while ($rest=~/\<REGION seq\_beg\=\"(\d+)\"\s+pdb\_beg\=\"\d+\"\s+seq\_end\=\"(\d+)\"\s+pdb\_end\=\"\d+\"\s+type\=\"(\w+)\"\/\>/mg)
{
	$start=$1;
	$end=$2;
	$type=$3;

	$TM_part_to_store = "$start-$end";
	
	$length_part="$start-$end";

	if($type==1)
	{ 
		substr($topo_initial, ($start-1), ($end-$start+1), ($side1 x ($end-$start+1)));
	}

	elsif($type==2)
	{ 
		substr($topo_initial, ($start-1), ($end-$start+1), ($opposite{$side1} x ($end-$start+1)));
	}

	elsif($type eq 'B')
	{ 
		push @all_TMs_line, $TM_part_to_store; 
	}

	else
	{ 
		substr($topo_initial, ($start-1), ($end-$start+1), ('U' x ($end-$start+1)));
	}
}