does this make sense?

Not completely.

1. *HDV**HYW*RW*WMYMRV* doesn't appear in your input.

   Did you mean *DV**HYW*RW*WMYMRV* (6*, 19) or H*DV**HYW*RW*WMYMRV* (6*,20)?

   And if the latter, why?

2. Why R*KR**YWHHWH...DYD* (4*, 19 length) instead of *KR**YWHHWH...DYD* (4*, 18 length)

Maybe this is something like your goal?

#! perl -slw
use strict;

my $seq = 'RKRMMWW*VWMWRYHDWMH*HR*DRMDMWHMWYVMWVRWMVBHWKVYWSMHYWY*HWVM
+VSKD'
    . 'HMDBYKMWRSMDSD*...**Y*WD*VWDRYHHYRYKRWWDDKDDH*DV**HYW*RW*WMYMRV
+*BWB';

my %uniq;
substr( $seq, $_, 25 ) =~ m[(\*.{8,23}\*)]
    and ++$uniq{ $1 } == 1
    and print "'$1'"
    for 0 .. length( $seq )-1;

__END__
C:\test>827470
'*VWMWRYHDWMH*HR*'
'*HWVMVSKDHMDBYKMWRSMDSD*'
'*...**Y*WD*'
'*WD*VWDRYHHYRYKRWWDDKDDH*'
'*VWDRYHHYRYKRWWDDKDDH*'
'*VWDRYHHYRYKRWWDDKDDH*DV*'
'*DV**HYW*RW*'
'*DV**HYW*RW*WMYMRV*'
'**HYW*RW*WMYMRV*'
'*HYW*RW*WMYMRV*'
'*RW*WMYMRV*'
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