In a Punnett square a capital letter stands for a allele.?

Capital letters on Punnett Squares represent dominant genes, while lowercase letters represent recessive genes. For example, if the trait "T" is a tall gene and the trait "t" is a short gene. When you get your results (if both parents are heterozygous for tallness, Tt) you get four possible results, 1 TT (homozygous tall), 2 Tt (twice, heterozygous tall Tt), and 1 tt (homozygous short). If there is a dominant gene there, that gene will be displayed. Only if there are two recessive genes will the recessive trait be displayed.