#!/usr/bin/perl -w                 

my $seq;

open (SEQ, "<$ARGV[0]");
open (REP, "<$ARGV[1]");
open (OUT, ">$ARGV[2]");

while (<SEQ>){
	$seq = $_;
	while (<REP>){
		print OUT if /$seq/;
	}

}

close (SEQ);
close (REP);
close (OUT);