************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 hnf4a.phase.inp hnf4a.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST hnf4a.phase.out_freqs : haplotype frequency estimates hnf4a.phase.out_pairs : most likely haplotype pairs for each individual hnf4a.phase.out_recom : estimates of recombination parameters hnf4a.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 87 Positions of loci: 84 85 353 437 1031 1037 1332 2207 2358 2837 2856 2913 3003 3691 3902 4432 5142 5281 6063 6126 6218 6515 6519 6560 6707 6740 6830 7185 7207 7790 7827 8499 8696 8738 9060 9412 9413 9427 10606 10738 10751 10767 11087 11310 11422 11584 11833 11898 12184 12227 12240 12272 12335 12483 12779 13779 14177 14627 14997 15098 15142 16409 17497 17846 18093 19341 19396 19559 20733 21224 21366 24618 28197 28610 29528 29868 30060 30066 30144 30595 30658 30745 31259 31290 31485 31652 32719 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file hnf4a.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACCAIIAGAICTTGGGCGGGAGCCCCCTCACAATAAAAAGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTAACGCGG 1 ITIC 1.000000 2 ACCAIIAGAICTTGGGCGGGAGCCCCCTCACAATAAAAAGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTAACGCGG 1 ITIG 1.000000 3 ACCAIIAGAICTTGGGCGGGAGCCCCCTCACAATATCAAGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTCATCCGG 1 ITIC 1.000000 4 ACCAIIAGAICTTGGGCGGGAGCCCCCTCACAATATCACGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTCATCTAT 1 ITIG 2.000000 5 ACCAIIAGAICTTGGGCGGGAGCCCCCTCACAATATCACGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTCATCTAT 2 ICIG 1.000000 6 ACCAIIAGAICTTGTGGGGGAGCCTCCCCACGATGAAGAGCGGCGGCCCGCGTCTGCCACGTCIGGAGGTGCTCTACTGTAG 4 ITIC 2.000000 7 ACCAIIAGAICTCGGGCGGGAGCCCCCTCACGATGAAGCGTGGCGGCCCGCGCCTACCACGTTIGGGGGAGCTTGAACGTAT 2 DCIG 1.000000 8 ACCAIIAGAICTCGGGCGGGAGCCCCCTCACGATGAAGCGTGGCGCCCCGCGCCTGCCACGCTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 9 ACCAIICGAICTCGGGCGGGAGCCCCCTCACGATGAAGAGCGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 2 ICIG 1.000000 10 ACCAIICGAICTCGGGGGGGAACCTCCCGACGATGAAGCGTAGCGGCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 2 DCIG 1.000000 11 ACCAIICGAICTCGGGGAAGTGCCCTCTCGTAGGGTCGAGCGGCGGCCCGCGCCCGCCACGCTDTAGGATATGTTCATCTAT 1 ICIG 1.000000 12 ACCAIICGAICTCGGGGAAGTGCCCTCTCGTAGGGTCGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTTAACGTAT 2 ICIG 1.000000 13 ACCAIICGAICTCGGGGAAGTGCCCTCTCGTAGGGTCGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTTAACGTAT 4 ICIG 2.000000 14 ACCAIICGAICTCGGGGAAGTGCCCTCTCGTAGGGTCGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAATGTAT 2 ICIG 1.000000 15 ACCAIICGADCTTGGGGGGGAGCCCCCTCACAATAAAAAGCGGCGGCCCGCGCCCGCCACGCTDTAGGATATGTTCATCTAT 2 ITIG 2.000000 16 ATCAIIAGAICTTGGGGGGGAGCCTCCCCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ITIG 1.000000 17 ATCAIIAGAICTTGGGGGGGAGCCTCCCCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGTTIGGGGGTGCTCGAACGCGG 1 ITIG 1.000000 18 ATCAIIAGAICTTGGGGGGGAACCTCCTGACGATGAAGCGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATGTAT 2 ITIG 1.000000 19 ATCAIIAGAICTTGGGGGAGAGCCTCCCCACAATGAAAAGCGGCGGCCCGCGCCTGCCACGTTIGGGGGTGCTCGAATGTAT 2 DCIG 1.000000 20 ATCAIDAGAICTTGGGGGGGAGCCTCCCCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ITIG 3.000000 21 ATCAIDAGAICTTGTGGGGGAGCCTCCCCACGATGAAGCGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTCATCTAT 1 ITIG 1.000000 22 ATCAIDAGAICTTAGGGGAGAGCGTCCTCACAATGAAGCTTGGCAGTTCGAACCCGGGCCATTDTAGGATATGTTAACGTAT 2 ICIC 2.000000 23 ATAAIIAGAICTTGGGCGGGAGCCCCCTCACAATATCAAGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTCATCTAT 1 ITIG 1.000000 24 ATAAIIAGAICTTGGCGGAAAGTGTCCTCACAATATCAAGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTAACGTAT 2 ICIG 1.000000 25 ATAAIIAGAICTTGGCGGAAAGTGTCCTCACAATATCAAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 26 ATAAIIAGAICTCGGGGGGGAACCTCCCGACGATGAAGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 27 ATAAIIAGAICTCGGGGGGGAACCTCCCGACGATGAAGCGTAGCGCCCCGCGCCTGCCACGTTIGGGGGAGCTTTAACGTAT 2 ICIG 1.000000 28 ATAAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGCGTAGCGGCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 2 DCIG 1.000000 29 ATAAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGCGTAGCGCCCCGCGCCTGCCACGCTDTAGGATGTGTTAATCTAT 2 DCIG 1.000000 30 ATAAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGCGTAGCGCCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 2 DCIC 2.000000 31 ATAAIICGAICTCGGGCGGGAGCCCCCTCACGATGAAGAGCGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ITIG 1.000000 32 ATAAIICGAICTCGGGCGGGAGCCCCCTCACGATGAAGAGCGGCGGCCCGCGCCTGCCACGCTDTAGGATACTCGAATGTAT 2 DTIG 1.000000 33 ATAAIICGAICTCGGGGAAGTGCCCTCTCGTAGGGTCGAGCGGCGGCCCGCGCCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 34 GTCAIIAGAICTTGTGGGGGAGCCTCCTCACGATGAAGAGCGGCGGCCCGCGTCTGCCACGTCIGGAGGTGCTCTACTGTAG 4 ITIC 1.000000 35 GTCAIIAGAICTCGGGGGGGAACCTCCCGACGATGAAGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTTAACGTAT 2 ICIG 1.000000 36 GTCAIIAGAICTCGGGGGGGAACCTCCCGACGATGAAGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIC 1.000000 37 GTCAIIAGAICTCGGGGGGGAACCTCCCGACGATGAAGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 38 GTCAIIAGAICTCGGGGGGGAACCTCCCGACGATGAAGCGTGATAGCTTGAGCTCGGGCGATTIGGGGGAGCTTGAACGTAT 2 ICIG 2.000000 39 GTCAIIAGAICTCGGGGGGGAACCTCCTGACGATGAAAAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 40 GTCAIIAGAICTCGGGGGGGAACCTCCTGACGATGAAACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ITIG 1.000000 41 GTCAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 42 GTCAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGCGTGATAGCTTGAGCTCGGGCGATCIGGAAGTGCTCTACTGTAG 4 ICIG 1.000000 43 GTCAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGCGTGATAGCTTGAGCTCGGGCGATCIGGAAGTGCTCTACTGTAG 4 ICDG 1.000000 44 GTCAIIAGAIACTGGCGGAAAGTGTCCTCACAATGAAGCGTAGCGGCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 2 DCIG 1.000000 45 GTCAIICGAICTTAGGGGGGAGCCCCCTCACAATAAAAAGCGGCGGCCCGCGTCTACCACGCTDTAGGATATGTTAACCCGG 1 ITIC 1.000000 46 GTCAIICGAICTTAGGGGGGAGCCTCCCCACGATGAAGCGCGGCGGCCCGCGCCTGCCACGCTIGGGGGAGCGTGAACGTAT 2 ICIG 1.000000 47 GTCAIICGAICTCGGGGGGGAACCTCCCGACGATGAAGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTTAACGTAT 2 ICIG 1.000000 48 GTCAIICGAICTCGGGGGGGAACCTCCCGACGATGAAGCGTGATAGCTTGAGCCCGGGCGATCIGGAAGTGCTCTACTGTAG 4 ICDG 1.000000 49 GTCAIICGAICTCGGGGGGGAACCTCCCGACGATGAAGCGTGATAGCTTGAGCTCGGGCGATTIGGGGGAGCTTTAACGTAT 2 ICIG 1.000000 50 GTCAIICGAICTCGGGGGGGAACCTCCCGACGATGAAGCGTGATAGCTTGAGCTCGGGCGATTIGGGGGAGCTTGAACGTAT 2 ICIG 3.000000 51 GTCAIICGAICTCGGGGGGGAACCTCCCGACGATGTCGCGTAGCGCCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 2 DCIC 1.000000 52 GTCAIICGAIACCGGGGGGGAACCTCCCGACGATGAAGCGTGATAGCTTGAGCTCGGGCGATTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 53 GTCAIDCGAICTCGGGCGGGAGCCCCCTCACAATATCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ICIC 1.000000 54 GTCAIDCGCDCTTGGGGGGGAGCCCCCTCACAATATCAAGCGGCGGCCCGCGTCTACCACGTTIGGGGGTGCTCGAACGCGG 2 ICIC 1.000000 55 GTCAIDCGCDCTTGGGGGGGAGCCCCCTCACAATATCACTTGGCAGTTTTAACCCGGGCCATTIGGGGGTGCTCGAACGCGG 1 ITIG 2.000000 56 GTCAIDCGCDCTTGGGGAAGAGCCCTCTCACAATGTCAAGCGGCGGTCCGCGTCTGCGACGTCIGGAGGTGCTCTACTGTAG 4 ICIG 1.000000 57 GTCAIDCAAICTCGGGGAAGTGCCCTTTCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ICDG 1.000000 58 GTCADICAAICTCGGGGAGGTGCCCTTTCGCAGGGTCACGCGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 2 ICDG 1.000000 59 GTCADICAAICTCGGGGAAGTGCCCTTTCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ITIG 1.000000 60 GTCADICAAICTCGGGGAAGTGCCCTTTCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ICDG 2.000000 61 GTCADICAAICTCGGGGAAGTGCCCTTTCGCAGGGTCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 2 ICIC 1.000000 62 GTCGIIAGAICTTGGGCGGGAGCCCCCTCACAATATCAAGCGGCGGCCCGCGCCCGCCACGCTDTAGGATATGTTCATCTAT 1 ICIG 1.000000 63 GTCGIIAGAICTTGGGCGGGAGCCCCCTCACAATATCACGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ICIC 1.000000 64 GTCGIIAGAICTTGGGCGGGAGCCCCCTCACAATATCACGTAGCGGCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 2 DCIG 1.000000 65 GTCGIIAGAICTTGTGGGGGAGCCTCCCCACGATGAAGAGCGGCGGCCCGCGCCTACCACGTTDGGGGGAGCTTGAACGTAT 2 ICIC 1.000000 66 GTCGIIAGAICTTGTGGGGGAGCCTCCCCACGATGAAGCGCGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 2 ITIG 1.000000 67 GTCGIIAGAICTTGTGGGGGAGCCTCCCCACGATGAAGCGCGGCGGCCCGCGCCTGCCACGCTIGGGGGAGCGTGAACGTAT 2 ICIG 3.000000 68 GTCGIIAGAICTTGTGGGGGAGCCTCCCCACGATGAAGCTTGGCAGTTTTAACCCGGGCGATCIGGAAGTGCTCGAATGTAG 2 ICIC 2.000000 69 GTCGIICGAICTCGGGGGGGAACCTCCTGACGATGAAGCGTGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 2 ITIG 1.000000 70 GTCGIICGAICTCGGGGGGGAACCTCCTGACGATGAAGCGTGGCGGCCCGCGCCTGCCACGCTDGAGGATATGTGCATCTAT 2 ITIG 1.000000 71 GTCGIICGAICTCGGGGAAGTGCCCTCTCGCAGGGTCGAGCGGCGGCCCGCGTCTACCACGTTDTAGGATATGTTCATCTAT 2 ICIG 1.000000 72 GTCGIICGAICTCGGGGAAGTGCCCTCTCGTAGGGTCGAGCGGCGGCCCGCGTCTACCACGTTIGGGGGAGCTTTAACGTAT 2 ICIG 2.000000 73 GTCGIICGAIACCGGCGGAAAGTGTCCTCACAATGAAGCGTAGCGCCCCGCGCCTGCCACGCTDTAGGATGTGTGCATCTAT 1 ICDG 1.000000 74 GTCGIDAGAICTTGTGGGGGAGCCTCCCCACGATGAAGCGCGGCGGCCCGCGCCTGCCACGCTDTAGGATATGTTCATCTAT 1 ICIC 1.000000 75 GTCGIDAGAICTTGTGGGGGAGCCTCCCCACGATGAAGCGCGGCGGCCCGCGCCTGCCACGCTIGGGGGAGCGTGAACGTAT 2 ICIG 1.000000 76 GTCGIDAGAICTTAGGGGAGAGCGTCCTCACAATGAAGCTTGGCAGTTTTAACCCGGGCCATTIGGGGGAGCTTGAACGTAT 2 ICIG 1.000000 77 GTCGIDCGCDCTTGGGGGGGAGCCCCCTCACAATATCACTTGGCAGTTTTAACCCGGGCCATTIGGGGGTGCTCGAACGCGG 2 ICIG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,20) DY02: (5,6) DY03: (9,56) DY04: (15,16) DY05: (18,68) DY06: (4,65) DY07: (32,45) DY08: (20,55) DY09: (6,66) DY10: (3,67) DY11: (35,44) DY12: (22,67) DY13: (21,74) DY14: (22,63) DY15: (19,67) DY16: (17,25) DY17: (24,76) DY18: (34,71) DY19: (54,77) DY20: (46,62) DY21: (2,55) DY22: (23,75) DY23: (20,68) DY24: (4,15) E101: (13,14) E102: (50,64) E103: (7,38) E104: (53,57) E105: (30,69) E106: (72,73) E107: (51,27) E108: (30,40) E109: (8,52) E110: (48,61) E111: (31,41) E112: (50,50) E113: (11,72) E114: (29,60) E115: (42,26) E116: (38,60) E117: (28,59) E118: (10,49) E119: (43,58) E120: (33,37) E121: (12,47) E122: (36,70) E123: (13,39) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A C C A I (I) A G A I C T T G G G C G G G A G C C C C C T C A C A A T A A A A A G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T A A C [G] C G G 1 I T I C A T C A I (D) A G A I C T T G G G G G G G A G C C T C C C C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G 0 DY02 A C C A I I A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A [C] G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I C I G A C C A I I A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G A G [C] G G C G G C C C G C G T C T G C C A C G T C I G G A G G T G C T C T A C T G T A G 4 I T I C 0 DY03 (A) (C) C A I I C G A I C T C G G G (C) (G) (G) G A G C C C (C) C T C A C (G) A T G (A) A (G) A G C G G C G G (C) C C G C G C C T G C (C) A C G C T D T A G G A T A T G T T C A T C T A T 2 I C I G (G) (T) C A I D C G C D C T T G G G (G) (A) (A) G A G C C C (T) C T C A C (A) A T G (T) [C] (A) A G C G G C G G (T) C C G C G T C T G C (G) A C G T C I G G A G G T G C T C T A C T G T A G 4 I C I G 0 DY04 A C C A I I C G A D C T T G G G G G G G A G C C C C C T C A C A A T A A A A A G C G G C G G C C C G C G C C C G C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I T I G A T C A I I A G A I C T T G G G G G G G A G C C T C C C C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G 0 DY05 [A] [T] C A I I A G A I C T T G G G G G G G A A C C T C C T G A C G A T G A A G C G [T] G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T G T A T 2 I T I G [G] T C [G] I I A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C T T G G C A G T T T T A A C C C G G G C G A T C I G G A A G T G C T C G A A T G T A G 2 I C I C 0 DY06 A C C A I I A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A [C] G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G G T C G I I A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G [A] G C G G C G G C C C G C G C C T A C C A C G T T D G G G G G A G C T T [G] A A C G T A T 2 I C I C 0 DY07 A T (A) A I I C G A I C T C G G G C G G G A G C C C C C T C A C G A T G A A G A G C G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A C T C G A A T G T A T 2 D T I G [G] T (C) A I I C G A I C T T A G G G G G G A G C C C C C T C A C A A T A A A A A G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T [A] A C C C G G 1 I T I C 0 DY08 A T C A I [D] A G A I C T T G G G G G G G A G C C T C C C C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G [G] [T] C A I [D] C G C D C T T G G G G G G G A G C C C C C T C A C A A T A T C A C T T G G C A G T T T T A A C C C G G G C C A T T I G G G G G T G C T C G A A C G C G G 1 I T I G 0 DY09 A C C A I I A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G A G [C] G G C G G C C C G C G T C T G C C A C G T C I G G A G G T G C T C T A C T G T A G 4 I T I C G T C G I I A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C G [C] G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I T I G 0 DY10 A C C A I I A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A A G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T C A T C (C) (G) (G) (1) I (T) I (C) G T C G I I A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C G C G G C G G C C C G C G C C T G C C A C G C T I G G G G G A G C G T G A A C G (T) (A) (T) (2) I (C) I (G) 0 DY11 G T C A I I A G A I (C) (T) (C) G G (G) G G (G) (G) A (A) (C) (C) T C C (C) (G) A C (G) A T G A A G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T (T) A A C G T A T 2 I C I G G T C A I I A G A I (A) (C) (T) G G (C) G G (A) (A) A (G) (T) (G) T C C (T) (C) A C (A) A T G A A G C G T A G C G G C C C G C G C C T G C C A C G C T D T A G G A T G T G T (G) C A T C T A T 2 D C I G 0 DY12 A T C A I (D) A G A I C T T A G G G G A G A G C G T C C T C A C A A T G A A G C T T G G C A G T T C G A A C C C G G G C C A T T D T A G G A T A T G T T A A C G T A T 2 I C I C G T C G I (I) A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C G C G G C G G C C C G C G C C T G C C A C G C T I G G G G G A G C G T G A A C G T A T 2 I C I G 0 DY13 (A) T C (A) I D A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G (G) T C (G) I D A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C G C G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C I C 0 DY14 A T C A I (D) A G A I C T T A G G G G A G A G C G T C C T C A C A A T G A A G C T T G G C A G T T C G A A C C C G G G C C A T T D T A G G A T A T G T T A A C G T A T 2 I C I C G T C G I (I) A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C I C 0 DY15 (A) T C (A) I I A G A I C T T G (G) G G G (A) G A G C C T C C C C A C (A) A T G A A (A) A G C G G C G G C C C G C G C C T G C C A C G T T I G G G G G T G C T C G A A T G T A T 2 D C I G (G) T C (G) I I A G A I C T T G (T) G G G (G) G A G C C T C C C C A C (G) A T G A A (G) C G C G G C G G C C C G C G C C T G C C A C G C T I G G G G G A G C G T G A A C G T A T 2 I C I G 0 DY16 A T C A I I A G A I C T T G G G G G G G A G C C T C C C C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G T T I G G G G G T G C T C G A A C G C G G 1 I T I G A T A A I I A G A I C T T G G C G G A A A G T G T C C T C A C A A T A T C A A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 DY17 A T A A I I A G A I C T T G G C G G A A A G T G T C C T C A C A A T A T C A A G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T A A C G T A T 2 I C I G G T C G I D A G A I C T T A G G G G A G A G C G T C C T C A C A A T G A A G C T T G G C A G T T T T A A C C C G G G C C A T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 DY18 G T C (A) I I A G A I C T T G T G G G G G A G C C T C C T C A C G A T G A A G A G C G G C G G C C C G C G T C T G C C A C G T C I G G A G G T G C T C T A C T G T A G 4 I T I C G T C (G) I I C G A I C T C G G G G A A G T G C C C T C T C G C A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T D T A G G A T A T G T T C A T C T A T 2 I C I G 0 DY19 G T C (A) I D C G C D C T T G G G G G G G A G C C C C C T C A C A A T A T C A A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G T G C T C G A A C G C G G 2 I C I (C) G T C (G) I D C G C D C T T G G G G G G G A G C C C C C T C A C A A T A T C A C T T G G C A G T T T T A A C C C G G G C C A T T I G G G G G T G C T C G A A C G C G G 2 I C I (G) 0 DY20 G T C (A) I I C G A I C T T A G G G G G G A G C C T C C C C A C G A T G A A G C G C G G C G G C C C G C G C C T G C C A C G C T I G G G G G A G C G T G A A C G T A T 2 I C I G G T C (G) I I A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A A G C G G C G G C C C G C G C C C G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C I G 0 DY21 A C C A I (I) A G A I C T T G G G C G G G A G C C C C C T C A C A A T A A A A A G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T A A C G C G G 1 I T I G G T C A I (D) C G C D C T T G G G G G G G A G C C C C C T C A C A A T A T C A C T T G G C A G T T T T A A C C C G G G C C A T T I G G G G G T G C T C G A A C G C G G 1 I T I G 0 DY22 (A) T (A) (A) I (I) A G A I C T T G G G C G G G A G C C C C C T C A C A A T A [T] [C] A A G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G (G) T (C) (G) I (D) A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C G C G G C G G C C C G C G C C T G C C A C G C T I G G G G G A G C G T G A A C G T A T 2 I C I G 0 DY23 A T C A I (D) A G A I C T T G G G G G G G A G C C T C C C C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G G T C G I (I) A G A I C T T G T G G G G G A G C C T C C C C A C G A T G A A G C T T G G C A G T T T T A A C C C G G G C G A T C I G G A A G T G C T C G A A T G T A G 2 I C I C 0 DY24 A C C A I I A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A C G C G G C G G C C C G C G T C T A C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G A C C A I I C G A D C T T G G G G G G G A G C C C C C T C A C A A T A A A A A G C G G C G G C C C G C G C C C G C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I T I G 0 E101 A C C A I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T (T) A A (C) G T A T (4) I C I G A C C A I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T (G) A A (T) G T A T (2) I C I G 0 E102 G T C A I I C G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T T I G G G G G A G C T T G A A C G T A T 2 I C I G G T C G I I A G A I C T T G G G C G G G A G C C C C C T C A C A A T A T C A C G T A G C G G C C C G C G C C T G C C A C G C T D T A G G A T G T G T G C A T C T A T 2 D C I G 0 E103 (A) (C) C A I I A G A I C T C G G G (C) G G G A (G) C C (C) C C (T) (C) A C G A T G A A G C G T G G C G G C C C G C G C C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 (D) C I G (G) (T) C A I I A G A I C T C G G G (G) G G G A (A) C C (T) C C (C) (G) A C G A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T T I G G G G G A G C T T G A A C G T A T 2 (I) C I G 0 E104 G T C A I D C G A I C T C G G G C G G G A G C C C C C T C A C A A T A T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C I C G T C A I D C A A I C T C G G G G A A G T G C C C T T T C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C D G 0 E105 A T A A I I A G A I A C T G G C G G A A A G T G T C C T C A C A A T G A A G C G T A G C G C C C C G C G C C T G C C A C G C T D T A G G A T G T G T G C A T C T A T 2 D C I C G T C G I I C G A I C T C G G G G G G G A A C C T C C T G A C G A T G A A G C G [T] G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I T I G 0 E106 G T C G I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T (T) A A C G T A T 2 I C I G G T C G I I C G A I A C C G G C G G A A A G T G T C C T C A C A A T G A A G C G T A G C G C C C C G C G C C T G C C A C G C T D T A G G A T G T G T (G) C A T C T A T 1 I C D G 0 E107 (G) T (C) A I I (C) G A I C T C G G G G G G G A A C C T C C C G A C G A T G (T) (C) G C G T A G C G C C C C G C G C C T G C C A C G C T D T A G G A T G T G T G C A T C T A T 2 D C I C (A) T (A) A I I (A) G A I C T C G G G G G G G A A C C T C C C G A C G A T G (A) (A) G C G T A G C G C C C C G C G C C T G C C A C G T T I G G G G G A G C T T T A A C G T A T 2 I C I G 0 E108 A T A A I I A G A I A C T G G C G G A A A G T G T C C T C A C A A T G A A (G) C G T (A) G C G (C) C C C G C G C C T G C C A C G C T D T A G G A T (G) T G T (G) C A T C T A T (2) (D) (C) I (C) G T C A I I A G A I C T C G G G G G G G A A C C T C C T G A C G A T G A A (A) C G T (G) G C G (G) C C C G C G C C T G C C A C G C T D T A G G A T (A) T G T (T) C A T C T A T (1) (I) (T) I (G) 0 E109 (A) (C) C A I I (A) G A I (C) (T) C G G G C G G G A G C C C C C T C A C G A T G A A G C G T G G C G (C) C C C G C G C C T G C C A C G C T I G G G G G A G C T T G A A C G T A T 2 I C I G (G) (T) C A I I (C) G A I (A) (C) C G G G G G G G A A C C T C C C G A C G A T G A A G C G T G A T A (G) C T T G A G C T C G G G C G A T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 E110 G T C A (I) I C (G) A I C T C G G G G G (G) G (A) (A) C C (T) (C) (C) (C) (G) (A) C (G) (A) (T) G (A) (A) (G) C G T G A T A G C T T G A G C C C G G G C G A T C I G G A A G T G C T C T A C T G T A G 4 I C D (G) G T C A (D) I C (A) A I C T C G G G G [A] (A) G (T) (G) C C (C) (T) (T) (T) (C) (G) C (A) (G) (G) G (T) (C) (A) C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I C I (C) 0 E111 (A) T (A) A I I C G A I C T C G G G C G G G A G C C C C C T C A C G A T G A A G A G C G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G (G) T (C) A I I A G A I A C T G G C G G A A A G T G T C C T C A C A A T G A A G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 E112 G T C A I I C G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T T I G G G G G A G C T T G A A C G T A T 2 I C I G G T C A I I C G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 E113 (A) (C) C (A) I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G C C [C] G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C I G (G) (T) C (G) I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T T A A C G T A T 2 I C I G 0 E114 A T A A I I A G A I A C T G G C G G A A A G T G T C C T C A C A A T G A A G C G T A G C G C C C C G C G C C T G C C A C G C T D T A G G A T G T G T T (A) A T C T A T 2 D C I G G T C A [D] [I] C A A I C T C G G G G A A G T G C C C T T T C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T (C) A T C T A T 1 I C D G 0 E115 (G) T (C) A I I A G A I (A) (C) (T) G G (C) G G (A) (A) A (G) (T) (G) T C C (T) (C) A C (A) A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T C I G G A A G T G C T C T A C T G T A G 4 I C I G (A) T (A) A I I A G A I (C) (T) (C) G G (G) G G (G) (G) A (A) (C) (C) T C C (C) (G) A C (G) A T G A A G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 E116 G T C A I I A G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T T I G G G G G A G C T T G A A C G T A T 2 I C I G G T C A D I C A A I C T C G G G G A A G T G C C C T T T C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I C D G 0 E117 (A) T (A) A I I A G A I A C T G G C G G A A A G T G T C C T C A C A A T G A A G C G T A G C G G C C C G C G C C T G C C A C G C T D T A G G A T G T G T G C A T C T A T 2 D C I G (G) T (C) A D I C A A I C T C G G G G A A G T G C C C T T T C G C A G G G T C A C G T G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 1 I T I G 0 E118 (A) (C) C A I I C G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G C G T A G C G G C C C G C G C C T G C C A C G C T D T A G G A T G T G T (G) C A T C T A T 2 D C I G (G) (T) C A I I C G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G C G T G A T A G C T T G A G C T C G G G C G A T T I G G G G G A G C T T (T) A A C G T A T 2 I C I G 0 E119 G T C A (I) I (A) (G) A I (A) (C) (T) G G (C) G (G) (A) (A) (A) G (T) (G) (T) (C) (C) T C (A) C A (A) (T) G (A) (A) (G) C G T G A T A G C T T G A G C T C G G G C G A T C I G G A A G T G C T C T A C T G T A G 4 I C D G G T C A (D) I (C) (A) A I (C) (T) (C) G G (G) G (A) (G) (G) (T) G (C) (C) (C) (T) (T) T C (G) C A (G) (G) G (T) (C) (A) C G C G G C G G C C C G C G C C T G C C A C G C T D T A G G A T A T G T T C A T C T A T 2 I C D G 0 E120 (A) T (A) A I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G (C) C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 I C I G (G) T (C) A I I A G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G A G C G G C G G C C C G C G (T) C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 I C I G 0 E121 A C C A I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T T A A C G T A T 2 I C I G G T C A I I C G A I C T C G G G G G G G A A C C T C C C G A C G A T G A A G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T T A A C G T A T 2 I C I G 0 E122 G T C A I I A G A I C T C G G G G G G G A A C C T C C (C) G A C G A T G A A G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T G A A C G T A T 2 I C I (C) G T C G I I C G A I C T C G G G G G G G A A C C T C C (T) G A C G A T G A A G C G T G G C G G C C C G C G C C T G C C A C G C T D G A G G A T A T G T G C A T C T A T 2 I T I (G) 0 E123 A C C A I I C G A I C T C G G G G A A G T G C C C T C T C G T A G G G T C G A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T T A A C G T A T (4) I C I G G T C A I I A G A I C T C G G G G G G G A A C C T C C T G A C G A T G A A [A] A G C G G C G G C C C G C G T C T A C C A C G T T I G G G G G A G C T T G A A C G T A T (2) I C I G 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 = C = = = (I) ? = ? = = = = = = = C = = = = = = = C = = ? ? A = = A T ? A A = ? ? ? ? = = = = = = = = = = T ? ? A ? = = = = = = = = = ? = = ? ? = = = = ? ? ? ? C ? ? = = = = C = T = = = (D) ? = ? = = = = = = = G = = = = = = = T = = ? ? G = = G G ? T C = ? ? ? ? = = = = = = = = = = C ? ? G ? = = = = = = = = = ? = = ? ? = = = = ? ? ? ? T ? ? = = = = G 0 DY02 ? ? = = = = = = = = = = = = G = C = = = = = = = C = = T = = = A = = A T C A ? ? ? ? = = = = = = ? ? ? ? ? = = A ? = = = = C T D T A G = A = A T G T ? C A = C = = ? 2 = C = G ? ? = = = = = = = = = = = = T = G = = = = = = = T = = C = = = G = = G A A G ? ? ? ? = = = = = = ? ? ? ? ? = = G ? = = = = T C I G G A = G = G C T C ? A C = G = = ? 4 = T = C 0 DY03 (A) (C) = = ? I = = A ? ? ? C = = ? (C) (G) (G) = = = = = = (C) = = = = = (G) = = = (A) ? (G) = = = = = = = = (C) = = = = = C ? = = ? (C) = = = C T D T A G = A = A T G ? ? C A = ? = = T 2 = = = = (G) (T) = = ? D = = C ? ? ? T = = ? (G) (A) (A) = = = = = = (T) = = = = = (A) = = = (T) ? (A) = = = = = = = = (T) = = = = = T ? = = ? (G) = = = T C I G G A = G = G C T ? ? A C = ? = = G 4 = = = = 0 DY04 = C = = = = C = = D = = = = = = = = = = = = = = C = = T = A = = A T A A A = A = C = = = = = = = = = = = = ? C = ? = = = = = = = = = = = = ? ? = = ? = = ? ? ? = = = 2 = = = = = T = = = = A = = I = = = = = = = = = = = = = = T = = C = G = = G G G T C = C = T = = = = = = = = = = = = ? T = ? = = = = = = = = = = = = ? ? = = ? = = ? ? ? = = = 1 = = = = 0 DY05 ? ? ? ? = = = = = = = = = = G = = = = = = A = = = = = T ? = = = = = = ? ? ? ? ? ? ? = = G = C C C G C G = ? ? = ? C A C G C T D T A G G A = A T G T T ? = = = = = T = = T = G ? ? ? ? = = = = = = = = = = T = = = = = = G = = = = = C ? = = = = = = ? ? ? ? ? ? ? = = A = T T T T A A = ? ? = ? G C G A T C I G G A A G = G C T C G ? = = = = = G = = C = C 0 DY06 A C = A = = = = = = = = = = G = C = ? = = = = = C = = ? ? ? ? ? = = A T ? ? ? ? ? ? = = = = = = = = = = T = = = ? = = = = C = = T A = = A T A T G = ? C = T C = ? = 1 = T = G G T = G = = = = = = = = = = T = G = ? = = = = = T = = ? ? ? ? ? = = G A ? ? ? ? ? ? = = = = = = = = = = C = = = ? = = = = T = = G G = = G A G C T = ? A = C G = ? = 2 = C = C 0 DY07 ? ? (A) = = = = = = = = = C G = = C = = = = = = = = = = = = = = G = = G ? ? ? = = = = = = = = = = = = = = C = = G ? = = = = = = = = = = = = = = C T C G ? = T G T ? ? 2 D = = G ? ? (C) = = = = = = = = = T A = = G = = = = = = = = = = = = = = A = = A ? ? ? = = = = = = = = = = = = = = T = = A ? = = = = = = = = = = = = = = T G T T ? = C C C ? ? 1 I = = C 0 DY08 ? ? ? = ? ? A = A I = = = = = = = = ? = = = = = T = ? C = G = = G ? G ? ? ? = G = = = = G ? ? C C G C G = ? T = ? C ? ? ? C = D T A = = A ? ? T G T T ? ? ? ? T ? ? = = = = ? ? ? ? = ? ? C = C D = = = = = = = = ? = = = = = C = ? T = A = = A ? A ? ? ? = T = = = = A ? ? T T T A A = ? C = ? G ? ? ? T = I G G = = G ? ? C T C G ? ? ? ? C ? ? = = = = ? 0 DY09 A C = A = = = = = = = = = ? = = = = = = = ? ? ? ? = = = = = = = = = = = = = ? ? ? ? = = = = ? = = = = = T = = = = = = = = T C I G G A = G = G C T C = A C = G = = G 4 = = = C G T = G = = = = = = = = = ? = = = = = = = ? ? ? ? = = = = = = = = = = = = = ? ? ? ? = = = = ? = = = = = C = = = = = = = = C T D T A G = A = A T G T = C A = C = = T 2 = = = G 0 DY10 A C = A = = = = = = = = = = G = C = = = = = = = C = = T = = = A = = A T C A A = = = = = = = = = = = = = T = = A = = = = = = = D T A = = A T A T = = T C = T C (C) (G) (G) (1) = (T) = (C) G T = G = = = = = = = = = = T = G = = = = = = = T = = C = = = G = = G A A G C = = = = = = = = = = = = = C = = G = = = = = = = I G G = = G A G C = = G A = C G (T) (A) (T) (2) = (C) = (G) 0 DY11 = = = = = = = = = = (C) (T) (C) = = (G) = ? (G) (G) = (A) (C) (C) = = = (C) (G) ? ? (G) = = = = = = A = C G = = = = ? = = = = = T = = A = = = = = T = I G G = = G A = C T = (T) A = C G = = = = I = = = = = = = = = = = = = (A) (C) (T) = = (C) = ? (A) (A) = (G) (T) (G) = = = (T) (C) ? ? (A) = = = = = = C = T A = = = = ? = = = = = C = = G = = = = = C = D T A = = A T = T G = (G) C = T C = = = = D = = = 0 DY12 A = = A = (D) = = = = = = = A G = = = A = = = = G = = = T = = = ? = = = = = = = T T = = = A = T T = = A A = = C = G G C = A T = D T A = = A T A T = = T = = = = = = = = = = = C G = = G = (I) = = = = = = = G T = = = G = = = = C = = = C = = = ? = = = = = = = G C = = = G = C C = = C G = = T = C C A = G C = I G G = = G A G C = = G = = = = = = = = = = = G 0 DY13 (A) = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = G (G) = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C 0 DY14 A = = A = (D) = = = = = = = A = = G = A = = = = G T = = = = = = ? = = G A ? G = T = = = = A = T T = = A A = = C = G G C = A T = = = = = = = = = = = = = A = C G = = = 2 = = = = G = = G = (I) = = = = = = = G = = C = G = = = = C C = = = = = = ? = = A T ? A = G = = = = G = C C = = C G = = T = C C A = G C = = = = = = = = = = = = = C = T C = = = 1 = = = = 0 DY15 (A) = = (A) = = = = = = = = = = (G) = = = (A) = = = = = = = = = = = = (A) = = = = = (A) A = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = T = = T C = = = T = = = = = D = = = (G) = = (G) = = = = = = = = = = (T) = = = (G) = = = = = = = = = = = = (G) = = = = = (G) C = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = A = = G T = = = C = = = = = I = = = 0 DY16 = = C = = = = = = ? ? ? = = = G = = G G = = C C = = = C = G = = G G G = = = C = T = = = = = = = = = = = C = = G = = = = = = = = = = = = = T = = = C = = = = = C G G 1 = T = = = = A = = = = = = ? ? ? = = = C = = A A = = T G = = = T = A = = A T A = = = A = C = = = = = = = = = = = T = = A = = = = = = = = = = = = = A = = = T = = = = = T A T 2 = C = = 0 DY17 A = A A = I = = = = = = = G = C = = = A = = T = = = = = = = = ? = = A T C A A G C = = = G = C C C G C G T = T A C C A = G C = D T A = = A T A T G = T = = = = = = = = = = = = G = C G = D = = = = = = = A = G = = = G = = C = = = = = = = = ? = = G A A G C T T = = = A = T T T T A A C = C G G G C = A T = I G G = = G A G C T = G = = = = = = = = = = = = 0 DY18 = = = (A) = = A = = = = = T = T = = G G = A = = = T C = = = A = G A T = A A = = = = = = = = = = = = = = = = = = G = = = = = = C I G G A = G = G C T C = A C = G = = G 4 = T = C = = = (G) = = C = = = = = C = G = = A A = T = = = C T = = = G = A G G = T C = = = = = = = = = = = = = = = = = = A = = = = = = T D T A G = A = A T G T = C A = C = = T 2 = C = G 0 DY19 = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G C = = = G = C C C G C G T = T A C C A = G = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T T = = = A = T T T T A A C = C G G G C = A = = = = = = = = = = = = = = = = = = = = = = = = = (G) 0 DY20 = = = (A) = = C = = = = = = A = = G = = = = = = = T = = C = = = G = = G A A G C = = = = = = = = = = = = = = = T = = = = = = = = I G G = = G A G C = = G A = C G = = = 2 = = = = = = = (G) = = A = = = = = = G = = C = = = = = = = C = = T = = = A = = A T C A A = = = = = = = = = = = = = = = C = = = = = = = = D T A = = A T A T = = T C = T C = = = 1 = = = = 0 DY21 A C = = = (I) A = A I = = = = = = C ? = = = = = = = = = = = ? ? = = = = A A = A G C = = = G = C C C G C G T = T A C C A = G C = D T A = = A = A T G T T = = = = = = = = = = = = G T = = = (D) C = C D = = = = = = G ? = = = = = = = = = = = ? ? = = = = T C = C T T = = = A = T T T T A A C = C G G G C = A T = I G G = = G = G C T C G = = = = = = = = = = = = 0 DY22 (A) = (A) (A) = (I) = = = = = = = = G = C = = = = = = = C = = T = = = A = = A ? ? ? A = = = = = = = = = = = = = T = = A = = = = = = = D T A = = A T A T = = T C = T C = = = 1 = T = = (G) = (C) (G) = (D) = = = = = = = = T = G = = = = = = = T = = C = = = G = = G ? ? ? C = = = = = = = = = = = = = C = = G = = = = = = = I G G = = G A G C = = G A = C G = = = 2 = C = = 0 DY23 A = = A = (D) = = = = = = = = G = = = = = = = = = = = = = = G = A G G = T C A = G = = = = G = C C C G C G = = T = C C A C G C T D T A G G A = A T G T T C = = C = = T 1 = T = G G = = G = (I) = = = = = = = = T = = = = = = = = = = = = = = A = G A T = A A G = T = = = = A = T T T T A A = = C = G G C G A T C I G G A A G = G C T C G A = = G = = G 2 = C = C 0 DY24 = = = = = = A = = I = = = = = = C = = = = = = = = = = = = = = = = = = ? ? ? C = = = = = = = = = = = = = T = T A = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = C = = D = = = = = = G = = = = = = = = = = = = = = = = = = ? ? ? A = = = = = = = = = = = = = C = C G = = = = = = = = = = = = = = = = = = = = = = = = = = 2 = = = = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = (C) = = = = (4) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = (T) = = = = (2) = = = = 0 E102 = = = A = = C = = ? = ? C = = = ? ? = = = A = = T = = C G = = G = = G A A G = = = G A T A = ? T T = A = = T C = G ? C G A T = I G G = = G A = C T = = A = C G = = = = I = = = = = = G = = A = = ? = ? T = = = ? ? = = = G = = C = = T C = = A = = A T C A = = = A G C G = ? C C = C = = C T = C ? A C G C = D T A = = A T = T G = = C = T C = = = = D = = = 0 E103 (A) (C) = = = = = = = = = = = = = = (C) ? = = = (G) = = (C) = = (T) (C) = = = = = = = = = = = = = G C G = ? C C = C = = C T A C C A C G = = = = = = = = = = = = = = = = = = = = = = (D) = = = (G) (T) = = = = = = = = = = = = = = (G) ? = = = (A) = = (T) = = (C) (G) = = = = = = = = = = = = = A T A = ? T T = A = = T C G G G C G A = = = = = = = = = = = = = = = = = = = = = = (I) = = = 0 E104 = = = = = = = G = = = = = = = = C ? G = A = = = = C C = = A = = A T A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I C = = = = = = = A = = = = = = = = G ? A = T = = = = T T = = G = = G G G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D G 0 E105 A = A A = = A = = = A C T = = C = = A A = G T G = = = = C = = A = = = = = = = ? ? ? = = = C = = = = = = = = = = = = = = = = = = = = = = = = G = = = G = = = = = = = = D C = C G = C G = = C = = = C T C = = G = = G G = A C C = = = = G = = G = = = = = = = ? ? ? = = = G = = = = = = = = = = = = = = = = = = = = = = = = A = = = T = = = = = = = = I T = G 0 E106 = = = = = = = = = = C T = = = G = ? = G T = C C C T = = = G T = G G = T C = A = C G = = = G = = = = = = T = ? A = = = = = T = I G G = = G A = C T = (T) A = C G = = = 2 = = I = = = = = = = = = = = A C = = = C = ? = A A = T G T C = = = A C = A T = A A = C = T A = = = C = = = = = = C = ? G = = = = = C = D T A = = A T = T G = (G) C = T C = = = 1 = = D = 0 E107 (G) = (C) = ? ? (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) (C) = = = = = = = = = = = = = = = = = = = ? = = = = C = D T A = = A T = T G = G C = T C = = = = D = = ? (A) = (A) = ? ? (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) (A) = = = = = = = = = = = = = = = = = = = ? = = = = T = I G G = = G A = C T = T A = C G = = = = I = = ? 0 E108 A = A = ? ? = = = = A C T = = C = = A A = G T G = = = = C = = A = = = = = (G) = = = (A) = = = (C) = = = = = = = = ? = = = = = = = = = = = = = = = (G) = = = (G) = = = = = = = (2) (D) (C) = (C) G = C = ? ? = = = = C T C = = G = = G G = A C C = = = = G = = G = = = = = (A) = = = (G) = = = (G) = = = = = = = = ? = = = = = = = = = = = = = = = (A) = = = (T) = = = = = = = (1) (I) (T) = (G) 0 E109 (A) (C) = = = = (A) = = = (C) (T) = = = = C = = = = G = = C = = T C = = = = = = = = = = = = = G C G (C) = C C = C = = ? T = C C A C G C = = = = = = = = = = = = = = = = = = = = = = = = = (G) (T) = = = = (C) = = = (A) (C) = = = = G = = = = A = = T = = C G = = = = = = = = = = = = = A T A (G) = T T = A = = ? C = G G C G A T = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 = = = = (I) = = (G) = = = = = = = = = ? (G) = (A) (A) = = (T) (C) (C) (C) (G) (A) = (G) (A) (T) = (A) (A) (G) = = = = A T A = = T T = A = = = C = G G C G A T C I G G A A G = G C T C = A C = G = = G 4 = = D (G) = = = = (D) = = (A) = = = = = = = = = ? (A) = (T) (G) = = (C) (T) (T) (T) (C) (G) = (A) (G) (G) = (T) (C) (A) = = = = G C G = = C C = C = = = T = C C A C G C T D T A G G A = A T G T = C A = C = = T 2 = = I (C) 0 E111 (A) = (A) = ? ? C = = = C T C = = G C = G G = = C C C = = = = = = G = = = = = = = = = = = = = = = = = = = = C = ? G = = = = = C = D T A = = A T A T G = T C = T C = = = 1 = T = = (G) = (C) = ? ? A = = = A C T = = C G = A A = = T G T = = = = = = A = = = = = = = = = = = = = = = = = = = = T = ? A = = = = = T = I G G = = G A G C T = G A = C G = = = 2 = C = = 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 (A) (C) = (A) ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = ? G = = = = = C = D T A = = A T A T G = = C = T C = = = 1 = = = = (G) (T) = (G) ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = ? A = = = = = T = I G G = = G A G C T = = A = C G = = = 2 = = = = 0 E114 A = A = ? ? A G = = A C T = = C = G = A A = T G T C C = = A = = A T = A A G = = = A = = = C = = = = = = = = = = = = = = = = = = = = = = = = G ? = = = (A) = = = = = = 2 D = I = G = C = ? ? C A = = C T C = = G = A = G T = C C C T T = = G = = G G = T C A = = = G = = = G = = = = = = = = = = = = = = = = = = = = = = = = A ? = = = (C) = = = = = = 1 I = D = 0 E115 (G) = (C) = = = = = = = (A) (C) (T) = = (C) = = (A) (A) = (G) (T) (G) = = = (T) (C) = = (A) = = = = = = C = T = A T A = = T T = A = C T C G G G C G A = C = = = A A = T = = = C T = C T = = = G 4 = = = = (A) = (A) = = = = = = = (C) (T) (C) = = (G) = = (G) (G) = (A) (C) (C) = = = (C) (G) = = (G) = = = = = = A = C = G C G = = C C = C = T C T A C C A C G = T = = = G G = A = = = T G = A C = = = T 2 = = = = 0 E116 = = = = I = A G = = = = = ? = ? = G G = A A = = T C C C G A = G A T = A A G = = = = A T A = = T T = A = = T C = G G C G A T = I G G = = G A G C T = G A = C ? = = = 2 = = I = = = = = D = C A = = = = = ? = ? = A A = T G = = C T T T C G = A G G = T C A = = = = G C G = = C C = C = = C T = C C A C G C = D T A = = A T A T G = T C = T ? = = = 1 = = D = 0 E117 (A) = (A) = I = A G = = A C T = = C = G = A A = T G T C C = = A = = A T = A A G = = = A = = = = ? = = = = = = = = = = = = = = = = = = = = = = = G = = = G = = = = = = = 2 D C = = (G) = (C) = D = C A = = C T C = = G = A = G T = C C C T T = = G = = G G = T C A = = = G = = = = ? = = = = = = = = = = = = = = = = = = = = = = = A = = = T = = = = = = = 1 I T = = 0 E118 (A) (C) = = = = = = = ? ? ? = = = = = = = = = ? ? ? = = = = = = = = = = ? ? ? ? = = = A G C G = = C ? ? ? ? = C T = C C A C G C = D T A = = A T = T G = (G) C = T C = = = = D = = = (G) (T) = = = = = = = ? ? ? = = = = = = = = = ? ? ? = = = = = = = = = = ? ? ? ? = = = G A T A = = T ? ? ? ? = T C = G G C G A T = I G G = = G A = C T = (T) A = C G = = = = I = = = 0 E119 = = = = (I) = (A) (G) = = (A) (C) (T) = = (C) = (G) (A) (A) (A) = (T) (G) (T) (C) (C) = = (A) = = (A) (T) = (A) (A) (G) = = T = A T A = = T T = A = = T C = G G C G A T C I G G A A G = G C T C = A C = G = = G 4 = = = = = = = = (D) = (C) (A) = = (C) (T) (C) = = (G) = (A) (G) (G) (T) = (C) (C) (C) (T) (T) = = (G) = = (G) (G) = (T) (C) (A) = = C = G C G = = C C = C = = C T = C C A C G C T D T A G G A = A T G T = C A = C = = T 2 = = = = 0 E120 (A) = (A) = = = C = = = = = = = = = = A A = T G = = C T = T C G T A G G = ? ? ? = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = (C) = = = A = = = = = = = = = = G G = A A = = T C = C G A C G A T = ? ? ? = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E121 A C = = ? ? = = = = = = = ? = = = A A = T G = = C T = T C G T ? G ? = T C = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = = ? ? = = = = = = = ? = = = G G = A A = = T C = C G A C ? A ? = A A = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E122 = = = A = = A = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = A = C = = = = = = = = = = = T = = A = = = = = T = I = G = = G A G C T = = A = C G = = = = = C = (C) = = = G = = C = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = C = T = = = = = = = = = = = C = = G = = = = = C = D = A = = A T A T G = = C = T C = = = = = T = (G) 0 E123 A C = = = = C = = ? ? ? = ? = = = A A = T G = = C T = = C G T A G G ? ? ? ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = T = = = = = = = (4) = = = = G T = = = = A = = ? ? ? = ? = = = G G = A A = = T C = = G A C G A T ? ? ? ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = G = = = = = = = (2) = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.99 = = = 0.87 ? = ? = = = = = = = 1.00 = = = = = = = 1.00 = = ? ? 1.00 = = 1.00 1.00 ? 1.00 1.00 = ? ? ? ? = = = = = = = = = = 1.00 ? ? 1.00 ? = = = = = = = = = ? = = ? ? = = = = ? ? ? ? 1.00 ? ? = = = = 1.00 ? ? = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = 1.00 = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 ? ? ? ? = = = = = = ? ? ? ? ? = = 1.00 ? = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 ? 1.00 1.00 = 1.00 = = ? 1.00 = 1.00 = 1.00 0.72 0.72 = = ? 0.95 = = 0.96 ? ? ? 0.96 = = ? 0.76 0.76 0.76 = = = = = = 0.76 = = = = = 0.76 = = = 0.76 ? 0.76 = = = = = = = = 0.76 = = = = = 1.00 ? = = ? 0.76 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? ? 1.00 1.00 = ? = = 1.00 1.00 = = = = = 0.97 = = = = 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 0.98 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 ? ? 0.74 = = = = = = = = = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = 1.00 = = 1.00 ? ? ? = = = = = = = = = = = = = = 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 = 1.00 1.00 = = = = = = = = ? = = = = = 1.00 = ? 1.00 = 1.00 = = 1.00 ? 1.00 ? ? ? = 1.00 = = = = 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 = ? 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 = 0.96 = = = = = = = = = ? = = = = = = = ? ? ? ? = = = = = = = = = = = = = ? ? ? ? = = = = ? = = = = = 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 0.91 0.91 = 0.91 = = = = = = = = = = 1.00 = 1.00 = = = = = = = 1.00 = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 0.64 0.64 0.64 0.87 = 0.87 = 0.63 = = = = = = = = = = 0.71 0.71 0.71 = = 0.71 = ? 0.71 0.71 = 0.71 0.71 0.71 = = = 0.71 0.71 ? ? 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 = 0.85 1.00 = 1.00 1.00 = = = = 1.00 = = = 1.00 = = 1.00 = 0.83 = = = = = = = 1.00 1.00 = = = 1.00 = = = = 1.00 = = = 1.00 = = = ? = = = = = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00 1.00 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 = = 0.57 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = = 0.96 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = 0.92 0.97 = = 0.97 = 0.83 = = = = = = = 1.00 = = 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = ? = = 1.00 1.00 ? 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 0.83 = = 0.83 = = = = = = = = = = 0.83 = = = 0.52 = = = = = = = = = = = = 0.89 = = = = = 0.76 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = 1.00 = = = = = 0.95 = = = = = = ? ? ? = = = 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 = = 0.91 = 0.91 0.91 = 1.00 = = = = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = = = = = ? = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 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 = = 0.94 = = = = = 0.94 = 0.94 = = 0.94 0.94 = 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 = 0.91 = 0.95 = = = 0.51 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 0.50 = = = 0.88 = = 0.90 = = = = = = 0.94 = = 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 = = = = 0.92 0.92 = = = 0.89 0.99 = 1.00 1.00 = = = = = = 1.00 ? = = = = = = = = = = = ? ? = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = 0.86 = 0.86 0.86 = 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 = = = 1.00 = 1.00 = = 0.96 = = 0.96 = 0.87 = = = = = = = = 1.00 = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = = = = = 1.00 = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = = = ? ? ? 1.00 = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.79 = = 0.75 = = = = 0.75 = = = = = = = 0.97 = = 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 = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = = = 0.72 0.72 = = = = = = = = = = = = = = 0.88 ? = = = 0.88 = = 0.88 = = 0.88 0.88 = = = = = = = = = = = = = 1.00 1.00 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 = = = = = = = = = = 0.95 = = = = = = = = 1.00 ? 1.00 = 1.00 = = = = 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 0.98 = 0.98 0.98 = = 0.97 = = = 0.98 0.98 0.97 = = 0.98 = = 0.98 0.98 = 0.98 0.98 0.98 = = = = 0.98 = = 0.98 = = = = = = = ? ? ? = = = 0.91 = = = = = = = = = = = = = = = = = = = = = = = = 0.91 = = = 0.91 = = = = = = = = 0.91 0.91 = 0.91 = = = = = = = = = = 0.97 0.97 = = = 0.97 = ? = 0.97 0.97 = 0.97 0.97 0.97 0.97 = = = 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 = 0.77 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 0.52 = 0.52 = ? ? 0.51 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 0.51 = = = = = = = = = = = = = = = = = = = ? = = = = 1.00 = 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 = ? ? = = = = 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = = = = = 0.83 = = = 0.89 = = = 0.89 = = = = = = = = ? = = = = = = = = = = = = = = = 0.89 = = = 0.89 = = = = = = = 0.89 0.89 0.89 = 0.89 0.66 0.66 = = = = 0.63 = = = 0.56 0.56 = = = = 0.91 = = = = 0.91 = = 0.91 = = 0.91 0.91 = = = = = = = = = = = = = 1.00 1.00 1.00 0.84 = 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 0.85 = 0.85 0.85 0.85 = 0.85 0.85 0.85 = = = = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 0.89 0.56 = 0.57 = ? ? 0.98 = = = 0.98 0.98 0.98 = = 0.98 0.98 = 0.98 0.98 = = 0.98 0.98 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 0.58 = 0.58 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = ? 1.00 = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 1.00 = 1.00 = ? ? 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 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 = = = = = = 0.94 0.94 = 0.94 = 0.58 = 0.58 = = = = = = = 0.68 0.68 0.68 = = 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 = = = = = = = = 0.97 = 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 1.00 1.00 1.00 = 1.00 1.00 = 1.00 ? = = = 1.00 = = 1.00 = 0.87 = 0.87 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 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 = = = = = = = ? ? ? = = = = = = = = = ? ? ? = = = = = = = = = = ? ? ? ? = = = 1.00 1.00 1.00 1.00 = = 1.00 ? ? ? ? = 1.00 1.00 = 1.00 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 = 1.00 1.00 = = = = 1.00 = = = = = = = 0.77 = 0.77 0.77 = = 0.77 0.77 0.77 = = 0.77 = 0.77 0.55 0.77 0.77 = 0.77 0.77 0.77 0.77 0.77 = = 0.77 = = 0.77 0.77 = 0.77 0.77 0.77 = = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = 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 = = = = 0.58 = 0.58 = = = 0.92 = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = ? ? ? = = = = = = = = = = = = = = 0.67 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.91 0.91 = = ? ? = = = = = = = ? = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 ? 1.00 ? = 1.00 1.00 = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.92 = = 0.96 = = = = = = = = = = = = = = = = = = = = 0.89 = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = 1.00 = = 1.00 = = = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = = 1.00 = 0.51 0.98 0.98 = = = = 0.99 = = ? ? ? = ? = = = 1.00 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 = = = = END PHASEPROBS