#name   complete(cs)    len(cs) simple(ss)  len(ss) pos(cs)
NAME1   A0AAA000AAA00A  14      AAAAAAAA    8        4,6            
NAME2   AAAA0AA00000A   13      AAAAAAA     7        7

##</code><code>##

$ perl -anle '
    print "$_ position(cs)" and next if /^#/;
    printf "%s",$_;
    for $pos_ss (split ",",$F[5]) {
        $char = substr($F[1],$pos_ss-1,1);
        @cs = split //,$F[3];
        @cs_idx = grep {$cs[$_] eq $char} 0..$#cs;
        push @res,++$cs_idx[$pos_ss-1];
    }
    printf "%14s\n", join ",",@res;
    @res=();
' file 

##</code><code>##

NAME1   A0AAA000AAA00A  14      AAAAAAAA    8        4,9	3,5
NAME2   AAAA0AA00000A   13      AAAAAAA     7        7          6