************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 casp5.phase.inp casp5.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST casp5.phase.out_freqs : haplotype frequency estimates casp5.phase.out_pairs : most likely haplotype pairs for each individual casp5.phase.out_recom : estimates of recombination parameters casp5.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 34 Positions of loci: 148 282 292 622 694 1009 1076 1935 1975 2395 2519 2605 2780 3083 3275 5312 5496 5565 5891 6143 6566 6774 8141 9008 9385 10622 11070 11099 11669 13869 13946 14284 15445 16781 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file casp5.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CTACGATTAGCCTCTATCTDAT 1 CGGTTATTAGC 1.000000 2 CTACGATTAGCCTCTATCTDAT 2 CGGTTATTGGC 1.000000 3 CTACGATTAGCCTCTATCTDAT 2 TGCCTATTGGC 1.000000 4 CTACGATTAGCCTCTATCTDAT 3 CGGTTAATAGC 1.000000 5 CTACGATTAGCCTCTATCTDAT 3 CGGTTATTGGC 3.000000 6 CTACGATTAGCCTCTATCTDAT 3 TACCTATAGTT 2.000000 7 CTACGATTAGCCTCTATCTITT 3 CGCTCATTGGT 3.000000 8 TCGTCGCAGACGCTCGTCCDTT 3 CGCTCTTTGGT 1.000000 9 TCGTCGCAGATGCTCGTCCDAT 1 CGGTTATTAGC 4.000000 10 TCGTCGCAGATGCTCGTCCDAT 1 TACCTATAGTT 1.000000 11 TCGTCGCAGATGCTCGTCCDAT 3 CGGTTAATAGC 49.000000 12 TCGTCGCAGATGCTCGTCCDAT 3 CGGTTATTAGC 2.000000 13 TCGTCGCAGATGCTCGTCCDAT 3 CGCTTATTGGT 1.000000 14 TCGTCGCAGATGCTCGTCCDAT 3 CGCTCATTGGT 2.000000 15 TCGTCGCAGATGCTCGTCCDAT 3 CGCTCTTTGGT 24.000000 16 TCGTCGCAGATGCTCGTCCDAT 3 CGCCTATAGTC 2.000000 17 TCGTCGCAGATGCTCGTCCDAT 3 TACCTATAGTT 3.000000 18 TCGTCGCAGATGCTCGTCCDAA 3 CGGTTAATAGC 4.000000 19 TCGTCGCAGATGCTCGTCCDAA 3 CGCTCTTTGGT 3.000000 20 TCGTCGCAGATGCTCGTCCDTT 3 CGCTCTTTGGT 3.000000 21 TCGTCGCAGATGCTCGTCCDTA 3 CGCTCTTTGGT 1.000000 22 TCGTCGCAGATGCTCGTCCIAT 1 CGGTTATTAGC 2.000000 23 TCGTCGCAGATGCTCGTCCIAT 3 CGGTTATTGGC 2.000000 24 TCGTCGCAGATGCTCGTCCITT 2 CGGTTATTGGC 1.000000 25 TCGTCGCAGATGCTCGGCCIAT 1 CGGTTATTAGC 1.000000 26 TCGTCGCAGGTGCTCGTCCDAT 3 CGGTTAATAGC 1.000000 27 TCGTCGCAGGTGCTCGTCCDAT 3 CGCTCTTTGGT 11.000000 28 TCGTCGCAGGTGCTCGTCCDAT 3 TACCTATAGTT 1.000000 29 TCGTCGCAGGTGCTCGTCCDAA 3 CGGTTAATAGC 1.000000 30 TCGTCGCAGGTGCTCGTCCDAA 3 CGCTCTTTGGT 3.000000 31 TCGTCGCAGGTGCTCGTCCDTT 2 CGGTTATTGGC 1.000000 32 TTGTCGCAGGCCCTCGTCCDAT 2 CGGTTATTGGC 3.000000 33 TTGTCGCAGGCCCTCGTCCDAT 3 CGGTTAATAGC 5.000000 34 TTGTCGCAGGCCCTCGTCCDAT 3 CGGTTATTGGC 3.000000 35 TTGTCGCAGGCCCTCGTCCDAT 3 CGCTTATTGGT 1.000000 36 TTGTCGCAGGCCCTCGTCCDAT 3 CGCTCTTTGGT 10.000000 37 TTGTCGCAGGCCCTCGTCCDAT 3 TACCTATAGTT 3.000000 38 TTGTCGCAGGCCCTCGTCCDTT 3 CGGTTAATAGC 2.000000 39 TTGTCGCAGGCCCTCGTCCIAT 3 CGCTCATTGGT 5.000000 40 TTGTCGCAGGCCCTCGTCCIAT 3 CGCTCTTTGGT 1.000000 41 TTGTCGCAGGCCCTCGTCCIAT 3 TACCTATAGTT 2.000000 42 TTGTCGCAGGCCCTCGTTCIAT 3 CGCTTATTGGT 3.000000 43 TTGTCGCAGGCCCTCGTTCITT 2 CGGTTATTGGC 1.000000 44 TTGTCGCAGGCCCTCGGTCDAT 3 CGGTTAATAGC 6.000000 45 TTGTCGCAGGCCCTCGGTCIAT 3 CGGTTAATAGC 4.000000 46 TTGTCGCAGGCCCTCGGTCIAT 3 CGCTTATTGGT 2.000000 47 TTGTCGCAGGCCCTCGGTCIAT 3 CGCTCATTGGT 1.000000 48 TTGTCGCAGGCCCTCGGTCIAT 3 CGCTCTTTGGT 1.000000 49 TTGTCGCTAGCCCTCGGTCIAT 3 CGCTCTTTGGT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,11) D002: (4,12) D003: (7,11) D004: (39,46) D005: (3,31) D006: (1,11) D007: (39,44) D008: (17,35) D009: (22,42) D010: (6,13) D011: (7,29) D012: (17,21) D013: (9,39) D014: (20,41) D015: (39,46) DY01: (5,6) DY02: (5,49) DY03: (24,47) DY04: (12,23) DY05: (42,43) DY06: (14,39) DY07: (9,36) DY08: (15,22) DY09: (5,9) DY10: (9,10) DY11: (7,32) DY12: (23,32) E101: (11,36) E102: (14,27) E103: (11,18) E104: (18,44) E105: (11,17) E106: (11,36) E107: (11,26) E108: (15,27) E109: (15,44) E110: (11,33) E111: (19,20) E112: (44,44) E113: (11,15) E114: (11,19) E115: (11,11) E116: (11,33) E117: (11,18) E118: (11,41) E119: (15,40) E120: (11,28) E121: (11,37) E122: (15,27) H101: (15,30) H102: (15,27) H103: (15,19) H104: (27,34) H105: (15,27) H106: (27,36) H107: (11,15) H108: (15,27) H109: (15,15) H110: (15,48) H111: (11,16) H112: (11,16) H113: (15,30) H114: (11,36) H115: (27,34) H116: (27,33) H117: (15,37) H118: (18,37) H119: (11,44) H120: (15,15) H121: (30,42) H122: (27,33) X101: (11,11) X102: (11,36) X103: (25,8) X104: (15,45) X105: (11,15) X106: (11,11) X107: (11,15) X108: (34,38) X109: (11,11) X110: (11,15) X111: (11,11) X112: (11,36) X113: (11,32) X114: (11,11) X115: (11,36) X116: (20,45) X117: (15,45) X118: (11,33) X119: (11,45) X120: (11,11) X121: (11,11) X122: (11,38) X123: (11,36) X124: (11,36) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C T A C G A T T A G C C T C T A T C T D A T (2) C G G T T A (T) T (G) G C T C G T C G C A G A T G C T C G T C C D A T (3) C G G T T A (A) T (A) G C 0 D002 C T A C G A T T A G C C T C T A T C T D A T 3 C G G T T A (A) T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A (T) T A G C 0 D003 C T A C G A T T A G C C T C T A T C T I T T 3 C G C T C A T T G G T T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 D004 T T G T C G C A G G C C C T C G T C C I A T 3 C G C T (C) A T T G G T T T G T C G C A G G C C C T C G G T C I A T 3 C G C T (T) A T T G G T 0 D005 C T A C G A T T A G C C T C T A T C T D (A) T 2 T G C C T A T T G G [C] T C G T C G C A G G T G C T C G T C C D (T) T 2 C G G T T A T T G G C 0 D006 C T A C G A T T A G C C T C T A T C [T] D A T (1) C G G T T A (T) T A G C T C G T C G C A G A T G C T C G T C C D A T (3) C G G T T A (A) T A G C 0 D007 T T G T C G C A G G C C C T C G (T) (C) C [I] A T 3 C G C T C A T T G G T T T G T C G C A G G C C C T C G (G) (T) C D A T 3 C G G T T A A T A G C 0 D008 T C G T C G C A G (A) (T) [G] C T C G T C C D A T [3] T A C C T A T A G T T T [T] G T C G C A G (G) (C) C C T C G T C C [D] A T [3] C G [C] T [T] A T T G G [T] 0 D009 T C G T C G C A G A T G C T C G T C C I A T 1 C G G T T A T T A G C T T G T C G C A G G C C C T C G T T C I A T 3 C G C T T A T T G G T 0 D010 C T A C G A T T A G C C T C T A T C T D A T 3 (T) (A) C (C) T A T (A) G (T) T T C G T C G C A G A T G C T C G T C C D A T 3 (C) (G) C (T) T A T (T) G (G) T 0 D011 C T A C G A T T A G C C T C T A T C T I T T 3 C G C T C A T T G G T T C G T C G C A G G T G C T C G T C C D A A 3 C G G T T A A T A G C 0 D012 T C G T C G C A G A T G C T C G T C C D (A) (T) 3 T A C C T A T A G T T T C G T C G C A G A T G C T C G T C C D (T) (A) 3 C G C T C T T T G G T 0 D013 T C G T C G C A G A T G C T C G T C C (D) A T 1 C G G T T A T T A G C T T G T C G C A G G C C C T C G T C C (I) A T 3 C G C T C A T T G G T 0 D014 T [C] G T C G C A G (A) (T) (G) C T C G T C C (D) (T) T 3 C G C T C T T T G G T T [T] G T C G C A G (G) (C) (C) C T C G T C C (I) (A) T 3 T A C C T A T A G T T 0 D015 T T G T C G C A G G C C C T C G T C C I A T 3 C G C T (C) A T T G G T T T G T C G C A G G C C C T C G G T C I A T 3 C G C T (T) A T T G G T 0 DY01 C T A C G A T T A G C C T C T A T C T D A T 3 C G G T T A T T G G C C T A C G A T T A G C C T C T A T C T D A T 3 T A C C T A T A G T T 0 DY02 C T A C G A T T A G C C T C T A T C T D A T 3 C G G T T A T T G G C T T G T C G C T A G C C C T C G G T C I A T 3 C G C T C T T T G G T 0 DY03 T (C) G T C G C A G (A) (T) (G) C T C G (T) (C) C I (T) T (2) C G (G) T (T) A T T G G C T (T) G T C G C A G (G) (C) (C) C T C G (G) (T) C I (A) T (3) C G (C) T (C) A T T G G [T] 0 DY04 T C G T C G C A G A T G C T C G T C C (D) A T 3 C G G T T A T T A G C T C G T C G C A G A T G C T C G T C C (I) A T 3 C G G T T A T T G G C 0 DY05 T T G T C G C A G G C C C T C G T T C I (A) T 3 C G C T T A T T G G T T T G T C G C A G G C C C T C G T T C I (T) T 2 C G G T T A T T G G C 0 DY06 T C G T C G C A G A T G C T C G T C C (D) A T 3 C G C T C A T T G G T T T G T C G C A G G C C C T C G T C C (I) A T 3 C G C T C A T T G G T 0 DY07 T (C) G T C G C A G (A) (T) (G) C T C G T C C [D] A T 1 C G G T T A T T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 DY08 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G A T G C T C G T C C I A T 1 C G G T T A T T A G C 0 DY09 C T A C G A T T A G C C T C T A T C T D A T (3) C G G T T A T T (G) G C T C G T C G C A G A T G C T C G T C C D A T (1) C G G T T A T T (A) G C 0 DY10 T C G T C G C A G A T G C T C G T C C D A T 1 C G G T T A T T A G C T C G T C G C A G A T G C T C G T C C D A T 1 T A C C T A T A G T T 0 DY11 C T A C G A T T A G C C T C T A T C T I T T 3 C G C T C A T T G G T T T G T C G C A G G C C C T C G T C C D A T 2 C G G T T A T T G G C 0 DY12 T C G T C G C A G A T G C T C G T C C (I) A T (3) C G G T T A T T G G C T T G T C G C A G G C C C T C G T C C (D) A T (2) C G G T T A T T G G C 0 E101 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 E102 T C G T C G C A G (A) T G C T C G T C C D A T 3 C G C T C A T T G G T T C G T C G C A G (G) T G C T C G T C C D A T 3 C G C T C T T T G G T 0 E103 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A A 3 C G G T T A A T A G C 0 E104 T C G T C G C A G A T G C T C G T C C D A A 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G G T C D A T 3 C G G T T A A T A G C 0 E105 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 T A C C T A T A G T T 0 E106 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 E107 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G G T G C T C G T C C D A [T] 3 C G G T T A A T A G C 0 E108 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G G T G C T C G T C C D A T 3 C G C T C T T T G G T 0 E109 T (C) G T C G C A G (A) (T) (G) C T C G (T) (C) C D A T 3 C G C T C T T T G G T T (T) G T C G C A G (G) (C) (C) C T C G (G) (T) C D A T 3 C G G T T A A T A G C 0 E110 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G T C C D A T 3 C G G T T A A T A G C 0 E111 T C G T C G C A G A T G C T C G T C C D (A) A 3 C G C T C T T T G G T T C G T C G C A G A T G C T C G T C C D (T) T 3 C G C T C T T T G G T 0 E112 T T G T C G C A G G C C C T C G G T C D A T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G G T C D A T 3 C G G T T A A T A G C 0 E113 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 E114 T C G T C G C A G A T G C T C G T C C D A (T) 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A (A) 3 C G C T C T T T G G T 0 E115 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 E116 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G T C C D A T 3 C G G T T A A T A G C 0 E117 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A A 3 C G G T T A A T A G C 0 E118 T (C) G T C G C A G (A) (T) (G) C T C G T C C (D) A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C (I) A T 3 T A C C T A T A G T T 0 E119 T C G T C G C A G A T G C T C G T C C (D) A T 3 C G C T C T T T G G T T T G T C G C A G G C C C T C G T C C (I) A T 3 C G C T C T T T G G T 0 E120 T C G T C G C A G (A) T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G (G) T G C T C G T C C D A T 3 T A C C T A T A G T T 0 E121 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 T A C C T A T A G T T 0 E122 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G G T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H101 T C G T C G C A G (A) T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G (G) T G C T C G T C C D A A 3 C G C T C T T T G G T 0 H102 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G G T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H103 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G A T G C T C G T C C D A A 3 C G C T C T T T G G T 0 H104 T (C) G T C G C A G G (T) (G) C T C G T C C D A T 3 C G C T C T T T G G T T (T) G T C G C A G G (C) (C) C T C G T C C D A T 3 C G G T T A T T G G C 0 H105 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G G T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H106 T C G T C G C A G G T G C T C G T C C D A T 3 C G C T C T T T G G T T T G T C G C A G G C C C T C G T C C D A T 3 C G C T C T T T G G T 0 H107 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H108 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G G T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H109 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H110 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T T G T C G C A G G C C C T C G G T C [I] A T 3 C G C T C [T] T T G G T 0 H111 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C C T A T A G T C 0 H112 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C C T A T A G T C 0 H113 T C G T C G C A G (A) T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G (G) T G C T C G T C C D A A 3 C G C T C T T T G G T 0 H114 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 H115 T (C) G T C G C A G G (T) (G) C T C G T C C D A T 3 C G C T C T T T G G T T (T) G T C G C A G G (C) (C) C T C G T C C D A T 3 C G G T T A T T G G C 0 H116 T (C) G T C G C A G G (T) (G) C T C G T C C D A T 3 C G C T C T T T G G T T (T) G T C G C A G G (C) (C) C T C G T C C D A T 3 C G G T T A A T A G C 0 H117 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G C T C T T T G G T T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 T A C C T A T A G T T 0 H118 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A (A) 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A (T) 3 T A C C T A T A G T T 0 H119 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G G T C D A T 3 C G G T T A A T A G C 0 H120 T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 H121 T C G T C G C A G G T G C T C G T C C D A A 3 C G C T C T T T G G T T T G T C G C A G G C C C T C G T T C I A T 3 C G C T T A T T G G T 0 H122 T (C) G T C G C A G G (T) (G) C T C G T C C D A T 3 C G C T C T T T G G T T (T) G T C G C A G G (C) (C) C T C G T C C D A T 3 C G G T T A A T A G C 0 X101 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X102 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 X103 T C G T C G C A G A (T) G C T C G (G) C C (I) A T 1 C G G T T A T T A G C T C G T C G C A G A (C) G C T C G (T) C C (D) T T 3 C G C T C T T T G G T 0 X104 T C G T C G C A G A T G C T C G T C C D A T 3 C G (C) T (C) (T) (T) T (G) G (T) T T G T C G C A G G C C C T C G G T C I A T 3 C G (G) T (T) (A) (A) T (A) G (C) 0 X105 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 X106 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X107 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 X108 T T G T C G C A G G C C C T C G T C C D (A) T 3 C G G T T A T T G G C T T G T C G C A G G C C C T C G T C C D (T) T 3 C G G T T A A T A G C 0 X109 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X110 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G C T C T T T G G T 0 X111 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X112 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 X113 T C G T C G C A G A T G C T C G T C C D A T (3) C G G T T A (A) T (A) G C T T G T C G C A G G C C C T C G T C C D A T (2) C G G T T A (T) T (G) G C 0 X114 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X115 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 X116 T (C) G T C G C A G (A) (T) [G] C T C G (T) (C) C (D) T T 3 C G (C) T (C) (T) (T) T [G] G (T) T (T) G T C G C A G (G) (C) C C T C G (G) (T) C (I) A T 3 C G (G) T (T) (A) (A) T A G (C) 0 X117 T (C) G T C G C A G (A) (T) (G) C T C G (T) (C) C (D) A T 3 C G C T C T T T G G T T (T) G T C G C A G (G) (C) (C) C T C G (G) (T) C (I) A T 3 C G G T T A A T A G C 0 X118 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G T C C D A T 3 C G G T T A A T A G C 0 X119 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G G T C I A T 3 C G G T T A A T A G C 0 X120 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X121 T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C T C G T C G C A G A T G C T C G T C C D A T 3 C G G T T A A T A G C 0 X122 T C G T C G C A G A T G C T C G T C C D (A) T 3 C G G T T A A T A G C T T G T C G C A G G C C C T C G T C C D (T) T 3 C G G T T A A T A G C 0 X123 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G T 0 X124 T (C) G T C G C A G (A) (T) (G) C T C G T C C D A T 3 C G G T T A A T A G C T (T) G T C G C A G (G) (C) (C) C T C G T C C D A T 3 C G C T C T T T G G 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 ? ? ? C G A T ? ? G C C T C T A = = T = = = (2) = = = = = = (T) = (G) = ? ? ? ? T C G C ? ? A T G C T C G = = C = = = (3) = = = = = = (A) = (A) = ? 0 D002 C T A C G A T ? ? G C C T C T A = = ? ? ? ? = = = = = = = (A) = = = ? T C G T C G C ? ? A T G C T C G = = ? ? ? ? = = = = = = = (T) = = = ? 0 D003 C T A C G ? ? T A G C C T C T A = = T ? ? ? = = = C = C = T = G = ? T C G T C ? ? A G A T G C T C G = = C ? ? ? = = = G = T = A = A = ? 0 D004 ? ? ? = = ? ? = = ? = = = ? ? = T C ? = = = = = ? = = (C) ? = = = ? ? ? ? ? = = ? ? = = ? = = = ? ? = G T ? = = = = = ? = = (T) ? = = = ? ? 0 D005 C T A C G A T T A = C C T C T A = = ? = (A) ? = T = C C = = = = = ? ? T C G T C G C A G = T G C T C G = = ? = (T) ? = C = G T = = = = = ? ? 0 D006 C T A C G A T T A G C C T C T A = = ? = = = (1) = = = ? ? = (T) = = = ? T C G T C G C A G A T G C T C G = = ? = = = (3) = = = ? ? = (A) = = = ? 0 D007 = = = = = = = = = = = = = = = = (T) (C) = ? ? ? = = = C = C = T = G = ? = = = = = = = = = = = = = = = = (G) (T) = ? ? ? = = = G = T = A = A = ? 0 D008 ? ? ? = ? ? ? = = (A) (T) ? ? ? ? ? ? ? ? ? ? ? ? T A ? ? ? = = A = T ? ? ? ? = ? ? ? = = (G) (C) ? ? ? ? ? ? ? ? ? ? ? ? C G ? ? ? = = T = G ? 0 D009 = C = = = = = = = A T G = = = = = C = = = = 1 = = G = = = = = A = C = T = = = = = = = G C C = = = = = T = = = = 3 = = C = = = = = G = T 0 D010 ? ? ? C G A T T A G C C T C T A = = T = = = = (T) (A) = (C) = = = (A) = (T) ? ? ? ? T C G C A G A T G C T C G = = C = = = = (C) (G) = (T) = = = (T) = (G) ? 0 D011 C T A C G A T T A = C C T C T A = = T I T T = = = C = C = T = G = T T C G T C G C A G = T G C T C G = = C D A A = = = G = T = A = A = C 0 D012 = = = = = = = = = = = = = = = = = = = = (A) (T) = T A = C T A = A = T ? = = = = = = = = = = = = = = = = = = = = (T) (A) = C G = T C T = T = G ? 0 D013 = C = = = = = = = A T G = = = = = = = (D) = = 1 = = G = T = = = A = C = T = = = = = = = G C C = = = = = = = (I) = = 3 = = C = C = = = G = T 0 D014 ? ? ? = = = = = = (A) (T) (G) = = = = = = = (D) (T) = = C G = T C T = T = G = ? ? ? = = = = = = (G) (C) (C) = = = = = = = (I) (A) = = T A = C T A = A = T = 0 D015 = = = = = = = = = = = = = = = = T C = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = G T = = = = = = = = = (T) = = = = = = 0 DY01 = = = = = = = = = = = = = = = = = = = = = = = C G G ? ? = = T = G C = = = = = = = = = = = = = = = = = = = = = = = T A C ? ? = = A = T T 0 DY02 C = A C G A T = = = = = T C T A T C T D = = = = = G = T A = = = = C T = G T C G C = = = = = C T C G G T C I = = = = = C = C T = = = = T 0 DY03 = (C) = = = = = = = (A) (T) (G) = = = = (T) (C) = = (T) = (2) ? = (G) = (T) = = = ? = ? = (T) = = = = = = = (G) (C) (C) = = = = (G) (T) = = (A) = (3) ? = (C) = (C) = = = ? = ? 0 DY04 = = = = = = = = = = = = = = = = = = = (D) = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = (I) = = = = = = = = = = = G = = 0 DY05 = = = = = = = = = = = = = = = = = = = = (A) = 3 = = C = ? = = = = = T = = = = = = = = = = = = = = = = = = = = (T) = 2 = = G = ? = = = = = C 0 DY06 ? ? ? = = = = = = A T G = = = = = = = (D) = = = = = = = = = = = = = = ? ? ? = = = = = = G C C = = = = = = = (I) = = = = = = = = = = = = = = 0 DY07 = (C) = = = = = ? ? (A) (T) (G) = = = = = = = ? = = 1 = = G = T A = = A = C = (T) = = = = = ? ? (G) (C) (C) = = = = = = = ? = = 3 = = C = C T = = G = T 0 DY08 = = = = = = = = = = = = = = = = = = = D = = 3 = = C = C T = = G = T = = = = = = = = = = = = = = = = = = = I = = 1 = = G = T A = = A = C 0 DY09 C T A C G A T T A G C C T C T A = = T = = = (3) = = = = = = = = (G) = = T C G T C G C A G A T G C T C G = = C = = = (1) = = = = = = = = (A) = = 0 DY10 = = = = = = = = = = = = = = = = = = = = = = = C G G T = = ? ? A G C = = = = = = = = = = = = = = = = = = = = = = = T A C C = = ? ? G T T 0 DY11 C = A C G A T T A = = = T C T A = = T I T = 3 = = C = C = = = = = T T = G T C G C A G = = = C T C G = = C D A = 2 = = G = T = = = = = C 0 DY12 = C = = = = = = = A T G = = = = = = = (I) = = (3) = = = = = = = = = = = = T = = = = = = = G C C = = = = = = = (D) = = (2) = = = = = = = = = = = 0 E101 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = = = = G = T A A = A = C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = = = = C = C T T = G = T 0 E102 = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = T = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = 0 E104 = C = = = = = = = A T G = = = = T C = = = A = = = = = = = = = = = = = T = = = = = = = G C C = = = = G T = = = T = = = = = = = = = = = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = C G G T = = A T A ? C = = = = = = = = = = = = = = = = = = = = = = = T A C C = = T A G ? T 0 E106 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = = = = G = T A A = A = C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = = = = C = C T T = G = T 0 E107 = = = = = = = = = A = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = ? = = = = = = = = = = = = 0 E108 = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = 0 E109 = (C) = = = = = = = (A) (T) (G) = = = = (T) (C) = = = = = = = C = C T T = G = T = (T) = = = = = = = (G) (C) (C) = = = = (G) (T) = = = = = = = G = T A A = A = C 0 E110 = C = = = = = = = A T G = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = G C C = = = = = = = = = = = = = = = = = = = = = = 0 E111 = = = = = = = = = = = = = = = = = = = = (A) A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) T = = = = = = = = = = = = 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = = = = = = = = = = = = = = = = = ? = = = ? = = G = T A A = A = ? = = = = = = = = = = = = = = = = = = ? = = = ? = = C = C T T = G = ? 0 E114 = = = = = = = = = = = = = = = = = = = = = (T) = = = G = T A A = A = C = = = = = = = = = = = = = = = = = = = = = (A) = = = C = C T T = G = T 0 E115 = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = 0 E116 = C = = = = = = = A T G = = = = = = = ? ? = = = = = = = = = = = = = = T = = = = = = = G C C = = = = = = = ? ? = = = = = = = = = = = = = 0 E117 = = = = = = = = = = = = = = = = = = ? ? = T = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = A = = = = = = ? = = = = = 0 E118 = (C) = = = = = = = (A) (T) (G) = = = = = = = (D) = = = C G G T = = A T A G C = (T) = = = = = = = (G) (C) (C) = = = = = = = (I) = = = T A C C = = T A G T T 0 E119 = C = = = = = = = A T G = = = = = = = (D) = = = = = = = = = = = = = = = T = = = = = = = G C C = = = = = = = (I) = = = = = = = = = = = = = = 0 E120 = = = = = = = = = (A) = = = = = = = = = = = = = C G G T = = A T ? G C = = = = = = = = = (G) = = = = = = = = = = = = = T A C C = = T A ? T T 0 E121 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = = C G G T = = A T A G C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = = T A C C = = T A G T T 0 E122 = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = 0 H101 = = = = = ? ? = = (A) = = = = = = = = = = = T = = = = = = = = = = = = = = = = = ? ? = = (G) = = = = = = = = = = = A = = = = = = = = = = = = 0 H102 = = = = = = = ? ? A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? G = = = = = = = = = = = = = = = = = = = = = = = = 0 H103 ? ? ? = = = = = = = = = = = = = = = ? = = T = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = ? = = A = = = = = = = = = = = = 0 H104 = (C) = = = = = = = = (T) (G) = = = = = = = = = = = = = C = C T = = = = T = (T) = = = = = = = = (C) (C) = = = = = = = = = = = = = G = T A = = = = C 0 H105 = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = 0 H106 = C = = = = = = = = T G = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = C C = = = = = = = = = = = = = = = = = = = = = = 0 H107 = = = = = = = = = = = = = = = = = = ? = = = = = = G = T A A = A = C = = = = = = = = = = = = = = = = = = ? = = = = = = C = C T T = G = T 0 H108 = = = = = ? ? = = A = ? ? = = = = = = = = ? = = = = = = ? = = = = = = = = = = ? ? = = G = ? ? = = = = = = = = ? = = = = = = ? = = = = = 0 H109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H110 = C = = = = = = = A T ? ? = = = T C = ? ? ? = = = = = = ? = = = = = = T = = = = = = = G C ? ? = = = G T = ? ? ? = = = = = = ? = = = = = 0 H111 = = = = = = = = = = = = = = = = = = = = = = = = = G T = = A T A G = = = = = = = = = = = = = = = = = = = = = = = = = = C C = = T A G T = 0 H112 = = = = = = = = = = = = = = = = = = = = = = = = = G T = = A T A G = = = = = = = = = = = = = = = = = = = = = = = = = = C C = = T A G T = 0 H113 = = = = = = = = = (A) = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = A = = = = = = = = = = = = 0 H114 = (C) = = = = = = = (A) (T) (G) = = = = = = = ? = = = = = G = T A A = A = ? = (T) = = = = = = = (G) (C) (C) = = = = = = = ? = = = = = C = C T T = G = ? 0 H115 = (C) = = = = = = = = (T) (G) = = = = = = ? = = = = = = C = C T = = = = ? = (T) = = = = = = = = (C) (C) = = = = = = ? = = = = = = G = T A = = = = ? 0 H116 = (C) = ? ? = = = = = (T) (G) = = = = = = = = = = = = = C = C T T = G = ? = (T) = ? ? = = = = = (C) (C) = = = = = = = = = = = = = G = T A A = A = ? 0 H117 = (C) = = = = = = = (A) (T) (G) = = = = = = = ? ? = = C G = T C T = T = G = = (T) = = = = = = = (G) (C) (C) = = = = = = = ? ? = = T A = C T A = A = T = 0 H118 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = (A) = C G G T = = A T A G C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = (T) = T A C C = = T A G T T 0 H119 = C = = = = = = = A T G = = = = T C = = = = = = = = = = = = = = = ? = T = = = = = = = G C C = = = = G T = = = = = = = = = = = = = = = ? 0 H120 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? 0 H121 = C = = = = = = = = T G = = = = = C = D = A = = = = = C T = = = = ? = T = = = = = = = = C C = = = = = T = I = T = = = = = T A = = = = ? 0 H122 = (C) = = = = = = = = (T) (G) = = = = = = = ? ? = = = = C = C T T = G = T = (T) = = = = = = = = (C) (C) = = = = = = = ? ? = = = = G = T A A = A = C 0 X101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X102 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = = = = G = T A A = A = C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = = = = C = C T T = G = T 0 X103 = = = = = ? ? = = = (T) = = = = = (G) = = (I) A = 1 = = G = T A = = A ? C = = = = = ? ? = = = (C) = = = = = (T) = = (D) T = 3 = = C = C T = = G ? T 0 X104 ? ? ? = = = = = = A T G = = = = T C = D = = = = = (C) = (C) (T) (T) = (G) = (T) ? ? ? = = = = = = G C C = = = = G T = I = = = = = (G) = (T) (A) (A) = (A) = (C) 0 X105 = = = = = = = = = = = = = = = = = = = = = = = = = G = T A A = A = C = = = = = = = = = = = = = = = = = = = = = = = = = C = C T T = G = T 0 X106 = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = 0 X107 = = = = = = = = = = = = = = = = = = = ? ? = = = = G = T A A = ? = ? = = = = = = = = = = = = = = = = = = = ? ? = = = = C = C T T = ? = ? 0 X108 = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = T = G = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = A = A = = 0 X109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X110 = = = = = = = = = = = = = = = = = = = = = = = = = G = T A A = A = C = = = = = = = = = = = = = = = = = = = = = = = = = C = C T T = G = T 0 X111 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X112 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = = = = G = T A A = A = C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = = = = C = C T T = G = T 0 X113 = C = = = = = = = A T G = = = = = = = = = = (3) = = = = = = (A) = (A) = = = T = = = = = = = G C C = = = = = = = = = = (2) = = = = = = (T) = (G) = = 0 X114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 X115 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = = = = ? = T A A = A = C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = = = = ? = C T T = G = T 0 X116 = (C) = = = = = = = (A) (T) ? ? = = = (T) (C) = (D) T = ? = = (C) = (C) (T) (T) = ? = (T) = (T) = = = = = = = (G) (C) ? ? = = = (G) (T) = (I) A = ? = = (G) = (T) (A) (A) = ? = (C) 0 X117 = (C) = = = = = = = (A) (T) (G) = = = = (T) (C) = (D) = = ? = = C = C T T = G = ? = (T) = = = = = = = (G) (C) (C) = = = = (G) (T) = (I) = = ? = = G = T A A = A = ? 0 X118 = C = = = = = = = A T G = = = = = = = = ? = = = = ? = = = ? ? = = = = T = = = = = = = G C C = = = = = = = = ? = = = = ? = = = ? ? = = = 0 X119 = C = = = ? ? = = A T ? ? = = = T C = D = = = = = = = = ? = = = = = = T = = = ? ? = = G C ? ? = = = G T = I = = = = = = = = ? = = = = = 0 X120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X121 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X122 = C = = = = = = = A T G = = = = = = = = (A) = = = = = = = = = = = = = = T = = = = = = = G C C = = = = = = = = (T) = = = = = = = = = = = = = 0 X123 = (C) = = = = = = = (A) (T) (G) = = = = = = = ? ? = = = = G = T A A = A = C = (T) = = = = = = = (G) (C) (C) = = = = = = = ? ? = = = = C = C T T = G = T 0 X124 = (C) = = = = = = = (A) (T) (G) = = = = = = = = = = ? = = G = T A ? ? A ? C = (T) = = = = = = = (G) (C) (C) = = = = = = = = = = ? = = C = C T ? ? G ? 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 1.00 1.00 1.00 1.00 = = 1.00 = = = 0.73 = = = = = = 0.73 = 0.73 = ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = ? ? ? ? = = = = = = = 0.52 = = = ? 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 ? = = = = = ? = = 0.72 ? = = = ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = ? = 0.73 ? = 1.00 = 1.00 1.00 = = = = = ? ? 1.00 1.00 1.00 1.00 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 = = = ? ? = 0.50 = = = ? = = = = = = = = = = = = = = = = 0.65 0.65 = ? ? ? = = = 1.00 = 1.00 = 1.00 = 1.00 = ? ? ? ? = ? ? ? = = 0.83 0.83 ? ? ? ? ? ? ? ? ? ? ? ? 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 = = = = 0.75 0.75 = 0.75 = = = 0.75 = 0.75 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = 0.99 = 0.99 = 0.99 = 0.99 = 0.99 = = = = = = = = = = = = = = = = = = = = 0.66 0.53 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 ? = 0.95 = = = = = = = 0.95 0.95 0.95 = = = = = = = 0.75 = = 1.00 = = 1.00 = 1.00 = = = 1.00 = 1.00 ? ? ? = = = = = = 0.71 0.71 0.71 = = = = = = = 0.59 0.71 = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = 0.72 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 ? ? = = 1.00 = 1.00 1.00 0.93 = 0.93 0.93 0.93 0.93 0.93 = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = 0.97 = 0.97 0.97 = = = = 0.97 = 0.81 = = = = = = = 0.81 0.81 0.81 = = = = 0.87 0.80 = = 0.87 = 0.80 ? = 0.80 = 0.80 = = = ? = ? = = = = = = = = = = = = = = = = = = = 0.88 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 0.89 = 1.00 = = 1.00 = ? = = = = = 1.00 ? ? ? = = = = = = 1.00 1.00 1.00 = = = = = = = 0.87 = = = = = = = = = = = = = = = 0.82 = = = = = ? ? 0.82 0.82 0.82 = = = = = = = ? = = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = 0.92 = = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 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 = = = = = = = = 0.89 = = = = = = = = = = = = = = = = = = = = = = = = = 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 0.99 0.99 = 0.99 = = 0.99 = 0.99 = = = = = 0.99 = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = 0.89 = = 0.81 = = = = = = = = = = = = 0.56 = = = = = = = 0.56 0.56 0.56 = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = 0.76 = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = 1.00 1.00 = = = 0.92 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 ? 1.00 = 0.56 = = = = = = = 0.56 0.56 0.56 = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 0.75 = = = = = = = 0.75 0.75 0.75 = = = = 0.75 0.75 = = = = = = = 1.00 = 1.00 1.00 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 = ? = = = = = = = = = = = = = = = = = = = = = 0.60 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = 1.00 = = = = = = ? = = = = = = 0.75 = = = = = = = 0.75 0.75 0.75 = = = = = = = 0.74 = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = 0.77 = = = = = = = = = = = = = = = = = = = = = = = 0.51 = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 ? 1.00 1.00 = 0.58 = = = = = = = 0.58 0.58 0.58 = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = 0.53 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = ? ? 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = ? = = 1.00 = = = = = = = = = = = = = 0.86 = = = = = = = = 0.86 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 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = = = = 0.51 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 0.59 = = = = = = = 0.59 0.59 0.59 = = = = = = = ? = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = ? = 0.87 = = = = = = = = 0.87 0.87 = = = = = = ? = = = = = = 1.00 = 1.00 1.00 = = = = ? = 0.78 = ? ? = = = = = 0.78 0.78 = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = ? = 0.66 = = = = = = = 0.66 0.66 0.66 = = = = = = = ? ? = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = 0.59 = = = = = = = 0.59 0.59 0.59 = = = = = = = = = 0.59 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = 1.00 1.00 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? = 1.00 = = = = = = = = 1.00 1.00 = = = = = 1.00 = 1.00 = 1.00 = = = = = 1.00 1.00 = = = = ? = 0.79 = = = = = = = = 0.79 0.79 = = = = = = = ? ? = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.56 = = = = = = = 0.56 0.56 0.56 = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = ? ? = = = 0.50 = = = = = 0.51 = = 0.80 0.93 = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 ? 1.00 ? ? ? = = = = = = 0.98 0.98 0.98 = = = = 0.98 0.98 = 0.96 = = = = = 0.61 = 0.61 0.61 0.61 = 0.61 = 0.61 = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.57 = = = = = = = 0.57 0.57 0.57 = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = 0.88 = = = = = = 0.88 = 0.88 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0.56 = = = = = = = 0.56 0.56 0.56 = = = = = = = = = = = = = ? = 1.00 1.00 1.00 = 1.00 = 1.00 = 0.84 = = = = = = = 0.84 0.84 ? ? = = = 0.83 0.83 = 0.70 0.98 = ? = = 0.90 = 0.90 0.90 0.90 = ? = 0.90 = 0.60 = = = = = = = 0.60 0.60 0.60 = = = = 0.60 0.60 = 0.58 = = ? = = 1.00 = 1.00 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 = = = = = = = = 0.86 = = = = = = = = = = = = = = 0.56 = = = = = = = 0.56 0.56 0.56 = = = = = = = ? ? = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = 0.56 = = = = = = = 0.56 0.56 0.56 = = = = = = = = = = ? = = 1.00 = 1.00 1.00 ? ? 1.00 ? 1.00 END PHASEPROBS