When I copied your data, I get single spaces instead of tab characters. Try to use split as follows:

use strict;
use warnings;

my $df = 10;
while (<DATA>) {
    chomp $_;
    my @values = split;
    foreach my $val (@values) {
        my $DNA_conc = $val * $df * 50;
        print $DNA_conc;
        print "\n";
    }
}

__DATA__
0.250   0.413   0.432   0.345   0.786   1.001   0.987 
0.984   0.125   0.678   0.243   0.657   0.342   0.743   
0.986   0.734   0.764   0.650   0.457   0.965   0.836
[download]

This is the output I get:

125
206.5
216
172.5
393
500.5
493.5
492
62.5
339
121.5
328.5
171
371.5
493
367
382
325
228.5
482.5
418
[download]