How about using split rather than index? Using cdarke's extended data shows that you have to use a third argument to split of -1 to allow the trailing empty element if the split term is at the end of the line.

$ perl -le '
> $str = q{YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]};
> @chunks = split m{(?<=N)\[115\]}, $str, -1;
> $posn = -1;
> print $posn += length for @chunks[ 0 .. $#chunks - 1 ];'
12
30
37
$
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I hope this is of interest.