************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 a4glt.phase.inp a4glt.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST a4glt.phase.out_freqs : haplotype frequency estimates a4glt.phase.out_pairs : most likely haplotype pairs for each individual a4glt.phase.out_recom : estimates of recombination parameters a4glt.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 84 Positions of loci: 995 1129 1132 1264 1352 1691 1739 1743 1899 2434 2464 2477 2511 2625 2637 3520 3846 4223 4303 4311 4432 4483 4642 4734 4754 4981 5339 5340 5367 5770 5813 5828 5956 6100 6163 6299 7338 11085 17738 17830 20273 20409 20412 20774 20843 20877 21223 21260 21489 21778 22732 22761 22775 22846 23037 23822 23842 23849 23897 24689 24747 27207 27434 27579 27598 28243 28501 28528 28928 29119 29722 29806 30228 30314 30342 30408 30517 30700 30768 30997 31134 31785 31882 32328 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file a4glt.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ICCAICCGIAADCCCGACTDTCTGTGCATAGCTTTAAGCAGGGGAAATAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 3.000000 2 ICCAICCGICADCCCGACTDTCTCTGCGTAGCTTTAACCAGAAACGGCACGTGGCIACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 3 ICCAICCGICADCCCGACTDGTTCTGCGTAGCGTTGAGCAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 2.000000 4 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 5 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAAAAGAAATACGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 6 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAAAAGAAATGCGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 7 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAAGAAAAGCACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 2.000000 8 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAAGAGCAACACAAGACIATTAGDCIATAGGCGAGCGDATGATCGT 1.000000 9 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAGAAACGGCACGTGGCIACTAGDCIGAAGAGCGGCADGCGGCTAC 1.000000 10 ICCAICCGICADCCCGACTDGTTCTGCGTAGGGTTGAGCAGGGGAAATAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 11 ICCAICCGICGDCCCGACTITCTCTGCGTAGGGTTGAGCGAAAGAAATACAAGGCIACTAGDCIGTAGAGGGGCGDGCGGCCGT 2.000000 12 ICCAICCGICGDCCCGACTITCTGGTTACAGCTTCAACCGAGAGAAACAGGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 13 ICCAICTGICGDTTCGACTDTCCCTGCGTCGCTTTGAGCAAAAGAAATGCGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 14 ICCAICTGICGDTTCGACTDTTCCTGCGTAGCTTTAAGCAAAAGAAATGCGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 15 ICCAICTGICGDTTCGACTDTTCCTGCGTAGCTTTAAGAAGAAACGGCACGAGGCIATTAGICIGTTGACGGGCGDGCGGCCGT 2.000000 16 ICCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGCGACGIGCGGCTAC 1.000000 17 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 18 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAAAAGAAATGCGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 19 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAAGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 7.000000 20 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAAGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDGCGATCGT 1.000000 21 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAAGAGAAACAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 22 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAGAAACGGCACGTGGCIACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 23 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCAGGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 24 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCGAAAGAAATAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 2.000000 25 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCGAGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 26 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCGAGAGAAACACAAGACIATTAGDCIGTAGAGGGGCGDGCGGCCGT 1.000000 27 ICCADCCAICGDCCCGACTITCTCTGCGTAACGTTGAGCGGGGGAAATAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 28 ICCADCCAICGDCCCGACTITTCCTGCGTAGCTTTAACCAAGAGAAACAGGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 29 ICTAIGCGIAAITCCGATTDTCTGGGTACAGCGTTGAGCAGAAACGGCACGAGGCIACTAGDTIGTAGAGGGGCGDGCGGCCGT 1.000000 30 ICTAIGCGIAAITCCGGCTDTCTCTGCGTAGCTTTAACCAGGGGAAATACGTGGCIACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 31 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCGTTGAGCAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 32 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACCAAGAGAAACAGGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 33 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACCGAGAGAAACAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 2.000000 34 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACCGAGAGAAACAGGTGGGIACTAGDCIGTATAGCGGCADGCGGCTAC 1.000000 35 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACCGGAAACGGCACGTGGCICCTGGICIGTTGAGGGGAGDGCGGCCGT 3.000000 36 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACAAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 37 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACAAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDGTGACCGT 1.000000 38 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACAAAAAGAAATGCGTGGCIACTAGDCIGTATAGCGGCADGCGGCTAC 1.000000 39 ICTAIGCGIAAITCGGGCTITTCCTGCGTAGCTTTAACAAAGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 40 ICTAIGCGICAITCGGGCTITTCCTGCGTAGCTTTAACCGGAAACGGCACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 41 ICTAIGCGICGITCCGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGCGGCGDGCGGCTAC 1.000000 42 ICTAIGCGICGITCGGGCTITTCCTGCGTAGCTTTAACCGAGAGAAACAGGTGGCICCTGGICIGTTGAGGGGAGDGCGGCCGT 2.000000 43 ICTAIGCGICGITCGGGCTITTCCTGCGTAGCTTTAACCGAGAGAAACAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 44 ICTAIGCGICGDCCCGGCTITTCCTGCGTAGCTTTAACCAAGAGAAACAGGTGGGIACTAGDCIGTATAGCGGCADGCGGCTAC 1.000000 45 IGTAIGCGIAAITTCGATTDTCTGGTTACAGCTTCAAGCAGAAACGGCACGTGGCIACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 46 IGTAIGCGIAAITTCCATTDTCTGGTTACAGCTTCAAGCAAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 47 IGTAIGCGIAAITTCCATTDTCTGGTTACAGCTTCAAGCAAAAGAAATACGTGGCICCTGGICIGTTGAGGGGAGDGCGGCCGT 1.000000 48 IGTAIGCGIAAITTCCATTDTCTGGTTACAGCTTCAAGCAAAAGAAATGCGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 49 IGTAIGCGIAAITTCCATTDTCTGGTTACAGCTTCAAGCGAAAGAAATACGAGACIACTGGICIGTTGACGGGCGDGCGGCCGT 1.000000 50 IGTAIGCGIAAITTCCATTDTCTGGTTACAGCTTCAACCGAAAGAAATACGAGACIACTGGICIGTTGACGGGCGDGCGGCCGT 1.000000 51 IGTCIGCGIAAITTCCATTDTCTGGTTACAGCTTCAACCGAAAGAAATACGTAGCIATTAGDCIATAGGGGAGCGDATGACCGT 2.000000 52 IGTCIGCGIAAITTCCATTDTCTGGTTACAGCTTCAACCGAGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 53 IGTCIGCGIAAITTCCATTDTCTGGTTACAGCTTCAACCGAGAGAAACAGGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 2.000000 54 IGTCIGCGIAAITTCCATTDTCTGGTTACAGCTTCAACCGAGAGAAACAGGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 55 IGTCIGCGIAAITTCCATTDTCTGGTTACAGCTTCAACCGAGAGAAACAGGTGGGIACTAGDCIGTATAGCGGCADGCGGCTAC 1.000000 56 DCCAICTGDCGDCCCGACTITCTGGTCATAGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGCGACGIGCGGCTAC 1.000000 57 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTTTAACCAAAAGAAATACATAGCIATTAGDCIATAGGGGAGCGDATGACCGT 1.000000 58 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAAGCAGGGGAAGTACGTGGCDACTAGDCIGAAGAGGGGCGDGCAGCCGT 1.000000 59 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAAGAGAAACACGTAGCIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 60 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAAGAGAAACAGGTGGGIACTAGDCIGTATAGCGGCADGCGGCTAC 1.000000 61 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATTAGDCIATAGGGGAGCGDATGATCGT 1.000000 62 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGGAACGIGCGGCTAC 1.000000 63 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGCGGCGDGCGGCTAC 3.000000 64 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGCGACGIGCGGCTAC 8.000000 65 DCCAICTGDCGDCCCGGTGDTCTGGTCATCGCTCTAGGCGGGGGAAGTACAAGACIATCAADTDGTATAGCGACGIGCGGCTAC 1.000000 66 DCCAICTGDCGDCCGGGTGDTCTGGTCATCGCTCTAGGCAGGGGAAGTACAAGACIATCAADTDGTATAGCGGCGDGCGGCTAC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (29,31) DY02: (9,14) DY03: (39,30) DY04: (32,50) DY05: (18,19) DY06: (8,35) DY07: (3,33) DY08: (5,35) DY09: (2,57) DY10: (17,33) DY11: (10,28) DY12: (6,11) DY13: (13,27) DY14: (1,51) DY15: (11,48) DY16: (24,40) DY17: (24,51) DY18: (26,35) DY19: (4,15) DY20: (3,21) DY21: (22,49) DY22: (7,45) DY23: (7,38) DY24: (36,37) E101: (19,64) E102: (64,66) E103: (20,42) E104: (15,64) E105: (19,25) E106: (19,43) E107: (19,60) E108: (54,63) E109: (19,34) E110: (16,59) E111: (23,64) E112: (53,64) E113: (63,65) E114: (19,63) E115: (1,47) E116: (58,64) E117: (12,56) E118: (53,55) E119: (44,64) E120: (42,64) E121: (1,41) E122: (46,62) E123: (52,61) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 I [C] [T] A I [G] C G I [A] [A] I T [C] [C] G A T T D T C T G G G T A C A [G] C [G] T T G A G C A G A A A C G G C A C G A G G C I A C T A G D T I G T A G A G G G G C G D G C G G C C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G [C] [G] T T G A G C A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY02 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A G A A A C G G C A C G T G G C I A C T A G D C I G A A G A G C G G C A D G C G G C T A C I C C A I C T G I C G D T T C G A C T D T T C C T G C G T A G C T T T A A G C A A A A G A A A T G C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY03 I C T A I G C G I A A I T C (G) G G [C] [T] (I) T (T) (C) C T G C G T A G C T T T A A C (A) A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T I C T A I G C G I A A I T C (C) G G [C] [T] (D) T (C) (T) C T G C G T A G C T T T A A C (C) A G G G G A A A T A C G T G G C I A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 DY04 I (C) T A I G C G I A A I T (C) (G) (G) (G) [C] T (I) T (T) (C) (C) (T) (G) (C) (G) (T) A G C T T (T) A A C C (A) A G A G A A A C A G G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I (G) T A I G C G I A A I T (T) (C) (C) (A) [T] T (D) T (C) (T) (G) (G) (T) (T) (A) (C) A G C T T (C) A A C C (G) A A A G A A A T A C G A G A C I A C T G G I C I G T T G A C G G G C G D G C G G C C G T 0 DY05 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A A A G A A A T G C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T 0 DY06 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A A G A G C A A C A C A A G A C I A T T A G D C I A T A G G C G A G C G D A T G A T C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G G A A A C G G C A C G T G G C I C C T G G I C I G T T G A G G G G A G D G C G G C C G T 0 DY07 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G C G T T G A G C A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G A G A G A A A C A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 DY08 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A A A A G A A A T A C G T [G] G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G G A A A C G G C A C G T G G C I C C T G G I C I G T T G A G G G G A G D G C G G C C G T 0 DY09 I C C A I C C G I [C] [A] D C C C G A C T D T C T C T G C G T A G C T T T A A C C A G A A A C G G C A C G T G G C I A C T A G D C I G A A G A G G G G C G D G C A G C C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T T T A A C C A A A A G A A A T [A] C A T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY10 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G A G A G A A A C A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 DY11 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A G G G G A A A T A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I C C A [D] C C [A] I [C] [G] [D] [C] C C G A C T I T T C C T G C G T A G C T T T A A C C A A G A G A A A C A G G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY12 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A A A A G A A A T G C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C C A I C C G I [C] [G] D C C C G A C T I T C T C T G C G T A G G G T T G A G C G A A A G A A A T A C A A G G C I A C T A G D C I G T A G A G G G G C G D G C G G C C G T 0 DY13 I C C A I C [T] G I [C] [G] D [T] [T] C G A C T D T C C C T G C G T C G C T T T G A G C A A A A G A A A T G C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C G G G G G A A A T A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 DY14 I C C A I C C G I [A] [A] D C C C G A C T D T C T G T G C A T A G C T T T A A G C A G G G G A A A T A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I G T [C] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C G A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY15 I C C A I C C G I [C] [G] D C C C G A C T I T C T C T G C G T A G G G T T G A G C G A A A G A A A T A C A A G G C I A C T A G D C I G T A G A G G G G C G D G C G G C C G T I G T [A] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A G C A A A A G A A A T G C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY16 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C G A A A G A A A T A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I C T A I G C G I [C] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G G A A A C G G C A C G T [A] G C I A [T] T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY17 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C [G] A A A G A A A T A [G] G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I G T [C] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C [G] A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T 0 DY18 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C G A G A G A A A C A C A A G A C I A T T A G D C I G T A G A G G G G C G D G C G G C C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G G A A A C G G C A C G T G G C I C C T G G I C I G T T G A G G G G A G D G C G G C C G T 0 DY19 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C [C] A I C T G I C G D T T C G A C T D T T C C T G C G T A G C T T T A A G A A G A A A C G G C A C G A G G C I A T T A G I C I G T T G A C G G G C G D G C G G C C G T 0 DY20 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G C G T T G A G C A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C [A] A G A G A A A C A [G] G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 DY21 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A G A A A C G G C A C G T G G C I A C T A G D C I G A A G A G G G G C G D G C A G C C G T I G T [A] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A G C G A A A G A A A T A C G A G A C I A C T G G I C I G T T G A C G G G C G D G C G G C C G T 0 DY22 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A A G A A A A G C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I [G] T A I G C G I [A] [A] I T [T] [C] G A T T D T C T G G T T A C A G C T T C A A G C A G A A A C G G C A C G T G G C I A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 DY23 I C C A I C C G I [C] [A] D C C C G A C T D G T T C T G C G T A G G G T T G A G C A A G A A A A G C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C T A I G C G I A A I T C G G G C T I T T C C T G C G T A G C T T T A A C A A A A A G A A A T G C G T G G C I A C T A G D C I G T A T A G C G G C A D G C G G C T A C 0 DY24 I C T A I G C G I A A I T C G G G C T I T T C C T G C G T A G C T T T A A C A A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A C C G T I C T A I G C G I A A I T C G G G C T I T T C C T G C G T A G C T T T A A C A A A A A G A A A T A C G T A G C I A T T A G D C I A T A G G G G A G C G D G T G A C C G T 0 E101 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E102 D C C A I C T G D C G D C C (C) G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C D C C A I C T G D C G D C C (G) G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G G C G D G C G G C T A C 0 E103 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D G C G A T C G T I C T A I G C G I [C] [G] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G A G A G A A A C A G G T G G [C] I C C T G G I C I G T T G A G G G G A G D G C G G C C G T 0 E104 I C [C] A I C T G I C G D T T C G A C T D T T C C T G C G T A G C T T T A A G A A G A A A C G G C A C G A G G C I A T T A G I C I G T T G A C G G G C G D G C G G C C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E105 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C G A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T 0 E106 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T I C T A I G C G I [C] [G] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G A G A G A A A C A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T 0 E107 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A (C) G T (A) G (C) I A (T) T A G D C I (A) T A (G) (G) G (G) (A) G C (G) D (A) (T) G (A) (T) (C) (G) (T) D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A A G A G A A A C A (G) G T (G) G (G) I A (C) T A G D C I (G) T A (T) (A) G (C) (G) G C (A) D (G) (C) G (G) (C) (T) (A) (C) 0 E108 I G T [C] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C G A G A G A A A C A G G T [G] G C [D] A C T A G D C I G A A G A G G G G C G D G C A G C C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G G C G D G C G G C T A C 0 E109 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T I C T A I G C G I [A] [A] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G A G A G A A A C A G G T G G G I A C T A G D C I G T A T A G C G G C A D G C G G C T A C 0 E110 (I) C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C (D) C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T 0 E111 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A G G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E112 I G T C I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C G A G A G A A A C A G G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E113 D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C (A) G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G G C G D G C G G C T A C D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C (G) G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E114 I C C A D C C A I C G D C C C G A C T I T C T C T G C G T A A C G T T G A G C A A G A G A A A C A C G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G G C G D G C G G C T A C 0 E115 I C C A I C C G I [A] [A] D C C C G A C T D T C T G T G C A T A G C T T T A A G C A G G G G A A A T A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I G T A I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A G C A A A A G A A A T A C G T G G C I C C T G G I C I G T T G A G G G G A G D G C G G C C G T 0 E116 D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A (A) G C A G G G G A A G T A C [G] [T] G [G] C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A (G) G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E117 I C C A [I] C C G I C G D C C C G A C T I T C T G G T T A C A G C T T C A A C C G A G A G A A A C A [G] G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T D C C A I C T G D C G D C C C G [A] C T I T C T G G T C A T A G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E118 I G T C I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C G A G A G A A A C A G G T A G C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T I G T C I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C G A G A G A A A C A G G T G G G I A C T A G D C I G T A T A G C G G C A D G C G G C T A C 0 E119 (I) C [T] A I (G) (C) G (I) C G D C C C G G C T I T T C C T G C G T A G C T T T A A C C A A G A G A A A C A G G T G G G I A C T A G D C I G T A T A G C G G C A D G C G G C T A C (D) C C A I (C) (T) G (D) C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E120 I C T A I G C G I [C] [G] I T C G G G C T I T T C C T G C G T A G C T T T A A C C G A G A G A A A C A G G T G G [C] I C C T G G I C I G T T G A G G G G A G D G C G G C C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G A C G I G C G G C T A C 0 E121 I C C A I C C G I [A] [A] D C C C G A C T D T C T G T G C A T A G C T T T A A G C A G G G G A A A T A G G T G G C D A C T A G D C I G A A G A G G G G C G D G C A G C C G T I C T A I G C G I [C] [G] [I] [T] C [C] G G T G D T C T G G T C A T C G C T C T A G G C A G G G G A A G T A C A A G A C I A T C A A D T D G T A T A G C G G C G D G C G G C T A C 0 E122 I G T [A] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A G C A (A) (A) (A) G A A (A) T A C (G) (T) (A) (G) C I A T (T) A (G) D (C) (I) (A) T A (G) (G) G G A (G) C G (D) (A) (T) G (A) C (C) (G) (T) D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A (G) (G) (G) G A A (G) T A C (A) (A) (G) (A) C I A T (C) A (A) D (T) (D) (G) T A (T) (A) G G A (A) C G (I) (G) (C) G (G) C (T) (A) (C) 0 E123 I G T [C] I G C G I A A I T T C C A T T D T C T G G T T A C A G C T T C A A C C G (A) G (A) G A A (A) (C) A C (G) (T) (A) (G) C I A T T A G D C I A T A G G G G A G C G D A T G A T C G T D C C A I C T G D C G D C C C G G T G D T C T G G T C A T C G C T C T A G G C A (G) G (G) G A A (G) (T) A C (A) (A) (G) (A) C I A T T A G D C I A T A G G G G A G C G D A T G A T 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 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = A ? ? D = C T G G = T A C ? ? ? ? = = = = = ? ? G = = A C G G C = = = A G = = = = C = = = = T = G = = = A = = G = = = = G C = G = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = G ? ? I = T C C T = C G T ? ? ? ? = = = = = ? ? A = = G A A A T = = = T A = = = = T = = = = C = A = = = G = = A = = = = A T = A = = = = 0 DY02 = = = = = = C = = ? ? ? ? ? ? = = = = = G = T = = = = = = = = G G = = G = = = = ? ? ? ? ? ? G C A = ? ? ? ? ? = = C = = = = = = G A = = A = C G = = A = G C = G = T A C = = = = = = T = = ? ? ? ? ? ? = = = = = T = C = = = = = = = = C T = = A = = = = ? ? ? ? ? ? A T G = ? ? ? ? ? = = T = = = = = = A T = = G = G A = = G = A T = A = C G T 0 DY03 = = = = = = = = = = = = = = (G) = = ? ? (I) = (T) (C) = = = = = = = = = = = = = = = (A) = A = A = = = = C = = = = A = = = = T = = = = = = A T = = G = = A = = = = A T G A T = = = = = = = = = = = = = = = = = (C) = = ? ? (D) = (C) (T) = = = = = = = = = = = = = = = (C) = G = G = = = = T = = = = G = = = = C = = = = = = G A = = A = = G = = = = G C A G C = = = 0 DY04 = (C) = = = = = = = = = = = (C) (G) (G) (G) ? ? (I) = (T) (C) (C) (T) (G) (C) (G) (T) = = = = = (T) = = = = (A) = G = = = = = C = G = T A G = = = T = ? = D = = A = A = G G = A = = = = A T = A = = = = = (G) = = = = = = = = = = = (T) (C) (C) (A) ? ? (D) = (C) (T) (G) (G) (T) (T) (A) (C) = = = = = (C) = = = = (G) = A = = = = = T = C = A G A = = = C = ? = I = = G = T = A C = G = = = = G C = G = = = = 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = T G = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = C A = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = T = = = 0 DY06 = = C = = C = = = ? ? D C = C = A ? ? D G = T = = = = = = = = G G = = G = G = A A G = G = A A = = = A A = A = = A T = A = D = = A = A = G C = A = C = = A T = A T = = = = = T = = G = = = ? ? I T = G = G ? ? I T = C = = = = = = = = C T = = A = C = G G A = A = G G = = = G T = G = = C C = G = I = = G = T = A G = G = A = = G C = G C = = = 0 DY07 = = C = = C = = = ? ? D C = C = A ? ? D G = T = = = = = = = = = G = = G = G = A ? ? ? = = = = T = C = = A = = I = T = = = = = = A T = = G = = A = = = = A T G A = = ? ? = = T = = G = = = ? ? I T = G = G ? ? I T = C = = = = = = = = = T = = A = C = G ? ? ? = = = = C = G = = G = = D = C = = = = = = G A = = A = = G = = = = G C A G = = ? ? 0 DY08 = = C = = C = = = ? ? ? ? ? ? = A ? ? D G = T = = = = = = = = G G = = G = G = A A = = G A A A T = = ? ? ? ? ? D ? ? ? A = D = = = A A = ? ? = = = C = ? = = ? = = = = ? = = T = = G = = = ? ? ? ? ? ? = G ? ? I T = C = = = = = = = = C T = = A = C = G G = = A C G G C = = ? ? ? ? ? I ? ? ? G = I = = = T T = ? ? = = = A = ? = = ? = = = = ? 0 DY09 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = A C T = = = = C T G = G = A = = = = = = = = = = G = = A C G ? ? ? ? G = G = = = = C = = = = = ? G A = = A = = G = = = = G C A G = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = G T G = = = = G G T = A = C = = = = = = = = = = A = = G A A ? ? ? ? A = A = = = = T = = = = = ? A T = = G = = A = = = = A T G A = = = = 0 DY10 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = A = = = = C T = = = = = = = A = G = = G = G = A = A = = = = = T = C = = A = = I = T = = = = = = A T = = G = = A = = = = A T G A = ? ? = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = G = = = = T C = = = = = = = G = T = = A = C = G = G = = = = = C = G = = G = = D = C = = = = = = G A = = A = = G = = = = G C A G = ? ? = 0 DY11 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? D G = T = = = = = = = = G G = = G = ? = = G = G = = = = T = = = = G = = D = C = ? ? = = = G A = = A = = G = = = = G C A G = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? I T = C = = = = = = = = C T = = A = ? = = A = A = = = = C = = = = A = = I = T = ? ? = = = A T = = G = = A = = = = A T G A = = = = 0 DY12 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? D G T = = = = = = = = = = = = = = = = = A = = = = = = = = G = G T A = = = = T = = = = = = A = = = G = = A = = = = A T = A = = ? = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? I T C = = = = = = = = = = = = = = = = = G = = = = = = = = A = A A G = = = = C = = = = = = G = = = A = = G = = = = G C = G = = ? = 0 DY13 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? D = = C = = = = = = C G = T = = = = = = A A A A = = = = = G C = = A = = I = T = ? ? = = = A T = = G = = A = = = = A T G A = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? I = = T = = = = = = A A = G = = = = = = G G G G = = = = = A G = = G = = D = C = ? ? = = = G A = = A = = G = = = = G C A G = = = = 0 DY14 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? G = C = = = = = = T G C = T = = = = = T = = G = A G G G = = = = = = G = = G = = D = C = = = = = = G A = = A = = G = = = = G C A G = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? C = T = = = = = = G T T = C = = = = = C = = C = G A A A = = = = = = C = = A = = I = T = = = = = = A T = = G = = A = = = = A T G A = = = = 0 DY15 ? ? ? ? ? C = = = ? ? ? ? ? ? G = ? ? I = = = C T G C G T = = G G = T G = = = G = = = = = = = = A = A A G = = = = C = = = = = = G = = = A = = G = = = = G C = G = = = = ? ? ? ? ? G = = = ? ? ? ? ? ? C = ? ? D = = = G G T T A C = = C T = C A = = = A = = = = = = = = G = G T A = = = = T = = = = = = A = = = G = = A = = = = A T = A = = = = 0 DY16 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = A = = = = C T = = = = = = = A = G = = G = G = = A = = G A A A T = G ? ? ? ? ? ? ? ? = ? ? = = = G ? ? ? A = = G = = = = G C A G = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = G = = = = T C = = = = = = = G = T = = A = C = = G = = A C G G C = C ? ? ? ? ? ? ? ? = ? ? = = = A ? ? ? G = = A = = = = A T G A = = = = 0 DY17 ? ? ? ? ? C = A = ? ? ? ? ? ? G = ? ? I = = = C T G C G T = A = G = T G = G = ? = = = = = = ? ? ? ? = = G = = D = C = ? ? = = ? G A = = A = = G = = = = G C A G = = = = ? ? ? ? ? G = G = ? ? ? ? ? ? C = ? ? D = = = G G T T A C = G = T = C A = C = ? = = = = = = ? ? ? ? = = A = = I = T = ? ? = = ? A T = = G = = A = = = = A T G A = = = = 0 DY18 ? ? ? ? ? C = A = ? ? ? ? ? ? = A = = = = C T = = = = = = = A = G = = G = G = = A G = G A A A = = = A A = A = = A T = ? ? D = = = = A = = = = = = C = = = = = = = = = = ? ? ? ? ? G = G = ? ? ? ? ? ? = G = = = = T C = = = = = = = G = T = = A = C = = G A = A C G G = = = G T = G = = C C = ? ? I = = = = T = = = = = = A = = = = = = = = = = 0 DY19 ? ? ? ? ? = C = = ? ? ? ? ? ? = = = = = G = T = = = = = = = = G G = = G = = C = A = = G A A A T = = = T A = = = = = = = = D = = A = A = G G = A = = = = A T = A = = = = ? ? ? ? ? = T = = ? ? ? ? ? ? = = = = = T = C = = = = = = = = C T = = A = = A = G = = A C G G C = = = A G = = = = = = = = I = = G = T = A C = G = = = = G C = G = = = = 0 DY20 ? ? ? ? ? = = G = ? ? ? ? ? ? ? = ? ? D G T = = = = = = = = G = = = = = = = ? ? = A = = = = ? ? ? ? = = A = = I = T = = = = = ? A T = = G = = A = = = = A T G A = = = = ? ? ? ? ? = = A = ? ? ? ? ? ? ? = ? ? I T C = = = = = = = = A = = = = = = = ? ? = G = = = = ? ? ? ? = = G = = D = C = = = = = ? G A = = A = = G = = = = G C A G = = = = 0 DY21 ? ? ? ? ? C = A = ? ? ? ? ? ? G = ? ? I = = = C T G C G T = A = G = T G = = = A G = = A C G G C = = = T = G = = = = = A = D = = = A A = = G = = = = = = = = A = = = = = ? ? ? ? ? G = G = ? ? ? ? ? ? C = ? ? D = = = G G T T A C = G = T = C A = = = G A = = G A A A T = = = A = A = = = = = G = I = = = T T = = C = = = = = = = = G = = = = = 0 DY22 ? ? ? ? ? C = = = ? ? ? ? ? ? = = C = = G T = C T G C G T = = G G = T G = = = = A G = = A A = = = = = = A = = = = T = = = = = = A T = = G = = A = = = = A T G A = = = = ? ? ? ? ? G = = = ? ? ? ? ? ? = = T = = T C = G G T T A C = = C T = C A = = = = G A = = C G = = = = = = G = = = = C = = = = = = G A = = A = = G = = = = G C A G = = = = 0 DY23 ? ? ? ? ? C = = = ? ? ? ? ? ? = A ? ? D G = T = = = = = = = = G G = = G = G C = = G = A = = G C A = = = A = = = = T = = = = = = A = = G G = G A = = G = A T = A = C G T ? ? ? ? ? G = = = ? ? ? ? ? ? = G ? ? I T = C = = = = = = = = C T = = A = C A = = A = G = = A T G = = = G = = = = C = = = = = = G = = T A = C G = = A = G C = G = T A C 0 DY24 ? ? ? ? ? = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = A = = = = = = = ? ? ? ? ? = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = G = = = = = = = 0 E101 I ? ? ? ? ? C A I = = = = = = = A ? ? I = = = C T G = G = A A = G T = G A = ? ? A = A = = = ? ? ? = G T A G = = = = T = G = C I A = = G G = G A G = = D A T = A T C G T D ? ? ? ? ? T G D = = = = = = = G ? ? D = = = G G T = A = C G = T C = A G = ? ? G = G = = = ? ? ? = A A G A = = = = C = A = T D G = = T A = C G A = = I G C = G C T A C 0 E102 ? = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = ? ? = = = = A = = I = = = = = = = = ? = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = ? ? = = = = G = = D = = = = = = = = 0 E103 ? ? ? ? ? C = A = ? ? D C = C = A = = = = C T = = = = = = = A = G = = G = G = A = = = = = = = = = C = = A = ? = A T = A = D ? = A = A = G = = A = C = = = = = A T = = = ? ? ? ? ? G = G = ? ? I T = G = G = = = = T C = = = = = = = G = T = = A = C = G = = = = = = = = = G = = G = ? = C C = G = I ? = G = T = A = = G = A = = = = = G C = = = 0 E104 ? ? ? ? ? = = = I = = = ? ? = = A C T = = T C C T G = G = A = = = T = = A = A = = A A A C G ? ? ? = G = = G = = = = T = G I ? I = = T G = C G = G = = D = = = = = ? ? ? ? ? ? ? ? = = = D = = = ? ? = = G T G = = C T G G T = A = C = = = C = = G = C = = G G G A A ? ? ? = A = = A = = = = C = A D ? D = = A T = G C = A = = I = = = = = ? ? ? 0 E105 = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 = = C = D C = A = ? ? D C = C = A = = = = C T = = = = = = = A = G = = G = G = A = = = = = = = = = C = = A = = I = T = ? ? = = = A T = = G = = A = = = = A T G A T = = = = = T = I G = G = ? ? I T = G = G = = = = T C = = = = = = = G = T = = A = C = G = = = = = = = = = G = = G = = D = C = ? ? = = = G A = = A = = G = = = = G C A G C = = = 0 E107 I ? ? ? ? = C A I ? ? ? ? ? ? = A ? ? I = = = C T G = G = A A = G T = G A = = = = = = = = = = = = (C) = = (A) = (C) = = (T) = = = = = = (A) = = (G) (G) = (G) (A) = = (G) = (A) (T) = (A) (T) (C) (G) (T) D ? ? ? ? = T G D ? ? ? ? ? ? = G ? ? D = = = G G T = A = C G = T C = A G = = = = = = = = = = = = (G) = = (G) = (G) = = (C) = = = = = = (G) = = (T) (A) = (C) (G) = = (A) = (G) (C) = (G) (C) (T) (A) (C) 0 E108 I ? ? ? ? G C = I ? ? I T T = C A = T = = = = = = = T = C A = = = T C = A C = G A = A = = = A C = G ? ? ? ? ? ? ? ? ? ? ? = C I = A = G = = G = = = = = = = A = = C G T D ? ? ? ? C T = D ? ? D C C = G G = G = = = = = = = C = T C = = = C T = G G = A G = G = = = G T = C ? ? ? ? ? ? ? ? ? ? ? = T D = T = T = = C = = = = = = = G = = T A C 0 E109 = = C = D C = A = ? ? D C = C = A = = = = C T = = = = = = = A = G = = G = G = A = = = = = = ? ? ? ? = = A = C = = T = = = = = ? A = = G G = G A = = G = A T = A T C G T = = T = I G = G = ? ? I T = G = G = = = = T C = = = = = = = G = T = = A = C = G = = = = = = ? ? ? ? = = G = G = = C = = = = = ? G = = T A = C G = = A = G C = G C T A C 0 E110 (I) ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = G = = = G T = = A A G A = = = = C ? ? = T D G = = T A = C G A = = I G C = G C T A C (D) ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = A = = = A C = = G T A G = = = = T ? ? = C I A = = G G = G A G = = D A T = A T C G T 0 E111 I ? ? ? ? = C A I = = = = = = = A ? ? I = = ? ? ? ? = G = A A = G T = G A = = = = = A = = = A C = = ? ? ? ? ? = = = T = G = C ? ? = = G G = G A G = = D A T = A T C G T D ? ? ? ? = T G D = = = = = = = G ? ? D = = ? ? ? ? = A = C G = T C = A G = = = = = G = = = G T = = ? ? ? ? ? = = = C = A = T ? ? = = T A = C G A = = I G C = G C T A C 0 E112 I ? ? ? ? G C = I ? ? I T T = C A = T = = = = = = = ? ? ? ? ? ? = ? ? ? ? C = G A = A = = = A C = G ? ? ? ? ? = = = T = G = C I A = = G G = G A G = = D A T = A T ? ? ? D ? ? ? ? C T = D ? ? D C C = G G = G = = = = = = = ? ? ? ? ? ? = ? ? ? ? G = A G = G = = = G T = C ? ? ? ? ? = = = C = A = T D G = = T A = C G A = = I G C = G C ? ? ? 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? G = = D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? A = = I = = = = = = = = 0 E114 I ? ? ? ? ? C A I = = = = = = = A ? ? I = = = C T G = G = A A = G T = G A = = = A = A = = = A C = = G T A G = = = = T ? ? = C I A = = G G = G A = = = = A T = A T C G T D ? ? ? ? ? T G D = = = = = = = G ? ? D = = = G G T = A = C G = T C = A G = = = G = G = = = G T = = A A G A = = = = C ? ? = T D G = = T A = C G = = = = G C = G C T A C 0 E115 = C C = = C = = = ? ? D C C = G = C = = = = = = T G C = T = = = = = T = = = = = G G G = = = = = = G = = = = = D A = = A = D = = = A A = = = = = = C = = = = A = = = = = = G T = = G = = = ? ? I T T = C = T = = = = = = G T T = C = = = = = C = = = = = A A A = = = = = = C = = = = = I C = = G = I = = = T T = = = = = = A = = = = G = = = = = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = ? ? ? ? ? D ? ? ? = G = C I = A = G = = G = G = = D = = A = = C G T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = ? ? ? ? ? I ? ? ? = A = T D = T = T = = C = A = = I = = G = = T A C 0 E117 I ? ? ? ? = C = I = = = = = = ? ? = = = = ? = = = = T = C = = = = T C = ? C ? ? A = A = = = ? ? ? ? G T A G = = = = T = G = C ? A = = G G = G A G = = D A T = A T C G T D ? ? ? ? = T = D = = = = = = ? ? = = = = ? = = = = C = T = = = = C T = ? G ? ? G = G = = = ? ? ? ? A A G A = = = = C = A = T ? G = = T A = C G A = = I G C = G C T A C 0 E118 = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = C = = T = ? ? = = = A = = G G = G A = = G = A T = A T C G T = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = G = = C = ? ? = = = G = = T A = C G = = A = G C = G C T A C 0 E119 (I) ? ? ? ? (G) (C) = (I) = = = = = = = = ? ? I = T C C T G = G = A = = = T = = A C = = A = A = = = A C = G G T = G G = = C T = G = C I = = = = = = = = G = A D = = = = = = = = (D) ? ? ? ? (C) (T) = (D) = = = = = = = = ? ? D = C T G G T = A = C = = = C = = G G = = G = G = = = G T = C A A = A C = = T C = A = T D = = = = = = = = A = G I = = = = = = = = 0 E120 I ? ? ? ? G C = I ? ? I T = G = = ? ? I = T C C T G = G = A = = = T = = A C = G ? ? ? = = = A C = G G T = ? ? = C C T G G ? ? I = = T G = = G = G A = D = = = = = C G T D ? ? ? ? C T = D ? ? D C = C = = ? ? D = C T G G T = A = C = = = C = = G G = A ? ? ? = = = G T = C A A = ? ? = A T C A A ? ? D = = A T = = C = A C = I = = = = = T A C 0 E121 = = C = = C = = ? ? ? ? ? ? ? = A C T = = = = = T G = = = A = = = T = = A = = = = = = = = = A = = G G T = G = D = C T = G = C I = A = G = = G = = = = = = = A = = C G T = = T = = G = = ? ? ? ? ? ? ? = G T G = = = = = G T = = = C = = = C = = G = = = = = = = = = G = = C A A = A = I = T C = A = T D = T = T = = C = = = = = = = G = = T A C 0 E122 I ? ? ? ? G C = I ? ? ? ? ? ? C A = T = = = = = = = T = C A = = = T C ? A = = = (A) (A) (A) = = = (A) = = = (G) (T) (A) (G) = = = = (T) = (G) = (C) (I) (A) = = (G) (G) = = = (G) = = (D) (A) (T) = (A) = (C) (G) (T) D ? ? ? ? C T = D ? ? ? ? ? ? G G = G = = = = = = = C = T C = = = C T ? G = = = (G) (G) (G) = = = (G) = = = (A) (A) (G) (A) = = = = (C) = (A) = (T) (D) (G) = = (T) (A) = = = (A) = = (I) (G) (C) = (G) = (T) (A) (C) 0 E123 I ? ? ? ? G C = I ? ? I T T = C A = T = = = = = = = T = C A = = = T C = A C = G (A) = (A) = = = (A) (C) = = (G) (T) (A) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D ? ? ? ? C T = D ? ? D C C = G G = G = = = = = = = C = T C = = = C T = G G = A (G) = (G) = = = (G) (T) = = (A) (A) (G) (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = 1.00 ? ? 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? ? ? ? = = = = = ? ? 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = = = 1.00 = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = = ? ? ? ? ? ? = = = = = 1.00 = 1.00 = = = = = = = = 1.00 1.00 = = 1.00 = = = = ? ? ? ? ? ? 1.00 1.00 1.00 = ? ? ? ? ? = = 1.00 = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = 0.51 = = ? ? 0.51 = 0.51 0.51 = = = = = = = = = = = = = = = 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 = = = = 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 = = = = 0.89 = 0.95 = = = = = 0.95 = 0.95 = 0.96 0.96 0.96 = = = 0.96 = ? = 0.96 = = 0.96 = 0.96 = 0.96 0.96 = 0.96 = = = = 0.96 0.96 = 0.96 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 1.00 = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = 1.00 = = = ? ? 1.00 1.00 = 1.00 = 1.00 ? ? 1.00 1.00 = 1.00 = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = ? ? 1.00 1.00 = 1.00 = 1.00 ? ? 1.00 1.00 = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 ? ? ? = = = = 1.00 = 1.00 = = 1.00 = = 1.00 = 1.00 = = = = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = ? ? = = 1.00 = = 1.00 = = = ? ? ? ? ? ? = 1.00 ? ? 1.00 1.00 = 1.00 = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = ? ? ? ? ? 1.00 ? ? ? 1.00 = 1.00 = = = 1.00 1.00 = ? ? = = = 1.00 = ? = = ? = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 ? ? ? ? 1.00 = 1.00 = = = = 1.00 = = = = = ? 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = 1.00 = = = = 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = 1.00 = 1.00 = = = = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = ? ? = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? 1.00 1.00 = 1.00 = = = = = = = = 1.00 1.00 = = 1.00 = ? = = 1.00 = 1.00 = = = = 1.00 = = = = 1.00 = = 1.00 = 1.00 = ? ? = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = = = = = 1.00 = = = 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 = = ? = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = ? ? 1.00 = = 1.00 = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 1.00 = = = = = 1.00 1.00 = = 1.00 = = 1.00 = 1.00 = ? ? = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = 1.00 = = 1.00 = = 1.00 = 1.00 = = = = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? 1.00 = = = ? ? ? ? ? ? 1.00 = ? ? 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = = = = = 1.00 = = = 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = 1.00 = = = = 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 ? ? ? ? ? ? ? ? = ? ? = = = 1.00 ? ? ? 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? 1.00 = 1.00 = ? ? ? ? ? ? 1.00 = ? ? 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 = ? = = = = = = ? ? ? ? = = 1.00 = = 1.00 = 1.00 = ? ? = = ? 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? 1.00 = 1.00 = ? ? ? ? ? ? = 1.00 = = = = 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 = = 1.00 1.00 = ? ? 1.00 = = = = 1.00 = = = = = = 1.00 = = = = = = = = = = ? ? ? ? ? = 1.00 = = ? ? ? ? ? ? = = = = = 1.00 = 1.00 = = = = = = = = 1.00 1.00 = = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 = 1.00 = = = = ? ? ? ? ? = = 1.00 = ? ? ? ? ? ? ? = ? ? 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = = = ? ? = 1.00 = = = = ? ? ? ? = = 1.00 = = 1.00 = 1.00 = = = = = ? 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = ? ? ? ? ? 1.00 = 1.00 = ? ? ? ? ? ? 1.00 = ? ? 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = = = = = ? ? ? ? ? 1.00 = = = ? ? ? ? ? ? = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = = = 1.00 = = = = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 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 = 0.96 = = 0.96 0.96 0.96 = = = 1.00 = = = = 1.00 = = = = = = 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? ? ? ? ? = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 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 = 0.97 0.97 = ? ? 1.00 = 1.00 = = = ? ? ? = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? = = = = = = = = = = = = = 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 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 ? ? ? = 1.00 = = 1.00 = = = = 1.00 = 1.00 1.00 ? 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = = = = ? ? ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 = ? ? 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = = = = 1.00 = = 1.00 = = 1.00 = 1.00 = ? ? = = = 1.00 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 ? ? ? ? = 1.00 1.00 1.00 ? ? ? ? ? ? = 1.00 ? ? 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = 0.81 = = 0.81 = 0.81 = = 0.81 = = = = = = 0.81 = = 0.81 0.81 = 0.81 0.81 = = 0.81 = 0.81 0.81 = 0.81 0.81 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 = 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 = = = 1.00 1.00 = 1.00 ? ? ? ? ? ? ? ? ? ? ? = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = ? ? 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = ? ? ? ? = = 1.00 = 1.00 = = 1.00 = = = = = ? 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 0.50 ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = 1.00 ? ? = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? ? ? = 1.00 1.00 1.00 = = = = = = = 1.00 ? ? 1.00 = = ? ? ? ? = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = 1.00 = = = 1.00 1.00 = = ? ? ? ? ? = = = 1.00 = 1.00 = 1.00 ? ? = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? ? ? 1.00 1.00 = 1.00 ? ? 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = ? ? ? ? ? ? = ? ? ? ? 1.00 = 1.00 1.00 = 1.00 = = = 1.00 1.00 = 1.00 ? ? ? ? ? = = = 1.00 = 1.00 = 1.00 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 = = = = = = = = 0.96 ? ? ? ? ? 0.96 0.96 0.96 = = = = = = = 0.96 ? ? 0.96 = = = 0.96 0.96 0.96 = 0.96 = 0.96 0.96 = 0.96 0.96 = 0.96 0.96 = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = 1.00 ? ? = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = = ? ? 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = = = = 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 ? ? ? ? = 0.97 = 0.97 = = = = = = ? ? = = = = ? = = = = 1.00 = 1.00 = = = = 1.00 1.00 = ? 1.00 ? ? 1.00 = 1.00 = = = ? ? ? ? 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 ? 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = 1.00 = ? ? = = = 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 0.77 ? ? ? ? 0.77 0.77 = 0.77 = = = = = = = = ? ? 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = 1.00 = 1.00 1.00 = = = = = = = = 1.00 ? ? ? ? 1.00 1.00 = 1.00 ? ? 1.00 1.00 = 1.00 = = ? ? 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = = 1.00 1.00 = 1.00 ? ? ? = = = 1.00 1.00 = 1.00 1.00 1.00 = ? ? = 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 = = 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = ? ? ? ? ? ? ? = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = 1.00 = = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 ? ? ? ? 1.00 1.00 = 1.00 ? ? ? ? ? ? 1.00 1.00 = 1.00 = = = = = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 ? 1.00 = = = 0.90 0.90 0.90 = = = 0.90 = = = 0.90 0.90 0.90 0.90 = = = = 0.90 = 0.90 = 0.90 0.90 0.90 = = 0.90 0.90 = = = 0.90 = = 0.90 0.90 0.90 = 0.90 = 0.90 0.90 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 0.85 = 0.85 = = = 0.85 0.85 = = 0.85 0.85 0.85 0.85 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS