I was bored :)

my $ref = 'agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg';

my @subseq_to_find = qw{
    gctagctag
    tagcatgctagctag
    gctagctgac
    tag
};

my @output;
for my $subseq ( @subseq_to_find ) {
    my $p = -1;
    MATCH: while (1) {
        $p = index $ref, $subseq, $p + 1;
        last if $p < 0;
        my $len = length $subseq;

        for ( @output ) {
            my $substr = \ substr $_, $p, $len;
            $$substr = $subseq and next MATCH
              unless $$substr =~ /\S/;
        }
        push @output, " " x length $ref;
        substr $output[-1], $p, $len, $subseq;
    }
}

print "$_\n" for $ref, @output;
[download]

Output:

agctagctagctagcatgctagctagctgatcgatgctagctagctgactgacgacg
 gctagctag tag   gctagctag         gctagctag
     gctagctag     tag tag             gctagctgac
   tag tag tagcatgctagctag           tag tag
[download]

Update: next SUBSEQ should be next MATCH. Added a smaller pattern to test the fix. I guess I'm still bored.