Tool for sequence search in databases

ClustalW 
Multiple sequence alignment program for DNA or proteins

GeneCards
Integrated database of human genes that provides concise genomic related information

Pre-designed primers and probes databases

Database of predesigned qPCR primers and probes

Primer bank
Database of predesigned qPCR primers and probes

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

Primer design tools

Tool for web-based primer design 

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

RealTimeDesign
Tool for web-based qPCR primer design

Exon Primer
Tool for designing exon-spanning primers

Tools for evaluating designed PCR systems

mFold
Tool for checking secondary structures of DNA or RNA

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

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

Tools for evaluating oligonucleotide properties

Tool for establishing the physical and chemical properties of oligonucleotides

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

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

Copy number calculator
Tool for calculating the number of copies of a template