my ($value, $col, $col2, $l_o_b, $left, $matchedID, $diff_three_prime, $diff_five_prime, $sequence);
open (EXONS_five, '>fasta_exons_five');
open (EXONS_three, '>fasta_exons_three');
my $i = 0;
foreach my $match(@exonic_matches) { 

$value = $exon_ID[$i];
$col = $exon_left{$value};
$col2 = $exon_right{$value};
my @three_prime_ss = split(",", $col);  
my @five_prime_ss = split(",", $col2); 
my @reverse_three = reverse(@three_prime_ss);
my @reverse_five = reverse(@five_prime_ss);


	if ($strands{$value} =~ m/\+/) {

	$diff_three_prime = $LBP[$i] - $three_prime_ss[$exons2{$value} - 1]; 
	$diff_five_prime = $LBP[$i] - $five_prime_ss[$exons2{$value} - 1]; 
	$matchedID = $ID{$LBP[$i]};
	
	if ($diff_three_prime !~ m/\-/ && $diff_three_prime <= 3) {
	
	$BP{$LBP[$i]} =~ s/\[[ACTG]\]/$alt[$i]/i; 
	
	$l_o_b = 20;
	##$right_of_boundary = 3;
	 
			$l_o_b = $l_o_b + $diff_three_prime; 

			$left = 51 - $l_o_b; 

	$sequence = substr($BP{$LBP[$i]}, $left, 23);
	##	print $sequence, "\n"; 
## POINT ONE: prints out correct sequence for condition ##
	}
		
	elsif ($diff_five_prime =~ m/\-/ && $diff_five_prime >= -3) {
	
	$BP{$LBP[$i]} =~ s/\[[ACTG]\]/$alt[$i]/i; 
	
	$l_o_b = 3;
	##$right_of_boundary = 6;
	 
			$l_o_b = $l_o_b + $diff_five_prime; 

			$left = 51 - $l_o_b; 
	
	$sequence = substr( $BP{$LBP[$i]}, $left, 9);
	##	print $sequence, "\n"; 
## POINT TWO: prints out what I want for this condition plus some repeats ##
		}
 }

	
		##	print $sequence, "\n"; 
## POINT THREE: prints out multiple sequences of the above ##
	my $seq_length = length($sequence);
	if ($seq_length == 9) {
	
	print EXONS_five (">" . "$match_exon{$matchedID}" . "\n", lc($sequence),"\n");	
	}
		else {
	print EXONS_three (">" . "$match_exon{$matchedID}" . "\n", lc($sequence),"\n");
	}
$i++;
}
	close (EXONS_five);
	close (EXONS_three);