... local our $q = $s - 1; fixes [the lexical bug].

It can even be fixed a bit more cleanly, and also fold in the added  s/// fixup at the end (still runs under 5.8.9):

c:\@Work\Perl\monks\Q.and>perl -wMstrict -le
"my @stops = (2,6);
 ;;
 my $tag = '___';
 ;;
 for (qw(ATCGGATCTGGC  A-C-G--CTGGC)) {
   my $seq = $_;
   printf qq{'$seq' -> };
   $seq =~ s{ ((?: [TAGC] [^TAGC]*){$_} [TAGC]) [^TACG]* }{$1$tag}xms
     for map $_-1, @stops;
   print qq{'$seq'};
   }
"
'ATCGGATCTGGC' -> 'AT___CGGA___TCTGGC'
'A-C-G--CTGGC' -> 'A-C___G--CTG___GC'
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