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	    }
	}

	push @position_match_array, $match;
	push @position_cover_array, $cover;
	push @position_depth_array, $depth;
	push @position_start_array, $alignment_start;
	push @position_end_array, ($alignment_end - 1);
	push @consensus_chunks, join("", @consensus_positions);

	#Sort position arrrays from largest to smallest fragment
	@index_sorted_size = sort { $position_cover_array[$b] <=> $position_cover_array[$a] } 0 .. $#position_cover_array;

	@position_cover_array = @position_cover_array[@index_sorted_size];
	@position_match_array = @position_match_array[@index_sorted_size];
	@position_depth_array = @position_depth_array[@index_sorted_size];
	@position_start_array = @position_start_array[@index_sorted_size];
	@position_end_array = @position_end_array[@index_sorted_size];
	@consensus_chunks = @consensus_chunks[@index_sorted_size];

	#Calcular coverage, identity and mean read depth from largest fragment
	if($position_cover_array[0] == 0) {
	    $identity_proportion = 0;
	} else {
	    $identity_proportion = $position_match_array[0] / $position_cover_array[0];
	}

	$coverage_proportion = $position_cover_array[0] / scalar(@protein_split);
	$mean_read_depth = $position_depth_array[0] / scalar(@protein_split);
	
	if($coverage_proportion > 0){