Engine
Primer design
Select a region; Primer3 proposes pairs. Melting temperature, GC content, product size and self-complementarity warnings sit in the table next to each pair, and the set you keep leaves as an order sheet in the format your vendor expects.
Primer3
design engine
IDT / Twist
order sheets
CPU
engine class
Free
to run
01
What the feature does
Primers are the least glamorous part of a design and one of the most common places for a project to lose a week. A pair whose melting temperatures do not match, a product too long to be convenient, a pair that binds itself happily — none of this is subtle, and all of it is easy to miss when the set is assembled by hand across a dozen junctions.
This engine is Primer3 behind a table. You mark the region you want covered, the engine proposes pairs, and each pair arrives with the properties you would otherwise be checking one at a time. Sort by whichever one matters, keep the set that fits, and send it onward as an order sheet.
02
In the interface
Select the region
Click a feature on the annotated map, choose a junction from the assembly, or type coordinates. Working from a construct in the catalog means the region already carries its annotation, so you are selecting a described thing rather than a span of numbers.
Set the targets
Melting temperature window, acceptable GC range, product size range, and how many pairs you want proposed. Defaults are sensible for verification work and every one of them is visible and editable before the run.
Read the pairs table
One row per pair, with melting temperature for each primer, the difference between them, GC content, product size and position. Sort on any column; the pair that is best on temperature is often not the best on product size, and the table lets you see that trade directly.
Check the warnings
Self-complementarity, hairpin potential and pair-to-pair interference are flagged per row rather than buried in a log. A flagged pair is not removed — it is marked, so the decision to use it anyway is a decision someone made.
Cover a whole construct
Running across every junction in an assembly produces one coherent set rather than a dozen separate jobs, with overlaps and gaps shown against the map so you can see what the set actually covers.
Export as an order sheet
The kept set exports as an IDT or Twist order sheet laid out the way those upload paths expect, or as GenBank, FASTA or SBOL when the primers belong with the construct record rather than with an order.
03
A worked example
- Region
- Insert junctions, construct SS-0421
- Melting temperature window
- 58–62 °C
- Target product size
- 450–750 bp
- Pairs proposed
- 20
- Pairs kept
- 5
- Warnings flagged
- 2 pairs, both excluded
- Export
- IDT order sheet
- Engine class
- CPU — no credits
Twenty proposals, five kept, two set aside on warnings and one dropped because its product landed too close to a neighbouring amplicon to be read apart easily. That last one is the judgement the table exists to support: nothing was wrong with the pair, it simply did not fit alongside the others.
The kept set stays attached to the construct version it was designed against. If the construct is edited afterwards, the primers are re-checked against the new sequence rather than silently inherited, which is one of the checks design validation runs.
04
Who runs it, and what it costs
Verification work is the common case — teams designing checks across the junctions of an assembly before anything is ordered. Ag-biotech groups run it in batch across a whole series and export one consolidated order sheet, which is considerably easier to reconcile against an invoice than twenty separate ones. Labs receiving a design from elsewhere use it to confirm that the primer set they were sent still matches the sequence they were sent with it.
Primer design is a CPU engine and free to run, at any volume and with unlimited exports. Prepaid credits — $25 for 250 credits, one credit for roughly one Standard job — apply only to GPU engines, and nothing in this feature touches them.
Ready to run it
Try this in the Splice Platform.
CPU engines are free to run. GPU engines run on prepaid credits.
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