Are you counting from 1 or zero? If from 1 then it should probably be this (to give the first match at 10 to 21 inclusive):

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);
    my $seg_start  = $seg_end - $seg_length + 1;

    print $seg. "|" . $seg_start . "-" . $seg_end . "\n";
}
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To say what you expect the answer to be when posting have a read of How to ask better questions using Test::More and sample data.

Counting from 0, as usual. If you check the first substring, then it starts (correctly) at 9, but it should end at 20, not 21, am I wrong? It has a length of 12, and it includes position 9.

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 . "-" . $seg_end . "\n";
}
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$ perl 11153140.pl 
BBBBBBBBBBBB|9-20
BBBBBBBBBBBBBB|29-42
BBBBBBBBBBBBBB|63-76
BBBBBBBB|79-86
$
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🦛

I added that and it works fine now, thank you!


my $seg_end    = pos ($seq)-1;
    my $seg_start  = $seg_end - $seg_length+1;
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