Why is DNA migration semi-logarithmic?

In agarose gel electrophoresis the distance a fragment travels is roughly proportional to the logarithm of its size, not its size directly. Small fragments move much faster, so plotting log size against distance gives an approximately straight line that can be interpolated.

How does the interpolation work?

The tool finds the two ladder bands that bracket each unknown by migration distance, then draws a straight line between their log-sized values and the matching distances. It reads the unknown distance off that line and converts back from log to base pairs.

What distance unit should I use?

Any consistent unit works: millimetres measured with a ruler, or pixels measured in image software. The estimate depends only on the ratios between distances, so the choice of unit cancels out as long as the ladder and samples share it.

Why must my band fall within the ladder range?

Interpolation is only reliable between known points. A band that migrates further or less than every ladder band would require extrapolation off the end of the fitted line, where the semi-log relationship breaks down, so the tool flags it rather than guessing.

How accurate is the estimate?

On a well-run gel with closely spaced ladder bands, semi-log interpolation is typically within a few percent. Accuracy falls near the gel limits, with very large or very small fragments, and when ladder bands are far apart, so treat sizes as estimates.

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.

Tips and notes

Measure all distances from the same edge of the well to the same edge of each band, and keep the unit consistent between ladder and samples. Closely spaced ladder bands around your expected size give the best accuracy because the local line is short and the semi-log approximation holds well. Bands that migrate beyond every ladder band cannot be interpolated and are flagged, since extrapolation off the fitted line is unreliable. The estimate is a guide for sizing PCR products and restriction fragments, not a replacement for sequencing.