An allele is a form of a gene at a particular position (locus) on a chromosome.15 It is the bit of coding DNA at that place.p6

Typical plants and animals have two sets of chromosomes, one set inherited from each parent.123 These organisms are called diploid. Since such organisms have two sets of chromosomes, they have (except on the sex chromosomes) two alleles at each gene locus.p6

If the two alleles are identical, the individual is called a homozygote and is said to be homozygous. If instead the two alleles are different, the individual is a heterozygote and is heterozygous.205

Dominance 
In a heterozygote the effect of one allele may completely ‘mask’ the other. That is, the phenotype produced by the two alleles in heterozygous combination is identical to that produced by one of the two homozygous genotypes.212 

The allele that masks the other is said to be dominant to the latter, and the alternative allele is said to be recessive to the former. This idea originates in the work of Gregor Mendel, the founder of genetics.

In other cases, both alleles contribute to the phenotype.

Example 
The inheritance of alleles, and their dominance, can be represented in a Punnett square.

An example is the gene for blossom colour in many species of flower. A single gene controls the colour of the petals, but there may be several different versions (or alleles) of the gene.

In this example, parents have the genotype Bb (capital letters show dominant alleles and lower-case letters to show recessive alleles). If B (capital) is found in their genotype, the flower will be red. Therefore, the only time a flower is not red is when the genotype is bb (there are no capital 'B's).

The probability of the flowers having different genotypes are: BB is 25%, Bb is 50%, and bb is 25%. The phenotype of the flower will always be red if a dominant B is in the genotype. Therefore, there is a 25% chance of getting a flower which is not red, and 75% chance of getting a flower which is red.

Recessive 

The pattern of inheritance of recessive genes is quite simple. If they are heterozygous with a dominant allele, the appearance (phenotype) is the same as a dominant homozygote. Only if both alleles are recessive does the recessive allele show in the phenotype b.

Incomplete dominance 
This is when the dominant allele is not completely dominant over the recessive allele. This means both the alleles have a degree of phenotypic expression in the hybrids. In this case the functional product formed is a little different or is intermediate between the product produced by to the dominant allele and the recessive allele.

For example: Mirabilis jalapa. The heterozygote of this plant produces flowers in the F1 generation of the colour pink in contrast to the red (dominant) and white (recessive) homozygotes.

Sex linkage 
Genes on the sex chromosomes are said to be sex linked. In the XY sex determination system of mammals, the X chromosomes carry a full set of genes, but the Y chromosomes carry few genes. Alleles or genes which are not sex-linked are called autosomal.

Different alleles at a locus 
There are three ways alleles at a locus may differ.p6 They are:
By origin. Alleles differ by origin if they come from the same locus on different chromosomes. Thus, for example, the two alleles at a particular locus in a diploid individual are always different by origin. They sit on different chromosomes.
By state. Alleles are different by state if they have different DNA sequences. This idea can be adjusted to need. For example, we may judge them as different only if the difference changes the amino acid sequence of a protein.
By descent. Alleles are different by descent if they do not share a common ancestor. Of course, all alleles have a common ancestor if one goes back far enough. What is meant is they share a fairly recent ancestor. 

Two alleles different by descent may or may not be of different state. For example, one may carry a mutation, so making its DNA sequence different.

Terms introduced 
 Allele
 Locus
 Homozygote
 Heterozygote
 Dominant
 Recessive
 Dominance (genetics)
 Punnett square
 Sex linkage
 Autosomal

Related pages 
Allele frequency

References 

Chromosomes