A solution that uses index and substr.

$ perl -le '
> $str = q{YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]};
> $posn = -1;
> while ( ( $posn = index $str, q{N[115]}, $posn ) > -1 )
> {
>     print +( $posn ++ );
>     substr $str, $posn, 5, q{};
> }'
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$
[download]

Making the solution more general and avoiding modifying the original string.

$ perl -Mstrict -wle '
> print for findPosns(
>    q{YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]},
>    q{N},
>    q{[115]}
>    );
> 
> sub findPosns
> {
>     my ( $str, $textKeep, $textThrow ) = @_;
> 
>     my $text  = $textKeep . $textThrow;
>     my $len   = length $textThrow;
>     my @posns = ();
>     my $posn  = -1;
>     while ( ( $posn = index $str, $text, $posn ) > -1 )
>     {
>         push @posns, $posn ++;
>         substr $str, $posn, $len, q{};
>     }
>     return @posns;
> }'
12
30
37
$
[download]

I hope this is useful.