OK. I said I didn't understand what you meant! How about this then (damn the hard-coded 5):

use strict;
use warnings;

my $string='YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]';
my $offset = 0;
my $substring = 'N[115]';
my @positions;

while (1) {
    my $pos = index($string, $substring, $offset);
    last if $pos < 0;
    $offset = $pos + length($substring);
    
    $pos -= 5 * @positions;
    push @positions,$pos;
}

print "Positions: @positions\n";
[download]

Gives:

Positions: 12 30 37
[download]

I added another N for testing.

Update:I have recieved a /msg puzzling about a line of code. Here is a description of $pos -= 5 * @positions;
We need to adjust the position by the length of [115] (5 characters), not just just once but for each position found. I use @positions in scalar context to get me the number of elements (scalar context is forced by the multiplication operator *). The first time around the loop the number of elements in @positions is zero, so $pos is not decremented. Subsequently it is decremented by 5 * number-of-items-found.