Primer Design Tool

Automated two-tailed RT-qPCR assay design for microRNAs and isomiRs with cooperative RNA:DNA thermodynamics.

microRNA Identifier

Mature Target RNA Sequence

▸ Advanced Settings & IsomiR Specificity

Calculate IsomiR Specificity

Assay Mode: Standard (Discriminate isomiRs) Target Specific IsomiR

Custom Variant / Off-Target Sequences (one per line)

Auto-Evaluate Canonical IsomiRs

Transcriptome Off-Target Scanner Persistent Cache

Na+ (mM)

Mg2+ (mM)

dNTPs (mM)

RT Primer (µM)

qPCR Primer (µM)

RT Temp (°C)

ΔG min (kcal/mol)

ΔG max (kcal/mol)

ΣΔG max (kcal/mol)

Top N Candidates

Tries per Pair

PRNG Seed

5' probe min (nt)

5' probe max (nt)

3' probe min (nt)

3' probe max (nt)

qPCR Tm min (°C)

qPCR Tm max (°C)