for ($aaa=0; $aaa<=$#unique_species; $aaa++) # The @unique_species is Chimp,Dog,Horse,Human,Monkey,Pig,Rat
				{
				@brk_species_name=split /\_/,$unique_species[$aaa];
				my $speciesName= lc($brk_species_name[0]);
				@{"$speciesName"."_brk"}=0; 
				foreach $cor(0..$#target_species) 
					{	
					if ("$target_species[$cor]" eq "$unique_species[$aaa]")
						{
						#print "$target_species[$cor]\t$unique_species[$aaa]\t$target_brk_cordinates[$cor]\n";
						 push @{"$speciesName"."_brk"},"$target_brk_cordinates[$cor]"; 
						}
					}
 				@{"$speciesName"."_brk"}=sortUniqueHash (@{"$speciesName"."_brk"});
				my $arrayEntries=checkNumber (@{"$speciesName"."_brk"});
				push (@allDecision, $arrayEntries);
				push (@allBreakpointCoordinates, @{"$speciesName"."_brk"}); 
			        @{"$speciesName"."_brk"}=join (',',@{"$speciesName"."_brk"});  ## it generate one string and enter in an array
				}
 	

                # Chimp,Dog,Horse,Human,Monkey,Pig,Rat same order as sps file names in matrix ....      Need to change ...

  		 @matrix=\(@species,@chromosome,@brk_cordinates,@brk_decision,@chimp_brk,@dog_brk,@horse_brk,@human_brk,@monkey_brk,@pig_brk,@rat_brk);

		#print "Print Using Array Index\n";
		for(my $i = 0; $i <= $#matrix; $i++){
   		# $#array_2d gives the highest index from the array
  		 for(my $j = 0; $j <= $#matrix ; $j++){    
      			print OUTFILE "$matrix[$i][$j] ";
  				 }
  			 print OUTFILE"\t";   
				}
				print OUTFILE "\n";
				


undef @target_species;  undef @species; undef @chromosome;undef @matrix; undef @brk_cordinates;  undef @target_brk_cordinates;  undef @da;   undef @brk_decision;
undef @dog_brk; undef @horse_brk; undef @monkey_brk; undef @pig_brk; undef @human_brk; undef @chimp_brk; undef @rat_brk; undef @mouse_brk; undef @pig_brk; undef @dog_brk; undef @horse_brk; undef @cattle_brk; undef @allBreakpointCoordinates; undef @all_sps_array;
undef @allDecision;  undef @matrix;