Extraction duplex structure

#!/usr/bin/perl -w

if (@ARGV==0){
  print STDERR "usage: features_mirna_positive.pl  <input file>\n";
  exit;
}

open (ST,">$ARGV[0].out");
open (INFO, $ARGV[0]);   #The output of find_transcripts

my $bait1=">";
my $bait2="Forward";
my $bait3="Performing Scan:";
my $header='';  
my $gene_iinfo=0;
my $line1 ='';	my $line2 ='';	my $line3 ='';	
my $line4 ='';	my $line5 ='';	my $line6 ='';  my $line7 ='';  my $line8='';  my $line9='';
my $line10 =''; my $line11 ='';
my $flag=0; my $count =0; 
while ($line1 = <INFO>){	
	if(($line1 =~m/$bait3/) && ($count ==0)){
		@sg_1 = split (/ /,$line1);
		$header_n = $sg_1[2];
		$gene_info_n = $sg_1[4];
		$header_n = join "",">",$header_n,"\t",$gene_info_n;
		$line3 = <INFO>;  $line4 = <INFO>;   
		$line5 = <INFO>;  $line6 = <INFO>;  
		$line7 = <INFO>;  $line8 = <INFO>;  
		$line9 = <INFO>;  $line10 =<INFO>;  $line11 = <INFO>;
		@energy = split(/ /,$line11);
		$line5 =~ s/\s+$//;
		$line5 = join "",$line5,"\t",$energy[3].$energy[5];
		print ST $header_n;
		print ST "$line5\n\n";  print ST $line9;  
		print ST $line8;  print ST "$line7\n";
		$count++;
	}
	if ($line1 =~m/$bait1/){
		@test=split (/\t/,$line1);
		$header = join "",$test[0],"\t",$test[1];		
		while ($line2=<INFO>){	
			if ($line2 =~/$bait2/){				
				if ($flag==0){ 
				print ST "$header\n"; 
				}
				if ($flag>=1){
				print ST "\n$header\n";				
				}
				$flag++;
#				print ST $line2;				
				$line3=<INFO>;	$line4=<INFO>;	
				$line5=<INFO>;	$line6=<INFO>;
				$line7 = <INFO>;  $line8 = <INFO>;
		                @energy = split(/ /,$line8);
		                $line2 =~ s/\s+$//;
		                $line2 = join "",$line2,"\t",$energy[3].$energy[5];  #add energy
				print ST "$line2\n";
				print ST $line3;  print ST $line6;	
				print ST $line5;  print ST "$line4";
				last;						     #send it to the while loop	
			}
		
		}
	}
}