my %class =(AGGAG => { name => 'sd' },
            TT    => { name => 'terminator' });  # I shortened the terminator for testing
$class{$_}{length} = length $_ for keys %class;

# ...

        $highlight{$name}{ pos($dna{$name}) - $class{$1}{length} } = $class{$1};

# ...

        my $class = $highlight{$key}{$pos};
        wrap(\@lines, $pos + $class->{length}, '</span>');
        wrap(\@lines, $pos, "<span class='$class->{name}'>");


##</code><code>##

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,