************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 nr1i2.phase.inp nr1i2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST nr1i2.phase.out_freqs : haplotype frequency estimates nr1i2.phase.out_pairs : most likely haplotype pairs for each individual nr1i2.phase.out_recom : estimates of recombination parameters nr1i2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 99 Positions of loci: 411 1040 1415 1683 1776 1962 2157 2337 2403 2425 2446 2979 3215 3382 3422 4348 4517 4758 4860 5140 5255 5694 6072 6081 8446 8565 9572 9759 10479 10492 10584 10823 11318 11754 12407 12441 12753 12958 14353 14935 14941 15007 15168 15447 16139 16219 16283 17075 18963 19104 19277 19459 19843 19979 20426 20504 20544 20937 20984 21048 21248 21434 21607 21661 25332 25851 25876 26728 26751 27033 27074 28139 28155 28265 28456 29404 29492 29984 30068 30406 30520 31237 31358 31687 33031 33635 33725 34112 34532 36174 36453 36808 36938 36960 37097 37196 37276 37633 37670 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file nr1i2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CACGIDGCIGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTGCTGAGTTTAGATTGCGAGGTCTTGACGACGTGCCAGCGCCGGCCCGGAT 1.000000 2 CACGIDGCIGTAACCATGCGGCGDGICGTGCGACTGCAGTGCCGTCCCTGTAGCACCCGGGCCGCTGGGCTCCGGCTATATGCCACCGCCAACTCAGAT 1.000000 3 CACGIDGCDGTAACCATGCGGCGDCICGTGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCGAGGCTCCTGCGACGTGTTAGCGCCGGCCCAGCC 1.000000 4 CACGIDGCDGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGCGTGGAATCAAAT 1.000000 5 CACGIDGCDGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGTGTCGGCCCAGCC 1.000000 6 CACGIDGCDGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCCGTGTCGGCCCAGCC 1.000000 7 CACGIDGCDGTAACCATGCGGCGDGITGTGTGACCCCGGTGCCGTCCCTGTTGAGCCCGGGCCGCGAGGCTCCGGCTACGTGCCACCGCCAACTCAGAT 1.000000 8 CACGIDGCDGTAACCATGCGGCGDGDCGTGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCGAGGCTCCTGCGACGTGTTAGCGCGGAATCAAAT 1.000000 9 CACGIDGCDGTAACCATGCGGCGDGDCGTGTATCCCTGGTGCCGACCCGGTAGAGTTTGAGTCACGAGACTCCGGCTACATACCAGTGTCGGCCCAGCC 1.000000 10 CACGIDGCDGTAACCATGCGGCGDGDCGTGTATCCCTGGTGCCGATCCGGTAGAGTTTGAGTCACGAGACTCCGGCTACATACCAGTGTCGGCCCAGCC 1.000000 11 CACGIDGCDGTAACCATGCGGCGDGDCGTGTATCCCTGGTGCCGATCCGGTAGAGTTTGAGTCACGAGGTCTTGATGACGTGCCAGCGCCGGCCCGGAT 3.000000 12 CACGIDGTIGTAACCATGCGGCGDCICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGTGTCGGCCCAGCC 1.000000 13 CACGIDGTIGTAACCATGCGGCGDCICATGTATCCCCGGTTTTATCTTTGCTGAGTTTAGATTGCGAGGTCTTGATGACGTGCCAGCGCCGGCCCGGAT 1.000000 14 CACGIDGTIGTAACCATGCGGCGDCICGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCACCGCCGACTCAGAT 1.000000 15 CACGIDGTIGTAACCATGCGGCGDCICGTGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCGAGGCTCCTGCGACGTGTTAGCGCCGGCCCAGCC 1.000000 16 CACGIDGTIGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGCGCCGGCCCGGAT 1.000000 17 CACGIDGTIGTAACCATGCGGCGDGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCTGCGACGTGTTAGCGCGGACCCAGAT 1.000000 18 CGCGIDACIGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGCGCCGGCCCGGAT 1.000000 19 CGCGIDACIGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTATATGCCAGTGTCGGCCCAGCC 1.000000 20 CGCGIDACIGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCTAGGCTCCGGCTATATGCCAGCGCGGAATCAAAT 1.000000 21 CGCGIDACIGTAACCATGCGGCGDGICATGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCTAGGCTCCGGCTATATGCCACCGCCAACTCAGAT 1.000000 22 CGCGIDACIGTAACCATGCGGCGDGICAAGTATCCCCGGTTTTGTCTTTGCTGAGTTTGGGTCGCGAGGTCTTGGCGACGTGCCACCGCCAACTCAGAT 1.000000 23 CGCGIDACIGTAACCATGCGGCGDGICAAGTATCCCCGGTTTTGTCTTTGCTGAGTTTGGGTCGCTAGGTCTTGGCGACGTGCCAGCGCCGGCCCAGAT 1.000000 24 CGCGIDACIGTAACCATGCGGCGDGITGTGCGACTGCAATGCCGTCCCGGTAGCACCCGGGCCGCGAGGCTCCGGCTATATGCCAGCGCCGGCCCAGCC 2.000000 25 CGAGIDACIGCAATTGCATCAGAIGICATGTATCCCCGGCTTTATCTTTATTGAGCCCGGGCCGCGAGGTCTTGGCGACGTGCCAGCGCCGGCCCGGAT 1.000000 26 CGAGIDACIGCAATTGCATCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCAGCGCGGAATTAAAT 4.000000 27 CGAGIDACIGCAATTGCATCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCCCCACCGACTCAGAT 8.000000 28 CGAGIDACIGCAATTGCATCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGTGTCGGCCCAGCC 1.000000 29 CGAGIDACIGCAATTGCATCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGGAACTCCGGCTGTATACCCCCACCGACTCAGAT 3.000000 30 CGAGIDACIGCAATTGCATCAGAIGICATGTATCCCCGGTGCCGATCCTGCTGAGTTTGGGTCGCGAGGTCTTGGCGACGTGCCAGCGCCGGCCCAGAT 1.000000 31 CGAGIDACIGCAATTGCATCAGAIGICAAGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTGTATACCCGCACCGACTCAGAT 1.000000 32 CGAGIDACIGCAATTGCATCAGAIGICAAGTATCCCCGGTTTTGTCTTTGCTGAGTTTGGGTCGTGAGGCTCCGGCGACGTGCCAGCGCGGAATTAAAT 1.000000 33 CGAGIDACIGCAATTGCATCAGAIGICGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGAAACTCCGGCTGTATACCCCCACCGACTCAGAT 1.000000 34 CGAGIDACIGCAATTGCATCAGAIGICGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCGCGCGGAATTAAAT 1.000000 35 CGAGIDACIGCAATTGCATCAGAIGICGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCCCACCGACTCAGAT 1.000000 36 CGAGIDACIGCAATTGCATCAGAIGICGTGTATACCCGGCTTTATCCTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCCCACCGACTCAGAT 1.000000 37 CGAGIDACIGCAATTGCATCAGAIGITATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCCCCACCGACTCAGAT 1.000000 38 CGAGIDACIGCAATTGCATCAGAIGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCCCCGCCGACTCAGAT 1.000000 39 CGAGIDACIGCAATTGCATCAGAIGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCCCCACCGACTCAGAT 5.000000 40 CGAGIDACIGCAATTGCATCAGAIGDCATGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCTAGGCTCCGGCTATATGCCAGCGCCGGCCCAGCC 1.000000 41 CGAGIDACIGTAATTGCATCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGTGTCGGCCCAGCC 1.000000 42 CGAGIDACIGTAATTGCATCAGAIGITGTGTGACCCCGGTGCCATCTTTGCTGAGTTTGGGTCGCTAGGCCCCGGCTATATGCCAGCGCGGAATCAAAT 1.000000 43 TGCADIACIATGATTGCGTCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGCGCGGAATCAAAT 1.000000 44 TGCADIACIATGATTGCGTCAGAIGICAAATATCCCCGGTTTTGTCTTTGCTGAGTTTGGGTCGTGAGGCTCCGGCTACGCGCCAGCGCGGAATTAAAT 1.000000 45 TGCADIACIATGATTGCGTCAGAIGICGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCCCACCGACTCAGAT 2.000000 46 TGCADIACIATGATTGCGTCAGAIGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCCCCACCGACTCAGAT 2.000000 47 TGCADIACIATGATTGCGTCAGAIGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGACTCCGGCTACATGCCAGCGTGGAATCAAAT 1.000000 48 TGCADIACIATGATTGCGTCAGAIGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGCGTGGAATCAAAT 1.000000 49 TGCADIACIATGATTGCGTCAGAIGDCAAGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTGTATACCCCCACCGACTCAGAT 2.000000 50 TGCADIACIATGATTGCGTCAGAIGDCAAATATCCCCGGTTTTGTCTTTGCTGAGTTTGGGTCGTGAGGCTCCGGCTACGCGCCAGCGCGGAACCAAAT 1.000000 51 TGCADIACIATGATTGCGTCAGAIGDCAAATATCCCCGGTTTTGTCTTTGCTGAGTTTGGGTCGTGAGGCTCCGGCTACGCGCCAGCGCGGAATTAAAT 3.000000 52 TGCADIACIATGATTGCGTCAGAIGDCGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCGCGCGGAATTAAAT 1.000000 53 TGCADIACIATGATTGCGTCAGAIGDCGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCCCACCGACTCAGAT 1.000000 54 TGCADIACIATGCCCATGCGGCGDGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAAACTCCGGCTGTATACCCCCACCGACTCAGAT 2.000000 55 TGCADIACIATGCCCATGCGGCGDGDCGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCCCCACCGACTCAGAT 2.000000 56 TGCADIACIATGCTTGCGTCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGCGCCGGCCCAGCC 1.000000 57 TGCADIACIATGCTTGCGTCAGAIGICATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGTCTTGACGACGTGCCAGCGCCGGCCCGGAT 1.000000 58 TGCADIACIATGCTTGCGTCAGAIGICATGTATCCCCGGTTTTATCTTTGCTGAGTTTAGATTGCGAGGTCTTGACGACGTGCCAGCGCCGGCCCGGAT 2.000000 59 TGCADIACIATGCTTGCGTCAGAIGICATGTATCCCCGGTTTTATCTTTGCTGAGTTTAGATTGCGAGGTCTTGATGACGTGCCAGCGCCGGCCCGGCC 1.000000 60 TGCADIACIATGCTTGCGTCAGAIGICAAGTATCCCCGGTTTTATCTTTGCTGAGTTTGGGTCGCGAGGCTCCTGCGACGTGTTAGCGCCAACTCAGAT 1.000000 61 TGCADIACIATGCTTGCGTCAGAIGICGTGTATACCCGGCTTTATCTTTGCTAAGTTTGGGTCGCGGAACTCCGGCTGTATACCACCGCCGACTCAGAT 1.000000 62 TGCADIACIATGCTTGCGTCAGAIGICGTGTATCCCTGGTGCCGATCCGGTAGAGTTTGAGTCACGAGACTCCGGCTACATACCAGTGTCGGCCCAGCC 2.000000 63 TGCADIACIATGCTTGCGTCAGAIGITGTGCGACTGCAATGCCGTCCCGGTAGCACCCGGGCCGCGAGGCTCCGGCTATATACCAGTGTCGGCCCAGCC 1.000000 64 TGCADIACIATGCTTGCGTCAGAIGITGTGCGACTGCAATGCCGTCCCGGTAGCACCCGGGCCGCGAGGCTCCGGCTATATGCCAGTGTCGGCCCAGCC 2.000000 65 TGCADIACIATGCTTGCGTCAGAIGDCATGTATCCCCGGTTTTATCTTTATTGAGCCCGGGCCGCGAGGCTCCGGCTACATGCCAGTGTCGGCCCAGCC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (5,14) DY02: (28,23) DY03: (13,18) DY04: (4,17) DY05: (10,11) DY06: (1,8) DY07: (56,59) DY08: (6,62) DY09: (15,42) DY10: (3,58) DY11: (11,57) DY12: (24,62) DY13: (64,65) DY14: (22,41) DY15: (20,43) DY16: (12,58) DY17: (16,40) DY18: (60,63) DY19: (7,61) DY20: (2,48) DY21: (21,24) DY22: (11,64) DY23: (19,47) DY24: (9,30) E101: (27,29) E102: (36,51) E103: (39,54) E104: (26,39) E105: (46,51) E106: (29,39) E107: (27,49) E108: (27,34) E109: (27,55) E110: (25,54) E111: (29,32) E112: (27,45) E113: (35,53) E114: (27,44) E115: (45,55) E116: (26,27) E117: (39,46) E118: (37,39) E119: (26,33) E120: (27,31) E121: (50,51) E122: (38,52) E123: (26,49) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C A C G I D G (C) (D) G T A A C C A T G C G G C G D G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T A C A T G C C A G T G T C G G C C C A G C C C A C G I D G (T) (I) G T A A C C A T G C G G C G D C I C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C A C C G C C G A C T C A G A T 0 DY02 C G (A) G I D A C I G (C) A A (T) (T) (G) (C) (A) (T) (C) (A) (G) (A) (I) G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C (G) A G G C T C C G G C T A C A T G C C A G T G T C G G C C C A G C C C G (C) G I D A C I G (T) A A (C) (C) (A) (T) (G) (C) (G) (G) (C) (G) (D) G I C A A G T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G C (T) A G G T C T T G G C G A C G T G C C A G C G C C G G C C C A G A T 0 DY03 C A C G I D G T I G T A A C C A T G C G G C G D C I C A T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T A G A T T G C G A G G T C T T G A T G A C G T G C C A G C G C C G G C C C G G A T C G C G I D A C I G T A A C C A T G C G G C G D G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T A C A T G C C A G C G C C G G C C C G G A T 0 DY04 C A C G I D G (C) (D) G T A A C C A T G C G G C G D G (I) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T A C A T G C C A G C G T G G A A T C A A A T C A C G I D G (T) (I) G T A A C C A T G C G G C G D G (D) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C T G C G A C G T G T T A G C G C G G A C C C A G A T 0 DY05 C A C G I D G C D G T A A C C A T G C G G C G D G D C G T G T A T C C C T G G T G C C G A T C C G G T A G A G T T T G A G T C A C G A G A C T C C G G C T A C A T A C C A G T G T C G G C C C A G C C C A C G I D G C D G T A A C C A T G C G G C G D G D C G T G T A T C C C T G G T G C C G A T C C G G T A G A G T T T G A G T C A C G A G G T C T T G A T G A C G T G C C A G C G C C G G C C C G G A T 0 DY06 C A C G I D G C (I) G T A A C C A T G C G G C G D G I C A T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T A G A T T G C G A G G T C T T G A C G A C G T G C C A G C G C C G G C C C G G A T C A C G I D G C (D) G T A A C C A T G C G G C G D G D C [G] T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T G G G T C G C G A G G C T C C T G C G A C G T G T T A G C G C G G A A T C A A A T 0 DY07 T G C A D I A C I A T G C T T G C G T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T A C A T G C C A G C G C C G G C C C (A) G C C T G C A D I A C I A T G C T T G C G T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T A G A T T G C G A G G T C T T G A T G A C G T G C C A G C G C C G G C C C (G) G C C 0 DY08 C A C G I D G C D G T A A C C A T G C G G C G D G I C (A) T G T A T C C C (C) G G T (T) (T) (T) (A) (T) (C) (T) (T) T (A) T (T) G A G (C) (C) (C) G (G) G (C) C (G) C G A G (G) C T C C G G C T A C A T (G) C C C G T G T C G G C C C A G C C T G C A D I A C I A T G C T T G C G T C A G A I G I C (G) T G T A T C C C (T) G G T (G) (C) (C) (G) (A) (T) (C) (C) [G] (G) T (A) G A G (T) (T) (T) G (A) G (T) C (A) C G A G (A) C T C C G G C T A C A T (A) C C A G T G T C G G C C C A G C C 0 DY09 C (A) (C) G I D (G) (T) I G T A A (C) (C) (A) (T) (G) [C] (G) (G) (C) (G) [D] (C) I C G T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T G G G T C G C G A G G C (T) C C T G C G A C G T G T T A G C G C C G G C C C A G C C C (G) (A) G I D (A) (C) I G T A A (T) (T) (G) (C) (A) [T] (C) (A) (G) (A) [I] (G) I T G T G T G A C C C C G G T G C C A T C T T T G C T G A G T T T G G G T C G C T A G G C (C) C C G G C T A T A T G C C A G C G C G G A A T C A A A T 0 DY10 C A C G I D G C D G T A A C C A T G C G G C G D (C) I C G T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T G G G T C G C G A G G C T C C T G C G A C G T G T T A G C G C C G G C C C A G C C T G C A D I A C I A T G C T T G C G T C A G A I (G) I C A T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T A G A T T G C G A G G T C T T G A C G A C G T G C C A G C G C C G G C C C G G A T 0 DY11 C A C G I D G C D G T A A C C A T G C G G C G D G D C G T G T A T C C C T G G T G C C G A T C C G G T A G A G T T T G A G T C A C G A G G T C T T G A T G A C G T G C C A G C G C C G G C C C G G A T T G C A D I A C I A T G C T T G C G T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G T C T T G A C G A C G T G C C A G C G C C G G C C C G G A T 0 DY12 C G C G I D A C I G T A A C C A T G C G G C G D G I T G T G C G A C T G C A A T G C C G T C C C G G T A G C A C C C G G G C C G C G A G G C T C C G G C T A T A T G C C A G C G C C G G C C C A G C C T G C A D I A C I A T G C T T G C G T C A G A I G I C G T G T A T C C C T G G T G C C G A T C C G G T A G A G T T T G A G T C A C G A G A C T C C G G C T A C A T A C C A G T G T C G G C C C A G C C 0 DY13 T G C A D I A C I A T G C T T G C G T C A G A I G (I) T G T G C G A C T G C A A T G C C G T C C C G G T A G C A C C C G G G C C G C G A G G C T C C G G C T A T A T G C C A G T G T C G G C C C A G C C T G C A D I A C I A T G C T T G C G T C A G A I G (D) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T A C A T G C C A G T G T C G G C C C A G C C 0 DY14 C G (C) G I D A C I G T A A (C) (C) (A) (T) (G) (C) (G) (G) (C) [G] (D) G I C A A G T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G C G A G G T C T T G G C G A C G T G C C A C C G C C A A C T C A G A T C G (A) G I D A C I G T A A (T) (T) (G) (C) (A) (T) (C) (A) (G) [A] (I) G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T A C A T G C C A G T G T C G G C C C A G C C 0 DY15 C G C G I D A C I G T A A C C A T G C G G C G D G I C A T G T A T C C C C G G T T T T A T C T T T (G) (C) T G A G (T) (T) (T) G G G (T) C G C (T) A G G C T C C G G C T A (T) A T G C C A G C G C G G A A T C A A A T T G C A D I A C I A T G A T T G C G T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T (A) (T) T G A G (C) (C) (C) G G G (C) C G C (G) A G G C T C C G G C T A (C) A T G C C A G C G C G G A A T C A A A T 0 DY16 C A C G I D G T I G T A A C C A T G C G G C G D (C) I C A T G T A T C C C C G G T T T T A T C T T T (A) (T) T G A G (C) (C) (C) (G) G (G) (C) (C) G C G A G G (C) (T) (C) (C) G (G) C (T) A C (A) T G C C A G (T) G (T) C G G C C C (A) G (C) (C) T G C A D I A C I A T G C T T G C G T C A G A I (G) I C A T G T A T C C C C G G T T T T A T C T T T (G) (C) T G A G (T) (T) (T) (A) G (A) (T) (T) G C G A G G (T) (C) (T) (T) G (A) C (G) A C (G) T G C C A G (C) G (C) C G G C C C (G) G (A) (T) 0 DY17 C A C G I D G T I G T A A C C A T G C G G C G D G (I) C A T G T A T C C C C G G T T T T A T C T T T (A) (T) T G A G (C) (C) (C) G G G (C) C G C (G) A G G C T C C G G C T A (C) A T G C C A G C G C C G G C C C (G) G (A) (T) C G A G I D A C I G C A A T T G C A T C A G A I G (D) C A T G T A T C C C C G G T T T T A T C T T T (G) (C) T G A G (T) (T) (T) G G G (T) C G C (T) A G G C T C C G G C T A (T) A T G C C A G C G C C G G C C C (A) G (C) (C) 0 DY18 T G C A D I A C I A T G C T T G C G T C A G A I G I C A A G T A T C C C C G G T T T T A T C T T T G C T G A G T T T G G G T C G C G A G G C T C C T G C G A C G T G T T A G C G C C (A) (A) C (T) C A G (A) (T) T G C A D I A C I A T G C T T G C G T C A G A I G I T G T G C G A C T G C A A T G C C G T C C C G G T A G C A C C C G G G C C G C G A G G C T C C G G C T A T A T A C C A G T G T C (G) (G) C (C) C A G (C) (C) 0 DY19 C A C G I D G C D G T A A C C A T G C G G C G D G I T G T G T G A C C C C G G T G C C G T C C C T G T T G A G C C C G G G C C G C G A G G C T C C G G C T A C G T G C C A C C G C C A A C T C A G A T T G C A D I A C I A T G C T T G C G T C A G A I G I C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C A C C G C C G A C T C A G A T 0 DY20 (C) (A) C (G) (I) (D) (G) C I (G) T (A) A (C) (C) (A) (T) G (C) (G) (G) (C) (G) (D) G (I) C G T G C G A C T G C A G T G C C G T C C C T G T A G C A C C C G G G C C G C T (G) G G C T C C G G C T A T A T G C C A C C G C C A A C T C A G A T (T) (G) C (A) (D) (I) (A) C I (A) T (G) A (T) (T) (G) (C) G (T) (C) (A) (G) (A) (I) G (D) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G (A) G G C T C C G G C T A C A T G C C A G C G T G G A A T C A A A T 0 DY21 C G C G I D A C I G T A A C C A T G C G G C G D G I C A T G T A T C C C C G G T T T T A T C T T T G C T G A G T T T G G G T C G C T A G G C T C C G G C T A T A T G C C A (C) C G C C (A) (A) C (T) C A G (A) (T) C G C G I D A C I G T A A C C A T G C G G C G D G I T G T G C G A C T G C A A T G C C G T C C C G G T A G C A C C C G G G C C G C G A G G C T C C G G C T A T A T G C C A (G) C G C C (G) (G) C (C) C A G (C) (C) 0 DY22 C A C G I D G C D G T A A C C A T G C G G C G D G D C G T G T A T C C C T G G T G C C G A T C C G G T A G A G T T T G A G T C A C G A G G T C T T G A T G A C G T G C C A G C G C C G G C C C G G A T T G C A D I A C I A T G C T T G C G T C A G A I G I T G T G C G A C T G C A A T G C C G T C C C G G T A G C A C C C G G G C C G C G A G G C T C C G G C T A T A T G C C A G T G T C G G C C C A G C C 0 DY23 C G C G I D A C I G T A A C C A T G C G G C G D G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G (G) C T C C G G C T A (T) A T G C C A G (T) G T (C) G (G) (C) (C) C A (G) (C) (C) T G C A D I A C I A T G A T T G C G T C A G A I G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G (A) C T C C G G C T A (C) A T G C C A G (C) G T (G) G (A) (A) (T) C A (A) (A) (T) 0 DY24 C A C G I D G C D G T A A C C A T G C G G C G D G D C G T G T A T C C C T G G T G C C G A (C) C C (G) G (T) (A) G A G T T T G (A) G T C (A) C G A G (A) (C) (T) (C) (C) G G C (T) A C (A) T (A) C C A G (T) G (T) C G G C C C A G (C) (C) C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T G C C G A (T) C C (T) G (C) (T) G A G T T T G (G) G T C (G) C G A G (G) (T) (C) (T) (T) G G C (G) A C (G) T (G) C C A G (C) G (C) C G G C C C A G (A) (T) 0 E101 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E102 (C) G (A) (G) (I) (D) A C I (G) C (A) A T T G C (A) T C A G A I G (I) C G T G T A T A C C C G G C T T T A T C (C) T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T (T) G (C) (A) (D) (I) A C I (A) [T] (G) A T T G C (G) T C A G A I G (D) C A A A T A T C C C C G G T T T T G T C (T) T T G C T G A G T T T G G G T C G T G A G G C T C C G G C T A C G C G C C A G C G C G G A A T T A A A T 0 E103 C G A G I D A C I G C A A T T G C A T C A G A I G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G C C C A T G C G G C G D G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E104 C G A G I D A C I G C A A T T G C A T C A G A I G (I) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C A G C G C G G A A T T A A A T C G A G I D A C I G C A A T T G C A T C A G A I G (D) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E105 T G C A D I A C I A T G A T T G C G T C A G A I G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G A T T G C G T C A G A I G D C A A A T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G T G A G G C T C C G G C T A C G C G C C A G C G C G G A A T T A A A T 0 E106 C G A G I D A C I G C A A T T G C A T C A G A I G (I) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T C G A G I D A C I G C A A T T G C A T C A G A I G (D) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E107 C G A G I D A C I G C A A T T G C A T C A G A I G (I) C A (T) G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A (A) (A) C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G A T T G C G T C A G A I G (D) C A (A) G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A (G) (G) C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E108 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C (C) C (A) C (C) G A (C) T (C) A (G) A T C G A G I D A C I G C A A T T G C A T C A G A I G I C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C (G) C (G) C (G) G A (A) T (T) A (A) A T 0 E109 C G A G I D A C I G C A A T T G C A T C A G A I G (I) C (A) T G T A T (C) C C C G G (T) T T T A T C T T T (A) (T) T (G) A G (C) (C) (C) G G G (C) C G C G (A) A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G C C C A T G C G G C G D G (D) C (G) T G T A T (A) C C C G G (C) T T T A T C T T T (G) (C) T (A) A G (T) (T) (T) G G G (T) C G C G (G) A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E110 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G (C) T T T A T C T T T A T T G A G C C C G G G C C G C G A (G) (G) (T) (C) (T) (T) G G C (G) (A) (C) (G) T (G) C C (A) (G) C (G) C C G (G) C (C) C (G) G A T T G C A D I A C I A T G C C C A T G C G G C G D G D C A T G T A T C C C C G G (T) T T T A T C T T T A T T G A G C C C G G G C C G C G A (A) (A) (C) (T) (C) (C) G G C (T) (G) (T) (A) T (A) C C (C) (C) C (A) C C G (A) C (T) C (A) G A T 0 E111 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T C G A G I D A C I G C A A T T G C A T C A G A I G I C A A G T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G T G A G G C T C C G G C G A C G T G C C A G C G C G G A A T T A A A T 0 E112 (C) G (A) (G) (I) (D) A C I (G) (C) (A) A T T G C (A) T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T (T) G (C) (A) (D) (I) A C I (A) (T) (G) A T T G C (G) T C A G A I G I C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E113 C G A G I D A C I G C A A T T G C A T C A G A I G (I) C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G A T T G C G T C A G A I G (D) C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E114 (C) G (A) (G) (I) [D] A C I (G) (C) (A) A T T G C (A) T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T (T) G (C) (A) (D) [I] A C I (A) (T) (G) A T T G C (G) T C A G A I G I C A A A T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G T G A G G C T C C G G C T A C G C G C C A G C G C G G A A T T A A A T 0 E115 T G C A D I A C I A T G A T T G C G T C A G A I G (I) C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G C C C A T G C G G C G D G (D) C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E116 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C A G C G C G G A A T T A A A T C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E117 C G A G I D A C I G C A A T T G C A T C A G A I G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T T G C A D I A C I A T G A T T G C G T C A G A I G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E118 C G A G I D A C I G C A A T T G C A T C A G A I G (I) T A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T C G A G I D A C I G C A A T T G C A T C A G A I G (D) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T 0 E119 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C (A) (G) C (G) C (G) G A (A) T (T) A (A) A T C G A G I D A C I G C A A T T G C A T C A G A I G I C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G A A A C T C C G G C T G T A T A C C (C) (C) C (A) C (C) G A (C) T (C) A (G) A T 0 E120 C G A G I D A C I G C A A T T G C A T C A G A I G I C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C C C A C C G A C T C A G A T C G A G I D A C I G C A A T T G C A T C A G A I G I C A A G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T G T A T A C C C G C A C C G A C T C A G A T 0 E121 T G C A D I A C I A T G A T T G C G T C A G A I G D C A A A T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G T G A G G C T C C G G C T A C G C G C C A G C G C G G A A C C A A A T T G C A D I A C I A T G A T T G C G T C A G A I G D C A A A T A T C C C C G G T T T T G T C T T T G C T G A G T T T G G G T C G T G A G G C T C C G G C T A C G C G C C A G C G C G G A A T T A A A T 0 E122 (C) G (A) (G) (I) D A C I (G) C (A) A T T G C (A) T C A G A I G D C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C C (C) C G C (C) G A (C) T (C) A (G) A T (T) G (C) (A) (D) [I] A C I (A) [T] (G) A T T G C (G) T C A G A I G D C G T G T A T A C C C G G C T T T A T C T T T G C T A A G T T T G G G T C G C G G A A C T C C G G C T G T A T A C C C (G) C G C (G) G A (A) T (T) A (A) A T 0 E123 (C) G (A) (G) (I) (D) A C I (G) (C) (A) A T T G C (A) T C A G A I G (I) C A T G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A A A C T C C G G C T G T A T A C C A G C G C G G A A T T A A A T (T) G (C) (A) (D) (I) A C I (A) (T) (G) A T T G C (G) T C A G A I G (D) C A A G T A T C C C C G G T T T T A T C T T T A T T G A G C C C G G G C C G C G A G G C T C C G G C T G T A T A C C C C C A C C G A C T C A G A 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 DY01 = = = = = = = (C) (D) ? ? = = = = = = = = = = = ? ? G = = ? = = = = = C = = = = = T = = = = ? = = = = A T = G = = C C C = = = C = = = = A G G = = = = = = = = A C = = G = = = ? ? = T = = G = C = = = C C = = = = = = = (T) (I) ? ? = = = = = = = = = = = ? ? C = = ? = = = = = A = = = = = C = = = = ? = = = = G C = A = = T T T = = = T = = = = G A A = = = = = = = = G T = = A = = = ? ? = C = = A = T = = = A T 0 DY02 = = (A) = = = = = = = (C) = = (T) (T) (G) (C) (A) (T) (C) (A) (G) (A) (I) = = ? = T = = = = = = = = = = = = = = A = = = = = A T = = = = C C C = = = C = = = (G) = = = C T C C = = = T = = A = = = = = ? ? = T = = = = = = = = C C = = (C) = = = = = = = (T) = = (C) (C) (A) (T) (G) (C) (G) (G) (C) (G) (D) = = ? = A = = = = = = = = = = = = = = G = = = = = G C = = = = T T T = = = T = = = (T) = = = T C T T = = = G = = G = = = = = ? ? = C = = = = = = = = A T 0 DY03 = A ? = = = G T = = = = = = = = = = = = = = = = C = ? = = = = = = = = = = = = = = = = = ? = = = = G C = = = = T T T A = A T T = = = = = = T C T T = A T G = = G = = = = = = = = = = = = = = = = = = = = G ? = = = A C = = = = = = = = = = = = = = = = G = ? = = = = = = = = = = = = = = = = = ? = = = = A T = = = = C C C G = G C C = = = = = = C T C C = G C T = = A = = = = = = = = = = = = = = = = = = = 0 DY04 = = = ? ? ? = (C) (D) = ? = = = = = = = = = = = = = = (I) = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = G = = T = = A = = C C = = = = T = = = A T = = A = = = = = ? ? ? = (T) (I) = ? = = = = = = = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = T = = G = = G = = T T = = = = C = = = C C = = G = = 0 DY05 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = A C T C C = G C T = = A = A = = = = T = T = = = = = = A = C C = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = G T C T T = A T G = = G = G = = = = C = C = = = = = = G = A T 0 DY06 = = = = = = = = (I) = ? = = = = = = = = = = = ? ? = I = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = A = A = T = = = = = = T C T T G A = = = = = = = C C = = = ? = C = G C C = G G = = = = = = = = = = (D) = ? = = = = = = = = = = = ? ? = D = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = G = G = C = = = = = = C T C C T G = = = = = = = T T = = = ? = G = A A T = A A = = 0 DY07 = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? ? = = = = = = = = = = = = = A T = = = = C C C G = G C C = = = = = = C T C C = G C ? = = A = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? ? = = = = = = = = = = = = = G C = = = = T T T A = A T T = = = = = = T C T T = A T ? = = G = = = = = = = = = = = = = = = (G) = = = 0 DY08 C A = G I D ? ? D G ? A A C C A T = C G G C ? ? = = = (A) = = = = = = = = (C) = = = (T) (T) (T) (A) (T) (C) (T) (T) ? (A) = (T) = = = (C) (C) (C) = (G) = (C) = (G) = = = = (G) = = ? ? ? ? = = = = = = (G) = = C = = = = = = = = = = = = = = T G = A D I ? ? I A ? G C T T G C = T C A G ? ? = = = (G) = = = = = = = = (T) = = = (G) (C) (C) (G) (A) (T) (C) (C) ? (G) = (A) = = = (T) (T) (T) = (A) = (T) = (A) = = = = (A) = = ? ? ? ? = = = = = = (A) = = A = = = = = = = = = = = = = = 0 DY09 = (A) (C) = = = (G) (T) = = = = = (C) (C) (A) (T) (G) ? (G) (G) (C) (G) ? (C) = C = = = = A T = = = = = = = T T T = = = = = = = = = = = = = = = = = = = = = = G = = = = (T) = = T = = G = C G = = T T = = = = = C = G C C = ? ? C C = (G) (A) = = = (A) (C) = = = = = (T) (T) (G) (C) (A) ? (C) (A) (G) (A) ? (G) = T = = = = G A = = = = = = = G C C = = = = = = = = = = = = = = = = = = = = = = T = = = = (C) = = G = = T = T A = = C C = = = = = G = A A T = ? ? A T 0 DY10 C A = G I D ? ? D G = A A C C A T = C G G C G D (C) = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = G = C = = = = = = C T C C T G = = = = = = = T T = = = = = = = = = = = A = C C T G = A D I ? ? I A = G C T T G C = T C A G A I (G) = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = A = T = = = = = = T C T T G A = = = = = = = C C = = = = = = = = = = = G = A T 0 DY11 C A = G I D ? ? D G = A A C C A T = C G G C ? D = D = G = = = = = = = = T = = = G C C G A T C C G G = A = = = T T T = A = T = A = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = T G = A D I ? ? I A = G C T T G C = T C A G ? I = I = A = = = = = = = = C = = = T T T A T C T T T A = T = = = C C C = G = C = G = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = 0 DY12 C = = G I D = = = G = A A C C A T = C G G C G D = = T = = = C G A = T G C A A = = = = = T C = = = = = = = C A C C C = G = C = G = = = = G = = = = = = = = = T = = G = = = = C = C = = = = = = = = = = T = = A D I = = = A = G C T T G C = T C A G A I = = C = = = T A T = C C T G G = = = = = A T = = = = = = = A G T T T = A = T = A = = = = A = = = = = = = = = C = = A = = = = T = T = = = = = = = = = = 0 DY13 = = = = = = = = = = = = = = = = = = = = = = = = = (I) T G = = C G A = T G = A A = G C C G ? ? ? C G G = A = C A = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (D) C A = = T A T = C C = G G = T T T A ? ? ? T T A = T = A G = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = 0 DY14 = = (C) = = ? = = = = = = = (C) (C) (A) (T) (G) (C) (G) (G) (C) ? (D) = = = = A = = = = = = = = = = = = = = G = = = = = G C = = = = T T T = = = T = = = = = = = T C T T = = = G = = G = = = = = C C = C = A A = T = = = A T = = (A) = = ? = = = = = = = (T) (T) (G) (C) (A) (T) (C) (A) (G) ? (I) = = = = T = = = = = = = = = = = = = = A = = = = = A T = = = = C C C = = = C = = = = = = = C T C C = = = T = = A = = = = = G T = T = G G = C = = = C C 0 DY15 C = = G I D = = = G = A = C C A T = C G G C G D = = = = = = = = = = = = = = = = = = = = = = = = = (G) (C) = = = = (T) (T) (T) = = = (T) = = = (T) = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = T = = A D I = = = A = G = T T G C = T C A G A I = = = = = = = = = = = = = = = = = = = = = = = = = (A) (T) = = = = (C) (C) (C) = = = (C) = = = (G) = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = 0 DY16 C A = G I D G T = G = A A C C A T = C G G C ? ? (C) = = = = = = = = = = = = = = = = = = = = = = = = (A) (T) = = = = (C) (C) (C) (G) = (G) (C) (C) = = = = = = (C) (T) (C) (C) = (G) = (T) = = (A) = = = = = = (T) = (T) = = = = = = (A) = (C) (C) T G = A D I A C = A = G C T T G C = T C A G ? ? (G) = = = = = = = = = = = = = = = = = = = = = = = = (G) (C) = = = = (T) (T) (T) (A) = (A) (T) (T) = = = = = = (T) (C) (T) (T) = (A) = (G) = = (G) = = = = = = (C) = (C) = = = = = = (G) = (A) (T) 0 DY17 = A C = = = G T = = T = = C C A T G C G G C ? ? = (I) = = = = = = = = = = = = = = = = = = = = = = = (A) (T) = = = = (C) (C) (C) = = = (C) = = = (G) = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = (G) = (A) (T) = G A = = = A C = = C = = T T G C A T C A G ? ? = (D) = = = = = = = = = = = = = = = = = = = = = = = (G) (C) = = = = (T) (T) (T) = = = (T) = = = (T) = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = (A) = (C) (C) 0 DY18 = = = = = = = = = = = = = = = = = = = = = = = = = = C A A = T A T = C C = G G = T T T A = = T T T = C T = A G T T T = = = T = = = = = = = = = = = T = = G = C G = G T T = = C = C = (A) (A) = (T) = = = (A) (T) = = = = = = = = = = = = = = = = = = = = = = = = = = T G T = C G A = T G = A A = G C C G = = C C G = T A = C A C C C = = = C = = = = = = = = = = = G = = T = T A = A C C = = T = T = (G) (G) = (C) = = = (C) (C) 0 DY19 C A = G I D ? ? D G = A A C C A T = C G G C G D = = T = = = = G A C = = = = = T G C C G = = C C = = T = G = = C C C = = = C = = = = A G G = = = = = = = = A C G = G = = = ? ? = = = A = = = = = = = = T G = A D I ? ? I A = G C T T G C = T C A G A I = = C = = = = A T A = = = = = C T T T A = = T T = = C = A = = T T T = = = T = = = = G A A = = = = = = = = G T A = A = = = ? ? = = = G = = = = = = = = 0 DY20 (C) (A) = (G) (I) (D) (G) = = (G) = (A) = (C) (C) (A) (T) = (C) (G) (G) (C) (G) (D) = (I) = G = = C G A = T G = A = = G C C G = = C C = G = A = C A = = = = = = = = = = T (G) = = = = = = = = = = = T = = = = = = C = = C C A = C = = = G = = (T) (G) = (A) (D) (I) (A) = = (A) = (G) = (T) (T) (G) (C) = (T) (C) (A) (G) (A) (I) = (D) = A = = T A T = C C = G = = T T T A = = T T = A = T = A G = = = = = = = = = = G (A) = = = = = = = = = = = C = = = = = = G = = T G G = A = = = A = = 0 DY21 = = = = = = = = = = = = = = = = = = = = = = = = = = C A = = T A T = C C = G G = T T T A = = T T T = C T = A G T T T = = = T = = = T = = = = = = = = = = = = = = = = = = = (C) = = = = (A) (A) = (T) = = = (A) (T) = = = = = = = = = = = = = = = = = = = = = = = = = = T G = = C G A = T G = A A = G C C G = = C C G = T A = C A C C C = = = C = = = G = = = = = = = = = = = = = = = = = = = (G) = = = = (G) (G) = (C) = = = (C) (C) 0 DY22 C A = G I D ? ? D G = A A C C A T = C G G C G D = D C = = = T A T = C C T G G = = = = = A T = = ? = = = = A G T T T = A = T = A = = = = = T C T T = A T G = C G = = = = = = C = C = = = = = = G = A T T G = A D I ? ? I A = G C T T G C = T C A G A I = I T = = = C G A = T G C A A = = = = = T C = = ? = = = = C A C C C = G = C = G = = = = = C T C C = G C T = T A = = = = = = T = T = = = = = = A = C C 0 DY23 C = = G I D = = = G = A = C C A T = C G G C G D = I = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = (T) = = = = = = = (T) = = (C) = (G) (C) (C) = = (G) (C) (C) T = = A D I = = = A = G = T T G C = T C A G A I = D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = (C) = = = = = = = (C) = = (G) = (A) (A) (T) = = (A) (A) (T) 0 DY24 = A C = = = G = D = ? = = C C A T G C G G C G D = D = ? = = = = = = = = T = = = = = = = = (C) = = (G) = (T) (A) = = = = = = = (A) = = = (A) = = = = (A) (C) (T) (C) (C) = = = (T) = = (A) = (A) = = ? = (T) = (T) = = = = = = = = (C) (C) = G A = = = A = I = ? = = T T G C A T C A G A I = I = ? = = = = = = = = C = = = = = = = = (T) = = (T) = (C) (T) = = = = = = = (G) = = = (G) = = = = (G) (T) (C) (T) (T) = = = (G) = = (G) = (G) = = ? = (C) = (C) = = = = = = = = (A) (T) 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? 0 E102 (C) = (A) (G) (I) (D) = = = (G) ? (A) = = = = = (A) = = = = = = = (I) = G T G = = = A = = = = = C = = = A = = (C) = = = = = A = = = = = = = = = = = C = G A A = = = = = = = = G T A T A = = C C = A = C = = C = C = G = = (T) = (C) (A) (D) (I) = = = (A) ? (G) = = = = = (G) = = = = = = = (D) = A A A = = = C = = = = = T = = = G = = (T) = = = = = G = = = = = = = = = = = T = A G G = = = = = = = = A C G C G = = A G = G = G = = A = T = A = = 0 E103 C = A G I D = = = G C A A T T G C A T C A G A I = = = = = = = = = ? = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C A D I = = = A T G C C C A T G C G G C G D = = = = = = = = = ? = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = = = = = = = = = = = = = = = = = = = = = = = = = (I) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G = G = G = = A = T = A = = = = = = = = = = = = = = = = = = = = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C = A = C = = C = C = G = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = T G = = = = = = = = = = = = = A = = = = = A T = = = = C C C = = = C = = C = = A A = = = = = = = = G T A T A = = C C = A = C = = C = C = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A A = = = = = = = = = = = = = G = = = = = G C = = = = T T T = = = T = = T = = G G = = = = = = = = A C G C G = = A G = G = G = = A = T = A = = 0 E106 = = = = = ? = = = = = = = = = = = = = = = = = = = (I) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 C = A G I D = = = G C A = = = = = A = = = = = = = (I) = = (T) = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C A D I = = = A T G = = = = = G = = = = = = = (D) = = (A) = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = = = = = = = = = = = = = ? = = = = = = A = = = = = C = = = = = T = = = = = = = = = A T = G = = C C C = = = C = = = = A = = = = = = = = = = = = = = = = = = (C) = (A) = (C) = = (C) = (C) = (G) = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = G = = = = = A = = = = = C = = = = = = = = = G C = A = = T T T = = = T = = = = G = = = = = = = = = = = = = = = = = = (G) = (G) = (G) = = (A) = (T) = (A) = = 0 E109 C = A G I D = = = G ? A A T T G C A T C A G A I = (I) = (A) = = = = = (C) = = = = = (T) = = = = = = = = = (A) (T) = (G) = = (C) (C) (C) = = = (C) = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C A D I = = = A ? G C C C A T G C G G C G D = (D) = (G) = = = = = (A) = = = = = (C) = = = = = = = = = (G) (C) = (A) = = (T) (T) (T) = = = (T) = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 C = A G I D = = = G ? A A T T G C A T C A G A I = I = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) (G) (T) (C) (T) (T) = = = (G) (A) (C) (G) = (G) = = (A) (G) = (G) = = = (G) = (C) = (G) = = = T = C A D I = = = A ? G C C C A T G C G G C G D = D = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) (A) (C) (T) (C) (C) = = = (T) (G) (T) (A) = (A) = = (C) (C) = (A) = = = (A) = (T) = (A) = = = 0 E111 = = = = = = = = = = = = = = = = = = = = = = = = = ? = = T = = = = = = = = = = = = = = A = = = = = A T = = = = C C C = = = C = = C = G A A = = = = = = = T G T A = A = = C C = A = C = = C = C = G = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = A = = = = = = = = = = = = = = G = = = = = G C = = = = T T T = = = T = = T = A G G = = = = = = = G A C G = G = = A G = G = G = = A = T = A = = 0 E112 (C) = (A) (G) (I) (D) = = = (G) (C) (A) = = = = = (A) = = = = = = = = = A = = = = = C = = = = = T = = = = = = = = = A T = G = = C C C = = = C = = = = A = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = (T) = (C) (A) (D) (I) = = = (A) (T) (G) = = = = = (G) = = = = = = = = = G = = = = = A = = = = = C = = = = = = = = = G C = A = = T T T = = = T = = = = G = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 E113 C = A G I ? = = = G C A = = = = = A = = = = = = = (I) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C A D ? = = = A T G = = = = = G = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 (C) = (A) (G) (I) ? = = = (G) (C) (A) = = = = = (A) = = = = = = = = = = T G = = = ? = = = = = = = = = A = = = = = A T = = = = C C C = = = C = = C = = A A = = = = = = = = G T A T A = = C C = A = C = = C = C = G = = (T) = (C) (A) (D) ? = = = (A) (T) (G) = = = = = (G) = = = = = = = = = = A A = = = ? = = = = = = = = = G = = = = = G C = = = = T T T = = = T = = T = = G G = = = = = = = = A C G C G = = A G = G = G = = A = T = A = = 0 E115 = = = = = = = = = = = = A T T G C = T C A G A ? = (I) = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C C A T = C G G C G ? = (D) = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G = G = G = = A = T = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C = A = C = = C = C = G = = 0 E117 C = A G I D = = = G ? A = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C A D I = = = A ? G = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E118 = = = = = = = = = = = = = = = = = = = = = = = = = (I) T = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (D) C = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 0 E119 = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = C = = = = = T = = = = ? ? ? = = A T = G = = C C C = = = C = = = = = = = = = = = = = = = = = = = = = = (A) (G) = (G) = (G) = = (A) = (T) = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = A = = = = = C = = = = ? ? ? = = G C = A = = T T T = = = T = = = = = = = = = = = = = = = = = = = = = = (C) (C) = (A) = (C) = = (C) = (C) = (G) = = 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = = = = A A = = = = = = = = = = = = = = = = C = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = = = = G G = = = = = = = = = = = = = = = = G = = = ? = = = = = = = = = 0 E121 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T T = = = = 0 E122 (C) = (A) (G) (I) ? = = = (G) ? (A) = = = = = (A) = = = = = = = = = A = = = = = ? = = = = = T = = = = = = = = = A T = G = = C C C = = = C = = = = A = = = = = = = = = = = = = = = = = = (C) = = = (C) = = (C) = (C) = (G) = = (T) = (C) (A) (D) ? = = = (A) ? (G) = = = = = (G) = = = = = = = = = G = = = = = ? = = = = = C = = = = = = = = = G C = A = = T T T = = = T = = = = G = = = = = = = = = = = = = = = = = = (G) = = = (G) = = (A) = (T) = (A) = = 0 E123 (C) = (A) (G) (I) (D) = = = (G) (C) (A) = = = = = (A) = = = = = = = (I) = = T = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A A = = = = = = = = = = = = = = = A G = G = G = = A = T = A = = (T) = (C) (A) (D) (I) = = = (A) (T) (G) = = = = = (G) = = = = = = = (D) = = A = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = = = = = = = = = = = = = = = C C = A = C = = C = C = G = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = 0.82 0.82 ? ? = = = = = = = = = = = ? ? 1.00 = = ? = = = = = 1.00 = = = = = 1.00 = = = = ? = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 = = 1.00 = = = ? ? = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 = = 0.54 = = = = = = = 0.54 = = 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 = = ? = 1.00 = = = = = = = = = = = = = = 1.00 = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 = = = 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 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = ? ? ? = 0.67 0.66 = ? = = = = = = = = = = = = = = 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 = = = = = = = = 0.89 = ? = = = = = = = = = = = ? ? = 1.00 = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 1.00 = = = ? = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? ? = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 ? = = 1.00 = = = = = = = = = = = = = = = 0.81 = = = 1.00 1.00 = 1.00 1.00 1.00 ? ? 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 ? ? = = = 0.87 = = = = = = = = 0.87 = = = 0.87 0.87 0.87 0.87 0.87 0.87 0.87 0.87 ? 0.87 = 0.87 = = = 0.87 0.87 0.87 = 0.87 = 0.87 = 0.87 = = = = 0.87 = = ? ? ? ? = = = = = = 0.87 = = 1.00 = = = = = = = = = = = = = = = 0.63 0.63 = = = 0.63 0.63 = = = = = 0.63 0.63 0.63 0.63 0.63 ? 0.63 0.63 0.63 0.63 ? 0.73 = 0.90 = = = = 0.90 0.90 = = = = = = = 0.90 0.90 0.90 = = = = = = = = = = = = = = = = = = = = = = 0.90 = = = = 0.54 = = 0.90 = = 0.90 = 0.90 0.90 = = 0.90 0.90 = = = = = 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 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 0.64 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 1.00 = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? ? 1.00 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 = 0.93 = = = = = = = = 0.93 = = = 0.93 0.93 0.93 0.93 0.93 0.93 0.93 0.93 0.93 0.93 = 0.93 = = = 0.93 0.93 0.93 = 0.93 = 0.93 = 0.93 = = = = = = = = = = = 0.93 = = = = = = = = = = = = = = = = = = = = = = = 0.95 = = 0.95 0.95 0.95 = = = 0.95 = 0.95 0.95 0.95 0.95 0.95 0.95 = 0.95 0.95 0.95 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.82 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 ? ? ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 0.60 = = ? = = = = = = = 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 ? 0.60 = = = = 0.99 = = = = = = = = = = = = = = 0.99 = = = = = 0.99 0.99 = = = = 0.99 0.99 0.99 = = = 0.99 = = = = = = = 0.97 0.97 0.97 0.97 = = = 0.97 = = 0.97 = = = = = 0.97 0.97 = 0.97 = 0.97 0.97 = 0.97 = = = 0.97 0.97 1.00 = = 1.00 1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 0.58 = = = = 0.58 0.58 0.58 = = = 0.58 = = = 0.58 = = = = = = = = = = = = 0.58 = = = = = = = = = = = = = = = = = = = = 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 ? ? 0.76 = = = = = = = = = = = = = = = = = = = = = = = = 0.76 0.76 = = = = 0.76 0.76 0.76 0.76 = 0.76 0.76 0.76 = = = = = = 0.76 0.76 0.76 0.76 = 0.76 = 0.76 = = 0.76 = = = = = = 0.76 = 0.76 = = = = = = 0.76 = 0.76 0.76 = 1.00 1.00 = = = 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? = 0.78 = = = = = = = = = = = = = = = = = = = = = = = 0.52 0.52 = = = = 0.52 0.52 0.52 = = = 0.52 = = = 0.52 = = = = = = = = = = = = 0.52 = = = = = = = = = = = = = = = = 0.52 = 0.52 0.52 = = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 = 1.00 1.00 = 1.00 1.00 1.00 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 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 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = 1.00 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = ? ? = = = 1.00 = = = = = = = = 0.54 0.54 = 0.54 0.54 0.54 0.54 = = 0.54 = 0.54 = 0.54 0.54 0.54 0.54 = 0.54 0.54 0.54 0.54 0.54 0.54 = 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 = = = = = = = = = = 0.94 0.54 = = = = = = = = = = = 0.95 = = = = = = 0.95 = = 0.95 0.95 0.95 = 0.95 = = = 0.95 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = 0.87 = = = = 0.87 0.87 = 0.87 = = = 0.87 0.87 0.98 0.98 = 0.98 0.98 0.98 ? ? 0.98 0.98 = 0.98 0.98 0.98 0.98 0.98 0.98 = 0.98 0.98 0.98 0.98 0.98 0.98 = 0.94 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 1.00 = = ? = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 = = = = = = = = = 0.56 = = = = = = = 0.60 = = 0.60 = 0.60 0.60 0.60 = = 0.60 0.60 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 = 0.98 = ? = = = = = = = = 1.00 = = = = = = = = 0.57 = = 0.62 = 0.62 0.62 = = = = = = = 0.62 = = = 0.62 = = = = 0.62 0.62 0.62 0.62 0.62 = = = 0.62 = = 0.62 = 0.62 = = ? = 0.62 = 0.62 = = = = = = = = 0.62 0.62 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? 0.80 = 0.80 0.80 0.80 0.80 = = = 0.80 ? 0.80 = = = = = 0.80 = = = = = = = 0.79 = 1.00 1.00 1.00 = = = 1.00 = = = = = 1.00 = = = 1.00 = = 0.53 = = = = = 1.00 = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = = = = = 1.00 = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = 0.87 = = 0.81 = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.81 0.81 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 1.00 = = = = = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = 0.71 = 0.71 = 0.71 = = 0.71 = 0.71 = 0.71 = = 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 ? 1.00 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 = 0.67 = = = = = 0.67 = = = = = 0.67 = = = = = = = = = 0.67 0.67 = 0.67 = = 0.67 0.67 0.67 = = = 0.67 = = = = 0.67 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 ? 1.00 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 = = = = = = = = = = = = = 0.52 = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 0.58 0.58 0.58 0.58 0.58 = = = 0.58 0.58 0.58 0.58 = 0.58 = = 0.58 0.58 = 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 = 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 = = 0.68 = 0.68 0.68 0.68 0.68 = = = 0.68 0.68 0.68 = = = = = 0.68 = = = = = = = = = 1.00 = = = = = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = = = 0.96 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 1.00 = 1.00 1.00 1.00 ? = = = 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = 0.70 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.64 = 0.64 0.64 0.64 ? = = = 0.64 0.64 0.64 = = = = = 0.64 = = = = = = = = = = 1.00 1.00 = = = ? = = = = = = = = = 1.00 = = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? = 0.59 = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.50 1.00 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = = = 1.00 = = = = ? ? ? = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 0.65 0.65 = 0.65 = 0.65 = = 0.65 = 0.65 = 0.65 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = = = ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = 0.77 = 0.77 0.77 0.77 ? = = = 0.77 ? 0.77 = = = = = 0.77 = = = = = = = = = 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 = 0.73 = 0.73 = = 0.88 = 0.88 0.88 0.88 0.88 = = = 0.88 0.88 0.88 = = = = = 0.88 = = = = = = = 0.79 = = 0.96 = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 0.96 = = = = = = = = = = = = = = = 0.98 0.98 = 0.98 = 0.98 = = 0.98 = 0.98 = 0.98 = = END PHASEPROBS