************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ikbke.phase.inp ikbke.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ikbke.phase.out_freqs : haplotype frequency estimates ikbke.phase.out_pairs : most likely haplotype pairs for each individual ikbke.phase.out_recom : estimates of recombination parameters ikbke.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 104 Positions of loci: 74 79 744 925 1311 1796 1977 1979 2152 2178 2263 3313 3676 3748 4479 4516 4632 4690 5423 5592 5655 5992 6186 6242 6352 6583 6700 6974 7200 7577 7616 7733 8157 8270 9059 9314 9557 9558 9674 9932 10707 10731 12475 12499 12704 12945 13389 13538 13570 13624 13839 14372 14499 14539 14784 14977 15388 16015 16022 17573 18735 18833 19093 20187 20973 22614 22625 23270 23465 23854 23976 24055 24114 24134 24747 24802 24952 25021 25137 25295 25321 25355 25659 25834 25940 26241 26447 26457 26578 26658 26675 26811 27354 27683 28176 28387 28479 28715 28875 28876 29049 29836 29837 30018 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ikbke.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCAACCCAGATCTATCCGCTGCAGTAAGGTCCGAIGCGCCATAGTACCTGCACCGCTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACITGGTCCT 1.000000 2 GCAACCCAGATCTATCCGCTGTACTGGGGCCCGAIGCGCCATGGTATCCGCATCACTTACGGCCGTGCGAGGGACAGGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 3 GCAACCCAGATCTATCCGCTGTACTAAGGTCCGAIGCGCCATAGTGCCTGCATCACTTGCGGTTTTGCGAGGGACATGGAAA 3 TCAGGTGTTCCGGICCTGTTC 1.000000 4 GCAACCCAGATTTATCCGCTGCAGTGAGGCTTAAIGCGCCATAGTGCCTACATCACTTGCGGCCTTTCGAGGCAAAGACGGA 2 CCAGGCACCACACICGGTCCT 2.000000 5 GCAACCCAGATTTATCCGCTGCGGTGAGGCTTAAIGCGCCATAGTGCCTACACCGCTTGCGGCCTTGCGAGGGACGTGGAAC 3 TCAAGTGTTCCGGITCTGTTC 3.000000 6 GCAACCCAGCTCCATCCGCGGCAGTGAGGCCCAAIGCACCGCAGTGTCCGCATCACTTGCGGCCTTGCGAGGGACGTGGAAC 3 TCAAGTGTTCCGGITCTGTTC 1.000000 7 GCAACCCAGCTCCATCCGCGGCAGTGAGGCCCAAIGCACCGCAGTGTCCGCATCACTTGCGGCCTTTCGAGGCAAAGACGGA 2 CCGGGTGCCCCGGICCTGTCC 2.000000 8 GCAACCCAGCTCCATCCGCGGCAGTGAGGCCCAAIGCGCCATAGTGCCCGGATCACTTGCGGTTGTGCAAGACACATGGAAA 3 TCAGGTGTTCCGGDTCTGTTC 1.000000 9 GCAACCCAGCTCCATCCGCGGCAGTAAGGCCCAAIGCACCACAGTGTCCGCATCACTTACGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 10 GCAACCCAGCTCCATCCGCGGCAGTAAGGCCCAAIGCACCACAGTGTCCGCATCACTTACGGCCTTGCGAGGGACATGGAAA 2 TCAGATGTCACACICGGTCCT 1.000000 11 GCAACCCAGCTCCATCCGCGGCAGTAAGGCCCAAIGCACCACAGTGTCCGCATCACTTGCGACTTTGTAAGACACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 12 GCAACCCAGCTCCATCCGCGGCAGGGAGGCCCAAIGCGCCATAGTGCCCGGATCACTTGCGGTTGTTCGAGGGACATGGAAA 2 CCGGGCACCACACICGGTCCT 1.000000 13 GCAACCCAGCTCCATCCGCTGCAGGAAGGCCCAAIGCATCACAGTGTCCGCATCGCTTGCGGCCGTGCGAGGGACAGACGGA 2 CCGGGCACCACACICGGTCCT 1.000000 14 GCAACCCGGATCTGTCCGTGGCAGGGAGACCCGAIACGCCATGACGCTCGCATCACACGCGGCTGTGTAAGACACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 15 GCAACCCGGATCTGTCCGTGGCAGGAAGGTCCGAIGCGCCATAGTACCTGCACCGCTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICCTTCCT 1.000000 16 GCAACCCGGATCTGTCCGTGGCAGGAAGACCCGAIATGCTATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 3.000000 17 GCAACCCGGATCTGTCCGTGGCAGGAAGACCCGAIATGCTATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 18 GCAACCCGGATCTGTCCGTGGCACGAAGGTCCGGIGCGCCATAGTACCTGCACTGCTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICCTTCCT 6.000000 19 GCAACCCGGATCTGTCCGTTGCAGGAAGACCCGAIATGCTATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACAGGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 20 GCAACCCGGATCTGTTAGCTGCAGTAAGGCCCAAIGCATCACAGTGTCCGCATCGCTTGCGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 21 GCAACCCGGATCTGTTAGCTGCACTAAGGCCCAAIGCATCACAGTGTCCGCATCGCTTGCGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 22 GCAACTCAAATCTATCCACTGCAGTGGGGCCCGAIGCGCCATAGTGCCTGCACCGCTTGCGGCCTTGTGGAGGGAAGACGGA 2 CCAGGCACCCCGGICCTGTCC 1.000000 23 GCAACTCAAATCTATCCACTGCACTGAGGCCCAAIGCACCACAGTGTCCGCATCGCTTGCGACCTTGTGAGACACATGGAAA 3 TTAGGTGTTCCGGICCTGTTC 4.000000 24 GCAACTCAAATCTATCCACTGCACTGGGGCCCAAIGCACCGCAGTGTCCGCATCACTTGCGGCCTTTCGAGGCACAGGGAAA 3 TTAGGTGCCCCGGICCTGTCC 3.000000 25 GCAACTCAAATCTATCCACTGCACTGGGGCCCAAIGCGCCATAGTGCCCGGATCACTTGCGGTTGTTCGAGGGACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 26 GCAATCCAGATCTATCCGCGGCGGGGAGACCCAAIGCGCCATAGTGCCTGCACCGCTTGCGGCCTTGCGAGGGACATGGAAA 3 TCGGGTGCCCCGGICCTGTCC 1.000000 27 GCAATCCAGATCTATCCGTTGCAGTGAGGCCCAAIGCACCGCAGTGTCCGCATCACTTGCGGCCTTTCGAGGCAAAGGCGGA 2 CCGGGTGCCCCGGICCTGTCC 1.000000 28 GCATCCCAGATCTATCCGCTGCAGTGAGACCCAAIGCGCCATAGTGCCTGCACCGCTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 29 GCATCCCAGATCTATCCGTGGTAGGGAGACCCGAIATGCCATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 2.000000 30 GCATCCCAGATCTATTAGCTGCAGTGAGGCCCAAIGCACCGCGGTATCCGCATCACTTACGGCCGTTCGAGGCAAAGACGGA 2 CCGGGTGCCCCGGICCTGTCC 1.000000 31 GCATCCCAGATCTATTAGCTGCAGTGAGGCCCAAIGCACCGCGGTATCCGCATCACTTACGGCCGTTCGAGGCAAAGACGGA 2 CTAGGTGCCCCGGICCTGTCC 1.000000 32 GCATCCCAGATCTATTAGCTGCAGTGAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 1.000000 33 GCATCCCAGATCTATTAGCTGCAGTAAGGCCCAAIGCATCACAGTGTCCGCATCGCTTGCGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 34 GCATCCCAGATCTATTAGCTGCAGTAAGGCCCAAIGCATCACAGTGTCCGCATCGCTTGCGGCCTTGCGAGGGACATGGAAA 2 TCAGATGTCACACICGGTCCT 1.000000 35 GCATCCCAGATCTATTAGCTGCAGTAAGGCCCAAIGCGCCATAGTACCTGCACCGTTTGGAGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 36 GCATCCCAGATCTATTAGCTGCAGTAAGGCCCAAIGCGCCATAGTGCCCGCATCACTTGCGGCCGTGCGAGGCACATGGAAA 3 TCAAGTGTTCCGGITCTGTTC 1.000000 37 GCATCCCAGATCTATTAGCTGCAGTAAGGCCCGAIATGCCATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 38 GCATCCCAGATCTATTAGCTGCAGTAAGGTCCGAIGCGCCATAGTACCTGCACCGCTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 39 GCATCCCAGATCTATTAGCTGCAGTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGCAGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 40 GCATCCCAGATCTATTAGCTGCAGTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGAGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 41 GCATCCCAGATCTATTAGCTGCACTAAGGCCCGAIATGCCATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 1.000000 42 GCATCCCAGATCTATTAGCTGCACTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGCGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 43 GCATCCCAGATCTATTAGCTGCACTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 2.000000 44 GCATCCCAGATCTATTAGCTGCACTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 4.000000 45 GCATCCCAGATCTATTAGCTGCACTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGAGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 4.000000 46 GCATCCCAGATCTATTAGCTGCACGAAGGCCCGAIGTGCTATGACGCTCGCGTCACACGCGGCCTTGCGAGGGACAGGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 2.000000 47 GCATCCCAGATCTATTAGCTGCGGTGAGGTCCGAIGCGCCATAGTGCCTGCATCACTTGCGGTTGTGCGAGGCACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 48 GCATCCCAGATCTATTAGCTGCGGTAAGGCCCAAIGCATCACAGTGTCCGCATCGCTTGCGGCCTTGCGAGGGACGTGGAAC 3 TCAAGTGTTCCGGITCTGTTC 1.000000 49 GCATCCCAGATCTATTAGCTGCGGTAAGGCCCAAIGCATCGCAGTGTCCGCATCGCTTGCGGCCTTGCGAGGGACGTGGAAC 3 TCAAGTGTTCCGGITCTGTTC 1.000000 50 GCATCCCAGATCTATTAGCTGCGGTAAGGCCCAAIGCGCCATAGTACCCGGATCGCTTGCGGTTGTGCGAGGCAAAGGCGGA 2 CCGGGTGTTCCGGDCCTGTTC 1.000000 51 GCATCCCAGATCTATTCGCGGCAGTAAGGCCCAAIGCACCACAGTGTCCGCATCGCTTGCGGCCTTGTGGAGGGAAGGCGGA 2 CCGGGTGCCCCGGICCTGTCC 2.000000 52 GCATCCCAGATCTGTCAGTGGCACTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGGGCCTTGCGAGGGACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 53 GCATCCCAGATCTGTCAGTGGCACTAAGGTCCGAIGCGCCATAGTACCTGCACCGTTTGGGGCCTTGCGAGGGACATGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 1.000000 54 GCTATCCAGACCTAGCCGCTGTAGGGAGGCCTAAIGCGCCATAGTGCCTACACCGCTTGCGGCCTTGTGGAGGGAAGACGGA 2 CCAGGCACCCCGGICCTGTCC 1.000000 55 GCTATCGAGACCTAGCCGCTACAGTGAGACCCGAIATGCCATGATGCTCGCGTCACACGCGGCTTTGTAAGACACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 56 GCTATCGAGACCTAGCCGCTACAGTGAGACCCGAIATGCCATGACGCTCGCGTCACACGCGGCTGTGTAAGACACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 57 GCTATCGAGACCTAGCCGCTACAGTAAGACCCGAIATGCCATGACGCTCGCGTCACACGCGGCTTTGTAAGACACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 58 GCTATCGAGACCTAGCCGCTACACTGAGACCCGAIACACCACAGTGTCCGCATCACTTACGGCCTTGCGAGGGACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 59 GCTATCGAGACCTAGCCGCTACACTGAAGTCCGADGCGCCATAGTGCCTGCACCGCTTGGGGCCTATCGAGGCACATGGAAA 3 TCAGGTGTTCTGGDCCTGTTC 1.000000 60 GCTATCGAGACCTAGCCGTGGCAGGGAAGTCCGADGCGCCATAGTGCCTGCACCGCTTGCGGCCTTGCGAGGGACATGGAAA 3 TCAGGTGTTCCGGICCTGTTC 1.000000 61 GCTATCGAGACCTAGCCGTGGCACTGAAGTCCGADGCGCCATAGTGCCTGCACCGCTTGGGGCCTATCGAGGCACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 62 ACAATCCAGATCTATCCGTTGCAGGGAGGCCCAAIGCGCCATGGTGCCCGGATCACTTGCGGTTTATTGGAGGGAAGACGGA 2 CCGGGCACCACACICGGTCCT 1.000000 63 ACAATCCAGATCTATCCGTTGCACTGAGGCCCAAIGCACCGCAGTGTCCGCATCACTTGCGGCCTTTCGAGGCACATGGAAA 1 TCAGATGTCACACICGGTCCT 1.000000 64 AGTATCCAGACCTAGCCGCTACACTGAAGTCCGADGCGCCATAGTGCCTGCACCGCTTGGGGCCTATCGAGGCACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 1.000000 65 AGTATCCAGACCTAGCCGCTATACTGAAGTCCGADGCGCCATAGTGCCTGCACCGCTTGGGGCCTATCGAGGCACATGGAAA 3 TCAGGTGTTCCGGDCCTGTTC 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (8,30) DY02: (5,7) DY03: (25,31) DY04: (1,28) DY05: (24,48) DY06: (36,13) DY07: (2,50) DY08: (23,33) DY09: (4,24) DY10: (23,55) DY11: (23,63) DY12: (38,47) DY13: (4,51) DY14: (14,51) DY15: (24,56) DY16: (6,58) DY17: (7,23) DY18: (27,34) DY19: (5,26) DY20: (49,62) DY21: (5,12) DY22: (11,22) DY23: (10,54) DY24: (9,57) E101: (16,53) E102: (17,59) E103: (37,60) E104: (18,44) E105: (15,45) E106: (18,44) E107: (45,65) E108: (44,45) E109: (32,61) E110: (3,35) E111: (39,42) E112: (52,64) E113: (18,46) E114: (44,46) E115: (41,43) E116: (18,40) E117: (16,19) E118: (21,29) E119: (20,29) E120: (43,65) E121: (18,65) E122: (18,45) E123: (16,65) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G C A A C C C A G C T C C A T C C G C G G C A G T G A G G C C C A A I G C G C C A T A G T G C C C G G A T C A C T T G C G G T T G T G C A A G A C A C A T G G A A A 3 T C A G G T G T T C C G G D (T) C T G T T C G C A T C C C A G A T C T A T T A G C T G C A G T G A G G C C C A A I G C A C C G C G G T A T C C G C A T C A C T T A C G G C C G T T C G A G G C A A A G A C G G A 2 C C G G G T G C C C C G G I (C) C T G T C C 0 DY02 G C A A C C C A G A T T T A T C C G C T G C G G T G A G G C T T A A I G C G C C A T A G T G C C T A C A C C G C T T G C G G C C T T G C G A G G G A C G T G G A A C 3 T C A A G T G T T C C G G I T C T G T T C G C A A C C C A G C T C C A T C C G C G G C A G T G A G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T T C G A G G C A A A G A C G G A 2 C C G G G T G C C C C G G I C C T G T C C 0 DY03 G C A A C T C A A A T C T A T C C A C T G C A C T G G G G C C C A A I G C G C C A T A G T G C C C G G A T C A C T T G C G G T T G T T C G A G G [G] A C A [T] G G A A A 3 T C A G G T G T T C C G G D C C T G T T C G C A T C C C A G A T C T A T T A G C T G C A G T G A G G C C C A A I G C A C C G C G G T A T C C G C A T C A C T T A C G G C C G T T C G A G G C A A A G A C [G] [G] A [2] C T A G G T G C C C C G G I C C T G T C C 0 DY04 G C A (A) C C C A G A T C T A T C C G C T G C A G T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I T G G T C C T G C A (T) C C C A G A T C T A T C C G C T G C A G T G A G A C C C A A I G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 DY05 G C A A C T C A A A T C T A T C C A C T G C A C T G G G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T T C G A G G C A C A G G G A A A 3 T T A G G T G C C C C G G I C C T G T C C G C A T C C C A G A T C T A T T A G C T G C G G T A A G G C C C A A I G C A T C A C A G T G T C C G C A T C G C T T G C G G C C T T G C G A G G G A C G T G G A A C 3 T C A A G T G T T C C G G I T C T G T T C 0 DY06 G C A (T) C C C A G (A) T C (T) A T (T) (A) G C T G C A G (T) A A G G C C C A A I G C (G) (C) C A (T) A G T G (C) C C G C A T C (A) C T T G C G G C C G T G C G A G G (C) A C A T G G A A A 3 T C A A G T G T T C C G G I T C T G T T C G C A (A) C C C A G (C) T C (C) A T (C) (C) G C T G C A G (G) A A G G C C C A A I G C (A) (T) C A (C) A G T G (T) C C G C A T C (G) C T T G C G G C C G T G C G A G G (G) A C A G A C G G A 2 C C G G G C A C C A C A C I C G G T C C T 0 DY07 G C A (A) C C C A G A T C T A T (C) (C) G C T G (T) (A) (C) T (G) G G G C C C G A I G C G C C A T G G T A T C C G C A T C (A) C T T A C G G C C G T G C G A G G (G) A (C) A G G (G) (A) (A) A (3) (T) C (A) G G T G T T C C G G D C C T G T T C G C A (T) C C C A G A T C T A T (T) (A) G C T G (C) (G) (G) T (A) A G G C C C A A I G C G C C A T A G T A C C C G G A T C (G) C T T G C G G T T G T G C G A G G (C) A (A) A G G (C) (G) (G) A (2) (C) C (G) G G T G T T C C G G [D] C C T G T T C 0 DY08 G C A A C T C A A A T C T A T C C A C T G C A C T G A G G C C C A A I G C A C C A C A G T G T C C G C A T C G C T T G C G A C C T T G T G A G A C A C A T G G A A A 3 T T A G G T G T T C C G G I C C T G T T C G C A T C C C A G A T C T A T T A G C T G C A G T A A G G C C C A A I G C A T C A C A G T G T C C G C A T C G C T T G C G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 DY09 G C A A C C C A G A T T T A T C C G C T G C A G T G A G G C T T A A I G C G C C A T A G T G C C T A C A T C A C T T G C G G C C T T T C G A G G C A A A G A C G G A 2 C C A G G C A C C A C A C I C G G T C C T G C A A C T C A A A T C T A T C C A C T G C A C T G G G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T T C G A G G C A C A G G G A A A 3 T T A G G T G C C C C G G I C C T G T C C 0 DY10 G C A A C T C A A A T C T A T C C A C T G C A C T G A G G C C C A A I G C A C C A C A G T G T C C G C A T C G C T T G C G A C C T T G T G A G A C A C A T G G A A A 3 T T A G G T G T T C C G G I C C T G T T C G C T A T C G A G A C C T A G C C G C T A C A G T G A G A C C C G A I A T G C C A T G A T G C T C G C G T C A C A C G C G G C T T T G T A A G A C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 DY11 G C A A C T C A A A T C T A T C C A C T G C A C T G A G G C C C A A I G C A C C A C A G T G T C C G C A T C G C T T G C G A C C T T G T G A G A C A C A T G G A A A 3 T T A G G T G T T C C G G I C C T G T T C A C A A T C C A G A T C T A T C C G T T G C A C T G A G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T T C G A G G [C] A [C] A [T] G G A A A [1] T C A G A T G T C A C A C I C G G T C C T 0 DY12 G C A T C C C A G A T C T A T T A G C T G C (A) G T (A) A G G T C C G A I G C G C C A T A G T (A) C C T G C A (C) C (G) C T T G (G) G G (C) (C) (T) T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T G C A T C C C A G A T C T A T T A G C T G C (G) G T (G) A G G T C C G A I G C G C C A T A G T (G) C C T G C A (T) C (A) C T T G (C) G G (T) (T) (G) T G C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 DY13 G C A A C C C A G A T T T A T C C G C T G C A G T G A G G C T T A A I G C G C C A T A G T G C C T A C A T C A C T T G C G G C C T T T C G A G G C A A A G A C G G A 2 C C A G G C A C C A C A C I C G G T C C T G C A T C C C A G A T C T A T T C G C G G C A G T A A G G C C C A A I G C A C C A C A G T G T C C G C A T C G C T T G C G G C C T T G T G G A G G G A A G G C G G A 2 C C G G G T G C C C C G G I C C T G T C C 0 DY14 G C A A C C C G G A T C T G T C C G T G G C A G G G A G A C C C G A I A C G C C A T G A C G C T C G C A T C A C A C G C G G C T G T G T A A G A C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C G C A T C C C A G A T C T A T T C G C G G C A G T A A G G C C C A A I G C A C C A C A G T G T C C G C A T C G C T T G C G G C C T T G T G G A G G G A A G G C G G A 2 C C G G G T G C C C C G G I C C T G T C C 0 DY15 G C A A C T C A A A T C T A T C C A C T G C A C T G G G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T T C G A G G C A C A G G G A A A 3 T T A G G T G C C C C G G I C C T G T C C G C T A T C G A G A C C T A G C C G C T A C A G T G A G A C C C G A I A T G C C A T G A C G C T C G C G T C A C A C G C G G C T G T G T A A G A C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 DY16 G C A A C C C A G C T C C A T C C G C G G C A (G) T G A G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T G C G A G G G A C (G) T G G A A (C) 3 T C A (A) G T G T T C C G G (I) (T) C T G T T C G C T A T C G A G A C C T A G C C G C T A C A (C) T G A G A C C C G A I A C A C C A C A G T G T C C G C A T C A C T T A C G G C C T T G C G A G G G A C (A) T G G A A (A) 3 T C A (G) G T G T T C C G G (D) (C) C T G T T C 0 DY17 G C A A C C C A G C T C C A T C C G C G G C A G T G A G G C C C A A I G C A C C G C A G T G T C C G C A T C A C T T G C G G C C T T T C G A G G C A A A G A C G G A 2 C C G G G T G C C C C G G I C C T G T C C G C A A C T C A A A T C T A T C C A C T G C A C T G A G G C C C A A I G C A C C A C A G T G T C C G C A T C G C T T G C G A C C T T G T G A G A C A C A T G G A A A 3 T T A G G T G T T C C G G I C C T G T T C 0 DY18 G C A (A) (T) C C A G A T C T A T (C) (C) G (T) T G C A G T (G) A G G C C C A A I G C A (C) C (G) C A G T G T C C G C A T C (A) C T T G C G G C C T T [T] C G A G G (C) A A A G G C G G A 2 C C G G G T G C C C C G G I C C T G T C C G C A (T) (C) C C A G A T C T A T (T) (A) G (C) T G C A G T (A) A G G C C C A A I G C A (T) C (A) C A G T G T C C G C A T C (G) C T T G C G G C C T T [G] C G A G G (G) A C A T G G A A A 2 T C A G A T G T C A C A C I C G G T C C T 0 DY19 G C A A C C C A G A T T T A T C C G C T G C G G T G A G G C T T A A I G C G C C A T A G T G C C T A C A C C G C T T G C G G C C T T G C G A G G G A C G T G G A A C 3 T C A A G T G T T C C G G I T C T G T T C G C A A T C C A G A T C T A T C C G C G G C G G G G A G A C C C A A I G C G C C A T A G T G C C T G C A C C G C T T G C G G C C T T G C G A G G G A C A [T] G G A A A [3] T C G G G T G C C C C G G I C C T G T C C 0 DY20 G C A T C C C A G A T C T A T T A G C T G C G G T A A G G C C C A A I G C A T C (G) C (A) G T G T C C G C A T C G C T T G C G G C C T T G C G A G G G A C G T G G A A C 3 T C A A G T G T T C C G G I T C T G T T C A C A A T C C A G A T C T A T C C G T T G C A G G G A G G C C C A A I G C G C C (A) T (G) G T G C C C G G A T C A C T T G C G G T T T A T T G G A G G G A A G A C G G A 2 C C G G G C A C C A C A C I C G G T C C T 0 DY21 G C A A C C C A G A T T T A T C C G C T G C G G (T) G A G G C T T A A I G C G C C A T A G T G C C T A C A C C G C T T G C G G C C T T G C G A G G G A C G T G G A A C 3 T C A A G T G T T C C G G I T C T G T T C G C A A C C C A G C T C C A T C C G C G G C A G (G) G A G G C C C A A I G C G C C A T A G T G C C C G G A T C A C T T G C G G T T G T T C G A G G G A C A T G G A A A 2 C C G G G C A C C A C A C I C G G T C C T 0 DY22 G C A A C (C) C A (G) (C) T C (C) A T C C (G) C (G) G C A G T (A) (A) G G C C C (A) A I G C (A) C C A (C) A G T [G] (T) C (C) G C A (T) C A C T T G C G (A) C T T T G T A A G A C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C G C A A C (T) C A (A) (A) T C (T) A T C C (A) C (T) G C A G T (G) (G) G G C C C (G) A I G C (G) C C A (T) A G T [G] (C) C (T) G C A (C) C G C T T G C G (G) C C T T G T G G A G G G A A G A C G G A 2 C C A G G C A C C C C G G I C C T G T C C 0 DY23 G C (A) A (C) C C A G (C) (T) C (C) A (T) C C G C (G) G (C) A G (T) (A) A G G C C (C) A A I G C (A) C C A (C) A G T G (T) C (C) (G) C A (T) C (A) C T T (A) C G G C C T T G C G A G G G A C A T G G A A A 2 T C A G A T G T C A C A C I C G G T C C T G C (T) A (T) C C A G (A) (C) C (T) A (G) C C G C (T) G (T) A G (G) (G) A G G C C (T) A A I G C (G) C C A (T) A G T G (C) C (T) (A) C A (C) C (G) C T T (G) C G G C C T T G T G G A G G G A A G A C G G A 2 C C A G G C A C C C C G G I C C T G T C C 0 DY24 G C A A C C C A G C T C C A T C C G C G G C A G T A A G G C C C A A I G C A C C A C A G (T) G T C C G C A T C A C T T A C G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T G C T A T C G A G A C C T A G C C G C T A C A G T A A G A C C C G A I A T G C C A T G A (C) G C T C G C G T C A C A C G C G G C T T T G T A A G A C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E101 G C A A C C C G G A T C T G T C C G T G G C A G G A A G A C C C G A I A T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A (G) G G A A A 3 T C A G G T G T T C T G G D C C T G T T C G C A T C C C A G A T C T G T C A G T G G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A (T) G G A A A 3 T C A G G T G T T C T G G D C C T G T T C 0 E102 G C A A C C C G G A T C T G T C C G T G G C A G G A A G A C C C G A I A T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A T G G A A A (1) T C A G (A) T G T (C) (A) (C) (A) (C) (I) C (G) (G) (T) (C) (C) (T) G C T A T C G A G A C C T A G C C G C T A C A C T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A (3) T C A G (G) T G T (T) (C) (T) (G) (G) (D) C (C) (T) (G) (T) (T) (C) 0 E103 G C A T C C C A G A T C T A T T A G C T G C A G T A A G G C C C G A I A T G C C A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A [T] G G A A A [1] T C A G A T G T C A C A C I C G G T C C T G C T A T C G A G A C C T A G C C G T G G C A G G G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G C G G C C T T G C G A G G G A C A [T] G G A A A 3 T C A G G T G T T C C G G I C C T G T T C 0 E104 G C A A C C C G G A T C T G T C C G T G G C A C G A A G G T C C G G I G C G C C A T A G T A C C T G C A C T G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C C T T C C T G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E105 G C A A C C C G G A T C T G T C C G T G G C A (G) G A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G (C) T T G G (G) G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C (C) (T) T C C T G C A T C C C A G A T C T A T T A G C T G C A (C) T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G (T) T T G G (A) G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C (G) (G) T C C T 0 E106 G C A A C C C G G A T C T G T C C G T G G C A C G A A G G T C C G G I G C G C C A T A G T A C C T G C A C T G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C C T T C C T G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E107 G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G A G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T A G T A T C C A G A C C T A G C C G C T A T A C T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E108 G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G A G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E109 G C (A) (T) (C) C (C) A G A (T) C T A (T) (T) (A) G (C) (T) G C A (G) T G A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C G C (T) (A) (T) C (G) A G A (C) C T A (G) (C) (C) G (T) (G) G C A (C) T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E110 G C A A C C C A G A T C T A T C C G C T G T A C T A A G G T C C G A I G C G C C A T A G T G C C T G C A T C A C T T G C G G T T T T G C G A G G G A C A T G G A A A 3 T C A G G T G T T C C G G I C C T G T T C G C A T C C C A G A T C T A T T A G C T G C A G T A A G G C C C A A I G C G C C A T A G T A C C T G C A C C G T T T G G A G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E111 G C A T C C C A G A T C T A T T A G C T G C A (G) T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G C A G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T G C A T C C C A G A T C T A T T A G C T G C A (C) T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G C G G C C T T G C G A G G G A C A T G G A A A [1] T C A G A T G T C A C A C I C G G T C C T 0 E112 G C A T C C C A G A T C T G T C A G T G G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T A G T A T C C A G A C C T A G C C G C T A C A C T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E113 G C A A C C C G G A T C T G T C C G T G G C A C G A A G G T C C G G I G C G C C A T A G T A C C T G C A C T G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C C T T C C T G C A T C C C A G A T C T A T T A G C T G C A C G A A G G C C C G A I G T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C 0 E114 G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T G C A T C C C A G A T C T A T T A G C T G C A C G A A G G C C C G A I G T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C 0 E115 G C A T C C C A G A T C T A T T A G C T G C A C T A A G G C C C G A I A T G C C A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C 0 E116 G C A A C C C G G A T C T G T C C G T G G C A (C) G A A G G T C C G G I G C G C C A T A G T A C C T G C A C T G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C C T T C C T G C A T C C C A G A T C T A T T A G C T G C A (G) T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G A G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E117 G C A A C C C G G A T C T G T C C G T G G C A G G A A G A C C C G A I A T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C G C A A C C C G G A T C T G T C C G T T G C A G G A A G A C C C G A I A T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A G G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E118 G C A (A) C C C (G) G A T C T (G) T T A G C T G C A C T A A G G C C C A A I G C A T C A C A G T G T C C G C A T C G C T T G C G G C C T T G C G A G G G A C A (G) G G A A A 3 T C A G G T G T T C C G G D C C T G T T C G C A (T) C C C (A) G A T C T (A) T C C G T G G T A G G G A G A C C C G A I A T G C C A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A (T) G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E119 G C A A C C C G G A T C T G T T A G C T G C A G T A A G G C C C A A I G C A T C A C A G T G T C C G C A T C G C T T G C G G C C T T G C G A G G G A C A [G] G G A A A 3 T C A G G T G T T C C G G D C C T G T T C G C A T C C C A G A T C T A T C C G T G G T A G G G A G A C C C G A I A T G C C A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A [T] G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E120 G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C A G T A T C C A G A C C T A G C C G C T A T A C T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E121 G C A A C C C G G A T C T G T C C G T G G C A C G A A G G T C C G G I G C G C C A T A G T A C C T G C A C T G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C C T T C C T A G T A T C C A G A C C T A G C C G C T A T A C T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C 0 E122 G C A A C C C G G A T C T G T C C G T G G C A C G A A G G T C C G G I G C G C C A T A G T A C C T G C A C T G C T T G G G G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C C T T C C T G C A T C C C A G A T C T A T T A G C T G C A C T A A G G T C C G A I G C G C C A T A G T A C C T G C A C C G T T T G G A G C C T T G C G A G G G A C A T G G A A A 1 T C A G A T G T C A C A C I C G G T C C T 0 E123 G C A A C C C G G A T C T G T C C G T G G C A G G A A G A C C C G A I A T G C T A T G A C G C T C G C G T C A C A C G C G G C C T T G C G A G G G A C A G G G A A A 3 T C A G G T G T T C T G G D C C T G T T C A G T A T C C A G A C C T A G C C G C T A T A C T G A A G T C C G A D G C G C C A T A G T G C C T G C A C C G C T T G G G G C C T A T C G A G G C A C A T G G A A A 3 T C A G G T G T T C C G G D C C T G T T C END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 DY01 = = = A = = = = = C = = C = = C C = = G = ? ? = = = = = = = = = = = = = = G = = A T A = ? G C = = = G = = = = ? = = G = = = T T = = G = A = = A = = C = T G G A A = 3 ? ? A = = = = T T = = = = D (T) = = = = T = = = = T = = = = = A = = T = = T A = = T = ? ? = = = = = = = = = = = = = = A = = G C G = ? A T = = = C = = = = ? = = A = = = C C = = T = G = = G = = A = G A C G G = 2 ? ? G = = = = C C = = = = I (C) = = = = C = 0 DY02 = = = = = = = = = A = T T = = = = = = T = = G = = = = = = = T T = = = = = G = = A T = = = = C = T A = = C = G = = ? ? = = = = = = = G = = = = = G = C G T G G A A C 3 ? ? ? ? ? ? = ? T ? = ? ? ? ? = = = = T = = = = = = = = = = C = C C = = = = = = G = = A = = = = = = = C C = = = = = A = = G C = = = = T = C G = = T = A = = ? ? = = = = = = = T = = = = = C = A A G A C G G A 2 ? ? ? ? ? ? = ? C ? = ? ? ? ? = = = = C = 0 DY03 = = = A = T = = A = ? = = = = C C A = = = = = C = = G = = = = = ? ? = = = G = = A T A = ? G C = = = G = = = = = = = G = = = T T = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? T C = = = = = T T = = = = D = = = = = T = = = = T = C = = G = ? = = = = T A G = = = = = G = = A = = = = = ? ? = = = A = = G C G = ? A T = = = C = = = = = = = A = = = C C = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? C T = = = = = C C = = = = I = = = = = C = 0 DY04 = = = (A) = = = = = = = = = = = = = = = = = = = = = A = = G T = = G = = ? ? ? = = = = = = = A = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = G = = A C = = A = = ? ? ? = = = = = = = G = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = 0 DY05 = = = A = T = = A = ? = = = = C C A = = = = A C = G G = = = = = = = = = = = C = G = = = = = = = = = = = = = A = = = = = = = = = = = T = = = = = C = = A G = = = = A = = T = G = = = C C = = = = = C = = = = C = = = = T = C = = G = ? = = = = T A G = = = = G G = A A = = = = = = = = = = = T = A = = = = = = = = = = = = = G = = = = = = = = = = = G = = = = = G = = G T = = = = C = = C = A = = = T T = = = = = T = = = = T = 0 DY06 = = = (T) = = = = = (A) = = (T) = = (T) (A) = = = = = = = (T) = = = = = = = = = = = = (G) (C) = = (T) = = = = (C) = = = = = = = (A) = = = = = = = = = = = = = = = = = (C) = = = T G G A A = 3 T = A A = T G T T C = G G = T C T G T T C = = = (A) = = = = = (C) = = (C) = = (C) (C) = = = = = = = (G) = = = = = = = = = = = = (A) (T) = = (C) = = = = (T) = = = = = = = (G) = = = = = = = = = = = = = = = = = (G) = = = G A C G G = 2 C = G G = C A C C A = A C = C G G T C C T 0 DY07 = = = (A) = = = = = = ? = = = = (C) (C) = = = = (T) (A) (C) = (G) G = = = = = G = = = = = = = = = G = ? = T = = = C = = = (A) = = = A = = = C C = = = = = = = = (G) = (C) = = = (G) (A) (A) = (3) (T) = (A) = = = = = = = = = = ? = = = = = = = = = = (T) = = = = = = ? = = = = (T) (A) = = = = (C) (G) (G) = (A) A = = = = = A = = = = = = = = = A = ? = C = = = G = = = (G) = = = G = = = T T = = = = = = = = (C) = (A) = = = (C) (G) (G) = (2) (C) = (G) = = = = = = = = = = ? = = = = = = = 0 DY08 = = = A = T = = A = ? = = = = C C A = = = = = C = G = = ? = ? = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = A = = = = = T = = = A C = = = = = = = = = 3 = T = = G = = = T C = G G = = C T G T T C = = = T = C = = G = ? = = = = T A G = = = = = G = A = = ? = ? = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = G = = = = = C = = = G G = = = = = = = = = 1 = C = = A = = = C A = A C = = G G T C C T 0 DY09 = = = = = C = = G = ? T = = = = = G = = = = = G = = A = = = T T = = = = = G = = A T = = = = C = T A = = = = = = = = = = = = = = = = = = = = = = = = A = = A C G G = 2 C C = = = C A = = A = A C = = G G T ? ? ? = = = = = T = = A = ? C = = = = = A = = = = = C = = G = = = C C = = = = = A = = G C = = = = T = C G = = = = = = = = = = = = = = = = = = = = = = = = C = = G G A A = 3 T T = = = T G = = C = G G = = C T G ? ? ? 0 DY10 = = A = C T C = A = T = = = T = = A = = G = = C = = = = G = = = A = = G C A = = = C A G = = T C = = = A = = G = T T = = = A = C = = = = G = = = = = = = = = = = = = = = T = = = = = = = = = = = I = = = = = = = = = T = T C G = G = C = = = G = = G = = A = = G = = = = A = = = G = = A T G = = = T G A = = C T = = = G = = A = A C = = = G = T = = = = A = = = = = = = = = = = = = = = C = = = = = = = = = = = D = = = = = = = 0 DY11 G = = = C T = = A = ? = = = = = = A C = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = G = = = = = = A = = = = G T = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = T = = G = = = T C = G G = = C T G T T C A = = = T C = = G = ? = = = = = = G T = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = A = = = = = = G = = = = T C = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = C = = A = = = C A = A C = = G G T C C T 0 DY12 = = = = = = = = = = = = = = = = = = = = = = (A) = = (A) = = = = = = = = = = = = = = = = = = = (A) = = = = = = (C) = (G) = = = = (G) = = (C) (C) (T) = = = = = = = G = = = = = = = = = 1 = = = = A = = = C A = A C I = G G T C C T = = = = = = = = = = = = = = = = = = = = = = (G) = = (G) = = = = = = = = = = = = = = = = = = = (G) = = = = = = (T) = (A) = = = = (C) = = (T) (T) (G) = = = = = = = C = = = = = = = = = 3 = = = = G = = = T C = G G D = C T G T T C 0 DY13 = = = A = = = = = = = T = = = C = = = T = = = = = G = = = = T T = = = = = G = = = T = = = = C = T A = = = = A = = = = = = = = = = = T C = A G = C A = = = A = = = = = = = A = = C A = = A = A C = = G G T C = T = = = T = = = = = = = C = = = T = = = G = = = = = A = = = = C C = = = = = A = = = C = = = = T = C G = = = = G = = = = = = = = = = = G T = G A = G G = = = G = = = = = = = G = = T G = = C = G G = = C T G T = C 0 DY14 = = = A = = = G = = = = = G = C = = T = = = = = G G = = A = = = G = = A = G = = = T G A C = C T = = = = = = A = A C = = = = = T G = = = A A G A C A C = T = G A A = 3 T = A = = = = T T = = = = D = = = = = T = = = = T = = = A = = = = = A = T = = C = = = = = T A = = G = = = A = = G = A = = = C A G T = T C = = = = = = G = T T = = = = = C T = = = G G A G G G A = G = C G G = 2 C = G = = = = C C = = = = I = = = = = C = 0 DY15 = = A = C T C = A = T = = = T = = A = = G = = C = = G = G = = = A = = G C A = = G C A G T = T C = = = A = = = = T T = = = = = C T = T C G = = G = = = = G = = = = = = = T = = = = = C C = = = = I = = = = = C = = = T = T C G = G = C = = = G = = G = = A = = G = = A = A = = = G = = A T G = = A T G A C = C T = = = G = = = = A C = = = = = T G = G T A = = A = = = = T = = = = = = = C = = = = = T T = = = = D = = = = = T = 0 DY16 = = A = C = C = = C T = C = T = = = = G G = = (G) = = = = G = = = A = = G = = = = G = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = (G) = = = = = (C) = = = = (A) = = = = = = = = = (I) (T) = = = = = = = = T = T = G = = A C = T = G = = = = T A = = (C) = = = = A = = = G = = A = = = = A = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = (A) = = = = = (A) = = = = (G) = = = = = = = = = (D) (C) = = = = = = 0 DY17 = = = = = C = = G C = = C = = = = G = G = = = G = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = A = = = = = = G = = = = T C = = = G = = A = G A C G G = 2 C C G = = = = C C = = = = = = = = = = C = = = = = = T = = A A = = T = = = = A = T = = = C = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = G = = = = = = A = = = = G T = = = A = = C = T G G A A = 3 T T A = = = = T T = = = = = = = = = = T = 0 DY18 = = = (A) (T) = = = = = = = = = = (C) (C) = (T) = = = = = = (G) = = = = = = = = = = = = (C) = (G) = = = = = = = = = = = = = (A) = = = = = = = = = = ? ? = = = = = (C) = A = G = C G G = = C = G = G = = C = C = G G = = C T G T = C = = = (T) (C) = = = = = = = = = = (T) (A) = (C) = = = = = = (A) = = = = = = = = = = = = (T) = (A) = = = = = = = = = = = = = (G) = = = = = = = = = = ? ? = = = = = (G) = C = T = G A A = = T = A = A = = T = A = A C = = G G T C = T 0 DY19 = = = = C = = = = = = T = = = = = = = T = = = = T = = = G = T T = = = ? ? ? = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = A A = = = T T = = = = = T = = = = T = = = = = T = = = = = = C = = = = = = = G = = = = G = = = A = C C = = = ? ? ? = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = G G = = = C C = = = = = C = = = = C = 0 DY20 G = = T C = = = = = = = = = = T A = C = = = G = T A = = = = = = = = = = = A T = (G) C (A) = = = T = = = C = = = G = = = = = = = C C = T G C = A G = = A C G T G G A A C 3 T = A A = T G T T C = G G = T C T G T T C A = = A T = = = = = = = = = = C C = T = = = A = G G = = = = = = = = = = = G C = (A) T (G) = = = C = = = G = = = A = = = = = = = T T = A T T = G A = = G A A G A C G G A 2 C = G G = C A C C A = A C = C G G T C C T 0 DY21 = = = = = = = = = A = T T = = = = = = T = = G = (T) = = = = = T T = = = = = = = = = = = = = = = = T A C = C = G = = = = = = = C C T = G = = = = = = = = G = = = = = C 3 T = A A = T G T T C = G G = T C T G T T C = = = = = = = = = C = C C = = = = = = G = = A = (G) = = = = = C C = = = = = = = = = = = = = = = = C G G = T = A = = = = = = = T T G = T = = = = = = = = A = = = = = A 2 C = G G = C A C C A = A C = C G G T C C T 0 DY22 = = = = = (C) = = (G) (C) = = (C) = = = = (G) = (G) = = = = = (A) (A) = = = = = (A) = = = = (A) = = = (C) = = = ? (T) = (C) = = = (T) = A = = = = = = (A) = T = = = = A A G A C A C = T G G A A = 3 ? ? = = = T G T T = = = = D = = = = = T = = = = = = (T) = = (A) (A) = = (T) = = = = (A) = (T) = = = = = (G) (G) = = = = = (G) = = = = (G) = = = (T) = = = ? (C) = (T) = = = (C) = G = = = = = = (G) = C = = = = G G A G G G A = G A C G G = 2 ? ? = = = C A C C = = = = I = = = = = C = 0 DY23 = = (A) = (C) = = = = (C) (T) = (C) = (T) = = = = (G) = (C) = = (T) (A) = = = = = (C) = = = = = (A) = = = (C) = = = = (T) = (C) (G) = = (T) = (A) = = = (A) = = = = = = = = C = A G = = A C = T G G A A = = T = = = A T G T = A = A C = = G G T C = T = = (T) = (T) = = = = (A) (C) = (T) = (G) = = = = (T) = (T) = = (G) (G) = = = = = (T) = = = = = (G) = = = (T) = = = = (C) = (T) (A) = = (C) = (G) = = = (G) = = = = = = = = T = G A = = G A = G A C G G = = C = = = G C A C = C = G G = = C T G T = C 0 DY24 = = A = C = C = = C T = C = T = = = = G G = = = = = = = G = = = A = = G C A = = = C A G (T) = T C = = = A = = = = T T A = = = = C = = = C G = = G G = = = = = = = = = 1 = = = = A = = = C A = A C I = G G T C C T = = T = T = G = = A C = T = G = = = = T A = = = = = = = A = = = G = = A T G = = = T G A (C) = C T = = = G = = = = A C G = = = = T = = = T A = = A C = = = = = = = = = 3 = = = = G = = = T C = G G D = C T G T T C 0 E101 = = = A = = = G = = = = = = = = C = = = = = = G G = = = ? C = = = = = A T = = T = = G A C G = T C = = G T = A C A C = C = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = A = = = = = = = = A = = = = = = C T = = = ? T = = = = = G C = = C = = A G T A = C T = = A C = G T T T = G = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = A = C = C G = = T = = G T = = = T G G = = G G A = G A C = = = = I A T = = T = = G A C = = T C = = G T = A = A C = C = = = = = T G = = = = = G = = = = = = = = = (1) = = = = (A) ? = = (C) (A) (C) (A) (C) (I) = (G) (G) (T) (C) (C) (T) = = T = T = G A = = C = = A G = = = C T A = = C T G = A G T = = = = D G C = = C = = A G T = = C T = = A C = G = T T = G = = = = = A T = = = = = C = = = = = = = = = (3) = = = = (G) ? = = (T) (C) (T) (G) (G) (D) = (C) (T) (G) (T) (T) (C) 0 E103 = = A T C = C = = = T = = = T T A = C T = = = = T A = G = C = = = = I A T = = = = = G A C = = T C = = G T = A = A C = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = A = = = C A = A C = = G G T C C T = = T A T = G = = = C = = = G C C = T G = = = = G G = A = T = = = = D G C = = = = = A G T = = C T = = A C = G = T T = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = G = = = T C = G G = = C T G T T C 0 E104 = = = A = = = G = = = = = G = C C = T G = = = = G = = = = = = = = G = = = = = = = = = = = = = = = = = = = T = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = = = = = = = T = = = A = = = = = A = T A = C T = = = = T = = = = = = = = A = = = = = = = = = = = = = = = = = = = C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = = = = 0 E105 = = = A = = = G = = = = = G = C C = T G = = = (G) G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) (T) = = = = = = = T = = = A = = = = = A = T A = C T = = = (C) T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) (G) = = = = 0 E106 = = = A = = = G = = = = = G = C C = T G = = = = G = = = = = = = = G = = = = = = = = = = = = = = = = = = = T = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = = = = = = = T = = = A = = = = = A = T A = C T = = = = T = = = = = = = = A = = = = = = = = = = = = = = = = = = = C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = = = = 0 E107 G C A T C = = = = = T = = = T T A = = = G C = = = A = G = = = = = = I = = = = = = = = = = A = = = = = = = = = T = = = = A = = = = T G = = = = = G = = = = = = = = = 1 = = = = A = = = C A = A C I = G G T C C T A G T A T = = = = = C = = = G C C = = = A T = = = G = A = = = = = = D = = = = = = = = = = G = = = = = = = = = C = = = = G = = = = A T = = = = = C = = = = = = = = = 3 = = = = G = = = T C = G G D = C T G T T C 0 E108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E109 = = (A) (T) (C) = (C) = = = (T) = = = (T) (T) (A) = (C) (T) = = = (G) = = = G = = = = = = I = = = = = = = = = = A = = = = = = = = = T = = = = = = = = = T G = = = = = G = = = G = = = = = = = = = = = = = = = = T = = = = = = = = = = = = (T) (A) (T) = (G) = = = (C) = = = (G) (C) (C) = (T) (G) = = = (C) = = = A = = = = = = D = = = = = = = = = = G = = = = = = = = = C = = = = = = = = = A T = = = = = C = = = T = = = = = = = = = = = = = = = = C = = = = = = = = = = 0 E110 = = = A = = = = = = = = = = = C C = = = = T = C = = = = = T = = G = = = = = = = = = = = = G = = = = = = T = A C = = = C G = T T = ? ? = = = = = = = = = = = = = = = 3 = = = = G = = = T C = G G = = C T G T T C = = = T = = = = = = = = = = = T A = = = = C = G = = = = = C = = A = = = = = = = = = = = = A = = = = = = C = G T = = = G A = C C = ? ? = = = = = = = = = = = = = = = 1 = = = = A = = = C A = A C = = G G T C C T 0 E111 = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 0 E112 G C A T C = = = = = T = = G T = A = T G G = = = = A = G = = = = = = I = = = = = = = = = = A = = = = = = = = = T = = = = = = = = = T G = = = = = G = = = = = = = = = 1 = = = = A = = = C A = A C I = G G T C C T A G T A T = = = = = C = = A G = C = C T A = = = = G = A = = = = = = D = = = = = = = = = = G = = = = = = = = = C = = = = = = = = = A T = = = = = C = = = = = = = = = 3 = = = = G = = = T C = G G D = C T G T T C 0 E113 = = = A = = = G = = = = = G = C C = T G = = = = = = = = = T = = = G = = C = = C = = A G T A = C T = = A C T G = T T = G = = = = = = = = = = = = = = = = T = = = = = 1 = = = = A = = = C A C A C I = = = T C C T = = = T = = = A = = = = = A = T A = C T = = = = = = = = = C = = = A = = T = = T = = G A C G = T C = = G T C A = A C = C = = = = = = = = = = = = = = = = G = = = = = 3 = = = = G = = = T C T G G D = = = G T T C 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = T = = = = T = = = = = = C = = C = = A G T A = C T = = A C = G T T T = G = = = = = = = = = = = = = = = = T = = = = = 1 = = = = A = = = C A C A C I = G G T C C T = = = = = = = = = = = = = = = = = = = = = = = = G = = = = C = = = = = = T = = T = = G A C G = T C = = G T = A C A C = C = = = = = = = = = = = = = = = = G = = = = = 3 = = = = G = = = T C T G G D = C T G T T C 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = A T = = = = = G A C G = T C = = G T = A C A C = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = G C = = = = = A G T A = C T = = A C = G T T T = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = = = A = = = G = = = = = G = C C = T G = = = (C) G = = = = = = = = G = = = = = = = = = = = = = = = = = = = T = C = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = ? ? ? = = = T = = = A = = = = = A = T A = C T = = = (G) T = = = = = = = = A = = = = = = = = = = = = = = = = = = = C = T = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = ? ? ? 0 E117 = = = ? = = = = = = = = = = = = = = = G = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 3 = = = = G = = = T C T G G D = C T G T T C = = = ? = = = = = = = = = = = = = = = T = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = A = = = C A C A C I = G G T C C T 0 E118 = = = (A) = = = (G) = = = = = (G) = T A = C T = C = C T A = = G = = = A = = G C A T = = C A G T = T C = = = A = = G = T T = = = = = = ? = = = = = = = = = = = (G) = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = (T) = = = (A) = = = = = (A) = C C = T G = T = G G G = = A = = = G = = A T G C = = T G A C = C T = = = G = = A = A C = = = = = = ? = = = = = = = = = = = (T) = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = 0 E119 = = = A = = = G = = = = = G = T A = C T = C = = T A = = G = = = A = = G C A T = = C A G T = T C = = = A = = G = T T = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = T = = = A = = = = = A = C C = T G = T = = G G = = A = = = G = = A T G C = = T G A C = C T = = = G = = A = A C = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 0 E120 G C A T C = = = = = T = = = T T A = = = G C = = = A = G = = = = = = I = = = = = = = = = = A = = = = = = = = = T = = = = = = = = = T G = = = = = G = = = G = = = = = = = = = = = = = = = = T = = = = = = = = = = A G T A T = = = = = C = = = G C C = = = A T = = = G = A = = = = = = D = = = = = = = = = = G = = = = = = = = = C = = = = = = = = = A T = = = = = C = = = T = = = = = = = = = = = = = = = = C = = = = = = = = = = 0 E121 G C A = C = = G = = T = = G T = = = T G G C = = G A = G = = = = = G I = = = = = = = = = = A = = = = = = = T = = = = = = = = = = = T G = = = = = G = = = = = = = = = 1 = = = = A = = = C A = A C I = = = T C C T A G T = T = = A = = C = = A G = = = C T A T = = T G = A = = = = = A D = = = = = = = = = = G = = = = = = = C = = = = = = = = = = = A T = = = = = C = = = = = = = = = 3 = = = = G = = = T C = G G D = = = G T T C 0 E122 = = = A = = = G = = = = = G = C C = T G = = = = G = = = = = = = = G = = = = = = = = = = = = = = = = = = = T = C = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = = = = = = = T = = = A = = = = = A = T A = C T = = = = T = = = = = = = = A = = = = = = = = = = = = = = = = = = = C = T = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = = = = 0 E123 G C A = C = = G = = T = = G T = = = T G G C = G G A = G A C = = = = I A T = = T = = G A C = = T C = = G T = A = A C = ? = = = = = T G = = = = = G = = = G = = = = = = = = = = = = = = = = T = = = = = = = = = = A G T = T = = A = = C = = A G = = = C T A T = C T G = A G T = = = = D G C = = C = = A G T = = C T = = A C = G = T T = ? = = = = = A T = = = = = C = = = T = = = = = = = = = = = = = = = = C = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = 0.95 = = = = = 0.95 = = 0.95 = = 0.95 0.95 = = 0.95 = ? ? = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = ? 1.00 1.00 = = = 1.00 = = = = ? = = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 ? ? 1.00 = = = = 1.00 1.00 = = = = 1.00 0.56 = = = = 1.00 = = = = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 1.00 = = = = = 1.00 = = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = ? ? = = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? ? ? ? ? = ? 1.00 ? = ? ? ? ? = = = = 1.00 = = = = 0.95 = 0.95 = = 0.95 = ? = = = = 0.95 0.95 0.95 = = = = = 0.95 = = 0.95 = = = = = ? ? = = = 1.00 = = 1.00 1.00 1.00 = ? 1.00 1.00 = = = 1.00 = = = = = = = 1.00 = = = 1.00 1.00 = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1.00 1.00 = = = = = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = = = 0.60 = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 = = ? ? ? = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 = = 1.00 = ? = = = = 1.00 1.00 1.00 = = = = 0.96 1.00 = 1.00 1.00 = = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = = = = = = 1.00 = = = = = 1.00 = = 1.00 1.00 = = = = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = = = 1.00 = = = = 0.53 = = = = = 0.53 = = 0.53 = = 0.53 0.53 = = = = = = = 0.55 = = = = = = = = = = = = 0.53 0.53 = = 0.53 = = = = 0.53 = = = = = = = 0.53 = = = = = = = = = = = = = = = = = 0.82 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 0.71 = = = = = = ? = = = = 0.71 0.71 = = = = 0.71 0.71 0.71 = 0.51 0.92 = = = = = 0.92 = = = = = = = = = 0.92 = ? = 0.92 = = = 0.92 = = = 0.67 = = = 0.92 = = = 0.92 0.92 = = = = = = = = 0.79 = 0.79 = = = 0.79 0.79 0.79 = 0.79 0.79 = 0.79 = = = = = = = = = = ? = = = = = = = = = = 1.00 = 1.00 = = 1.00 = ? = = = = 1.00 1.00 1.00 = = = = = 1.00 = 1.00 = = ? = ? = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = 1.00 1.00 = = = = = = = = = 1.00 = 1.00 = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = = 1.00 = ? 1.00 = = = = = 1.00 = = = = = 1.00 = = 1.00 = = = 1.00 1.00 = = = = = 1.00 = = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 ? ? ? = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 = = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 = ? = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = = = 1.00 1.00 = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = 1.00 = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = 0.54 = = 0.53 = = = = = = = = = = = = = = = = = = = 0.80 = = = = = = 0.80 = 0.80 = = = = 0.80 = = 0.80 0.80 0.80 = = = = = = = 0.96 = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = = = = = 1.00 = = = 1.00 = = = 1.00 = = = = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 = = = 1.00 = = = = 1.00 = 1.00 1.00 = = = = 1.00 = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = = = = 1.00 1.00 = = 1.00 = = = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 = = 1.00 = = 1.00 = = 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = = 1.00 = = = = = = = 1.00 = = = = = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = = 0.99 = 0.99 = 0.99 = = 0.99 0.99 = 0.99 = 0.99 = = = = 0.99 0.99 = = 0.58 = = = = 1.00 = = = 1.00 = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = 0.70 = = = = = 0.70 = = = = 0.70 = = = = = = = = = 0.70 0.70 = = = = = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 = = = = 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = = = = = = = = = = 1.00 = = = = 0.65 0.65 = = = = = = = = = = 0.65 0.65 = 0.65 = = = = = = 0.70 = = = = = = = = = = = = 0.70 = 0.70 = = = = = = = = = = = = = 0.70 = = = = = = = = = = ? ? = = = = = 0.70 = 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = = 1.00 = = = = = = 1.00 = = = = = = = 1.00 = = = = 1.00 = = = 1.00 = 1.00 1.00 = = = ? ? ? = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = 1.00 1.00 = = = 1.00 1.00 = = = = = 1.00 = = = = 1.00 = 0.99 = = 0.99 0.99 = = = = = = = = = = 0.99 0.99 = 0.99 = = = 0.97 = 0.99 0.99 = = = = = = = = = = = 0.99 0.99 = 0.51 0.99 0.68 = = = 0.99 = = = 0.99 = = = 0.99 = = = = = = = 0.99 0.99 = 0.98 0.98 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = 1.00 = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 0.71 = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = = = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = 0.66 = = 0.66 0.66 = = 0.66 = = = = 0.66 = 0.66 = = = = = 0.74 0.54 = = = = = 0.54 = = = = 0.54 = = = 0.54 = = = ? 0.54 = 0.54 = = = 0.54 = 0.92 = = = = = = 0.54 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 ? ? = = = 1.00 1.00 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = = 0.59 = 0.59 = = = = 0.59 0.59 = 0.59 = 0.59 = = = = 0.59 = 0.61 = = 0.59 0.57 = = = = = 0.57 = = = = = 0.57 = = = 0.57 = = = = 0.57 = 0.57 0.57 = = 0.57 = 0.57 = = = 0.57 = = = = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = 0.99 = 0.99 = 0.99 = = 0.99 0.99 = 0.99 = 0.99 = = = = 0.99 0.99 = = = = = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 0.85 = 1.00 1.00 = = = 1.00 = = = = 1.00 1.00 1.00 = = = = 0.93 = = = 0.93 0.93 = = 0.93 0.93 = = = = = = = = = 0.93 = = = = 0.93 = = = 0.93 0.93 = 0.93 0.93 0.93 = 0.93 0.93 0.93 0.93 0.93 0.93 = = = 1.00 = = = 1.00 = = = = = = = = 1.00 = = = = = = 1.00 1.00 = = = ? 1.00 = = = = = 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = 0.69 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = = = = = 1.00 = = = = = = = = = 0.68 = = = = 0.68 ? = = 0.68 0.68 0.58 0.68 0.68 0.68 = 0.68 0.68 0.68 0.68 0.68 0.68 = = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 0.66 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.71 = = = = 0.71 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.62 0.62 = = = = = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = 1.00 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.85 0.85 0.85 = 0.85 = = = 0.85 = = = 0.85 0.85 0.85 = 0.85 0.85 = = = 0.87 = = = 0.94 = = = = = = 0.94 = = = = = = = = = = 0.94 = = = = = = = = = 0.94 = = = = = = = = = 0.94 0.94 = = = = = 0.94 = = = 0.94 = = = = = = = = = = = = = = = = 0.94 = = = = = = = = = = = = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 = = = = = 1.00 = = 1.00 = = = = = = = = = = = = 1.00 = = = = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = ? ? = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 0.68 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 0.90 0.90 0.90 0.90 0.90 = = = = = 0.90 = = 0.90 0.90 = 0.90 = 0.90 0.90 0.90 = = = = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = 1.00 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = = = = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = 0.96 = = = = = 0.96 = = = = 0.96 = = = 0.96 0.96 0.96 0.96 0.96 0.96 = 0.96 0.96 0.96 0.96 0.96 0.96 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 0.73 1.00 = = = = = = = = 0.97 = = = = = = = = = = = = = = = = = = = 0.97 = 0.97 = = = = 0.97 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 0.97 = ? ? ? = = = ? = = = = = = = = = = = = = = = 1.00 = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 0.70 = = = 0.73 = = = = = 0.73 = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = = = = = = ? = = = = = = = = = = = 0.57 = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = 0.97 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = 1.00 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = 1.00 1.00 = = = = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = = = = = = = = = = 1.00 = = = = = = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = = 1.00 = = = 1.00 = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = ? = = = = = 1.00 1.00 = = = = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = END PHASEPROBS