Gel Electrophoresis Band Size Calculator
Sizing DNA or RNA fragments from gel electrophoresis requires plotting the log of the ladder band sizes against their migration distances to create a standard curve, then interpolating the unknown band's size from its migration distance. This calculator performs least-squares linear regression on log(size) vs migration distance using your ladder data, then estimates the size of your unknown band. Enter ladder band sizes (bp) and their migration distances (mm), then enter the migration distance of the unknown band.
Band sizing method
log10(size in bp) = a + b * migration distance (mm)
The calculator performs ordinary least-squares linear regression of log10(size) against migration distance for all ladder bands. It then solves for the unknown size: estimated size = 10^(a + b * distance). This is the standard analytical method described by Sharp et al. (1973) and used in all standard molecular biology references.
Tips for accurate gel sizing
- Run the gel until the largest ladder band has migrated at least 20 mm from the well for resolution.
- Use at least 4 to 6 ladder bands that bracket your unknown band size.
- Measure migration distances from the centre of the well to the centre (brightest point) of each band.
- Check the R-squared value from this calculator: values above 0.99 indicate a reliable standard curve.
- Do not extrapolate beyond the ladder range; only interpolate within it.
Gel electrophoresis sizing: frequently asked questions
How does gel electrophoresis separate DNA fragments by size?
In agarose gel electrophoresis, DNA fragments migrate through the gel matrix under an electric field. Smaller fragments migrate faster and travel further from the well. The migration distance is inversely related to the log of the fragment size in base pairs.
What is the standard relationship between migration distance and fragment size?
The relationship is log(size in bp) vs migration distance (mm) is approximately linear for fragments within the linear range of the gel. A standard curve (regression line) is generated from ladder bands with known sizes, then used to interpolate unknown fragment sizes.
What agarose percentage should I use for different fragment sizes?
For fragments of 5,000 to 50,000 bp, use 0.5 to 0.8% agarose. For 200 to 5,000 bp, use 1 to 1.5% agarose. For fragments below 500 bp, use 2 to 3% agarose. For very small fragments (less than 100 bp), consider PAGE instead of agarose.
What DNA ladder should I use?
Common ladders include the 1 kb Plus DNA Ladder (sizes from 100 bp to 12,000 bp), the 100 bp ladder (sizes from 100 to 3,000 bp), and the Lambda HindIII digest (sizes from 125 to 23,130 bp). Choose a ladder whose range covers your expected fragment sizes.
Can this calculator be used for RNA gels?
Yes. The same log-linear interpolation approach applies to denaturing RNA gels. Use an RNA ladder with known sizes and measure migration distances in the same way. The fragment sizes returned will be in nucleotides (nt) rather than base pairs (bp).
Official sources
- Sharp P.A., Sugden B., Sambrook J. (1973). Detection of two restriction endonuclease activities in Haemophilus parainfluenzae: Biochemistry, NCBI PubMed Central.
- NCBI NIH gel electrophoresis protocols: NCBI Bookshelf: Molecular Cloning Methods.
Reviewed by the CalculatorHub team, edited by James Graham, 14 June 2026. See our methodology.