my %endpoints;
$endpoints{ $-[0] } = $+[0] 
    while $chromosome =~ m[(CG.*?AT)]g;

##</code><code>##

my %endpoints;
$endpoints{ $-[0] - 1 } = $+[0] - $-[0] - 1
    while $chromosome =~ m[(CG.*?AT)]g;

...
while( my( $begin, $end ) =  each %exon_endpoints ) {
    print substr( $chromosome, $begin, $end ), "\n\n";
}


##</code><code>##

my @exons;
push @exons, eval "\\substr( \$chromosome, 
                   $-[0] - 1,
                   $+[0] - $-[0] - 1 )"
    while $chromosome =~ m[(CG.*?AT)]g;

...
for( @exons ) {
    print $$_, "\n\n";
}