Advanced Fragment Size Calculator

Fragment Size Input Form

Enter ladder values and unknown band migration distances. Use commas, spaces, or new lines between values.

Sample Name

Distance Unit

Regression Mode

Gel Concentration (%)

Run Voltage (V)

Auto-sort ladder by migration distance

Marker Fragment Sizes (bp)

Marker Migration Distances

Unknown Band Distances

Ladder Band	Known Size (bp)	Migration Distance (mm)	log10(Size)
Band 1	10000	12	4.00000
Band 2	5000	23	3.69897
Band 3	3000	32	3.47712
Band 4	1500	44	3.17609
Band 5	500	66	2.69897

Formula Used

Standard curve model:
log10(Fragment Size in bp) = m × Migration Distance + b

Estimated fragment size:
Fragment Size = 10^{(m × Unknown Distance + b)}

This calculator uses semi-log regression, a common gel electrophoresis sizing approach. Known ladder sizes are transformed with log10, then regressed against measured migration distances.

A negative slope usually appears because smaller fragments migrate farther. The R² value helps you judge how well ladder measurements align with the fitted line.

How to Use This Calculator

Measure migration distances for each ladder band from the well to the band center.
Enter ladder fragment sizes and distances in matching order.
Enter one or more unknown sample band distances.
Choose the same unit you used during measurement.
Click the calculate button to generate sizes, regression statistics, and the standard curve plot.
Review whether each unknown result is interpolated or extrapolated.
Download the generated CSV or PDF report for documentation.

FAQs

1. What does this fragment size calculator estimate?

It estimates DNA fragment sizes from gel migration distances by fitting a semi-log standard curve using known ladder bands.

2. Why is log10 used for fragment size?

DNA migration commonly shows an approximately linear relationship between migration distance and the logarithm of fragment size over a practical sizing range.

3. What is the difference between interpolation and extrapolation?

Interpolation means the unknown band falls within the ladder distance range. Extrapolation means it falls outside, so confidence is usually lower.

4. How many ladder points should I enter?

At least three are required, but more well-spaced ladder bands usually improve curve stability and final fragment size estimates.

5. Can I use pixels instead of millimeters?

Yes. Consistency matters more than the specific unit. Use one unit for both ladder distances and unknown band distances.

6. What does the R² value tell me?

R² shows how closely the ladder data follow the fitted regression line. Values closer to 1 generally indicate a stronger fit.

7. Can this size RNA or protein bands?

The method is tailored to DNA fragment sizing assumptions. Other molecule types may require different standards, gels, and calibration behavior.

8. Why do my results look unrealistic?

Check band measurements, ladder order, distorted lanes, overloaded samples, and whether unknown bands lie far beyond the ladder range.