$VAR1 = {
          '27069_1' => {
                              'stop' => 214601666,
                              'start' => 214600991
                            },
          '14644_1' => {
                              'stop' => 166950686,
                              'start' => 166950125
                            },
}


##</code><code>##

$tss{$ch[0]}{$id}={
                start=>$start,
                stop=>$stop
        }; 


##</code><code>##

for(keys(%the_hash)){
                my $ch=$_;
                my @a=keys(%{$tss{$ch}});
                my $tid=pop(@a);
                my $s=$tss{$ch}{$tid}{'start'}; 
                my $st=$tss{$ch}{$tid}{'stop'};
                foreach(keys(%{$tss{$ch}})){my $k=$_;
                if($tss{$ch}{$k}{'start'} eq $s and $tss{$ch}{$k}{'stop'} eq $st #and $_ ne $tid
                ){  
                        delete($tss{$ch}{$k});
                }
..... and so on