IDT SciTools® Web Tools

These software applications determine the properties of any oligo sequence entered, as well as facilitate the intelligent design of assay conditions, all at the click of a button. The suite is easy to use and makes it simple to add each optimized oligonucleotide to an ongoing order list ready for purchase.

Oligo Analysis Tools

OligoAnalyzer® Tool
Identifies oligonucleotide properties, including melting temperature, hairpins, dimers and mismatches
UNAFold Tool
Secondary structure analysis
Dilution Calculator
Find the volume needed to dilute your oligo stock to a lower concentration
Resuspension Calculator
Find the volume needed to resuspend a dry oligo to a desired concentration

qPCR and PCR Amplification

PrimeTime® Predesigned qPCR Assay Database
Selects qPCR primers and probe sequences for human, mouse, and rat gene expression assays based on up-to-date sequence data
PrimerQuest® Tool
Allows highly customized designs for PCR primers and qPCR assays
RealTime PCR Tool
Selects custom qPCR assays for any species
PrimeTime Multiplex Dye Selection Tool


rhAmp™ Genotyping Design Tool
Choose predesigned rhAmp SNP Assays or design assays for SNPs not currently included in the predesigned assay library

CRISPR Genome Editing

Alt-R® Predesigned Cas9 crRNA Selection Tool
Selects guaranteed crRNAs targeting human, mouse, rat, zebrafish, or nematode genes
Alt-R Custom Cas9 crRNA Design Tool
Designs custom crRNAs to sequences from any species
CRISPR-Cas9 Design Checker
Assesses on- and off-targeting potential of user-designed protospacer sequences

Gene Regulation and Knockdown

Predesigned DsiRNA Selection Tool
Selects DsiRNAs and TriFECTa® RNAi Kits for your human, rat, or mouse targets
Custom DsiRNA Design Tool
Generates DsiRNAs for any sequence from any species

Gene Design

Codon Optimization Tool
Automates codon optimization of a gene to the species of your choice

Please use following format when citing SciTools:

PrimerQuest® program, IDT, Coralville, USA. Retrieved 12 December, 2012.