use strict;
use warnings;

##</code><code>##

use strict;
use warnings;
use Bio::SeqIO;

my $seq_file = 'D:/Motif Search/sequence.txt';
my $mot_file = 'D:/Motif Search/motif.txt';

my $in = Bio::SeqIO->new(     #sequences object
    -format => 'fasta',
    -file   => $seq_file,
);

my $mot = Bio::SeqIO->new(   #motifs object
    -format => 'fasta',
    -file   => $mot_file
);

my @motifs;
while ( my $motif = $mot->next_seq ) {  #read in motifs
    my $motif_string = $motif->seq;     #stringify motifs
    push @motifs, $motif_string;
}


while ( my $seq = $in->next_seq ) {
    my $string = $seq->seq;
    foreach my $motif (@motifs) {
        if ( $string =~ /$motif([agct]+)[AGCT]/ ) {
            print "'$motif' ", length $1, " bases away at ", $seq->id,
              "\n";
        }
    }
}

##</code><code>##