# Restriction Fragment Length Calculator 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. > Canonical page: https://elysiatools.com/en/tools/restriction-fragment-length - **Category:** Education - **Keywords:** restriction fragment length, restriction digest calculator, plasmid double digest, restriction map fragments, dna cut fragments bp, circular plasmid digestion, linear dna fragments, 4 cutter 256 bp, 6 cutter 4096 bp, agarose gel fragment size, molecular biology, lab calculator ## 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. ## Inputs - **Substrate Topology** (select): Circular plasmids give n fragments from n cuts; linear DNA gives n+1. - **Input Mode** (select): Enter exact cut positions, or just the number of cut sites for an average estimate. - **Substrate Length (bp)** (number): Total length of the substrate (plasmid or linear DNA) in base pairs. - **Cut Positions (bp, comma-separated)** (text): Cut coordinates counted from base 1 (positions mode); each must be strictly inside the substrate and unique. - **Cut Site Count** (number): Number of cut sites (count mode); fragments = n circular or n+1 linear. - **Decimal Places** (number) ## 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 - Select the substrate topology: circular plasmid or linear DNA. - Choose exact cut positions or cut-site count as the input mode. - Enter the substrate length in base pairs and provide the required positions or site count. - The 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. ## Frequently asked questions ### How many fragments result from n cuts? A circular substrate produces n fragments, while linear DNA produces n+1 fragments. ### How do I enter exact cut positions? Enter unique, comma-separated coordinates counted from base 1, such as 1000, 2000. ### What does the cut-site count mode calculate? It calculates the expected fragment count and average fragment length assuming an even distribution of cut sites. ### Does the calculator account for circular wrap-around? Yes. For circular substrates, it includes the fragment that crosses the origin. ### What are the expected frequencies of four- and six-base recognition sites? In random DNA, a four-base site is expected about once every 256 bp and a six-base site about once every 4096 bp. ## Related tools - [Amino Acid Composition Analyzer](https://elysiatools.com/en/tools/amino-acid-composition): Per-residue counts and mol%, group tallies, Kyte–Doolittle GRAVY score, and ProtParam MW from a sequence. 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