Keep track of the positions in an array:

use warnings;
use strict;

my @lines = <DATA>;

my @pos;
foreach my $line (@lines) {
    chomp $line;
    my @columns = split( /\s+/, $line );
    my $score = $columns[1];
    if ($score < 50) {
        push @pos, $columns[0];
    }
    else {
        print "@pos[0, -1]\n" if @pos;
        @pos = ();
    }
}
print "@pos[0, -1]\n" if @pos;

__DATA__
1  50
2  50
3  1
4  10
5  49
6  8
7  50
8  5
9  5
10  40
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Note: I changed \t to \s+ just to create a self-contained example.