Free Oligo Tools
Select the tool that matches the sequence task: Tm Calculator for melting temperature, Primer Analyzer for primer review, Secondary Structure Predictor for hairpin or primer-dimer checks, GC Content Analyzer for composition risk, Oligo Dilution Calculator for resuspension and working stocks, and Batch Sequence QC for large sequence sets.
Calculation methods and privacy
The calculators are organized around common oligonucleotide design tasks: melting temperature, GC composition, molecular weight, secondary structure, dilution, batch QC, coverage, and vendor-file preparation. Use a focused calculator when the input is simple, or use Batch Sequence QC when the sequence set is large.
Tm calculations and related method pages document published thermodynamic assumptions, including nearest-neighbor parameters for DNA oligonucleotides. Structure tools report hairpin and dimer risk using threshold-based interpretation, not a synthesis guarantee.
Sequence calculations run in your browser. The site does not need to upload sequence text, result rows, or order files for analysis.
Planning an Oligo Pool?
Use the main oligo pool guide when the question is broader than one calculator: application fit, design constraints, synthesis method, QC interpretation, and vendor choice.
Oligo Pool Guide
Definition, applications, design, QC, vendors, and calculators
Synthesis Planning
Method choice, quotes, budget, and post-delivery checks
QC Metrics
Uniformity, dropout, error rate, and representation thresholds
Research References
Method notes, calculation references, and literature links
Choose a Tool by Task
| I want to... | Use this tool | Key output |
|---|---|---|
| Calculate primer Tm with NEB, IDT, or Twist-style settings | Tm Calculator | Nearest-neighbor Tm, salt correction, and batch results |
| Run a combined primer check | Primer Analyzer | Tm, GC%, MW, hairpin, dimer, mismatch, and BLAST link |
| Review a primer with detailed oligo-analysis output | Primer Analyzer | Combined primer review with client-side calculations |
| Calculate only GC% or flag GC outliers before ordering | GC Content Analyzer | GC%, base composition, batch outlier risk |
| Calculate Tm for 1 primer | Tm Calculator | Tm (°C), ΔH, ΔS, ΔG, suggested Ta |
| Analyze a primer pair (Tm + dimers) | Primer Analyzer | Pair Tm, ΔTm, self/cross-dimer ΔG |
| Check hairpins, self-dimers, or primer dimerization risk | Structure Predictor | Hairpin/dimer ΔG, structural diagrams |
| QC an entire oligo pool (1000+ sequences) | Batch Sequence QC | Pass/fail per sequence, pool statistics |
| Get a compact MW, OD260, and property sheet | Oligo Properties | MW, ε₂₆₀, OD260 conversions, GC%, reverse complement |
| Convert file format for vendor ordering | Vendor Format Adapter | IDT/Twist/GenScript-ready order file |
| Resuspend or dilute primers, probes, or oligo pools | Dilution Calculator | Stock concentration, working dilution, and printable bench protocol |
How the Tools Compare with NEB, IDT, and Primer3
Use this table to choose between a quick Tm calculation, combined primer analysis, batch QC, and vendor-file preparation.
| Feature | OligoPool.com | NEB | IDT OligoAnalyzer | Primer3 |
|---|---|---|---|---|
| Tm Algorithm | SantaLucia 1998 | SantaLucia 1998 | SantaLucia 1998 | SantaLucia 1998 |
| Batch Processing | Up to 10,000 sequences | Single-sequence web calculator | Single-sequence analysis form | Available through command-line use |
| Secondary Structures | Hairpin and dimer checks | Not the main purpose | Hairpin, self-dimer, and hetero-dimer options | Primer design constraints |
| Pool/Library QC | Composition, structure, error, and coverage checks | Tm-focused | Limited | Primer picking, not pool QC |
| Account Required | No | No | Sign-in or registration requested | No (CLI) |
| Calculation Location | Runs in the browser | Web application | Account-based web tool | Local CLI or hosted interface |
| Vendor Format Export | IDT, Twist, and GenScript formats | Not a vendor order formatter | IDT only | Primer design output |
Compare with NEB, IDT, and Common Tm Calculators
Use these comparison pages when buffer assumptions, account requirements, privacy, or output format affect the tool you choose.
vs NEB Tm Calculator
Tm method, salt settings, batch handling, and privacy
vs IDT OligoAnalyzer
Primer checks, account requirements, batch QC, and privacy
Free Oligo Tools
Pick a tool by task, output, and privacy requirement
Tm Methods Compared
Nearest-neighbor, salt correction, Wallace, and GC approximation
Core Calculators
Common calculations for oligonucleotide design, resuspension, and bench preparation
Tm Calculator
Calculate melting temperature using nearest-neighbor thermodynamics. Supports salt and DMSO corrections.
GC Content Analyzer
Analyze GC percentage with batch processing. Identify extreme compositions and risk levels.
Molecular Weight Calculator
Calculate molecular weight, extinction coefficient, and concentration conversions. Supports modifications.
Dilution Calculator
Calculate resuspension volumes, dilutions, and pool-specific concentrations with printable protocols.
Oligo Properties Calculator
Quick property sheet for MW, GC%, OD260 conversions, reverse complement, and a compact Tm summary.
Sequence Analysis
Primer, structure, and batch checks for sequences that need more than one value
Secondary Structure Predictor
Use as the dedicated hairpin calculator and primer dimer check with ΔG threshold interpretation.
Primer Analyzer
Primer review including Tm, GC%, molecular weight, self-complementarity, and dimer checks.
Batch Sequence QC
Analyze up to 10,000 sequences for quality issues. Detect homopolymers, low complexity regions, and more.
Quality Control
Oligo pool checks for yield, representation, sequencing depth, and coverage planning
Synthesis Error Rate Calculator
Predict full-length product percentage from coupling efficiency and compare coupling-yield assumptions.
Pool Uniformity Estimator
Estimate dropout rate and concentration variation. Get QC sequencing depth recommendations.
Coverage Calculator
Calculate required oligos for CRISPR libraries, tiling applications, and custom coverage strategies.
Format Conversion
Clean sequence files and prepare order formats after design checks are complete
Why Use OligoPool.com Tools?
No Account Required
Open a calculator, enter a sequence, and review results without registration or ads.
Local Sequence Handling
Calculations run in the browser, so sequence text does not need to be uploaded for analysis.
Published Method Basis
Tm and related calculations reference established thermodynamic methods, including SantaLucia parameters.
Batch-Ready Analysis
Use batch QC and composition checks when a pool or library contains thousands of sequences.
Method References
Review method comparisons, calculation assumptions, and salt-correction behavior before using calculated values in a protocol.
Planning an Oligo Pool?
Start with the oligo pool guide when the question is bigger than one calculator. Use the vendor comparison after design rules, QC expectations, and application fit are clear.