A Free Multiple Primer Analyzer Alternative
You have a list of primers — ordered last year, inherited from a departing postdoc, or pulled from three different papers — and the question is which of them will fight each other in one tube. SeqBench's Oligo Pool Screen takes up to 384 of them and checks every pair, plus each oligo against itself, with no account and nothing to install.
The difference that matters is what it does with a hit. A pairing that caps a primer's 3' end can be extended into a primer-dimer product that then amplifies away your reaction; one that only sequesters the middle of a primer just lowers the effective concentration. The two are held to different thresholds and counted separately, rather than being listed together and left to you.
SeqBench vs Thermo Fisher Multiple Primer Analyzer
| Aspect | SeqBench | Multiple Primer Analyzer |
|---|---|---|
| Access model | Web app, no account | Web form, no account |
| Price | Free | Free |
| Melting temperature | Nearest-neighbour (SantaLucia 1998) at the Na+, Mg2+, dNTP and primer concentrations you set | Yes |
| Hairpin detection | Yes — ΔG, the number of paired bases, whether the 3' end is involved, and the base-pair diagram | Yes |
| Self-dimer detection | Yes — same readout as the hairpin, with the alignment drawn | Yes |
| Cross-dimer between two oligos | Yes — the most stable heterodimer between a named pair | Yes |
| Whole-set screen | Yes — up to 384 oligos, every pair screened, from a FASTA paste or a named list | Yes, for a short list pasted into the form |
| 3' end vs internal pairing | Scored against two separate ΔG thresholds, because a dimer that sequesters a primer internally is not the same problem as one that caps its 3' end | Reports the pairings; the distinction is yours to make |
| Duplicate oligos in a set | Flagged by name — identical sequences in one pool are reported before anything else | Not reported |
| Tm spread across the set | Reported for the whole pool, which is the number that decides one annealing temperature | Per-primer Tm only |
| Where it runs | Single-oligo and pairwise analysis run in your browser; the whole-set screen runs on the server because it is quadratic in the pool size | On the Thermo Fisher server |
| Genome off-target check | A separate tool, against bundled reference genomes — not part of the dimer screen | No |
| Designing primers from a template | A separate tool — this one screens oligos you already have | No — analysis only |
| API and AI-agent access | Yes — the same functions behind a JSON REST endpoint and an MCP server | No public API |
Comparison is simplified and provided in good faith — check Thermo Fisher for current behaviour. Multiple Primer Analyzer is a tool of Thermo Fisher Scientific and is not affiliated with SeqBench.
What this is for
- Checking a multiplex panel before you order it
- Finding out why one reaction in a plate keeps producing a low band
- Auditing an inherited primer list for duplicates and Tm spread
- Screening an oligo pool too large to paste into a form one pair at a time
What it deliberately is not
- A primer designer — that starts from a template, and is its own tool
- A genome specificity check — that needs a reference, and is its own tool
- A prediction of whether your PCR will work; it reports pairings and their ΔG
Related primer tools
Nearest-neighbor Tm, ΔG, hairpins and primer dimers for any oligo or primer pair.
Screen a whole oligo pool for cross-dimers between members, each oligo's own hairpin and self-dimer, duplicates and Tm spread.
Estimate primer Tm, GC% and molecular weight from a sequence.
Design ranked PCR primer pairs from a template, with Tm, GC and dimer checks.
Choose one primer pair per target so no two cross-dimerise, every amplicon is separable on the gel, and one annealing temperature serves the whole panel.
Enter a template and two primers to predict the PCR product, its size and position.
Frequently asked questions
Is there a free alternative to Thermo Fisher's Multiple Primer Analyzer?
Yes. SeqBench's Oligo Analyzer covers one primer — nearest-neighbour Tm, ΔG, ΔH, ΔS, hairpin and self-dimer with the base pairs drawn — and the Oligo Pool Screen covers a whole set, screening every pair in a pool of up to 384 oligos for cross-dimers as well as each oligo against itself. Neither needs an account.
Why does it treat a 3' end dimer differently from an internal one?
Because they fail differently. A pairing that caps a primer's 3' end blocks extension, or worse, gets extended into a primer-dimer product that then amplifies exponentially and consumes the reaction. A pairing that only sequesters the middle of a primer reduces the effective concentration and shifts the Tm, which is a milder problem. The screen therefore holds 3'-end pairings to a stricter ΔG threshold than internal ones and reports the two counts separately.
How many primers can I screen at once?
Up to 384 — four 96-well plates. The work is quadratic in the pool size (384 oligos is 73,536 pairs), which is why the whole-set screen runs on the server while single-oligo and pairwise analysis run in the browser.
Does it check my primers against a genome?
Not in the dimer screen — that is a separate tool that scans bundled reference genomes for off-target binding sites. Keeping them apart is deliberate: whether two primers stick to each other is a question about the oligos, answerable in the browser from the sequences alone, while whether a primer sticks somewhere it should not is a question about a genome and needs one.
Will it design primers for me?
That is a different tool. This one screens oligos you already have, which is the case a Multiple Primer Analyzer covers — you have ordered primers, or inherited a list, and want to know which combinations will fight each other. The primer designer starts from a template instead.
What does the Tm spread tell me?
Whether one annealing temperature can serve the whole set. Individual Tm values matter far less than the gap between the highest and the lowest: a pool spanning 16 °C has no annealing temperature at which every primer is working properly, and that is a design problem no amount of cycling optimisation fixes.