Primer binding track

Where the selected pair binds on the template, and what it produces, drawn on the template's own coordinates.

What it doesCopy Anchor Link

A primer pair is reported as two sequences, two melting temperatures and a product length. Those numbers are correct and they do not answer the question you actually have, which is whether the product covers the thing you care about — the insert, the junction, the mutation, the deletion you are screening for.

This puts the pair on the template. One lane holds the two primers, drawn over the bases they bind and pointing the way they read; the lane above holds the product they flank. Against the map's coordinates you can see at a glance whether the amplicon spans a feature, clips its edge, or sits beside it.

For a sequencing walk the upper lane is not an amplicon but a read — a walk primer has no partner, so there is no product to draw, and what it actually gives you is a readable window that begins some distance past the primer where the trace is not yet callable. That window, with the dead zone already removed, is what is shown.

When you'd use thisCopy Anchor Link

• Before ordering a screening primer set. A colony-PCR product has to differ between the two outcomes you are distinguishing, and that is a statement about where it lands.
• To check a junction is covered. An amplicon that stops at the junction tells you nothing about it; one that spans it does.
• To place a sequencing walk. Reads have to overlap, and the overlap is visible here in a way that a list of start positions is not.
• When a pair looks good and fails. A primer binding somewhere other than where you assumed is the first thing to rule out.

What this computesCopy Anchor Link

• The binding span and strand of each primer of the selected pair, on the template's own coordinates.
• The product they flank, with its length and the annealing temperature the designer computed for the pair.
• For a sequencing walk, the readable window each primer yields, with the uncallable region next to the primer excluded rather than counted as read.

What it does not doCopy Anchor Link

It draws the pair you have selected, on the template you designed against. It is not a specificity check: whether these primers also bind somewhere else — on this molecule or in a genome — is a separate question the designer's own screening answers, and a single clean-looking pair here can still have a second site off the drawing.