my %data;

while (<DATA>)
{
	chomp;
	
	my ($firstnum, $secondnum, $thingy, @bits) = split /\s/;	
	my $key = sprintf("%s\x00%s\x00%s", $firstnum, $secondnum, $thingy);

	for my $i (0 .. $#bits)
	{
		$data{$key}[$i] = [] unless exists $data{$key}[$i];
		push @{ $data{$key}[$i] }, $bits[$i];
	}
}

foreach my $key (sort keys %data)
{
	print join q[ ], split "\x00", $key;
	print q[ ];
	print join q[ ], map { join '/', @$_ } @{ $data{$key} };	
	print "\n";
}

__DATA__
1 51 Brahui A C A A T 
1 51 Brahui A C A G T 
3 51 Brahui A C A G C 
3 51 Brahui A C G A T 
5 51 Brahui A C G A T 
5 51 Brahui A C G G C 
7 51 Brahui A C G A T 
7 51 Brahui A C G G T 
9 51 Brahui A C G G T 
9 51 Brahui A C G G T