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, Batch Sequence QC for large sequence sets, and Vendor Format Adapter for vendor-specific order files.
Browse all 19 active tools. If you need a number now, do not start with this index. Open the dedicated calculator first, then return here only when you need to choose between Tm, primer review, structure risk, GC composition, dilution, batch QC, or vendor-file preparation.
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.
Calculations run in your browser by default. Dashboard History can store the full input snapshot when auto-save, session, or account history is enabled; Library saves and membership/API workflows can send sequence assets by design.
Choose by Workflow
Start with the workflow when the job has multiple checks. Use the tool table below only when you already know the exact calculator you need. Core workflows include PCR Primer Workflow, Build Pool Architecture, Run Pool Pre-Order QC, CRISPR Guide QC Workflow, and Vendor Order Prep Workflow. For pool-risk follow-up, open the Error Rate Calculator, Coverage Calculator, or Vendor Format Adapter.
PCR Primer Workflow
Tm, GC, hairpin, dimer, MW, and dilution checks for primer-pair ordering decisions.
Build Pool Architecture
Assemble inserts, adapters, barcodes, primers, and motifs before pool-scale QC.
Run Pool Pre-Order QC
Screen sequence quality, export passing rows, and prepare vendor formatting after review.
Estimate Synthesis Yield
Estimate full-length yield, truncation burden, and pool-scale error risk before ordering.
Plan Coverage Depth
Estimate library coverage, redundancy, and dropout risk for pooled experiments.
CRISPR Guide QC Workflow
Coverage planning, MOI scale, guide QC, synthesis fields, and stable CRISPR library order prep.
Vendor Order Prep Workflow
Vendor-specific IDT, Twist, GenScript, or Dynegene export after QC and vendor selection.
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. Combined primer review with client-side calculations |
| Calculate only GC% or flag GC outliers before ordering | GC Content Analyzer | GC%, base composition, and batch outlier risk |
| Get a compact MW, OD260, and property sheet | Oligo Properties Calculator | MW, epsilon260, OD260 conversions, GC%, and reverse complement |
| Calculate DNA/RNA molecular weight and mass conversions | Molecular Weight Calculator | Molecular weight, nmol/ug conversion, and sequence mass |
| Check hairpins, self-dimers, or primer dimerization risk | Secondary Structure Predictor | Hairpin and dimer risk with structure interpretation |
| QC an entire oligo pool before synthesis ordering | Batch Sequence QC | Pass/fail rows, pool statistics, privacy-safe review packet, and handoff exports |
| Estimate synthesis error burden for a pool | Error Rate Calculator | Full-length yield, truncation burden, and expected error count |
| Model representation spread across an oligo pool | Uniformity Estimator | Representation skew, dropout risk, and uniformity interpretation |
| Estimate read depth and redundancy coverage | Coverage Calculator | Coverage probability, redundancy targets, and dropout risk |
| Resuspend or dilute primers, probes, or oligo pools | Dilution Calculator | Stock concentration, working dilution, and printable bench protocol |
| Generate index barcodes with distance and diversity checks | Barcode / Index Designer | Barcode FASTA/CSV, pairwise distance, GC range, and base diversity |
| Build synthesis-ready pool constructs from inserts and adapters | Oligo Pool Architecture Builder | Full constructs, length/GC flags, CSV/FASTA, and explicit Library save |
| Plan a DMS or saturation mutagenesis library | DMS / Degenerate Library Planner | Variant count, codon diversity, stop risk, and screening burden |
| Analyze NGS read-count representation after pool construction | NGS Pool Representation QC | Dropout, zero-count rows, Gini, CV, and fold representation |
| Plan pooled CRISPR screen scale before ordering | CRISPR Library Planner | MOI, seed cells, cells per guide, controls, and bottleneck status |
| Tile NGS capture or MPRA probes across target regions | Probe Tiling Designer | Tiled probe constructs, GC/length flags, CSV/FASTA, and explicit Library save |
| Convert FASTA, CSV, TSV, or plain sequence files | Format Converter | Clean generic sequence formats before QC or vendor-specific order formatting |
| Generate vendor-specific order-file columns after QC | Vendor Format Adapter | IDT, Twist, GenScript, or Dynegene-ready review file |
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 | 1,000 free / 50,000 member 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 for free runs; login/license for member limits | No | Sign-in or registration requested | No (CLI) |
| Calculation Location | Browser by default; saves/API are explicit | 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
Thermodynamics
Run sequence-level checks that are saved into calculation history.
Tm Calculator
Melting temperature, salt correction, and batch Tm.
GC Content Analyzer
Single and batch GC distribution checks.
Molecular Weight Calculator
DNA/RNA molecular weight and mass conversion.
Oligo Properties Calculator
Combined GC, Tm, MW, and sequence property review.
Secondary Structure Predictor
Hairpin, self-dimer, and structure-risk screening.
Primer Analyzer
Primer suitability, end stability, and design checks.
Pool QC
Audit pooled designs, coverage, dilution, and synthesis risk.
Batch Sequence QC
Batch upload and paste quality control workflow.
Error Rate Calculator
Estimate pool synthesis error burden.
Uniformity Estimator
Model representation spread across oligo pools.
Coverage Calculator
Estimate read depth and redundancy coverage.
Dilution Calculator
Resuspension, dilution, and pool mixing calculations.
Workflow
Prepare sequence files, vendor formats, and exploratory checks.
Barcode / Index Designer
Generate distance-aware barcodes and save index sets to the sequence library.
Oligo Pool Architecture Builder
Assemble inserts, barcodes, adapters, and motifs into full constructs.
DMS / Degenerate Library Planner
Estimate degenerate codon diversity, stop burden, and screening scale.
NGS Pool Representation QC
Analyze read-count representation, dropout, Gini skew, and QC flags.
CRISPR Library Planner
Plan MOI, cells per guide, replicate scale, controls, and bottlenecks.
Probe Tiling Designer
Tile NGS capture or MPRA probes and save generated probe constructs.
Format Converter
Convert FASTA, CSV, TSV, and plain sequence formats.
Vendor Format Adapter
Adapt sequence orders for vendor submission formats.
Why Use OligoPool.com Tools?
Free Tier Without Account
Open the free calculator tier, enter a sequence, and review results without registration; member limits use a license.
Browser-Default Handling
Public calculations run in the browser by default; History, Library, and API paths use explicit save or request actions.
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.