Guides

The 4-step design wizard

Every primer-panel design in Primer Architect goes through the same four steps. Each step is independently validatable so you can flip back and forth without losing context.

Step 1 — Select reference

Pick the organism reference assembly. Twelve curated genomes are live:

Mammalian — human (GRCh38.p14), mouse (GRCm39), pig (Sscrofa11.1), Chinese hamster (CriGri-PICR).
Other vertebrates — chicken (GRCg7b), zebrafish (GRCz11).
Invertebrates / model organisms — drosophila (BDGP6.46), C. elegans (WBcel235).
Plants — arabidopsis (TAIR10), maize (Zm-B73-REFERENCE-NAM-5.0).
Microbial — yeast (R64-1-1), E. coli K-12 (U00096.3).

You can also upload your own FASTA or GenBank file — the picker has an Upload custom genome action at the bottom. GenBank inputs (.gb, .gbff) are converted to FASTA in your browser before upload. Once indexed it appears in the same picker tagged yours, and the trash icon next to it removes it from storage.

Step 2 — Select target sequence

Choose the gene to amplify, either:

By gene: type the gene symbol or an alias (e.g. TP53 or p53). A curated short-list of common oncology targets is suggested.
By disease: pick a disease from the curated list; we'll show the associated genes.

Step 3 — Select target bases

The interactive gene track shows your target's exons and a draggable selection band that defines the amplified range.

Click + drag on the track to define a new range.
Drag the highlighted band to move the selection.
Drag either edge to resize.
Type exact Initial / Final base values to override.

Step 4 — Scheme parameters

Amplicon length — target size for each amplicon; ±10 % range.
Number of pools — multiplex pools to avoid primer-pair collisions.
Target overlap — defaults to ~10 % of amplicon size; override for tighter coverage.
Min base frequency — minimum allele frequency to keep in primer design.
Backtrack — try alternative paths to prevent gaps (slower).
High-GC — relax the upper GC threshold for high-GC genomes.

What happens after submit

The design call can take up to 5 minutes. Behind the scenes, the design engine runs with your parameters and returns a primer/amplicon manifest. You land on the results page, where you can:

Explore the primer list, pool breakdown, and amplicon coverage map.
Run an Off-target check — bowtie2 against the chosen genome with a tunable mismatch budget (0 / ≤1 / ≤2 / ≤3).
Run a Variants check— scan each primer's 3' last 5 nt against gnomAD v4 common variants (MAF threshold 5% / 1% / 0.1%). Variants at the 3' end cause silent dropout in carrier patients, so flagging them lets you redesign before ordering.
Export to BED, TSV, CSV, or a robot-ready format (Opentrons, Hamilton, Echo, 96-well plate map).