my %class =(AGGAG => { name => 'sd' },
            TT    => { name => 'terminator' });  # I shortened the ter
+minator 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}'>");
[download]

($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,
[download]

Thanks; this does the job perfectly. I was trying to do the same by creating another hash, called %size where I was recording the length of the patterns and then use those instead of the "5" but could not make it work. Many thanks again. and also to the other Monks taking the time to reply.