In that case, subtract 1 from the end value and you are good to go:

use strict;
use warnings;

my $seq =
  'dddddddddBBBBBBBBBBBBDDDDDDDDBBBBBBBBBBBBBBddddddddddddddddddddBBBB
+BBBBBBBBBBDDBBBBBBBBddddddddddddd';

while ($seq =~ /(B+)/g) {
    my $seg        = $1;
    my $seg_length = length ($seg);
    my $seg_end    = pos ($seq) - 1;
    my $seg_start  = $seg_end - $seg_length + 1;

    print $seg. "|" . $seg_start . "-" . $seg_end . "\n";
}
[download]

$ perl 11153140.pl 
BBBBBBBBBBBB|9-20
BBBBBBBBBBBBBB|29-42
BBBBBBBBBBBBBB|63-76
BBBBBBBB|79-86
$
[download]