Gel Electrophoresis Calculator
Estimate a DNA fragment's size from how far it ran on a gel, calibrated against two ladder bands — the semi-log relationship that every gel is read with.
Fragments migrate a distance proportional to the log of their size: small fragments run far, large ones barely move.
How the gel electrophoresis calculator works
Fragments migrate a distance proportional to the log of their size: small fragments run far, large ones barely move. Two known ladder bands define the line, and the unknown's distance is read off it.
The relationship is only linear over the gel's resolving range, which depends on the agarose percentage. A 1% gel separates 500 bp to 10 kb well; use 2% for anything under 500.
Formula: log(size) is linear in distance: size = 10^(a + b × distance)
Worked examples
| Inputs | Estimated fragment size (bp) | Note |
|---|---|---|
| A band between 1 and 3 kb markers | 1,732 | about 1,700 bp |
| Closer to the small marker | 1,170 | just over 1 kb |
| Beyond the ladder | 534 | extrapolated |
FAQFrequently asked questions
How do I estimate fragment size from a gel?
Plot log size against distance for the ladder bands, draw the line, and read the unknown off it. Two bands bracketing the unknown are enough for a good estimate.
Why log size?
Because migration through the gel matrix falls off logarithmically with fragment length over the useful range. Outside it the relationship bends.
What agarose percentage should I use?
One per cent for 500 bp to 10 kb; two per cent for small fragments; 0.7% for large ones. The resolving range row gives the working limits.
How accurate is this?
About 10% when the unknown lies between two ladder bands close to it. Extrapolating beyond the ladder, or using distant bands, doubles that.
What about supercoiled plasmids?
They run anomalously fast. This estimate is for linear DNA only — cut the plasmid first if you need its true size.
Where these figures come from
- NCBI Bookshelf — Molecular Biology of the Cell — growth kinetics and molecular conventions
- National Human Genome Research Institute — the US genomics research institute
Last checked: September 2026. Formulas are the standard textbook forms; assumptions are stated on each page because they are where these models break.