use strict;
use warnings;

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

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

print "Positions: @positions\n";