A seq1 20
B seq2 25
B seq2 80
B seq1 40
C seq1 25
D seq2 30
E seq2 45

##</code><code>##

A B C
B D E

##</code><code>##

A Seq1 20 B seq1 40 C seq1 25
B seq2 25 D seq2 30 E seq2 45
B seq2 80 D seq2 30 E seq2 45

##</code><code>##

#file opening
open(AB,"try_fimo.txt")||die("cannot open");
open(BC,"try_fimo2.txt")||die("cannot open");

#storing file in an array
@data=<AB>;
chomp(@data);
@data2=<BC>;
chomp(@data2);

#reading file line by line
foreach $line(@data)
 {
 
  foreach $line2(@data2)
    {
    
     if($line2=~/(.*?)\s+(.*?)\s+(.*)/)
      {
     
        $t1=$1; #eg. in first row from file2 i.e.ABC, it will first take A followed by B & C 
        $t2=$2;
        $t3=$3;
      }
     if($line=~/(.*?)\s+(.*?)\s+(.*)/)
      {
      
         if($1 eq $t1)
         
           {
           #storing each column in seperate array based on match
            push(@tf1,$1);
             push(@seq1,$2);
              push(@dis1,$3);
            # print $1,"\t",$2,"\t",$3,"\t";
             
            }
        
        
                 if($1 eq $t2)
	         
	          {
                      push(@tf2,$1);
                        push(@seq2,$2);
                         push(@dis2,$3);
	             
                   }
                   
                   
                            if($1 eq $t3)
				         
			    	{
                                   push(@tf3,$1);
                        	      push(@seq3,$2);
                         		push(@dis3,$3);       
				             
                  		 }
                   
             }      

                   
      }
      
      
      
  }

#comparison using loops

      for($i=0;$i<@tf1;$i++)
        {
        
          for($j=0;$j<@tf2;$j++)
             {
             
               for($k=0;$k<@tf3;$k++)
                 {
                 
                   if(($seq1[$i] eq $seq2[$j]) && ($seq1[$i] eq $seq3[$k]))
                      {
                      
                        if(($tf1[$i] ne $tf2[$j]) && ($tf1[$i] ne $tf3[$k]))
                          {
                            print $tf1[$i],"\t",$seq1[$i],"\t",$dis1[$i],"\t",$tf2[$j],"\t",$seq2[$j],"\t",$dis2[$j],"\t",$tf3[$k],"\t",$seq3[$k],"\t",$dis3[$k],"\n";
                          
                          }
                            
                         
                        }
                        
                   }
                   
                   
              }
              
              
          
         }