1.txt

@gi
AGAT
+
AAAA	1:1.txt

@gi
CATT
+
AAAAA	3:1.txt

##</code><code>##

2.txt

@gi
AGAT
+
AAAA	1:2.txt

@gi
TACA
+
AAAA	2:2.txt

##</code><code>##


output.txt

@gi
AGAT
+
AAAA	2	1:1.txt	1:2.txt
@gi
CATT
+
AAAAA	3	3:1.txt
@gi
TACA
+
AAAA	2	2:2.txt



##</code><code>##

#!/usr/bin/env perl
use strict;
use warnings;

my %compare;

$/="";
my $key;
my $value;

while (<>) {
chomp;
   ( $key, $value ) = split('\t', $_);
   
   my @lines = split /\n/, $key;
   my $key1 = $lines[1];
   
    
    push( @{ $compare{$key1} }, $value );
 

}


foreach my $key1 ( sort keys %compare ) {

my $tot = 0;
my $file_count = @ARGV;

for my $val ( @{$compare{$key1}} ) {
        $tot += ( split /:/, $val )[0];
    }   
    
if ( @{ $compare{$key1} } >= $file_count) {


        print join( "\t", $key, $tot, @{ $compare{$key1} } ), "\n\n";
    }
}