************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 adamt.phase.inp adamt.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST adamt.phase.out_freqs : haplotype frequency estimates adamt.phase.out_pairs : most likely haplotype pairs for each individual adamt.phase.out_recom : estimates of recombination parameters adamt.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 67 Positions of loci: 221 223 614 2066 2418 3413 3776 3858 4464 5547 6078 6105 6413 6505 7214 7412 7550 7792 9374 9775 12588 13215 15978 16468 16920 16936 17083 17169 17609 17739 18270 18374 18623 18718 18983 19214 19498 19761 19925 20175 20224 20342 21201 21576 21895 23029 23283 24328 25045 25160 25395 25504 25659 25878 26166 27609 28391 28979 29164 30461 33555 33775 37016 38119 38241 38332 38726 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file adamt.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CAACCCACCCGAIGADTCC 2 DGICGCTTCTGGAGAGTAGTCCCAACCATGTACATTCCCGCGTCGGC 3.000000 2 CAACGCACCTGAIGAITGT 2 IGICGCCTCTGGAGAGTAGTCCCAACCATGCACATTCCCGTGCCGCC 1.000000 3 CAACGCACTTGAIGAITGT 2 IGICGCCTCTGGAGAGTAGTCCCAACCATGCACATTCCCGTGCCGCC 1.000000 4 CAACGCACTTGAIGAITGT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGTCCCGTGCCGCC 3.000000 5 CGACCCACCCGAIGGDTCT 2 DGICGTCTCTAGACAGCAGTCCCGGCCTTGCACATCTTCGCGTCGGC 1.000000 6 CGACCCACCCGAIGGDTCT 2 DGICGTCTCTAGACAGCAGTCCCGGCCTTGTACAGTCCCGTGCCAGC 2.000000 7 CGACCCACCCGAIGGDTCT 2 DGICGTCTCTAGACAGCAGTCCCGGCCTTGTACATCTTCGCGTCGGC 2.000000 8 CGACCCACCCGADGADCCT 2 DGICGCCTCTGGAGAGTAGTCCCAACCAAACACAGTCCCGTGCCAGC 1.000000 9 CGACCCACCCGADGADCCT 2 DGICGCCTCTGGAGAGTAGTCCCAACCAAACATAGTCCCGTGCCAGC 3.000000 10 CGACCCACCCATDTADCCT 2 IGDGTCCCGCGCAGACTGGTCCCAACCATGCACGTTCCGGCCCCGGA 1.000000 11 CGACCCACCTGAIGAITCT 2 IGICGCCTCTGGTGAGTAGCCCCAACCAAACATAGTCCCGTGCCAGC 2.000000 12 CGACCCACCTGAIGAITCT 2 IGICGCCTCTGGTGAGTAGCCCCAACCAAACATAGTCCCGTGCCGCC 1.000000 13 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAACGATGCGCAGTCCCGTGCCAGC 2.000000 14 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGTCCCGTGCCGCC 11.000000 15 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGTCCCGTGCAGCC 2.000000 16 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGCTTCGCGTCGGC 3.000000 17 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCATTCCCGCGTCGGC 1.000000 18 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATGATGCACAGTCCCGTGCCAGC 1.000000 19 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATGATGCACAGTCCCGTGCCGCC 2.000000 20 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATGATGCACAGTCCCGCGTCGGC 2.000000 21 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATGATGCGCAGTCCCGTGCCAGC 1.000000 22 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATGCCAATGATGCACAGTCCCCTGCCAGC 3.000000 23 CGACCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATGCCAATGATGCACAGTCCGCTGCCAGC 1.000000 24 CGACCCACCTGAIGAITCT 3 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGTCCCGTGCCGCC 1.000000 25 CGACCCACCTAADTADCCT 2 IGIGTCCCGCGGAGAGTAGTCCCAACCATGTACGTTCCGGCCCCGGA 1.000000 26 CGACCCATCCGAIGAITCT 1 DGICGCCTCTGGAGAGTAGTCTTAACCATGCGCATTCCCGCGTCGGC 2.000000 27 CGACCCGCTCGAIGGDTCT 2 DGICGTCTCTGGACAGCAGTCCCGGCCATGCACAGCTTCGCGTCGGC 1.000000 28 CGATCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATGCCAATGTTGCACAGTCCCCTGCCAGC 1.000000 29 CGATCCACTCGAIGADTCC 2 DGICGCTTCTGGAGAGTAGTCCCAACCATGCACAGTCCCGTGCCAGC 1.000000 30 CGATCCACTCGAIGGDTCT 2 DGICGTCTCTGGACAGCAGTCCCGGCCATGTACATCTTCGCGTCGGC 1.000000 31 CGGCCCACCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGTCCCGTGCAGCC 1.000000 32 CGGCCCATCCGAIGAITCT 1 DGICGCCTCTGGAGAGTAGTCTTAACCATGCGCAGTCCCGTGCCGCC 3.000000 33 CGGCCCATCCGAIGAITCT 1 DGICGCCTCTGGAGAGTAGTCTTAACCATGCGCATTCCCGTGCCGCC 1.000000 34 CGGCCCATCCGAIGAITCT 1 DGICGCCTCTGGAGAGTAGCCCCAACCATGCACATTCCCGTGCCGCC 1.000000 35 CGGCCCATCCGAIGAITCT 1 DGICGCCTCTGGAGAGTAGCCCCAACCATGCGCAGTCCCGTGCCGCC 1.000000 36 CGGCCTATCCATDTADCCT 2 IGDGTCCCGCGCAGACTGGTCCCAACCATGCACGGTCCCCTGCCAGC 1.000000 37 CGGCCTATCCATDTADCCT 2 IGDGTCCCGCGCAGACTGGTCCCAACCATGCACGTTCCGGCCCCGGA 12.000000 38 CGGCCTATCCATDTADCCT 2 IGDGTCCCGCGCAGACTGGTCCCAACGATGCACGTTCCGGTGCAGCC 3.000000 39 CGGCCTATCTGAIGAITCT 2 ICICGCCTCTGGTGGGTAATCCCAATCATGCGCAGTCCCGTGCCGCC 2.000000 40 TGACCCGCTCGAIGGDTCT 2 DGICGTCTCTGGACAGCAGTCCCGGCCATGCACATCTTCGCGTCGGC 1.000000 41 TGACCCGCTCGAIGGDTCT 2 DGICGTCTCTGGACAGCAGTCCCGGCCATGTACATCTTCGCGTCGGC 1.000000 42 TGACCCGCTCGAIGGDTCT 2 DGICGTCTCTGGACAGCAGTCCCGGCGATGTACAGTCCCGTGCCAGC 6.000000 43 TGATCCACTCGAIGADTCC 2 DGICGCTTCTGGAGAGTAGTCCCAACCATGCACAGTCCCGTGCCGGC 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (3,6) DY02: (8,42) DY03: (16,32) DY04: (9,16) DY05: (30,32) DY06: (4,33) DY07: (6,26) DY08: (26,34) DY09: (1,24) DY10: (32,42) DY11: (1,27) DY12: (2,20) DY13: (11,35) DY14: (21,37) DY15: (4,41) DY16: (14,40) DY17: (12,42) DY18: (4,16) DY19: (1,42) DY20: (11,17) DY21: (13,42) DY22: (9,29) DY23: (13,20) DY24: (9,42) E101: (36,39) E102: (14,37) E103: (7,15) E104: (37,37) E105: (23,37) E106: (19,43) E107: (38,39) E108: (38,43) E109: (37,37) E110: (14,37) E111: (31,22) E112: (15,18) E113: (14,37) E114: (14,14) E115: (14,37) E116: (14,43) E117: (5,22) E118: (10,14) E119: (14,22) E120: (14,38) E121: (7,19) E122: (37,37) E123: (28,25) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C A A C G C A C (T) T G A I G A I T G T 2 I G I C G C C T C T G G A G A G T A G T C C C A A C C A T G C A C A T T C C C G T G C C G C C C G A C C C A C (C) C G A I G G D T C T 2 D G I C G T C T C T A G A C A G C A G T C C C G G C C T T G T A C A G T C C C G T G C C A G C 0 DY02 C G A C C C A C C C G A D G A D C C T 2 D G I C G C C T C T G G A G A G T A G T C C C A A C C A A A C A C A G T C C C G T G C C A G C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C G A T G T A C A G T C C C G T G C C A G C 0 DY03 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G C T T C G C G T C G G C C G G C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G T C T T A A C C A T G C G C A G T C C C G T G C C G C C 0 DY04 C G A C C C A C C C G A D G A D C C T 2 D G I C G C C T C T G G A G A G T A G T C C C A A C C A A A C A T A G T C C C G T G C C A G C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G C T T C G C G T C G G C 0 DY05 C G A T C C [A] C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C C A T G T A C A T C T T C G C G T C G G C C G G C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G T C T T A A C C A T G C G C A G T C C C G T G C C G C C 0 DY06 C A A C G C A C T T G A I G A I T G T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A (G) T C C C G T G C C G C C C G G C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G T C T T A A C C A T G C G C A (T) T C C C G T G C C G C C 0 DY07 C G A C C C A C C C G A I G G D T C T 2 D G I C G T C T C T A G A C A G C A G T C C C G G C C T T G T A C A G T C C C G T G C C A G C C G A C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G T C T T A A C C A T G C G C A T T C C C G C G T C G G C 0 DY08 C G A C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G T C T T A A C C A T G C G C A T T C C C G C G T C G G C C G G C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G C C C C A A C C A T G C A C A T T C C C G T G C C G C C 0 DY09 C A A C C C A C C C G A I G A D T C C (2) D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G T A C A T T C C C G C G T C G G C C G A C C C A C C T G A I G A I T C T (3) I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C 0 DY10 C G G C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G T C T T A A C C A T G C G C A G T C C C G T G C C G C C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C G A T G T A C A G T C C C G T G C C A G C 0 DY11 C A A C C C A C C C G A I G A D T C C 2 D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G T A C A (T) T C C C G C G T C G G C C G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C C A T G C A C A (G) C T T C G C G T C G G C 0 DY12 C A A C G C A C C T G A I G A I T G T 2 I G I C G C C T C T G G A G A G T A G T C C C A A C C A T G C A C A T T C C C G T G C C G C C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T G A T G C A C A G T C C C G C G T C G G C 0 DY13 C G A C C C A C C T G A I G A I T C T 2 I G I C G C C T C T G G T G A G T A G C C C C A A C C A A A C A T A G T C C C G T G C C A G C C G G C C C A T C C G A I G A I T C T 1 D G I C G C C T C T G G A G A G T A G C C C C A A C C A T G C G C A G T C C C G T G C C G C C 0 DY14 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A (T) (G) A T G C G C A G T C C C G T G C C A G C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A (C) (C) A T G C A C G T T C C G G C C C C G G A 0 DY15 C A A C G C A C T T G A I G A I T G T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C C A T G T A C A T C T T C G C G T C G G C 0 DY16 (C) G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C (T) G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C C A T G C A C A T C T T C G C G T C G G C 0 DY17 C G A C C C A C C T G A I G A I T C T 2 I G I C G C C T C T G G T G A G T A G C C C C A A C C A A A C A T A G T C C C G T G C C (G) (C) C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C G A T G T A C A G T C C C G T G C C (A) (G) C 0 DY18 C A A C G C A C T T G A I G A I T G T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G C T T C G C G T C G G C 0 DY19 C A A C C C A C C C G A I G A D T C C 2 D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G T A C A T T C C C G C G T C G G C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C G A T G T A C A G T C C C G T G C C A G C 0 DY20 C G A C C C A C C T G A I G A I T C T 2 I G I C G C C T C T G G T G A G T A G C C C C A A C C A A A C A T A G T C C C G T G C C A G C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A T T C C C G C G T C G G C 0 DY21 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A C G A T G C G C A G T C C C G T G C C A G C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C G A T G T A C A G T C C C G T G C C A G C 0 DY22 C G A C C C A C C C G A D G A D C C T 2 D G I C G C C T C T G G A G A G T A G T C C C A A C C A A A C A T A G T C C C G T G C C A G C C G A T C C A C T C G A I G A D T C C 2 D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G C A C A G T C C C G T G C C A G C 0 DY23 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A C G A T G C G C A G T C C C G T G C C A G C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T G A T G C A C A G T C C C G C G T C G G C 0 DY24 C G A C C C A C C C G A D G A D C C T 2 D G I C G C C T C T G G A G A G T A G T C C C A A C C A A A C A T A G T C C C G T G C C A G C T G A C C C G C T C G A I G G D T C T 2 D G I C G T C T C T G G A C A G C A G T C C C G G C G A T G T A C A G T C C C G T G C C A G C 0 E101 C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G G T C C C C T G C C A G C C G G C C T A T C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C 0 E102 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E103 C G A C C C A C C C G A I G G D T C T 2 D G I C G T C T C T A G A C A G C A G T C C C G G C C T T G T A C A T C T T C G C G T C G G C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C A G C C 0 E104 C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E105 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T G C C A A T G A T G C A C A G T C C G C T G C C A G C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E106 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T G A T G C A C A G T C C C G T G C C G C C T G A T C C A C T C G A I G A D T C C 2 D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G C A C A G T C C C G T G C C G G C 0 E107 C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C G A T G C A C G T T C C G G T G C A G C C C G G C C T A T C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C 0 E108 C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C G A T G C A C G T T C C G G T G C A G C C T G A T C C A C T C G A I G A D T C C 2 D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G C A C A G T C C C G T G C C G G C 0 E109 C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E110 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E111 C G (G) C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C A G C C C G (A) C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T G C C A A T G A T G C A C A G T C C C C T G C C A G C 0 E112 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C A G C C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T G A T G C A C A G T C C C G T G C C A G C 0 E113 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E114 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C 0 E115 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E116 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C T G A T C C A C T C G A I G A D T C C 2 D G I C G C T T C T G G A G A G T A G T C C C A A C C A T G C A C A G T C C C G T G C C G G C 0 E117 C G A C C C A C C C G A I G G D T C T 2 D G I C G T C T C T A G A C A G C A G T C C C G G C C (T) T G C A C A T C T T C G C G T C G G C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T G C C A A T G (A) T G C A C A G T C C C C T G C C A G C 0 E118 C G A C C C A C C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C 0 E119 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T G C C A A T G A T G C A C A G T C C C C T G C C A G C 0 E120 C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T C A T G C G C A G T C C C G T G C C G C C C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C G A T G C A C G T T C C G G T G C A G C C 0 E121 C G A C C C A C C C G A I G G D T C T 2 D G I C G T C T C T A G A C A G C A G T C C C G G C C T T G T A C A T C T T C G C G T C G G C C G A C C C A C C T G A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T C C C A A T G A T G C A C A G T C C C G T G C C G C C 0 E122 C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A C G G C C T A T C C A T D T A D C C T 2 I G D G T C C C G C G C A G A C T G G T C C C A A C C A T G C A C G T T C C G G C C C C G G A 0 E123 C G A (T) C C A C C T (G) A I G A I T C T 2 I C I C G C C T C T G G T G G G T A A T G C C A A T G T T G C A C A G T C C C C T G C C A G C C G A (C) C C A C C T (A) A D T A D C C T 2 I G I G T C C C G C G G A G A G T A G T C C C A A C C A T G T A C G T T C C G G C C C C G G 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 = A = = G = = = (T) T = = = = A I = G = = I = = = = C = = = = G = = G = = T = = = = = = A A = = A = = C = = = T = = = = = = = = = G C = = G = = C = = = (C) C = = = = G D = C = = D = = = = T = = = = A = = C = = C = = = = = = G G = = T = = T = = = G = = = = = = = = = A G = 0 DY02 C = = = = = A = C = = = D = A = C = = = = = = = = C = = = = = = = G = = T = = = = = = A A = C = A A C = = = = = = = = = ? = = = = = = T = = = = = G = T = = = I = G = T = = = = = = = = T = = = = = = = C = = C = = = = = = G G = G = T G T = = = = = = = = = ? = = = = = = 0 DY03 = = A = = = = C = T = = = = = = = = = 2 I C ? = = = = = = = = = T = ? = = = A = = C C = = T = = = = = = = = = C T T = = C = T = = G = = = G = = = = T = C = = = = = = = = = 1 D G ? = = = = = = = = = A = ? = = = G = = T T = = C = = = = = = = = = T C C = = T = C = = C = 0 DY04 = = = = = = = = = C = = D = = D C = = = D G = = = = = = = = = = A = A = = = G = = = = = = C ? = A A = A T = = T C C = = T = C = A = = = = = = = = = = = T = = I = = I T = = = I C = = = = = = = = = = T = G = = = A = = = = = = T ? = T G = G C = = C T T = = C = T = G = = 0 DY05 = = A T = = ? ? T = = = = = G D = = = 2 = = = = = T = = = = = = = C = = C = = = = C C G G = = = = = T A = = T C T T = = C = T = = G = = = G C = = ? ? C = = = = = A I = = = 1 = = = = = C = = = = = = = G = = T = = = = T T A A = = = = = C G = = G T C C = = T = C = = C = 0 DY06 = A A = G = = C T T = = = = = = = G = 2 I C = = = = = = = = = = T = G = = = A = = C C = = T = = = = = = = = (G) = = = = = = = = = = = = = G G = C = = T C C = = = = = = = C = 1 D G = = = = = = = = = = A = A = = = G = = T T = = C = = = = = = = = (T) = = = = = = = = = = = = 0 DY07 = = = = = = = C = = = = = = G D = = = 2 = = = = = T = = = = A = = C = = C = = = = C C G G = = T = = T A = = G = = = = = T = C = A = ? = = = = = = = T = = = = = = A I = = = 1 = = = = = C = = = = G = = G = = T = = = = T T A A = = A = = C G = = T = = = = = C = T = G = ? 0 DY08 = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = T T = = = = = = = = G = = = = = ? = = C = T = = G = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C C = = = = = = = = A = = = = = ? = = T = C = = C = 0 DY09 = A = = = = = = = C = = = = = D = = C (2) D G = = = = T = = = = = A = A = = = G = = = = = = C = = = = T A = = T = = = = = C = T = = G = = G = = = = = = = T = = = = = I = = T (3) I C = = = = C = = = = = T = G = = = A = = = = = = T = = = = C G = = G = = = = = T = C = = C = 0 DY10 C = G = = = A T C = = = = = A I = = = 1 = = = = = C = = = = = = = G = = T = = = = T T A A = C = = = C G = = = = = = = = = = = = G C = T = A = = = G C T = = = = = G D = = = 2 = = = = = T = = = = = = = C = = C = = = = C C G G = G = = = T A = = = = = = = = = = = = A G = 0 DY11 = A = = ? = A = C = ? ? = = A = = = C = = = = = = C T = = = = = = G = = T = = = = = = A A = = = = = T = = = (T) T C C = = = = = = = = = = G = = ? = G = T = ? ? = = G = = = T = = = = = = T C = = = = = = C = = C = = = = = = G G = = = = = C = = = (G) C T T = = = = = = = = = 0 DY12 = A = = G = = = = = = = = = = = = G = = = G = = = = = = = = = = A = A = = = G = = = = = = C C = = = = = = = T = = = = = T = C = = C = = G = = C = = = = = = = = = = = = C = = = C = = = = = = = = = = T = G = = = A = = = = = = T G = = = = = = = G = = = = = C = T = = G = 0 DY13 = = A = = = = C = T = = = = = = = = = 2 I = = = = = = = = = = = T = = = = = = = = = = = = = = = A A = A T = = = = = = = = = = = A G = = = G = = = = T = C = = = = = = = = = 1 D = = = = = = = = = = = A = = = = = = = = = = = = = = = T G = G C = = = = = = = = = = = G C = 0 DY14 = = A = = C = C = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = (T) (G) = = ? ? G = A G = = = C = T G = = A = C = = G = = T = T = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = (C) (C) = = ? ? A = G T = = = G = C C = = G = A 0 DY15 C A = = G = A = = T = = = = A I = G = = I C = = = C = = = = = = T G G = T = A = = = = A A T = = = = C G = = G T C C = = T = C = = C = T G = = C = G = = C = = = = G D = C = = D G = = = T = = = = = = A C A = C = G = = = = G G C = = = = T A = = T C T T = = C = T = = G = 0 DY16 (C) = = = = = A = C T = = = = A I = = = = I C = = = C = = = = = = T G G = T = A = = = = A A T = = = = = G = = G T C C = = T = C = = C = (T) = = = = = G = T C = = = = G D = = = = D G = = = T = = = = = = A C A = C = G = = = = G G C = = = = = A = = T C T T = = C = T = = G = 0 DY17 C = = = = = A = C T = = = = A I = = = = I = = = = C = = = = = = T G = = T = = C = = = A A = C = A A C = T = = = = = = = = = = = (G) (C) = T = = = = = G = T C = = = = G D = = = = D = = = = T = = = = = = A C = = C = = T = = = G G = G = T G T = C = = = = = = = = = = = (A) (G) = 0 DY18 = A = = G = = = T = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T ? C ? ? T = C = = C = = G = = C = = = C = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C ? T ? ? C = T = = G = 0 DY19 C A = = = = A = C = = = = = A = = = C = = = = = = C T = = = = = = G = = T = = = = = = A A = C = = = = = = = T = = = = = C = T = G = = T G = = = = G = T = = = = = G = = = T = = = = = = T C = = = = = = C = = C = = = = = = G G = G = = = = = = = G = = = = = T = C = A = = 0 DY20 = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = A = = = G C = = = = = C = = A A = A T = G = = = = = T = C = A = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = G = = = A T = = = = = T = = T G = G C = T = = = = = C = T = G = = 0 DY21 C = = = = = A = C T = = = = A I = = = = I C = = = C = = = = = = T G G = T = A = = = = A A = = = = = C G = = = = = = = = = = = = = = = T = = = = = G = T C = = = = G D = = = = D G = = = T = = = = = = A C A = C = G = = = = G G = = = = = T A = = = = = = = = = = = = = = = 0 DY22 = = = C = = = = C = = = D = = = C = T = = = = = = = C = = = = = = = = = = = = = = = = = = = = = A A = = T = = = = = = = = = = = = = = = = = T = = = = T = = = I = = = T = C = = = = = = = T = = = = = = = = = = = = = = = = = = = = = T G = = C = = = = = = = = = = = = = = 0 DY23 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = G = = = = = = = = T = C = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = A = = = = = = = = C = T = G = = 0 DY24 C = = = = = A = C = = = D = A = C = = = = = = = = C = = = = = = = G = = T = = = = = = A A = C = A A C = T = = = = = = = = = = = = = = T = = = = = G = T = = = I = G = T = = = = = = = = T = = = = = = = C = = C = = = = = = G G = G = T G T = C = = = = = = = = = = = = = = 0 E101 = = = = = = = = = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = C = = = = = A = G = = = = = C = = = = A G = = = = = = = = = = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = T = = = = = G = A = = = = = G = = = = G C = 0 E102 = = A = = C = C = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = T = = = = = G = A G = = = C = T G = = = C C = = G = = T = T = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = C = = = = = A = G T = = = G = C C = = = G A 0 E103 = = = = = = = = = C = = = = G D = = = = D G = = = T = = = = A = A C A = C = G = = = = G G C = T = = T A = = T C T T = = C = T C = G = = = = = = = = = = T = = = = A I = = = = I C = = = C = = = = G = T G G = T = A = = = = A A T = A = = C G = = G T C C = = T = C A = C = 0 E104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 = = A = = C = C = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = G = = = = T G = = = = = = A G = = = = C T G = = A = C = = G = = T = T = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = C = = = = C C = = = = = = G T = = = = G C C = = G = A 0 E106 C = = C = = = = C T = = = = = I = = T = I C = = = = C = = = = = T = G = = = A = = = = = = T G = = = = = = = = = = = = = = = = = = C = T = = T = = = = T C = = = = = D = = C = D G = = = = T = = = = = A = A = = = G = = = = = = C C = = = = = = = = = = = = = = = = = = G = 0 E107 = = = = = = = = = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = C G = = = = A = G T = = = G = = = = A = = = = = = = = = = = = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = T C = = = = G = A G = = = C = = = = C = = = 0 E108 C = G C = T = T C = A T D T = = C = ? = I = D G T = C C G C = C = = = C = G = = = = = = = = G = = = = = = G T = = = G = = = = A = C = T = A T = C = C T = G A I G = = T = ? = D = I C G = T T C T = G = = = G = A = = = = = = = = C = = = = = = A G = = = C = = = = C = G = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0 E110 = = A = = C = C = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = T = = = = = G = A G = = = C = T G = = = C C = = G = = T = T = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = C = = = = = A = G T = = = G = C C = = = G A 0 E111 = = (G) = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = C = = = = G = = = = = = = G = = = A G C = = = (A) = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = G = = = = A = = = = = = = C = = = C A G = 0 E112 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = C = = = = G = = = = = = = = = = = A G C = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = G = = = = A = = = = = = = = = = = C A G = 0 E113 = = A = = C = C = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = ? T = = = = = G = A G = = = C = T G = = = C C = = G = = T = T = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = ? C = = = = = A = G T = = = G = C C = = = G A 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 = = A = = C = C = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = T = = = = = G = A G = = = C = T G = = = C ? = = G = = T = T = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = C = = = = = A = G T = = = G = C C = = = G ? 0 E116 C = = C = = = = C T = = = = = I = = T = I C = = = = C = = = = = T = G = = = A = = = = = = T = = = = = G = = = = = = = = = = = = = C = T = = T = = = = T C = = = = = D = = C = D G = = = = T = = = = = A = A = = = G = = = = = = C = = = = = A = = = = = = = = = = = = = G = 0 E117 = = = = = = = = = C = = = = G D = = = = D G = = = T = = = = A = A C A = C = G = C = = G G C C (T) = = = = = = T C T T = G C = T = G = = = = = = = = = = = T = = = = A I = = = = I C = = = C = = = = G = T G G = T = A = G = = A A T G (A) = = = = = = G T C C = C T = C = A = = 0 E118 = = = = = = = = = C A T D T = D C = = = = G D G T = = C G C = C A = A C = G G = = = = = = C = = = = = A = G ? = = = G = C C = = = G A = = = = = = = = = T G A I G = I T = = = = C I C G = = T C T = G T = G G = A A = = = = = = T = = = = = G = A ? = = = C = T G = = = C C 0 E119 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = C = = = = = C = = = = G = = = = = = = G = = = = G C = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = G = = = = = G = = = = A = = = = = = = C = = = = A G = 0 E120 = = A = = C = C = T G A I G = I T = = = = ? I C G = = T C T = G T = G G = A A = = = = = = T C = = = = G = A G = = = C = = = = C = = = = = G = = T = T = C A T D T = D C = = = = ? D G T = = C G C = C A = A C = G G = = = = = = C G = = = = A = G T = = = G = = = = A = = = 0 E121 = = = = = = ? ? = ? = = = = G D = = = = D G = = = T = = = = A = A C A = C = G = = = = G G C C T = = T = = = T C T T = = C = T = = G = = = = = = = ? ? = ? = = = = A I = = = = I C = = = C = = = = G = T G G = T = A = = = = A A T G A = = C = = = G T C C = = T = C = = C = 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E123 = = = (T) = = = = = = (G) = I G = I T = = = = ? = C G = = T C T = = T = G = ? = A = G = = = = T G T = = C = = A G = = = C C T G = = A = C = = = (C) = = = = = = (A) = D T = D C = = = = ? = G T = = C G C = = A = A = ? = G = C = = = = C C A = = T = = G T = = = G G C C = = G = A 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 = = = 0.65 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 = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = = = = = ? = = = = = = = = 1.00 = = = = 1.00 = 1.00 = = = = = = = = = 1.00 1.00 1.00 ? = = = = = = = = = 1.00 = ? = = = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = = = = = = 1.00 = = 1.00 = = 1.00 1.00 = = = 1.00 1.00 = = = = = = = = = = 1.00 = 1.00 = = = 1.00 = = = = = = 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 = = = = = = = = 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 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 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 = = = 0.52 1.00 1.00 1.00 = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = = 1.00 = 1.00 = = = 1.00 = = = = = = 1.00 1.00 = = = = = = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = = 1.00 = = = = 1.00 = 1.00 = = = = = = = = = 1.00 1.00 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = 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 = = = = = = 0.81 0.83 = = ? ? 0.90 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = 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 = = 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 = = = = = = = = = = = 0.51 0.51 = = 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 1.00 = 1.00 1.00 = 1.00 = = = = = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 = = = 1.00 = 1.00 = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = = = = = = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = 1.00 = 1.00 = = = 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 = = = = = = = 1.00 = = 1.00 = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 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 = = 0.98 = 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 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = 1.00 = = = 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 1.00 = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = ? = 1.00 = 1.00 1.00 1.00 = 1.00 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 = = 0.98 = 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 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = 0.50 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = = 1.00 = = = = = = = 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 0.93 = = = = 0.93 = = = = = = = = = = = 0.98 1.00 1.00 = = = 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 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 ? 1.00 = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = 1.00 = = = 1.00 = = = = = = 1.00 = = = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 = = = 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 = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 = = = = = 1.00 = 1.00 ? = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = = 1.00 = = = = = = = 1.00 = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = ? 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 1.00 = = = = = = = = = ? ? = ? = = = = 1.00 1.00 = = = = 1.00 1.00 = = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.53 = = = = = = 0.80 = 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 1.00 1.00 = = 1.00 = 1.00 END PHASEPROBS