Thanks Cristoforo,

I modified the code as suggested by you but I thing the program is giving me error of uninitialized values.

#!/usr/bin/perl -w                                                    
+                           
use strict;
use warnings;

my $matchfile = "match_super.dat";
my $ctfile = "M23263_rna_300-1.dat_1.ct";

my @match;my %data;my $fragment; my $pos;
open (A, "<", $matchfile) or die "Check the file $!\n";
while (my $line = <A>)
{
    chomp $line;
    (undef, $fragment, undef, $pos) = split(/\t/, $line);
    $data{$pos} = $fragment;
}
close (A);

my ($num1, $base, $num2, $num3, $connect, $num4);
open (B, "<", $ctfile) or die "Check the file $!\n";
while (my $ctline = <B>)
{
    chomp $ctline;
    if ($ctline =~ /^(\d+\s+dG.*)/)
    {
#       print "$1\n"; next;                                           
+                           
        next;
    }
    $pos = (split /\s+/)[0];
    print "$data{$pos} $pos\n" if $data{$pos};
}
close (B);
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Error: 
Use of uninitialized value $pos in hash element at ./second_str_map.pl
+ line 29, <B> line 298.
Use of uninitialized value $_ in split at ./second_str_map.pl line 28,
+ <B> line 299.
Use of uninitialized value $pos in hash element at ./second_str_map.pl
+ line 29, <B> line 299.
Use of uninitialized value $_ in split at ./second_str_map.pl line 28,
+ <B> line 300.
Use of uninitialized value $pos in hash element at ./second_str_map.pl
+ line 29, <B> line 300.
Use of uninitialized value $_ in split at ./second_str_map.pl line 28,
+ <B> line 301.
Use of uninitialized value $pos in hash element at ./second_str_map.pl
+ line 29, <B> line 301.
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