You just need to match your label and save that in a variable:
my $label;
# reads each line
while (my $line = <INFILE>){
...
if ($line =~ />(.*)/){
$label = $1;
# Calculates percent
} else{
...
print "The percentage of G's and C's for $label, @seq[1] is $percent\n";
}
}