************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 casrx.phase.inp casrx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST casrx.phase.out_freqs : haplotype frequency estimates casrx.phase.out_pairs : most likely haplotype pairs for each individual casrx.phase.out_recom : estimates of recombination parameters casrx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 133 Positions of loci: 1281 1453 1497 1780 2339 2377 2627 2698 2955 3268 3274 3368 3486 3643 4270 4375 5091 5195 5438 12804 13142 13291 13855 13873 14126 14165 14316 26279 27204 27386 27400 27484 27935 28141 36812 36924 37402 37420 37913 38203 38362 38873 39202 39229 39434 39624 39668 46760 46984 47573 48104 48145 48751 48860 49204 49429 49524 49527 49579 49595 52404 53253 53536 53763 53770 54139 66097 66401 66411 66689 66756 67549 68012 68307 68358 68365 71606 71831 72096 72214 74215 74795 74820 74950 75718 75959 75997 76000 76012 76391 76747 77538 78694 79008 79155 79169 79707 79749 81074 81084 81300 81301 81803 82787 83072 83270 83486 92712 92897 92939 93065 93106 95548 99341 99599 100132 100192 100336 100564 100711 101643 101718 102510 103222 103297 103563 103684 104078 104519 104597 104702 105356 106346 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file casrx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTIIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 2.000000 2 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 3 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTIIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 4 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGCCCICTCTACGGADGACTGT 1.000000 5 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTTAATCIACTTATAACTIIIGACATAGTTGAGGCTGTCGTTCCGAGCAAGCCCICTCTACGGADGACTGC 1.000000 6 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTIIIGATTCGAGGGAGACCGTCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 7 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 8 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTIIIGACATAGGGAAAGTCGTCGTCTCGAGCAAGCCCICTCCCCGCTDGACTGC 2.000000 9 AACDTACGGTCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTDIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 1.000000 10 AACDTACGGTCAGGIIGCAGCDACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTDIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 1.000000 11 AACDTACGGTCAGGIIGCAGCDTACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGACACCCIGTCTCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 12 AACDTACGGTCAGGIIGCAGCDTACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACTTCGACCIACTGCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCTCTIGACCAC 1.000000 13 AACDTACGGTCAGGIIGCAGCDTACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACTTCGACCIACTGCGAGTTIDIGACATAGTTGAGGCTATCGTCCCGGGCGAGCCCDTTTTCCTCTIGACCAC 1.000000 14 AACDTACGGTCAGGIIGCAGCDTACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACTTCGACCIACTGCGAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 2.000000 15 AACDTACGGTCAGGIIGCAGCDTACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACTTCGACCIACTGCGAGCTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 16 AACDTACGGTCAGGIIGCAGCDTCCTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGACACCCIGTCTCGAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 17 AACDTACGGTCAGGIIGCAGCIACCTGCGACGGTCIGGCAGACGGTGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTDIIGATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 1.000000 18 AACDTACGGTCAGGIIGCTGCDTACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACTTCGACCIACTGCGAGCTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 19 AACDTACGGTCAGGIIGCTGCIACCTGCGACGGTCIGGCAGACGGTGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGCCCICTCTACGGADGACTGT 1.000000 20 AACDTACGGTCAGGIIGGAGCIACCTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTTAATCIACTTATAACTIIIGACATAGTTGAGGCTGTCGTTCCGAGCAAGCCCICTCTACGGADGACTGC 1.000000 21 AACDTACGGTCAGGIIGGAGCIACCTGCGGGAACCDGGCAAACGATGAGGGGGCCGCGGCACGACACCCIGTCTCGAGTTIDIGACATAGTTGAGGCTATCGTCCCGGGTGAGCCCDTTTTCCTCTIGACCGC 1.000000 22 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGATTGC 1.000000 23 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 24 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTIIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 1.000000 25 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 5.000000 26 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCCCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 27 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCTCGAGCAAGCCCICTCCCCGCTDGACTGC 3.000000 28 AACDTACGGTAAGGIIGGAGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 29 AACDTACGGTAAGGIIGGTGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 30 AACDTACGGTAAGGIIGGTGTIACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDDDGACATAGTTGAGGCTGTCGTCCCGAGCGAGCCCDTTTTCCGCTIGACCGC 1.000000 31 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTIIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 32 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTIDIGACATAGGGGAAGTCGTCGTCCCGAGCAAGCCCICTCTCCGCTDGACTGC 1.000000 33 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTDIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 34 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCCCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 35 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 36 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTDIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 1.000000 37 AACDTACGATCAGGIIGCAGCDAACTGCAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTDIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGT 1.000000 38 AACDCACAGTCAGGIIGGAGCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTIIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 39 AACDCACAGTCAGGIIGGAGCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 40 AACDCACAGTCAGGIIGGAGCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTDIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 41 AACDCACAGTCAGGIIGGAGCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 42 AACDCACAGTCAGGIIGGAGCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTDDDGACATAGTTGAGGCTGTCGTCCCGAGCGAGCCCDTTTTCCGCTIGACCGC 2.000000 43 AACDCACAGTCAGGIIGGATCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTIIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 44 AACDCACAGTCAGGIIGGATCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTIIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTAC 1.000000 45 AACDCACAGTCAGGIIGGATCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTIDIGACATAGTTGAGGCTATCGTCCCGGGCGAGCCCDTTTTCCTCTIGACCAC 1.000000 46 AACDCACAGTCAGGIIGGATCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTDDDGACATAGTTGAGGCTGTCGTCCCGAGCGAGCCCDTTTTCCGCTIGACCGC 1.000000 47 AACDCACAGTCAGGIIGGTTCIACTCGCGGGAACTDGGCAAACCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTIIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 48 AACDCACAGTCAGGIIGGTTCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTDIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 3.000000 49 AACDCACAGTCAGGIIGGTTCIACTCGCGGGAACTDGGCAAACCATAAGAGGATCGCGCCACGTCAACCIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCTCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 50 GACITCCGGTCAGGIIAGATCIACTCACGACAATCIAGCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 51 GACITCCGGTCAGGIIAGATCIACTCACGACAATCIAGCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAACTDIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 52 GACITCCGGTCAAGDIAGAGCDACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACCIACTGCGGGTCDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGCCCICTCTACGGADGACTGT 4.000000 53 GACITCCGGTCAAGDIAGTGCDACCTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACCIACTGCGGGTCDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGCCCICTCTACGGADGACTGT 1.000000 54 GATITACGGTCAGGDIAGAGTIACCTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTDIIAATTCGAGGGTAGTCGTCGTCCCAAACACACCTICCCTCCGCTDGATTGC 1.000000 55 GATITACGGTCAGGDIAGAGTIACCTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGCCCICTCTACGGADGACTGT 1.000000 56 GATITCCGGTCAGGDIAGAGCDACTTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 57 GATITCCGGTCAGGDIAGAGCDACTTGCAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCCCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 58 GATITCCGGTCAGGDIAGAGCDACTTGCGGCGATCIGGTGGACGGAGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTIIIGACATAGGGAAAGTCGTCGTCTCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 59 GATITCCGGTCAGGDIAGAGCDACTTGCGGCGATCIGGTGGACGGAGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTDIIAATTCGAGGGTAGTCGTCGTCCCAAGCACACCCICTCTCCGCTDGATTGC 1.000000 60 GATITCCGGTCAGGDIAGAGCDACTTGCGGCGATCIGGTGGACGGAGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 61 GATITCCGGTCAGGDIAGAGCDACTTGCGGCGATCIGGTGGACGGAGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTDIDAATTCGAGGGTAGTCGTCGTCCCAAGCACACCTICTCTCCGCTDGATTGC 1.000000 62 GATITCCGGTCAGGDIAGAGCDACTTGCGGCGATCIGGTGGACGGAGGTGGGGCCATCGCACGACACTCDATTTATAACTIIIGACATAGGGGAAGTCGTCGTCCCGAGCAAGCCCICTCTCCGCTDGACTGC 1.000000 63 GATITCCGGTCAGGDIAGAGTIACCTGCAGCAGCTDGGCAAATCATAAGAGGACCGCGCCACGTCAACCIACTGCGAGTTIDIGACATAGTTGAGGCTATCGTCCCGGGCGAGCCCDTTTTCCTCTIGACCAC 2.000000 64 GGCITCCGGACTGGIDAGAGCIACCTACAGCAGCTDGGCAAACCATAAGAGGACCGCGCCACGTCAACTIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCCCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 65 GGCITCCGGACTGGIDAGTGCDACCTATGGCAATCIGGCAGGCGGTGGTGAGGCAATCGTGTGATACTCIATTTATAACTDDDGACATAGTTGAGGCTGTCGTCCCGAGCGAGCCCDTTTTCCGCTIGACCGC 1.000000 66 GGCITCCGGACTGTIDAGAGCIACCTACAGCAGCTDGGCAAACCATAAGAGAACCGCGCCACGTCAACCIACTGCGAGTTDIIGACATAGGGAAAGTCGTCGTCCCGAGCAAGCCCICTCCCCGCTDGACTGC 1.000000 67 GGCITCCGGACTGTIDAGAGCIACCTACGACAATCIAGCAGGCGGTGGTGAGGCAATCGTGTGATACTCDACTTATAACTDIIGGCATAGGGGAGGTCGTGGGTCCGAGCAAGACCICTCTAGGGADCACTGT 1.000000 68 GGCITCCGGACTGTIDAGAGCIACCTATGACAATCIAGCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAACTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 69 GGCITCCGGACTGTIDAGAGCIACCTATGACAATCIAGCAGGCGGTGGTGAGGCCATCGCACGACACCCIGTCTCGAGTTIDDGACATAGTTGAGGCTGTCGTCCCGAGCGAGCCCDTTTTCCGCTIGACCGC 1.000000 70 GGCITCCGGACTGTIDAGTGCDACCTATGGCAATCIGGCAGGCGGTGGTGAGGCAATCGTGTGATACTCIATTTATAACTIDDGACATAGTTGAGGCTGTCGTCCCGAGCGAGCCCDTTTTCCGCTIGACCGC 1.000000 71 GGCITCCGGACTGTIDAGTGCIACCTACGGCGATCIGGTGGACGGTGGTGGGGCCATCGCACGACACCCIGTCTCGAGTTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 72 GGCITCCGGACTGTIDAGTGCIACCTACGGGAACCDGGCAAACGATGAGGGGGCCGCGGCACGACACCCIGTCTCGAGTTDDIGACATAGTTGAGGCTATCGTCCCGGGCGAGCCCDTTTTCCTCTIGACCGC 1.000000 73 GGCITCGGGACTGTIDAGAGCDACCTATGACAATCIGCCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAACTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 74 GGCITCGGGACTGTIDAGAGCDACCTATGACAATCIACCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAGTTDDIGACATAGTTGAGGCTATCGTCCCGGGTGAGCCCDTTTTCCTCTIGACCGC 1.000000 75 GGCITCGGGACTGTIDAGAGCDACCTATGACAATCIACCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAACTIIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 1.000000 76 GGCITCGGGACTGTIDAGAGCDACCTATGACAATCIACCAGGCGGTGGTGAGGCAATCGTGTGATACTCDATTTATAACTDIIGATTCGAGGGAGACCGGCATCCTGAGTAAGCTCITTTTCCGCTDGGCCGC 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (6,59) DY02: (1,51) DY03: (4,53) DY04: (1,69) DY05: (3,64) DY06: (9,57) DY07: (19,62) DY08: (61,72) DY09: (20,70) DY10: (52,56) DY11: (2,29) DY12: (33,36) DY13: (7,32) DY14: (34,66) DY15: (8,35) DY16: (31,68) DY17: (5,71) DY18: (60,67) DY19: (48,52) DY20: (8,52) DY21: (10,26) DY22: (27,37) DY23: (17,28) DY24: (24,52) E101: (40,42) E102: (22,38) E103: (15,50) E104: (14,25) E105: (23,63) E106: (25,45) E107: (27,46) E108: (25,54) E109: (44,63) E110: (39,73) E111: (49,76) E112: (27,30) E113: (25,48) E114: (43,55) E115: (12,42) E116: (47,75) E117: (14,18) E118: (13,21) E119: (41,48) E120: (11,58) E121: (16,25) E122: (74,76) E123: (65,76) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A T C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T [I] I I (G) A T T C G A G G G [A] (G) (A) (C) C G T C (A) T C C (T) (G) A G (T) A (A) (G) C (T) C I (T) T (T) T C C G C T D G (G) (C) (C) G C G A T I T C C G G T C A G G D I A G A G C D A C T T G C G G C G A T C I G G T G G A C G G A G G T G G G G C C A T C G C A C G A C A C C C I G T C T C G A G T T [D] I I (A) A T T C G A G G G [T] (A) (G) (T) C G T C (G) T C C (C) (A) A G (C) A (C) (A) C (C) C I (C) T (C) T C C G C T D G (A) (T) (T) G C 0 DY02 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T (I) I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C G A C I T C C G G T C A G G I I A G A T C I A C T C A C G A C A A T C I A G C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T (D) I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C 0 DY03 A A C D T A C G G T C A G G I I G C (A) G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T G A C I T C C G G T C A A G D I A G (T) G C D A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G G G T C D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T 0 DY04 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T I I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C G G C I T C C G G A C T G T I D A G A G C I A C C T A T G A C A A T C I A G C A G G C G G T G G T G A G G C C A T C G C A C G A C A C C C I G T C T C G A G T T I D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C 0 DY05 (A) (A) C (D) T (A) C G G [T] C (A) G G I (I) (G) (C) A G C (D) A (A) C T (G) C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T (I) I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G A C C I C T C T A G G G A D C A C T G T (G) (G) C (I) T (C) C G G [A] C (T) G G I (D) (A) (G) A G C (I) A (C) C T (A) C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T (D) I I G A C A T A G G G A A A G T C G T C G T C C C G A G C A A G C C C I C T C C C C G C T D G A C T G C 0 DY06 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A T C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C G A T I T C C G G T C A G G D I A G A G C D A C T T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C C C G A G C A A G C C C I C T C C C C G C T D G A C T G C 0 DY07 A A C D T A C G G T C A G G I I G C T G C I A C C T G C G [A] C G G T C I G G C A G A C G G T G G T G G G G C C A T C G C A C G A C A C C C I G T C T C G A G T T D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T G A T I T C C G G T C A G G D I A G A G C D A C T T G C G G C G A T C I G G T G G A C G G A G G T G G G G C C A T C G C A C G A C A C T C D A T T T A T A A C T I I I G A C A T A G G G G A A G T C G T C G T C C C G A G C A A G C C C I C T C T C C G C T D G A C T G C 0 DY08 G A T I T C C G G T C A G G D I A G A G C D A C T T G C G G C G A T C I G G T G G A C G G A G G T G G G G C C A T C G C A C G A C A C C C I G T C T C G A G T T D I [D] A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C G G C I T C C G G A C T G T I D A G T G C I A C C T A C G G G A A C C D G G C A A A C G A T G A G G G G G C C G C G G C A C G A C A C C C I G T C T C G A G T T D D I G A C A T A G T T G A G G C T A T C G T C C C G G G C G A G C C C D T T T T C C T C T I G A C C G C 0 DY09 A A C D T A C G G T C A G G I I G G A G C I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T T A A T C I A C T T A T A A C T I I I G A C A T A G T T G A G G C T G T C G T T C C G A G C A A G C C C I C T C T A C G G A D G A C T G C G G C I T C C G G A C T G T I D A G T G C D A C C T A T G G C A A T C I G G C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C I A T T T A T A A C T I D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C 0 DY10 G A C I T C C G G T C A A G D I A G A G C D A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G G G T C D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T G A T I T C C G G T C A G G D I A G A G C D A C T T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T [D] I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 DY11 A A C D T A C G G T (C) A G G I I G (C) (A) G (C) (D) A (A) C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C (C) I A C T G C G A G T T [D] I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G A C C I C T C T A G G G A D C A C T G T A A C D T A C G G T (A) A G G I I G (G) (T) G (T) (I) A (C) C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C (T) I A C T G C G A G T T [D] I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 DY12 A A C D T A C G A T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C A A C D T A C G A T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C 0 DY13 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A T C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D T A C G A T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T I D I G A C A T A G G G G A A G T C G T C G T C C C G A G C A A G C C C I C T C T C C G C T D G A C T G C 0 DY14 A A C D T A C G A T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C C C G A G C A A G C C C I C T C C C C G C T D G A C T G C G G C I T C C G G A C T G T I D A G A G C I A C C T A C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C C C G A G C A A G C C C I C T C C C C G C T D G A C T G C 0 DY15 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A T C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T [I] I I G A C A T A G G G A A A G T C G T C G T C T C G A G C A A G C C C I C T C C C C G C T D G A C T G C A A C D T A C G A T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T [D] I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G A C C I C T C T A G G G A D C A C T G T 0 DY16 A A C D T A C G [A] T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G [A] A C C G C G C C A C G T C A A C C I A C T G C G A G T T (I) I I G (G) (C) (A) (T) (A) (G) G G G A G (G) (T) C G [T] [G] [G] (G) (T) C (C) G A G (C) A A G (A) (C) C I (C) T (C) T (A) (G) G (G) (A) D (C) (A) C (T) G (T) G G C I T C C G G A C T G T I D A G A G C I A C C T A T G A C A A T C I A G C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T (D) I I G (A) (T) (T) (C) (G) (A) G G G A G (A) (C) C G [G] [C] [A] (T) (C) C (T) G A G (T) A A G (C) (T) C I (T) T (T) T (C) (C) G (C) (T) D (G) (G) C (C) G (C) 0 DY17 A A C D T A C G [G] T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T T A A T C I A C T T A T A A C T I I I G A C A T A G T T G A G G C T G T C G T T C C G A G C A A G C C C I C T C T A C G G A D G A C T G C G G C I T C C G G A C T G T I D A G T G C I A C C T A C G G C G A T C I G G T G G A C G G T G G T G G G G C C A T C G C A C G A C A C C C I G T C T C G A G T T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 DY18 G A T I T C C G G T C A G G D I A G A G C D A C T T G C G G C G A T C I G G T G G A C G G A G G T G G G G C C A T C G C A C G A C A C C C I G (T) C T C G A G T T D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G A C C I C T C T A G G G A D C A C T G T G G C I T C C G G A C T G T I D A G A G C I A C C T A C G A C A A T C I A G C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A (C) T T A T A A C T D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G A C C I C T C T A G G G A D C A C T G T 0 DY19 A A C D C A C A G T C A G G I I G G (T) T C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T [D] I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C G A C I T C C G G T C A A G D I A G (A) G C D A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G G G T C D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T 0 DY20 A A C D T A C G G T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A T C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T (I) I I G A C A T A G G G A A A G T C G T C G T C T C G A G C A A G C C C I C T C C C C G C T D G A C T G C G A C I T C C G G T C A A G D I A G A G C D A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G G G T C (D) I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T 0 DY21 A A C D T A C G G T C A G G I I G C A G C D A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C A A C D T A C G G T A A G G I I G G A G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C C C G A G C A A G C C C I C T C C C C G C T D G A C T G C 0 DY22 A A C D T A C G G T A A G G I I G G A G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C T C G A G C A A G C C C I C T C C C C G C T D G A C T G C A A C D T A C G A T C A G G I I G C A G C D A A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G T C A A C C I A C T G C G A G T T D I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G T 0 DY23 A A C D T A C G G T C A G G I I G C A G C I A C C T G C G [A] C G G T C I G G C A G A C G G T G G T G G G G C C A T C G C A C G A C A C C C I G T C T C G A G T T [D] I I G A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C A A C D T A C G G T A A G G I I G G A G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T [D] I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G A C C I C T C T A G G G A D C A C T G T 0 DY24 A A C D T A C G G T A A G G I I G G A G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T I I D A A T T C G A G G G T A G T C G T C G T C C C A A G C A C A C C T I C T C T C C G C T D G A T T G C G A C I T C C G G T C A A G D I A G A G C D A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G G G T C D I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T 0 E101 A A C D C A C A G T C A G G I I G G A [G] C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T D I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C A A C D C A C A G T C A G G I I G G A [G] C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T D D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C 0 E102 A A C D (T) A C (G) G T (A) A G G I I G G A G (T) I A C (C) (T) G C (A) G (C) A (G) C T D G G C A A A C C A T A A G A G G A (C) C G C G C C A C G T C A A C (T) I A C T G C G A G T T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G A T T G C A A C D (C) A C (A) G T (C) A G G I I G G A [G] (C) I A C (T) (C) G C (G) G (G) A (A) C T D G G C A A A C C A T A A G A G G A (T) C G C G C C A C G T C A A C (C) I A C T G C G A G T T I I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C 0 E103 A A C D T A C G G T C A G G I I G C A G C D T A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C T T C G A C C I A C T G C G A G (C) T [D] I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C G A C I T C C G G T C A G G I I A G A T C I A C T C A C G A C A A T C I A G C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A G (T) T [D] I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 E104 A A C D T A C G G T C A G G I I G C A G C D T A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C T T C G A C C I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D T A C G G T A A G G I I G G A G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 E105 (A) A (C) (D) T (A) C G G T (A) A G G (I) I (G) G A G T I A C C T G C A G C A G C T D G G C A A A (C) C A T A A G A G G A C C G C G C C A C G T C A A C (T) I A C T G C G A G T T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C (G) A (T) (I) T (C) C G G T (C) A G G (D) I (A) G A G T I A C C T G C A G C A G C T D G G C A A A (T) C A T A A G A G G A C C G C G C C A C G T C A A C (C) I A C T G C G A G T T I D I G A C A T A G T T G A G G C T A T C G T C C C G G G C G A G C C C D T T T T C C T C T I G A C C A C 0 E106 A A C D (T) A C (G) G T (A) A G G I I G G A (G) (T) I A C (C) (T) G C (A) G (C) A (G) C T D G G C A A A C C A T A A G A G G A (C) C G C G C C A C G T C A A C (T) I A C T G C G A G T T (D) I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D (C) A C (A) G T (C) A G G I I G G A (T) (C) I A C (T) (C) G C (G) G (G) A (A) C T D G G C A A A C C A T A A G A G G A (T) C G C G C C A C G T C A A C (C) I A C T G C G A G T T (I) D I G A C A T A G T T G A G G C T A T C G T C C C G G G C G A G C C C D T T T T C C T C T I G A C C A C 0 E107 A A C D (T) A C (G) G T (A) A G G I I G G A (G) (T) I A C (C) (T) G C (A) G (C) A (G) C T D G G C A A A C C A T A A G A G G A (C) C G C G C C A C G T C A A C (T) I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C T C G A G C A A G C C C I C T C C C C G C T D G A C T G C A A C D (C) A C (A) G T (C) A G G I I G G A (T) (C) I A C (T) (C) G C (G) G (G) A (A) C T D G G C A A A C C A T A A G A G G A (T) C G C G C C A C G T C A A C (C) I A C T G C G A G T T D D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C 0 E108 (A) A (C) [D] T A C G G T (A) A G G (I) I (G) G A G T I A C C T G C A G C A G C T D G G C A A A (C) C A T A A G A G G A C C G C G C C A C G T C A A C (T) I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C (G) A (T) [I] T [A] C G G T (C) A G G (D) I (A) G A G T I A C C T G C A G C A G C T D G G C A A A (T) C A T A A G A G G A C C G C G C C A C G T C A A C (C) I A C T G C G A G T T D I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C 0 E109 A A C D C A C A G T C A G G I I G G A [T] C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T I I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T A C G A T I T C C G G T C A G G D I A G A G T I A C C T G C A G C A G C T D G G C A A A T C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T I D I G A C A T A G T T G A G G C T A T C G T C C C G G G C G A G C C C D T T T T C C T C T I G A C C A C 0 E110 A A C D C A C A G T C A G G I I G G A G C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C G G C I T C G G G A C T G T I D A G A G C D A C C T A T G A C A A T C I G C C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 E111 A A C D C A C A G T C A G G I I G G T T C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T D I I G A (C) (A) (T) (A) (G) G G (A) A (A) (G) (T) C G (T) C (G) T C (T) (C) G A G (C) A A G C (C) C I (C) T (C) (C) C C G C T D G (A) C (T) G C G G C I T C G G G A C T G T I D A G A G C D A C C T A T G A C A A T C I A C C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T D I I G A (T) (T) (C) (G) (A) G G (G) A (G) (A) (C) C G (G) C (A) T C (C) (T) G A G (T) A A G C (T) C I (T) T (T) (T) C C G C T D G (G) C (C) G C 0 E112 A A C D T A C G G T A A G G I I G G (A) G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G A C A T A G G G A A A G T C G T C G T C T C G A G C A A G C C C I C T C C C C G C T D G A C T G C A A C D T A C G G T A A G G I I G G (T) G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C 0 E113 A A C D (T) A C (G) G T (A) A G G I I G G (A) (G) (T) I A C (C) (T) G C (A) G (C) A (G) C T D G G C A A A C C A T A A G A G G A (C) C G C G C C A C G T C A A C (T) I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D (C) A C (A) G T (C) A G G I I G G (T) (T) (C) I A C (T) (C) G C (G) G (G) A (A) C T D G G C A A A C C A T A A G A G G A (T) C G C G C C A C G T C A A C (C) I A C T G C G A G T T D I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C 0 E114 (A) A (C) (D) (C) A C (A) G T C A G G (I) I (G) G A (T) (C) I A C (T) (C) G C (G) G (G) A (A) C T D G G C A A A (C) C A T A A G A G G A (T) C G C G C C A C G T C A A C C I A C T G C G A G T T (I) I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C (G) A (T) (I) (T) A C (G) G T C A G G (D) I (A) G A (G) (T) I A C (C) (T) G C (A) G (C) A (G) C T D G G C A A A (T) C A T A A G A G G A (C) C G C G C C A C G T C A A C C I A C T G C G A G T T (D) I I G G C A T A G G G G A G G T C G T G G G T C C G A G C A A G C C C I C T C T A C G G A D G A C T G T 0 E115 A A C D T A C G G T C A G G I I G C A G C D T A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C T T C G A C C I A C T G C G A G [T] T I I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C T C T I G A C C A C A A C D C A C A G T C A G G I I G G A G C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T D D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C 0 E116 A A C D C A C A G T C A G G I I G G T T C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C C I A C T G C G A G T T I I I (A) A T T C G A G G G (T) (A) (G) (T) C G (T) C (G) T C C (C) (A) A (A) (C) A (C) (A) C (C) (T) I (C) (C) (C) T C C G C T D G (A) (T) (T) G C G G C I T C G G G A C T G T I D A G A G C D A C C T A T G A C A A T C I A C C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T I I I (G) A T T C G A G G G (A) (G) (A) (C) C G (G) C (A) T C C (T) (G) A (G) (T) A (A) (G) C (T) (C) I (T) (T) (T) T C C G C T D G (G) (C) (C) G C 0 E117 A A C D T A C G G T C A G G I I G C (A) G C D T A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C T T C G A C C I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D T A C G G T C A G G I I G C (T) G C D T A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C T T C G A C C I A C T G C G A G C T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 E118 A A C D T A C G G T C A G G I I G C A G C D T A C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C T T C G A C C I A C T G C G A G [T] T I D I G A C A T A G T T G A G G C T A T C G T C C C G G G C G A G C C C D T T T T C C T C T I G A C C A C A A C D T A C G G T C A G G I I G G A G C I A C C T G C G G G A A C C D G G C A A A C G A T G A G G G G G C C G C G G C A C G A C A C C C I G T C T C G A G T T I D I G A C A T A G T T G A G G C T A T C G T C C C G G G T G A G C C C D T T T T C C T C T I G A C C G C 0 E119 A A C D C A C A G T C A G G I I G G (A) (G) C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D C A C A G T C A G G I I G G (T) (T) C I A C T C G C G G G A A C T D G G C A A A C C A T A A G A G G A T C G C G C C A C G T C A A C C I A C T G C G A G T T D I I A A T T C G A G G G T A G T C G T C G T C C C A A A C A C A C C T I C C C T C C G C T D G A T T G C 0 E120 A A C D T A C G G T C A G G I I G C A G C D T (A) C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G A C A C C C I G T C T C G A G T T I I I G A (T) (T) (C) (G) (A) G G (G) A (G) (A) (C) C G (G) C (A) T C (C) (T) G A G (T) A A G C (T) C I (T) T (T) (T) C C G C T D G (G) C (C) G C G A T I T C C G G T C A G G D I A G A G C D A (C) T T G C G G C G A T C I G G T G G A C G G A G G T G G G G C C A T C G C A C G A C A C C C I G T C T C G A G T T I I I G A (C) (A) (T) (A) (G) G G (A) A (A) (G) (T) C G (T) C (G) T C (T) (C) G A G (C) A A G C (C) C I (C) T (C) (C) C C G C T D G (A) C (T) G C 0 E121 A A C D T A C G G T C A G G I I G C A G C D T C C T G C A G C A G C T D G G C A A A C C A T A A G A G A A C C G C G C C A C G A C A C C C I G T C T C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C A A C D T A C G G T A A G G I I G G A G T I A C C T G C A G C A G C T D G G C A A A C C A T A A G A G G A C C G C G C C A C G T C A A C T I A C T G C G A G T T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 E122 G G C I T C G G G A C T G T I D A G A G C D A C C T A T G A C A A T C I A C C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A G T T D D I G A C A T A G T T G A G G C T A T C G T C C C G G G T G A G C C C D T T T T C C T C T I G A C C G C G G C I T C G G G A C T G T I D A G A G C D A C C T A T G A C A A T C I A C C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G C 0 E123 G G C I T C C G G A C T G (G) I D A G T G C D A C C T A T G G C A A T C I G G C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C I A T T T A T A A C T D D D G A C A T A G T T G A G G C T G T C G T C C C G A G C G A G C C C D T T T T C C G C T I G A C C G C G G C I T C G G G A C T G (T) I D A G A G C D A C C T A T G A C A A T C I A C C A G G C G G T G G T G A G G C A A T C G T G T G A T A C T C D A T T T A T A A C T D I I G A T T C G A G G G A G A C C G G C A T C C T G A G T A A G C T C I T T T T C C G C T D G G C C G 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 D = A ? ? ? = = = = = I = G C = = = = = A C = = = A = = A G C T D = = C A A = T C A T A A G A = = A = ? G C G C = = = = T = = A = = = A C T G = = = = = = ? = = (G) = = = = = = = = = ? (G) (A) (C) = = = = (A) = = = (T) (G) = = (T) = (A) (G) = (T) = = (T) = (T) = = = = = = = = (G) (C) (C) = = G = T I = C ? ? ? = = = = = D = A G = = = = = C T = = = G = = G A T C I = = T G G = C G G A G G T G = = G = ? A T C G = = = = A = = C = = = G T C T = = = = = = ? = = (A) = = = = = = = = = ? (A) (G) (T) = = = = (G) = = = (C) (A) = = (C) = (C) (A) = (C) = = (C) = (C) = = = = = = = = (A) (T) (T) = = 0 DY02 A = = D = A = = = ? ? = = = = = G C = G = D = A C T G = A G = = G C T D G = = = A A = C A = A A G A G = A = C G C G C C A C = T C = A C = I = C = G C G = G T = (I) = D ? = = = = = = = = = = = = = = = = = = = ? = = = = G = = = = = = = = = T = = = = = = = = = = = = = = G = = I = C = = = ? ? = = = = = A G = T = I = C T C A = G A = = A T C I A = = = G G = G G = G G T G A = G = A A T C G T G T = A T = C T = D = T = T A T = A C = (D) = I ? = = = = = = = = = = = = = = = = = = = ? = = = = A = = = = = = = = = C = = = = = = = = = = = = = = 0 DY03 A = = D = A = = = ? ? = G = I = G C (A) = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = A = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = I = C = = = ? ? = A = D = A G (T) = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = G = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY04 A A = D = A = = = ? ? A = G = I G C = = = D = A = = G C A G = = G C T D G = = = A A = C A = A A G A G = A = = G C G C = = = = T = = A = = = A C T G = = = = = = = I ? ? = T T C G A G G = T A = T C = = = = = = = = A = = = A C A = = T I C = C = = = = = = D = = T T = = G G = I = C = = = ? ? T = T = D A G = = = I = C = = A T G A = = A T C I A = = = G G = G G = G G T G A = G = = A T C G = = = = A = = C = = = G T C T = = = = = = = D ? ? = C A T A G T T = A G = C T = = = = = = = = G = = = G A G = = C D T = T = = = = = = I = = C C = = 0 DY05 (A) (A) = (D) = (A) = = = ? ? (A) = = = (I) (G) (C) = = = (D) = (A) = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (I) = = = G = = = = = = = G = G = = = = = G = G T = = = = = = = = = A = = = = = = T A G = G A = C = = = = T (G) (G) = (I) = (C) = = = ? ? (T) = = = (D) (A) (G) = = = (I) = (C) = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (D) = = = A = = = = = = = A = A = = = = = C = T C = = = = = = = = = C = = = = = = C C C = C T = G = = = = C 0 DY06 A = C D = A = = = = = = = = I = G C ? = = = = A C = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = D ? = T T C G A = = G T = = = = = = = = = = = = A = = = = C A = = T = = = = T = = = = = = = = T = = = G = T I = C = = = = = = = = D = A G ? = = = = C T = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = I ? = C A T A G = = A A = = = = = = = = = = = = G = = = = A G = = C = = = = C = = = = = = = = C = = = 0 DY07 A = C D = A = = = ? ? = = = I = G C T = = I = = C = = = = ? ? ? ? = = = = = C A = = = = = T = = = = = = = = = = = = = = = = = = = = = C = I ? ? C = C G = G T = D = = = G = = = = = = = = = G = = = = = G = G T = = = = = = = = = = = = = = = = = A ? = G A = = = = = = ? G = T I = C = = = ? ? = = = D = A G A = = D = = T = = = = ? ? ? ? = = = = = T G = = = = = A = = = = = = = = = = = = = = = = = = = = = T = D ? ? T = A T = A C = I = = = A = = = = = = = = = A = = = = = C = T C = = = = = = = = = = = = = = = = = C ? = C T = = = = = = ? 0 DY08 = A T = = = = = = ? ? A = G D I = = A = = D = = T = G = = = C G = T = I = = T G G = = = G A = G T = ? ? = = = A T C = = = = = = = = = = = = = = = = = = = = ? ? = I ? ? = T T C ? ? G G ? T A = T C G = = = = = = = A A = = A C A = = T I C = C = = = G = = D = = T T = = = G C = = = = = = ? ? T = T I D = = T = = I = = C = A = = = G A = C = D = = C A A = = = A T = A G = ? ? = = = G C G = = = = = = = = = = = = = = = = = = = = ? ? = D ? ? = C A T ? ? T T ? A G = C T A = = = = = = = G G = = G A G = = C D T = T = = = T = = I = = C C = = 0 DY09 A A = D = A ? ? ? T = A = G = I G = A = = I = = = = G C A = = = G C T D = = = = A A = C A = A A G A G A A = C G C G C C A C = ? ? = ? = = = = C = = = = = = = ? = I ? ? = = = = = = = = = = = = = = = = = = = T = = = = = = A = = = = ? I C = C = A = = G A D = = = T = = G G = I = C ? ? ? A = T = T = D A = T = = D = = = = A T G = = = A T C I = = = = G G = G G = G G T G A G G = A A T C G T G T = ? ? = ? = = = = T = = = = = = = ? = D ? ? = = = = = = = = = = = = = = = = = = = C = = = = = = G = = = = ? D T = T = C = = C T I = = = C = = 0 DY10 = = C = = = = = = ? ? = A = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = ? = = = = G = = C ? = = = G C A T A G = = = = = G T = = T G G G T = C = = = C = = = = C = = C = C = A = = G A = = A = T = T = = T = = = = = = ? ? = G = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = ? = = = = A = = T ? = = = A T T C G A = = = = = A C = = G C A T C = T = = = T = = = = T = = T = T = C = = C T = = G = C = C 0 DY11 = = = = = = = = = = (C) = = = = = = (C) (A) = (C) (D) = (A) = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = (C) = = ? = = = = = = = = ? = = = ? C A T A G = = = = = G T = = T G G G T = C = = = C = = = A C = = C = C = A G = G A = C A = T = T = = = = = = = = = = (A) = = = = = = (G) (T) = (T) (I) = (C) = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = (T) = = ? = = = = = = = = ? = = = ? T T C G A = = = = = A C = = G C A T C = T = = = T = = = C T = = T = T = C C = C T = G G = C = C 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I ? = = = = = = = = = ? ? ? = = = = = = = = = = = = A = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D ? = = = = = = = = = ? ? ? = = = = = = = = = = = = G = = = = = = = = = T = = = = = = = = = = = = = = 0 DY13 = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = ? G = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = I ? ? = ? ? ? ? ? ? = = = G A C = = G = A = = = T = = = T = = = = T = = T = T = = = = = = = = G = C = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = ? A = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = D ? ? = ? ? ? ? ? ? = = = A G T = = T = G = = = C = = = C = = = = C = = C = C = = = = = = = = A = T = = 0 DY14 A A = D = A = = A T = A = G = I G C = = = D = A = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = I = C = = G A = T = T = D A G = = = I = C = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY15 = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = ? ? = = = = = = = = = = = = = = ? ? ? ? = = ? = = = = = = = ? = = = A = = = = = = = A = A = = = = = C = T C T = = = = = = = = C = = = = = = C C C = C T = G = = = = C = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = ? ? = = = = = = = = = = = = = = ? ? ? ? = = ? = = = = = = = ? = = = G = = = = = = = G = G = = = = = G = G T C = = = = = = = = A = = = = = = T A G = G A = C = = = = T 0 DY16 A A = D = A ? ? ? ? ? A = G = I G C = ? = D ? ? ? ? ? C A G = = G C T D G = = = A A = C ? ? ? A G A ? ? A = C G C G C C A C = T C = A C = I = C = G C G = G ? ? (I) = = = (G) (C) (A) (T) (A) (G) = = = ? ? (G) (T) = ? ? ? ? (G) (T) = (C) = = = (C) = = = (A) (C) = = (C) = (C) = (A) (G) = (G) (A) = (C) (A) = (T) = (T) G G = I = C ? ? ? ? ? T = T = D A G = ? = I ? ? ? ? ? T G A = = A T C I A = = = G G = G ? ? ? G T G ? ? G = A A T C G T G T = A T = C T = D = T = T A T = A ? ? (D) = = = (A) (T) (T) (C) (G) (A) = = = ? ? (A) (C) = ? ? ? ? (T) (C) = (T) = = = (T) = = = (C) (T) = = (T) = (T) = (C) (C) = (C) (T) = (G) (G) = (C) = (C) 0 DY17 A A = D = A ? ? ? T = A = G = I G C A = = D = A = = G = A = = A G C ? D = = C A A = = C A = A A G A ? ? A = = G C G C = = = = T T = ? T = = A C T = A T = A C = = = = = = C A T A G T T = = = G = T = T = G = T = C = = = C = = = = C = = C = C = A = = G A = = A = T = = G G = I = C ? ? ? A = T = T = D A G T = = I = C = = A = G = = G A T ? I = = T G G = = G G = G G T G ? ? G = = A T C G = = = = A C = ? C = = G T C = C G = G T = = = = = = T T C G A G G = = = A = C = G = A = C = T = = = T = = = = T = = T = T = C = = C T = = G = C = = 0 DY18 = A T = = = = = = T = A = G D I = = = = = D = = T = G = = G = G = = = = G = T G = A = = = A = = = = G = = = C = = = = C A C = = C = = C = I G (T) C = C G = G T = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = = = = A = T = T I D = = = = = I = = C = A = = A = A = = = = A = C A = G = = = T = = = = A = = = A = = = = T G T = = T = = T = D A (C) T = A T = A C = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY19 A = = D C A = A = = = = G = I = G = (T) T = I = = T C = = G = G = A = ? = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = A = = T ? = = A A T T C G A = = = T A = = = = = C = T C = = A = A = = C A = = T = = C = = C = = C T = = = T = = C G = = I T C = G = = = = A = D = A = (A) G = D = = C T = = A = C = G = ? = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = G = = C ? = = G G C A T A G = = = A G = = = = = G = G T = = G = G = = A G = = C = = T = = A = = G A = = = C = = T 0 DY20 A = = D = A = = = = = = G = I = G C = = = = = A = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = A = = T (I) = = = A = = = = = = = A = A = = = = = C = T C T = = = = = = = = = = = = = = = C C = = C T = = = = = = C G = = I = C = = = = = = A = D = A G = = = = = C = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = G = = C (D) = = = G = = = = = = = G = G = = = = = G = G T C = = = = = = = = = = = = = = = T A = = G A = = = = = = T 0 DY21 = = = = = = = = ? = C = = = = = = C = = C D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = D ? = T T C G A = = G T = = = = = = = = = = = = A = = = = C A = = T = = = = T = = = = = = = = T = = = = = = = = = = = ? = A = = = = = = G = = T I = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = I ? = C A T A G = = A A = = = = = = = = = = = = G = = = = A G = = C = = = = C = = = = = = = = C = = = 0 DY22 = = = = = = = = G ? ? = = = = = = G = = T I = C = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = ? ? ? = = T = = = ? = = = = = = = = = I ? = ? ? ? ? ? = = ? A = = = = = = = = = = T = G ? = = = A G = = C = = = = C = = = = = = = = C = = C = = = = = = = = A ? ? = = = = = = C = = C D = A = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = ? ? ? = = C = = = ? = = = = = = = = = D ? = ? ? ? ? ? = = ? T = = = = = = = = = = C = A ? = = = C A = = T = = = = T = = = = = = = = T = = T 0 DY23 = = = = = = = = = ? ? = = = = = = C = = C = = = = = = = G ? ? ? ? T C I = = = = G = = G G = G G T G = = G = ? ? ? ? ? ? = = = A = = C = C = G T C T = = = = = = ? = = = ? T T C G A = = = T A = = = = = C = T C = = A = = = = C A C = T = = = = = C C = C T = G = T = = C = = = = = = = = = ? ? = = = = = = G = = T = = = = = = = A ? ? ? ? C T D = = = = A = = C A = A A G A = = A = ? ? ? ? ? ? = = = T = = A = T = A C T G = = = = = = ? = = = ? C A T A G = = = A G = = = = = G = G T = = G = = = = A G A = C = = = = = A G = G A = C = C = = T 0 DY24 A = = D = A = = = ? ? = G = I = G = = = T I = = = = = = = = = = = ? = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = T = = = = = = = A = = T I = D ? A T T C G A = = = T A = = = ? ? ? ? T C = = A = = = = C A = = T = = = = = C = = C T = = = T = = C G = = I = C = = = ? ? = A = D = A = = = C D = = = = = = = = = = = ? = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = C = = = = = = = G = = C D = I ? G C A T A G = = = A G = = = ? ? ? ? G T = = G = = = = A G = = C = = = = = A = = G A = = = C = = T 0 E101 = = = ? ? = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I ? ? = T T C G A G G = T A = T C = = = = = = = = A = A = A C A = = ? I C C C = = = = = = D = = T T = = = = = ? ? = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D ? ? = C A T A G T T = A G = C T = = = = = = = = G = G = G A G = = ? D T T T = = = = = = I = = C C = = 0 E102 = = = = (T) = = (G) = = (A) = = = = = = = = ? (T) = = = (C) (T) = = (A) = (C) = (G) = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = G = = = = = = = = = A G A C = = G = A = = = T G = G T = A G = T C = T T T = = = = = = = = = = = = = = = = = (C) = = (A) = = (C) = = = = = = = = ? (C) = = = (T) (C) = = (G) = (G) = (A) = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = A = = = = = = = = = T A G T = = T = G = = = C A = A C = C A = C T = C C C = = = = = = = = = = = = = 0 E103 A = = D = A = = = = = = = = = = G C = G = D T A C T G = A G = = G C T D G = = = A A = C A = A A G A G A A = C G C G C C A C T T C G A C = I = C = G C G = = (C) = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = G = = I = C = = = = = = = = = = A G = T = I A C T C A = G A = = A T C I A = = = G G = G G = G G T G A G G = A A T C G T G T G A T A C T = D = T = T A T = = (T) = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0 E104 = = = = = = = = = = C = = = = = = C = = C D T A = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = T = = G = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = G = = T I A C = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = G = = A = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 (A) = (C) (D) = (A) = = = = (A) = = = (I) = (G) = = = = = = = = = = = = ? ? ? = = = = = = = = = = (C) = = ? ? = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = I ? ? = ? ? ? ? ? G G = = = A = C G G = A = = = T = A = T A = = = T = I = = = = = = G = = D ? ? ? = G = (G) = (T) (I) = (C) = = = = (C) = = = (D) = (A) = = = = = = = = = = = = ? ? ? = = = = = = = = = = (T) = = ? ? = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = D ? ? = ? ? ? ? ? T T = = = G = T A T = G = = = C = G = C G = = = C = D = = = = = = T = = I ? ? ? = A = 0 E106 = ? ? = (T) = = (G) = = (A) = = = = = = = = (G) (T) = = = (C) (T) = = (A) = (C) = (G) = = = = = = = = = = = = = = = = = ? ? = (C) = = = = = = = = = = = = = = (T) = = = = = = = = = = = (D) I ? ? = ? ? ? ? ? G G = = = A = C G G = A = = = T = A = T A = = = T = I = = = = = = G = = D = G = = G = = ? ? = (C) = = (A) = = (C) = = = = = = = = (T) (C) = = = (T) (C) = = (G) = (G) = (A) = = = = = = = = = = = = = = = = = ? ? = (T) = = = = = = = = = = = = = = (C) = = = = = = = = = = = (I) D ? ? = ? ? ? ? ? T T = = = G = T A T = G = = = C = G = C G = = = C = D = = = = = = T = = I = A = = A = 0 E107 = ? ? = (T) = = (G) = = (A) = = = = = = = = (G) (T) = = = (C) (T) = = (A) = (C) = (G) = = = = = = = = = = = ? ? ? = = = = = = (C) = = = = = = = = = = = = = = (T) = = = = = = = = = = = = I ? ? = = = = = = G G A = A = T C = = = = = = T = = = = = A = = = = = I C = C C = = = = = D = = = T = = = ? ? = (C) = = (A) = = (C) = = = = = = = = (T) (C) = = = (T) (C) = = (G) = (G) = (A) = = = = = = = = = = = ? ? ? = = = = = = (T) = = = = = = = = = = = = = = (C) = = = = = = = = = = = = D ? ? = = = = = = T T G = G = C T = = = = = = C = = = = = G = = = = = D T = T T = = = = = I = = = C = = 0 E108 (A) = (C) ? ? ? = = = = (A) = = = (I) = (G) = = = = = = = = = = = = = = = = = = ? = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = ? ? ? = = ? ? = = = G = = = = = = = = = A G A C = = G = A = = = T G = G T = A G = T C = T T T = = = = = = = = G C C = = (G) = (T) ? ? ? = = = = (C) = = = (D) = (A) = = = = = = = = = = = = = = = = = = ? = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = ? ? ? = = ? ? = = = A = = = = = = = = = T A G T = = T = G = = = C A = A C = C A = C T = C C C = = = = = = = = A T T = = 0 E109 A = C D C A ? ? = = = = = = I = G = = ? C = = = T C = = G = G = A = = = = = = = = = C = = = = = = = = = = T = = = = = = = = ? = = = ? = = = = = = = = = = = ? ? = I = A ? ? ? ? ? ? G G = T A = T C G = = = = = = = A A A = A C A = = ? I C C C = = = G = = D = = T T = = G = T I T C ? ? = = = = = = D = A = = ? T = = = C T = = A = C = G = = = = = = = = = T = = = = = = = = = = C = = = = = = = = ? = = = ? = = = = = = = = = = = ? ? = D = G ? ? ? ? ? ? T T = A G = C T A = = = = = = = G G G = G A G = = ? D T T T = = = T = = I = = C C = = 0 E110 A A = D C A C A = ? ? A = G = I G = = = = I = = T C G C = G G = = C T D = G = = A A = C A = A A G A G = A T ? G C G C C A C = T C = ? ? = I = ? = G C G = G ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = I T C G G = ? ? T = T = D A = = = = D = = C T A T = A C = = T C I = C = = G G = G G = G G T G A = G C ? A T C G T G T = A T = ? ? = D = ? = T A T = A ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 A A = D C A C A = T = A = G = I G = T T = I = = T C G C = G G = = C T D G G = = A A = C A = A A G A G = A T C G C G C C A C = T C = A C = I = C = G C G = G T = = = = = = (C) (A) (T) (A) (G) = = (A) = (A) (G) (T) = = (T) = (G) = = (T) (C) = = = (C) = = = = (C) = = (C) = (C) (C) = = = = = = = (A) = (T) = = G G = I T C G G = A = T = T = D A = A G = D = = C T A T = A C = = T C I A C = = G G = G G = G G T G A = G C A A T C G T G T = A T = C T = D = T = T A T = A C = = = = = = (T) (T) (C) (G) (A) = = (G) = (G) (A) (C) = = (G) = (A) = = (C) (T) = = = (T) = = = = (T) = = (T) = (T) (T) = = = = = = = (G) = (C) = = 0 E112 = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = ? = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I ? ? = = = = = = G G A = A = T C = = = = = = T = = = = = A = = = = = I C = C C = = = = = D = = = T = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = ? = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D ? ? = = = = = = T T G = G = C T = = = = = = C = = = = = G = = = = = D T = T T = = = = = I = = = C = = 0 E113 = = = = (T) = = (G) = = (A) = = = = = = = (A) (G) (T) = = = (C) (T) = = (A) = (C) = (G) = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = G = = = = = = = = = A G A C = = G = A = = = T G = G T = A G = T C = T T T = = = = = = = = G C C = = = = = = (C) = = (A) = = (C) = = = = = = = (T) (T) (C) = = = (T) (C) = = (G) = (G) = (A) = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = A = = = = = = = = = T A G T = = T = G = = = C A = A C = C A = C T = C C C = = = = = = = = A T T = = 0 E114 (A) = (C) (D) (C) = = (A) = = = = = = (I) = (G) = = (T) (C) = = = (T) (C) = = (G) = (G) = (A) = = = = = = = = = (C) = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = (I) = = A A T T C G A = = = T A = = = = = C = T C = = A = A = = C A = = T = = C = ? C = = C T = = = T = = C (G) = (T) (I) (T) = = (G) = = = = = = (D) = (A) = = (G) (T) = = = (C) (T) = = (A) = (C) = (G) = = = = = = = = = (T) = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = (D) = = G G C A T A G = = = A G = = = = = G = G T = = G = G = = A G = = C = = T = ? A = = G A = = = C = = T 0 E115 = = = = T = = G = = = = = = = = = C = = = D T A C T = = A = C = G = = = = = = = = = = = = = = = = = = A = C = = = = = = = = T = = G = = = = = = = = = = = = ? ? I I ? ? ? T T C G A G G = = = A = C = G = A = = = T = = = T A = = = T = I = = = = = = T = = = = = = = A = = = = = C = = A = = = = = = = = = G = = = I A C T C = = G = G = A = = = = = = = = = = = = = = = = = = G = T = = = = = = = = G = = A = = = = = = = = = = = = ? ? D D ? ? ? C A T A G T T = = = G = T = T = G = = = C = = = C G = = = C = D = = = = = = G = = = = = = = G = 0 E116 A A = D C A C A = ? ? A = G = I G = T T = I = = T C G C = G G = = C T D G G = = A A = C A = A A G A G = A = C G C G C C A C = T C = A C = I = C = ? ? ? = G ? ? = = = (A) = = = = = = = = ? (T) (A) (G) (T) = = (T) = (G) = = = (C) (A) = (A) (C) = (C) (A) = (C) (T) = (C) (C) (C) = = = = = = = = (A) (T) (T) = = G G = I T C G G = ? ? T = T = D A = A G = D = = C T A T = A C = = T C I A C = = G G = G G = G G T G A = G = A A T C G T G T = A T = C T = D = T = ? ? ? = A ? ? = = = (G) = = = = = = = = ? (A) (G) (A) (C) = = (G) = (A) = = = (T) (G) = (G) (T) = (A) (G) = (T) (C) = (T) (T) (T) = = = = = = = = (G) (C) (C) = = 0 E117 = = = = = = ? ? ? = = = = = = = = = (A) ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = ? ? ? = = = = = = = = = (T) ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 E118 = = = = = = = = = = = = = = = = = C = ? = ? T A = = = = A = C = G = T = = = = = = = = C = = A = = A = A A = = = = = C = = = T T = G A = = = A C T ? ? ? = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = A ? = = = = = = = = = = = = = = = = = G = ? = ? A C = = = = G = G = A = C = = = = = = = = G = = G = = G = G G = = = = = G = = = G A = A C = = = G T C ? ? ? = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = G ? 0 E119 = = = = = = = = = = = = = = = = = = (A) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = G = = = = = = = = = A G A C = = G = A = = = T G ? ? ? = ? ? = T C = T T T = = = = = = = = G C C = = = = = = = = = = = = = = = = = = = = (T) (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = A = = = = = = = = = T A G T = = T = G = = = C A ? ? ? = ? ? = C T = C C C = = = = = = = = A T T = = 0 E120 A = C D = A = = = = = = = = I = G C = = = = T (A) C = = = A = = A G C T D = = C A A = = C A T A A G A = A A = = G C G C = = = = = = = = = = = = = = = = = = = = = = = = = = (T) (T) (C) (G) (A) = = (G) = (G) (A) (C) = = (G) = (A) = = (C) (T) = = = (T) = = = = (T) = = (T) = (T) (T) = = = = = = = (G) = (C) = = G = T I = C = = = = = = = = D = A G = = = = A (C) T = = = G = = G A T C I = = T G G = = G G A G G T G = G G = = A T C G = = = = = = = = = = = = = = = = = = = = = = = = = = (C) (A) (T) (A) (G) = = (A) = (A) (G) (T) = = (T) = (G) = = (T) (C) = = = (C) = = = = (C) = = (C) = (C) (C) = = = = = = = (A) = (T) = = 0 E121 = = = = = = = = = = C = = = = = = C = = C D T = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = A = = C = C ? G T C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = G = = T I A = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = T = = A = T ? A C T G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G T = = D = = = C ? ? ? ? T T = = = G = T A T = G = = = C = G = = G = = = C = D = = = = = = T = ? I = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C = = I = = = T ? ? ? ? G G = = = A = C G G = A = = = T = A = = A = = = T = I = = = = = = G = ? D = G = = = = 0 E123 = = = = = = C = = = = = = (G) = = = = T ? = = = = = = = = = G = = = = = = G G = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = I = = = = = = = = = = = D ? ? = C A T A G T T ? ? ? ? = T ? ? ? ? = = = C = = = C G = = = C = D = = = = = = = = = I = A = = = = = = = = = = G = = = = = = (T) = = = = A ? = = = = = = = = = A = = = = = = A C = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = D = = = = = = = = = = = I ? ? = T T C G A G G ? ? ? ? = C ? ? ? ? = = = T = = = T A = = = T = I = = = = = = = = = D = G = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 1.00 = 1.00 1.00 = 1.00 ? ? ? = = = = = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 = = = = = = = = = ? 0.57 0.57 0.57 = = = = 0.57 = = = 0.57 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 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 0.78 = 1.00 ? = = = = = = = = = = = = = = = = = = = ? = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 = = = ? ? = 1.00 = 1.00 = 1.00 1.00 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 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = = = 1.00 ? ? = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = = 1.00 1.00 = = 0.52 0.52 = 0.52 = 0.52 = = = ? ? 0.52 = = = 0.52 0.52 0.52 = = = 0.52 = 0.52 = = 0.52 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.72 = = = 1.00 = = = = = = = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 = = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = = 1.00 = 1.00 1.00 ? = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 1.00 ? = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = = = = = = 1.00 = = = = 1.00 1.00 = = 1.00 = = = = 1.00 = = = = = = = = 1.00 = = = 1.00 = 1.00 1.00 = 1.00 = = = ? ? = = = 1.00 = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = ? ? ? ? = = = = = 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 ? ? 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 ? = 1.00 1.00 = = = = = = ? = 1.00 1.00 = = = = = = ? ? 1.00 = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = ? ? = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = ? ? = 1.00 ? ? = 1.00 1.00 1.00 ? ? 1.00 1.00 ? 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 ? ? ? 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = ? ? = ? = = = = 1.00 = = = = = = = ? = 1.00 ? ? = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = = = ? 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 = = = = = = ? ? = 1.00 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = ? = = = = 1.00 = = 1.00 ? = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 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 = 0.58 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 = = 1.00 = 1.00 = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = ? ? = = = = = = = = = = = = = = ? ? ? ? = = ? = = = = = = = ? = = = 1.00 = = = = = = = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = 1.00 ? ? ? ? ? 1.00 = 1.00 = 1.00 1.00 1.00 = ? = 1.00 ? ? ? ? ? 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 ? ? ? 1.00 1.00 1.00 ? ? 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 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 = = = 0.71 0.71 0.71 0.71 0.71 0.71 = = = ? ? 0.71 0.71 = ? ? ? ? 0.71 0.71 = 0.71 = = = 0.71 = = = 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 = = 1.00 = 1.00 = = 1.00 1.00 1.00 ? 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 ? ? 1.00 = = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = ? 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = 1.00 = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = 1.00 = = 1.00 = 1.00 = = 1.00 = 1.00 = = = = 1.00 = 1.00 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 = 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 1.00 1.00 1.00 = = = 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 = = = 1.00 = = 1.00 0.94 = = 0.94 = 0.94 = = = = = = 0.94 = 0.94 = 0.94 0.94 = = = = = 0.94 = = = = = = = = = = = = = = = = = = 0.94 = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = 0.94 = = 0.94 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 1.00 = = 1.00 = = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = 1.00 ? ? = = = = = = 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = ? ? ? = = 1.00 = = = ? = = = = = = = = = 1.00 ? = ? ? ? ? ? = = ? 1.00 = = = = = = = = = = 1.00 = 1.00 ? = = = 1.00 1.00 = = 1.00 = = = = 1.00 = = = = = = = = 1.00 = = 1.00 = = = = = = = = = ? ? = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 ? ? ? ? 1.00 1.00 1.00 = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = ? ? ? ? ? ? = = = 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = ? = = = ? 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = = = ? ? = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = = = = = = = = = = = ? = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = = ? ? ? ? 1.00 1.00 = = 1.00 = = = = 1.00 1.00 = = 1.00 = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = 1.00 = = = ? ? = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? ? = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = 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 = = 0.56 = = 0.56 = = = = = = = = ? 0.56 = = = 0.56 0.56 = = 0.56 = 0.56 = 0.56 = = = = = = = = = = = = = = = = = = = = 0.56 = = = = = = = = = = = = = = 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 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 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 = 0.83 = = = = 0.83 = = = 0.83 = 0.83 = = = = = = = = = = = = ? ? ? = = = = = = = = = = 0.83 = = ? ? = = = = = = = = = = = = = = = = = = = = = 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 = = ? ? = 0.59 = = 0.59 = = 0.59 = = = = = = = = 0.59 0.59 = = = 0.59 0.59 = = 0.59 = 0.59 = 0.59 = = = = = = = = = = = = = = = = = ? ? = 0.59 = = = = = = = = = = = = = = 0.59 = = = = = = = = = = = 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 = = ? ? = 0.67 = = 0.67 = = 0.67 = = = = = = = = 0.67 0.67 = = = 0.67 0.67 = = 0.67 = 0.67 = 0.67 = = = = = = = = = = = ? ? ? = = = = = = 0.67 = = = = = = = = = = = = = = 0.67 = = = = = = = = = = = = 1.00 ? ? = = = = = = 1.00 1.00 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 = 0.60 ? ? ? = = = = 0.60 = = = 0.60 = 0.60 = = = = = = = = = = = = = = = = = = ? = = = = = = 0.60 = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 ? ? = = = = = = 1.00 = 1.00 = = ? 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = = = = = ? = = = ? = = = = = = = = = = = ? ? = 1.00 = 1.00 ? ? ? ? ? ? 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = ? 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = ? ? 1.00 = 1.00 = 1.00 1.00 = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = ? ? = 1.00 = ? = 1.00 1.00 1.00 = 1.00 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 0.59 0.59 = = 0.59 = 0.59 = = 0.59 0.59 = = = 0.59 = = = = 0.59 = = 0.59 = 0.59 0.59 = = = = = = = 0.59 = 0.59 = = = = = = = = = = = = = = = = = = = = 0.61 = = = = = = = = = = = = = = = = = = = = = = = = ? = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? ? = = = = = = 1.00 1.00 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 = = 0.70 = = 0.70 = = = = = = = 0.57 0.70 0.70 = = = 0.70 0.70 = = 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 = = 0.53 = 0.53 0.53 0.53 = = 0.53 = = = = = = 0.53 = 0.53 = = 0.53 0.53 = = = 0.53 0.53 = = 0.53 = 0.53 = 0.53 = = = = = = = = = 0.53 = = = = = = = = = = 0.53 = = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 = = = 1.00 = = 1.00 = = = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = ? ? 1.00 1.00 ? ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = ? ? 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 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 = = = = = = = = ? 0.51 0.51 0.51 0.51 = = 0.51 = 0.51 = = = 0.51 0.51 = 0.51 0.51 = 0.51 0.51 = 0.51 0.51 = 0.51 0.51 0.51 = = = = = = = = 0.51 0.51 0.51 = = = = = = = = ? ? ? = = = = = = = = = 0.55 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = ? = ? 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 = = 1.00 = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = 1.00 = = = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 ? ? ? = ? ? = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = 1.00 = 1.00 1.00 = = = = 1.00 0.88 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 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 = = 0.53 = 0.53 0.53 0.53 = = 0.53 = 0.53 = = 0.53 0.53 = = = 0.53 = = = = 0.53 = = 0.53 = 0.53 0.53 = = = = = = = 0.53 = 0.53 = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = 1.00 = = 1.00 = 1.00 ? 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = 1.00 ? ? ? ? 1.00 1.00 = = = 1.00 = 1.00 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 = = = = END PHASEPROBS