PrimerAnalyser tool for comprehensive primer analyze

Comprehensive analysis of a single oligonucleotide: standard and mixed bases, DNA/RNA, methylated, locked (LNA) and phosphorothioated nucleotides. Results update instantly as you type.

Type or paste sequence (5′→3′):

Parameters for Tm calculation:

Primer concentration (0.01–5 µM):
Total salt (Na⁺, K⁺, NH₄⁺, Tris⁺; 1–1000 mM):
Mg²⁺ concentration (0–10 mM):
Dimer detection sensitivity (1–10):

Dilution calculator:

Target volume (µl):
Target concentration (µM):
Volume of the stock (µl):
MQ water or TE buffer (µl):

Amount of oligo:

OD (A₂₆₀):
Mass (µg):
nmol:

Preparing stock solution:

Stock concentration (µM):

To export results: select all (Ctrl-A), copy (Ctrl-C), paste (Ctrl-V).

Features

Dimers

Standard IUB/IUPAC degenerate codes:

B = C, G, T

D = A, G, T

H = A, C, T

K = G, T

M = A, C

N = A, C, G, T

R = A, G

S = G, C

V = A, C, G

W = A, T

Y = C, T

U = Uracil

I = Inosine

LNA codes: E = LNA-dA, F = LNA-dC, J = LNA-dG, L = LNA-dT.

Melting temperature Tm (°C)

Extinction coefficient ε (L/mol·cm)

GC content (%)

Molecular weight (g/mol)

Linguistic complexity (LC% and YR%)

Amount per OD unit (nmol/OD₂₆₀)

Length (nt) and base composition

Mass per OD unit (µg/OD₂₀₀)

Self-dimers and G-quadruplex detection

Dilution & resuspension calculator

LC% — measures the "vocabulary richness" of a genetic text by counting nucleotide combinations relative to the theoretical maximum. 100% = highest level.

YR% — measures the "vocabulary richness" of genetic text by counting purine/pyrimidine combinations relative to the theoretical maximum. 100% = maximum level.

Full documentation, parameter explanations, and troubleshooting: Help → PrimerAnalyser.

Accepted nucleotide codes

Calculated properties

Linguistic complexity (LC% and YR%)