I might do something along these lines for the first and second loops:

print "Number of pairs for top of punnett square:";
chomp( $numTop = <STDIN> );
my @top = (0) x $numTop;

for ( @top )
{
  print "Enter pairs ( xx ): ";
  chomp( $_ = <STDIN> );
}
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And definitely don't use the C style for loop for that last loop. Use for my $t (@top) {, etc. Then you don't have to worry about off by one errors, or having to index your array to get to the elements.