I wondered what would happen if other letters had square bracketed numbers, I solved that in this way. Seems a regex is the "wrong" solution but it was what struck me first.

use strict;
use warnings;

my $string='YYSFTVME[13]TDPVN[115]HMVGVISVE[13]GRPGLFWFN[115]ISGGDKN[1
+15]';
my $substring = 'N[115]';

my @chars = $string =~ /(.(?:\[\d+\])?)/gxms;

my @positions;
foreach my $i (0..$#chars) {
    push @positions, $i if $chars[$i] eq $substring;
}

print "Positions: @positions\n";
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