************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 mosc2.phase.inp mosc2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mosc2.phase.out_freqs : haplotype frequency estimates mosc2.phase.out_pairs : most likely haplotype pairs for each individual mosc2.phase.out_recom : estimates of recombination parameters mosc2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 27 Positions of loci: 805 1040 1144 1380 1435 1443 2232 7798 8058 8663 8979 9442 9619 9643 15089 15143 15368 16095 16264 16707 16855 34390 35634 35739 36299 37026 37111 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mosc2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCAGTTGACTTAATAAGCGAACTCGAA 1.000000 2 GCAGTTGACTTTATAAGCGAATTCATA 1.000000 3 GCAGTTGACTTTATAAGCGAATTCATG 5.000000 4 GCAGTTGACTTTATAAGTAAATTCATG 2.000000 5 GCAGTTGGCTTAATAAGCGAGCTCGAA 58.000000 6 GCAGTTGGCTTAATAAGCGAGTTCATG 1.000000 7 GCAGTTGGCTTAATAAGCGAACACGAA 2.000000 8 GCAGTTGGCTTAATAAGTAAGCTGGAA 1.000000 9 GCAGTTGGCTTTATAAGCGAGCTCGAA 1.000000 10 GCAGTTGGCTTTACAAGCGAACTCGAA 1.000000 11 GCAGTTGGCTTTGTAAGCGAACTCGAA 3.000000 12 GCAGTTGGCTTTGTAAGTAAACTCGAA 1.000000 13 GCAGTTGGCTTTGTAAGTAAACAGGAA 4.000000 14 GCAGTTGGCCCAATAGACGGGCTCGAA 2.000000 15 GCAGTTGGCCCAACAGGCGGACTCGAA 1.000000 16 GCAGTTGGTTTAATAAGCGAGCTCGAA 1.000000 17 GCAGTTGGTTTTACCAATAAACTCGAA 2.000000 18 GCGGTTGACTTTATAAGTAAATTCATG 1.000000 19 GGAGTTGACTTAATAAGCGAACTCGAA 1.000000 20 GGAGTTGGCTTAATAAGCGAGCTCGAA 3.000000 21 GGAGTTGGCCCAATAGGCGGACTCGAA 1.000000 22 GGAGTTGGCCCAACAGGCGGACTCGAA 2.000000 23 GGAGTTGGCCCAGTAGGCGGACTCGAA 1.000000 24 GGAGTTGGCCCAGTAGGCGGACACGAA 1.000000 25 GGGGTCGACTTAATAAGTAAGCTGGAA 2.000000 26 GGGGTCGACTTTATAAATAAATTGGAA 1.000000 27 GGGGTCGACCCTATAGGCGGATTCATG 1.000000 28 GGGGTCGGCTTAATAAGCGAGCTCGAA 3.000000 29 GGGGTCGGCTTAATAAGCGAACTCGAA 2.000000 30 GGGGTCGGCTTAATCAATAAGCTCGAA 1.000000 31 GGGGTCGGTTTAATCAATAAGCTCGAA 1.000000 32 GGGGTCGGTTTAATCAATAAACTCGAA 1.000000 33 GGGGTCCGCTTAATAAGCGAGTTCATG 3.000000 34 GGGGTCCGCTTAATAAGTAAACAGGAA 1.000000 35 GGGGTCCGCCCAATAGGCGGACTCGAA 2.000000 36 GGGGTCCGTTTAATAAGCGAGCTCGAA 2.000000 37 GGGGTCCGTTTTACAAGTAAACTCGAA 1.000000 38 GGGGTCCGTTTTACCAATAAACTCGAA 29.000000 39 GGGGTCCGTTTTACCAATAAATTCATG 3.000000 40 GGGGGCGACTTTATAAGTAAATTCATG 2.000000 41 GGGCTCGGCTTAATAAGCGAGCTCGAA 1.000000 42 GGGCTCGGCTTAATAAGTAAACTCGAA 2.000000 43 GGGCTCGGCCCAATAGACGGGCTCGAA 2.000000 44 GGGCTCGGCCCTATAAGTAAATTCATG 1.000000 45 GGGCTCCGCTTAATAAGCGAGCTCGAA 2.000000 46 GGGCGCGACTTAATAAGTAAACTCGAA 1.000000 47 GGGCGCGACTTTATAAGTGAATTCATG 1.000000 48 GGGCGCGACTTTATAAGTAAATTCAAA 1.000000 49 GGGCGCGACTTTATAAGTAAATTCATG 8.000000 50 GGGCGCGGCTTAATAAGCGAGCTCGAA 2.000000 51 GGGCGCGGCTTAATAAGTAAACTCGAA 4.000000 52 GGGCGCGGCTTTATAAGTAAATTCATG 1.000000 53 GGGCGCGGCTTTACAAGTAAACTCGAA 2.000000 54 CGGGTCGGCTTAATAAGCGAGCTCGAA 2.000000 55 CGGGTCGGCTTTGTAAGTGAACAGGAA 1.000000 56 CGGGTCGGCTTTGTAAGTAAACAGGAA 5.000000 57 CGGCGCGACTTTATAAGTAAATTCATA 1.000000 58 CGGCGCGGCTCTATAGACGGGCTCGAA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (9,5) D002: (2,3) D003: (4,16) D004: (3,10) D005: (32,43) D006: (3,43) D007: (25,54) D008: (5,40) D009: (20,18) D010: (29,51) D011: (5,51) D012: (31,49) D013: (5,28) D014: (5,53) D015: (5,14) DY01: (7,57) DY02: (1,25) DY03: (42,46) DY04: (7,11) DY05: (3,5) DY06: (5,34) DY07: (11,11) DY08: (5,52) DY09: (45,51) DY10: (14,27) DY11: (24,58) DY12: (26,44) E101: (5,42) E102: (29,45) E103: (8,56) E104: (28,51) E105: (3,28) E106: (5,5) E107: (5,5) E108: (5,39) E109: (5,5) E110: (5,5) E111: (5,48) E112: (5,30) E113: (41,53) E114: (5,38) E115: (5,5) E116: (38,47) E117: (5,55) E118: (5,5) E119: (5,5) E120: (17,56) E121: (5,38) E122: (5,5) H101: (33,38) H102: (19,33) H103: (20,38) H104: (5,38) H105: (5,5) H106: (38,38) H107: (5,37) H108: (38,49) H109: (5,5) H110: (20,38) H111: (5,54) H112: (36,38) H113: (38,38) H114: (5,36) H115: (5,38) H116: (5,5) H117: (5,17) H118: (5,38) H119: (5,39) H120: (5,5) H121: (5,38) H122: (5,6) X101: (5,38) X102: (22,38) X103: (13,38) X104: (21,35) X105: (38,49) X106: (13,23) X107: (5,38) X108: (5,13) X109: (22,38) X110: (49,56) X111: (38,38) X112: (50,50) X113: (38,56) X114: (5,40) X115: (12,33) X116: (49,49) X117: (4,35) X118: (13,38) X119: (5,49) X120: (38,49) X121: (5,56) X122: (5,38) X123: (5,38) X124: (15,39) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G C A G T T G [G] C T T T [A] T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 D002 G C A G T T G A C T T T A T A A G C G A A T T C A T A G C A G T T G A C T T T A T A A G C G A A T T C A T G 0 D003 G C A G T T G A (C) T T T A T A A G T A A A T T C A T G G C A G T T G G (T) T T A A T A A G C G A G C T C G A A 0 D004 G C A G T T G A C T T T A T A A G C G A A T T C A T G G C A G T T G G C T T T A C A A G C G A A C T C G A A 0 D005 G G G G T C G G T T T A A T C A A T A A (A) C T C G A A G G G C T C G G C C C A A T A G A C G G (G) C T C G A A 0 D006 G C A G T T G A C T T T A T A A G C G A A T T C A T G G G G C T C G G C C C A A T A G A C G G G C T C G A A 0 D007 G G G G T C G A C T T A A T A A G T A A G C T G G A A C G G G T C G G C T T A A T A A G C G A G C T C G A A 0 D008 G C A G T T G G C T T A A T A A G C G A G C T C G A A G [G] [G] [G] [G] [C] G A C T T T A T A A G [T] [A] A A T T C A T G 0 D009 G (G) (A) G T T G G C T T A A T A A G C G A G C T C G A A G (C) (G) G T T G A C T T T A T A A G T A A A T T C A T G 0 D010 G G G G T C G G C T T A A T A A G C G A A C T C G A A G G G C G C G G C T T A A T A A G T A A A C T C G A A 0 D011 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G C G C G G C T T A A T A A G T A A A C T C G A A 0 D012 G G G G T C G G T T T A A T C A A T A A G C T C G A A G G G C G C G A C T T T A T A A G T A A A T T C A T G 0 D013 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C G G C T T A A T A A G C G A G C T C G A A 0 D014 G C A G T T G G C T T A A (T) A A G C G A G C T C G A A G G G C G C G G C T T [T] A (C) A A G T A A A C T C G A A 0 D015 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C C C A A T A G A C G G G C T C G A A 0 DY01 (G) C A G T T G G C T T A A T A A G C G A A C A C G A A (C) G G C G C G A C T T T A T A A G T A A A T T C A T A 0 DY02 G C A G T T G A C T T A A T A A G C G A A C T C G A A G G G G T C G A C T T A A T A A G T A A G C T G G A A 0 DY03 G G G C (T) C G G C T T A A T A A G T A A A C T C G A A G G G C (G) C G A C T T A A T A A G T A A A C T C G A A 0 DY04 G C A G T T G G C T T A A T A A G C G A A C A C G A A G C A G T T G G C T T T G T A A G C G A A C T C G A A 0 DY05 G C A G T T G A C T T T A T A A G C G A A T T C A T G G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 DY06 G (C) (A) G T (T) (G) G C T T A A T A A G (C) (G) A G C T (C) G A A G (G) (G) G T (C) (C) G C T T A A T A A G (T) (A) A A C [A] (G) G A A 0 DY07 G C A G T T G G C T T T G T A A G C G A A C T C G A A G C A G T T G G C T T T G T A A G C G A A C T C G A A 0 DY08 G (C) (A) (G) (T) (T) G G C T T A A T A A G C G A G C T C G A A G (G) (G) (C) (G) (C) G G C T T T A T A A G T A A A T T C A T G 0 DY09 G G G C (T) C (C) G C T T A A T A A G C G A G C T C G A A G G G C (G) C (G) G C T T A A T A A G T A A A C T C G A A 0 DY10 G (C) (A) G T (T) G (G) C C C (A) A T A G (A) C G G G (C) T C (G) (A) (A) G (G) (G) G T (C) G (A) C C C (T) A T A G (G) C G G A (T) T C (A) (T) (G) 0 DY11 (G) G A G T T G G C C C (A) G T A G G C G G A C (A) C G A A (C) G G C G C G G C T C (T) A T A G A C G G G C (T) C G A A 0 DY12 G G G (G) T C G (A) C (T) (T) T A T A A (A) T A A A T T (G) (G) (A) (A) G G G (C) T C G (G) C (C) (C) T A T A A (G) T A A A T T (C) (A) (T) (G) 0 E101 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G C T C G G C T T A A T A A G T A A A C T C G A A 0 E102 G G G (G) T C (G) G C T T A A T A A G C G A A C T C G A A G G G (C) T C (C) G C T T A A T A A G C G A G C T C G A A 0 E103 G C A G T T G G C T T A A T A A G T A A G C T G G A A C G G G T C G G C T T T G T A A G T A A A C A G G A A 0 E104 G G G G T C G G C T T A A T A A G C G A G C T C G A A G G G C G C G G C T T A A T A A G T A A A C T C G A A 0 E105 G (C) (A) G T (T) G A C T T T A T A A G C G A A T T C A T G G (G) (G) G T (C) G G C T T A A T A A G C G A G C T C G A A 0 E106 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E107 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E108 G C A G T T G G C T T A A T A A G C G A G (C) T C (G) (A) (A) G G G G T C C G T T T T A C C A A T A A A (T) T C (A) (T) (G) 0 E109 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E110 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E111 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G C G C G A C T T T A T A A G T A A A T T C A A A 0 E112 G (C) (A) G T (T) G G C T T A A T A A G C G A G C T C G A A G (G) (G) G T (C) G G C T T A A T C A A T A A G C T C G A A 0 E113 G G G C (T) C G G C T T (A) A (T) A A G C G A G C T C G A A G G G C (G) C G G C T T (T) A (C) A A G T A A A C T C G A A 0 E114 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 E115 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E116 G G G G T C C G T T T T A C C A A T (A) A A C T C G A A G G G C G C G A C T T T A T A A G T (G) A A T T C A T G 0 E117 G C A G T T G G C T T A A T A A G C G A G C T C G A A C G G G T C G G C T T T G T A A G T G A A C A G G A A 0 E118 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E119 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 E120 G C A G T T G G T T T T A C C A A T A A A C T C G A A C G G G T C G G C T T T G T A A G T A A A C A G G A A 0 E121 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 E122 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 H101 G G G G T C C G C T T A A T A A G C G A G (T) T C (A) (T) (G) G G G G T C C G T T T T A C C A A T A A A (C) T C (G) (A) (A) 0 H102 G G (A) G T (T) (G) (A) C T T A A T A A G C G A (A) C T C G A A G G (G) G T (C) (C) (G) C T T A A T A A G C G A (G) T T C A T G 0 H103 G G A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H104 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H105 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 H106 G G G G T C C G T T T T A C C A A T A A A C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H107 G (C) (A) G T (T) (G) G (C) T T A A T A A G C G A G C T C G A A G (G) (G) G T (C) (C) G (T) T T T A [C] A A G T A A A C T C G A A 0 H108 G G G G T C C G T T T T A C C A A T A A A C T C G A A G G G C G C G A C T T T A T A A G T A A A T T C A T G 0 H109 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 H110 G G A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H111 G C A G T T G G C T T A A T A A G C G A G C T C G A A C G G G T C G G C T T A A T A A G C G A G C T C G A A 0 H112 G G G G T C C G T T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H113 G G G G T C C G T T T T A C C A A T A A A C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H114 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T A A T A A G C G A G C T C G A A 0 H115 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H116 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 H117 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G T T T T A C C A A T A A A C T C G A A 0 H118 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H119 G C A G T T G G C T T A A T A A G C G A G (C) T C (G) (A) (A) G G G G T C C G T T T T A C C A A T A A A (T) T C (A) (T) (G) 0 H120 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G C T C G A A 0 H121 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 H122 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T A A T A A G C G A G T T C A T G 0 X101 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X102 G G A G T T G G C C C A A C A G G C G G A C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X103 G C A G T T G G C T T T G T A A G T A A A C A G G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X104 G G A G T T G G C C C A A T A G G C G G A C T C G A A G G G G T C C G C C C A A T A G G C G G A C T C G A A 0 X105 G G G G T C C G T T T T A C C A A T A A A C T C G A A G G G C G C G A C T T T A T A A G T A A A T T C A T G 0 X106 G C A G T T G G C T T T G T A A G T A A A C A G G A A G G A G T T G G C C C A G T A G G C G G A C [T] C G A A 0 X107 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X108 G C A G T T G G C T T A A T A A G C G A G C T C G A A G C A G T T G G C T T T G T A A G T A A A C A G G A A 0 X109 G [G] A G T T G G C C C A A C A G G C G G A C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X110 G G G C G C G A C T T T A T A A G T A A A T T C A T G C G G G T C G G C T T T G T A A G T [A] A A C A G G A A 0 X111 G G G G T C C G T T T T A C C A A T A A A C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X112 G G G C G C G G C T T A A T A A G C G A G C T C G A A G G G C G C G G C T T A A T A A G C G A G C T C G A A 0 X113 G G G G T C C G T T T T A C C A A T A A A C T C G A A C G G G T C G G C T T T G T A A G T A A A C A G G A A 0 X114 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G G C G A C T T T A T A A G T A A A T T C A T G 0 X115 G C A G T T G G C T T (T) (G) T A A G (T) (A) A (A) (C) T C (G) (A) (A) G G G G T C C G C T T (A) (A) T A A G (C) (G) A (G) (T) T C (A) (T) (G) 0 X116 G G G C G C G A C T T T A T A A G T A A A T T C A T G G G G C G C G A C T T T A T A A G T A A A T T C A T G 0 X117 G C A G T T G A C T T T A T A A G T A A A T T C A T G G G G G T C C G C C C A A T A G G C G G A C T C G A A 0 X118 G C A G T T G G C T T T G T A A G T A A A C A G G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X119 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G C G C G A C T T T A T A A G T A A A T T C A T G 0 X120 G G G G T C C G T T T T A C C A A T A A A C T C G A A G G G C G C G A C T T T A T A A G T A A A T T C A T G 0 X121 G C A G T T G G C T T A A T A A G C G A G C T C G A A C G G G T C G G C T T T G T A A G T A A A C A G G A A 0 X122 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X123 G C A G T T G G C T T A A T A A G C G A G C T C G A A G G G G T C C G T T T T A C C A A T A A A C T C G A A 0 X124 G [C] A G T T G G C C C A A C A G G C G G A (C) T C (G) (A) (A) G G G G T C C G T T T T A C C A A T A A A (T) T C (A) (T) (G) END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 D001 = = = = = = = ? = = = T ? ? = = = = = = = = = = = = = = = = = = = = ? = = = A ? ? = = = = = = = = = = = = = 0 D002 = ? = = = = = = = = = ? = = = = = = = = = = = = = = A = ? = = = = = = = = = ? = = = = = = = = = = = = = = G 0 D003 = = = = = = = A (C) = = T = = = = = T A = A T = = A T G = = = = = = = G (T) = = A = = = = = C G = G C = = G A A 0 D004 = = = = = = = A = = = = = T = = = = = = = T = = A T G = = = = = = = G = = = = = C = = = = = = = C = = G A A 0 D005 = = = G = = = = T T T = = = C A = T A A (A) = = = = = = = = = C = = = = C C C = = = A G = C G G (G) = = = = = = 0 D006 = C A G = T = A = T T T = = = A G = = A A T ? = A T G = G G C = C = G = C C A = = = G A = = G G C ? = G A A 0 D007 G = = = = = = A = = = = = = = = = T A = = = = G = = = C = = = = = = G = = = = = = = = = C G = = = = C = = = 0 D008 = ? ? ? ? ? = G = ? ? A = = ? ? ? ? ? ? G C = = G A A = ? ? ? ? ? = A = ? ? T = = ? ? ? ? ? ? A T = = A T G 0 D009 = (G) (A) = = = = G = = = A = = ? ? = C ? = G C = = G A A = (C) (G) = = = = A = = = T = = ? ? = T ? = A T = = A T G 0 D010 = = = G T = = = = = = = = = ? ? = C G = = = = = = = = = = = C G = = = = = = = = = ? ? = T A = = = = = = = = 0 D011 = C A G T T = = = = = ? = = = = = C G = G = = = = = = = G G C G C = = = = = ? = = = = = T A = A = = = = = = 0 D012 = = = G T = = G T = = A = = ? ? ? = = ? G C = = G A A = = = C G = = A C = = T = = ? ? ? = = ? A T = = A T G 0 D013 = C A = = T = = = = = = = = = = = = = = = = = = = = = = G G = = C = = = = = = = = = = = = = = = = = = = = = 0 D014 = C A G T T ? = = = = ? = (T) = = = C G = G = ? = = = = = G G C G C ? = = = = ? = (C) = = = T A = A = ? = = = = 0 D015 = = = = = = = = = T T = = = ? ? ? = = A = = ? = = = = = = = = = = = = = C C = = = ? ? ? = = G = = ? = = = = 0 DY01 (G) ? A G T T ? G = = = A ? ? ? ? ? C G ? = C A = G A = (C) ? G C G C ? A = = = T ? ? ? ? ? T A ? = T T = A T = 0 DY02 = C A = = T = = = = = = = = = = = C G = A = = C = = = = G G = = C = = = = = = = = = = = T A = G = = G = = = 0 DY03 = = = = (T) = = G = = = = ? ? = = = = = = = = = = = = = = = = = (G) = = A = = = = ? ? = = = = = = = = = = = = = 0 DY04 = = = = = = = = = = = A A = = = = = = = = = A = = = = = = = = = = = = = = = T G = = = = = = = = = T = = = = 0 DY05 = = = = = = = A = = = T = = = = = = = = A T ? = A T G = = = = = = = G = = = A = = = = = = = = G C ? = G A A 0 DY06 = (C) (A) = = (T) (G) = = = = = = = = = = (C) (G) = G = ? (C) = = = = (G) (G) = = (C) (C) = = = = = = = = = = (T) (A) = A = ? (G) = = = 0 DY07 = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = 0 DY08 = (C) (A) (G) (T) (T) = = = = = A = = = = = C G = G C = = G A A = (G) (G) (C) (G) (C) = = = = = T = = = = = T A = A T = = A T G 0 DY09 = = = = (T) = (C) = = = = = = = = = = C G = G = = = = = = = = = = (G) = (G) = = = = = = = = = = T A = A = = = = = = 0 DY10 = (C) (A) = = (T) = (G) = = = (A) = = = = (A) = = = G (C) = = (G) (A) (A) = (G) (G) = = (C) = (A) = = = (T) = = = = (G) = = = A (T) = = (A) (T) (G) 0 DY11 (G) = A G T T = = = C = (A) G = = = G = = = A = (A) = = = = (C) = G C G C = = = T = (T) A = = = A = = = G = (T) = = = = 0 DY12 = = = (G) = = = (A) = (T) (T) = = = = = (A) = = = = = = (G) (G) (A) (A) = = = (C) = = = (G) = (C) (C) = = = = = (G) = = = = = = (C) (A) (T) (G) 0 E101 = C A G = T = = = = = = = = = = = C G = G = ? = = = = = G G C = C = = = = = = = = = = = T A = A = ? = = = = 0 E102 = = = (G) = = (G) = = = = = = = = = = = = = A ? ? = = = = = = = (C) = = (C) = = = = = = = = = = = = = G ? ? = = = = 0 E103 G C A = = T = = = = = A A = = = = = = = G = ? = = = = C G G = = C = = = = = T G = = = = = = = A = ? = = = = 0 E104 = = = G T = = = = = = = = = = = = C G = G = ? = = = = = = = C G = = = = = = = = = = = = T A = A = ? = = = = 0 E105 = (C) (A) = = (T) = A = = = T = = = = = = = ? A T = = A T G = (G) (G) = = (C) = G = = = A = = = = = = = ? G C = = G A A 0 E106 = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = 0 E107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = C A = = T G = C = = A = T A = G C G = G (C) = = (G) (A) (A) = G G = = C C = T = = T = C C = A T A = A (T) = = (A) (T) (G) 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0 E111 = C A G T T = G = = = A = = = = = C G = G C ? = G = ? = G G C G C = A = = = T = = = = = T A = A T ? = A = ? 0 E112 = (C) (A) = = (T) = = = = = = = = A = G C G ? = = ? = = = = = (G) (G) = = (C) = = = = = = = = C = A T A ? = = ? = = = = 0 E113 = = = = (T) = = = = = = (A) = (T) = = = C G = G = = = = = = = = = = (G) = = = = = = (T) = (C) = = = T A = A = = = = = = 0 E114 = C A = = T G = C = = A = T A = G C G = G = = = = = = = G G = = C C = T = = T = C C = A T A = A = = = = = = 0 E115 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E116 = = = G T = C G T = = = = C C = A = (A) = = C = = G A A = = = C G = G A C = = = = T A = G = (G) = = T = = A T G 0 E117 G C A = = T = = = = = A A = = = = C = = G = T C = = = C G G = = C = = = = = T G = = = = T = = A = A G = = = 0 E118 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0 E119 = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = 0 E120 G C A = = T = = T = = = A C C = A = = = = = ? C = = = C G G = = C = = C = = = G T A = G = = = = = ? G = = = 0 E121 = C A = = T G = C = = A ? ? A = G C G ? ? = = = = = = = G G = = C C = T = = T ? ? C = A T A ? ? = = = = = = 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H101 = = = = = = = = C = = A = T A = G C G = G (T) = = (A) (T) (G) = = = = = = = = T = = T = C C = A T A = A (C) = = (G) (A) (A) 0 H102 = = (A) = = (T) (G) (A) = = = = = = = = = = = = (A) C = = G A A = = (G) = = (C) (C) (G) = = = = = = = = = = = = (G) T = = A T G 0 H103 = = A = = T G = C = = A = T A = G C G = G = = = = = = = = G = = C C = T = = T = C C = A T A = A = = = = = = 0 H104 = C A = = T G = C = = A = T A = G C G = G = = = = = = = G G = = C C = T = = T = C C = A T A = A = = = = = = 0 H105 = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = 0 H106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H107 = (C) (A) = = (T) (G) = (C) = = A ? ? ? ? = C ? = G = = = = = = = (G) (G) = = (C) (C) = (T) = = T ? ? ? ? = T ? = A = = = = = = 0 H108 = = = G T = C ? ? = = = ? ? C = A = = = = C = = G A A = = = C G = G ? ? = = = ? ? A = G = = = = T = = A T G 0 H109 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = 0 H110 = = A = = T G = C = = A ? ? A = G C G = G = = = = = = = = G = = C C = T = = T ? ? C = A T A = A = = = = = = 0 H111 G C A = = T = = = = = = ? ? = = = = ? = = = = = = = = C G G = = C = = = = = = ? ? = = = = ? = = = = = = = = 0 H112 = = = = = = = = = = = A = T A = G C G = G = = = = = = = = = = = = = = = = = T = C C = A T A = A = = = = = = 0 H113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H114 = C A = = T G = C = = = = = = = = = = = = = = = = = = = G G = = C C = T = = = = = = = = = = = = = = = = = = 0 H115 = C A = = T G = C = = A ? ? A = G C G = G = = = = = = = G G = = C C = T = = T ? ? C = A T A = A = = = = = = 0 H116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H117 = = = = = = = = C = = A = T A = G C G = G = = = = = = = = = = = = = = T = = T = C C = A T A = A = = = = = = 0 H118 = C A = = T G = C = = A = T A = G C G = G = = = = = = = G G = = C C = T = = T = C C = A T A = A = = = = = = 0 H119 = C A = = T G = C = = A = T A = G C ? = G (C) = = (G) (A) (A) = G G = = C C = T = = T = C C = A T ? = A (T) = = (A) (T) (G) 0 H120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H121 = C A = = T G = C = = ? ? ? A = G C ? = G = = = = = = = G G = = C C = T = = ? ? ? C = A T ? = A = = = = = = 0 H122 = = = = = = = = = = = = = = = = = = = = = C = = G A A = = = = = = = = = = = = = = = = = = = = = T = = A T G 0 X101 = ? A = = T G = C = = A ? ? A = G C G ? G = = = = = = = ? G = = C C = T = = T ? ? C = A T A ? A = = = = = = 0 X102 = = A = = T G = C C C A = = A G G C G G = = = = = = = = = G = = C C = T T T T = = C A A T A A = = = = = = = 0 X103 = C A = = T G = C = = = G T A = G = = = = = A G = = = = G G = = C C = T = = = A C C = A = = = = = T C = = = 0 X104 = = A = = T G = = = = = = = = = = = = = = = = = = = = = = G = = C C = = = = = = = = = = = = = = = = = = = = 0 X105 = = = G T = C G T = = = = C C = A = = = = ? = = G A A = = = C G = G A C = = = = T A = G = = = = ? = = A T G 0 X106 = C = = = = = = = T T T = = = A = T A A = = ? G = = = = G = = = = = = = C C A = = = G = C G G = = ? C = = = 0 X107 = C A = = T G = C = = A = T A = G C G = G ? = = = = = = G G = = C C = T = = T = C C = A T A = A ? = = = = = 0 X108 = = = = = = = = = = = A A = = = = C G = G = ? C = = = = = = = = = = = = = = T G = = = = T A = A = ? G = = = 0 X109 = ? A = = T G = C C C A = = A G G C G G = = = = = = = = ? G = = C C = T T T T = = C A A T A A = = = = = = = 0 X110 G = = C G = = A = = = = A = = = = ? ? = = T T C A T G C = = G T = = G = = = = G = = = = ? ? = = C A G G A A 0 X111 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X112 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0 X113 G = = = = = C = T = = = ? ? C = A = = = = = T C = = = C = = = = = G = C = = = ? ? A = G = = = = = A G = = = 0 X114 = C A = T T = G = = = A = = ? ? ? C G = G C = = G A A = G G = G C = A = = = T = = ? ? ? T A = A T = = A T G 0 X115 = C A = = T G = = = = (T) (G) = = = = (T) (A) = (A) (C) = = (G) (A) (A) = G G = = C C = = = = (A) (A) = = = = (C) (G) = (G) (T) = = (A) (T) (G) 0 X116 = ? = = = = = = = = = = ? ? = = = = = = = = = = = = = = ? = = = = = = = = = = ? ? = = = = = = = = = = = = = 0 X117 = ? A = = T G A = T T T = = = A = T A A = T = = A T G = ? G = = C C G = C C A = = = G = C G G = C = = G A A 0 X118 = C A = = T G ? ? = ? = G T A = G = ? = = = A G = = = = G G = = C C ? ? = ? = A C C = A = ? = = = T C = = = 0 X119 = ? A G T T = G = = = A = = = = = C G = G C = = G A A = ? G C G C = A = = = T = = = = = T A = A T = = A T G 0 X120 = ? = G T = C G T = = = = C C = A = = = = C = = G A A = ? = C G = G A C = = = = T A = G = = = = T = = A T G 0 X121 G ? A = = T = = = = = A A = = = = C G = G = T C = = = C ? G = = C = = = = = T G = = = = T A = A = A G = = = 0 X122 = ? A = = T G = C = = A = T A = G C G = G = = = = = = = ? G = = C C = T = = T = C C = A T A = A = = = = = = 0 X123 = ? A = = T G = C = = A = T A = G C G = G ? = = = = = = ? G = = C C = T = = T = C C = A T A = A ? = = = = = 0 X124 = ? ? ? ? ? G = C ? ? A = = ? ? G C G ? = (C) ? = (G) (A) (A) = ? ? ? ? ? C = T ? ? T = = ? ? A T A ? = (T) ? = (A) (T) (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 = = = = = = = 0.99 0.74 = = 1.00 = = = = = 0.99 0.99 = 1.00 1.00 = = 1.00 1.00 1.00 = = = = = = = 0.95 = = = = = 0.94 = = = = = = = 1.00 = = 1.00 1.00 1.00 = = = 0.99 = = = = 0.99 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 0.71 = = = = = = = 0.91 0.91 0.91 = 0.91 = 0.99 = 0.99 0.99 0.99 = = = 0.99 0.99 = = 0.99 0.99 0.99 ? = 0.99 0.99 0.99 0.96 = = = = = = 0.99 = = = = = = = = = 1.00 1.00 = = = = 1.00 = = = = ? ? ? ? ? = 1.00 = ? ? 1.00 = = ? ? ? ? ? ? 1.00 1.00 = = 1.00 1.00 1.00 = 0.50 0.51 = = = = 1.00 = = = 1.00 = = ? ? = 1.00 ? = 1.00 1.00 = = 1.00 1.00 1.00 = = = 0.98 0.97 = = = = = = = = = ? ? = 1.00 1.00 = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = = ? = = = = = 0.99 0.99 = 0.99 = = = = = = = = = 0.99 0.99 = = 1.00 0.99 = = 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 ? = = = = ? = 0.78 = = = 1.00 1.00 = 1.00 = ? = = = = = = = = = = = = = 1.00 1.00 = = = ? ? ? = = 1.00 = = ? = = = = 0.60 ? 1.00 1.00 1.00 1.00 ? 0.98 = = = 1.00 ? ? ? ? ? 1.00 1.00 ? = 0.98 0.98 = 0.98 0.98 = = 0.94 0.94 = = 0.94 = = = = = = = = = = = 1.00 1.00 = 0.98 = = 1.00 = = = = = = = 0.74 = = 1.00 = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = 0.97 = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = 1.00 1.00 ? = 1.00 1.00 1.00 = 0.79 0.79 = = 0.79 0.79 = = = = = = = = = = 0.73 0.73 = 0.95 = ? 0.70 = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = 0.77 0.77 0.77 0.77 0.77 = = = = = 1.00 = = = = = 1.00 1.00 = 1.00 0.98 = = 0.98 0.98 0.98 = = = = 0.78 = 0.88 = = = = = = = = = = 1.00 1.00 = 0.99 = = = = = = = 0.84 0.84 = = 0.84 = 0.88 = = = 0.70 = = = = 0.89 = = = 0.90 0.71 = = 0.71 0.71 0.71 0.72 = 1.00 1.00 1.00 1.00 = = = 0.94 = 0.76 0.99 = = = 1.00 = = = 1.00 = 0.75 = = = = = = = 0.69 = = = 0.69 = 0.67 0.67 = = = = = 0.68 = = = = = = 0.82 0.83 0.83 0.83 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = 0.92 0.92 = 0.92 = ? = = = = = = = 0.90 = = 0.70 = = = = = = = = = = = = = 0.96 ? ? = = = = 0.94 0.94 0.94 = = 0.94 = = = = = 1.00 1.00 = = = = = = = 1.00 = ? = = = = = = = 0.96 0.94 = = = = = = = = = = = = 1.00 1.00 = 0.99 = ? = = = = = 0.79 0.79 = = 0.79 = 1.00 = = = 1.00 = = = = = = = ? 1.00 1.00 = = 1.00 1.00 1.00 = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 0.96 = = 0.96 0.96 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 0.54 = = 0.54 0.54 0.54 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0.98 0.98 0.98 0.98 0.98 = 1.00 = = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 ? = 1.00 = ? = 0.63 0.63 = = 0.63 = = = = = = = = 1.00 = 1.00 1.00 1.00 ? = = ? = = = = = = = = 0.75 = = = = = = 0.63 = 0.74 = = = 0.98 0.98 = 1.00 = = = = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 = 0.53 = = 1.00 = = 1.00 1.00 1.00 0.97 0.97 0.97 = = 0.97 = = = = = 1.00 1.00 = = = = 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = 0.96 0.96 0.96 = = 0.96 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = = = ? 1.00 = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = 1.00 ? ? 1.00 = 1.00 1.00 1.00 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 0.72 = = 0.72 0.72 0.72 = = 0.88 = = 0.88 0.89 0.82 = = = = = = = = = = = = 0.79 0.92 = = 0.92 0.92 0.92 = = 0.99 = = 0.99 0.99 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.73 0.73 = = 0.73 0.73 = 0.73 = = 1.00 ? ? ? ? = 0.97 ? = 0.97 = = = = = = = = = 1.00 1.00 = 1.00 ? ? = = = ? ? 1.00 = 1.00 = = = = 0.98 = = 0.98 0.98 0.98 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = 0.99 = = 0.99 0.99 = 1.00 = = 1.00 ? ? 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = 0.99 1.00 1.00 = = 1.00 = = = = = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 1.00 = 0.98 = = = = = = = = = = = = = = = = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = 1.00 ? ? 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = 0.96 0.96 = = 0.96 0.96 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 ? = 1.00 0.55 = = 0.55 0.55 0.55 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = ? ? ? 1.00 = 1.00 1.00 ? = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = ? 0.99 = = 0.99 1.00 = 1.00 = = 1.00 ? ? 1.00 = 1.00 1.00 1.00 ? 1.00 = = = = = = = = 0.99 = = 0.99 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = = = = = 1.00 = = 1.00 0.99 = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = ? = = 1.00 1.00 1.00 = 0.99 = = = = = = = 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = = ? 1.00 = = = = 0.99 0.99 = = 0.99 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 ? = = = = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 1.00 = 1.00 = ? 1.00 = = = = ? 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 = = = = 1.00 = = = = ? ? = = 1.00 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 = 0.91 0.92 = 1.00 = = = 1.00 = = ? ? ? 0.99 0.99 = 1.00 1.00 = = 1.00 1.00 1.00 = 0.97 0.97 = = 0.97 0.97 = = = = 0.80 0.80 = = = = 0.80 0.80 = 0.80 0.74 = = 0.74 0.74 0.74 = ? = = = = = = = = = = ? ? = = = = = = = = = = = = = = ? 0.92 = = 0.92 0.92 1.00 = 0.99 0.99 1.00 = = = 0.99 = 0.99 0.99 0.99 = 1.00 = = 1.00 1.00 1.00 = 0.99 0.99 = = 0.99 0.99 ? ? = ? = 1.00 1.00 1.00 = 1.00 = ? = = = 1.00 1.00 = = = = ? 0.98 0.98 0.98 0.98 = 1.00 = = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = ? = 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = 1.00 = = 1.00 1.00 1.00 0.95 ? 0.95 = = 0.95 = = = = = 1.00 1.00 = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = = ? 0.99 = = 0.99 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = ? 0.99 = = 0.99 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 ? = = = = = = ? ? ? ? ? 1.00 = 1.00 ? ? 1.00 = = ? ? 1.00 1.00 1.00 ? = 0.68 ? = 0.68 0.68 0.68 END PHASEPROBS