Punnett Square Calculator
Map every possible allele combination from two parents and instantly see genotype ratios, phenotype probabilities, and carrier percentages. Supports monohybrid (one gene) and dihybrid (two independent genes) crosses, with options for complete dominance, incomplete dominance, codominance, and X-linked inheritance.
Worked example
Aa x Aa (complete dominance): the four cells are AA, Aa, Aa, aa giving a 1:2:1 genotype ratio and 3:1 phenotype ratio. AaBb x AaBb (dihybrid): 16 cells, phenotype classes are 9 A-dom B-dom : 3 A-dom b-rec : 3 a-rec B-dom : 1 a-rec b-rec.
How the Punnett square works
A Punnett square is a grid used to predict the probability that offspring inherit particular allele combinations. For a monohybrid cross (one gene), each parent contributes one of their two alleles to each gamete. The 2 x 2 grid has four cells, each equally probable at 25%. Counting how many cells contain each genotype (AA, Aa, aa) gives the genotype ratio. Because a dominant allele (A) masks the effect of a recessive allele (a) under complete dominance, both AA and Aa individuals show the dominant phenotype, so the dominant percentage is the count of those cells divided by four.
Dihybrid crosses and independent assortment
A dihybrid cross tracks two genes simultaneously. When the genes sit on different chromosomes (or far apart on the same one), they assort independently per Mendel's second law. Each parent produces four gamete types (e.g., AB, Ab, aB, ab for an AaBb parent), giving a 4 x 4 grid of 16 equally probable offspring cells. Under complete dominance for both genes, the classic phenotype ratio is 9:3:3:1 (nine show both dominant traits, three each show one dominant and one recessive, and one shows both recessives). This calculator computes those four phenotype class probabilities for any dihybrid combination.
Incomplete dominance and codominance
Not all traits follow simple dominant-recessive inheritance. With incomplete dominance, heterozygotes (Aa) show a blended phenotype, neither fully dominant nor fully recessive. An Aa x Aa cross then yields a 1:2:1 phenotype ratio rather than the classic 3:1. Codominance is similar in grid structure but the heterozygote expresses both alleles distinctly rather than blending them, the ABO blood type system is a well-known example where A and B alleles are codominant over each other. Select either mode in this calculator to see the three-class phenotype split.
X-linked inheritance
X-linked traits are encoded on the X chromosome. Males (XY) are hemizygous, meaning they have only one copy, so a single recessive allele is sufficient to produce the phenotype. Females (XX) need two recessive copies to be affected and may be carriers with one copy. In this calculator, choose X-linked recessive to flag the carrier status of heterozygous offspring and to note that hemizygous males in the Aa row of the grid are affected, not carriers. Common X-linked recessive conditions include hemophilia A and red-green color blindness.
Custom trait names and practical uses
Entering a dominant and recessive trait name (e.g., Round seeds and Wrinkled seeds) labels the insight panel with real-world language rather than abstract letters. This is useful for students preparing lab reports or breeders analyzing livestock coat color, disease resistance, or other heritable traits. Remember that the ratios are theoretical expectations over many offspring. A litter of four kittens, for example, may deviate substantially from the 3:1 ratio by chance.
Limitations
This calculator models one or two genes at a time with standard Mendelian assumptions. It does not handle genetic linkage (where two genes on the same chromosome are inherited together more often than expected), epistasis (where one gene masks or modifies the effect of another), or polygenic traits like height and skin tone that involve dozens of loci. Penetrance and expressivity variation also affect real-world phenotype frequencies. For clinical genetic counseling involving human disease alleles, always consult a qualified medical geneticist.
Common cross outcomes at a glance
| Parent 1 | Parent 2 | Genotype ratio (AA:Aa:aa) | Dominant % | Recessive % |
|---|---|---|---|---|
| AA | AA | 4 : 0 : 0 | 100% | 0% |
| AA | Aa | 2 : 2 : 0 | 100% | 0% |
| AA | aa | 0 : 4 : 0 | 100% | 0% |
| Aa | AA | 2 : 2 : 0 | 100% | 0% |
| Aa | Aa | 1 : 2 : 1 | 75% | 25% |
| Aa | aa | 0 : 2 : 2 | 50% | 50% |
| aa | AA | 0 : 4 : 0 | 100% | 0% |
| aa | Aa | 0 : 2 : 2 | 50% | 50% |
| aa | aa | 0 : 0 : 4 | 0% | 100% |
Genotype and phenotype ratios for the nine possible monohybrid crosses under complete dominance. Percentages round to one decimal place.
Frequently asked questions
What does the 3:1 phenotype ratio mean in an Aa x Aa cross?
When two heterozygous carriers reproduce, each offspring independently has a 75% chance of inheriting at least one dominant allele (AA or Aa) and expressing the dominant phenotype, and a 25% chance of inheriting two recessive alleles (aa) and expressing the recessive phenotype. This 3:1 ratio is a long-run probability, not a guarantee for any specific family.
What is the difference between genotype and phenotype ratios?
The genotype ratio describes the proportion of offspring with each specific allele combination (AA : Aa : aa). The phenotype ratio describes the proportion that actually shows each observable trait. Because AA and Aa both display the dominant trait under complete dominance, the phenotype ratio collapses those two genotype classes into one, giving 3:1 instead of 1:2:1.
How do I use this for a dihybrid cross?
Switch the cross type to Dihybrid, then select genotypes for both gene A and gene B for each parent. The calculator builds a 4 x 4 grid of 16 cells and reports the probability of each of the four phenotype classes (both dominant, A-dominant only, B-dominant only, both recessive). For AaBb x AaBb parents the classic result is 9:3:3:1.
What is incomplete dominance and how does it change the ratio?
With incomplete dominance, neither allele is fully dominant. Heterozygotes (Aa) show an intermediate phenotype rather than the dominant one. An Aa x Aa cross under incomplete dominance produces a 1:2:1 phenotype ratio (25% dominant, 50% intermediate, 25% recessive) instead of the 3:1 ratio seen with complete dominance. Classic examples include flower color in snapdragons and four-o'clock plants.
Can this calculator predict eye color or other polygenic traits?
No. Eye color, height, and skin tone are polygenic traits controlled by many loci simultaneously. A single-gene or two-gene Punnett square captures only a tiny fraction of the variation. This tool is most accurate for clearly Mendelian single-gene traits such as ABO blood type, cystic fibrosis carrier status, or the seed traits Mendel studied in peas.
What are X-linked recessive traits and how does the ratio differ?
X-linked recessive traits are encoded on the X chromosome. Because males have only one X (hemizygous), they are affected by a single recessive allele, while females need two copies to be affected but may be carriers with one. If a carrier female (X^A X^a) mates with an unaffected male (X^A Y), 50% of sons are affected and 50% of daughters are carriers. Common examples are hemophilia A, Duchenne muscular dystrophy, and red-green color blindness.