************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 il1f8.phase.inp il1f8.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il1f8.phase.out_freqs : haplotype frequency estimates il1f8.phase.out_pairs : most likely haplotype pairs for each individual il1f8.phase.out_recom : estimates of recombination parameters il1f8.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 89 Positions of loci: 129 393 661 1656 1934 1979 2106 2677 3102 3126 3620 3769 3820 3881 4021 4338 4991 6058 7275 7400 7841 8009 8398 8834 12348 12461 12722 13248 13745 14016 14112 16518 16632 17207 17227 17645 21212 21297 21518 21527 21852 22145 22147 22278 22764 23089 23236 23388 23815 24211 24305 24442 24783 25049 25572 26564 27204 27386 27604 27649 28145 28497 28735 28836 29176 29750 30014 30077 30347 31071 31476 32531 32873 33200 33420 33764 34998 35013 35291 35716 35734 35736 35848 36657 36833 37069 38845 39076 39810 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il1f8.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCCACCCGCGCCGGCTCTCIAIATCIGITTTAACCAACGCTCAGTAGGGGCTTGCGCCCDCAGGAGGTTGCCAGCCAGGGCACCCCGCA 6.000000 2 CCCACCCGCGCCGGCTCTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGCGTCCICACATGATTGTTAACCGCGACAACGCGTA 1.000000 3 CCCACCCGCGCCGGCTCTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGCGTCCICACATGATTGTTAACCGCGACAATGCGTA 6.000000 4 CCCACCCGCGCCGGCTCTCIAIATCIGITTTACCCGACGCTCAGTAGGGGCTCGGGCCCDCAGGAGGTTGCCAGCCAGGGCACCCCGCA 1.000000 5 CCCACCCGCGCCGGCTCTCIAIATCIGITTTACCCGGCGATCATTAGGGGCTCGGGCTCICACGAGATTGCCAGCCACGGCAACCTGTA 1.000000 6 CCCACCCGCGCCGGTTCTCIAIATCIGITTTAACCAACGCTCAGTAGGGGCTTGCGCCCDCAGGAGGTTGCCAGCCAGGGCACCCCGCA 2.000000 7 CCCACCCGCGCCGGTTCTCIAIATCIGITTTAACCAACGCTCAGTAGGGGCTTGCCCTCICTCGAGATTCCCGGATACGGTTACCTATA 1.000000 8 CCCACCCGCGCCGGTTCTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGCGTCCICACATGATTGTTAACCGCGACAATGCGTA 7.000000 9 CCCACCCGCGCCGGTTCTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGGGTCCICACATGATTGTTAACCGCGACAATGCGTA 3.000000 10 CTAACCCGCGCCGGCTCTCIAIACTDCICCCACCCGGCGCTCGGTGTGGGTTTGGGCTCICACGAGATTGCCAGCCACAGCAACCTGTG 1.000000 11 CTAACCCGCGCCGGCTCTCIAIACTDCICCCACCCGGCGCTCGGTGTGGGTTTGGGCTTICACGAGATTGCCAGCCACAGCAACCTGTG 1.000000 12 CTAACCCGCGCCGGCTCTCIAIACTDCICCCACCCGGCGCTCGGTGTTCGTTTGGGCCCDCACGAAGTTGCCAGCCAGGGCACCCCGCA 1.000000 13 CTAACCCGCGCCGGCTCTCIAIACTDCICCCACCCGGCGCTCGGCGGGGGCTTGGGCTCICACGAGGTTGCCAGCCACGGCAACCTGTA 1.000000 14 CTAACCCGCGCCGGCTCTCIAIACTDCICCCACTCGACGCTCAGTAGGGGCTTGCCCTCICTCGAGATTCCCGGATACGGTTACCTATA 1.000000 15 CTAACCCGCGCCGGCTCTCIADATCIGITTTGCCCGGCTCCCGGTGGGGCCGTGGGCTTICACGAGATTGCCAGCCACAGCAACCTGTG 1.000000 16 CTAACCCGCGCCGGCTCTCIADATCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGGCTTICACGAGATTGCCAGCCACAGCAACCTGTG 1.000000 17 CTAACCCGCGCCGGCTCTCIADATCIGICCCGCCCGGCTCCGGGTGGGGCCGTGCGCTCICACGAGATTGCCAGCCACGGCACCCTGTA 1.000000 18 CTAACCCGCGCCGGCTCTCIADATCIGICCCGCCCGGCTCCGGGTGGGGCCGTGCGCTCICACGAGATTGCCAGCCACGGCAACCTGTA 1.000000 19 CTAACCCGCGCCGGCTCTTIGICTCIGITTTACCCGGCTCTGGGTGGGGGTTTGGCCTCICTCGAGATTCCCGGATACGGTTACCTATA 2.000000 20 CTAACCCGCGCCGGCTCTTIGICTCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGGCCCICACGAGATTGCCAGCCACGGCAACCTGTA 1.000000 21 CTAACCCGCGCCGGCTCTTIGICTCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGGCTCICTCGAGATTGCCAGCCAGGGCACCCCGCA 1.000000 22 CTAACCCGCGCCGGCTCTTIGICTCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGCCTCICTCGAGATTCCCGGATACGGTTACCTGTA 1.000000 23 CTAACCCGCGCCGGCTCTTIGICTCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGCCTCICTCGAGATTCCCGGATACGGTTACCTATA 2.000000 24 CTAACCCGCGCCGGCTCATDGICTCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGGCCCDCACGAAGTTGCCAGCCAGGGCACCCCGCA 2.000000 25 CTAACCCGCGCCGGCTCATDGICTCIGITTTGCCCGGCTCCGGGTGGGGCCGTGGGCTTICACGAGACCGCCAGCCACAGCAACCTGTA 1.000000 26 CTAACCCGCGCCGGCTCATDGICCTDCICCCACCCGGCGCTCGGTGTTGGTTTGCGCTCICACGAGATTGCCAGCCACGGCACCCTGTA 2.000000 27 CTAACCCGCGTCGACTCTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGCGTCCICACATGATTGTTAACCGCGACAATGCGTA 1.000000 28 CTAACCCGCGTCGACTCTCIADACTDCDCCCACTTGGTTCCGGGCGGGGGCTTCCGCTTIGACGAGACCGCCAGCCACAGCAACCTGTA 5.000000 29 CTAACCCGCGTCGACTCTCIADACTDCDCCCACTTGGTTCCGGGCGGGGGCTTCGGCTTIGACGAGACCGCCAGCCACAGCAACCTATA 1.000000 30 CTAACCCGCGTCGACTCTCIADACTDCDCCCACTTGGTTCCGGGCGGGGGCTTCGGTCCICACATGATTGTTAACCGCGACAATGCGTA 1.000000 31 CTAACCCGCGTCGACTCTCIADACTDCDCCCACTTGGTTCCGGGCGGGGGCTTCGCCTCICTCGAGATTCCCGGATACGGTTACCTATA 9.000000 32 CTAACCCGCGTCGACTCTCIADACTDCDCCCACTTGGTTCCGGGCGGGGGCTTCGCCTCICTCATGATTGTTAACCGCGACAATGCGTA 1.000000 33 TCCTCCTGTACCCGCACTCIAIATCIGITTTACCCGATGCTCAGTAGGGGCTTGCGCTCICACGAGATTGCCAGCCACGGCAACCTGTA 1.000000 34 TCCTCCTGTACCCGCACTCIAIATCIGITTTACCCGGCGCTCGGCGGGGGCTTGGGCTCICACGAGATTGCCAGCCACGGCAACCTGTA 1.000000 35 TCCTCTTGTACCCGCACTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGCGCTCICTCGAGATTGCCAGCCAGGGCACCCCGCA 2.000000 36 TCCTCTTGTACCCGCACTCIAIATCIGITTTACCCGGCGATCATTAGGGGCTTGCCCTCICTCGAGATTCCCGGATACGGTTACCTATA 1.000000 37 TCCTCTTGTACCCGCACTCIAIATCIGITTTACCCGGCGATCATTAGGGGCTCGCGTCCICACATGATTGTTAACCGCGACAATGCGTA 3.000000 38 TCCTCTTGTACCCGCACTCIAIATCIGITTTACCCGGCGATCATTAGGGGCTCGGGCTTICACGAGACCGCCAGCCACAGCAACCTGTA 1.000000 39 TTAATCCACGCTGGCTTTCIAIATCIGITTTACCCGATGCTCAGTAGGGGCTTGGGCTCICACGAGGTTGCCAGCCAGGGCACCCCGCA 1.000000 40 TTAATCCACGTTGGCTCTCIAIACTDCICCCACCCGGCGCTCGGTGTGGGTTTGCGCCCDCAGGAGGTTGCCAGCCAGGGCACCCCGCA 1.000000 41 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCAACGCTCAGTAGGGGCTTGCGTCCICACATGATTGTTAACCGCGACAACGCGTA 4.000000 42 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCGATGCTCAGTAGGGGCTTGGGCCCDCACGAGATTCCCGGATACGGTTACCTATA 1.000000 43 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCGATGCTCAGTAGGGGCTTGGGCCCDCACGAAGTTGCCAGCCAGGGCACCCCGCA 1.000000 44 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCGATGCTCAGTAGGGGCTTGGGCTTICACGAGATTGCCAGCCACAGCAACCTGTG 1.000000 45 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCGGCGCTCAGTGTTGGTTTGGGCTCICTCGAGATTGCCAGCCAGGGCACCCCGCA 1.000000 46 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCGGCGCTCGGTGTTCGTTTGCGCTTIGACGAGACCGCCAGCCACAGCAACCTGTA 2.000000 47 TTAATCCACGTTGGCTTTCIAIATCIGITTTACCCGGCGCTCGGTGTTCGTTTGCCCTCICTCGAGATTCCCGGATACGGTTACCTATA 2.000000 48 TTAATCCACGTTGGCTTTCIAICTCIGITTTACCCGATGCTCAGTAGGGGCTTGGGCTTICACGAGATTGCCAGCCACAGCAACCTGTG 1.000000 49 TTAATCCACGTTGGCTTTCIAICTCIGITTTACCCGGCGCTCGGTGTTCGTTTGCGCTTIGACGAGACCGCCAGCCACAGCAACCTGTA 1.000000 50 TTAATCCACGTTGGCTTTTIGICTCIGICCCGCCCGGCTCCGGGTGGGGCCGTGGGCCCDCACGAAGTTGCCAGCCAGGGCACCCCGCA 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (6,35) DY02: (36,48) DY03: (24,44) DY04: (5,43) DY05: (9,16) DY06: (9,34) DY07: (1,11) DY08: (33,40) DY09: (10,26) DY10: (21,25) DY11: (12,50) DY12: (4,15) DY13: (14,39) DY14: (19,20) DY15: (1,23) DY16: (26,50) DY17: (19,23) DY18: (18,22) DY19: (1,41) DY20: (13,17) DY21: (1,35) DY22: (1,38) DY23: (24,42) DY24: (6,45) E101: (7,31) E102: (8,41) E103: (31,31) E104: (28,41) E105: (8,8) E106: (3,30) E107: (8,32) E108: (9,28) E109: (8,8) E110: (28,47) E111: (3,29) E112: (3,37) E113: (27,31) E114: (28,31) E115: (3,31) E116: (31,47) E117: (31,46) E118: (28,49) E119: (8,46) E120: (3,37) E121: (3,41) E122: (2,37) E123: (1,31) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C C C A C C C G C G C C G G (T) T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A T C C T C T T G T A C C C G (C) A C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G C T C I C T C G A G A T T G C C A G C C A G G G C A C C C C G C A 0 DY02 T C C T C T T G T A C C C G C A C T C I A I (A) T C I G I T T T A C C C G G C G A T C A T T A G G G G C T T G [C] C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A T T A A T C C A C G T T G G C T T T C I A I (C) T C I G I T T T A C C C G A T G C T C A G T A G G G G C T T G G G C T T I C A C G A G A T T G C C A G C C A C A G C A A C C T G T G 0 DY03 C T A A C C C G C G C C G G C T C A T D G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G G C C C D C A C G A A G T T G C C A G C C A G G G C A C C C C G C A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G A T G C T C A G T A G G G G C T T G G G C T T I C A C G A G A T T G C C A G C C A C A G C A A C C T G T G 0 DY04 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C G G C G A T C A T T A G G G G C T C G G G C (T) C (I) C A C G A (G) (A) T T G C C A G C C A (C) G G C A (A) C C (T) G (T) A T T A A T C C A C G [T] T G G C T T T C I A I A T C I G I T T T A C C C G A T G C T C A G T A G G G G C T T G G G C (C) C (D) C A C G A (A) (G) T T G C C A G C C A (G) G G C A (C) C C (C) G (C) A 0 DY05 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G G G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C T A A C C C G C G C C G G C T C T C I A D A T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G G C T T I C A C G A G A T T G C C A G C C A C A G C A A C C T G T G 0 DY06 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G G G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A T C C T C C T G T A C C C G C A C T C I A I A T C I G I T T T A C C C G G C G C T C G G C G G G G G C T T G G G C T C I C A C G A G A T T G C C A G C C A C G G C A A C C T G T A 0 DY07 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A C T A A C C C G C G C C G G C T C T C I A I A C T D C I C C C A C C C G G C G C T C G G T G T G G G T T T G G G C T T I C A C G A G A T T G C C A G C C A C A G C A A C C T G T G 0 DY08 T C C T C C T G T A C C C G C A C T C I A I A T C I G I T T T A C C C G A T G C T C A G T A G G G G C T T G C G C (T) C (I) C A (C) G A G (A) T T G C C A G C C A (C) G G C A (A) C C [T] G (T) A T T A A T C C A C G T T G G C T C T C I A I A C T D C I C C C A C C C G G C G C T C G G T G T G G G T T T G C G C (C) C (D) C A (G) G A G (G) T T G C C A G C C A (G) G G C A (C) C C [C] G (C) A 0 DY09 C T A A C C C G C G C C G G C T C T C I A I A C T D C I C C C A C C C G G C G C T C G G T G T G G G T T T G G G C T C I C A C G A G A T T G C C A G C C A C A G C A A C C T G T G C T A A C C C G C G C C G G C T C A T D G I C C T D C I C C C A C C C G G C G C T C G G T G T T G G T T T G C G C T C I C A C G A G A T T G C C A G C C A C G G C A C C C T G T A 0 DY10 C T A A C C C G C G C C G G C T C (T) T (I) G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G G C T C I C T C G A G A T T G C C A G C C A G G G C A C C C C G C A C T A A C C C G C G C C G G C T C (A) T (D) G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G G C T T I C A C G A G A C C G C C A G C C A C A G C A A C C T G T A 0 DY11 C T A A C C C G C G C C G G C T C T C I A I A C T D C I C C C A C C C G G C G C T C G G T G T T C G T T T G G G C C C D C A C G A A G T T G C C A G C C A G G G C A C C C C G C A T T A A T C C A C G T T G G C T T T T I G I C T C I G I C C C G C C C G G C T C C G G G T G G G G C C G T G G G C C C D C A C G A A G T T G C C A G C C A G G G C A C C C C G C A 0 DY12 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C G A C G C T C A G T A G G G G C T (C) G G G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A C T A A C C C G C G C C G G C T C T C I A D A T C I G I T T T G C C C G G C T C C C G G T G G G G C C G (T) G G G C T T I C A C G A G A T T G C C A G C C A C A G C A A C C T G T G 0 DY13 C T A A C C C G C G C C G G C T C T C I A I A C T D C I C C C A C T C G A C G C T C A G T A G G G G C T T G [C] C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A T T A A T C C A C G C T G G C T T T C I A I A T C I G I T T T A C C C G A T G C T C A G T A G G G G C T T G [G] G C T C I C A C G A G G T T G C C A G C C A G G G C A C C C C G C A 0 DY14 C T A A C C C G C G C C G G C T C T T I G I C T C I G I T T T [A] C C C G G C T C T G G G T G G G G G T T T G G C C (T) C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A C T A A C C C G C G C C G G C T C T T I G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G G C (C) C I C A C G A G A T T G C C A G C C A C G G C A A C C T G T A 0 DY15 C C C A C C C G C G C C G G [C] T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A C T A A C C C G C G C C G G C T C T T I G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 DY16 C T A A C C C G C G C C G G C T C A T D G I C C T D C I C C C A C C C G G C G C T C G G T G T T G G T T T G C G C T C I C A C G A G A T T G C C A G C C A C G G C A C C C T G T A T T A A T C C A C G T T G G C T T T T I G I C T C I G I C C C G C C C G G C T C C G G G T G G G G C C G T G G G C C C D C A C G A A G T T G C C A G C C A G G G C A C C C C G C A 0 DY17 C T A A C C C G C G C C G G C T C T T I G I C T C I G I T T T [A] C C C G G C T C T G G G T G G G G G T T T G G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A C T A A C C C G C G C C G G C T C T T I G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 DY18 C T A A C C C G C G C C G G C T C T C I A D A T C I G I [C] [C] [C] G C C C G G C T C C G G G T G G G G C C G T G C (G) C T C I C (A) C G A G A T T (G) C C (A) G (C) C A C G G (C) (A) A C C T G T A C T A A C C C G C G C C G G C T C T T I G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G (C) C T C I C (T) C G A G A T T (C) C C (G) G (A) [T] A C G G (T) (T) A C C T G T A 0 DY19 C C C A C C C G C G C C G G [C] T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A C G C G T A 0 DY20 C T A A C C C G C G C C G G C T C T C I A I A C T D C I C C C A C C C G G C G C T C G G C G G G G G C T T G G G C T C I C A C G A G (G) T T G C C A G C C A C G G C A (A) C C T G T A C T A A C C C G C G C C G G C T C T C I A D A T C I G I C C C G C C C G G C T C C G G G T G G G G C C G T G C G C T C I C A C G A G (A) T T G C C A G C C A C G G C A (C) C C T G T A 0 DY21 C C C A C C C G C G C C G G [C] T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A T C C T C T T G T A C C C G C A C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G C T C I C T C G A G A T T G C C A G C C A G G G C A C C C C G C A 0 DY22 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A T C C T C T T G T A C C C G C A C T C I A I A T C I G I T T T A C C C G G C G A T C A T T A G G G G C T C G [G] G C T T I C A C G A G A C C G C C A G C C A C A G C A A C C T G T A 0 DY23 C T A A C C C G C G C C G G C T C A T D G I C T C I G I T T T G C C C G G C T C C G G G T G G G G C C G T G G G C C C D C A C G A (A) (G) T T (G) C C (A) G (C) (C) A (G) G G (C) (A) (C) C C (C) (G) (C) A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G A T G C T C A G T A G G G G C T T G G G C C C D C A C G A (G) (A) T T (C) C C (G) G (A) (T) A (C) G G (T) (T) (A) C C (T) (A) (T) A 0 DY24 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G (C) G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G G C G C T C A G T G T T G G T T T G (G) G C T C I C T C G A G A T T G C C A G C C A G G G C A C C C C G C A 0 E101 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 E102 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A C G C G T A 0 E103 C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 E104 C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A C G C G T A 0 E105 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A 0 E106 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G (C) G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C (G) G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A 0 E107 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C A T G A T T G T T A A C C G C G A C A A T G C G T A 0 E108 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G G G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A 0 E109 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A 0 E110 C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C C (G) C T (T) I (G) (A) C G A G A (C) (C) (G) C C (A) G (C) (C) A C (A) G (C) (A) A C C T (G) T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G G C G C T C G G T G T T C G T T T G C (C) C T (C) I (C) (T) C G A G A (T) (T) (C) C C (G) G (A) (T) A C (G) G (T) (T) A C C T (A) T A 0 E111 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G (C) G (T) (C) (C) I (C) A C (A) (T) G A (T) (T) G (T) (T) A (A) C C (G) C (G) (A) C A A (T) (G) (C) (G) T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C (G) G (C) (T) (T) I (G) A C (G) (A) G A (C) (C) G (C) (C) A (G) C C (A) C (A) (G) C A A (C) (C) (T) (A) T A 0 E112 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A T C C T C T T G T A C C C G C A C T C I A I A T C I G I T T T A C C C G G C G A T C A T T A G G G G C T C G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A 0 E113 C T A A C C C G C G T C G A C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 E114 C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 E115 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 E116 C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G G C G C T C G G T G T T C G T T T G C C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A 0 E117 C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G G C G C T C G G T G T T C G T T T G C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A 0 E118 C T A A C C C G C G T C G A C T C T C I A D (A) C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A T T A A T C C A C G T T G G C T T T C I A I (C) T C I G I T T T A C C C G G C G C T C G G T G T T C G T T T G C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A 0 E119 C C C A C C C G C G C C G G T T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C G G C G C T C G G T G T T C G T T T G C G C T T I G A C G A G A C C G C C A G C C A C A G C A A C C T G T A 0 E120 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A T C C T C T T G T A C C C G C A C T C I A I A T C I G I T T T A C C C G G C G A T C A T T A G G G G C T C G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A 0 E121 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A T G C G T A T T A A T C C A C G T T G G C T T T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A C G C G T A 0 E122 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A C C C A A C G C T C A G T A G G G G C T T G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A (C) G C G T A T C C T C T T G T A C C C G C A C T C I A I A T C I G I T T T A C C C G G C G A T C A T T A G G G G C T C G C G T C C I C A C A T G A T T G T T A A C C G C G A C A A (T) G C G T A 0 E123 C C C A C C C G C G C C G G C T C T C I A I A T C I G I T T T A A C C A A C G C T C A G T A G G G G C T T G C G C C C D C A G G A G G T T G C C A G C C A G G G C A C C C C G C A C T A A C C C G C G T C G A C T C T C I A D A C T D C D C C C A C T T G G T T C C G G G C G G G G G C T T C G C C T C I C T C G A G A T T C C C G G A T A C G G T T A C C T A T A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 DY01 C = = A = C C = C G = = G = (T) T = = = = = = = = = = = = ? ? ? = A = = = = = = = = = = = = = = = = = = = ? = = = = C = D = A G = = = G = = = = = = = = = = = = = = = = = = = = = = T = = T = T T = T A = = C = (C) A = = = = = = = = = = = = ? ? ? = C = = = = = = = = = = = = = = = = = = = ? = = = = T = I = T C = = = A = = = = = = = = = = = = = = = = = = = = = = 0 DY02 = C C T C T T G T A C C C = = A C = = = = = (A) = = = = = = = = = = = = = G C = A = = = T = = = = = = = = = = ? C = = C = = T = = = = = = = C = = G = A T = = G = T T = = = = A = A = T A A T C C A C G T T G = = T T = = = = = (C) = = = = = = = = = = = = = A T = C = = = G = = = = = = = = = = ? G = = T = = A = = = = = = = G = = A = C C = = A = C A = = = = G = G 0 DY03 C = = = C = = G = = C C = = = = C A T D G = C = = = = = ? ? ? G = = = = G C T = C G G = = G = = = C = ? = = = = = C C D = = = = = A G = = = = = = = = = = G G = = = C = = C = C A T = = = T = = A = = T T = = = = T T C I A = A = = = = = ? ? ? A = = = = A T G = T C A = = A = = = G = ? = = = = = T T I = = = = = G A = = = = = = = = = = C A = = = A = = T = T G 0 DY04 C C C = C = = G = = ? ? = = = = C = = = = = = = = = = = ? = = = = = = = G C = A = = = T = = = = = = = = C ? = = = (T) = (I) = = = = = (G) (A) = = = = = = = = = = (C) = = = = (A) = = (T) = (T) ? T T A = T = = A = = ? ? = = = = T = = = = = = = = = = = ? = = = = = = = A T = C = = = G = = = = = = = = T ? = = = (C) = (D) = = = = = (A) (G) = = = = = = = = = = (G) = = = = (C) = = (C) = (C) ? 0 DY05 = C C = = = = = = = = = = = T = = = = = = I = = = = = = = = = A = = = A A = G = T C A = = A = = = G = T = = = = T C C = = ? = A T = = = = = T T = A = = G = G A = = = T G C = = A = T A = = = = = = = = = = = C = = = = = = D = = = = = = = = = G = = = G G = T = C G G = = G = = = C = G = = = = C T T = = ? = G A = = = = = C C = G = = A = A G = = = C C T = = G 0 DY06 C = = A = = C = C G = = G = T T = = = = = = = = = = = = = = = = = = = A A = = = = = A = T A = = = = = = = = = = T C = = = = = A T = = = = = T T = A = = G = = A = = = T G C = = = T = = T = = T = T A = = C = C A = = = = = = = = = = = = = = = = = = = G G = = = = = G = C G = = = = = = = = = = C T = = = = = G A = = = = = C C = G = = A = = G = = = C C T = = = 0 DY07 = C C = = = = = = = = = = = = = = = = = = = = T C I G = T T T = A = = A A = = = = = A = = A G = = = C = = = C = = C C D = = G = = = G = = = = = = = = = = G G = = = C = = C = C A = T A = = = = = = = = = = = = = = = = = = = = C T D C = C C C = C = = G G = = = = = G = = G T = = = T = = = G = = T T I = = C = = = A = = = = = = = = = = C A = = = A = = T = T G 0 DY08 = C C T C = T G T A C C C = = A = = = = = = = T C I G = T T T = = = = = A T = = = = A = = A G = ? = C = = ? = = = (T) = (I) = = (C) = = = (A) = = = = ? = = ? ? = (C) = = = = (A) = ? ? = (T) = = T A A T = C A C G T T G = = T = = = = = = = C T D C = C C C = = = = = G C = = = = G = = G T = ? = T = = ? = = = (C) = (D) = = (G) = = = (G) = = = = ? = = ? ? = (G) = = = = (C) = ? ? = (C) = 0 DY09 = = = = = = = = = = = = = = = = = T ? I A = A = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = A = = = A = = = = = G = = = = = = = = = = = = = = = = = A ? D G = C = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = G = = = C = = = = = A 0 DY10 = = = = = = = = = = = = = = = = = (T) = (I) = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = T = = = = = T T = = = = = = = = G G = = = C = = C = C = = = = = = = = = = = = = = = = = = (A) = (D) = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = A = = = = = C C = = = = = = = = C A = = = A = = T = T = 0 DY11 C = = = C = = G = = C C = = ? = C = C = A = A C T D C = = = = A = = = = = = G = T C = = = = T T C G T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = T = = A = = T T = = ? = T = T = G = C T C I G = = = = G = = = = = = T = C G = = = = G G G C C G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY12 = C C = = = = = = = = = = = = = = = = = = I = = = = = = = = = A = = = = A = G = T = A = = A = = = G = T (C) ? = ? = C C D = = G = = = G = = = = = = = = = = G G = = = C = = C = C A = T A = = = = = = = = = = = = = = = = = = D = = = = = = = = = G = = = = G = T = C = G = = G = = = C = G (T) ? = ? = T T I = = C = = = A = = = = = = = = = = C A = = = A = = T = T G 0 DY13 C = = = C = = G = = = ? = = ? = C = = = = = = C T D C = C C C = = T = = = C = = = = = = = = = = = = = ? = = ? C = = = = = T = = = = A = = C = = G = A T = C = = T T A = ? ? A T = T = = = T = = A = = = ? = = ? = T = = = = = = T C I G = T T T = = C = = = T = = = = = = = = = = = = = ? = = ? G = = = = = A = = = = G = = G = = A = C C = G = = C A C = ? ? G C = 0 DY14 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = ? = = = = T = = = = = = = = G T T = = = C = (T) = = = T = = = = = = = C = = G = A T = = = = T T = = = = A = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = ? = = = = C = = = = = = = = C C G = = = G = (C) = = = A = = = = = = = G = = A = C C = = = = C A = = = = G = = 0 DY15 = C C = = = = = = = ? ? ? ? ? = = = C = A = A = = = = = = = = A A = = A A = G = T C A = = A = = = G = T = = ? G = C = D = A G = = = G = = G = = A = C C = G = = C A C = = C G C = = T A = = = = = = = ? ? ? ? ? = = = T = G = C = = = = = = = = G C = = G G = T = C G G = = G = = = C = G = = ? C = T = I = T C = = = A = = C = = G = A T = C = = T T A = = T A T = 0 DY16 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? A = D ? ? ? ? T D C = = = = A = = = = = = G = T C = = = = T T = G T ? = ? C = = T = I = = = = = G A = = = = ? ? = = = = C = = = = = = = T = T = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? T = I ? ? ? ? C I G = = = = G = = = = = = T = C G = = = = G G = C C ? = ? G = = C = D = = = = = A G = = = = ? ? = = = = G = = = = = = = C = C = 0 DY17 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = T = = = = = = = = G T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = C = = = = = = = = C C G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY18 = = = = = = = = = = = = = = = = = = C = A D A = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = C (G) = = = = = (A) = = = = = = = (G) = = (A) = (C) ? = = = = (C) (A) = = = = = = = = = = = = = = = = = = = = = = = = = T = G I C = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = G (C) = = = = = (T) = = = = = = = (C) = = (G) = (A) ? = = = = (T) (T) = = = = = = = 0 DY19 C C C = C = = G = = C C = = ? = C = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = ? = = = = C = = D = = G G A = G = = = C C = G = = A G = G = = C = C = = C = T T A = T = = A = = T T = = ? = T = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = ? = = = = T = = I = = C A T = A = = = T T = A = = G C = A = = A = G = = T = 0 DY20 = = = = = = = = = = = = = = = = = = ? ? ? I = C T D C = = = = A = = = = = = G = T C = = C = = = = G = T = = G = = = = = = = = = = = (G) = = = = = = = = ? = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? D = T C I G = = = = G = = = = = = T = C G = = T = = = = C = G = = C = = = = = = = = = = = (A) = = = = = = = = ? = = = = = = (C) = = = = = = 0 DY21 C = = A = C C = C G = = G = ? T = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = ? = = = = = C = D = A G = = = G = = = = = = = = = = = = = = = = = = = = = = T = = T = T T = T A = = C = ? A = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = ? = = = = = T = I = T C = = = A = = = = = = = = = = = = = = = = = = = = = = 0 DY22 C = = A = C C = C G = = G = = T = = = = = = = = = = = = = = = = A = = A A = = C = = = G = = = = = = = = T = ? = = C C D = = G = = = G T T = = = = = = = = G G = = = C = = C = C = T = = T = T T = T A = = C = = A = = = = = = = = = = = = = = = = C = = G G = = A = = = T = = = = = = = = C = ? = = T T I = = C = = = A C C = = = = = = = = C A = = = A = = T = T = 0 DY23 C = = = C = = G = = C C = = = = C A T D G = C = = = = = = = = G = = = = G C T = C G G = = G = = = C = G = = = ? = = = = = = = = = (A) (G) = = (G) = = (A) = (C) (C) = (G) = = (C) (A) (C) = = (C) (G) (C) = T = = = T = = A = = T T = = = = T T C I A = A = = = = = = = = A = = = = A T G = T C A = = A = = = G = T = = = ? = = = = = = = = = (G) (A) = = (C) = = (G) = (A) (T) = (C) = = (T) (T) (A) = = (T) (A) (T) = 0 DY24 C C C = C = = G = = C C = = T = C = = = = = = = = = = = = = = = A = = A A = = = = = = = = A G G = = C = = = (C) = = C = D = A G = = = G = = = = = = = = = = = = = = = = = = = = = = T T A = T = = A = = T T = = C = T = = = = = = = = = = = = = = = C = = G G = = = = = = = = G T T = = T = = = (G) = = T = I = T C = = = A = = = = = = = = = = = = = = = = = = = = = = 0 E101 = C C = = = = = = = C = = G T = = = = = = I = T C I G I T T T = A C C ? A C G = T C A = T A = = = = = = = G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A = = = = = = = T = = A C = = = = = = D = C T D C D C C C = C T T ? G T T = C G G = C G = = = = = = = C G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 C C C = C = = G = = C C = = T = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = T T A = T = = A = = T T = = C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 C = = = C = = G = = = C = A ? = C = = = = D = C T D C D C C C = = T T G G T T = C G G = C G = = = = = = = C = = C T T = G = = G A = = C C = C C = G = = A = A G = = = = C T = = = T = = = T = = A = = = T = G ? = T = = = = I = T C I G I T T T = = C C A A C G = T C A = T A = = = = = = = G = = T C C = C = = A T = = T T = T T = A = = G = G A = = = = G C = = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 = C C = = = = = = = C = = G = = = = = = = I = T C I ? I T T T = = C C A A C G = T C A = T A = = = = = = = G (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A = = = = = = = T = = A = = = = = = = D = C T D ? D C C C = = T T G G T T = C G G = C G = = = = = = = C (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = C C = = = = = = = C = = G T = = = = = = I = T C I G I T T T = = C C A A C G = T C A = T A = = = = = = = ? C G T C = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A = = = = = = = T = = A C = = = = = = D = C T D C D C C C = = T T G G T T = C G G = C G = = = = = = = ? G C C T = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = C C = = = = = = = C = = G T = = = = = = I = T C I G I T T T = = C C A A C G = T C A = T A = = = = = ? = ? G = T C C = C = = A T = = T T = T T = A = = G = G A = = = T ? ? = = = = T A = = = = = = = T = = A C = = = = = = D = C T D C D C C C = = T T G G T T = C G G = C G = = = = = ? = ? C = C T T = G = = G A = = C C = C C = G = = A = A G = = = C ? ? = = = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 C = = = C = = G = = = C = A = = C = = = = D = C T D C D C C C = = T T ? = T T = C G = = C = G G G = C = = C = (G) = = (T) = (G) (A) = = = = = (C) (C) (G) = = (A) = (C) (C) = = (A) = (C) (A) = = = = (G) = = T = = = T = = A = = = T = G = = T = = = = I = T C I G I T T T = = C C ? = C G = T C = = T = T T C = T = = G = (C) = = (C) = (C) (T) = = = = = (T) (T) (C) = = (G) = (A) (T) = = (G) = (T) (T) = = = = (A) = = 0 E111 = C C = = = = = = = C = = G = = = = = = = I = T ? ? G I T T T = = C C A A C G = T C A = T A = = = = = = = G (C) = (T) (C) (C) = (C) = = (A) (T) = = (T) (T) = (T) (T) = (A) = = (G) = (G) (A) = = = (T) (G) (C) (G) = = = T A = = = = = = = T = = A = = = = = = = D = C ? ? C D C C C = = T T G G T T = C G G = C G = = = = = = = C (G) = (C) (T) (T) = (G) = = (G) (A) = = (C) (C) = (C) (C) = (G) = = (A) = (A) (G) = = = (C) (C) (T) (A) = = 0 E112 C = = ? = C C = C G = = G = = ? ? = = = = = = = = = = = ? ? ? = = = = A A = = C = = = G = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = ? = T T = T A = = C = = ? ? = = = = = = = = = = = ? ? ? = = = = G G = = A = = = T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = = = = = = = = = = = = = = = = = = = = I = T C I G I T T T = = C C A A C G = T C A = T A = = = = = = = ? C G T C = = = A = A T = = = = G T T A A C C G = = A C A = T G C G = = = = = = = = = = = = = = = = = = = = = = = D = C T D C D C C C = = T T G G T T = C G G = C G = = = = = = = ? G C C T = = = T = G A = = = = C C C G G A T A = = G T T = C C T A = = 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = C G = = T = G A = = = = = C C G = = A = C C = = A = C A = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = G C = = C = C T = = = = = T T C = = G = A T = = G = T T = = = = A = = 0 E115 = C C = = = = = = = C = = G = = = = = = = I = T C I G I T T T = = C C A A C G = T C A = T A = = = = = = = G C G T C = = = A = A T = = = = G T T A A C C G = = A C A = T G C G = = = T A = = = = = = = T = = A = = = = = = = D = C T D C D C C C = = T T G G T T = C G G = C G = = = = = = = C G C C T = = = T = G A = = = = C C C G G A T A = = G T T = C C T A = = 0 E116 C = = = C = = G = = = C = A = = C = = = = D = C T D C D C C C = = T T = = T T = C G = = C = G G G = C = = C G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = T = = A = = = T = G = = T = = = = I = T C I G I T T T = = C C = = C G = T C = = T = T T C = T = = G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 C = = = C = = G = = = C = A = = C = = = = D = C ? D C D C C C = = ? ? = = T T = C G = = C = G G G = C = = ? G C = = C = C T = = = = = T T C = = G = A T = = G = T T = = = = ? = = T = = = T = = A = = = T = G = = T = = = = I = T ? I G I T T T = = ? ? = = C G = T C = = T = T T C = T = = ? C G = = T = G A = = = = = C C G = = A = C C = = A = C A = = = = ? = = 0 E118 C = = = C = = G = = = C = A = = C = = = = D (A) C T D ? D C C C = = T T ? = T T = C G = = C = G G G = C = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = T = = A = = = T = G = = T = = = = I (C) T C I ? I T T T = = C C ? = C G = T C = = T = T T C = T = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E119 C C C = C = = G = = C C = = T = C = = = = = = = ? ? = = = = = = = = = A A = = = = = A = = A G G G = C ? = = = = T C C = C = = A T = = T T = T T = A = = G = G A = = = T G C = = = T T A = T = = A = = T T = = C = T = = = = = = = ? ? = = = = = = = = = G G = = = = = G = = G T T C = T ? = = = = C T T = G = = G A = = C C = C C = G = = A = A G = = = C C T = = = 0 E120 C = = A = C C = C G = = G = = T = = = = = = = = = = = = = = = = = = = A A = = C = = = G = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = T = = T = T T = T A = = C = = A = = = = = = = = = = = = = = = = = = = G G = = A = = = T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0 E121 C C C = C = = G = = C C = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = ? = = = T T A = T = = A = = T T = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = ? = = = 0 E122 C = = A = C C = C G = = G = = T = = = = = = = = = = = = = = = = = = = A A = = C = = = G = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) ? ? = = = T = = T = T T = T A = = C = = A = = = = = = = = = = = = = = = = = = = G G = = A = = = T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) ? ? = = = 0 E123 = C C = = = = = = = C = = G = = = = = = = I = T C I G I T T T = A C C A A C G = T C A = T A = = = = = ? = G C G = C = D = A G = = = G = = G = = A = C C = G = = C A C = = C G C = = T A = = = = = = = T = = A = = = = = = = D = C T D C D C C C = C T T G G T T = C G G = C G = = = = = ? = C G C = T = I = T C = = = A = = C = = G = A T = C = = T T A = = T A T = 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 = 0.80 1.00 = = = = = = = = = = = = ? ? ? = 1.00 = = = = = = = = = = = = = = = = = = = ? = = = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 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 = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = = = = ? 1.00 = = 1.00 = = 1.00 = = = = = = = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = ? ? ? 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = ? = = = = = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = = = = = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 = = ? ? = = = = 1.00 = = = = = = = = = = = ? = = = = = = = 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = = 1.00 ? = = = 0.71 = 0.71 = = = = = 0.71 0.71 = = = = = = = = = = 0.71 = = = = 0.71 = = 0.71 = 0.71 ? = 0.95 0.95 = = = = = = = = = = = 0.95 = = = = = = 0.95 = = = = = = = = = 0.95 = = = 0.95 0.95 = 0.95 = 0.95 0.95 0.95 = = 0.95 = = = 0.95 = 0.95 = = = = 1.00 1.00 1.00 = = ? = 1.00 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = = = = = = = = = 0.97 0.97 = = = = = 0.97 0.97 = = = = = 0.97 0.97 = 0.97 = = 0.97 = = 0.97 = = = 0.97 0.97 0.97 = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = = = = = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = = 1.00 = = 1.00 1.00 = ? = 1.00 = = ? = = = 0.51 = 0.51 = = 0.51 = = = 0.51 = = = = ? = = ? ? = 0.51 = = = = 0.51 = ? ? = 0.51 = = = = = = = = = = = = = = = = = = 1.00 ? 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = 0.50 = 0.50 = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = 1.00 1.00 = = = = = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = ? = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = = = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 0.96 = = = = = = = = = = = = = = = = = = 0.96 = = = = = = = = = 0.96 = = = = 0.96 = 0.96 = 0.96 = 0.96 = = 0.96 = = = 0.96 = 0.96 0.62 ? = ? = 0.96 0.96 0.96 = = 0.96 = = = 0.96 = = = = = = = = = = 0.96 0.96 = = = 0.96 = = 0.96 = 0.96 0.96 1.00 = = = 1.00 = = 1.00 = = = ? = = ? = 1.00 = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = = = = = = = = = = = ? = = ? 1.00 = = = = = 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 = = = 1.00 = 0.82 = = = 1.00 = = = = = = = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 = = = = = = = ? ? ? ? ? = = = 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = 1.00 = = ? 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1.00 = 1.00 ? ? ? ? 1.00 1.00 1.00 = = = = 1.00 = = = = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 ? = ? 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 = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = 0.95 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 = 1.00 = = = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = ? ? ? 1.00 = 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 = = = = = = = = ? = = = = = = 0.71 = = = = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 = ? 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = ? = = = = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 = = = 1.00 = = = = = = = = 1.00 = ? = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = 1.00 = = = ? = = = = = = = = = 0.51 0.51 = = 0.51 = = 0.51 = 0.51 0.51 = 0.51 = = 0.51 0.51 0.51 = = 0.51 0.51 0.51 = 0.97 0.97 0.97 = 0.97 = = 0.97 = = 0.97 0.97 = = 0.94 = 0.97 = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = 1.00 1.00 1.00 = = 1.00 = = = 0.90 = = 0.95 = 0.95 = 0.95 0.95 = = = 0.95 = = = = = = = = = = = = = = = = = = = = = = = 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 0.94 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 ? = 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = ? 0.97 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 1.00 = = 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = ? = ? 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 ? = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 = 0.87 = = 0.87 = 0.87 0.87 = = = = = 0.87 0.87 0.87 = = 0.87 = 0.87 0.87 = = 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 = 1.00 1.00 = = = = = = = 1.00 0.56 = 0.87 0.87 0.87 = 0.87 = = 0.87 0.87 = = 0.87 0.87 = 0.87 0.87 = 0.87 = = 0.87 = 0.87 0.87 = = = 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 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 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 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = 1.00 0.99 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = 1.00 = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 = = ? ? = = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = = ? 1.00 1.00 = = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = 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 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = 1.00 1.00 ? = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = = = = = = = ? ? = = = = = = = = = 1.00 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 ? = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 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 = ? = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.60 ? ? = = = = 1.00 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = ? = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = END PHASEPROBS