Oligo Analyzer – Tm & Dimer Calculator
Nearest-neighbor Tm, ΔG, hairpins and primer dimers for any oligo or primer pair.
🌐 Nothing you paste is logged or stored — every tool is also callable via REST & MCP, and in bulk from the batch tools
A nearest-neighbor oligo analyzer for PCR primers: paste a single oligo, a forward/reverse pair, or a whole list, and get SantaLucia 1998 Tm, GC%, and dH/dS/dG37, plus a primer dimer and hairpin screen covering self-dimers and cross-dimers, each drawn as a base-paired alignment. Set the oligo, Na+, Mg2+ and dNTP concentrations to match your reaction; batch results export as CSV.
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Tm uses SantaLucia (1998) nearest-neighbour thermodynamics with a salt correction for Na⁺ and a monovalent-equivalent for Mg²⁺/dNTP. Hairpin and dimer ΔG are screening estimates — confirm critical designs with a dedicated secondary-structure tool. A 3′-end dimer/hairpin is the most likely to disrupt PCR.
Working on a whole construct rather than one oligo? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
How to use the Oligo Analyzer tool
- 1Pick a mode with the "Single oligo", "Primer pair" or "Batch" buttons at the top of the tool.
- 2Set the reaction conditions bar (Oligo nM, Na+ mM, Mg2+ mM, dNTP mM) by hand, or click a preset: Standard PCR, qPCR, or Isothermal / Gibson.
- 3Paste your sequence(s). Batch mode accepts one oligo per line, FASTA, or "name,sequence" rows.
- 4Read the results: Single oligo gives Tm (NN), dG37 and Hairpin / Self-dimer cards; Primer pair adds each primer's Tm, the delta-Tm (flagged when above 5 C), the forward x reverse cross-dimer and each primer's hairpin; Batch gives a per-oligo table with an Export CSV button. A dG below about -6 kcal/mol, or any structure marked "involves 3' end", is the one to worry about.
Frequently asked questions
How is the nearest-neighbor Tm calculated?
Using SantaLucia (1998) unified nearest-neighbor ΔH/ΔS parameters, with an entropy salt correction for Na⁺ and a monovalent-equivalent for Mg²⁺ (corrected for dNTP chelation). It is more accurate than the Wallace or salt-adjusted formulas, especially for primer-length oligos.
What counts as a problematic dimer or hairpin?
A more negative ΔG means a more stable structure. As a rough guide, ΔG below about −6 kcal/mol is worth attention, and any structure that involves the 3′ end is the most likely to interfere with extension. These are screening estimates — confirm critical designs with a dedicated folding tool.
Can I analyze many oligos at once?
Yes. Batch mode accepts one oligo per line, FASTA, or “name,sequence” rows, computes Tm, GC, ΔG and structure for each, and exports a CSV.