Primer Analyzer: Tm, Hairpin, Dimer and Detailed Metrics

Compare vs IDT

Use this page when a basic Tm calculator is not enough. Analyze a primer in one pass for nearest-neighbor Tm, GC%, molecular weight, extinction coefficient, hairpin risk, self-dimer risk, BLAST handoff, and single-base mismatch effects. If you are comparing assumptions against IDT OligoAnalyzer, public analysis runs in the browser by default; Dashboard History may store snapshots when saving is enabled. If you only need a vendor-style Tm value, use the Tm Calculator; if structure risk is the main question, use the Secondary Structure Predictor. Use the Tm method review and the ΔG threshold reference when you need calculation references.

Open first

Get to the sequence result faster

Use the workbench below for a single primer review, or switch to method and structure pages when the question is narrower.

Paste sequenceJump to the workbench and enter the primer.Open Check structuresMove to focused hairpin and dimer screening.Open Compare methodsReview why Tm tools disagree before recalculating.Open

Sequence

Track modification annotations for design context; confirm modification-specific thermodynamics in the vendor workflow.

Leave blank for single-primer Tm, GC, MW, hairpin, self-dimer, BLAST, or mismatch review.

Bases 0

Analyze sequences in batch

Use batch QC for larger primer or oligo sets.

Parameters

µM
mM
mM
mM

Choose a function

Enter a sequence and select an analysis function to see results.

What it checks

Tm, GC%, MW, extinction coefficient, hairpin, self-dimer, single-base mismatch effects, and BLAST handoff.

What output you get

Detailed metrics, threshold context, reverse complement, OD conversions, and structure-risk signals for lab review.

IDT relation

Compare outputs when checking assumptions against IDT OligoAnalyzer; use vendor tools when ordering or modification catalogs decide the final choice.

Privacy

Browser by default; History may save snapshots for browser-default primer review.

Example input: paste a 5' to 3' primer such as ATGCGTACGTTAGCCTGA, choose PCR or qPCR settings, then run Analyze for all-in-one output. Use single-metric pages only when one result needs a deeper explanation.

What Is the Primer Analyzer?

Use the Primer Analyzer when you need a single page to review primer Tm, GC%, molecular weight, hairpins, self-dimers, hetero-dimers with a second DNA sequence, single-base mismatch effects, and BLAST handoff before ordering or troubleshooting primers. It is for sequence output, while comparison pages are for choosing between tools.

If you searched for OligoAnalyzer, OligoEvaluator, or an oligo analysis tool, start here when you need the sequence result. Use comparison pages only when you are choosing between tools.

Paste a 5' to 3' DNA or RNA sequence, choose SpecSheet, PCR, qPCR, or Custom conditions, then review thermodynamics, base composition, mass, concentration conversion, complement sequence, and structure-risk signals. Public analysis can run without sign-in; Dashboard History may store an input snapshot when auto-save, session, or account history is enabled, and explicit sequence-library saves use the account-backed workflow. Hairpin, dimer, and mismatch checks are DNA-focused.

If you are comparing assumptions against IDT OligoAnalyzer, use this page as a browser-based primer review screen. Use vendor tools when ordering, modifications, or catalog-specific options determine the final decision. If the task is only melting temperature, use the Tm Calculator instead.

Use the Primer Analyzer when a basic Tm calculator is not enough and you need an all-in-one oligo analyzer for PCR or qPCR primer validation. In one review it reports nearest-neighbor Tm, GC content, molecular weight, extinction coefficient, OD conversions, reverse complement sequence, and structure risk signals.

For DNA primers, the analyzer can also run hairpin, self-dimer, hetero-dimer with a second sequence, BLAST handoff for external specificity review, and single-base Tm mismatch analysis. Use the dedicated single-metric pages when a result needs deeper interpretation.

Use the Primer Analyzer for BLAST specificity checking after the browser-default review. The public analysis path does not require an account; use the external BLAST handoff when database-backed specificity is the next decision.

How to Use the Primer Analyzer

  1. Enter your primer sequence (5' to 3') in the input field and choose DNA or RNA as the sequence type.
  2. Select a parameter preset (SpecSheet, PCR, qPCR, or Custom) that matches your application.
  3. Review the real-time property readouts as you type.
  4. Review the results panel: Tm values, GC%, molecular weight, extinction coefficient, and OD conversions.
  5. Use Hairpin to check for stem-loop formation, Self-Dimer for self-complementarity, and Hetero-Dimer after entering a second DNA primer.
  6. Use the BLAST handoff to open NCBI with the sequence for external specificity review.
  7. Open the dedicated GC, molecular-weight, Tm, or structure pages when one metric needs deeper interpretation.

Frequently Asked Questions

Is this a good IDT OligoAnalyzer alternative for primer analysis?
Yes for many single-primer and primer-pair review tasks. This page covers the core checks researchers usually want from OligoAnalyzer-style output: nearest-neighbor Tm, GC%, molecular weight, extinction coefficient, hairpin risk, self-dimer checks, hetero-dimer checks when a second DNA sequence is entered, BLAST handoff, and single-base mismatch analysis. It runs in the browser for public analysis; Dashboard History may store an input snapshot when saving is enabled, and explicit sequence-library saves use the account-backed workflow. IDT may still fit better when you want its ordering ecosystem or broader modification catalog.
Can I get detailed primer output here?
The Primer Analyzer is built for detailed primer review: it returns Tm, GC%, molecular weight, extinction coefficient, OD conversion values, reverse complement context, hairpin, self-dimer, hetero-dimer when a second DNA sequence is entered, single-base mismatch effects, and BLAST handoff options. Use it when you need one lab review screen before ordering or troubleshooting primers.
What should I enter before using the Primer Analyzer?
Enter a primer sequence in 5' to 3' orientation, choose DNA or RNA, select the parameter preset closest to your experiment, and set Na+, Mg2+, dNTP, and oligo concentration. Use modification selectors as design annotations, then confirm modification-specific thermodynamics in the vendor workflow. Example input: ATGCGTACGTTAGCCTGA. If you only need one metric after the all-in-one review, open the dedicated Tm, GC, molecular-weight, or structure page for deeper interpretation.
Which Tm value should I trust for PCR primer decisions?
Use the nearest-neighbor Tm as your primary decision metric for PCR and qPCR work. In this tool, Basic and Salt-adjusted values are best treated as quick context checks rather than the final answer. Choose the PCR or qPCR preset whenever possible so Na+, Mg2+, dNTP, and oligo concentration assumptions stay close to your real reaction conditions.
What makes a good PCR primer?
Good PCR primers commonly fall in these ranges: 18-25 bases, nearest-neighbor Tm around 58-62°C, GC content around 40-60%, no long homopolymer runs, a modest 3' GC clamp, no stable hairpins, no strong self-dimers, and primer-pair Tm values close to each other. The analyzer reports these criteria as a design screen; confirm assay-critical primers experimentally.
How do I design primers for GC-rich templates?
GC-rich templates (>65% GC) present challenges: primers will have high Tm and strong secondary structures. Strategies: (1) use shorter primers (18-20 nt) to keep Tm reasonable; (2) add DMSO (2-5%) or betaine (1-1.5 M) to destabilize secondary structures; (3) use high-fidelity polymerases optimized for GC-rich templates (e.g., KAPA HiFi, Q5); (4) increase denaturation temperature to 98°C; (5) open the Secondary Structure Predictor with DMSO correction to verify structure destabilization.
What is Tm mismatch analysis?
Tm mismatch mode estimates single-base primer substitution effects and reports the largest predicted Tm changes. It does not model template mismatches, multi-mismatch sets, or IUPAC degeneracy; use it as a local sensitivity screen before database-backed specificity review.

Related Tools

Tm Calculator

Use the dedicated Tm calculator when you need batch analysis, buffer-specific control, or a Tm-focused result.

Secondary Structure Predictor

Use the dedicated structure page when the main task is a hairpin calculator, primer dimer check, or ΔG threshold decision.

Molecular Weight Calculator

Open the MW calculator when you only need mass, extinction coefficient, and OD260 conversion details.

GC Content Analyzer

Use the GC calculator when base composition, GC clamp, or extreme GC content is the main design question.

OligoAnalyzer Alternatives

Choose between all-in-one primer analysis, focused structure checks, GC review, and vendor-specific workflows.

Review request

Check a result or ordering detail

Send the calculation, settings, or pool submission detail that needs a second look.

Related reading

Continue with the page or tool that matches the next decision in your experiment.

Tm Method ReviewΔG Threshold Method ReferenceSecondary Structure TutorialOligoPool vs IDT OligoAnalyzerOligoAnalyzer Alternatives