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using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;

namespace Rextester
{
    public class Program
    {
        private static char[] firstAlleles1;
        private static char[] secondAlleles1;
        private static char[] firstAlleles2;
        private static char[] secondAlleles2;
        
        public static void Main(string[] args)
        {
            //Input is already entered.
            //Console.WriteLine("Genotype combination 1:");
            string genotypeCollection1 = Console.ReadLine();
            //Input is already entered.
            //Console.WriteLine("Genotype combination 2:");
            string genotypeCollection2 = Console.ReadLine();
            Console.Write("\n\n");
            
            int genotypeCount = genotypeCollection1.Length / 2;
            
            string[] genotypes1 = new string[genotypeCount];
            string[] genotypes2 = new string[genotypeCount];
            
            firstAlleles1 = new char[genotypeCount];
            secondAlleles1 = new char[genotypeCount];
            firstAlleles2 = new char[genotypeCount];
            secondAlleles2 = new char[genotypeCount];
            
            for (int i = 0; i < genotypeCount; i++)
            {
                genotypes1[i] = genotypeCollection1.Substring(i * 2, 2);
                genotypes2[i] = genotypeCollection2.Substring(i * 2, 2);
            }
            
            for (int i = 0; i < genotypeCount; i++)
            {
                firstAlleles1[i] = genotypes1[i][0];
                secondAlleles1[i] = genotypes1[i][1];
                firstAlleles2[i] = genotypes2[i][0];
                secondAlleles2[i] = genotypes2[i][1];
            }
            
            string[] combinations1 = getCombinations(new string[] { string.Empty }, firstAlleles1.Length - 1, firstAlleles1, secondAlleles1);
            string[] combinations2 = getCombinations(new string[] { string.Empty }, firstAlleles2.Length - 1, firstAlleles2, secondAlleles2);
            
            string[,] results = new string[combinations1.Length, combinations2.Length];
            for (int i = 0; i < combinations1.Length; i++)
            {
                for (int k = 0; k < combinations2.Length; k++)
                {
                    string crossResult = string.Empty;
                    for (int m = 0; m < genotypeCount; m++)
                    {
                        if ((int)combinations1[i][m] <= (int)combinations2[k][m])
                        {
                            crossResult += combinations1[i][m].ToString() + combinations2[k][m].ToString();
                        }
                        else
                        {
                            crossResult += combinations2[k][m].ToString() + combinations1[i][m].ToString();
                        }
                    }
                    results[i, k] = crossResult;
                }
            }
            
            Console.WriteLine("Punnet square of possible results of a {0} x {1} cross:\n\n", genotypeCollection1, genotypeCollection2);
            
            Console.Write(new string(' ', genotypeCount + 1));
            foreach (string alleleCombination in combinations1)
            {
                Console.Write(alleleCombination + new string(' ', genotypeCount + 1));
            }
            
            for (int i = 0; i < combinations2.Length; i++)
            {
                Console.Write("\n" + combinations2[i] + ' ');
                for (int k = 0; k < combinations1.Length; k++)
                {
                    Console.Write(results[i, k] + ' ');
                }
            }
            
            //Only for running on a computer
            //Console.ReadKey(true);
        }
        
        private static string[] getCombinations(string[] currentArray, int allelePosition, char[] firstAlleles, char[] secondAlleles)
        {
            if (allelePosition >= 0)
            {
                string[] newCombinations = new string[currentArray.Length * 2];
                for (int i = 0; i < currentArray.Length; i++)
                {
                    newCombinations[i] = firstAlleles[allelePosition] + currentArray[i];
                    newCombinations[i + currentArray.Length] = secondAlleles[allelePosition] + currentArray[i];
                }
                return getCombinations(newCombinations, allelePosition - 1, firstAlleles, secondAlleles);
            }
            else
            {
                return currentArray;
            }
        }
    }
}

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Compilation time: 0.12 sec, absolute running time: 0.11 sec, cpu time: 0.09 sec, average memory usage: 21 Mb, average nr of threads: 5