sub wrap {
    my ($lines, $pos, $markup) = @_;
    my $idx = int($pos / 50);
    substr $lines->[$idx], $pos % 50, 0, $markup;
}


my %dna;
my $name1 = "name1";
my $name2 = "name2";

$dna{$name1} = "ATATTATCCCCCTATATATGGAGGGAGAGGGGGGGGGGGGGGGGGGGGGGGGGGGAGAGAGGAGATTTTTTTTTTTTTTTT";
$dna{$name2} = "ATATATTATATATATTATATTCGCGCGCGCGGCGCGCGCGGCGCGCGCGTTTTTTTTTTTTTTAGGAGAGAGAGGGAGGAGGAGAGGGGAGT";

my %class =(AGGAG => 'sd',
            TTTTT => 'terminator');
my $regex = join '|', keys %class;
$regex = qr/((?i:$regex))/;

my %highlight;
for my $name (keys %dna)  {
    while ($dna{$name} =~ /$regex/g) {
        $highlight{$name}{ pos($dna{$name}) - 5 } = $class{$1};
    }
}

for my $key (keys %highlight)  {
    print "<p> <b>$key</b><input type='radio' name='selected_intergenic' value='$dna{$key}'/> </p>";
    my @lines = unpack '(A50)*', $dna{$key};
    for my $pos (sort { $b <=> $a } keys %{ $highlight{$key} }) {
        my $class = $highlight{$key}{$pos};
        wrap(\@lines, $pos + 5, '</span>');
        wrap(\@lines, $pos, "<span class='$class'>");
    }
    print join "<br />", @lines;
}