#!/usr/bin/perl
use strict;
use warnings;
use Inline::Files;

my %data;
while (<A>) {
    chomp;
    my (undef, $fragment, undef, $pos) = split /\t/;
    $data{$pos} = $fragment;
}

<B>; # throw away header '300     dG = -62.54 ...'
while (<B>) {
    my $pos = (split /\t/)[0];
    print "$data{$pos} $pos\n" if $data{$pos};
}

__A__
1-Match:    GGTGTTGTATGCCTTTAAA    5    3545
2-Match:    GGAAAGTCAAGCCCATCTA    9    3254
3-Match:    GTTCTTATTTGCACCTACT    6    180
4-Match:    GATGAGGAACAGCAACCTT    5    844
__B__
300     dG = -62.54   [initially -70.70] gi178893_M23263_rna_300-1 
1    G    0    2    0    1
2    A    1    3    0    2
3    A    2    4    0    3
4    U    3    5    0    4
5    U    4    6    0    5
6    C    5    7    0    6
7    C    6    8    0    7
8    G    7    9    34    8
9    G    8    10    33    9
........
........
179    A    178    180    231    179
180    G    179    181    230    180
181    U    180    182    229    181
........
........
[download]

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);
[download]

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.
[download]

Change

$pos = (split /\s+/)[0];

to

$pos = (split /\s+/, $ctline)[0];