Off-target analyzer

Scan primers against a reference genome

Paste a list of primer sequences and a target assembly. Each primer gets aligned (bowtie2, `-k 200`) and any unintended binding sites are reported with chromosomal coordinates and mismatch counts. A primer with more than a couple of hits at low mismatch is a specificity risk — redesign before ordering.

Primers
One primer per line as name sequence, or as FASTA (>name on its own line), or comma-separated. Sequences must be ACGTN, ≥15 nt. Max 200 primers per run.
0 parsed
Scan settings

12 live genomes. Cold-start ~70 s for non-human services; human is always-warm.

Higher budgets catch weaker binders but report many more hits.