my (@rep1,@rep2,@rep3);

my $prefix = qr/[ACTG]{3}/;
my $rep1 = qr/TTGT/;
my $rep2 = qr/GGTT/;
my $rep3 = qr/ACCT/;
my $postfix = qr/[ACTG]{2}/;

while (my $line = <DATA>) {
    if ($line =~ /^$prefix
                   $rep1
                   $postfix/x )
    {
     push @rep1, $line;    # ignoring, for regex instruction, 
                           #  the need to push your cached line, etc...
    }
    elsif  ($line =~ /^$prefix
                 $rep2
                 $postfix/x )
    {
                 ....