Dear Liverpole,
First of all thanx for taking interest in this. Following is the code the way you asked. Now it is showing these errors
lobal symbol "@energy" requires explicit package name at monk.pl line 29. Type of arg 1 to push must be array (not concatenation (.) or string) at monk.pl line 29, near "})" Execution of monk.pl aborted due to compilation errors.
By the way, to rephrase my question, as 'second reply' has rightly put it, I am looking to change the array name dynamically... How this can be possible? Pl help..

#!/usr/bin/perl -w
use strict;
my $dinu_r;
my $energy;
my @energy1;
my @energy2;
my @energy3;
my @energy4;
my @energy5;
my $i;
for (my $x=1; $x<=5; $x++)
{
open (AA, "shuffle$x")or die "Can't open input  ($!)\n"; # LINE A

my $Sequence;
   $i=length($Sequence);
while (<AA>)
{
  $Sequence=$_;
}
close(AA);

my %Winenergy = Energy($Sequence,$dinu_r);
open (OUT, ">shuffle$x.stb");  # LINE B

foreach my $el1(sort{$a <=> $b} keys %Winenergy)
{
  push(@energy.$x , $Winenergy{$el1}); #LINE C
#  print OUT "$el1\t $Winenergy{$el1}\n";
}
#print OUT "\n";
close (OUT);
}

 sub Energy{

my ($sequence,$dinu_r) = @_;
my %dinu = %$dinu_r;
my $frame=1;
my $win=15;
my $lensequence = length($sequence); #length of the genome sequence
my $limit1 = $lensequence-$win+1; #no of windows
my $wincenpos = 1+($win-1)/2; #centre postion for the first window
my %winenergy = ();
my $j = 0; #starting position of the window
while($j<$limit1)
{
  my $winseq = substr($sequence,$j,$win);
  my $energy = 0;
  for(my $k =0; $k < $win-1; $k++)
  {
    my $dinucle_temp = substr($winseq,$k,2);
    my $dinucle = uc($dinucle_temp);
    $energy = $energy + $dinu{$dinucle};
  }#end for $k
  my $wincentre = $j+$wincenpos;
   $winenergy{$wincentre} = $energy;
  $j = $j+$frame;
}#end for $j
return %winenergy;
}
open(FILE,">total_shuffle.stb");
my $m=8;
for(my $j=0;$j<$i;$j++)
{
my $avg = ($energy1[$j]+$energy2[$j]+$energy3[$j]+$energy4[$j]+$energy
+5[$j])/5;
        print FILE "$m\t$avg\n";
$m++;
}
close (FILE);
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