##
ACTG..
TGAT..
G-T is a mispair
##
##
my @dna; # contains the sequence
my @comp; # contains the complement
while (@dna) {
foreach my $base (@dna) {
++$counter;
}
foreach my $base2 (@comp) {
++$counter2;
}
if (($base[$counter] == 'A') && ($base2[$counter2] !~ 'T') {
print "mismatch : $base[$counter] \t $base2[$counter2]\n";
}
# etc
}