Plan denaturation, annealing, and extension times with confidence. Estimate copies, mass, concentration, and runtime quickly. Review cycle-by-cycle growth for smarter wet-lab setup choices daily.
| Scenario | Initial Copies | Cycles | Efficiency % | Decay % | Length bp | Volume µL | Adjusted Copies | DNA ng | Time |
|---|---|---|---|---|---|---|---|---|---|
| Short clean amplicon | 100 | 35 | 95.0 | 0.8 | 250 | 25 | 1.246E+11 | 34.1495 | 00:44:45 |
| Medium fragment assay | 500 | 30 | 90.0 | 0.5 | 450 | 20 | 4.012E+10 | 19.7854 | 00:39:30 |
| Fast screening reaction | 1,000 | 28 | 85.0 | 1.2 | 150 | 50 | 3.358E+9 | 0.5521 | 00:37:24 |
1. Constant efficiency model: Copies = Initial Copies × (1 + Efficiency)Cycles.
2. Decay adjusted model: Each cycle uses a reduced efficiency. Effective Efficiency = Base Efficiency × (1 − Decay × Previous Cycles).
3. Cycle factor: Cycle Factor = 1 + Effective Efficiency.
4. Updated copies: New Copies = Previous Copies × Cycle Factor.
5. Suggested extension: Suggested Extension Seconds = Amplicon Length ÷ Polymerase Speed.
6. Estimated DNA mass: DNA ng = Copies × bp × 660 ÷ Avogadro Constant × 109.
7. Estimated concentration: Concentration = DNA ng ÷ Reaction Volume µL.
This calculator gives planning estimates. Real PCR yield depends on template quality, primer design, reagent balance, instrument behavior, and plateau effects.
PCR performance depends on both chemistry and timing. Very short denaturation or annealing stages can reduce product quality, while long extension stages increase total runtime without always improving yield. A practical cycle calculator helps you balance amplification quality against instrument availability and daily workflow targets.
Ideal doubling rarely continues across every cycle. Primer depletion, inhibitor carryover, polymerase fatigue, and product competition gradually reduce performance. That is why this tool reports both constant efficiency growth and decay adjusted growth. The comparison helps you judge how optimistic a simple doubling model might be.
Copy count alone can feel abstract during laboratory planning. Estimated DNA mass and concentration make the output easier to connect with downstream steps such as gel loading, cleanup, cloning, or sequencing preparation. These values remain theoretical, but they provide a better planning framework than cycle count alone.
It estimates final copy number, fold amplification, run time, DNA mass, concentration, and cycle-by-cycle growth using both constant and decay adjusted efficiency models.
One assumes the same efficiency every cycle. The other reduces efficiency gradually. The second estimate is usually more realistic for longer runs.
No. Perfect doubling is an ideal assumption. Real reactions lose efficiency because of reagent limits, product competition, suboptimal primers, and template issues.
It models a small drop in amplification strength from one cycle to the next. It helps you avoid overestimating yield in later cycles.
The calculator divides amplicon length by polymerase speed. This gives a practical minimum extension estimate for your chosen fragment size.
No. It is a theoretical estimate based on molecule count and fragment length. Actual recovered mass depends on chemistry, cleanup, and measurement method.
It can help with timing and broad amplification expectations, but it does not replace proper qPCR efficiency analysis, baseline handling, or Cq interpretation.
Total runtime affects throughput, instrument scheduling, and thermal exposure. A small timing change per cycle can significantly alter the full run length.
Important Note: All the Calculators listed in this site are for educational purpose only and we do not guarentee the accuracy of results. Please do consult with other sources as well.