Electrophoresis DNA Ladder Band Size Estimator

When you run DNA on an agarose gel beside a molecular weight ladder, you can read off approximate fragment sizes by comparing how far each band travelled. This tool turns that visual comparison into a number by fitting the well-known semi-logarithmic relationship between fragment size and migration distance.

How it works

Across most of a gel’s range the migration distance of a fragment is linearly related to the logarithm of its size:

distance is approximately proportional to log10(size)

For each unknown band, the tool finds the two ladder bands whose distances bracket it, then interpolates on the log scale:

log10(size) = log10(s1) + (d - d1) / (d2 - d1) x (log10(s2) - log10(s1))
size        = 10 ^ log10(size)

Here d1 and d2 are the bracketing ladder distances with sizes s1 and s2, and d is the unknown band’s distance.

Worked example

Suppose you run a 1% agarose gel with a 1 kb DNA ladder alongside a PCR product. Using a ruler on a printed gel image, you measure these ladder band positions from the top edge of the well:

Your unknown PCR band sits at 34 mm. It falls between the 1,500 bp band (31 mm) and the 1,000 bp band (37 mm). Interpolating on the log scale:

log10(size) = log10(1500) + (34 − 31) / (37 − 31) × (log10(1000) − log10(1500))
            = 3.176 + 0.5 × (3.000 − 3.176)
            = 3.176 − 0.088
            = 3.088
size        = 10^3.088 ≈ 1,224 bp

So the fragment is approximately 1,200 bp. This is consistent with a PCR product designed to amplify a 1.2 kb region. If your expected product was 800 bp, you would instead suspect a non-specific amplification product.

Getting accurate measurements from gel images

The most common source of error in band sizing is inconsistent measurement. Use these practices for the best results:

• Measure from the same reference edge. Always measure from the bottom edge of the well to the top edge of each band, or always to the center — what matters is consistency.
• Use pixel coordinates in image software. Rather than a physical ruler, load the gel photo into ImageJ or similar and use the measurement tool for pixel distances. This avoids parallax and image distortion.
• Straighten the gel image first. Even slight tilts introduce systematic errors, especially for bands near the edges of the gel.
• Do not compare across different gel runs. Ladder and samples must be on the same gel; migration depends on agarose percentage, buffer, and run conditions, which differ between gels.

Choosing the right agarose percentage

Gel percentage determines the size range you can resolve well:

Choose a gel percentage that puts your expected fragment size in the middle of the ladder range — this is where the semi-log fit is most linear and your size estimate is most accurate. Bands near the top or bottom of the ladder’s range have the largest interpolation error.