An OligoAnalyzer Alternative That Does Not Ask You to Sign In
SeqBench's Oligo Analyzer gives you SantaLucia nearest-neighbour Tm, GC%, hairpins and dimers from a pasted sequence, with no account to create. IDT's OligoAnalyzer is a genuinely good tool and free to use — but its own page opens by asking you to sign in or create an account first.
The difference that matters beyond the login is one row down the table: OligoAnalyzer works an oligo at a time, and this screens a whole 384-oligo plate pair by pair. Three things IDT does and this does not are in the table too, rather than left for you to find out.
SeqBench vs IDT OligoAnalyzer
| Aspect | SeqBench | IDT OligoAnalyzer |
|---|---|---|
| Access model | Web app — paste an oligo and read the answer, no account, no sign-in | Free web tool, but its own page says: sign in or create an IDT account to start using it |
| Price | Free | Free, once you have an account |
| Melting temperature | Yes — SantaLucia 1998 nearest-neighbour, and it moves with the oligo, Na+, Mg2+ and dNTP concentrations you actually pipette rather than a fixed default | Yes — their own nearest-neighbour model with a salt correction |
| Hairpin detection | Yes — the ΔG, the number of base pairs, whether the 3' end is caught in it, and the fold drawn as a base-paired diagram | Yes, with folded structures and their ΔG |
| Self-dimer detection | Yes — drawn as an aligned duplex, with a warning when the pairing involves the 3' end | Yes |
| Hetero-dimer between two oligos | Yes — paste both and the most stable cross-pairing is drawn with its ΔG | Yes, one pair at a time |
| A whole plate of oligos at once | Yes — up to 384 oligos, and it screens every pair rather than every oligo, so a 96-well plate is one run instead of 4,560 lookups. Duplicate sequences and the Tm spread across the set come back with it | One oligo at a time, plus a second for the hetero-dimer check |
| 3' end versus internal pairing | Yes — a pairing that involves a 3' end is held to a stricter ΔG bar than one that only sequesters the primer internally, because only one of the two stops extension | Structures are reported; judging the 3' end is left to you |
| GC content and molecular weight | Yes — GC%, single-strand molecular weight, and ΔH, ΔS and ΔG37 for the duplex | Yes |
| Extinction coefficient, ug/OD and nmol/OD | Molecular weight for every oligo, with a conversion cheat sheet on the site covering the A260 relationships. If you are resuspending a tube from its OD reading, IDT's tool is the right one | Yes — extinction coefficient, ug/OD and nmol/OD |
| Tm across mismatches | Tm for the oligo as given, responding to your salt, Mg2+ and dNTP concentrations | Yes — Tm variation over mismatched targets |
| Off-target specificity | An e-PCR-style screen you pick the background for: four bundled lab genomes (E. coli K-12 MG1655, B. subtilis 168, the human mitochondrion, M. hyorhinis), or the human or mouse transcriptome — MANE Select and RefSeq Select, one transcript per gene, so a hit names a different GENE. No queue and no account; the nuclear genome is not covered in any mode | Hands the oligo to NCBI BLAST |
| Where it runs | The single-oligo analysis and the two-oligo dimer check run in your browser, so nothing is uploaded; the 384-oligo pool screen runs on the server because the work grows with the square of the pool | On IDT's servers, against your signed-in account |
| API and AI-agent access | Yes — a JSON REST endpoint and an MCP server, no key and no account | Yes — the SciTools Plus API, with an account and a key |
Comparison is simplified and provided in good faith — check idtdna.com for current behavior. OligoAnalyzer and SciTools are products of Integrated DNA Technologies and are not affiliated with SeqBench.
Where SeqBench is the better fit
- You do not have an IDT account, or you are on a machine that is not yours
- You have a plate of primers, not one oligo, and want every pair checked
- You want the 3'-end pairings separated from the harmless internal ones
- You want the Tm to move with the salt and Mg2+ you are actually using
- You want the same analysis from a script or an AI agent without a key
Related primer tools
Frequently asked questions
Can I analyse an oligo without an IDT account?
Here, yes — paste the sequence and the answer is on the screen, with nothing to sign into. IDT's OligoAnalyzer page states that you sign in or create an IDT account to start using it. That account is free, and if you order oligos from IDT you almost certainly have one; this page exists for the case where you do not, or where you are on a shared machine, or where you just want the number now.
Is the Tm the same number IDT gives?
Close, not identical, and you should expect that of any two implementations. Both are nearest-neighbour models; this one is SantaLucia 1998 with a salt correction, and it takes the oligo, Na+, Mg2+ and dNTP concentrations as inputs so the number matches the reaction you are actually setting up. Two calculators using different salt corrections or different default concentrations will differ by a degree or two, which is why the concentrations are on the page rather than hidden.
Can I check a whole plate of primers rather than one oligo?
Yes, and that is the main thing this does that OligoAnalyzer does not. Paste a FASTA block or a spreadsheet column of up to 384 oligos and every pair is screened — 96 oligos is 4,560 pairs, which is not a thing anyone checks by hand. It reports each conflicting pair with its ΔG, flags pairings that involve a 3' end under a stricter threshold than internal ones, lists duplicate sequences, and gives the Tm spread across the set.
What does the off-target screen cover?
Pick one of three backgrounds. Four bundled lab genomes — E. coli K-12 MG1655, B. subtilis 168, the human mitochondrion and M. hyorhinis — answer host background for bacterial work. The human and mouse TRANSCRIPTOMES (MANE Select and RefSeq Select, one transcript per gene) answer the question most people bring to Primer-BLAST: does this pair also amplify another gene? Because the set holds one transcript per gene, a hit is a different gene rather than the fifteenth isoform of your own. What no background covers is the nuclear genome itself, so an off-target in an intron, a promoter, an intergenic region or genomic-DNA carry-over is out of scope — for that, NCBI BLAST or Primer-BLAST is free and is the route.
Can I work out a resuspension volume from an A260 reading?
Molecular weight is reported for every oligo, and this site carries a conversion cheat sheet covering the A260 relationships — extinction coefficient, ug/OD and nmol/OD — so a spectrophotometer reading turns into a working stock with one lookup.
Is my sequence sent anywhere?
The single-oligo analysis and the two-oligo dimer check run entirely in your browser — the same code, executed locally, with no request leaving the page. The 384-oligo pool screen runs on the server because screening every pair is quadratic work; that request is analysed in memory and the sequences are not logged or stored.