RealTimeDesign
Tool for web-based qPCR primer design

ClustalW
Multiple sequence alignment program for DNA or proteins

Beacon Designer Free Edit
Online tool for analyzing SYBR® Green primers and TaqMan® probes

Poland
Determine Tm for your amplicon before running a HRM assay.

Primer3
Tool for web-based primer design

Netprimer
Tool for analyzing primers for Tm, secondary structures and primerdimer formation

BLAST
Tool for sequence search in databases

Ensembl
Annotation of several eukaryotic genomes

mFold
Tool for checking secondary structures of DNA or RNA

Oligonucleotide Properties Calculator
Tool for establishing the physical and chemical properties of oligonucleotides

Ambion DNA/RNA Concentration Conversion Calculator
Tool for converting between different concentration units

DNA/RNA Absorption Concentration Calculator
Tool for converting measured absorption to concentration of DNA or RNA in your sample

RTPrimerDB- primer and probe database
Database of predesigned QPCR primers and probes

Real-time PCR primer and probe sets
Database of predesigned QPCR primers and probes

Exon Primer
Tool for designing exon-spanning primers

Primer-BLAST
Finding primers specific to your PCR template (using Primer3 and BLAST)