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Free! Primer Analysis Software

"I wish I had analyzed my primers before ordering for the third time. Now I check all my primers with NetPrimer before ordering" -Stacey McCann, Cancer Biology Program, Stanford University

About NetPrimer

NetPrimer combines the latest primer analysis algorithms with a web-based interface allowing the user to analyze primers over the Internet. All primers are analyzed for primer melting temperature using the nearest neighbor thermodynamic theory to ensure accurate Tm prediction. Primers are analyzed for all primer secondary structures including hairpins, self-dimers, and cross-dimers in primer pairs. This ensures the availability of the primer for the reaction as well as minimizing the formation of primer dimer. The program eases quantitation of primers by calculating primer molecular weight and optical activity. To facilitate the selection of an optimal primer, each primer is given a rating based on the stability of its secondary structures. A comprehensive analysis report can be printed for individual primers or primer pairs.

Major Features

  • Primer Melting Temperature (Tm): Predicts primer melting temperature using the accurate nearest neighbor thermodynamic algorithm.

  • Primer Properties: Tm , molecular weight, GC%, optical activity (both in nmol/A260 & µg/A260), DG, 3' end stability, DH, DS, and 5' end DG.

  • Primer Secondary Structures: Hairpins, dimers, cross dimers, palindromes, repeats and runs.

  • Primer Rating: Quantitative prediction of the efficiency of a primer.

  • Comprehensive Report: Prints complete primer analysis for an individual primer or primer pair

  • Primer Pairs: Analyze individual primers or primer pairs.

  • Comprehensive Help: Details all the formulas and references used in primer analysis algorithm.

Our Other Products

AlleleID®: For designing qPCR assays and microarray experiments. Supports primer/probe design on nucleotide sequence alignments, exon junctions for bacterial identification, selective cDNA amplification and much more.

Array Designer: Design efficient and specific probes for SNP detection, SNP genotyping and microarray gene expression profiling.

Beacon Designer™: For designing real time PCR assays.

PrimerPlex: Multiplex SNP Genotyping oligo design tool for suspension array systems such as Luminex xMAP® technology.

Primer Premier: Comprehensive PCR primer design software.

SimGlycan®: For glycan analysis and structure prediction.

SimLipid: Lipid characterization tool.

SimVector: Draw plasmid maps and simulate cloning experiments.

Xpression Primer: Tagged primers, sequencing primers, nested PCR for in-vitro expression analysis.

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