Use Primer Dimer Risk when you 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. Enter Primer A and Primer B using the definitions and units below so the result can be reproduced.

Primer A

A sequence, category, or text value.

Primer B

A sequence, category, or text value.

The published tool contract uses this rule: Heuristic primer-dimer screen that aligns one primer with the reverse complement of the other and flags four or more contiguous complementary bases.

Max complementary overlap

The calculated max complementary overlap.

Dimer risk

Whether dimer risk is true.

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

Retain the original Primer A and Primer B values and their units alongside the result. Self-Dimer Tm Risk is useful when you instead need to 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 Hairpin Risk provides another view by helping you 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.

• 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.

• Primer Hairpin Risk

  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.

• GC Clamp Check

  Check the GC clamp of a primer by counting guanine and cytosine bases among the last five nucleotides.