence values and their units alongside the result. Primer Dimer Risk is useful when you instead need to heuristic primer-dimer screen that aligns one primer with the reverse complement of the other and flags four or more contiguous complementary bases. Self-Dimer Tm Risk provides another view by helping you screen a primer for self-dimer risk by aligning it with its reverse complement, finding the longest contiguous complementary run, and flagging runs of at least five bases.

• Primer Dimer Risk

  Heuristic primer-dimer screen that aligns one primer with the reverse complement of the other and flags four or more contiguous complementary bases.

• Self-Dimer Tm Risk

  Screen a primer for self-dimer risk by aligning it with its reverse complement, finding the longest contiguous complementary run, and flagging runs of at least five bases.

• Hairpin Tm Estimate

  Estimate primer hairpin stability by searching the sequence against its own reverse complement for the longest internal inverted-repeat stem of three to eight non-overlapping bases and applying the Wallace rule of four degrees per GC pair and two per AT pair.