************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 ppara.phase.inp ppara.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ppara.phase.out_freqs : haplotype frequency estimates ppara.phase.out_pairs : most likely haplotype pairs for each individual ppara.phase.out_recom : estimates of recombination parameters ppara.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 100 Positions of loci: 1837 2027 2100 2628 3343 3552 4644 8330 8557 9273 16195 16574 16631 17081 17372 17420 17464 17467 17864 17922 17927 22140 22409 25220 25273 26162 26174 26224 26233 26389 26967 26968 27294 32817 32885 33432 34208 34376 34790 34970 34992 35002 38731 38743 39413 47237 47238 47474 47875 47951 48063 48346 48348 55224 61435 61550 62065 62203 62233 62887 63277 63382 63548 63724 64144 64750 65352 65623 66220 66470 66553 66582 67105 67159 67287 67700 68451 68683 68932 68949 69424 70039 75438 75694 75876 75910 76098 76198 77215 77423 77608 80486 80492 80550 80913 82302 82789 83932 83944 84103 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ppara.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACTGACGICTAGDCTAAGGGCGGTCATAADCTGGTCAATAGGCTGCGGTATGGAATATATTGCGCGTACAACGCGCGGGCCCAGATCTTTDTCCCCGACT 1.000000 2 ACTGACGICTAGDCTAAGGGCGGTCATAADGCGGTCAACGAACTGCGGTATGGAGTATACTGCGTGTACAACGCGCAGGTACGGGTACCTICCCCTGGCC 1.000000 3 ACTGACGICTAGDCTAGGGGCGGTCATAADGCGGTCAACGAATCATGATGTGAGATAAACTGGGCTCGGTACGTACGGGCCCAGACATCTICCCCTAGCT 1.000000 4 ACTGACGITCACDCTGGAGGCTGTCATAADGCGGTCAACGAACTGTGATGTGAAATAAATTACGCGTACAACACGCAGGCACATATACCTICGCCTAGGT 2.000000 5 ACTGACGITCACDCTGGAGGCTGTCATCADGCGGTCAACGAACTGCGATATGGAGTATACTGCGTTTACAACGCGCAGGCACGGGCATCTICCCCTAGCT 1.000000 6 ACTGACGITCACDCTGGAGGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGACACAGACATCTICCCCTAGCT 1.000000 7 ACTGACGITCACDCTGGAGGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 10.000000 8 ACTGACGITCACDCTGGAGGCTGTCATCADGCGGTCAACGAACTGTGACGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 9 ACTGACGITCACDCTGGAGGCTGTCATCADGCGGTCAACGGACTGTGATGGGAAATAAATTACGCGTACATCGTACGGGCACATATACCTICGCCTAGGT 1.000000 10 ACTGACGITCACDCTGGAGGCTGTCACCADGCGGTCAACGAACTGCGGTATGGGATATACTGGGCTCGGTACGTACGGGCCCAGATCTTTDTCCCCGACT 1.000000 11 ACTGACGITCACDCTGGAGGCTGTCACCADGCGGTCAACGAACTGTGATGGGGAGTATACTGCGTGTACAACGCGCAGGTACAGATCCTTDTCCCCGACT 1.000000 12 ACTGACGITCACDCTGGAGGCTGTCACCADGCGGTCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACATATACCTICGCCTAGGT 1.000000 13 ACTGACGITCACDCTGGAGGCTGTAATCADCTGGCCAACGAATCACGATATGGAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 14 ACTGACGITCACDCTGGAGGCTGCCATAADGCGGTCAACGAACTGTGATGTGAAATGTTCCGCACTTAGATCGTACGGGCATAGATCTTTDTCCCTAGCT 1.000000 15 ACTGACGITCACDTTGGGGGCTGTCATAGDCTGGCCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACGGGTATCTICCCCTGGCC 1.000000 16 ACTGACGITCACDTTGGGGGCTGTCATAGDGCGGTTAGTAAACCACGATATGGAATAAATTACGCGTACAACACGCAGGCACAGGTATCTICCCCTGACT 1.000000 17 ACTGACGITCGCICTGGGGGCTGTCGTAADGCGGCCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACATATACCTICGCCTAGGT 1.000000 18 ACTGACGITCGCICTGGGGGCTGTAGTAADGCGGTCAACGAACCACGATATGGAGTATACTGCGTGTACAACGCGCAGGTACGGGCATCTICCCCTAGCT 1.000000 19 ACTGAGGICTACDCTGGGGGCTGTCATAAIGCGGTCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACAGATACCGDCCCCTAGCT 1.000000 20 ACTGAGGICTACDTTGGGGGCGGTCATAADGCGGTCAACGAATCACGATATGGAATGTACTGCGCGTGCAATGCGTGGGCACAGATCTTTDTCCCCGACT 1.000000 21 ACTGAGGICTACDTTGGGGGCGGTCATAAIGCGGTCAACGAACTGCGGTATGGAGTATACTGCGTGTACAACGCGCAGGTACAGGTATCTICCCCTGGCC 1.000000 22 ACTGAGGICTACDTTGGGGGCTGTCATAADCTAACTAACGAACCACGATAGGAAATGTTCTGCACTTACATCGTACGGGCACAGATCTTTDTCCCCGACT 1.000000 23 ACTGAGGICTACDTTGGGGGCTGTCACCADGCGGTCAACGAACTGTGATGTGAAATATATTGCGCGTACAACGCGCGGGCCCAGATCTTTDTCCCCGACT 1.000000 24 ACTGAGGICTAGDCTAGGGGCTGTCACCADGCGGTCAGTGAGCCACGATATAGAATGTTCCGCACTTACATCGTACGGGCATAGATCTTTDTCCCCGACT 1.000000 25 ACTGAGGICTGCICTGGGGGCTGTCGCCADGCGGTCAACAAGCTGTGATGTGAAATGTACTGCGCGTGCAATGCGTGGGCACAGATCTTTDTCCCCGACT 1.000000 26 ACTGAGGITTACDCTGGAGATTGTCATCADGCGGTCAACGAACTGTGATGGGAAACGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 27 ACTGAGGITTACDCTGGAGATTGTCATCADGCGGTCAACGAACTGTGACGGGAAATGTTCTGCACTTACATCGTACGGGCATAGGCATTTDCCATTGGCT 1.000000 28 ACTGAGGITTACDCTGGAGATTGTCATCAICTGGCCAACGAACCGCAATAGAGAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 29 ACTGAGGITTACDCTGGAGATTGTCGTCADGCGGTCGACGAACCACGATATAGAATAAATTACGCGTACAACACGCAGGCACAGATCTTTDTCCCCGACT 1.000000 30 ACTGAGGITTACDCTGGAGATTGTAATCAICTGGCCAACGAACCGCAATAGAGAATAAATTACGCGTACAACACGCAAGCACATATACCTICGCCTAGGT 1.000000 31 ACTGAGGITTACDCTGGACGCTACCATAADGCGGTCAACGAACTGTGATATGAGATATACTGGGCTCGGAACGTACGGGCCCAGATACCGDCCCCTAGCT 1.000000 32 ACTGAGGITTGCICTGGGGGCTGCCATAADGCGGTCAACGAACTGTGATGTGAAATGTTCCGCACTTACATCGTACGGGCATAGATCTTTDTCCCCGACT 1.000000 33 ACTGAGGDCTACDCTGGAGGCTGTCACCADGCGGTCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACGGGTACCTICCCCTGGCC 1.000000 34 ACTGAGGDCTACDCTGGACGCTGTCATAADCTAACTAACGAACCACGATAGGAAATGTTCTGCACTTACATCGTACGGGCACAGATCTTTDCGCCTAGGT 1.000000 35 ACTGAGGDCTACDCTGGACGCTGTCATAADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 36 ACTGAGGDCTACDCTGGACGCTGTCATAGDCTGGCCAACGAACTGTGATGTGAAATATACTGCGCGTACAACGCGCGGGCACATATACCTICGCCTAGGT 1.000000 37 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGCCGACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 38 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGCCGACGAACCACGATATAGAATAAATTACGCGTACAACACGCAGGCACATATACCTICGCCTAGGT 2.000000 39 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGCGATATAGAATAAATTACGCGTACAACACGCAAGCACAGGTATTTDCCATTGGCT 1.000000 40 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATAAATTACGCGTACAACACGCAAGCACAGGTATTTDCCATTGGCT 1.000000 41 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACGTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 42 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATAGATATCTICCCCTAGCT 1.000000 43 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATAGGTATTTDCCCTTGGCT 1.000000 44 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATAGGTATTTDCCATTGGCT 2.000000 45 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 6.000000 46 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAACGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 47 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGACGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 48 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACCGCAATAGAGAATAAATTACGCGTACAACACGCAAGCACAGGTATTTDCCATTGGCT 3.000000 49 ACTGAGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGGACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 2.000000 50 ACTGAGGDCTACDCTGGACGCTGTCACCADGCGGTCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACATATACCTICGCCTAGGT 1.000000 51 ACTGAGGDCTACDCTGGACGCTGTCGTCADGCGGTCGACGAACCACGATAGAGAATGTTCTGCACTTACATCGTACGGACACAGATCTTTDTCCCCGACT 1.000000 52 ACTGAGGDCTACDCTGGACGCTGTAATCAICTGGCCAACGAACCGCAATAGAGAATAAATTACGCGTACAACACGCAAGCACATATACCTICGCCTAGGT 2.000000 53 ACTGAGGDCTACDCTGGACGCTATCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATAGGTATTTDCCATTGGCT 1.000000 54 ACTGAGGDCTACDCTGGACGCTATCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 5.000000 55 ACTGAGGDCTACDCTGGGGGCTGTCATAADGCGGTCAACGAACTGTGATATGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 56 ACTGAGGDCTACDCTGGGGGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGACACAGACATCTICCCCTAGCT 1.000000 57 ACTGAGGDCTACDCTGGGGGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 58 ACTGAGGDCTACDCTGGGGGCTGTCACCADGCGGTCAACGAGCTGTGATGTGAAATGTTCTGCACTTACATCGTACGGACACAGATACCGDCCCCTAGCT 1.000000 59 ACTGGGGDCTACDCTGGACGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 2.000000 60 ACTGGGGDCTACDCCGGGGGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAATGTTCTGCACTTACATCGTACGGGCACATATACCTICGCCTAGGT 1.000000 61 ACTGGGGDCTACDCCGGGGGCTGTCATCADGCGGTCAACGAACTGTGATGGGAAACGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 2.000000 62 ACTGGGGDCTACDCCGGGGGCTGTCATCADGCGGTCAACGAACCATGATGGGAAATGTTCTGCACTTACATCGTACGGGCATATATACCTICGCCTAGGT 1.000000 63 GCCGACGICTAGDCTAAGGGTGGTCATAADGCGGTCAACGAACTGTGATGTGAAATGTTCTGCACTTACATCGTACGGGCACAGATCTTTDTCCCCGACT 1.000000 64 GTCCAGAICCACDCTGGAGGCTGTCATAADGCGGTCAACGAACTGTGATGTGAGATATACTGGGCTCGGTACGTACGGGCACAGACATCTICCCCTAGCT 1.000000 65 GTCCAGAICTACDCTGGAGGCTGTCATAGDGCGGTTAGTAAACCACGATATGGAATGTTCTGCACTTACATCGTACGGGCACATATACCTICGCCTAGGT 1.000000 66 GTCCAGAICTACDCTGGAGGCTGTCACCADGCGGTCAACGAATCACGATATGGAATGTACTGCGCGTGCAATGCGTGGGCACAGATCTTTDTCCCCGACT 1.000000 67 GTCCAGAICTACDCTGGGGGCTGTCATAADCTAACTAACGAACCATGATAGGAAATATATTGCGCGTACAACGCGCGGGCCCAGATACCTICGCCTGGGT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,6) D002: (58,65) D003: (66,67) D004: (25,49) D005: (22,56) D006: (32,34) D007: (35,24) D008: (9,14) D009: (15,29) D010: (2,64) D011: (17,20) D012: (13,3) D013: (12,18) D014: (48,31) D015: (21,26) D016: (19,55) D033: (5,36) D034: (7,11) D035: (33,63) D036: (57,59) D037: (4,43) D038: (10,51) D039: (4,23) D040: (16,52) E001: (47,54) E002: (41,45) E003: (7,45) E004: (7,8) E005: (45,54) E006: (39,59) E007: (7,48) E008: (45,54) E009: (44,54) E010: (7,45) E011: (44,48) E012: (27,38) E013: (38,60) E014: (7,61) E015: (52,54) E016: (7,42) E017: (30,53) E018: (7,61) E019: (45,49) E020: (46,28) E021: (7,7) E022: (37,62) E023: (40,50) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A C T G A C G I C T A G D C T A A G G G C G G T C A T A A D C T G G [T] C A A T A G G C T G C G G T A T G G A A T A T A T T G C G C G T A C A A C G C G C G G G C C C A G A T C T T T D T C C C C G A C T A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C A G A [C] A T C T I C C C C T A G C T 0 D002 (A) (C) [T] (G) A G (G) (D) C T A C D C T G G (G) G G C T G T C A C C A D G C G G T C A A C G A (G) C T G T G A T G T G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C A (G) A T A C C (G) (D) C (C) C C T A G (C) T (G) (T) [C] (C) A G (A) (I) C T A C D C T G G (A) G G C T G T C A T A G D G C G G [T] [T] A G T A A (A) C C A C G A T A T G G A A T G T T C T G C A C T T A C A T C G T A C G G G C A C A (T) A T A C C (T) (I) C (G) C C T A G (G) T 0 D003 G T C C A G A I C T A C D C T G G (A) G G C T G T C A C C A D G C G G T C A A C G A A T C A C G A T A T G G A A T G T A C T G C G C G T G C A A T G C G T G G G C A C A G A T C T T T D T C C C C G A C T G T C C A G A I C T A C D C T G G (G) G G C T G T C A T A A D C T A A C T A A C G A A C C A T G A T A G G A A A T A T A T T G C G C G T A C A A C G C G C G G G C C C A G A T A C C T I C G C C T G G G T 0 D004 A C T G A G G (I) C T (G) C (I) C T G G (G) (G) G C T G T C G C C A D G C G G T C A A C A (A) G C T G T G A T G T G A A A T G T A C T G C G C G T G C A A T G C G T G G G C A C A G A T C T T T D T C C C C G A C T A C T G A G G (D) C T (A) C (D) C T G G (A) (C) G C T G T C A T C A D G C G G T C A A C G (G) A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 D005 A C T G A G G (I) C T A C D (T) T G G G G G C [T] G T C A T A A D C T A A C T A A C G A A C C A C G A T A G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A C A G A T C T T T D T C C C C G A C T A C T G A G G (D) C T A C D (C) T G G G G G C [T] G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C A G A [C] A T C T I C C C C T A G C T 0 D006 A C T G A G G [I] (T) T (G) C (I) C T G G (G) (G) G C T G C C A T A A D G C G G T C A A C G A A C T G T G A T G T G A A A T G T T C C G C A C T T A C A T C G T A C G G G C A [T] A G A T C T T T D (T) (C) C C (C) (G) (A) (C) T A C T G A G G [D] (C) T (A) C (D) C T G G (A) (C) G C T G T C A T A A D C T A A C T A A C G A A C C A C G A T A G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A C A G A T C T T T D (C) (G) C C (T) (A) (G) (G) T 0 D007 A C T G A G G (D) C T A (C) D C T (G) G (A) (C) G C T G T C A (T) (A) A D G C G G T C A A C G A (A) C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G (I) C T A (G) D C T (A) G (G) (G) G C T G T C A (C) (C) A D G C G G T C A G T G A (G) C C A C G A T A T A G A A T G T T C C G C A C T T A C A T C G T A C G G G C A [T] A G A T C T T T D T C C C C G A C T 0 D008 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G G A C T G T G A T G G G A A A T A A A T T A C G C G T A (C) A T C G T A C G G G C A (C) A (T) A T (A) (C) (C) T I (C) (G) C C T A G (G) T A C T G A C G I T C A C D C T G G A G G C T G C C A T A A D G C G G T C A A C G A A C T G T G A T G T G A A A T G T T C C G C A C T T A (G) A T C G T A C G G G C A (T) A (G) A T (C) (T) (T) T [D] (T) (C) C C [T] A G (C) T 0 D009 A C T G A C G I T C A C D T T G G G G G C T G T C A T A G D C T G G (C) C A A C G A A C T G T G A T G T G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C G G G T A T C T I C C C C T G G C C A C T G A G G I T T A C D C T G G A G A T T G T C G T C A D G C G G (T) C G A C G A A C C A C G A T A T A G A A T A A A T T A C G C G T A C A A C A C G C A G G C A C A G A T C T T T D T C C C C G A C T 0 D010 (A) (C) (T) (G) A (C) (G) I C (T) A (G) D C T (A) (A) (G) G G C (G) G T C A T A A D G C G G T C A A C G A A C T G (C) G (G) T (A) T G (G) (A) (G) T A T A C T G (C) G (T) (G) (T) (A) (C) (A) A C G (C) (G) C (A) G G (T) A C (G) G (G) (T) A (C) C T I C C C C T (G) G C (C) (G) (T) (C) (C) A (G) (A) I C (C) A (C) D C T (G) (G) (A) G G C (T) G T C A T A A D G C G G T C A A C G A A C T G (T) G (A) T (G) T G (A) (G) (A) T A T A C T G (G) G (C) (T) (C) (G) (G) (T) A C G (T) (A) C (G) G G (C) A C (A) G (A) (C) A (T) C T I C C C C T (A) G C (T) 0 D011 A C T G A (C) G I (T) (C) (G) C (I) (C) T G G G G G C (T) G T C G T A A D G C G G C C A A C G A A C T G T G A T G T G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C A T A T A C C T I C G C C T A G G T A C T G A (G) G I (C) (T) (A) C (D) (T) T G G G G G C (G) G T C A T A A D G C G G T C A A C G A A T C A C G A T A T G G A A T G T A C T G C G C G T G C A A T G C G T G G G C A C A G A T C T T T D T C C C C G A C T 0 D012 A C T G A C G I (T) (C) A (C) D C T (G) G (A) G G C (T) G T (A) A T (C) A D (C) (T) G G (C) C A A C G A A T C A (C) G A T (A) T G (G) A A T G (T) T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A C G I (C) (T) A (G) D C T (A) G (G) G G C (G) G T (C) A T (A) A D (G) (C) G G (T) C A A C G A A T C A (T) G A T (G) T G (A) G A T A (A) A C T G G G C T C G G T A C G T A C G G G C C C A G A C A T C T I C C C C T A G C T 0 D013 A C T G A C G I T C (A) C (D) C T G G (A) G G C T G T (C) (A) (C) (C) A D G C G G T C A A C G A A C (T) (G) (T) G A T (G) T G (A) A A T G T T C T G C A C T T A C A T C G T A C G G A C A C (A) (T) (A) (T) A (C) C T I C (G) C C T A G (G) T A C T G A C G I T C (G) C (I) C T G G (G) G G C T G T (A) (G) (T) (A) A D G C G G T C A A C G A A C (C) (A) (C) G A T (A) T G (G) A G T A T A C T G C G T G T A C A A C G C G C A G G T A C (G) (G) (G) (C) A (T) C T I C (C) C C T A G (C) T 0 D014 A C T G A G G (D) (C) T A C D C T G G A C G C T (G) (T) C A T (C) A D G C G G T C A A C G A A C C G C A A T A G A G A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A G G T A T T T D C C A T T G G C T A C T G A G G (I) (T) T A C D C T G G A C G C T (A) (C) C A T (A) A D G C G G T C A A C G A A C T G T G A T A T G A G A T A T A C T G G G C T C G G A A C G T A C G G G C C C A G A T A C C G D C C C C T A G C T 0 D015 A C T G A G G I (C) T A C D (T) T G G (G) G (G) (C) (G) G T C A T A A (I) G C G G T C A A C G A A C T G C G G T A T G G A G T A T A C T G C G T G T A C A A C G C G C A G G T A C A (G) (G) T A (T) C T I C (C) C C T (G) G (C) (C) A C T G A G G I (T) T A C D (C) T G G (A) G (A) (T) (T) G T C A T C A (D) G C G G T C A A C G A A C T G T G A T G G G A A A C G T T C T G C A C T T A C A T C G T A C G G G C A T A (T) (A) T A (C) C T I C (G) C C T (A) G (G) (T) 0 D016 A C T G A G G (I) C T A C D C T G G G G G C T G T C A T A A (I) G C G G T C A A C G A A C T G T G A T (G) T G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C A G A T A C C G D C C C C T A G C T A C T G A G G (D) C T A C D C T G G G G G C T G T C A T A A (D) G C G G T C A A C G A A C T G T G A T (A) T G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 D033 A C T G A (C) G (I) [T] (C) A C D C T G G A (G) G C T G T C A T (C) (A) D (G) (C) G G (T) C A A C G A A C T G C G A T A T G G A G T A T A C T G C G T T T A C A A C G C G C A G G C A C G G G C A T C T I C C C C T A G C T A C T G A (G) G (D) [C] (T) A C D C T G G A (C) G C T G T C A T (A) (G) D (C) (T) G G (C) C A A C G A A C T G T G A T G T G A A A T A T A C T G C G C G T A C A A C G C G C G G G C A C A T A T A C C T I C G C C T A G G T 0 D034 A C T G A C G I T C A C D C T G G A G G C T G T C A (T) C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A (T) A T (A) C (C) T (I) (C) (G) C C (T) (A) (G) (G) T A C T G A C G I T C A C D C T G G A G G C T G T C A (C) C A D G C G G T C A A C G A A C T G T G A T G G G G A G T A T A C T G C G T G T A C A A C G C G C A G G T A C A (G) A T (C) C (T) T (D) (T) (C) C C (C) (G) (A) (C) T 0 D035 (A) C (T) G A (G) G (D) C T A (C) D C T (G) (G) (A) G G (C) (T) G T C A (C) (C) A D G C G G T C A A C G A A C T G T G A T G T G A A A T G T T C T G C A C T T A C A T C G T A C G G (A) C A C (G) G (G) T (A) (C) (C) T (I) (C) C C C (T) G (G) C (C) (G) C (C) G A (C) G (I) C T A (G) D C T (A) (A) (G) G G (T) (G) G T C A (T) (A) A D G C G G T C A A C G A A C T G T G A T G T G A A A T G T T C T G C A C T T A C A T C G T A C G G (G) C A C (A) G (A) T (C) (T) (T) T (D) (T) C C C (C) G (A) C (T) 0 D036 A C T G (A) G G D C T A C D C T G G G G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G (G) G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 D037 A C T G A (C) G (I) (T) (C) A C D C T G G A (G) G C T G T C A T A A D G C G G T C A A C G A A C T G T G A T G T G A A A T A A A T T A C G C G T A C A A C A C G C A G G C A C A (T) (A) T A (C) (C) T (I) C (G) C (C) T (A) G (G) T A C T G A (G) G (D) (C) (T) A C D C T G G A (C) G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A (G) (G) T A (T) (T) T (D) C (C) C (T) T (G) G (C) T 0 D038 A C T G A (C) G (I) (T) (C) A C D C T G G A (G) G C T G T C (A) (C) C A D G C G G T C (A) A C G A A C (T) (G) C G (G) T A (T) (G) G (G) A T (A) T (A) C T G (G) (G) C T (C) (G) (G) (T) (A) C G T A C G G (G) C (C) C A G A T C T T T D T C C C C G A C T A C T G A (G) G (D) (C) (T) A C D C T G G A (C) G C T G T C (G) (T) C A D G C G G T C (G) A C G A A C (C) (A) C G (A) T A (G) (A) G (A) A T (G) T (T) C T G (C) (A) C T (T) (A) (C) (A) (T) C G T A C G G (A) C (A) C A G A T C T T T D T C C C C G A C T 0 D039 A C T G A (C) G I (T) (C) A C D (C) T G G (A) G G C T G T C A T A A D G C G G T C A A C G A A C T G T G A T G T G A A A T A A A T T A C G C G T A C A A C A C G C A G G C A C A T A T A C C T I C G C C T A G G T A C T G A (G) G I (C) (T) A C D (T) T G G (G) G G C T G T C A C C A D G C G G T C A A C G A A C T G T G A T G T G A A A T A T A T T G C G C G T A C A A C G C G C G G G C C C A G A T C T T T D T C C C C G A C T 0 D040 A C T G A (C) G (I) (T) (C) A C D (T) T G G (G) (G) G C T G T C A T A G D G C G G [T] [T] A G T A A A C C A C G A T A T G G A A T A A A T T A C G C G T A C A A C A C G C A G G C A C A G G T A T C T I C C C C T G A C T A C T G A (G) G (D) (C) (T) A C D (C) T G G (A) (C) G C T G T A A T C A I C T G G C C A A C G A A C C G C A A T A G A G A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A T A T A C C T I C G C C T A G G T 0 E001 A C T G A G G D C T A C D C T G G A C G C T (G) T C A T C A D G C G G T C A A C G A A C T G T G A C G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T (A) T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E002 A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C G T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E003 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E004 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A C G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E005 A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T A T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E006 A C T G (A) G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G (C) G A T (A) (T) (A) (G) A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A G G T A T T T D C C A T T G G C T A C T G (G) G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G (T) G A T (G) (G) (G) (A) A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E007 A C T G A (C) G (I) (T) (C) A C D C T G G A (G) G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A (G) G (D) (C) (T) A C D C T G G A (C) G C T G T C A T C A D G C G G T C A A C G A A C C G C A A T A G A G A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A G G T A T T T D C C A T T G G C T 0 E008 A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T A T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E009 A C T G A G G D C T A C D C T G G A C G C T (G) T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A G G T A T T T D C C A T T G G C T A C T G A G G D C T A C D C T G G A C G C T (A) T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E010 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E011 A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A G G T A T T T D C C A T T G G C T A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C C G C A A T A G A G A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A G G T A T T T D C C A T T G G C T 0 E012 A C T G A G G (I) (T) T A C D C T G G A (G) (A) (T) T G T C A T C A D G C G G T C A A C G A A C T G T G A C G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A (G) (G) (C) A (T) (T) T (D) C (C) (A) (T) T (G) G (C) T A C T G A G G (D) (C) T A C D C T G G A (C) (G) (C) T G T C A T C A D G C G G C C G A C G A A C C A C G A T A T A G A A T A A A T T A C G C G T A C A A C A C G C A G G C A C A (T) (A) (T) A (C) (C) T (I) C (G) (C) (C) T (A) G (G) T 0 E013 A C T G (A) G G D C T A C D C (T) G G (A) (C) G C T G T C A T C A D G C G G C C G A C G A A C C A C G A T A T A G A A T A A A T T A C G C G T A C A A C A C G C A G G C A C A T A T A C C T I C G C C T A G G T A C T G (G) G G D C T A C D C (C) G G (G) (G) G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A C A T A T A C C T I C G C C T A G G T 0 E014 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A (T) G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G G G G D C T A C D C C G G G G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A (C) G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E015 A C T G A G G D C T A C D C T G G A C G C T (G) T A A T C A I C T G G C C A A C G A A C C G C A A T A G A G A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T (A) T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E016 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A (T) A T A (C) C T I C (G) C C T A G (G) T A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A (G) A T A (T) C T I C (C) C C T A G (C) T 0 E017 A C T G A G G (I) (T) T A C D C T G G A (G) (A) (T) T (G) T A A T C A I C T G G C C A A C G A A C C G C A A T A G A G A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A (T) (A) T A (C) (C) T (I) C (G) (C) (C) T (A) G (G) T A C T G A G G (D) (C) T A C D C T G G A (C) (G) (C) T (A) T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A (G) (G) T A (T) (T) T (D) C (C) (A) (T) T (G) G (C) T 0 E018 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A (T) G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G G G G D C T A C D C C G G G G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A (C) G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E019 A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G D C T A C D C T G G A C G C T G T C A T C A D G C G G T C A A C G G A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E020 A C T G A G G (D) (C) T A C D C T G G A (C) (G) (C) T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A (C) G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A G G (I) (T) T A C D C T G G A (G) (A) (T) T G T C A T C A I C T G G C C A A C G A A C C G C A A T A G A G A A (T) G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E021 A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G A C G I T C A C D C T G G A G G C T G T C A T C A D G C G G T C A A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E022 A C T G (A) G G D C T A C D C (T) G G (A) (C) G C T G T C A T C A D G C G G C C G A C G A A C T G T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T A C T G (G) G G D C T A C D C (C) G G (G) (G) G C T G T C A T C A D G C G G T C A A C G A A C C A T G A T G G G A A A T G T T C T G C A C T T A C A T C G T A C G G G C A T A T A T A C C T I C G C C T A G G T 0 E023 A C T G A G G D C T A C D C T G G A C G C T G T C A (T) C A D G C G G T C A A C G A A C T G T G A T G (G) G A A A T A A A T T A C G C G T A C A A C A C G C A A G C A C A G G T A T T T D C C A T T G G C T A C T G A G G D C T A C D C T G G A C G C T G T C A (C) C A D G C G G T C A A C G A A C T G T G A T G (T) G A A A T G T T C T G C A C T T A C A T C G T A C G G A C A C A T A T A C C T I C G C C T A G G T 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 D001 = = ? = = = = = C T = G = = = A A G = = = G = = = = = A = = C T = ? ? ? = = T A G G = = = C = G = A T = G = = ? A = A T = = = G = G = = = = A = = C G = = = G = C = = = = ? C = T = D T = = = C G A = = = = ? = = = = = T C = C = = = G G A = = = T = = = = = C = = G C = ? ? ? = = C G A A = = = T = A = G G = A = = ? G = T C = = = A = T = = = = T = = T A = = = A = A = = = = ? A = C = I C = = = T A G = = 0 D002 (A) (C) ? (G) = = (G) (D) = = = = = = = = = (G) = = = = = = = = C C A = = = = ? ? ? = A C G = (G) = T G T = = = G = = A = = = = = = = = = = = = = = = = = = = = = = ? = = A = = = = (G) ? ? ? ? = (G) (D) = (C) = = = = = (C) = (G) (T) ? (C) = = (A) (I) = = = = = = = = = (A) = = = = = = = = T A G = = = = ? ? ? = G T A = (A) = C A C = = = A = = G = = = = = = = = = = = = = = = = = = = = = = ? = = G = = = = (T) ? ? ? ? = (T) (I) = (G) = = = = = (G) = 0 D003 = = ? = = = = = = = = = = = = = = (A) = = = = = = = = C C = = G C G G T C = = ? ? ? ? T = = C = = = = T = G = = = G = = C = = = = = = = G = = = T = = ? T = = = = A = = = = = C T T = D T C = = C = A C ? = = ? = = = = = = = = = = = = = = (G) = = = = = = = = T A = = C T A A C T = = ? ? ? ? C = = T = = = = G = A = = = A = = T = = = = = = = A = = = C = = ? C = = = = C = = = = = A C C = I C G = = T = G G ? 0 D004 = = ? = = = = (I) = = (G) = (I) = = = = (G) (G) = = = = = = G C = = = = = = = = = = = = A (A) G = = = = = = = = T = = = = = = = A = = = = G = G = G = = A T = C ? T = = = = = C = G = = C ? T = D T C = = C G A C = = = ? = = = = (D) = = (A) = (D) = = = = (A) (C) = = = = = = A T = = = = = = = = = = = = G (G) A = = = = = = = = G = = = = = = = T = = = = A = T = A = = T C = T ? C = = = = = T = T = = A ? C = I C G = = T A G G = 0 D005 = = = = = = = (I) = = = = = (T) = = = = = = = ? ? = = = = A = = C T A A C T = ? ? ? ? ? = C A C = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = ? C ? T = D T = = = C G A = = = = = = = = = (D) = = = = = (C) = = = = = = = ? ? = = = = C = = G C G G T C = ? ? ? ? ? = T G T = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = ? A ? C = I C = = = T A G = = 0 D006 = = = = = = = ? (T) = (G) = (I) = = = = (G) (G) = = = = C = = = = = = G C G G T C = = = = = = = T G T = = = G T = = = = = = = = = C = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = (T) (C) = = (C) (G) (A) (C) = = = = = = = = ? (C) = (A) = (D) = = = = (A) (C) = = = = T = = = = = = C T A A C T = = = = = = = C A C = = = A G = = = = = = = = = T = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = (C) (G) = = (T) (A) (G) (G) = 0 D007 = = = = = = = (D) = ? = (C) = = = (G) = (A) (C) = = = = = = = (T) (A) = = = = = = = = = A C = = (A) = T G T = = ? G G G A = = = = = = ? T = = = = = = = = = = = = = = = = = = = = ? = T = = A C C = I C G = = T A G G = = = = = = = = (I) = ? = (G) = = = (A) = (G) (G) = = = = = = = (C) (C) = = = = = = = = = G T = = (G) = C A C = = ? A T A G = = = = = = ? C = = = = = = = = = = = = = = = = = = = = ? = G = = C T T = D T C = = C G A C = 0 D008 = = ? = = = = = = = = = = = = ? ? ? = = = = = T = = = C = = = = = = = = = = = = G = = = = = = = = = G = = = = = A A A T T A = G = G = = (C) = = = = = = = = = = = = (C) = (T) = = (A) (C) (C) = ? (C) (G) = = ? = = (G) = = = ? = = = = = = = = = = = = ? ? ? = = = = = C = = = A = = = = = = = = = = = = A = = = = = = = = = T = = = = = G T T C C G = A = T = = (G) = = = = = = = = = = = = (T) = (G) = = (C) (T) (T) = ? (T) (C) = = ? = = (C) = 0 D009 = = = = = C = = = C = = = T = = = G = G C = = = = A = A G = C T = = (C) = A = = = = = = T G T = = = G = G A = = = G T T C = G = A = T = = ? ? T = G T A = ? = A = = = G = G = A = C = ? C = = = T = G = ? = = = = = G = = = T = = = C = = = A = A T = = = = G = C A = G C = = (T) = G = = = = = = C A C = = = A = A G = = = A A A T = A = G = G = = ? ? A = A C G = ? = G = = = A = A = C = T = ? T = = = C = A = ? 0 D010 (A) (C) (T) (G) = (C) (G) = = (T) = (G) = = = (A) (A) (G) = = = (G) = = = = = = = = = = = = = = = = ? = = = = = = (C) = (G) = (A) = = (G) (A) (G) = = = = = = = (C) = (T) (G) (T) (A) (C) (A) = = = (C) (G) = (A) = = (T) = = (G) = (G) (T) = (C) = = = = = = = = (G) = = (C) (G) (T) (C) (C) = (G) (A) = = (C) = (C) = = = (G) (G) (A) = = = (T) = = = = = = = = = = = = = = = = ? = = = = = = (T) = (A) = (G) = = (A) (G) (A) = = = = = = = (G) = (C) (T) (C) (G) (G) (T) = = = (T) (A) = (G) = = (C) = = (A) = (A) (C) = (T) = = = = = = = = (A) = = (T) 0 D011 = = = = = (C) = = (T) (C) (G) = (I) (C) = = = = = = = (T) = = = G = = = = = = = = C = = = = = = = C T G T = = = G = = A = = = = = T = = = = A = T ? A = = T C = T ? C = = A = = = = T = = A C C = ? C G = = T A G G = = = = = = (G) = = (C) (T) (A) = (D) (T) = = = = = = = (G) = = = A = = = = = = = = T = = = = = = = T C A C = = = A = = G = = = = = A = = = = G = G ? G = = A T = C ? T = = G = = = = G = = C T T = ? T C = = C G A C = 0 D012 = ? ? = = = = = (T) (C) = (C) = = = (G) = (A) = = = (T) = = (A) = = (C) = = (C) (T) = = (C) = = = = = = = = = = (C) = = = (A) = = (G) A = = G (T) T = = = C A = = T A C A T = = = = = = = = = A T = T = T = C = = = = G = = = = = G = = ? ? = = = = = (C) (T) = (G) = = = (A) = (G) = = = (G) = = (C) = = (A) = = (G) (C) = = (T) = = = = = = = = = = (T) = = = (G) = = (A) G = = A (A) A = = = G G = = C G G T A = = = = = = = = = C C = G = C = T = = = = C = = = = = C = 0 D013 = = = = = = = = = = (A) = (D) = = = = (A) = = = = = = (C) (A) (C) (C) = = = = = = = = = = = = = = = (T) (G) (T) = = = (G) = = (A) = A = G = T = = = = A C T = = = = T = = T A ? G = A C = = (A) (T) (A) (T) = (C) ? ? ? = (G) = = = = = (G) ? = = = = = = = = = = (G) = (I) = = = = (G) = = = = = = (A) (G) (T) (A) = = = = = = = = = = = = = = = (C) (A) (C) = = = (A) = = (G) = G = A = A = = = = G T G = = = = A = = C G ? A = G T = = (G) (G) (G) (C) = (T) ? ? ? = (C) = = = = = (C) ? 0 D014 = = ? ? = = = (D) (C) = = = = = = = = = = = = = (G) (T) = = = (C) = = = = = = = = = = = = = = = C = C A = = = G A G A = = = A = T = A C = = G T A C = = = A C G ? A A = = A = = = G = = T T T = = = A T = G = = = = = ? ? = = = (I) (T) = = = = = = = = = = = = = (A) (C) = = = (A) = = = = = = = = = = = = = = = T = T G = = = T G A G = = = T = C = G G = = T C G G = = = G T A ? G G = = C = = = A = = C C G = = = C C = A = = = 0 D015 = = = = = = = = (C) = = = = (T) = = = (G) = (G) (C) (G) = = = = = A = (I) = = = = = = = = ? = ? ? = = = C = G = A T = G = G T A = A = = = = G T G = = = = A = = C G = A = = T = C = (G) (G) = = (T) = = = = (C) = = = (G) = (C) (C) = = = = = = = = (T) = = = = (C) = = = (A) = (A) (T) (T) = = = = = C = (D) = = = = = = = = ? = ? ? = = = T = A = G G = A = A C G = T = = = = A C T = = = = T = = T A = G = = C = T = (T) (A) = = (C) = = = = (G) = = = (A) = (G) (T) 0 D016 = = ? ? = = = (I) = = = = = = ? = = = ? ? ? = = = = = = = = (I) = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = ? = = = A = = ? = G = = = = = G D = C = = = = = C = = = ? ? = = = (D) = = = = = = ? = = = ? ? ? = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = ? = = = G = = ? = T = = = = = T I = G = = = = = G = 0 D033 = = = = = (C) = (I) ? (C) = = = = = = = = (G) = = = = = = = = (C) (A) = (G) (C) = = (T) = = = = = = = = = = C ? = = A = = G = G = = = = = = = = = T T = = = = = = = = = = A = = = = = G G G C = T = = = = C = = = ? = C = = = = = = (G) = (D) ? (T) = = = = = = = = (C) = = = = = = = = (A) (G) = (C) (T) = = (C) = = = = = = = = = = T ? = = G = = A = A = = = = = = = = = C G = = = = = = = = = = G = = = = = A T A T = C = = = = G = = = ? = G = 0 D034 = = = = = = = ? = = ? = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = A = A = G = T ? = = = A C T = = = = T = = T A = G = = C = T = (T) = = (A) = (C) = (I) (C) (G) = = (T) (A) (G) (G) = = = = = = = = ? = = ? = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = G = G = A = A ? = = = G T G = = = = A = = C G = A = = T = C = (G) = = (C) = (T) = (D) (T) (C) = = (C) (G) (A) (C) = 0 D035 (A) = (T) = = (G) = (D) = = = (C) = = = (G) (G) (A) = = (C) (T) = = = = (C) (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = (G) = (G) = (A) (C) (C) = (I) (C) = = = (T) = (G) = (C) (G) = (C) = = (C) = (I) = = = (G) = = = (A) (A) (G) = = (T) (G) = = = = (T) (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = (A) = (A) = (C) (T) (T) = (D) (T) = = = (C) = (A) = (T) 0 D036 = = = = (A) = = = = = = = = = = = = G G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = A C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D037 = = = = = (C) = (I) (T) (C) = = = = = = = = (G) = = = = = = = = A = = = = = = = = = = ? ? ? ? = = = = = = = = T = = = = = A A A T = A = G = G = = = = A = A C G = A = = = = C = (T) (A) = = (C) (C) = (I) = (G) = (C) = (A) = (G) = = = = = = (G) = (D) (C) (T) = = = = = = = = (C) = = = = = = = = C = = = = = = = = = = ? ? ? ? = = = = = = = = G = = = = = G T T C = G = A = T = = = = T = G T A = G = = = = T = (G) (G) = = (T) (T) = (D) = (C) = (T) = (G) = (C) = 0 D038 = = = = = (C) = (I) (T) (C) = = = = = = = = (G) = = = = = = (A) (C) = = = = = = = = = (A) = = = = = = (T) (G) = = (G) = = (T) (G) = (G) = = (A) = (A) = = = (G) (G) = ? (C) (G) (G) (T) (A) = = = = = = = (G) = (C) = = = = = = = = = = = = = = = = = = = = = = = = (G) = (D) (C) (T) = = = = = = = = (C) = = = = = = (G) (T) = = = = = = = = = (G) = = = = = = (C) (A) = = (A) = = (G) (A) = (A) = = (G) = (T) = = = (C) (A) = ? (T) (A) (C) (A) (T) = = = = = = = (A) = (A) = = = = = = = = = = = = = = = = = = = 0 D039 = = = = = (C) = = (T) (C) = = = (C) = = = (A) = = = = = = = = T A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = A = = = = = = = = = = A = = = A = = = A = = T = = A C ? ? I C G = = T A G G = = = = = = (G) = = (C) (T) = = = (T) = = = (G) = = = = = = = = C C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = G = = = = = = = = = = G = = = G = = = C = = G = = C T ? ? D T C = = C G A C = 0 D040 = = ? ? = (C) = (I) (T) (C) ? = = (T) = = = (G) (G) = = = = = C = = A G D G C = ? ? ? = G T A = = = = A = G = = = T G = = = = = = = = = = = = = = = = = = = = = = = = = G = ? = = = G G = = T = = = = C = = = G A C = = = ? ? = (G) = (D) (C) (T) ? = = (C) = = = (A) (C) = = = = = A = = C A I C T = ? ? ? = A C G = = = = G = A = = = G A = = = = = = = = = = = = = = = = = = = = = = = = = A = ? = = = T A = = C = = = = G = = = A G G = 0 E001 = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E003 = = = = = C = I T C = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = D C T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = (A) (T) (A) (G) = = = A A A T = A = G = G = = = = A = A C G = A A = = = C = G G = = T T = D = C A T = G = C = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = (G) (G) (G) (A) = = = G T T C = G = A = T = = = = T = G T A = G G = = = T = T A = = C C = I = G C C = A = G = 0 E007 = = = ? = (C) = (I) (T) (C) = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = ? ? = T = T G = = G = G A = = = G T T C = G = A = T = = = = T = G T A = G G = = = T = T A = = C ? ? ? = G C C = A = G = = = = ? = (G) = (D) (C) (T) = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = ? ? = C = C A = = A = A G = = = A A A T = A = G = G = = = = A = A C G = A A = = = C = G G = = T ? ? ? = C A T = G = C = 0 E008 = = = = = = = = = = ? = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = = ? = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = = T T = D = C A T = G = C = = = ? = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A = = C C = I = G C C = A = G = 0 E010 = = = = = C = I T C = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = D C T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = T G = = G = G A = = = G T T C = G = A = T = = = = T = G T A = G G = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C A = = A = A G = = = A A A T = A = G = G = = = = A = A C G = A A = = = C = = = = = = = = = = = = = = = = = = 0 E012 = = ? = = = = (I) (T) = = = = = = = = = (G) (A) (T) = = = = = = = = = = = = = T = A = = = = = = T G T = = C G G G A = = = G T T C = G = A = T = = = = T = G T A = G = = = = T = (G) (G) (C) = (T) (T) = (D) = (C) (A) (T) = (G) = (C) = = = ? = = = = (D) (C) = = = = = = = = = (C) (G) (C) = = = = = = = = = = = = = C = G = = = = = = C A C = = T A T A G = = = A A A T = A = G = G = = = = A = A C G = A = = = = C = (T) (A) (T) = (C) (C) = (I) = (G) (C) (C) = (A) = (G) = 0 E013 = = ? = (A) = = = = = = = = = (T) = = (A) (C) = = = = = = = = = = = = = = = C = G = = = = = = C A C = = = A T A G = = = A A A T = A = G = G = = = = A = A C G = A = = = = = = = = = = = = = = = = = = = = = = = = = ? = (G) = = = = = = = = = (C) = = (G) (G) = = = = = = = = = = = = = = = T = A = = = = = = T G T = = = G G G A = = = G T T C = G = A = T = = = = T = G T A = G = = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = ? A C = I T ? = = = = T = = A = = = ? ? = = = = = = ? ? ? = ? ? = = = = = = = = = = = = = = = = = = = = (T) = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? ? = = = = = = ? G G = D C ? = = = = C = = G = = = ? ? = = = = = = ? ? ? = ? ? = = = = = = = = = = = = = = = = = = = = (C) = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? ? = = = 0 E015 = = ? = = = = = = = = = = = = = = = = = = = (G) = A = = = ? I C T = = C = = = = = = = = C = C A = = A = A G = = = A A A T = A = G = G = = = = A = A C G = A A = = = C = = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = = = = = = = = = = (A) = C = = = ? D G C = = T = = = = = = = = T = T G = = G = G A = = = G T T C = G = A = T = = = = T = G T A = G G = = = T = = = = = = = = = = = = = ? = = = = 0 E016 = = ? = = C = I T C = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = (C) = = = = (G) = = ? = = (G) = = = ? = = G = D C T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = (T) = = = = (C) = = ? = = (C) = 0 E017 = = = = = = = (I) (T) = = = = = = = = = (G) (A) (T) = (G) = A = = = ? I C T = = C = = = = = = = = C = C A = = A = A G = = = A A A T = A = G = G = = = = A = A C G = A A = = = C = (T) (A) = = (C) (C) = (I) = (G) (C) (C) = (A) = (G) = = = = = = = = (D) (C) = = = = = = = = = (C) (G) (C) = (A) = C = = = ? D G C = = T = = = = = = = = T = T G = = G = G A = = = G T T C = G = A = T = = = = T = G T A = G G = = = T = (G) (G) = = (T) (T) = (D) = (C) (A) (T) = (G) = (C) = 0 E018 = = = ? A C = I T C = = = = T = = A = = = = = ? = = = = = = ? ? = = = = = = = = ? = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? G G = D C T = = = = C = = G = = = = = ? = = = = = = ? ? = = = = = = = = ? = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E020 = = = = = = = (D) (C) = = = = = = = = = (C) (G) (C) = = = = = = = ? D G C = = T = = = = = = = = T = T G = = G = G A = = (C) = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = (I) (T) = = = = = = = = = (G) (A) (T) = = = = = = = ? I C T = = C = = = = = = = = C = C A = = A = A G = = (T) = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E021 = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E022 = = = = (A) = = = = = = = = = (T) = = (A) (C) = = = = = = = = = = = = = = = C = G = = = = = = T G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = (G) = = = = = = = = = (C) = = (G) (G) = = = = = = = = = = = = = = = T = A = = = = = = C A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E023 = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = A A A T = A = G = G = = = = A = A C G = A A G = = = = G G = = T T = D ? C A T = G = C = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = G T T C = G = A = T = = = = T = G T A = G G A = = = = T A = = C C = I ? G C C = A = 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 = = 0.59 0.59 ? 0.59 = = 0.59 0.59 = = = = = = = = = 0.56 = = = = = = = = 0.98 0.98 0.98 = = = = ? ? ? = 0.98 0.98 0.98 = 0.57 = 0.98 0.98 0.98 = = = 0.98 = = 0.98 = = = = = = = = = = = = = = = = = = = = = = ? = = 0.97 = = = = 0.85 ? ? ? ? = 0.85 0.85 = 0.85 = = = = = 0.85 = = = ? = = = = = = = = = = = = = = 0.62 = = = = = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = ? ? ? ? 1.00 = = 1.00 = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = = = = 1.00 = = = 1.00 = = ? 1.00 = = = = 1.00 = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 ? = = ? = = = = 0.66 = = 0.69 = 0.69 = = = = 0.69 0.69 = = = = = = 1.00 1.00 = = = = = = = = = = = = 1.00 0.52 1.00 = = = = = = = = 1.00 = = = = = = = 1.00 = = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 = 1.00 ? 1.00 = = = = = 1.00 = 1.00 = = 1.00 ? 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = = 0.54 = = = = = 0.54 = = = = = = = ? ? = = = = 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 = = = = = = = = = ? 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 = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = 0.62 0.62 = = 0.62 0.62 0.62 0.62 = = = = = = = = 0.56 = ? = 0.56 = = = 0.56 = 0.56 0.56 = = = = = = = 0.64 0.53 = = = = = = = = = 0.96 0.96 = = 0.60 = 0.96 0.96 0.96 = = ? 0.96 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 1.00 = = = ? = = = = = = = = = = = = ? ? ? = = = = = 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 = = = = = = = = = = = = 0.57 = 0.78 = = 0.78 0.78 0.78 = ? 0.78 0.78 = = ? = = 0.78 = = = = = = 1.00 = = = 1.00 = = = 1.00 = = = 1.00 = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 0.64 = 1.00 = = = = = = 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = ? ? 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 0.76 0.76 0.76 = 0.76 0.76 = = 0.74 = 0.76 = = = 0.76 0.76 0.76 = = = 0.76 = = = = = = = = = = = = = = = = ? = = = = = = 0.81 = 0.81 = 0.81 = = 0.81 0.69 0.69 = = = = = = = 0.69 = 0.69 0.69 0.69 0.69 0.69 0.69 = = = 0.69 0.69 = 0.69 = = 0.69 = = 0.61 = 0.61 0.74 = 0.74 = = = = = = = = 0.74 = = 0.74 = = = = = 0.86 = = 0.86 0.86 0.84 = 0.84 0.84 = = = = = = = 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 = = ? ? = = = = = 0.50 0.50 = 0.50 = = = 0.50 = 0.50 = = = 0.50 = = 0.50 = = 0.50 = = 0.50 0.50 = = 0.50 = = = = = = = = = = 0.62 = = = 0.62 = = 0.62 1.00 = = 1.00 0.56 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 = = = = = 1.00 = = = = = = = = = = = 0.56 = 0.56 = = = = 0.56 = = = = = = 0.60 0.53 0.64 0.64 = = = = = = = = = = = = = = = 0.89 0.89 0.89 = = = 0.89 = = 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 = = 0.84 0.84 0.84 0.84 = 0.84 ? ? ? = 0.84 = = = = = 0.84 ? = = ? ? = = = 0.50 0.50 = = = = = = = = = = = = = 0.59 0.90 = = = 0.90 = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 ? 1.00 1.00 = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 = = = = = = = = = = = 0.76 = = = = 0.76 = = = 0.76 = 0.76 0.76 0.82 = = = = = 1.00 = 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 = 1.00 = 0.86 0.86 = = 0.86 = = = = 0.86 = = = 0.86 = 0.86 0.86 = = ? ? = = = 0.51 = = = = = = ? = = = ? ? ? = = = = = = = = 0.67 = = = = = = = = = = = = = = = = = = = 0.81 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 1.00 = = ? = 1.00 = = = = = 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = = 0.55 = 0.55 ? 0.55 = = = = = = = = 0.55 = = = = = = = = 0.75 0.75 = 0.75 0.75 = = 0.75 = = = = = = = = = = 0.91 ? = = 0.91 = = 0.91 = 0.95 = = = = = = = = = 0.95 0.95 = = = = = = = = = = 0.95 = = = = = 0.95 0.95 0.95 0.95 = 0.95 = = = = 0.95 = = = ? = 0.95 = = = = = = = = ? = = ? = = = = = = = = = = = = = = = 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 = 0.81 = = 0.81 = 0.81 = 0.81 0.81 0.81 = = 0.81 0.81 0.81 0.81 = 0.64 = 0.64 = = 0.75 = 0.75 = = = 0.75 = = = 0.75 0.75 0.75 = = 0.66 0.75 = = = = 0.78 0.78 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.78 = = = 0.80 = 0.80 = 0.80 0.74 0.80 = 0.80 0.80 = = = 0.80 = 0.80 = 0.80 = = = = 0.70 = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.77 = 0.77 0.77 0.77 = = = = = = = = 0.77 = = = = = = = = 1.00 = = = = = = = = = = ? ? ? ? = = = = = = = = 1.00 = = = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = 1.00 = 0.75 0.75 = = 0.75 0.75 = 0.75 = 0.75 = 0.75 = 0.75 = 0.75 = = = = = = 0.64 = 0.64 0.64 0.64 = = = = = = = = 0.64 = = = = = = 0.81 0.73 = = = = = = = = = 0.85 = = = = = = 0.85 0.85 = = 0.85 = = 0.53 0.85 = 0.90 = = 0.90 = 0.90 = = = 0.90 0.90 = ? 0.90 0.90 0.90 0.90 0.90 = = = = = = = 0.90 = 0.87 = = = = = = = = = = = = = = = = = = = = = = = = 0.71 = = 0.71 0.71 = = = 0.71 = = = 0.71 = = = = = = = = 0.91 0.91 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = ? ? = 0.89 = 0.89 0.89 0.89 ? = = 0.89 = = = 0.89 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 = ? = = = 0.92 0.92 = = 0.92 = = = = 0.92 = = = 0.92 0.92 0.92 = = = = = = = = = = = = = = = = = = = = = = = 0.70 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.55 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.78 = = = 0.78 0.78 0.78 0.78 = = = 1.00 1.00 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 = = 0.92 0.92 = 0.92 = 0.92 0.92 0.92 = 0.92 = 0.92 = = = = ? = 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 = 0.97 0.97 = = 0.97 ? ? ? = 0.97 0.97 0.97 = 0.97 = 0.97 = = = = = = = = = = = ? = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 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 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = 0.55 0.55 = = = = = = = = = 0.55 0.55 0.55 = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 = = 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 = 0.60 0.60 0.50 = 0.60 0.60 = 0.60 = 0.60 0.60 0.60 = 0.60 = 0.60 = = = ? = 0.63 = = = = = = = = = 0.62 = = 0.62 0.62 = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = ? 1.00 1.00 = 1.00 1.00 ? = = = = 1.00 = = 1.00 = = = ? ? = = = = = = ? ? ? = ? ? = = = = = = = = = = = = = = = = = = = = 0.78 = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = 0.79 = 1.00 = = = ? 1.00 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = ? = = = = = = ? = = 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 = = = 0.51 = = = = 0.51 = = ? = = 0.51 = = = = = = = = 0.55 0.55 = = = = = = = = = 0.55 0.55 0.55 = 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 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = 0.63 0.63 = = 0.63 0.63 = 0.63 = 0.63 0.63 0.63 = 0.63 = 0.63 = = = = ? 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = = = = = ? = = = = = = ? ? = = = = = = = = ? = = = = = = = = = = = = = = 0.78 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 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 = = 0.54 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0.57 = = = = = = = = = 0.57 = = 0.57 0.57 = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.84 = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = 0.94 0.94 = = 0.94 0.94 = 0.94 ? 0.94 0.94 0.94 = 0.94 = 0.94 = END PHASEPROBS