You can store the lengths in the %class hash:
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}'>");
($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,