************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mpgxx.phase.inp mpgxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mpgxx.phase.out_freqs : haplotype frequency estimates mpgxx.phase.out_pairs : most likely haplotype pairs for each individual mpgxx.phase.out_recom : estimates of recombination parameters mpgxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 32 Positions of loci: 323 570 573 651 652 800 1700 1738 1775 1973 2017 2028 2405 2947 2948 3331 3414 3604 3644 3860 4220 4985 4996 5260 6363 6696 7191 7207 7495 8892 9008 9638 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mpgxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGCCGGTDACDACGTTGACTGGAAAAAGCTGC 2.000000 2 CGCCGGTDACDACACTGACTGGAGAAAGTTGC 2.000000 3 CGCCGGTDACDACACTGACTGGAGAAAGCTGC 49.000000 4 CGCCGGTDACDACACTGACTGGAGAAAGCTGT 1.000000 5 CGCCGGTDACDACACTGACTGGAGAAAGCCAT 4.000000 6 CGCCGGTDACDACACTGACTGGAAAAAGCTGC 33.000000 7 CGCCGGTDACDACACTGACTGGAAAAAGCCAT 3.000000 8 CGCCGGTDACDACACTGACTGGAATGCACTGT 4.000000 9 CGCCGGTDACDACACTGACTGGGGAGCGCTGC 1.000000 10 CGCCGGTDACDACACTGACTGGGAAAAGCTGC 2.000000 11 CGCCGGTDACDACACTGACTGGGATGCGCTGC 1.000000 12 CGCCGGTDACDACACTGACTGGGATGCACTGC 2.000000 13 CGCCGGTDACDACACTGACTGGGATGCACTGT 1.000000 14 CGCCGGTDACDACACTGACTGCAGTGCACTGT 1.000000 15 CGCCGGTDACDACACTGACTGCGAAAAGCTGC 1.000000 16 CGCCGGTDACDACACTGACCGGAGAAAGCTGC 1.000000 17 CGCCGGTDACDACACTCACTGGAGAAAGCTGC 6.000000 18 CGCCGGTDACDATACTGACTGGAGAAAGCTGC 1.000000 19 CGCCGGTDACDATACTGACTGGAAAAAGCTGC 3.000000 20 CGCCGGCIGTIGCGTTGACCGGAGTGCATCAT 2.000000 21 CGCTGGTDACDACACTGACTGGAAAAAGCTGC 1.000000 22 CGCTGGCIATDGTGTCCGGCGGGGAAAGCTGC 1.000000 23 CGCTGGCIATDGTGTCCGGCGCAAAGAGCTGC 1.000000 24 CGCTGGCIATDGTACTGACCGCAGTGCACTGT 1.000000 25 CATCGGTDACDACACCCGGCAGAATGCACTGT 1.000000 26 CATTGGTDACDACACCCGGCAGGGAGAGCTGC 1.000000 27 CATTGACIGTIGTGTCCGGCGGGAAGCGCTGC 1.000000 28 GGCCGGCDACDACACTCAGCGGAGTGCATCAT 2.000000 29 GGCCGGCDACDACACTCAGCGGAATGCACTGC 1.000000 30 GGCCGGCDACDACACTCAGCGCGGTGCATCAT 1.000000 31 GGCCGGCDACDACACTCAGCGCGAAAAGCTGC 1.000000 32 GGCCGGCDACDACACTCAGCGCGATGCATCAT 13.000000 33 GGCCGGCDACDACACTCAGCGCGATGCACTGT 1.000000 34 GATTGGCIATDGTGTCCGGCACGGAAAGCTGC 1.000000 35 GATTGGCIGTIGCACTGACCGCAGTGCACTGT 3.000000 36 GATTGGCIGTIGCACTGACCGCGATGCATCAT 1.000000 37 GATTGGCIGTIGCACTGACCGCGATGCACTGT 1.000000 38 GATTGACIGCDATGTTGACTGGGATGCATCAT 1.000000 39 GATTGACIGTIGCGTTGACTGGGAAAAGCTGC 1.000000 40 GATTGACIGTIGTGTTGACTGGAGAAAGCTGC 1.000000 41 GATTGACIGTIGTGTTGACTGGAAAAAGCTGC 7.000000 42 GATTGACIGTIGTGTCCGGCGGGAAGAGTTGC 1.000000 43 GATTGACIGTIGTGTCCGGCGGGAAGCACTGC 2.000000 44 GATTGACIGTIGTACTGACTGGAAAAAGCTGC 1.000000 45 GATTCGTDACDATGTTGACTGCAGTGCACTGT 1.000000 46 GATTCGCIATDGTGTCCGGCGCGATGCATCAT 1.000000 47 GATTCGCIATDGTGTCCGGCGCGATGCACTGC 1.000000 48 GATTCGCIATDGTGTCCGGCACAGTGCACTGT 2.000000 49 GATTCGCIATDGTGTCCGGCACAATGCACTGT 1.000000 50 GATTCGCIATDGTGTCCGGCACGGAAAGTTGC 1.000000 51 GATTCGCIATDGTGTCCGGCACGGAAAGCTGC 3.000000 52 GATTCGCIATDGTGTCCGGCACGATGCACTGT 3.000000 53 GATTCGCIATDGTACCCGGCACAGTGCACTGT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (3,3) P002: (6,29) P003: (42,46) P004: (27,43) P005: (6,7) P006: (3,6) P007: (6,41) P008: (6,41) P009: (6,10) P010: (5,19) P011: (48,52) P012: (8,32) P013: (6,7) P014: (6,19) P015: (3,14) P016: (1,41) P017: (33,36) P018: (48,51) P019: (3,32) P020: (6,8) P021: (26,51) P022: (17,35) P023: (6,32) P024: (3,17) P025: (6,17) P026: (1,6) P027: (6,6) P028: (3,3) P029: (23,49) P030: (6,32) P031: (3,17) P032: (20,37) P033: (2,28) P034: (3,6) P035: (3,5) P036: (30,32) P037: (3,32) P038: (3,11) P039: (3,32) P040: (3,3) P041: (10,38) P042: (20,50) P043: (15,31) P044: (3,5) P045: (6,7) P046: (3,6) P047: (3,32) P048: (6,6) P049: (2,32) P050: (16,52) P051: (3,3) P052: (3,28) P053: (6,21) P054: (3,19) P055: (4,41) P056: (8,12) P057: (8,25) P058: (3,6) P059: (45,47) P060: (3,6) P061: (35,53) P062: (3,6) P063: (6,32) P064: (34,51) P065: (22,35) P066: (3,17) P067: (3,3) P068: (3,41) P069: (41,41) P070: (3,17) P071: (3,6) P072: (3,32) P073: (6,40) P074: (32,39) P075: (6,44) P076: (3,9) P077: (3,3) P078: (6,32) P079: (3,6) P080: (24,43) P081: (3,6) P082: (3,5) P083: (3,3) P084: (3,3) P085: (3,3) P086: (3,6) P087: (12,13) P088: (3,18) P089: (6,52) P090: (3,3) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P002 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G G C C G G C D A C D A C A C T C A G C G G A A [T] G C A C T G C 0 P003 [G] A T T G A C I G T I G T G T C C G G C G G G A A G A G T T G C [G] [A] [T] T [C] G C I A T D G T G T C C G G C G [C] [G] [A] T G C A T C A T 0 P004 C A T T G A C I G T I G T G T C C G G C G G G A [A] G C G [C] T G C G A T T G A C I G T I G T G T C C G G C G G G A A G C A C T G C 0 P005 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C C A T 0 P006 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P007 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G A T T G A C I G T I G T G T T G A C T G G A A A A A G C T G C 0 P008 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G A T T G A C I G T I G T G T T G A C T G G A A A A A G C T G C 0 P009 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G G A A A A G C T G C 0 P010 C G C C G G T D A C D A (C) A C T G A C T G G A [G] A A A G C C A T C G C C G G T D A C D A (T) A C T G A C T G G A [A] A A A G C T G C 0 P011 G A T T C G C I A T D G T G T C C G G C A C [A] [G] T G C A C T G T G A T T C G C I A T D G T G T C C G G C A C [G] [A] T G C A C T G T 0 P012 C G C C G G T D A C D A C A C T G A C T G G A A T G C A C T G T G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P013 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C C A T 0 P014 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A T A C T G A C T G G A A A A A G C T G C 0 P015 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G C C G C C G G T D A C D A C A C T G A C T G C A G T G C A C T G T 0 P016 C G C C G G T D A C D A C G T T G A C T G G A A A A A G C T G C G A T T G A C I G T I G T G T T G A C T G G A A A A A G C T G C 0 P017 G G C C G G C D A C D A C A C T C A G C G C G A T G C A [C] T G T G A T T G G C I G [T] I G C A C T G A C C G C G A T G C A T C A T 0 P018 G A T T C G C I A T D G T G T C C G G C A C A G T G C A C T G T G A T T C G C I A T D G T G T C C G G C A C G G A A A G [C] T G C 0 P019 C G C C G G T D A C D A C A C T G A C T G G A (G) A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G (A) T G C A T C A T 0 P020 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A T G C A C T G T 0 P021 C A T [T] G [G] T D A C D A C A C C C G G C A G G G A G A G [C] T G C G A T T [C] G C I A T D G T G T C C G G C A C G G A A A G [C] T G C 0 P022 C G C C G G T D A C D A C A C T C A C T G G A G A A A G C T G C G A T T G G C I G [T] I G C A C T G A C C G C A G T G C A C T G T 0 P023 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P024 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T C A C T G G A G A A A G C T G C 0 P025 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T C A C T G G A G A A A G C T G C 0 P026 C G C C G G T D A C D A C G T T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P027 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P028 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P029 (C) (G) (C) T G G C I A T D G T G T C C G G C (G) C A A (A) G (A) (G) C T G (C) (G) (A) (T) T C G C I A T D G T G T C C G G C (A) C A A (T) G (C) (A) C T G (T) 0 P030 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P031 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T C A C T G G A G A A A G C T G C 0 P032 C G C C G G C I G T I G C G T T G A C C G G A G T G C A T C A T G A T T G G C I G T I G C A C T G A C [C] G C G A T G C A C T G T 0 P033 C G C C G G T D A C D A C A C T G A C T G G A G A A A G T T G C G G C C G G C D A C D A C A C T C A G C G G A G T G C A T C A T 0 P034 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P035 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C C A T 0 P036 G G C C G G C D A C D A C A C T C A G C G C G G T G C A T C A T G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P037 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G [A] T G C A T C A T 0 P038 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G [G] [A] T G C G C T G C 0 P039 C G C C G G T D A C D A C A C T G A C T G G A (G) A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G (A) T G C A T C A T 0 P040 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P041 [C] [G] [C] [C] G G (T) (D) (A) C D A (C) (A) (C) T G A C T G G G A (A) (A) (A) (G) [C] T (G) (C) [G] [A] [T] [T] G [A] (C) (I) (G) C D A (T) (G) (T) T G A C T G G G A (T) (G) (C) (A) [T] [C] (A) (T) 0 P042 C G C C G G C I G T I G C G T T G A C C G G A G T G C A T C A T G A T T C G C I A T D G T G T C C G G C A C G G A A A G T T G C 0 P043 C G C C G G T D A C D A C A C T G A C T G C G A A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G A A A A G C T G C 0 P044 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C C A T 0 P045 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C C A T 0 P046 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P047 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G C G G C C G G C D A C D A C A C T C A G C G [C] [G] [A] T G C A T C A T 0 P048 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P049 C G C C G G T D A C D A C A C T G A C T G G A G A A A G T T G C G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P050 C G C C G G T D A C D A C A C T G A C C G G (A) [G] A A A G C T G C G A T T C G C I A T D G T G T C C G G C A C (G) [A] T G C A C T G T 0 P051 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P052 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C G G C C G G C D A C D A C A C T C A G C G G A G T G C A T C A T 0 P053 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C C G C T G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P054 C G C C G G T D A C D A (C) A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A (T) A C T G A C T G G A [A] A A A G C T G C 0 P055 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G (T) G A T T G A C I G T I G T G T T G A C T G G A A A A A G C T G (C) 0 P056 C G C C G G T D A C D A C A C T G A C T G G A A T G C A C T G T C G C C G G T D A C D A C A C T G A C T G G G A T G C A C T G C 0 P057 C G C C G G T D A C D A C A C T G A C T G G A A T G C A C T G T C [A] [T] C G G T D A C D A C A C C C G G C A G A [A] T G C A C T G T 0 P058 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P059 G A T T C G T D A C D A T G T T G A C T G C (A) [G] T G C A C T G (T) G A T T C G C I A T D G T G T C C G G C G C (G) [A] T G C A C T G (C) 0 P060 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P061 G A T T (G) G C I (G) [T] (I) G (C) A C T G A C C G C A G T G C A C T G T G A T T (C) G C I (A) T (D) G (T) A C C C G G C A C A G T G C A C T G T 0 P062 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A [A] A A A G C T G C 0 P063 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P064 [G] A T T G [G] C I A T D G T G T C C G G C A C G G A A A G C T G C G A T T C G C I A T D G T G T C C G G C A C G G A A A G C T G C 0 P065 C G C [T] G G C I A T D G T G T C C G G C G G G G A A A G C T G C G A T T G G C I G [T] I G C A C T G A C C G C A G T G C A C T G T 0 P066 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G C C G C C G G T D A C D A C A C T C A C T G G A G A A A G C T G C 0 P067 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P068 C G C C G G T D A C D A C A C T G A C T G G A [G] A A A G C T G C G A T T G A C I G T I G T G T T G A C T G G A [A] A A A G C T G C 0 P069 G A T T G A C I G T I G T G T T G A C T G G A A A A A G C T G C G A T T G A C I G T I G T G T T G A C T G G A A A A A G C T G C 0 P070 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T C A C T G G A G A A A G C T G C 0 P071 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P072 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P073 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G A T T G A C I G T I G T G T T G A C T G G A G A A A G C T G C 0 P074 G G C C G G C D A C D A C A C T C A G C G C G [A] T G C A T C A T G A T T G A C I G T I G C G T T G A C T G G G [A] A A A G C T G C 0 P075 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G A T T G A C I G T I G T A C T G A C T G G A A A A A G C T G C 0 P076 C G C C G G T D A C D A C A C T G A C T G G (A) G A A (A) G C T G C C G C C G G T D A C D A C A C T G A C T G G (G) G A G (C) G [C] T G C 0 P077 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P078 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G G C C G G C D A C D A C A C T C A G C G C G A T G C A T C A T 0 P079 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P080 C G C T G G C I A T D G T [A] [C] T G A C C G C A G T G C A C T G T G A T T G A C I G T I G T G T C C G G C G G G A A G C A C T G C 0 P081 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P082 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C C A T 0 P083 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P084 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P085 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C 0 P086 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C 0 P087 C G C C G G T D A C D A C A C T G A C T G G G A T G C A C T G C C G C C G G T D A C D A C A C T G A C T G G G [A] T G C A C T G T 0 P088 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A T A C T G A C T G G A G A A A G C T G C 0 P089 C G C C G G T D A C D A C A C T G A C T G G A A A A A G C T G C G A T T C G C I A T D G T G T C C G G C A C G A T G C A C T G T 0 P090 C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C C G C C G G T D A C D A C A C T G A C T G G A G A A A G C T G C END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 P001 ? = = = = ? = = = = = = = ? ? = = = = = = = = = ? = = = ? ? = ? ? = = = = ? = = = = = = = ? ? = = = = = = = = = ? = = = ? ? = ? 0 P002 C = = = = ? T = = = = = = ? ? = G = C ? = = = = ? A A G ? = = = G = = = = ? C = = = = = = ? ? = C = G ? = = = = ? G C A ? = = = 0 P003 ? ? ? ? ? ? ? = ? ? I = = ? ? = = = = = = ? ? ? ? = A G = T G C ? ? ? ? ? ? ? = ? ? D = = ? ? = = = = = = ? ? ? ? = C A = C A T 0 P004 C = = = = ? ? = ? = = = = = = = = = = ? = = = = ? = = G ? = = ? G = = = = ? ? = ? = = = = = = = = = = ? = = = = ? = = A ? = = ? 0 P005 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? ? G C = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? ? A T 0 P006 = = = = = ? ? = = = = = = = = = = = = = = = = G = = = = = ? ? = = = = = = ? ? = = = = = = = = = = = = = = = = A = = = = = ? ? = 0 P007 C G C C = ? ? D ? ? D A C A C = = = = = = = = = = = = = = = = = G A T T = ? ? I ? ? I G T G T = = = = = = = = = = = = = = = = = 0 P008 ? ? C ? ? ? ? D ? ? D A C A C = = = = ? = = = = = = = = = = = = ? ? T ? ? ? ? I ? ? I G T G T = = = = ? = = = = = = = = = = = = 0 P009 ? ? ? = = = = = = = = = = = = = = = = = = = A = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = G = = = = = = = = = 0 P010 = = = = = = = = = = = = (C) = = = = = = = = = = ? = = = = = C A T = = = = = = = = = = = = (T) = = = = = = = = = = ? = = = = = T G C 0 P011 = = = = = ? = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = ? ? ? = = = = = = = = 0 P012 C = = = = ? T = = = = = = = = = G = C T = G A = = = = = ? T G = G = = = = ? C = = = = = = = = = C = G C = C G = = = = = ? C A = 0 P013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C A T 0 P014 = = = = = ? = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = T = = = = = = = = = = = = = = = = = = = 0 P015 = = = = = ? = = = = = = = = = = = = = = = G = ? A A A G = = = C = = = = = ? = = = = = = = = = = = = = = = C = ? T G C A = = = T 0 P016 C G C ? = ? ? ? ? ? ? ? C = = = = = = = = = = = = = = = ? = = = G A T ? = ? ? ? ? ? ? ? T = = = = = = = = = = = = = = = ? = = = 0 P017 = ? ? ? ? ? = D ? ? D A = = = = C = G = = = = = = = = = ? ? G = = ? ? ? ? ? = I ? ? I G = = = = G = C = = = = = = = = = ? ? A = 0 P018 = = = = = ? = = = = = = = = = = = = = = = = A = T G C A ? = = T = = = = = ? = = = = = = = = = = = = = = = = G = A A A G ? = = C 0 P019 ? ? ? ? ? ? ? = = = = = = = = = G = C T = G A (G) A A A G C T G C ? ? ? ? ? ? ? = = = = = = = = = C = G C = C G (A) T G C A T C A T 0 P020 = = = = = ? = = = = = = = = = = = = = = = = = = A A A G ? = = C = = = = = ? = = = = = = = = = = = = = = = = = = T G C A ? = = T 0 P021 C = = ? ? ? T D = C = A C A C = = = = ? = G = = = G = = ? = = = G = = ? ? ? C I = T = G T G T = = = = ? = C = = = A = = ? = = = 0 P022 C G C ? = ? T D ? ? D A = = = = C = = T = G = = A A A G = = = C G A T ? = ? C I ? ? I G = = = = G = = C = C = = T G C A = = = T 0 P023 C = = = = ? T = = = = = = = = = G = C T = G A = A A A G C T G C G = = = = ? C = = = = = = = = = C = G C = C G = T G C A T C A T 0 P024 = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = 0 P025 ? ? ? ? ? ? = = = = = = = ? ? = G = = = = = = A ? = = = = ? = = ? ? ? ? ? ? = = = = = = = ? ? = C = = = = = = G ? = = = = ? = = 0 P026 = = = = = = = = = = = = ? G T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? A C = = = = = = = = = = = = = = = = = 0 P027 ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P028 ? = = = = ? = = = = = = = = = = = = = = = ? ? = = = = = ? = = = ? = = = = ? = = = = = = = = = = = = = = = ? ? = = = = = ? = = = 0 P029 (C) (G) (C) = G ? = = = = = = = = = = = = = = (G) = = = (A) = (A) (G) = = = (C) (G) (A) (T) = C ? = = = = = = = = = = = = = = (A) = = = (T) = (C) (A) = = = (T) 0 P030 C = = = = ? ? = = = = = = = = = G = C ? = G A = A A A G C T G C G = = = = ? ? = = = = = = = = = C = G ? = C G = T G C A T C A T 0 P031 = = = = = ? = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = C = = = = = = = = = = = = = = = 0 P032 ? G C C = = = = = = = = = G T = = = = ? = G A G = = = = T C A = ? A T T = = = = = = = = = A C = = = = ? = C G A = = = = C T G = 0 P033 ? ? ? ? ? ? T = = = = = = = = = G = C T = = = ? A A A G = T G C ? ? ? ? ? ? C = = = = = = = = = C = G C = = = ? T G C A = C A T 0 P034 = = = = = ? = = = = = = = = = = = = = = = = = G = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = = A = = = = = ? = = 0 P035 = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = T G C = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = C A T 0 P036 = = = = = = = = = = = = = = = = = = = = = = = G = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = ? = = 0 P037 C = = = = = T = = = = = = = = = G = C ? = G A ? A A A G ? ? ? C G = = = = = C = = = = = = = = = C = G ? = C G ? T G C A ? ? ? T 0 P038 = = = = = ? = = = = = = = = = = = = = = = = ? ? A A A = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? ? T G C = = = = = 0 P039 C = = = = ? T = = = = = = = = = G = C ? = G A (G) A A A G C T G C G = = = = ? C = = = = = = = = = C = G ? = C G (A) T G C A T C A T 0 P040 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P041 ? ? ? ? ? ? (T) (D) (A) = = = (C) (A) (C) = = = = = = = = = (A) (A) (A) (G) ? ? (G) (C) ? ? ? ? ? ? (C) (I) (G) = = = (T) (G) (T) = = = = = = = = = (T) (G) (C) (A) ? ? (A) (T) 0 P042 C G C C G = = = G ? I = C = ? T G A C = G G A = T G C A = C A T G A T T C = = = A ? D = T = ? C C G G = A C G = A A A G = T G C 0 P043 C ? ? = = = T = = = = = = = = = G = C ? = = = = = = = = = = = = G ? ? = = = C = = = = = = = = = C = G ? = = = = = = = = = = = = 0 P044 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? T G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? C A T 0 P045 = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = T G C = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = C A T 0 P046 = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = ? = 0 P047 C = = = = = T = = = = = = = = = G = C T ? ? ? ? A A A G C T G C G = = = = = C = = = = = = = = = C = G C ? ? ? ? T G C A T C A T 0 P048 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P049 C ? ? ? ? ? T = = = = = = ? ? ? ? ? ? ? = ? A G A A A G = T G C G ? ? ? ? ? C = = = = = = ? ? ? ? ? ? ? = ? G A T G C A = C A T 0 P050 C G C C G ? ? D = C = A C A C T G A C = G G (A) ? A A A G = = = C G A T T C ? ? I = T = G T G T C C G G = A C (G) ? T G C A = = = T 0 P051 ? = = ? ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = ? = = ? ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = 0 P052 C = = = = ? T = = = = = = = = = G = C T = = = = A A A G C T G C G = = = = ? C = = = = = = = = = C = G C = = = = T G C A T C A T 0 P053 = = = C = ? = = = = = = = ? ? = = = = = = = = = = = = = = ? ? = = = = T = ? = = = = = = = ? ? = = = = = = = = = = = = = = ? ? = 0 P054 = = = = = ? = = = = = = (C) = = = = = = = = ? ? ? = = = = = = = = = = = = = ? = = = = = = (T) = = = = = = = = ? ? ? = = = = = = = = 0 P055 C G C C = ? ? ? ? ? D A C A C = = = = = = ? ? ? = = = = = = = (T) G A T T = ? ? ? ? ? I G T G T = = = = = = ? ? ? = = = = = = = (C) 0 P056 = = = = = ? = = = = = = = = = = = = = = = = A = = = = = = = = T = = = = = ? = = = = = = = = = = = = = = = = G = = = = = = = = C 0 P057 ? ? ? ? ? ? = = = = = = = = = T G A C T G = = ? = = = = ? = = = ? ? ? ? ? ? = = = = = = = = = C C G G C A = = ? = = = = ? = = = 0 P058 = ? ? ? ? = = = = = = = ? ? ? ? ? = = = = = = G = = = = = = = = = ? ? ? ? = = = = = = = ? ? ? ? ? = = = = = = A = = = = = = = = 0 P059 = = = = = = T D = C = A = = = T G A C T = = (A) ? = = = = = = = (T) = = = = = = C I = T = G = = = C C G G C = = (G) ? = = = = = = = (C) 0 P060 = = = = = ? = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = A = = = = = = = = 0 P061 = = = = (G) = = = (G) ? (I) = (C) = = T G A C = G = = = = = = = = = = = = = = = (C) = = = (A) ? (D) = (T) = = C C G G = A = = = = = = = = = = = 0 P062 = ? ? ? ? ? = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = ? ? ? = = = = = = = = 0 P063 C = = = = = T = = = = = = = = = G = C ? = G A = A A A G C T G C G = = = = = C = = = = = = = = = C = G ? = C G = T G C A T C A T 0 P064 ? = = = G ? = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = C ? = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 P065 C G C ? ? ? = = A ? D = T G T C C G G = = G G = A A A G ? ? = C G A T ? ? ? = = G ? I = C A C T G A C = = C A = T G C A ? ? = T 0 P066 = = = = = = = = = = = = = = = = G = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = ? = = = = = = = = 0 P067 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P068 C G C C = ? T D ? ? D A C A ? = = = = = = = = ? = = = = ? = = = G A T T = ? C I ? ? I G T G ? = = = = = = = = ? = = = = ? = = = 0 P069 = = = = = = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? = = = = = = = = = 0 P070 = = = = = = = = = ? ? ? = = = = G = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = C = = = = = = = = = = = = = = = 0 P071 = = = = = ? = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = A = = = = = = = = 0 P072 C = = = = ? T = = = = = = = = = G = C T = G A G A A A G C T G C G = = = = ? C = = = = = = = = = C = G C = C G A T G C A T C A T 0 P073 ? ? ? ? ? ? ? ? ? ? D A C ? ? = = = = = = ? ? A = = = = ? = = = ? ? ? ? ? ? ? ? ? ? I G T ? ? = = = = = = ? ? G = = = = ? = = = 0 P074 = G C C = G = D ? ? D A = A ? = C = G C = C = ? T G C A ? C A T = A T T = A = I ? ? I G = G ? = G = C T = G = ? A A A G ? T G C 0 P075 ? G C ? ? ? T D ? ? D A C = = = = = = = = = = = = = = = = = = = ? A T ? ? ? C I ? ? I G T = = = = = = = = = = = = = = = = = = = 0 P076 = = = = = ? = = = = = = = = = = = = = = = = (A) = = A (A) = ? = = = = = = = = ? = = = = = = = = = = = = = = = = (G) = = G (C) = ? = = = 0 P077 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = ? 0 P078 C ? ? ? ? = T = = = = = = = = = G = C T = G A = A A A G C T G C G ? ? ? ? = C = = = = = = = = = C = G C = C G = T G C A T C A T 0 P079 = = = = = ? = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = A = = = = = = = = 0 P080 C G C = = ? = = A ? D = = ? ? ? G ? C = = ? ? ? T = = = = = = T G A T = = ? = = G ? I = = ? ? ? C ? G = = ? ? ? A = = = = = = C 0 P081 = ? ? ? ? ? = = = = = = = = = = = = = = = = = G = = = = ? ? ? = = ? ? ? ? ? = = = = = = = = = = = = = = = = = A = = = = ? ? ? = 0 P082 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = T G C = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = C A T 0 P083 ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P084 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = 0 P085 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P086 = ? ? ? ? ? = = = = = = = = = = = = = = = = = G = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = A = = = = = = = = 0 P087 = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = C = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = T 0 P088 = = = = = ? = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = T = = = = = = = = = = = = = = = = = = = 0 P089 C ? ? ? ? ? T D = C = A C A C T G A C ? G G A = A A A G ? ? = C G ? ? ? ? ? C I = T = G T G T C C G G ? A C G = T G C A ? ? = T 0 P090 = ? ? ? ? = = = = ? = = ? = = = = = = = = = = = = = = = ? = = = = ? ? ? ? = = = = ? = = ? = = = = = = = = = = = = = = = ? = = = 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 0.99 0.99 = = = = = = = = = = = = = = = = = ? ? 1.00 ? ? ? ? 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 = = = = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = 0.86 = = = = = = = = = = ? = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0.99 = ? 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 ? = ? ? ? ? ? ? ? 1.00 = = = = = = = = = = = = = = = ? = = = = ? ? ? ? ? = 1.00 ? ? 1.00 1.00 = = = = 1.00 = 1.00 = = = = = = = = = ? ? 1.00 = = = = = = ? = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 ? = = 1.00 ? ? ? ? ? ? ? = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 0.90 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 0.91 = = ? ? ? 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = ? = 1.00 = = = 1.00 = = ? = = = 1.00 1.00 1.00 ? = ? 1.00 1.00 ? ? 1.00 1.00 = = = = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = = = ? 1.00 = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = ? ? = 0.93 = = = = = = 1.00 ? = = = = ? = = = = = = = = = = = = = = ? 1.00 1.00 = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = ? ? = = = = = ? = = = 0.90 0.90 0.90 = 0.90 ? = = = = = = = = = = = = = = 0.88 = = = 0.65 = 0.65 0.65 = = = 0.65 1.00 = = = = ? ? = = = = = = = = = 1.00 = 1.00 ? = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = ? = = = = = = = = = = 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 = = = ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = = = = ? = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = ? = = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 ? = 1.00 1.00 ? 0.99 0.99 0.99 0.99 ? ? ? 0.99 = = = = = ? = = = = = = = = = = = = = = = = ? ? 1.00 1.00 1.00 = = = = = 1.00 = = = = ? 1.00 = = = = = = = = = 1.00 = 1.00 ? = 1.00 1.00 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? 0.78 0.78 0.78 = = = 0.76 0.76 0.76 = = = = = = = = = 0.74 0.74 0.74 0.74 ? ? 0.74 0.74 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 ? ? ? ? ? 1.00 = = = = = = ? ? ? ? ? ? ? = ? 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 0.87 ? 0.92 0.92 0.92 0.92 = = = 0.92 ? = = ? ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = 0.93 = = = = ? 0.96 = = = = = = = = = 0.96 = 0.96 0.96 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = ? = = = = = = = ? ? = = = = = = = = = = = = = = ? ? = = = = = = ? = = = = = = 0.79 = = = = = = = = ? ? ? = = = = = = = = 1.00 1.00 1.00 1.00 = ? ? ? ? ? 1.00 1.00 1.00 1.00 1.00 = = = = = = ? ? ? = = = = = = = 0.51 = = = = = ? = = = = = = = = = = = = = = = = 0.95 = = = = = = = = 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 = = 0.62 ? = = = = = = = 0.66 = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = 0.87 = = = 0.87 ? 0.87 = 0.87 = = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = ? ? ? = = = = = = = = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 ? = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = = 1.00 ? = = = = = = = = ? = = = = = = = = = = = = = = = = = 0.95 0.95 0.95 ? ? ? = = 1.00 ? 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 0.98 1.00 = 0.98 0.98 0.98 0.98 ? ? = 0.98 = = = = = = = = = = = = = = = = 1.00 = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = ? 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 ? = = = = = = = = ? = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? ? ? = = = = 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = = = = ? 1.00 = = = = = = = = = 1.00 = 1.00 1.00 = 0.99 0.99 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 = ? 0.91 0.91 0.91 0.91 ? 0.91 0.91 0.91 ? 1.00 1.00 ? ? ? 1.00 1.00 ? ? 1.00 1.00 0.92 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0.83 = = 1.00 0.87 = ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = ? 1.00 ? ? ? ? = 1.00 = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 1.00 1.00 = = ? = = 1.00 ? 1.00 = = ? ? ? 1.00 ? 1.00 = = ? ? ? 1.00 = = = = = = 1.00 = ? ? ? ? ? = = = = = = = = = = = = = = = = = 1.00 = = = = ? ? ? = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = 1.00 = = = = = ? = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 ? ? ? ? ? 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 = 0.95 0.95 0.95 0.95 ? ? = 0.95 = ? ? ? ? = = = = ? = = ? = = = = = = = = = = = = = = = ? = = = END PHASEPROBS