Real Sanger (chain-termination) sequencing mixes a template strand, primer, DNA polymerase, normal dNTPs, and a small spike of chain-terminating dideoxynucleotides (ddNTPs) that lack the 3'-OH needed to add the next base. Across a huge population of parallel primer-extension reactions, every incorporation event is an independent coin flip between a normal dNTP and a ddNTP:
P(this copy terminates exactly at position n)
= (1 − p)^(n − 1) · p
p = ddNTP:dNTP ratio (the slider)
This simulator runs that exact stochastic process on a real random A/T/G/C template for a chosen number of parallel strand-copies. Each copy independently walks base-by-base and stops the instant a ddNTP wins the flip, recording the terminating base — the complement of the template base at that position, matching what a real newly-synthesized strand would incorporate. The population of terminated fragments is then size-sorted (capillary electrophoresis separates strictly by length — shorter fragments migrate faster and are detected first) and colour-coded per fragment's terminal base using the real 4-colour Sanger convention, producing a live chromatogram trace and a reconstructed base-call sequence.
- Template length — how many bases must be read; longer templates need more coverage to sequence cleanly to the end.
- ddNTP : dNTP ratio — the real trade-off at the heart of Sanger sequencing: too low and most copies run off the end before terminating (few short fragments, poor early-read resolution); too high and almost every copy terminates in the first few bases, starving later positions of coverage and truncating the usable read — exactly like an over- or under-spiked real reaction.
- Strand-copy population — real reactions use trillions of template copies; this simulator uses a much smaller finite population so you can see the statistical "gaps" (positions no copy happened to terminate at) that a small or badly-tuned reaction leaves behind, rendered as a dropout in the trace.
Real-world relevance: exactly this chain-termination principle (invented by Frederick Sanger, 1977 Nobel Prize) sequenced the first genomes and, in its automated fluorescent-ddNTP capillary form, remains the gold-standard method for short, high-accuracy reads (plasmid checks, clinical variant confirmation) even in the next-generation-sequencing era.