use strict;
use warnings;

my $YBL027W = 'GUAUGUUUAACAGUGAUACUAAAUUUUGAACCUUUCACAAGAUUUAUCUUUAAAU
+AUGUUAUGA';

my $seq = shift || 'GUAUG';
my @pos;
while( $YBL027W =~ m/\Q$seq\E/gis ){
    push @pos, pos($YBL027W) - length( $seq );
}


print regex => $/;
printf '       \%d0', $_ for 1 .. 8;
print $/, ( 0 .. 9 ) x 8, $/;
print $YBL027W,$/;


my $req = ' ' x length $YBL027W;

substr($req, $_, 1, '^')
    for @pos;
print  $req, $/;
print "@pos $/";

@pos = ();

for(
    my $lindex = index( $YBL027W, $seq);
    $lindex != -1;
    $lindex = index( $YBL027W, $seq, $lindex + length $seq)
        # + length $seq   so it matches the m//atch solution
        # otherwise UUU in UUUU would match twice ( [UUU]U and U[UUU] 
+)
) {
    push @pos, $lindex;
}


print $/, index => $/;
printf '       \%d0', $_ for 1 .. 8;
print $/, ( 0 .. 9 ) x 8, $/;
print $YBL027W,$/;

$req = ' ' x length $YBL027W;

substr($req, $_, 1, '^')
    for @pos;
print  $req, $/;
print "@pos $/";

__END__
loose$ perl substring.pl
regex
       \10       \20       \30       \40       \50       \60       \70
+       \80
0123456789012345678901234567890123456789012345678901234567890123456789
+0123456789
GUAUGUUUAACAGUGAUACUAAAUUUUGAACCUUUCACAAGAUUUAUCUUUAAAUAUGUUAUGA
^
0

index
       \10       \20       \30       \40       \50       \60       \70
+       \80
0123456789012345678901234567890123456789012345678901234567890123456789
+0123456789
GUAUGUUUAACAGUGAUACUAAAUUUUGAACCUUUCACAAGAUUUAUCUUUAAAUAUGUUAUGA
^
0

loose$ perl substring.pl  UUUAA
regex
       \10       \20       \30       \40       \50       \60       \70
+       \80
0123456789012345678901234567890123456789012345678901234567890123456789
+0123456789
GUAUGUUUAACAGUGAUACUAAAUUUUGAACCUUUCACAAGAUUUAUCUUUAAAUAUGUUAUGA
     ^                                          ^
5 48

index
       \10       \20       \30       \40       \50       \60       \70
+       \80
0123456789012345678901234567890123456789012345678901234567890123456789
+0123456789
GUAUGUUUAACAGUGAUACUAAAUUUUGAACCUUUCACAAGAUUUAUCUUUAAAUAUGUUAUGA
     ^                                          ^
5 48

loose$
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