my %sequences;  # this will be a hash of arrays

while (<DATA>) {
    @fields = split;
    for ( my $i=0; $i<@fields; $i+=2 ) {
        push @{$sequences{$fields[$i]}}, $fields[$i+1];
    }
}

for my $tag ( sort keys %sequences ) {
    my $i = 0;
    for my $val ( @{$sequences{$tag}} ) {
        printf( "%s [ %d ] : %s\n", $tag, $i+1, $sequences{$tag}[$i++] );
    }
}

__DATA__
A 100 B 200 C 400 A 150 C 250 D 550 B 350
A 200 B 300 C 500 A 600 B 700 C 800 D 900