my @third_fragments = grep -v ($rsite3), $second_fragments[$i]
	
		my @final_fragment1 = $seqname."_".$i."_1";	
		my @final_fragment2 = $seqname."_".$i."_2";	
		$final_fragments{$final_fragment1} = $third_fragments[0];
		$final_fragments{$final_fragment2} = $third_fragments[scalar @third_fragments - 1];