PEGYNDRQAVNGSFYKLTFAPTFKVGSIGDFFSRPEIRFYTSWMDWSKKLNNYA
......................................................

##</code><code>##

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)));
	}
}

##</code><code>##

413     1-6
413     7-15
413     16-34
413     35-46
413     47-53
413     54-67
413     68-83
413     84-85
413     86-95
413     96-112
413     113-118
413     119-133
413     134-142
413     143-153
413     154-160
413     161-174
413     175-181
413     182-186
413     187-193
413     194-217
413     218-224
413     225-237
413     238-244
413     245-266
413     267-273
413     274-282
413     283-290
413     291-304
413     305-311
413     312-320
413     321-328
413     329-347
413     348-355
413     356-369
substr outside of string at myscript.pl