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PCR, qPCR & Molecular Biology

Declared PCR Product Boundary Workbench

Calculate a linear or origin-crossing circular amplicon span from declared one-based inclusive product boundaries on a known template coordinate system.

Biology · experimental measurements

Make the coordinate convention and every retained segment explicit without pretending to discover primer binding, orientation, specificity or an experimental product.

Private calculations in your browser · explicit inputs and model boundaries
Example preview · Linear ampliconDeclared product interval
121–860740 bp

The bar is the inclusive distance between the two entered boundaries on the linear template.

  1. 1EnterProvide the known values
  2. 2CalculateResults update automatically
  3. 3VerifyReview the details and units
Try an example

Enter values in bp.

Enter values in one-based coordinate.

Enter values in one-based coordinate.

Calculation result

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Enter valid values to see the result.

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Understand the relationship

The reasoning behind the result

Inclusive coordinates count both boundary bases

L = b − a + 1

The added one retains both declared endpoints.

Coordinate arithmetic cannot establish how the endpoints were obtained.

A circular interval can cross the origin

Lwrap = (N − a + 1) + b

The directed span is split into the tail from a through N and the head from 1 through b.

The result depends on the declared direction and origin.

A product is an experimental claim

Primer specificity, orientation, secondary structure, template variation and reaction conditions determine whether an amplicon is produced.

This workbench reports only an entered map interval.

Follow the numbers

Map a circular origin-crossing interval

  1. Retain coordinates 4,800 through 5,000 as the first segment.
  2. Retain coordinates 1 through 225 as the second segment.
  3. Add 201 and 225 inclusive bases.

The declared circular span is 426 bp; this is not a product prediction.

Quick guide

How to use this calculator

  1. Use one coordinate system and enter the product boundaries, not merely primer 3′ endpoints unless those are also the intended product boundaries.
  2. Choose circular only when the directed product is allowed to cross coordinate 1.
  3. Verify primer binding, orientation and product identity independently.

Calculation method

Calculation and interpretation

Make the coordinate convention and every retained segment explicit without pretending to discover primer binding, orientation, specificity or an experimental product.

Linear size = end − start + 1. Circular origin-crossing size = (template length − start + 1) + end.

Worked example

Map a circular origin-crossing interval

The declared circular span is 426 bp; this is not a product prediction.

Linear size = end − start + 1. Circular origin-crossing size = (template length − start + 1) + end.

Supported inputs

Precision and limits

One-based inclusive convention

Every coordinate lies from 1 through the entered template length and both endpoints are counted.

Declared direction

For circular templates, start greater than end means the directed interval crosses coordinate 1.

No primer search

Sequences, binding sites, mismatches and strand orientation are not inferred.

No experimental product prediction

The result does not establish specificity, amplification, yield or a gel band.

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