Exact or averaged restriction-fragment sizes: circular substrates give n fragments from n cuts (wrapping the origin), linear DNA n+1, from cut positions or a site count. Includes 4/6-base recognizer frequencies (256/4096 bp) and agarose resolution advice. Sambrook & Russell / REBASE derived. Educational use only.
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Key facts
Category
Education
Input types
select, number, text
Output type
json
Sample coverage
4
API ready
Yes
Overview
The Restriction Fragment Length Calculator estimates DNA fragment sizes after restriction digestion. Choose circular plasmid or linear DNA, then enter exact cut positions for fragment lengths or provide a cut-site count for an average estimate.
When to use
Predict fragment sizes for a circular plasmid single or double digest.
Calculate the fragments produced when linear DNA is cut at known coordinates.
Estimate fragment count and average size when only the number of restriction sites is known.
How it works
1Select the substrate topology: circular plasmid or linear DNA.
2Choose exact cut positions or cut-site count as the input mode.
3Enter the substrate length in base pairs and provide the required positions or site count.
4The calculator returns fragment sizes, fragment count, mean length, minimum and maximum lengths, and the conserved total length.
Use cases
Planning plasmid restriction digests and checking expected band sizes.
Interpreting restriction maps for linear DNA or PCR products.
Comparing predicted fragment sizes with agarose gel observations for educational or experimental planning.
Examples
1. pUC19 circular double digest
Molecular biology student
Background
A 2686 bp circular pUC19 plasmid has restriction sites at positions 1000 and 2000.
Problem
Determine the fragment sizes expected from the two cuts.
How to use
Select Circular plasmid and Cut positions, enter 2686 as the substrate length, and enter 1000, 2000 as the cut positions.