While you wait for BioPerl to download and install, and then work out how to use it, this might do the job :)

#! perl -slw
use strict;

open MOTIFS, '<', '845226.motif' or die $!;
my @motifs = <MOTIFS>;
close MOTIFS;
chomp @motifs;

open SEQS, '<', '845226.fasta' or die $!;

while( my $seqID =  <SEQS> ) {
    chomp $seqID;
    $seqID =~s[^>][];

    my $seq = '';
    {
        local $/ = ">";
        chomp( $seq .= <SEQS> );
        $seq =~ tr[\n][]d;
    }
    for my $motif ( @motifs ) {
        if( $seq =~ m[$motif([^A-Z]+)[A-Z]] ) {
            print "$seqID contains $motif; distance ", length( $1 );
        }
    }
}
close SEQS;

__END__
C:\test>845226
uc002yje.1 chr21:13973492-13976330  contains gccccac; distance 88
uc002yje.1 chr21:13973492-13976330  contains gccccac; distance 92
uc002yje.1 chr21:13973492-13976330  contains gggggaaaaaacc; distance 2
+0
uc002yje.1 chr21:13973492-13976330  contains gccccac; distance 90
uc002yje.1 chr21:13973492-13976330  contains agagggccc; distance 4
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