$string1 = "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIIMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMIIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMOMMMMMMMMMMMMM";

$string2 = "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMMMMMOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMIIIIIMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMIIIMMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMIIIMMMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMIIIMMMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMIIIMMMMMMMMMMMMOOOOOOOOOOOOOOOMMMMMMMMMMIIIIIIMMMMMMMMMMMMOOOOOOOOOOOOOOOOOMMMMMMMMMMMMII";

##</code><code>##

#N-terminal
$Nterm_topo=substr($string2,0,1);
$Nterm_pred=substr($string1,0,1);

#TM number and orientation for $string2
$TM_topo=0;
$all_tms='';
while($string2=~/M+/g)
{
$TM_topo++;
$start_tm=$-[0]; 
$end_tm=$+[0]-1;
				$all_tms.=$start_tm."-".$end_tm."#";
}
chop $all_tms;

#TM number and orientation for $string1
$TM_pred=0;
while($string1=~/(M+)/g) { $TM_pred++; }	

################ Orientation ############################
$correct_TM_location=0;
@split_tms_real=split(/#/, $all_tms);

for ($i=0;$i<=$#split_tms_real;$i++)
{
$corresp_TM_real=$split_tms_real[$i];
if($corresp_TM_real=~/(\d+)\-(\d+)/) 
  { 
     $start_real=$1; $end_real=$2;
     $real_length=$end_real-$start_real+1;
     $substr_pred=substr($string1,$start_real, $real_length);
					$count_M=$substr_pred=~tr/M//;

if($count_M>=5) {$correct_TM_location++;}
				}					
}				

if( $Nterm_topo eq $Nterm_pred  $TM_topo==$TM_pred && $TM_pred==$correct_TM_location) 
{
   $correct_topo++; 
}