What's wrong with my code below ?

You appear to be trying to use what I think of as a "meta-for loop" to get the effect of $l nested for loops. No programming language I know of implements this directly.

    for ( my $i = 0 ; $i < $l ; $i++ ) {

        foreach my $nucl (@nucleotides) {

            substr( $cand_motif, $i, 1 ) = $nucl;
            push @enumerated_motifs, $cand_motif;

            #print "$cand_motif\n";
        }

    }
[download]

In a language that implemented the "meta-for" construct you could write something like

    meta_for ( my $i = 0 ; $i < $l ; $i++ ) {

        foreach my $nucl (@nucleotides) {
            substr( $cand_motif, $i, 1 ) = $nucl;

    } # meta_for

            push @enumerated_motifs, $cand_motif;

            #print "$cand_motif\n";

    meta_end_for ( my $i = 0 ; $i < $l ; $i++ ) {

        } # foreach

    } # meta_end_for
[download]

Of course, parsing the above code as written presents serious difficulties. Probably a different syntax would be required.

Update: Probably the best way to implement this (Update2: i.e. the "meta-for" construct) in Perl would be to use eval.

    my $code = "xyzzy";
    for ( my $i = 0 ; $i < $l ; $i++ ) {

        $code =~ s/xyzzy/
        foreach my \$nucl (\@nucleotides) {
            substr( \$cand_motif, $i, 1 ) = \$nucl;
            xyzzy
        }
/;

    }
        $code =~ s/xyzzy/
            push \@enumerated_motifs, \$cand_motif;
            #print "\$cand_motif\\n";
/;

    eval $code;
[download]

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