Create, find, and manage primers

For a step-by-step forward-primer save, cancel, detach, and reattach workflow, see Create, detach, and reattach a forward primer.

Open the Primers drawer

Open a nucleotide sequence. On the far-right sequence tool rail, find the Tools section and select Primers. It is the fourth tool in that section, below Annotations; point to an icon to see its label. In the drawer that opens to the left of the rail, choose Attached, Find, or Create. If saved primers do not load, the drawer shows Retry.

Create a primer from a selection

1. Open a nucleotide sequence and select the intended binding region.
2. Right-click the selection.
3. Select Create Forward Primer → or Create Reverse Primer ←.
4. Review the sequence, direction, length, melting temperature (Tm), GC percentage, mismatch information, and available reaction-condition fields.
5. Enter a name, review the metadata, and choose a save location.
6. Select Save Primer.

The saved primer remains available to later library and Registry workflows.

Create a primer manually

For a standalone DNA or RNA oligo, use Create and use DNA and RNA oligos.

Adjust direction and binding length

The primer form contains → Forward and ← Reverse direction controls. It also contains an editable 3′ length value and Increase length and Decrease length controls. Binding site returns the sequence viewer to the proposed binding range.

Review primer calculations

The form shows Length, Tm, and GC values. With template context, it can also show an exact-match or mismatch summary. When the selected local model supports them, the form shows reaction-condition inputs beside the calculation.

These displayed values and warnings are design aids. Use reaction conditions that match your protocol. To configure the local model, see Configure primer Tm calculations.

Edit primer metadata and modifications

The editor includes Edit primer name, Metadata, and Add schema field controls. Its modification picker also has a shared Clear action for active filters.

For a standalone DNA or RNA oligo workflow, see Create and use DNA and RNA oligos.

Find and attach saved primers

1. Right-click the sequence or a selected region and select Attach Primers.
2. In Find Primers, review Entire sequence, Custom region, or Use selection when that scope is available.
3. For a custom region, review the Start and End values.
4. Review the 3′ match length, minimum effective Tm, and maximum mismatch controls.
5. Use Filter by name... and select Both, Forward, or Reverse to filter the displayed results.
6. Select Find Primers.
7. Review each proposed binding and select Attach beside each primer that you want to bind.
8. Open Attached to review the resulting bindings.

The Find Primers panel starts with Entire sequence when no range is selected. Starting Attach Primers from a sequence selection can expose a selected-region scope. Opening Primers from the toolbar and opening Attach Primers from the canvas can start with different scope states.

Attach multiple results

After you attach one primer, the Find session stays open so that you can attach other matching results.

Retry loading or searching

The Attached view has Retry when saved primers fail to load. The Find Primers view has a separate Retry when it cannot reach the primer matcher. A failed load or search does not mean that the workspace has no saved or matching primers.

Manage an attached primer

The Attached view can show the saved primer's sequence, direction, status, binding range, and chemistry details.

The sequence context menu can show Copy bases, Copy for IDT, Edit Primer, and Detach Primer when the selected primer and workspace state support those actions.