$/="//\n";
while(<>)
{
	if($_=~/^(\d+)\s+(.*)/m)
	{$seq_length=$1; $ID=$2;}

	$seq='';
	while($_!~/([A_z]+)/mg) 
	{  $part1=$1; $seq.=$seq.$part1; } 

 	$top='';
	while($_=~/([S\.]+)/mg) {$part2=$1; $top.=$top.$part2;}

	print ">$ID\n$seq\n$top\n";
}
$/="\n";