SantaLucia 1998 nearest-neighbor parameters and salt correction, with Primer3-compatible symmetry and magnesium corrections.
Tm is not an optimized annealing temperature. This tool does not assess specificity, hairpins or dimers. Supports unmodified A/C/G/T DNA, 2–60 bases. Methods: SantaLucia (1998), doi:10.1073/pnas.95.4.1460; von Ahsen et al. (2001), doi:10.1093/clinchem/47.11.1956. Validated against Primer3 2.6.1 oligotm (SantaLucia/SantaLucia).
How to use this tool
Enter primer sequences in the 5′ to 3′ direction and the reaction concentrations. Compare results using the same conditions.
Calculate mass, molar concentration or final solution volume.
ECOTECH LAB TOOLS
Buffer Dilution Calculator
Calculate stock and diluent volumes using C₁V₁ = C₂V₂.
ECOTECH LAB TOOLS
Master Mix Calculator
Scale your reaction setup and include a pipetting allowance.
Primer Dimer Predictor
Inspect self-dimer and cross-dimer complementarity. Enter A, C, G and T only (8–100 bases).
Example sequences illustrate complementarity; they are not an assay design. Sequence-based screen of ungapped Watson–Crick complementarity, including 3′ ends. Not a thermodynamic ΔG prediction; does not model hairpins, mismatches or bulges. Confirm secondary structures with OligoAnalyzer.
Primer Pair Compatibility Checker
Compare Tm, GC content, length and complementarity under the same reaction conditions.
Example sequences illustrate complementarity; they are not an assay design. Sequence-based screen of ungapped Watson–Crick complementarity, including 3′ ends. Not a thermodynamic ΔG prediction; does not model hairpins, mismatches or bulges. Confirm secondary structures with OligoAnalyzer.
Tm uses the same SantaLucia model as our Primer Tm Calculator. This screen does not establish target specificity. Check specificity with Primer-BLAST ↗
ΔΔCt Calculator
Enter technical replicates separated by commas, spaces or new lines. Compare one sample with one calibrator.
Fold change = 2−ΔΔCt. Assumes approximately 100% and comparable target/reference amplification efficiencies and a validated stable reference gene. Run biological replicates separately; do not pool them as technical replicates. Non-detects cannot be replaced by zero. Method: Livak & Schmittgen (2001).
Housekeeping Gene Finder Beta
Explore candidate controls and combinations by organism, target RNA, material and tissue of origin. Review the supporting sources and experimental context before choosing controls.
Restriction Site Finder
Locate recognition sites for the 13 FlashDigest enzymes in our catalog, plus an optional custom motif.
Reports recognition-site starts (1-based), not cleavage coordinates. Checks both strands and circular junctions. Sequence matches do not account for methylation, reaction conditions or digestion efficiency. DpnI requires methylated recognition sites; a GATC match alone does not establish cleavage.
Reverse Complement Tool
Reverse-complement a DNA sequence, preserving IUPAC ambiguity codes.
RCF ↔ RPM Calculator
Convert rotational speed and relative centrifugal force using your rotor radius.
RCF = 1.118 × 10−5 × radius (cm) × RPM². Use the radius specified by the rotor manufacturer (maximum radius for maximum RCF). Check rotor and tube speed limits.
Cell Seeding Calculator
Prepare a cell suspension at your chosen viable cell count and volume per well.
Stock concentration is the total cell count before viability correction. If your measured concentration already counts viable cells only, enter 100% viability. This calculation does not predict cell growth or confluence.
