What is a Punnett square and how is it used?

A Punnett square is something used to find out how traits
are passed down.  Punnett squares were the result of the work by Mendel on pea plants
and he realized many different things about how traits pass down.  An example:  Say you
want to cross a plant that is tall to one that is short.  The short trait is recessive
in pea plants and the tall trait is dominant.  (Remember that the dominant trait will
show in the plant over the recessive, it only needs one allele from a parent, while the
recessive can only show when it's totally recessive.)  Since the short trait is
recessive, we know that the short plant must have two short alleles from its "parents".
 The tall plant could have two tall, or one tall and one short allele, since the tall
trait is dominant.  I'll show both examples.

First, let's
look at a short plant, which would have two short alleles, this is also called
homozygous recessive.  We'll use lower case t to mean the recessive trait.  And we'll
cross it with a tall plant that is homozygous dominant, or it has two tall alleles.
 We'll use upper case T to mean the dominant trait.  So we make a table separating the
two alleles from both plants, one across the top and one down the left side.  We fill in
the table by using the allele at the top of each column in each spot below it and using
the allele at the left of the row in each spot to the
right.

T T

t Tt
Tt

t Tt Tt

Sorry,
you'll have to imagine lines in between the columns and rows. What you end up with is
what would be the genotypes (the two alleles) of the progeny (the children).  When you
cross this example, each progeny ends up with Tt, which means it has one tall and one
short allele (this is called heterozygous).  Again, since tall is dominant, the plants
will look tall (their phenotypes).

#2  Now let's
cross the short plant (homozygous recessive tt) with the tall plant that has one tall
and one short allele (heterozygous Tt).

T
t

t Tt tt

t Tt
tt

This time, half of the progeny (children)
will have the Tt genotype (heterozygous), while the other half have the tt genotype
(homozygous recessive).  The Tt half will look tall since tall is dominant, while the tt
half will look short.

Just like all probability,
these numbers aren't exact in real life, but the more you experiment with, the closer it
gets to those numbers.

Hopefully this gives you
a good start.