Use Self-Dimer Tm Risk when you 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. Enter Sequence using the definitions and units below so the result can be reproduced.

Sequence

Primer sequence of at least eight nucleotides using only uppercase A, C, G and T.

The published tool contract uses this rule: 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.

Longest self-complement run

Length in bases of the longest perfect complementary run across all self-alignments.

Dimer risk

True when the longest self-complementary run is at least five bases.

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. 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.

• 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.

• 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.

• Nearest Neighbor Tm Approx

  Approximate primer melting temperature with a salt-adjusted nearest-neighbor style formula.