************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 fmo5x.phase.inp fmo5x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fmo5x.phase.out_freqs : haplotype frequency estimates fmo5x.phase.out_pairs : most likely haplotype pairs for each individual fmo5x.phase.out_recom : estimates of recombination parameters fmo5x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 29 Positions of loci: 420 522 739 816 1255 9269 10297 11107 11838 12922 13089 13724 14080 17463 17949 24249 24253 24405 24569 24704 24722 25305 26264 35373 35406 35987 36877 41460 41597 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fmo5x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AAACGATGGGTICTCACACGTACCGTCIT 1.000000 2 AAACGACCGACDCTTGGATGCGTCGTCIC 2.000000 3 AAGCCACCGACICTTGCATGCGCCGTADC 1.000000 4 AAGCCACCGACDCTTGCATGCGCCGTADC 2.000000 5 AAGCCACCGACDCTTGCATGCGCCATADC 2.000000 6 AAGCGGTCGGTICTCACACGTACCGCADC 5.000000 7 AAGTCATCGGTICTCACACGTACCGTADC 6.000000 8 AAGTCATGGGTICTCACACGTACCGTCIT 11.000000 9 AAGTCACCGACDCTTGGATGCGTCGTADC 1.000000 10 AAGTCACCGACDCTTGGATGCGTCGTCIC 5.000000 11 AAGTCACCGACDCTTGGATGCGTCGCADC 1.000000 12 AAGTCGTCGGTICTCACACGTACCGCADC 7.000000 13 AAGTCGTCAGTICTCACACTTACCGTADC 20.000000 14 ATACGATGGGTICTCACACGTACCGTCIT 5.000000 15 ATACGATGGGTICTCACACGTACCATCIT 2.000000 16 ATACGATGGGTICTCACACGTACGATCIT 1.000000 17 ATACGATGGGTICCCACACGTACCGTCIT 17.000000 18 ATACGATGGGTICCCACACGTACCGTCDT 1.000000 19 ATACGATGGGTICCCACACGTACGATCIT 5.000000 20 ATACGATGGGTDCCCACACGTACCGTCIT 7.000000 21 ATACGGTCGGTICTCACACTTACCGTADC 4.000000 22 GAGTCATGGGTICTCACACGTACCGTCIT 16.000000 23 GAGTCATGGGTICTCACACGTACGATCIT 3.000000 24 GAGTCATGGGTICTCAGCCGTACCGTCIT 1.000000 25 GAGTCATGGGTITTCACACGTACCGTCIT 1.000000 26 GAGTCATGGGTITTCACCCGTACCGTCIT 35.000000 27 GAGTCATGGGTITTCACCCGTACGATCIT 2.000000 28 GAGTCGTCGGTICTCACACTTACCGTADC 3.000000 29 GAGTCGTCAGTICTCACACTTACCGTADC 2.000000 30 GTACGATGGGTICTCACACGTACCGTCIT 20.000000 31 GTACGATGGGTICTCACCCGTACCGTCIT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (7,14) D002: (3,14) D003: (21,30) D004: (9,30) D005: (13,23) D006: (8,22) D007: (6,14) D008: (17,30) D009: (14,16) D010: (21,28) D011: (12,21) D012: (6,15) D013: (8,17) D014: (8,19) D015: (13,30) DY01: (4,7) DY02: (6,8) DY03: (7,8) DY04: (13,14) DY05: (7,8) DY06: (8,30) DY07: (8,11) DY08: (6,8) DY09: (7,28) DY10: (21,30) DY11: (7,28) DY12: (8,8) E101: (13,30) E102: (13,30) E103: (4,30) E104: (15,30) E105: (17,26) E106: (5,22) E107: (2,17) E108: (13,31) E109: (13,30) E110: (17,26) E111: (13,17) E112: (17,22) E113: (10,30) E114: (5,30) E115: (22,26) E116: (19,30) E117: (27,30) E118: (10,17) E119: (13,17) E120: (13,30) E121: (10,17) E122: (13,17) H101: (20,20) H102: (13,27) H103: (13,26) H104: (19,26) H105: (17,26) H106: (25,26) H107: (2,26) H108: (18,20) H109: (17,20) H110: (6,22) H111: (13,30) H112: (26,30) H113: (13,20) H114: (23,30) H115: (10,30) H116: (13,17) H117: (19,19) H118: (17,26) H119: (20,22) H120: (17,26) H121: (10,23) H122: (17,20) X101: (1,26) X102: (26,26) X103: (22,26) X104: (12,22) X105: (12,22) X106: (26,26) X107: (12,26) X108: (26,26) X109: (26,26) X110: (13,22) X111: (22,29) X112: (13,26) X113: (22,29) X114: (12,22) X115: (26,26) X116: (22,26) X117: (24,26) X118: (26,26) X119: (22,22) X120: (12,26) X121: (12,26) X122: (26,26) X123: (13,26) X124: (13,26) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A A G T C A T C G G T I C T C A C A C G T A C C G T A D C A T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 D002 A A G C C A C C G A C I C T T G C A T G C G C C [G] T A D C A T A C G A T G G G T I C T C A C A C G T A C C [G] T C I T 0 D003 (A) T A C G G T C G G T I C T C A C A C [T] T A C C G T A D C (G) T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 D004 A A G T C A C C G A C D C T T G G A T G C G T C G T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 D005 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G A G T C A T G G G T I C T C A C A C G T A C G A T C I T 0 D006 A A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 D007 A A G C G G T C G G T I C T C A C A C G T A C C G C A D C A T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 D008 A T A C G A T G G G T I C [C] C A C A C G T A C C G T C I T G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 D009 A T A C G A T G G G T I C T C A C A C G T A C C G T C I T A T A C G A T G G G T I C T C A C A C G T A C G A T C I T 0 D010 A T A C G G T C G G T I C T C A C A C [T] T A C C G T A D C [G] A G T C G T C G G T I C T C A C A C T T A C C G T A D C 0 D011 A A G T C G T C G G T I C T C A C A C G T A C C G (C) A D C A T A C G G T C G G T I C T C A C A C [T] T A C C G (T) A D C 0 D012 A A G C G G T C G G T I C T C A C A C G T A C C G C A D C A T A C G A T G G G T I C T C A C A C G T A C C A T C I T 0 D013 A A G T C A T G G G T I C T C A C A C G T A C C G T C I T A T A C G A T G G G T I C C C A C A C G T A C C G T C I T 0 D014 A A G T C A T G G G T I C T C A C A C G T A C C G T C I T A T A C G A T G G G T I C [C] C A C A C G T A C G A T C I T 0 D015 A (A) (G) (T) (C) G T C [A] G T I C T C A C A C T T A C C G T A D C [G] (T) (A) (C) (G) A T G G G T I C T C A C A C G T A C C G T C I T 0 DY01 A A G C C A C C G A C D C T T G C A T G C G C C [G] T A D C A A G T C A T C G G T I C T C A C A C G T A C C G T A D C 0 DY02 A A G C G G T C G G T I C T C A C A C G T A C C G C A D C A A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 DY03 A A G T C A T C G G T I C T C A C A C G T A C C G T A D C A A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 DY04 A (A) (G) (T) (C) G T C [A] G T I C T C A C A C T T A C C G T A D C A (T) (A) (C) (G) A T G G G T I C T C A C A C G T A C C G T C I T 0 DY05 A A G T C A T C G G T I C T C A C A C G T A C C G T A D C A A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 DY06 (A) A G T C A T G G G T I C T C A C A C G T A C C G T C I T (G) T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 DY07 A A G T C A T G G G T I C T C A C A C G T A C C G T C I T A A G T C A C C G A C D C T T G G A T G C G T C G C A D C 0 DY08 A A G C G G T C G G T I C T C A C A C G T A C C G C A D C A A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 DY09 A A G T C A T C G G T I C T C A C A C G T A C C G T A D C [G] A G T C G T C G G T I C T C A C A C T T A C C G T A D C 0 DY10 A T A C G G T C G G T I C T C A C A C [T] T A C C G T A D C [G] T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 DY11 A A G T C A T C G G T I C T C A C A C G T A C C G T A D C [G] A G T C G T C G G T I C T C A C A C T T A C C G T A D C 0 DY12 A A G T C A T G G G T I C T C A C A C G T A C C G T C I T A A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 E101 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E102 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E103 A A G C C A C C G A C D C T T G C A T G C G C C [G] T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E104 A T A C G A T G G G T I C T C A C A C G T A C C A T C I T G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E105 A T A C G A T G G G T I C C C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 E106 A A G C C A C C G A C D C T T G C A T G C G C C [A] T A D C G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 E107 A A A C G A C C G A C D C T T G G A T G C G T C G T C I C A T A C G A T G G G T I C C C A C A C G T A C C G T C I T 0 E108 (A) (A) (G) (T) (C) G T C A G T I C T C A C (A) C T T A C C G T A D C (G) (T) (A) (C) (G) A T G G G T I C T C A C (C) C G T A C C G T C I T 0 E109 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E110 A T A C G A T G G G T I C C C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 E111 A A G T C G T C [A] G T I C T C A C A C T T A C C G T A D C A T A C G A T G G G T I C [C] C A C A C G T A C C G T C I T 0 E112 A T A C G A T G G G T I C C C A C A C G T A C C G T C I T G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 E113 A A G T C A C C G A C D C T T G G A T G C G T C G T C I C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E114 A A G C C A C C G A C D C T T G C A T G C G C C [A] T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E115 G A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 E116 A T A C G A T G G G T I C C C A C A C G T A C G A T C I T G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E117 G A G T C A T G G G T I T T C A C C C G T A C (G) (A) T C I T G T A C G A T G G G T I C T C A C A C G T A C (C) (G) T C I T 0 E118 A A G T C A C C G A C D C T T G G A T G C G T C G T C I C A T A C G A T G G G T I C C C A C A C G T A C C G T C I T 0 E119 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C A T A C G A T G G G T I C [C] C A C A C G T A C C G T C I T 0 E120 (A) A G T C G T C A G T I C T C A C A C T T A C C G T A D C (G) T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 E121 A A G T C A C C G A C D C T T G G A T G C G T C G T C I C A T A C G A T G G G T I C C C A C A C G T A C C G T C I T 0 E122 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C A T A C G A T G G G T I C C C A C A C G T A C C G T C I T 0 H101 A T A C G A T G G G T D C C C A C A C G T A C C G T C I T A T A C G A T G G G T D C C C A C A C G T A C C G T C I T 0 H102 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G A G T C A T G G G T I T T C A C C C G T A C G A T C I T 0 H103 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 H104 A T A C G A T G G G T I C C C A C A C G T A C (G) (A) T C I T G A G T C A T G G G T I T T C A C C C G T A C (C) (G) T C I T 0 H105 A T A C G A T G G G T I C C C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 H106 G A G T C A T G G G T I T T C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 H107 A A A C G A C C G A C D C T T G G A T G C G T C G T C I C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 H108 A T A C G A T G G G T (I) C C C A C A C G T A C C G T C D [T] A T A C G A T G G G T (D) C C C A C A C G T A C C G T C I T 0 H109 A T A C G A T G G G T I C [C] C A C A C G T A C C G T C I T A T A C G A T G G G T D C C C A C A C G T A C C G T C I T 0 H110 A A G C G G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 H111 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 H112 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 H113 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C A T A C G A T G G G T D C C C A C A C G T A C C G T C I T 0 H114 G A G T C A T G G G T I C T C A C A C G T A C (G) (A) T C I T G T A C G A T G G G T I C T C A C A C G T A C (C) (G) T C I T 0 H115 A A G T C A C C G A C D C T T G G A T G C G T C G T C I C G T A C G A T G G G T I C T C A C A C G T A C C G T C I T 0 H116 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C A T A C G A T G G G T I C C C A C A C G T A C C G T C I T 0 H117 A T A C G A T G G G T I C C C A C A C G T A C G A T C I T A T A C G A T G G G T I C C C A C A C G T A C G A T C I T 0 H118 A T A C G A T G G G T I C C C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 H119 A T A C G A T G G G T D C C C A C A C G T A C C G T C I T G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 H120 A T A C G A T G G G T I C C C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 H121 A A G T C A C C G A C D C T T G G A T G C G T C G T C I C G A G T C A T G G G T I C T C A C A C G T A C G A T C I T 0 H122 A T A C G A T G G G T I C [C] C A C A C G T A C C G T C I T A T A C G A T G G G T D C C C A C A C G T A C C G T C I T 0 X101 A A A C G A T G G G T I (C) T C A C (A) C G T A C C G T C I T G A G T C A T G G G T I (T) T C A C (C) C G T A C C G T C I T 0 X102 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X103 G A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X104 A A G T C G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 X105 A A G T C G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 X106 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X107 A A G T C G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X108 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X109 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X110 (A) A G T C G T C A G T I C T C A C A C T T A C C G T A D C (G) A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 X111 G A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C G T C A G T I C T C A C A C T T A C C G T A D C 0 X112 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X113 G A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C G T C A G T I C T C A C A C T T A C C G T A D C 0 X114 A A G T C G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 X115 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X116 G A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X117 G A G T C A T G G G T I (C) T C A G C C G T A C C G T C I T G A G T C A T G G G T I (T) T C A C C C G T A C C G T C I T 0 X118 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X119 G A G T C A T G G G T I C T C A C A C G T A C C G T C I T G A G T C A T G G G T I C T C A C A C G T A C C G T C I T 0 X120 A A G T C G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X121 A A G T C G T C G G T I C T C A C A C G T A C C G C A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X122 G A G T C A T G G G T I T T C A C C C G T A C C G T C I T G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X123 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T 0 X124 A A G T C G T C A G T I C T C A C A C T T A C C G T A D C G A G T C A T G G G T I T T C A C C C G T A C C G T C I T END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 D001 = A G T C = ? C = = = = = = = = = = = = = = = = = = A ? ? = T A C G = ? G = = = = = = = = = = = = = = = = = = C ? ? 0 D002 = A G = C = ? C = A C = = = T G = = T = C G = ? ? = ? ? C = T A = G = ? G = G T = = = C A = = C = T A = ? ? = ? ? T 0 D003 (A) = = = = G = C = = = = = = ? ? ? ? ? ? ? = ? = = = A ? C (G) = = = = A = G = = = = = = ? ? ? ? ? ? ? = ? = = = C ? T 0 D004 A A G T C = ? C = A C D = = T G G = T = C G T = = = A D C G T A C G = ? G = G T I = = C A C = C = T A C = = = C I T 0 D005 ? = = = = G = C A = = = = ? = = = = = T = = = C G = A D C ? = = = = A = G G = = = = ? = = = = = G = = = G A = C I T 0 D006 A = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D007 = A G = = G = C = = = = = = = = = = = = = = = = = C A D C = T A = = A = G = = = = = = = = = = = = = = = = = T C I T 0 D008 A = = = = = = = = = = = = ? = = = = = = = = = = = = = = = G = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 D009 = = = = = = = = = = = = = = = = = = = = = = = C G = = = = = = = = = = = = = = = = = = = = = = = = = = = G A = = = = 0 D010 ? T A C G = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = ? A G T C = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = 0 D011 = A G T C = = = ? = = = = = = ? ? ? ? ? ? = = = = (C) = = = = T A C G = = = ? = = = = = = ? ? ? ? ? ? = = = = (T) = = = 0 D012 = A G = = G = C = = = = = = = = = = = = = = = = G C A D C = T A = = A = G = = = = = = = = = = = = = = = = A T C I T 0 D013 = A G T C = = = = = = = = T = = = = = = = = = = = = = ? ? = T A C G = = = = = = = = C = = = = = = = = = = = = = ? ? 0 D014 = A G T C = = = = = = = = ? = = = = = = = = = C G = = = = = T A C G = = = = = = = = ? = = = = = = = = = G A = = = = 0 D015 ? (A) (G) (T) (C) G ? C ? = = = = = = = = = = T = = = = = = A D C ? (T) (A) (C) (G) A ? G ? = = = = = = = = = = G = = = = = = C I T 0 DY01 = = = C = = C = = A C D = = T G = = T = C G = ? ? ? ? ? ? = = = T = = T = = G T I = = C A = = C = T A = ? ? ? ? ? ? 0 DY02 = = = C G ? ? C ? = = = = = = = = = = = = = = ? ? C A D C = = = T C ? ? G ? = = = = = = = = = = = = = = ? ? T C I T 0 DY03 = = = = = = = C ? = = = = ? = = = = = = = = = = = = A ? ? = = = = = = = G ? = = = = ? = = = = = = = = = = = = C ? ? 0 DY04 = (A) (G) (T) (C) G = C ? = = = = = = ? ? ? ? ? ? = = = = = A D C = (T) (A) (C) (G) A = G ? = = = = = = ? ? ? ? ? ? = = = = = C I T 0 DY05 = = = = = = = C = = = = = = = = = = = = = = = = = = A D C = = = = = = = G = = = = = = = = = = = = = = = = = = C I T 0 DY06 (A) A G T C = = = = = = = = = = = = = = = = = = = = = = = = (G) T A C G = = = = = = = = = = = = = = = = = = = = = = = = 0 DY07 = = = = = = T G = G T I = = C A C = C = T A ? = = T C I T = = = = = = C C = A C D = = T G G = T = C G ? = = C A D C 0 DY08 = = = C G G = C = = = = = ? = = = = = = = = = = = C A D C = = = T C A = G = = = = = ? = = = = = = = = = = = T C I T 0 DY09 ? = = = = A = = = = = = = = = = = = = G = = ? = = = = ? ? ? = = = = G = = = = = = = = = = = = = T = = ? = = = = ? ? 0 DY10 ? = = = = G = C = = = = = = ? ? ? ? ? ? ? = = = = = A D C ? = = = = A = G = = = = = = ? ? ? ? ? ? ? = = = = = C I T 0 DY11 ? = = = = A = = = = = = = = = = = = = G = = = = = = = = = ? = = = = G = = = = = = = = = = = = = T = = = = = = = = = 0 DY12 = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0 E101 A A G T C G = C A = = = = = = ? ? ? ? ? ? = = = = = A D C G T A C G A = G G = = = = = = ? ? ? ? ? ? = = = = = C I T 0 E102 A A G T C G = C A = = = = = = = = = = T = = ? = = = A D C G T A C G A = G G = = = = = = = = = = G = = ? = = = C I T 0 E103 A A G = C = C C = A C D = = T G = = T = C G = ? ? = ? ? C G T A = G = T G = G T I = = C A = = C = T A = ? ? = ? ? T 0 E104 A = = = = = = = = = = = = ? = = = = = = = = = = A = = = = G = = = = = = = = = = = = ? = = = = = = = = = = G = = = = 0 E105 A T A C G = = = = = = = C C = = = ? ? ? ? = ? ? ? = = = = G A G T C = = = = = = = T T = = = ? ? ? ? = ? ? ? = = = = 0 E106 A = = C = = ? C ? A C D = = T G = = T = C G ? ? ? ? ? ? ? G = = T = = ? G ? G T I = = C A = = C = T A ? ? ? ? ? ? ? 0 E107 = A = = = = C C = A C D = T T G G = T = C G T = ? = = = C = T = = = = T G = G T I = C C A C = C = T A C = ? = = = T 0 E108 (A) (A) (G) (T) (C) G = C A = = = = = = = = (A) = T = = ? = = = A D C (G) (T) (A) (C) (G) A = G G = = = = = = = = (C) = G = = ? = = = C I T 0 E109 A A G T C G = C A = = = = = = = = = = T = = = = = = A D C G T A C G A = G G = = = = = = = = = = G = = = = = = C I T 0 E110 A T A C G = = = = = = = C C = = = A = = = = = = = = = ? ? G A G T C = = = = = = = T T = = = C = = = = = = = = = ? ? 0 E111 = A G T C G = C ? = = = = ? = = = = = T = = ? ? ? = A D C = T A C G A = G ? = = = = ? = = = = = G = = ? ? ? = C I T 0 E112 A T A C G = = = = = = = = C ? = = = = = = = ? = = ? = = = G A G T C = = = = = = = = T ? = = = = = = = ? = = ? = = = 0 E113 A A G T C = C C = A C D = ? T G G = T = C G T = = = = = C G T A C G = T G = G T I = ? C A C = C = T A C = = = = = T 0 E114 A A G = C = C C = A C D = = T G = = T = C G ? ? ? ? ? ? C G T A = G = T G = G T I = = C A = = C = T A ? ? ? ? ? ? T 0 E115 = = = = = = = = = = = = C = = = = A = = = = = = = = = = = = = = = = = = = = = = = T = = = = C = = = = = = = = = = = 0 E116 A = = = = = = = = = = = = C = = = = = = = = = G A = = = = G = = = = = = = = = = = = T = = = = = = = = = C G = = = = 0 E117 = A G T C = = = = = = = T = = = = C = = = = = (G) (A) = = = = = T A C G = = = = = = = C = = = = A = = = = = (C) (G) = = = = 0 E118 = A G T C = C C = A C D = T T G G = T = C G T = = = = = C = T A C G = T G = G T I = C C A C = C = T A C = = = = = T 0 E119 = ? G T C G = C A = = = = ? = = = = = T = = = = = = A D ? = ? A C G A = G G = = = = ? = = = = = G = = = = = = C I ? 0 E120 (A) A G T C G = C A = = = = = = = = = = T = = = ? ? = A D C (G) T A C G A = G G = = = = = = = = = = G = = = ? ? = C I T 0 E121 = A G T C = C C = A C D = T ? G G = T = C G T = = = = ? ? = T A C G = T G = G T I = C ? A C = C = T A C = = = = ? ? 0 E122 = A G T C G = C ? = = = = T = = = = = T = = = = = = A D ? = T A C G A = G ? = = = = C = = = = = G = = = = = = C I ? 0 H101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H102 A = = = = G = C A = = = C = = = = A = T = = = C G = A D C G = = = = A = G G = = = T = = = = C = G = = = G A = C I T 0 H103 A = = = = G = C A = = = C = = = = A = T = = ? = = = A D C G = = = = A = G G = = = T = = = = C = G = = ? = = = C I T 0 H104 A T A C G = = = = = = = C C = = = A = = = = = (G) (A) = = = = G A G T C = = = = = = = T T = = = C = = = = = (C) (G) = = = = 0 H105 A T A C G = = = = = = = C C = = = A = = = = = = = = = = = G A G T C = = = = = = = T T = = = C = = = = = = = = = = = 0 H106 = = = = = = = = = = = = = ? = = = A = = = = = = = = = = = = = = = = = = = = = = = = ? = = = C = = = = = = = = = = = 0 H107 A = A C G = C C = A C D C = T G G A T = C G T = = = = = C G = G T C = T G = G T I T = C A C C C = T A C = = = = = T 0 H108 = = = = = = = = = = = (I) = = = = = = = = = = ? = = = = D ? = = = = = = = = = = = (D) = = = = = = = = = = ? = = = = I ? 0 H109 = = = = = = = = = = = I = ? = = = = = = = = = ? ? = = = ? = = = = = = = = = = = D = ? = = = = = = = = = ? ? = = = ? 0 H110 A = = C G G = C = = = = = = = = = = = = = = = = = C A D C G = = T C A = G = = = = = = = = = = = = = = = = = T C I T 0 H111 A A G T C G = C A = = = = = = = = = = T = = = = = = A D C G T A C G A = G G = = = = = = = = = = G = = = = = = C I T 0 H112 = A G T C = = = = = = = T = = = = C = = = = = = = = = = = = T A C G = = = = = = = C = = = = A = = = = = = = = = = = 0 H113 = A G T C G = C A = = I = T = = = ? ? ? ? = = = = = A D C = T A C G A = G G = = D = C = = = ? ? ? ? = = = = = C I T 0 H114 = A G T C = = = = = = = = ? = = = = = = = = = (G) (A) = = = = = T A C G = = = = = = = = ? = = = = = = = = = (C) (G) = = = = 0 H115 A A G T C = C C ? A C D = ? T G G = T = C G T = = = = = C G T A C G = T G ? G T I = ? C A C = C = T A C = = = = = T 0 H116 = A G T C G = C A = = = = T = ? ? = = T = = = = = = A ? ? = T A C G A = G G = = = = C = ? ? = = G = = = = = = C ? ? 0 H117 = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = 0 H118 A T A C G = = = = = = = C C = = = A = = = = = = = = = = = G A G T C = = = = = = = T T = = = C = = = = = = = = = = = 0 H119 A T A C G = = = = = = D = C ? = = = = = = = = = = = = = = G A G T C = = = = = = I = T ? = = = = = = = = = = = = = = 0 H120 A T A C G = = = = = = = C C = = ? A = = = = = = = = = = = G A G T C = = = = = = = T T = = ? C = = = = = = = = = = = 0 H121 A = = = = = C C = A C D = = T G G = T = C G T C G = = = C G = = = = = T G = G T I = = C A C = C = T A C G A = = = T 0 H122 = = = = = = = = = = = I = ? = = = = = = = = = ? ? = = = ? = = = = = = = = = = = D = ? = = = = = = = = = ? ? = = = ? 0 X101 A = A C G = = = ? = = = (C) = = = = (A) = = = = = = = = = ? ? G = G T C = = = ? = = = (T) = = = = (C) = = = = = = = = = ? ? 0 X102 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? 0 X103 = = = = = = = = = = = = C = = = = A = = = = = = = = = = = = = = = = = = = = = = = T = = = = C = = = = = = = = = = = 0 X104 A = = = = G = C = = = = = = = = = ? ? ? ? = = = = C A D C G = = = = A = G = = = = = = = = = ? ? ? ? = = = = T C I T 0 X105 A = = = = G = C = = = = = = = = = = = = = = = = = C A D C G = = = = A = G = = = = = = = = = = = = = = = = = T C I T 0 X106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X107 A = = = = G = C ? = = = C = = = = A = = = = ? = = C A D C G = = = = A = G ? = = = T = = = = C = = = = ? = = T C I T 0 X108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X109 = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0 X110 (A) = = = = G = C A = = = = = = ? ? ? ? ? ? ? ? = = = A D C (G) = = = = A = G G = = = = = = ? ? ? ? ? ? ? ? = = = C I T 0 X111 = = = = = A = G G = = = = = = = = = = G = = = = = = C I T = = = = = G = C A = = = = = = = = = = T = = = = = = A D C 0 X112 A = = = = G = C A = = = C = = = = A = T = = = = = = A ? ? G = = = = A = G G = = = T = = = = C = G = = = = = = C ? ? 0 X113 = = = = = A = G G = = = = = = = = = = G = = = = = = C I T = = = = = G = C A = = = = = = = = = = T = = = = = = A D C 0 X114 A = = = = G = C = = = = = = = = = = = = = = = = = C A D C G = = = = A = G = = = = = = = = = = = = = = = = = T C I T 0 X115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X116 = = = = = = = = = = = = C = = ? ? ? = ? ? = = = = = = = = = = = = = = = = = = = = T = = ? ? ? = ? ? = = = = = = = = 0 X117 = = = = = = = = = = = = (C) = = = G = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = C = = = = = = = = = = = = 0 X118 ? = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? = = = = ? = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? = = = = 0 X119 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X120 A = = = = G = C = = = = C = = = = A = = = = = = = C A D C G = = = = A = G = = = = T = = = = C = = = = = = = T C I T 0 X121 A = = = = G = C = = = = C = = = = A = = = = = = = C A D C G = = = = A = G = = = = T = = = = C = = = = = = = T C I T 0 X122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X123 A = = = = G = C A = = = C = = = = A = T = = = = = = A D C G = = = = A = G G = = = T = = = = C = G = = = = = = C I T 0 X124 A = = = = G = C A = = = C ? = = = A = T = = = = = = A D C G = = = = A = G G = = = T ? = = = C = G = = = = = = C I T END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.98 0.98 0.98 0.98 = ? 1.00 = = = = = = = = = = = = = = = = = = 1.00 ? ? = 1.00 1.00 = 1.00 = ? 1.00 = 1.00 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = ? ? = ? ? 1.00 0.90 = = = = 1.00 = 1.00 = = = = = = ? ? ? ? ? ? ? = ? = = = 1.00 ? 1.00 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 = = = 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 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 1.00 = = = = ? 1.00 1.00 1.00 1.00 = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = 1.00 1.00 1.00 1.00 = = = ? = = = = = = ? ? ? ? ? ? = = = = 0.90 = = = = 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = 0.98 = = = = = = = = = = = = = ? ? = 0.99 0.99 0.99 0.99 = = = = = = = = ? = = = = = = = = = 0.94 0.94 = = = = ? 0.83 0.83 0.83 0.83 1.00 ? 1.00 ? = = = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00 1.00 = ? ? ? ? ? ? = = = 0.99 0.99 ? ? 1.00 ? = = = = = = = = = = = = = = ? ? 1.00 1.00 1.00 1.00 = = = = = = = 1.00 ? = = = = ? = = = = = = = = = = = = 1.00 ? ? = 0.72 0.72 0.72 0.72 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 ? = = 0.97 0.97 0.97 0.97 = = = 0.99 0.99 1.00 = 1.00 = = = = = ? = = = = = = = = = = = 1.00 1.00 1.00 1.00 ? = = = = 1.00 = = = = = = = = = = = = = 1.00 = = ? = = = = ? ? ? = = = = 1.00 = 1.00 = = = = = = ? ? ? ? ? ? ? = = = = = 1.00 1.00 1.00 ? = = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0.91 0.95 0.95 0.95 0.95 1.00 = 1.00 1.00 = = = = = = ? ? ? ? ? ? = = = = = 1.00 1.00 1.00 0.91 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 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 0.89 0.83 0.83 0.83 0.83 1.00 = 1.00 1.00 = = = = = = = = 0.71 = 1.00 = = ? = = = 1.00 1.00 1.00 0.91 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 = = = = = = = = = ? ? = 0.92 0.92 0.92 0.92 1.00 = 1.00 ? = = = = ? = = = = = 1.00 = = ? ? ? = 1.00 1.00 1.00 0.97 1.00 1.00 1.00 1.00 = = = = = = = = 0.97 ? = = = = = = = ? = = ? = = = 0.95 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 = = = = = = = = = = = 0.92 = = = = = = = = = = = = 0.92 = = = = = = = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 = = = = = = = 0.98 = = = = 0.98 = = = = = 0.80 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 = ? 0.98 0.98 0.98 1.00 = 1.00 1.00 = = = = ? = = = = = 1.00 = = = = = = 1.00 1.00 ? 0.88 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 = = = = = 0.83 0.83 = = = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 1.00 = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 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 = = = = = = = = = = ? = = = = 1.00 ? = = = = = = = = = = = 1.00 = ? = = = = = = = = = ? ? = = = ? 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 0.91 0.96 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 = = = = = = = 0.99 = = = = 0.99 = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = = ? ? ? ? = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = ? = = = = = = = = = 0.88 0.88 = = = = 0.94 0.98 0.98 0.98 0.98 = 1.00 1.00 ? 1.00 1.00 1.00 = ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 = ? ? = = 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 = = = = = = 0.98 = 0.98 ? = = = = = = = = = = = = = = 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 = ? = = = = = = = = = ? ? = = = ? 0.99 = 1.00 1.00 1.00 = = = ? = = = 0.84 = = = = 0.84 = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = = 0.97 = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 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 0.97 = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = ? ? ? = ? ? = = = = = = = = = = = = = = = = = = = = 0.62 = = = 1.00 = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = 1.00 = = = = 1.00 = = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = = = 1.00 = = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = 1.00 = 1.00 = = = = = = 1.00 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