************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 psd4x.phase.inp psd4x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST psd4x.phase.out_freqs : haplotype frequency estimates psd4x.phase.out_pairs : most likely haplotype pairs for each individual psd4x.phase.out_recom : estimates of recombination parameters psd4x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 104 Positions of loci: 337 1099 1308 2254 2872 3003 3104 3179 3242 3253 3689 3993 4168 4246 4527 4616 4618 4668 4893 5470 5664 5698 5706 5710 5711 5813 5850 6106 6164 6250 6479 6549 7625 7823 7882 8006 8532 8588 10206 10394 10723 11124 11282 12212 12502 12648 12717 12748 12928 13346 13693 13913 14438 14903 15205 15273 15701 15777 15898 16138 16345 16525 16639 16791 17896 17926 18202 18290 18602 18821 18879 19025 19357 19359 19541 19819 20013 20034 20180 20738 20963 22368 23143 23952 24101 24396 24428 24450 24691 24940 25323 25518 25677 26815 27265 27385 27492 27627 27643 28082 28159 29835 30653 32519 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file psd4x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGTCCCCDCCGCCCGCACTTCCCGDACCGGGACGGAGAACGCCCGAGGACAGCCGGACCA 4 GGGGGC 3 ACGTCTTGTTGAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 2 CGTCCCCDCCGCCCGTATCCCCGGIACCGGAACGGGGAAAGTGCGAGGACAGCAGAATTC 2 GGGGGT 3 GGGTCCCGCTGAT 4 CAATAAGTAGCGCAGIAADCGT 1.000000 3 CGTCCCCDCCGCCCGTATCCCCGGIACCGGAACGGGGAAAACGCGAGGACAGCAGAATTC 2 GGGGGT 3 GGGTCCCGCTGAT 4 CAATAAGTAGCGCAGIAADCGT 1.000000 4 CGTCCCCDCCGCCCGTATCCTAGGIACCGGAACGGAGAACGCCCGAGGACAGTCGGACCA 4 GGGGGC 3 ACGTCTTGTTGAT 1 CAATAAGTAGCGCAGIAADTGC 1.000000 5 CGTCCCCDCCGCCCGTATCCTAGGIACCGGAACGGAGAACGCCCGAGGACAGTCGGACCA 4 GGGGGC 3 ACGTCTTGTTGAT 2 GGCCGGAACACCGTADCGICGT 1.000000 6 CGTCCCCDCCGCCCGTATCCTAGGIACCGTAACAGAGAACGCCCAAGAGCAGCCAGACCA 4 GGGGGC 3 GGGTCCCATCAAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 7 CGTCCCCDCCGCCCGTATCCTAGGIACCGTAACAGAGAACACCCGAGGACTGCAGAATTC 2 GGGGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGITTT 2.000000 8 CGTCCCCDCCGCCCGTATCCTAGGIACCGTAACAGAGAACACCCGAGGACTGCAGAATTC 2 GGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGTGCAGIAADCGC 1.000000 9 CGTCCCCDCCGCCCGTATCCTAGGIACCGTAACAGAGAACACCCGAGGACTGCCGGATTC 1 AGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 10 CGTCCCCDCCGCCCGTATCCTAGGIACCGTAACAGAGAACACCCGAGGACTGCCGGATTC 1 AGGGGT 3 GGGTCCCACCGAC 2 GGATGAGTAGCGCTGDAADCGC 2.000000 11 CGTCCCCDCCGCCCGTATCCTAGGIACCGTAACAGAGAACACCCGAGGACTGCCGGACCA 4 GGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGCGCAGIAADCGT 1.000000 12 CGTCCCGDCCGCCCGTATCCTAGGIGCCGGAGCGGAGAACGCCCGAGGACAGCCGGACCA 4 GCAGGC 3 ACGTCTTGTTGAT 1 CAATAAGTAGTGCAGIAADCGC 1.000000 13 CGTCCCGDCCGCCCGTATCCTAGGIGCCGGAGCGGAGAACGCCCGAGGACAGCCGGACCA 4 GCAGGC 3 ACGTCTTGTTGAT 2 GGATGAGTAGCGCTGDAADCGC 4.000000 14 CGTCCCGDTCGCCCGCACCTCCCGDACTGGAACGGAGAACGCCCGAGGACAGCCGGACCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 CAATAAGTAGTGCAGIAADCGC 1.000000 15 CGTCCCGDTCGCCCGCACCTCCCGDACTGGAACGGAGAACGCCCGAGGACAGCCGGACCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 16 CGTCCCGICGGCTCGTTTCCCCGGIACCAGAACGGGGAACGCCCGAGGACAGCAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 1.000000 17 CGTCCCGICGGTTCGTTTCCCCGGIACCAGAACGAGGAACGCCCAAGAGCAGCCAGACCA 4 GGGGGC 3 GGGTCCCATCAAT 2 GGATGAGTAGCGCTGDAGICGC 1.000000 18 CGTCCCGICGGTTCGTTTCCCCGGIACCAGAACGAGGAACGCCCAAGAGCAGCCAGACCA 4 GGGGCC 3 ACGGCCTGCTGAT 2 GGATGAGTAGCGCTGDAADCGC 3.000000 19 CGTCCCGICGGTTCGTTTCCCCGGIACCAGAACGAGGAACGCCCAAGAGCAGCCAGACCA 4 GGGGCC 3 ACGGCCTGCTGAT 2 GGATGAGTAGCGCTGDAGICGC 1.000000 20 CGTCCCGICGGTTCGTTTCCCCGGIACCAGAACGAGGAACGCCCAAGAGCAGCCAGACCA 4 GGGGCC 3 ACGGCCTGCTGGT 1 CAATAAGTAGTGCAGIAADCGC 1.000000 21 CGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGAGAACGCCCGAGGACAGCCGGACCA 4 GGGGGC 4 GCATTCTGTTGAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 22 CGTCTCGDTCGCCCGCACTCCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGGGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICTT 1.000000 23 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGGGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICTT 3.000000 24 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGGGGC 3 ACGTCTTGTTGAT 1 CAATAAGTAGTGCAGIAADCGC 2.000000 25 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGGGGC 3 ACGTCTTGTTGGT 4 CGATGAGTAGCGCTGDAADCGC 1.000000 26 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGGGGC 4 GCATTCTGTTGAT 1 CAATAAGTAGTGCAGIAADCGC 2.000000 27 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 1.000000 28 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAGAATTC 2 GGATGC 3 ACGTCCTGTTGAT 2 GGATGAGTAGCGCTGDAADCGC 2.000000 29 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACAAGACCA 2 GGGGGT 3 GGGTTCTATCAAT 4 CGATGAGTAGCGCTGDAADCGC 2.000000 30 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGAGATCGTGCAGCGAAAACCGGATCC 2 GGGGGC 1 ACGTCCTGTTAAC 1 CAATAAGTAGCGCAGIAADCGC 1.000000 31 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGGGAAAGCGCAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 32 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGGGAAAGCGCGAGGACAGCAGAGTTC 2 GGGGGT 3 GGGTCCCGCTGGT 1 CAATAAGTAGTGCAGIAADCGC 1.000000 33 CGTCTCGDTCGCCCGCACTTCCCGDACCGGGACGGGGAAAGCGCGAGGACAGCAGAGTTC 2 GGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 34 CGTCTCGDTCGCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 3.000000 35 CGTCTCGDTCGCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTGGT 2 GGATGAGTAGCGCTGDAGICGC 1.000000 36 CGTCTCGDTCTCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGGGGC 3 ACGTCCTGCTGAT 2 GGCCGGAACACCGTADCGICGT 1.000000 37 CGTCTCGDTCTCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 38 CGTCTCGDTCTCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGAGICADCGT 1.000000 39 CGTCTCGDTCTCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 9.000000 40 CGTCTCGDTCTCCCACACTTCCCGDACCGGGACGGAGATCGTGAAGCGAAAACCGGGCCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 GGCCGGAACACCGTADCGICGT 1.000000 41 CGTCTCGDTCTCCCACACTTCCCTDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 42 CGTCTCGDTCTCCCACACTTCCCTDACCGGGACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 1.000000 43 CGTTCCGDCCGCCCGCACCTCCCGDACCGGAACGGAGAACGCCCGAGGACAGCCGAACCA 4 GGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 44 CGTTCCGDCCGCCCGCACCTCCCGDACCGGAACGGAGAACGCCCGAGGACAGCCGGGCCC 2 GGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGCGCAGIAADCGC 1.000000 45 CGTTCCGDCCGCCCGTATCCCCGGIACCGGGACGGGGATCGCGCGGCGACAGCAGAATTC 2 AGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGTGCAGIAADCGC 1.000000 46 CGTTCCGDCCGCCCGTATCCCCGTIACCGGGACGGAGAACGCCCGAGGACAGCCGGGCCA 4 GGGGGC 3 ACGTCCTGCTGGT 4 CGATGAGTAGCGCTGDAADCGC 2.000000 47 CGTTTCGDCCGCCCGTATCCCCGTIACCGGGACGGGGATCGCGCGGCGACAGCAGAATTC 2 AGGGGT 3 GGGTCCCACCGAT 1 CAATAAGTAGTGCAGIAADCGC 1.000000 48 CGCCCCGDCCGCCTGTATCCTAGGIACCGGAACGGAGAACGCCCGAGGACAGCCGGACCA 4 GGGGGC 4 GCATTCTGTTGAT 2 GGCCGGAACACCGTADCGICTT 1.000000 49 CGCCCCGDCCGCCTGTATCCTAGGIACCGGAACGGAGAACGCCCGAGGACAGCCGGACCA 4 GGGGGC 4 GCATTCTGTTGAC 1 CAATAAGTAGCGCAGIAADCGC 1.000000 50 CGCCCCGDCCGCCTGTATCCTAGGIACCGGAACGGAGAACGCCCGAGGACAGTCGGACCA 4 GGGGGC 3 ACGTCTTGTTGAT 2 GGCCGGAACACCGTADCGICGT 4.000000 51 CCTCCCGICGGCTCGTTTCCCCGGIACCAGAATGAGGGACGCCCGAGAACAGCCAGACCA 2 GGGGGT 3 GGGTCCCATCAAT 1 CAATAAGTAGCGCAGIAADCGC 2.000000 52 CCTCCCGICGGCTCGTTTCCCCGGIACCAGAATGAGGGACGCCCGAGAACAGCCAGACCA 2 GGGGGT 3 GGGTCCCATCAAT 1 CAATAAGTAGCGCAGIAADTGC 2.000000 53 CCTCCCGICGGCTCGTTTCCCCGGIACCAGAATGAGGGACGCCCGAGAACAGCCAGACCA 2 GGGGGT 3 GGGTCCCATCAAC 2 GGATGAGTAGCGCAGIAADCGC 1.000000 54 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGAGATCGTGAAGCGAAAACAGAATTC 2 GGAGGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 1.000000 55 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAACAGAATTC 2 GGATGC 3 ACGTCCTGTTAAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 56 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAGCCGGGCCA 4 GGGGGC 3 ACGTCTTGTTGAT 2 GGCCGGAACACCGTADCGICGT 2.000000 57 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAGCCGGGCCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 58 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAGCCGGGCCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 GGCCGGAACACCGAGICADCGT 1.000000 59 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAGCCGGGCCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 GGCCGGAACACCGTGDAADCGT 1.000000 60 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAGCCGGGCCA 4 GGATGC 3 ACGTCCTGCTAAT 2 GGCCGGAACACCGTADCGICGT 1.000000 61 TGTCCAGDTCGCCCGCACCTCCCGDATTGGAACGGACAACGCCCGAGGACAGCCGGGCCA 4 GGATGC 3 ACGTCCTGTTAAT 2 GGATGAGTAGCGCTGDAADCGC 2.000000 62 TGTCCAGDTCGCCCGTATCCCCGTIACCGGGACGGGGATCGCGCGGCGACAGCAGGATCC 2 GGGGGC 3 ACGTCCTGTTAAT 2 GGATGAGTAGCGCTGDAADCGC 1.000000 63 TGTCTAGDTCGCCCGCACCTCCCGDATTGGAACGGAGATCGTGCAGCGAAAGCCGGGCCA 4 GGGTGC 3 ACGTCCTGTTGAT 2 CAATAAGTAGCGCAGIAADCGC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (2,22) DY02: (3,6) DY03: (47,52) DY04: (33,43) DY05: (23,52) DY06: (31,45) DY07: (7,46) DY08: (14,25) DY09: (7,8) DY10: (13,53) DY11: (9,18) DY12: (23,24) DY13: (24,44) DY14: (18,23) DY15: (10,20) DY16: (17,19) DY17: (1,15) DY18: (18,46) DY19: (21,32) DY20: (11,62) DY21: (27,48) DY22: (49,51) DY23: (10,51) DY24: (30,35) E101: (5,39) E102: (26,39) E103: (28,50) E104: (34,37) E105: (29,63) E106: (13,28) E107: (34,61) E108: (29,39) E109: (26,56) E110: (13,39) E111: (12,38) E112: (56,61) E113: (50,54) E114: (34,39) E115: (13,42) E116: (36,39) E117: (4,58) E118: (39,39) E119: (41,50) E120: (59,55) E121: (16,57) E122: (40,60) E123: (39,50) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C G T C C C C D C C G C C C G T A T C C C C G G I A C C G G A A C G G G G A A A G T G C G A G G A C A G C A G A A T T C 2 G G G G G T 3 G G G T C C C G C T G A T 4 C A A T A A G T A G C G C A G I A A D C G T C G T C T C G D T C G C C C G C A C T C C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C T T 0 DY02 C G T C C C C D C C G C C C G T A T C C C C G G I A C C G G A A C G G G G A A A A C G C G A G G A C A G C A G A A T T C 2 G G G G G T 3 G G G T C C C G C T G A T 4 C A A T A A G T A G C G C A G I A A D C G T C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G G C 3 G G G T C C C A T C A A T 1 C A A T A A G T A G C G C A G I A A D C G C 0 DY03 C G T T (T) C G D C C G C C C G T A T C C C C G (T) I A C C G G G A C G G G G A T C G C G C G G C G A C A G C A G A A T T C 2 A G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G T G C A G I A A D C G C C C T C (C) C G I C G G C T C G T T T C C C C G (G) I A C C A G A A T G A G G G A C G C C C G A G A A C A G C C A G A C C A 2 G G G G G T 3 G G G T C C C A T C A A T 1 C A A T A A G T A G C G C A G I A A D T G C 0 DY04 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G G G A A A G C G C G A G G A C A G C A G A G T T C 2 G G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G C G C A G I A A D C G C C G T T C C G D C C G C C C G C A C C T C C C G D A C C G G A A C G G A G A A C G C C C G A G G A C A G C C G A A C C A 4 G G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G C G C A G I A A D C G C 0 DY05 C G T C T C G D T C G C C C G C A C T [T] C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I (C) T T C C T C C C G I C G G C T C G T T T C C C C G G I A C C A G A A T G A G G G A C G C C C G A G A A C A G C C A G A C C A 2 G G G G G T 3 G G G T C C C A T C A A T 1 C A A T A A G T A G C G C A G I A A D (T) G C 0 DY06 C G T C (T) C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G G G A A A G C G C A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 1 C A A T A A G T A G C G C A G I A A D C G C C G T T (C) C G D C C G C C C G T A T C C C C G G I A C C G G G A C G G G G A T C G C G C G G C G A C A G C A G A A T T C 2 A G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G T G C A G I A A D C G C 0 DY07 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C A C C C G A G G A C T G C A G A A T T C 2 G G G G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I T T T C G T T C C G D C C G C C C G T A T C C C C G T I A C C G G G A C G G A G A A C G C C C G A G G A C A G C C G G G C C A 4 G G G G G C 3 A C G T C C T G C T G G T 4 C G A T G A G T A G C G C T G D A A D C G C 0 DY08 C G T C C C G D T C G C C C G C A C C T C C C G D A C T G G A A C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G G G (T) G C 3 A C G T C (C) T G T T G (A) T (2) C (A) A T (A) A G T A G (T) G C (A) G (I) A A D C G C C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G (G) G C 3 A C G T C (T) T G T T G (G) T (4) C (G) A T (G) A G T A G (C) G C (T) G (D) A A D C G C 0 DY09 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C A C C C G A G G A C T G C A G A A T T C 2 G G G G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I T T T C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C A C C C G A G G A C T G C A G A A T T C 2 G G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G T G C A G I A A D C G C 0 DY10 C G T C C C G D C C G C C C G T A T C C T A G G I G C C G G A G C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G C A G G C 3 A C G T C T T G T T G A T 2 G G A T G A G T A G C G C (T) G (D) A A D C G C C C T C C C G I C G G C T C G T T T C C C C G G I A C C A G A A T G A G G G A C G C C C G A G A A C A G C C A G A C C A 2 G G G G G T 3 G G G T C C C A T C A A C 2 G G A T G A G T A G C G C (A) G (I) A A D C G C 0 DY11 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C A C C C G A G G A C T G C C G G A T T C 1 A G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G C G C A G I A A D C G C C G T C C C G I C G G T T C G T T T C C C C G G I A C C A G A A C G A G G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G C C 3 A C G G C C T G C T G A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 DY12 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C T T C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 3 A C G T C T T G T T G A T 1 C A A T A A G T A G T G C A G I A A D C G C 0 DY13 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 3 A C G T C T T G T T G A T 1 C A A T A A G T A G T G C A G I A A D C G C C G T T C C G D C C G C C C G C A C C T C C C G D A C C G G A A C G G A G A A C G C C C G A G G A C A G C C G G G C C C 2 G G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G C G C A G I A A D C G C 0 DY14 C G T C C C G I C G G T T C G T T T C C C C G G I A C C A G A A C G A G G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G C C 3 A C G G C C T G C T G A T 2 G G A T G A G T A G C G C T G D A A D C G C C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C T T 0 DY15 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C A C C C G A G G A C T G C C G G A T T C 1 A G G G G T 3 G G G T C C C A C C G A C 2 G G A T G A G T A G C G C T G D A A D C G C C G T C C C G I C G G T T C G T T T C C C C G G I A C C A G A A C G A G G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G C C 3 A C G G C C T G C T G G T 1 C A A T A A G T A G T G C A G I A A D C G C 0 DY16 C G T C C C G I C G G T T C G T T T C C C C G G I A C C A G A A C G A G G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G G C 3 G G G T C C C A T C A A T 2 G G A T G A G T A G C G C T G D A G I C G C C G T C C C G I C G G T T C G T T T C C C C G G I A C C A G A A C G A G G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G C C 3 A C G G C C T G C T G A T 2 G G A T G A G T A G C G C T G D A G I C G C 0 DY17 C G T C C C C D C C G C C C G C A C T T C C C G D A C C G G G A C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G G G (G) G C 3 A C G T C (T) T G T T G A T 2 G G A T G A G T A G C G C T G D A A D C G C C G T C C C G D T C G C C C G C A C C T C C C G D A C T G G A A C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G G G (T) G C 3 A C G T C (C) T G T T G A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 DY18 C G T C C C G I C G G T T C G T T T C C C C G G I A C C A G A A C G A G G A A C G C C C A [A] G A G C A G C C A G A C C A 4 G G G G C C 3 A C G G C C T G C T G A T 2 G G A T G A G T A G C G C T G D A A D C G C C G T T C C G D C C G C C C G T A T C C C C G T I A C C G G G A C G G A G A A C G C C C G A G G A C A G C C G G G C C A 4 G G G G G C 3 A C G T C C T G C T G G T 4 C G A T G A G T A G C G C T G D A A D C G C 0 DY19 C G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G G G G G C 4 G C A T T C T G T T G A T 1 C A A T A A G T A G C G C A G I A A D C G C C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G G G A A A G C G C G A G G A C A G C A G A G T T C 2 G G G G G T 3 G G G T C C C G C T G G T 1 C A A T A A G T A G T G C A G I A A D C G C 0 DY20 (C) G T C C (C) (C) D (C) C G C C C G T A T C C (T) (A) G (G) I A C C G (T) (A) A C (A) G (A) G A (A) C (A) C (C) C G (A) (G) G A C (T) G C (C) G G A (C) C (A) (4) G G G G G T 3 G G G T C C C A C C G A T 1 C A A T A A G T A G C G C A G I A A D C G T (T) G T C C (A) (G) D (T) C G C C C G T A T C C (C) (C) G (T) I A C C G (G) (G) A C (G) G (G) G A (T) C (G) C (G) C G (G) (C) G A C (A) G C (A) G G A (T) C (C) (2) G G G G G C 3 A C G T C C T G T T A A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 DY21 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C (G) T C G C C C C G D C C G C C T G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G G G G G C 4 G C A T T C T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C (T) T 0 DY22 C G C C C C G D C C G C C T G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G G G G G C 4 G C A T T C T G T T G A (C) 1 C A A T A A G T A G C G C A G I A A D C G C C C T C C C G I C G G C T C G T T T C C C C G G I A C C A G A A T G A G G G A C G C C C G A G A A C A G C C A G A C C A 2 G G G G G T 3 G G G T C C C A T C A A (T) 1 C A A T A A G T A G C G C A G I A A D C G C 0 DY23 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G T A A C A G A G A A C A C C C G A G G A C T G C C G G A T T C 1 A G G G G T 3 G G G T C C C A C C G A (C) (2) (G) (G) A T (G) A G T A G C G C (T) G (D) A A D C G C C C T C C C G I C G G C T C G T T T C C C C G G I A C C A G A A T G A G G G A C G C C C G A G A A C A G C C A G A C C A 2 G G G G G T 3 G G G T C C C A T C A A (T) (1) (C) (A) A T (A) A G T A G C G C (A) G (I) A A D C G C 0 DY24 C G T C T C G D T C G C C C (G) C A C T T C C C G D A C C G G G A C G G A G A T C G T G (C) A G C G A A A A C (C) G (G) A T (C) C 2 G G (G) G G C (1) A C G T C C T G T T A A C (1) (C) (A) A T (A) A G T A G C G C (A) G (I) A (A) (D) C G C C G T C T C G D T C G C C C (A) C A C T T C C C G D A C C G G G A C G G A G A T C G T G (A) A G C G A A A A C (A) G (A) A T (T) C 2 G G (A) G G C (3) A C G T C C T G C T G G T (2) (G) (G) A T (G) A G T A G C G C (T) G (D) A (G) (I) C G C 0 E101 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G T C G G A C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C G T C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E102 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 4 G C A T T C T G T T G A T 1 C A A T A A G T A G T G C A G I A A D C G C C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E103 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G A T G C 3 A C G T C C T G T T G A T 2 G G A T G A G T A G C G C T G D A A D C G C C G C C C C G D C C G C C T G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G T C G G A C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E104 C G T C T C G D T C (G) C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T C G T C T C G D T C (T) C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 E105 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A A G A C C A 2 G G G G G T 3 G G G T T [C] T A T C A A T 4 C G A T G A G T A G C G C T G D A A D C G C T G T C T A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A G A T C G T G C A G C G A A A G C C G G G C C A 4 G G G T G C 3 A C G T C C T G T T G A T 2 C A A T A A G T A G C G C A G I A A D C G C 0 E106 C G T C C C G D C C G C C C G T A T C C T A G G I G C C G G A G C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G C A G G C 3 A C G T C T T G T T G A T 2 G G A T G A G T A G C G C T G D A A D C G C C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G A T G C 3 A C G T C C T G T T G A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 E107 C G T C T C G D T C G C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G A T G C 3 A C G T C C T G T T A A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 E108 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A A G A C C A 2 G G G G G T 3 G G G T T C T A T C A A T 4 C G A T G A G T A G C G C T G D A A D C G C C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E109 C G T C T C G D T C G C C C G C A C T T C C C G D A C C G G G A C G G A G A T C G T G C A G C G A A A A C A G A A T T C 2 G G G G G C 4 G C A T T C T G T T G A T 1 C A A T A A G T A G T G C A G I A A D C G C T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E110 C G T C C C G D C C G C C C G T A T C C T A G G I G C C G G A G C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G C A G G C 3 A C G T C T T G T T G A T 2 G G A T G A G T A G C G C T G D A A D C G C C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E111 C G T C C C G D C C G C C C G T A T C C T A G G I G C C G G A G C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G C A G G C 3 A C G T C T T G T T G A T (1) (C) (A) (A) (T) (A) (A) (G) (T) (A) (G) (T) (G) (C) A G I (A) A D C G (C) C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T (2) (G) (G) (C) (C) (G) (G) (A) (A) (C) (A) (C) (C) (G) A G I (C) A D C G (T) 0 E112 T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C G T T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G A T G C 3 A C G T C C T G T T A A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 E113 C G C C C C G D C C G C C T G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G T C G G A C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C G T T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E114 C G T C T C G D T C G C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E115 C G T C C C G D C C G C C C G T A T C C T A G G I G C C G G A G C G G A G A A C G C C C G A G G A C A G C C G G A C C A 4 G C A G G C 3 A C G T C T T G T T G A T 2 G G (A) (T) G (A) (G) (T) (A) (G) C (G) (C) T (G) D (A) (A) (D) C G (C) C G T C T C G D T C T C C C A C A C T T C C C T D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G (C) (C) G (G) (A) (A) (C) (A) C (C) (G) T (A) D (C) (G) (I) C G (T) 0 E116 C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G (G) G G C 3 A C G T C C T G C T G A T 2 G G C C G G A A C A C C G T A D C G I C G T C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G (A) G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E117 C G T C C C C D C C G C C C G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G T C G G A C C A 4 G G G G G C 3 A C G T C T T G T T G A T 1 C A A T A A G T A G C G C A G I A A D T G C T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G G T G C 3 A C G T C C T G T T G A T 2 G G C C G G A A C A C C G A G I [C] A D C G T 0 E118 C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G [T] A [D] C [G] I C G T 0 E119 C G T C T C G D T C T C C C A C A C T T C C C T D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G (A) (T) G (A) (G) (T) (A) (G) C (G) (C) T (G) D (A) (A) (D) C G (C) C G C C C C G D C C G C C T G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G T C G G A C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G (C) (C) G (G) (A) (A) (C) (A) C (C) (G) T (A) D (C) (G) (I) C G (T) 0 E120 T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A (G) C (C) G (G) (G) (C) (C) (A) (4) G G G T G C 3 A C G T C C T G T T (G) A T 2 G G C C G G A A C A C C G T G D A A D C G T T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A (A) C (A) G (A) (A) (T) (T) (C) (2) G G A T G C 3 A C G T C C T G T T (A) A T 2 G G A T G A G T A G C G C T G D A A D C G C 0 E121 C G T C C C G I C G G C T C G T T T C C C C G G I A C C A G A A C G G G G A A C G C C C G A G G A C A G C A G A A T T C 2 G G (A) G G C 3 A C G T C C T G C T (A) A T 2 G G (C) (C) G (G) (A) (A) (C) (A) C (C) (G) T (A) D (C) (G) (I) C G (T) T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G (G) T G C 3 A C G T C C T G T T (G) A T 2 G G (A) (T) G (A) (G) (T) (A) (G) C (G) (C) T (G) D (A) (A) (D) C G (C) 0 E122 C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C C G G G C C A 4 G G (G) T G C 3 A C G T C C T G (T) T (G) A T 2 G G C C G G A A C A C C G T A D C G I C G T T G T C C A G D T C G C C C G C A C C T C C C G D A T T G G A A C G G A C A A C G C C C G A G G A C A G C C G G G C C A 4 G G (A) T G C 3 A C G T C C T G (C) T (A) A T 2 G G C C G G A A C A C C G T A D C G I C G T 0 E123 C G T C T C G D T C T C C C A C A C T T C C C G D A C C G G G A C G G A G A T C G T G A A G C G A A A A C A G A A T T C 2 G G A G G C 3 A C G T C C T G C T A A T 2 G G C C G G A A C A C C G T A D C G I C G T C G C C C C G D C C G C C T G T A T C C T A G G I A C C G G A A C G G A G A A C G C C C G A G G A C A G T C G G A C C A 4 G G G G G C 3 A C G T C T T G T T G A T 2 G G C C G G A A C A C C G T A D C G I C 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 DY01 = = = = C = C = C = = = = = = T = T C = = = G = I = = = = = A = = = = G = = A A = = = = G A G = = C = G = = = = = = = = = = = = = = T = G G = = = = C = = = G = = 4 ? ? A T A A G T A G = G C A G I A A D = G = = = = = T = G = T = = = = = = C = C T = = = C = D = = = = = G = = = = A = = T C = = = = A G C = = A = A = = = = = = = = = = = = = = C = A C = = = = T = = = A = = 2 ? ? C C G G A A C A = C G T A D C G I = T = 0 DY02 = = = = = = = = = = = = = = = = = = = = C C = = = = = = = G = = = G = G = = = A A = G ? ? ? ? ? A = ? ? ? A G A = T T C 2 = = = = = T = = = = = ? = = G C T G = = 4 = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = T A = = = = = = = T = = = A = A = = = C G = C ? ? ? ? ? G = ? ? ? C A G = C C A 4 = = = = = C = = = = = ? = = A T C A = = 1 = = = = = = = = = = = = = = = = = = = = = C 0 DY03 ? G = T (T) = = D = C = = C = = = A = = = = = = (T) = = = = G = G = C = G = = A T = = = G = = G C G = = = = = A G A = T T C = A = = = = = = = = = = = = = = C = G = = = ? ? = = = = ? = = = T = = = = = = = = C = = ? C = C (C) = = I = G = = T = = = T = = = = = = (G) = = = = A = A = T = A = = G A = = = C = = A G A = = = = = C A G = C C A = G = = = = = = = = = = = = = = T = A = = = ? ? = = = = ? = = = C = = = = = = = = T = = 0 DY04 = = = C T = = = T = = = = = = = = = T = = = = = = = = = = = G = = = = G = ? = A = = G = = = = = = = = = = A = = G T T C 2 = = = = = = = = = = = ? ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = T C = = = C = = = = = = = = = C = = = = = = = = = = = A = = = = A = ? = C = = C = = = = = = = = = = C = = A C C A 4 = = = = = = = = = = = ? ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = 0 DY05 ? G = = T = = D T C = = C = = C A C T ? = = C = D = = = G = G = C = G A = ? T = = T G = A G C G = A = A = A G A = T T C = = = = = = C = A C = = = = T G C T = = = 2 G G C C ? ? ? A C A = C G T A D C G I (C) T T ? C = = C = = I C G = = T = = T T T C ? = = G = I = = = A = A = T = A G = ? A = = C C = G A G A = C = G = C A G = C C A = = = = = = T = G G = = = = C A T C = = = 1 C A A T ? ? ? T A G = G C A G I A A D (T) G C 0 DY06 = = = C (T) = = = T = = = = = = C = C T T = = C = D = = = = = = = = = = = = = A A = = = = A = = = = A = A = = = = = = = = = G = A = = C = A C = = = = T G = T A = = = = = = = = = = = = = C = = = = = = = = = = = = = = T (C) = = = C = = = = = = T = T C C = = G = I = = = = = = = = = = = = = T C = = = = G = = = = C = G = = = = = = = = = A = G = = T = G G = = = = C A = C G = = = = = = = = = = = = = T = = = = = = = = = = = 0 DY07 = = = C = = C = = = = = = = = = = = = = T A = G = = = = = T A = = A = = = = = = A = = = = = = = = = T = = A = A A T T C 2 = = = = = = = = = = = = = = = = = A A = 2 G = ? ? = G A A C A = C G = A = C G I T T T = = = T = = G = = = = = = = = = = = = = C C = T = = = = = G G = = G = = = = = = G = = = = = = = = = A = = C = G G C C A 4 = = = = = = = = = = = = = = = = = G G = 4 C = ? ? = A G T A G = G C = G = A A D C G C 0 DY08 = = = = C = = = = = = ? = = = = = = C = = = = = = = = T = = A = = = = = = = A = = C C = G A G = = C = G = C = G = C C A 4 = = = (T) = = = = = = = = (C) = = = = = (A) = (2) = (A) ? = (A) = = = = = (T) = = (A) = (I) = = = = = = = = = = T = = = = = = ? = = = = = = T = = = = = = = = C = = G = = = = = = = T = = T G = A G C = = A = A = A = A = T T C 2 = = = (G) = = = = = = = = (T) = = = = = (G) = (4) = (G) ? = (G) = = = = = (C) = = (T) = (D) = = = = = = 0 DY09 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = A C = = = = T G = T A = = 2 G G C C G G A A C A C C G T A D C G I T T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = G G = = = = C A = C G = = 1 C A A T A A G T A G T G C A G I A A D C G C 0 DY10 ? G = = = = = D = C = = C = = = A ? ? = T A = = = G = ? ? ? = G C = G A = A = = = = = = = = = G = = = = = = G = = = = = 4 = C A = = C = A C = = = T T G = T G = T = = = = = = = = = = = = = = (T) = (D) = = = = = = ? C = = = = = I = G = = T = = = T ? ? = C C = = = A = ? ? ? = A T = A G = G = = = = = = = = = A = = = = = = A = = = = = 2 = G G = = T = G G = = = C C A = C A = C = = = = = = = = = = = = = = (A) = (I) = = = = = = 0 DY11 = = = = = = C D = C = C C = = = A = = = T A = = = = = = G T ? = = A G A = = = = A = = ? ? ? ? ? A = T = = = G = = T T C 1 A = = = G T = G G = T = = C A = C = = = 1 C A = = A = = = = = = = = A = I = = = = = = = = = = = = G I = G = T T = = = T = = = C C = = = = = = A G ? = = G A G = = = = G = = ? ? ? ? ? G = A = = = A = = C C A 4 G = = = C C = A C = G = = T G = T = = = 2 G G = = G = = = = = = = = T = D = = = = = = 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = C = A = = 2 G G C C G G A A C A C C G T A D C G I ? T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = T = G = = 1 C A A T A A G T A G T G C A G I A A D ? G C 0 DY13 = = = C T = = ? ? ? = = = = = = = = T = = = = = = = = = = = G = = = = = = ? T = = T G = A G C = = A = A = A = A A T T = = = = = = = C = A C = = = T T G T T = = = = = = = = = = = = = = T = = = = = = = = = = = = = = T C = = ? ? ? = = = = = = = = C = = = = = = = = = = = A = = = = = = ? A = = C C = G A G = = C = G = C = G G C C = = = = = = = T = G G = = = C C A C C = = = = = = = = = = = = = = C = = = = = = = = = = = 0 DY14 = = = = C = = I C G = T T = = T T ? C C = = G = I = = = A = A = = = A G = = A = = C C ? ? ? ? ? G C = G = C A G = C C A 4 = = = = C = = = = = G = = = = = = G = = = = = A T = A G T A G = G C = G = A A D = G C = = = = T = = D T C = C C = = C A ? T T = = C = D = = = G = G = = = G A = = T = = T G ? ? ? ? ? A A = A = A G A = T T C 2 = = = = G = = = = = T = = = = = = A = = = = = C C = G A A C A = C G = A = C G I = T T 0 DY15 = = = = = = C D = C = C C = = = A = = = T A = = = = = = G T = = = A G A = = = = A = = ? ? ? ? ? A = T = = = G = = T T C 1 A = = = G T = G G = T = = C A = C = A C 2 G G = = G = = = = = C = = T = D = = = = = = = = = = = = G I = G = T T = = = T = = = C C = = = = = = A G = = = G A G = = = = G = = ? ? ? ? ? G = A = = = A = = C C A 4 G = = = C C = A C = G = = T G = T = G T 1 C A = = A = = = = = T = = A = I = = = = = = 0 DY16 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = G = = G G = T = = C A T C A = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = C = = A C = G = = T G C T G = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY17 = = = = = = C = C = = = = = = = = = T = = = = = = = = C = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = (T) = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = G = T = = = = = = = = = C = = = = = = = = T = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = (C) = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 DY18 = = = C = = = I = G = ? T = = = T = = = = = = G = = = = A = A = = = A G = = = = = = = ? ? ? ? ? G = = = = = A = A = = = = = = = = C = = = = = G = = = = = = = A = 2 G = = = = = = = = = = = = = = = = = = = = = = = = T = = = D = C = ? C = = = A = = = = = = T = = = = G = G = = = G A = = = = = = = ? ? ? ? ? A = = = = = G = G = = = = = = = = G = = = = = T = = = = = = = G = 4 C = = = = = = = = = = = = = = = = = = = = = 0 DY19 = = = = C A = = = = = = = = = = = = C = = = = = = = T T = = A = = = = A = = = C = = C = = = = = = = = = = C = G A C C A 4 = = = = = C 4 = C A = T = T = T = = A = = = = = = = = = = = = C = = = = = = = = = = = = = = = T C = = = = = = = = = = = = T = = = = = = = C C = = G = = = = G = = = A = = G = = = = = = = = = = A = A G T T C 2 = = = = = T 3 = G G = C = C = C = = G = = = = = = = = = = = = T = = = = = = = = = = = 0 DY20 (C) = = = = (C) (C) = (C) = = = = = = = = = = = (T) (A) = (G) = = = = = (T) (A) = = (A) = (A) = = (A) = (A) = (C) = = (A) (G) = = = (T) = = (C) = = = (C) = (A) (4) = = = = = T = G G = = = = C A C C G = = 1 ? ? = = A = = = = = = = = A = I = = = = = T (T) = = = = (A) (G) = (T) = = = = = = = = = = = (C) (C) = (T) = = = = = (G) (G) = = (G) = (G) = = (T) = (G) = (G) = = (G) (C) = = = (A) = = (A) = = = (T) = (C) (2) = = = = = C = A C = = = = T G T T A = = 2 ? ? = = G = = = = = = = = T = D = = = = = C 0 DY21 = = T = T = = = T = = = = C = C = C T T C C C = D = = = = = G = = = = = = ? T = = T G = A G C = = A = A = A = A = T T C 2 = = A = = = 3 A = G = C = = = C = A = = = = = = = = = = = = = = = = = = = = = = = (G) = = = C = C = = = C = = = = T = T = T C C T A G = I = = = = = A = = = = = = ? A = = C C = G A G = = C = G = C = G = C C A 4 = = G = = = 4 G = A = T = = = T = G = = = = = = = = = = = = = = = = = = = = = = = (T) = 0 DY22 ? G C = = = = D = C = = C T = = A = = = T A = = = = = = G = = = C = G A = A = = = = = = = = = G = = = = = = G = = = = = 4 = = = = = C 4 = C A = T = T G = T G = (C) = = = = = = = = = = = = = = = = = = = = = = = ? C T = = = = I = G = = T C = = T = = = C C = = = = = = A = = = T = A G = G = = = = = = = = = A = = = = = = A = = = = = 2 = = = = = T 3 = G G = C = C A = C A = (T) = = = = = = = = = = = = = = = = = = = = = = = 0 DY23 ? G = = = = ? D = C = = C = = = A = = = T A = = = = = = G T = = C A G A = A = = A = = = = = = G = = T = = = G = = T T C 1 A = = = = = = = = = = = = = = C = G = (C) (2) (G) (G) = = (G) = ? = = = = = = (T) = (D) = = = = = = ? C = = = = ? I = G = = T = = = T = = = C C = = = = = = A G = = T G A G = G = = G = = = = = = A = = A = = = A = = C C A 2 G = = = = = = = = = = = = = = T = A = (T) (1) (C) (A) = = (A) = ? = = = = = = (A) = (I) = = = = = = 0 DY24 = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = (C) = (G) = = (C) = = = = (G) = = = (1) = = = = = = = = T = A A C (1) (C) (A) = = (A) = = = = = = = = (A) = (I) ? (A) (D) = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = (A) = (A) = = (T) = = = = (A) = = = (3) = = = = = = = = C = G G T (2) (G) (G) = = (G) = = = = = = = = (T) = (D) ? (G) (I) = = = 0 E101 = = = = C = C = C = G = = = G T = T C C T A G = I = = = = = A = = = = = = = A = = C C C G A G = = C = G T ? = G = C C A 4 = = G = = = = = = = = = T = = T = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = G = T = T = = = A C = C T T C C C = D = = = = = G = = = = = = = T = = T G A A G C = = A = A C ? = A = T T C 2 = = A = = = = = = = = = C = = C = A = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = = = = = = = = G = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = G = = = 4 G = A = T = = = T = G = = 1 C A A T A A G T A G T G C A G I A A D = = C = = = = = = = = = = T = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = A = = = 3 A = G = C = = = C = A = = 2 G G C C G G A A C A C C G T A D C G I = = T 0 E103 = = T = T = = = T = = = = C = C = C T T C C C = D = = = = = G = = = = = = = T = = T G = A G C = = A = A C A = A = T T C 2 = = A T = = = = = = = = C = = = = = = = = = = A T = A G T A G = G C = G = A A D = = C = = C = C = = = C = = = = T = T = T C C T A G = I = = = = = A = = = = = = = A = = C C = G A G = = C = G T C = G = C C A 4 = = G G = = = = = = = = T = = = = = = = = = = C C = G A A C A = C G = A = C G I = = T 0 E104 = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C = G A A C A = C G = A = C G I = = T = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A T = A G T A G = G C = G = A A D = = C 0 E105 C = = = = C = ? ? ? = = = = = = = = T = = = = = = = C C = = G = = = = = = ? = = = = = = = = = = = = = A = A A = A = = = 2 = = = G = T = G G = = ? ? ? A = C A = = 4 = G = = G = = = = = = = = T = D = = = = = = T = = = = A = ? ? ? = = = = = = = = C = = = = = = = T T = = A = = = = = = ? = = = = = = = = = = = = = G = C G = G = = = 4 = = = T = C = A C = = ? ? ? G = T G = = 2 = A = = A = = = = = = = = A = I = = = = = = 0 E106 = = = = C = = = C = = = = = = T = T C C T A G = I G = = = = A G = = = = = = A = = C C = G A G = = C = G = C = G = C C A 4 = C = G = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = T = = = = = = C = C T T C C C = D A = = = = G A = = = = = = T = = T G = A G C = = A = A = A = A = T T C 2 = G = T = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 C = = = T C = = = = = = = = A = = = T = = = = = = = C C = = G = = = = = G = T = = T G A A G C = = A = A = A = A A T T C 2 = = = G = = = = = = = = = = = C = = = = = = = C C = G A A C A = C G = A = C G I = = T T = = = C A = = = = = = = = G = = = C = = = = = = = T T = = A = = = = = C = A = = C C C G A G = = C = G = C = G G C C A 4 = = = T = = = = = = = = = = = T = = = = = = = A T = A G T A G = G C = G = A A D = = C 0 E108 = = = = = = = = = = G = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = A G = C C A = = = G = = T = G G = = ? ? ? A T C = = = 4 C = A T = A G T A G = G C = G = A A D = = C = = = = = = = = = = T = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = G A = T T C = = = A = = C = A C = = ? ? ? G C T = = = 2 G = C C = G A A C A = C G = A = C G I = = T 0 E109 C = = = T C = = = = = = = = = = = = T = = = = = = = C C = = G = = = = = G = T = = T G = A G C = ? ? = A = A = A A T T C 2 = = = = = = 4 G = A = T C = = = = = = = 1 C A A T A A G T A G T G C ? ? ? ? A D = = C T = = = C A = = = = = = = = = = = = C = = = = = = = T T = = A = = = = = C = A = = C C = G A G = ? ? = G = C = G G C C A 4 = = = = = = 3 A = G = C T = = = = = = = 2 G G C C G G A A C A C C G ? ? ? ? G I = = T 0 E110 = = = = C = = = C = G = = = G T = T C C T A G = I G = = = = A G = = = = = = A = = C C C G A G = = C = G = C = G = C C A 4 = C = = = = = = = = = = T = = T = G = = = = = A T = A G T ? ? = G C = G = A A D = = C = = = = T = = = T = T = = = A C = C T T C C C = D A = = = = G A = = = = = = T = = T G A A G C = = A = A = A = A = T T C 2 = G = = = = = = = = = = C = = C = A = = = = = C C = G A A ? ? = C G = A = C G I = = T 0 E111 = = = = C = = = C = G = = = G T = T C C T A G = I G = = = = A G = = = = = = A = = C C C G A G = = C = G = C = G = C C A 4 = C = = = = = = = = = = T = = T = G = = (1) (C) (A) (A) (T) (A) (A) (G) (T) (A) (G) (T) (G) (C) = = = (A) = = = = (C) = = = = T = = = T = T = = = A C = C T T C C C = D A = = = = G A = = = = = = T = = T G A A G C = = A = A = A = A = T T C 2 = G = = = = = = = = = = C = = C = A = = (2) (G) (G) (C) (C) (G) (G) (A) (A) (C) (A) (C) (C) (G) = = = (C) = = = = (T) 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G = = = = = = = = T = = = = G = = = = = C C = G A A ? ? = C G = A = C G I = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A T = = = = = = = = C = = = = A = = = = = A T = A G T ? ? = G C = G = A A D = = C 0 E113 C = C = = C = = C = = = = T = T = T = C T A G = I = C C = = = = = = = = = ? A = = C C C G A G = = C = G T ? = G = C C A 4 = = G = = = = = = = = = T = = T = G = = = = = = = = = = = = = = = = = = = = = = = = = T = T = = A = = T = = = = C = C = C = T C C C = D = T T = = = = = = = = = ? T = = T G A A G C = = A = A C ? = A = T T C 2 = = A = = = = = = = = = C = = C = A = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 = = = = C = = = C = G = = = G T = T C C T A G G I G = = = = A G = = = = = = A = = C C C G A G = = C = G = C = G = C C A 4 = C = = = = = = = = = = T = = T = G = = = = = (A) (T) = (A) (G) (T) (A) (G) = (G) (C) = (G) = (A) (A) (D) = = (C) = = = = T = = = T = T = = = A C = C T T C C C T D A = = = = G A = = = = = = T = = T G A A G C = = A = A = A = A = T T C 2 = G = = = = = = = = = = C = = C = A = = = = = (C) (C) = (G) (A) (A) (C) (A) = (C) (G) = (A) = (C) (G) (I) = = (T) 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 C = = = = C C = C = = = = = = T = T = C T A G = I = C C = = = = = = = = G = = = = = = = = = = = = = = = T = = = A = = = = = = = G = = = = = = = = T = = = = = = = 1 ? A A T A A G T A G = G C ? ? = ? = = T = C T = = = = A G = T = = = = = = C = C = T C C C = D = T T = = = = = = = = C = = = = = = = = = = = = = = = C = = = G = = = = = = = T = = = = = = = = C = = = = = = = 2 ? G C C G G A A C A = C G ? ? = ? = = C = T 0 E118 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = 0 E119 = = T = T = = = T = T = = C A C = ? T T C C C T D = = = = = G = = = = = = = T = = T G A A G C = = A = A C A = A = T T C 2 = = A = = = = = = = = = C = = C = A = = = = = (A) (T) = (A) (G) (T) (A) (G) = (G) (C) = (G) = (A) (A) (D) = = (C) = = C = C = = = C = G = = T G T = ? C C T A G G I = = = = = A = = = = = = = A = = C C C G A G = = C = G T C = G = C C A 4 = = G = = = = = = = = = T = = T = G = = = = = (C) (C) = (G) (A) (A) (C) (A) = (C) (G) = (A) = (C) (G) (I) = = (T) 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = (C) = (G) (G) (C) (C) (A) (4) = = G = = ? = = = = = = = = = = = (G) = = = = = C C = G A A ? ? = C G = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = (A) = (A) (A) (T) (T) (C) (2) = = A = = ? = = = = = = = = = = = (A) = = = = = A T = A G T ? ? = G C = = = = = = = = C 0 E121 C = = = = ? = I C G = = T = = T T T = C = = G = I = C C A = = = = = = G G ? = = = = = = = = = = ? ? = = = A = A A T T C 2 = = (A) G = = = = = = = = = = = C = (A) = = = = = (C) (C) = (G) (A) (A) (C) (A) = (C) (G) = (A) = (C) (G) (I) = = (T) T = = = = ? = D T C = = C = = C A C = T = = C = D = T T G = = = = = = A C ? = = = = = = = = = = ? ? = = = C = G G C C A 4 = = (G) T = = = = = = = = = = = T = (G) = = = = = (A) (T) = (A) (G) (T) (A) (G) = (G) (C) = (G) = (A) (A) (D) = = (C) 0 E122 C = = = T C = = = = T = = = A = = = T = = = = = = = C C = = G = = = = = G = T = = T G A A G C = = A = A = = = = = = = = = = = (G) = = = = = = = = = = = = (T) = (G) = = = = = = = = = = = ? ? = = = = = = = = = = = = T = = = C A = = = = G = = = G = = = C = = = = = = = T T = = A = = = = = C = A = = C C C G A G = = C = G = = = = = = = = = = = (A) = = = = = = = = = = = = (C) = (A) = = = = = = = = = = = ? ? = = = = = = = = = = = = 0 E123 = = T = T = = = T = T = = C A C = C T T C C C = D = = = = = G = = = = = = = T = = T G A A G C = = A = A C A = A = T T C 2 = = A = = = = = = = = = C = = C = A = = = = = = = = = = = = = = = = ? ? = = = = = = = = = C = C = = = C = G = = T G T = T C C T A G = I = = = = = A = = = = = = = A = = C C C G A G = = C = G T C = G = C C A 4 = = G = = = = = = = = = T = = T = G = = = = = = = = = = = = = = = = ? ? = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = 0.98 = 0.99 = 0.99 = = = = = = 0.99 = 0.99 0.99 = = = 0.99 = 0.99 = = = = = 0.99 = = = = 0.99 = = 0.99 0.99 = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = = = = 1.00 = = = 1.00 = = 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 ? ? ? ? ? 1.00 = ? ? ? 1.00 1.00 1.00 = 1.00 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 = = = = = = 0.56 = = = = 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 = 1.00 = = = ? ? = = = = ? = = = 1.00 = = = = = = = = 1.00 = = = = = 1.00 1.00 = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = 1.00 = = = = 1.00 = ? = 1.00 = = 1.00 = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = ? ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = ? 1.00 = = 0.99 = = 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 ? = = 1.00 = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = ? 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 ? ? ? 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.69 1.00 1.00 = = = 1.00 0.80 = = = 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = = = = 1.00 = 1.00 = = = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = 0.94 = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = = 1.00 = = = = = = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = ? ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = = = = = ? = = = = = = 1.00 = = = = = = = = 1.00 = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = 0.75 = = = = = = = = 0.75 = = = = = 0.61 = 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 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = = 1.00 ? ? = 1.00 1.00 = = = 1.00 = ? ? ? = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = 1.00 = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = 0.51 = 0.51 = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = 1.00 1.00 = = = = = = 1.00 1.00 ? = = 1.00 1.00 1.00 = = = = 1.00 = = ? ? ? ? ? 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 = = = 1.00 1.00 = = ? ? ? = = = = = = = = 1.00 = = = = = = = = = = = 1.00 = = = = = = ? 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = 0.97 = 0.97 0.97 = = = 0.97 0.97 0.97 0.97 0.97 = = = = = = = = = = = = = = 0.91 = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 ? 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 = = 1.00 1.00 ? ? ? ? ? 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = = = = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = 1.00 1.00 = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 = = ? ? ? ? ? 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = = 1.00 = = 1.00 = 1.00 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = 0.99 = = = = = = = = = 1.00 = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 = = 1.00 = = = = 1.00 = = = 1.00 = = 1.00 = = = = = = = = = = 1.00 = 1.00 1.00 1.00 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 = 0.79 = = = = = = = = = = = 0.79 0.79 = 0.70 = = = = = 0.79 0.79 = = 0.79 = 0.79 = = 0.79 = 0.79 = 0.79 = = 0.79 0.79 = = = 0.79 = = 0.78 = = = 0.68 = 0.68 0.68 = = = = = 0.95 = 0.95 0.95 = = = = 0.95 0.95 0.95 0.95 0.95 = = 0.95 ? ? = = 0.95 = = = = = = = = 0.95 = 0.95 = = = = = 0.95 = = 1.00 = 1.00 = = = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = = ? 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 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 = 1.00 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 = 0.55 0.65 0.65 0.65 = = 0.65 = ? = = = = = = 0.65 = 0.65 = = = = = = = = = = = = = = = = = = = = 0.62 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.62 = = = = = = = = = 0.69 = 0.69 = = 0.69 = = = = 0.69 = = = 0.62 = = = = = = = = 0.92 = 0.92 0.92 0.91 0.88 0.88 0.88 = = 0.88 = = = = = = = = 0.88 = 0.88 ? 0.88 0.88 = = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 ? = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = 1.00 = = = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 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 = 1.00 1.00 = 1.00 = = = 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = = ? ? ? 1.00 = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = = = = 1.00 = 1.00 = = = = = = = = = = 1.00 = = = 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = = = = = = = 1.00 = = = 1.00 = = = = = = = 1.00 1.00 = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 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 0.94 = 0.94 0.94 0.94 0.94 0.94 = 0.94 0.94 = 0.94 = 0.94 0.94 0.94 = = 0.94 = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = = ? ? ? 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 = = = 1.00 1.00 = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = ? ? = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? ? ? 1.00 1.00 = = 1.00 = = = = 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = = 1.00 = 1.00 = = = = = 0.95 0.95 = 0.95 0.95 0.95 ? ? = 0.95 0.95 = 0.95 = 0.95 0.95 0.95 = = 0.95 = = = = 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = = 1.00 = 1.00 = = 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 1.00 = = = = = = = = 1.00 = = = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 ? ? = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 = = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = ? 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 ? = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 0.96 1.00 1.00 = = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 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 0.67 = 0.67 0.67 0.67 0.67 0.67 = 0.67 0.67 = 0.67 = 0.67 0.67 0.67 = = 0.67 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.90 = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = 1.00 = = = = = = = = 1.00 = = = = = = = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? ? = ? = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = 1.00 = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = ? 1.00 1.00 1.00 1.00 1.00 0.98 1.00 = = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 = = = = = 0.67 0.67 = 0.67 0.67 0.67 0.67 0.67 = 0.67 0.67 = 0.67 = 0.67 0.67 0.67 = = 0.67 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 = 0.51 = 0.51 0.51 0.51 0.51 0.51 0.51 = = 0.91 = = ? = = = = = = = = = = = 0.85 = = = = = 1.00 1.00 = 1.00 1.00 1.00 ? ? = 1.00 1.00 = = = = = = = = 1.00 0.91 = = = = ? = 0.91 0.91 0.91 = = 0.91 = = 0.91 0.91 0.91 = 0.91 = = 0.91 = 0.91 = 0.91 0.91 0.91 = = = = = = 0.91 0.91 ? = = = = = = = = = = ? ? = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 0.57 1.00 = = = = = = = = = = = 1.00 = 0.57 = = = = = 0.80 0.80 = 0.80 0.80 0.80 0.80 0.80 = 0.80 0.80 = 0.80 = 0.80 0.80 0.80 = = 0.80 1.00 = = = 1.00 1.00 = = = = 1.00 = = = 1.00 = = = 1.00 = = = = = = = 1.00 1.00 = = 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = 0.59 = = = = = = = = = = = = 0.56 = 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 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = ? ? = = = = = = = END PHASEPROBS