List of haplotypes found in best reconstruction, with frequencies in parentheses. 1: G A C C C I G A T G A A C C T C G G T G G C C C T A A I A G T T T G A C C T C C G C T C A T A T C C G T T G C G A A A G G G A C T A G C C C C C T T G G C G C T A G A G (1) 2: G A C C C I G A T G C A C C T C G G T G G C T C T A A I A G G T T C A C C T C C A C T T A T A C C C G T T G C G A A A G G G C C T T G C C C C C C T G G C G C T G G A G (1) 3: G A C C C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G C T T C T A C C C G T T G C G A A A G G G A C T T G C C C C C C T G G C C C T A G A G (1) 4: G A C C C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G G C C A T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T G C T G G A G (1) 5: G A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G C C A C A C C C G C G G C G A A A G G G A C T T G T C C C C C T A G C G C T G G A G (6) 6: T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C C G C A G (2) 7: G A T C C D G A T G A A T C C C G G T G G C T C T G A I A G T A D G A C C T T C G C T T A T A C A C G T T G C G G A A G G G A C T T G C T C T C C T G G C G C T G G A G (2) 8: G G C C T I G A T G C G C C C C A G T G G C T T T A A I G G T T T G G C C T C C G C T T C T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G (1) 9: G G C C C I G A T T A A C C C C G G T A G C T C T A A I A A G T T G A C C T C C G G T C A T A T C T G T T A C G A A A G G G A C T T G C C C C C T T G G C G C T A G A G (1) 10: G G C C C I G A T G A A C C C C G G T G G C C T T A A I G G T T T G G C C T C C G C T T A T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G (1) 11: G A C C C D G A T G A A T C C C G G T G G C T C T G A I A G T T T G A C C T T C G C T T A T A C A C G T T G C G G A A G G G A C T T G C T C T C C T G A C G C T G G A G (2) 12: G A T T C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G G C C A T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T G C T G G A G (1) 13: T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T C T A C C C G T T G T T A A A G G G A T T T G C C C C T C T G G C G T T G G G G (2) 14: G A C T C I G A T G A A C C C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C C G C A G (3) 15: G G C C C I G A T T A A C C C T G G T G G C T C C A A I A G T T T G A C T T C C A C T T A T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T G C T A G A G (2) 16: G A T C C I G A T G A A T C C C G A T G G C T C T A A I A G T T T G A C C T C C G G T C A T A C C C G T T G C G A A A G G G A C T T G C C C C C C T G G C C C T G G A G (1) 17: T A C T C D G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T C T A C C C G T T G T T A A T G G G A T T T G C C C C T C T G G C G T T G G G G (1) 18: G A C C T D A A T G C G C C T C G G T G G C T C T A A I A G G T T C A C C T C C A C T T A T A C C C G T T G C G A A A G G G C C T T G C C C C C C T G A C G C T G G A G (1) 19: G A C C T D A A T T C G C C C C A G T G G C T T T A A I G G T T T G G C C T C C G C T T C T A C C C G C T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G (1) 20: T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T A T A C C C G T T G T T A A T G G G A T T T G C C C C T C T G G C G T T G G G G (1) 21: G A C T C I G A A G A A C A C T G G T G G C T C C A A I A G T T T G A C T T C C A C T T A T A C C C A T T G C G A A A G G G A C T A G C C C C C C T G G C C C T A G A G (1) 22: G A C C T D A A T T C G C C C C A G T G G C T T T A A I G G T T T G G C C T C C G C T T C T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G (1) 23: G A C T C I G A A G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G G G C C T T G C C C C C C T G G C G C T G G A G (1) 24: G A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G T C A T A T C T G T T A C G A A A G G G A C T T G C C C C C T T G G C G C T A G A G (2) 25: T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T C T A C C C G T T G T T A A T G G G A T T T G C C C C T C T G G C G T T G G G G (1) 26: G A T C C D G A T G A A T C C C G G T G G C T C T G A I A G T T T G A C C T T C G C T T A T A C A C G T T G C G A A A G G G A C T T G C T C T C C T G G C G C T G G A G (1) 27: T A C T C I G A T G A A C A C C G A T G G C T C T G A I A G T T T G A C C T T C G C T T A T A C A C G T T G C G A G A G G G A C T T G C T C T C C T G G C G C T G G A G (2) 28: G G C C C I G A T T A A C C C T G G T G G C T C C A A I A G T T T G A C T T C C G C T T C T A C C C G T T G T T A A A G G G A T T T G C C C C T C T G G C G T T G G G G (1) 29: G G C C C I G A T T A A C C C C G G T A G C T C T A A I G G G T T G A C C T C C G G T C A T A T C T G T T A C G A A A G G G A C T T G C C C C C T T G G C G C T A G A G (1) 30: G A C C C I G G T G A A C C C C A G T G G C T T T A A I G G T T T G G C C T C C G C T T C T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G (1) 31: G A C T C I G A T G A A C C C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C T G G A G (1) 32: G G C C C I G A T G A A C C C C G G T G G C T C C A T I A A G T T G A C C A C C G G T C C T A C C C G T T G T T G A A G G G A C T T G C C C C T C T A G C G C T G G G G (1) 33: G A C C C I G G T G A A C C C C A G T G G C T T T A A I G G T T T G G C C T C C G C T T A T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G (1) 34: G A C T C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G C T T A T A C A C G C T G C G A A A G G G A C T T G C T C T C C T G G C G C T G G A G (1) Summary of best reconstruction (numbers refer to the list of haplotypes given above) D001: (1,2) D002: (3,4) D003: (5,6) D004: (7,8) D005: (9,10) D006: (11,12) D007: (13,13) D008: (14,15) D009: (16,17) D010: (5,18) D011: (19,20) D012: (5,21) D013: (22,15) D014: (14,23) D015: (24,25) D016: (26,27) D033: (28,27) D034: (5,29) D035: (24,14) D036: (7,6) D037: (30,31) D038: (5,11) D039: (32,33) D040: (5,34) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: D001 G A C C C I G A T G A A C C T C G G T G G C (C) C T A A I A G T T T G A C C T C C G [C] T (C) A T A (T) C C G T T G C G A A A G G G A C T (A) G C C C C C (T) T G G C G C T [A] G A G G A C C C I G A T G [C] A C C T C G G T G G C (T) C T A A I A G G T T C A C C T C C A C T (T) A T A (C) C C G T T G C G A A A G G G C C T (T) G C C C C C (C) T G G C G C T G G A G D002 G A C C C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G (C) T (T) (C) T A C C C G T T G C G A A A G G G A C T T G C C C C C C T G G C (C) C T (A) G A G G A C C C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G (G) C (C) (A) T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T (G) C T (G) G A G D003 (G) A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G C C A C A C C C G C G G C G A A A G G G A C T T G T C C C C C T A G C G C T G G A G (T) A C T C I G A T G A A C [A] C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C C G C A G D004 G (A) T C C (D) G A T G A A T C C C G G T G G C T C T G A I A G T A D G A C C T T C G C T T A T A C A C G T T G C G G A A G G G A C T T G C T C T C C T G G C G C T G G A G G (G) C C [T] (I) G A T [G] C G C C C C A G T G G C T T T A A I G G T T T [G] G C C T C C G C T T C T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G D005 G G C C C I G A T T A A C C C C G G T A G C (T) C T A A I [A] [A] [G] T T G A C C T C C G G T C A T A T C T G T T A C G A A A G G G A C T T G C C C C C T T G G C G C T A G A G G G C C C I G A T G A A C C C C G G T G G C (C) T T A A I G G T T T [G] G C C T C C G C T T A T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G D006 G A (C) (C) C D G A T G A A T C C C G G T G G C T C T G A I A G T T T G A C C T T C G (C) T (T) A T A C A C G T T G C G G A A G G G A C T T G C T C T C C T G A C G C T G G A G G A (T) (T) C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G (G) C (C) A T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T G C T G G A G D007 T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T C T A C C C G T T G T T A A A G G G A T T T G C C C C T C T G G C G T T G G G G T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T C T A C C C G T T G T T A A A G G G A T T T G C C C C T C T G G C G T T G G G G D008 G A C T C I G A T G A A C C C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C C G C A G G G C C C [I] G A T T A A C C C T G G T G G C T C C A A I A G T T T G A C T T C C A C T T A T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T G C T A G A G D009 G A (T) C C (I) G A T G A A (T) C C C G (A) T G G C T C T A A I A G T T T G A C C T C C G (G) T (C) (A) T A C C C G T T G C G A A (A) G G G A C T T G C C C C C C T G G C C C T G G A G T A (C) T C (D) G A T G A A (C) A C C G (G) T A G C C C T A A D A G T T T G A A C T C C G (C) T (T) (C) T A C C C G T T G T T A A (T) G G G A T T T G C C C C T C T G G C G T T G G G G D010 G A C C (C) (I) (G) G T G A (A) C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G C (C) A C A C C C G C G G C G A A A G G G A C T T G T C C C C C T A (G) C G C T G G A G G A C C (T) (D) (A) A T G C (G) C C T C G G T G G C T C T A A I A G [G] T T C A C C T C C A C T (T) A T A C C C G T T G C G A A A G G G C C T T G C C C C C C T G (A) C G C T G G A G D011 G A C C T (D) A A T [T] C G C C C C A G T G G C T T T A A I G G T T T [G] G C C T C C G C T T (C) T A C C C G (C) T G C G A A (A) G G G A T T T G C C C C C C T G G C G T T G G A G T A C T C (I) G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T (A) T A C C C G (T) T G T T A A (T) G G G A T T T G C C C C T C T G G C G T T G G G G D012 G A C (C) C I G G (T) G A A C (C) C (C) G G T G A T T C (T) A T I A A G T T G A C (C) A C A (G) (G) C (C) A C A C C C (G) C G G C G A A A G G G A C T (T) G T C C C C C T A G C G C T (G) G A G G A C (T) C I G A (A) G A A C (A) C (T) G G T G G C T C (C) A A I A G T T T G A C (T) T C C (A) (C) T (T) A T A C C C (A) T T G C G A A A G G G A C T (A) G C C C C C C T G G C C C T (A) G A G D013 G (A) C C T (D) (A) A T [T] C G C C C C A G T G G C T T T A A I G G T T T [G] G C C T C C G C T T C T A C C C G T T G C G A A A G G G A T T T G C C C C C C T G G C G T T G G A G G (G) C C C (I) (G) A T T A A C C C T G G T G G C T C C A A I A G T T T G A C T T C C A C T T A T A C C C G T T G C G A A A G G A A C G T A C C A C C C C G G T G C T A G A G D014 G A C T C I G A (T) G A A C (C) C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G (A) G (A) C T T G C C C C C C T G G C G C C G C A G G A C T C I G A (A) G A A C (A) C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G (G) G (C) C T T G C C C C C C T G G C G C T G G A G D015 G A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G T C A T A T C T G T T A C G A A (A) G G G A C T T G C C C C C T T G G C G C T A G A G T A C T C I G A T G A A C A C C G G T A G C C C T A A D A G T T T G A A C T C C G C T T C T A C C C G T T G T T A A (T) G G G A T T T G C C C C T C T G G C G T T G G G G D016 (G) A (T) (C) C D G A T G A A T (C) C C G G T G G C T C T G A I A G T T T G A C C T T C G C T T A T A C A C G T T G C G A A A G G G A C T T G C T C T C C T G G C G C T G G A G (T) A (C) (T) C I G A T G A A C (A) C C G A T G G C T C T G A I A G T T T G A C C T T C G C T T A T A C A C G T T G C G A G A G G G A C T T G C T C T C C T G G C G C T G G A G D033 (G) (G) C (C) C I G A T (T) A A C (C) C (T) G G T G G C T C (C) A A I A G T T T G A C (T) T C C G C T T C T A C C C G T T G T T A A A G G G A T T T G C C C C T C T G G C G T T G G G G (T) (A) C (T) C I G A T (G) A A C (A) C (C) G A T G G C T C (T) G A I A G T T T G A C (C) T T C G C T T A T A C A C G T T G C G A G A G G G A C T T G C T C T C C T G G C G C T G G A G D034 G A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G C C A C A C C C G C G G C G A A A G G G A C T T G T C C C C C T A G C G C T G G A G G G C C C I G A T T A A C C C C G G T A G C T C T A A I [G] [G] [G] T T G A C C T C C G G T C A T A T C T G T T A C G A A A G G G A C T T G C C C C C T T G G C G C T A G A G D035 G A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G T C A T A T C T G T T A C G A A A G G G A C T T G C C C C C T T G G C G C T A G A G G A C T C I G A T G A A C C C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C C G C A G D036 (G) A T C C D G A T G A A T (C) C C G G T G G C T C T G A I A G T A D G A C C T T C G C T T A T A C A C G T T G C G G A A G G G A C T T G C T C T C C T G G C G C T G G A G (T) A C T C I G A T G A A C (A) C C G G T A G C C C T A A D A G T T T G A A C T C C G G T C A T A C C C G C T G C G A G A G A G A C T T G C C C C C C T G G C G C C G C A G D037 G A C C C I G (G) T G A A C C C C (A) G T G G C (T) T T A A I G G T T T [G] G C C T C C G C T T (C) T A C C C G T T G C G A A A G (G) G A [T] T T G C C C C C C T G G C G T T G G A G G A C T C I G (A) T G A A C C C C (G) G T A G C (C) C T A A D A G T T T G A A C T C C G G T C (A) T A C C C G C T G C G A G A G (A) G [A] C T T G C C C C C C T G G C G C T G G A G D038 G A C C C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G C C A C A C C C G C G G C G A A A G G G A C T T G T C C C C C T A G C G C T G G A G G A C C C D G A T G A A T C C C G G T G G C T C T G A I A G T T T G A C C T T C G C T T A T A C A C G T T G C G G A A G G G A C T T G C T C T C C T G A C G C T G G A G D039 G (G) C C C I G (A) T G A A C C C C (G) G T G G C T C (C) A (T) I A (A) (G) T T G A C C (A) C [C] G (G) T (C) (C) T A C C C G T T G (T) (T) (G) A A G G G A (C) T T G C C C C (T) C T (A) G C G (C) T G G (G) G G (A) C C C I G (G) T G A A C C C C (A) G T G G C T T (T) A (A) I G (G) (T) T T [G] G C C (T) C C G (C) T (T) (A) T A C C C G T T G (C) (G) (A) A A G G G A (T) T T G C C C C (C) C T (G) G C G (T) T G G (A) G D040 G A C (C) C I G G T G A A C C C C G G T G A T T C T A T I A A G T T G A C C A C A G G C C A C A C C C G C G G C G A A A G G G A C T T G T C C C C C T A G C G C T G G A G G A C (T) C I G A T G A A C C C C G G T G G C T C T A A I A G T T T G A C C T C C G C T T A T A C A C G C T G C G A A A G G G A C T T G C T C T C C T G G C G C T G G A G Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = D001 = = = = = = = = = = ? = = ? = = ? = = = = = (C) = ? ? = = ? = T = = G = = = = = = G ? = (C) = = = (T) = = = = = = = = = = = = = = A = = (A) = = = = = = (T) = = = = = = = ? = = = = = = = = = = = = = ? = = ? = = ? = = = = = (T) = ? ? = = ? = G = = C = = = = = = A ? = (T) = = = (C) = = = = = = = = = = = = = = C = = (T) = = = = = = (C) = = = = = = = ? = = = D002 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = (C) T (T) (C) = = = = = = = = = = = = = = = = G = ? T = G = = C = = = T = = C (C) = = (A) = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = (G) C (C) (A) = = = = = = = = = = = = = = = = A = ? G = A = = A = = = C = = T (G) = = (G) = = = D003 (G) = = C = = = G = = ? = = ? = = = = = G A T T = = = T I = A G = = = = ? ? A = A ? ? C = = ? = = = = = = G = = = = A ? ? ? = = = = = = T = = = = = = A = = = = T = G = = (T) = = T = = = A = = ? = = ? = = = = = A G C C = = = A D = G T = = = = ? ? T = C ? ? T = = ? = = = = = = T = = = = G ? ? ? = = = = = = C = = = = = = G = = = = C = C = = D004 = (A) ? = ? (D) = = = ? A A ? = = = G = = = = = = ? = G = = A = = A D ? A = = = T = = = = = A = = = A = = = = = = = G = = = = = = C = = = = T ? T = = = = = = = C = = = = = = (G) ? = ? (I) = = = ? C G ? = = = A = = = = = = ? = A = = G = = T T ? G = = = C = = = = = C = = = C = = = = = = = A = = = = = = T = = = = C ? C = = = = = = = T = = = = = D005 = = = = = = ? = = T = = ? = = = = = = A = = (T) C = = = = ? ? ? = = ? A = = = = = = G = C = = = T = ? = = = A = = = = = = = = = C = = = = = = = = T = = = = = C = A = ? = = = = = = = ? = = G = = ? = = = = = = G = = (C) T = = = = ? ? ? = = ? G = = = = = = C = T = = = C = ? = = = G = = = = = = = = = T = = = = = = = = C = = = = = T = G = ? = D006 = = (C) (C) = ? = = = = = = T = = = = = = ? = = = = = G = = = = = = = = = = = = T = = (C) T (T) = = = = A = = = = = = = G = = = = G = = T = G = T C T = = T = A C = = = = = = = = = (T) (T) = ? = = = = = = C = = = = = = ? = = = = = A = = = = = = = = = = = = C = = (G) C (C) = = = = C = = = = = = = A = = = = A = = G = A = C A C = = C = G T = = = = = = = D007 = = = ? ? ? = = = = = = = = = ? ? ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = ? ? ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D008 = A = T ? ? = = = G = = = = = C = = = A = = C = T = = D = = = = = = = A C = = = G G = C = = = = = = = C ? = = = = G = = A G = = T = G = = C = = = T = = C = = C G C = = = G = C ? ? = = = T = = = = = T = = = G = = T = C = = I = = = = = = = C T = = = A C = T = = = = = = = T ? = = = = A = = G A = = G = A = = A = = = C = = T = = T A G = = D009 G = (T) C = (I) = = = = = = (T) C = = = (A) = G = = T = = = = I = = = = = = ? C = = = = = (G) = (C) (A) = = = = = = = = = C G = = (A) = = = = C = = = = = = = C = = = = = C C = = = A = T = (C) T = (D) = = = = = = (C) A = = = (G) = A = = C = = = = D = = = = = = ? A = = = = = (C) = (T) (C) = = = = = = = = = T T = = (T) = = = = T = = = = = = = T = = = = = G T = = = G = D010 = = = = (C) (I) (G) G = ? A (A) = = C = = = = = A T = = = = T = = ? ? = = G = = = A = A G G C (C) = C = = = = = C G = = = ? ? = = = = A = = = = T = = = = = = A (G) = = = = = = = = = = = = (T) (D) (A) A = ? C (G) = = T = = = = = G C = = = = A = = ? ? = = C = = = T = C A C T (T) = T = = = = = T T = = = ? ? = = = = C = = = = C = = = = = = G (A) = = = = = = = = D011 G = = C T (D) A = = ? C G = C = = A = = G = ? T T = = = I G = = = = ? G C = = = = = = = = (C) = = = = = = (C) = = C G = = (A) = = = = = = = = = = = = C = = = = = = = = = = A = T = = T C (I) G = = ? A A = A = = G = = A = ? C C = = = D A = = = = ? A A = = = = = = = = (A) = = = = = = (T) = = T T = = (T) = = = = = = = = = = = = T = = = = = = = = = = G = D012 = = = (C) = = = G (T) = = = = (C) = (C) = = = = A T = = (T) = T = = A G = = = = = (C) A = A (G) (G) C (C) = C = = = = (G) C G = = = = = ? ? = = = = = (T) = T = = = = = = A = = G = = (G) = = = = = = (T) = = = A (A) = = = = (A) = (T) = = = = G C = = (C) = A = = G T = = = = = (T) T = C (A) (C) T (T) = T = = = = (A) T T = = = = = ? ? = = = = = (A) = C = = = = = = G = = C = = (A) = = = D013 = (A) = = T (D) (A) = = ? C G = = = C A = = = = = = T T = = = G = = = = ? G = C = = = G = = = C = = = = = = = = = = = = = = = = G = T T = G = = C = = = T = = C = T = G = = = = (G) = = C (I) (G) = = ? A A = = = T G = = = = = = C C = = = A = = = = ? A = T = = = A = = = A = = = = = = = = = = = = = = = = A = C G = A = = A = = = C = = T = C = A = = = D014 = = = = = = = = (T) = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = (A) = = = = = = = = = = = = = = = = C = C = = = = = = = = = = (A) = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = (C) = = = = = = = = = = = = = = = = T = G = = D015 G = = C = = = G = = = = = C = = = = = G A T T = = = T I = A G = = = = C = A = A = G = C A = = T = T = = = A C G = = (A) = = = = C = = = = = = = C T = = = = = C = A = A = T = = T = = = A = = = = = A = = = = = A G C C = = = A D = G T = = = = A = T = C = C = T C = = C = C = = = G T T = = (T) = = = = T = = = = = = = T C = = = = = T = G = G = D016 (G) = (T) (C) = D = = = = = = T (C) = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = (C) (T) = I = = = = = = C (A) = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = D033 (G) (G) = (C) = = = = = (T) = = = (C) = (T) = G = = = = = = (C) A = = = = = = = = = = (T) = C = = = = = C = = = C = = = = = T T = A = = = = = T = = = = C = C T = = = = = = T = = = G = (T) (A) = (T) = = = = = (G) = = = (A) = (C) = A = = = = = = (T) G = = = = = = = = = = (C) = T = = = = = A = = = A = = = = = C G = G = = = = = C = = = = T = T C = = = = = = C = = = A = D034 = A = = = = = G = G = = = = = = = = = ? A T = = = = T = ? ? ? = = = = = = A = A = = C = = C = C = C = C G G = = = = = = = = = = = = = T = = = = C = A = = = = = G = = = = G = = = = = A = T = = = = = = = = = ? G C = = = = A = ? ? ? = = = = = = T = C = = T = = T = T = T = T T A = = = = = = = = = = = = = C = = = = T = G = = = = = A = = = D035 = = = C = = = G = = = = = = = = = = = G A T T = = = T I = A G = = = = C = A = A = = = = = = = T = T = T = A = = = A = = G = = = = = = = = = = = T = = = = = = T A G = = = = = T = = = A = = = = = = = = = = = A G C C = = = A D = G T = = = = A = T = C = = = = = = = C = C = C = G = = = G = = A = = = = = = = = = = = C = = = = = = C G C = = D036 (G) = T C = D = = = = = = T (C) = = = = = G = = T = = G = I = = = A D = = C = = T = = C = T = = = = A = = T = = = = G A = = G = = = = = = = T = T = = = = = = = = T = G = = (T) = C T = I = = = = = = C (A) = = = = = A = = C = = A = D = = = T T = = A = = C = = G = C = = = = C = = C = = = = A G = = A = = = = = = = C = C = = = = = = = = C = C = = D037 = = ? C = = = (G) = = = = = = = = (A) = = G ? ? (T) T = = = I G = = = = ? G C = = = = = C = T (C) = = = = = = T = = = = = A = = (G) = ? ? = = = = = = = = = = = = = = T = = = = = = = ? T = = = (A) = = = = = = = = (G) = = A ? ? (C) C = = = D A = = = = ? A A = = = = = G = C (A) = = = = = = C = = = = = G = = (A) = ? ? = = = = = = = = = = = = = = C = = = = = D038 = = = = = I = G = = = = C = = = = = = = A T = = = A T = = A G = = = = = = A C A = G C C = C = = C = = C G = = = A = = = = = = = = = = T C = C = = = ? G = = = = = = = = = = = = = D = A = = = = T = = = = = = = G C = = = G A = = G T = = = = = = T T C = C T T = T = = A = = T T = = = G = = = = = = = = = = C T = T = = = ? A = = = = = = = = D039 = (G) = = = = = (A) = = = = = = = = (G) = = = = = = C (C) = (T) = A (A) (G) = = ? A = = (A) = ? = (G) = (C) (C) = = = = = = = = = (T) (T) (G) = = = = = = (C) = = = = = = = (T) = = (A) = = = (C) = = = (G) = = (A) = = = = = (G) = = = = = = = = (A) = = = = = = T (T) = (A) = G (G) (T) = = ? G = = (T) = ? = (C) = (T) (A) = = = = = = = = = (C) (G) (A) = = = = = = (T) = = = = = = = (C) = = (G) = = = (T) = = = (A) = D040 = = = (C) = = ? G = = = = = = = = = = = = A T = = = = T = = A G = = = = = = A = A = G C C = C = = C = = = G = = = = = = = = = = = = = = T C = C = = = A = = = = = = = = = = = = (T) = = ? A = = = = = = = = = = = = G C = = = = A = = G T = = = = = = T = C = C T T = T = = A = = = T = = = = = = = = = = = = = = C T = T = = = G = = = = = = = = = Phase probabilities at each site with phase known positions indicated by = = = = = = = = = = = = = = = = = = = = = = = 0.5 = = = = = = = 0.9 = = 0.97 = = = = = = 0.95 = = 0.62 = = = 0.53 = = = = = = = = = = = = = = 0.98 = = 0.52 = = = = = = 0.52 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.73 1 0.68 0.72 = = = = = = = = = = = = = = = = 1 = = 1 = 1 = = 1 = = = 1 = = 1 0.89 = = 0.69 = = = 0.89 = = 1 = = = 1 = = = = = = = = = = = 1 1 1 1 = = = 1 1 = 1 1 = = = = = = 1 = 1 = = 1 = = = = = = = = = 1 = = = = 1 = = = = = = = = = 1 = = = = = = 1 = = = = 1 = 1 = = = 0.65 = = = 0.74 = = = = 0.98 0.98 = = = = 1 = = = = = = = = 1 = = 1 = = 0.97 0.97 = 1 = = = 1 = = = = = 0.97 = = = 1 = = = = = = = 0.99 = = = = = = 1 = = = = 1 = 1 = = = = = = = 1 = = = = = = = = = = = = = = 1 = = = = = = = = = 0.96 = = 0.85 1 = = = = = = = = = = 1 = = = = = = 1 = 0.99 = = = 1 = = = = = 1 = = = = = = = = = 0.98 = = = = = = = = 1 = = = = = 1 = 1 = = = = = 0.55 0.57 = = = = = = = = 1 = = = = = = = = = = = = 1 = = = = = = = = = = = = 1 = = 0.86 1 0.84 = = = = 1 = = = = = = = 0.91 = = = = 1 = = 1 = 1 = 1 1 1 = = 1 = 0.9 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.94 = 1 = = = = = 0.99 = = = = = 1 = = = 1 = = 1 = 1 = = 1 = = = = = = = 1 1 = = = 1 1 = 1 = = = = = = = 1 = = = = = 1 = = 1 1 = = 1 = 1 = = 1 = = = 1 = = 1 = = 1 1 1 = = 1 = 0.54 1 = 0.56 = = = = = = 0.54 1 = = = 0.5 = 1 = = 1 = = = = 1 = = = = = = = 1 = = = = = 0.68 = 0.7 0.53 = = = = = = = = = 1 1 = = 0.87 = = = = 0.98 = = = = = = = 1 = = = = = 0.96 1 = = = 1 = = = = = 0.66 0.64 0.65 1 = = 0.94 0.64 = = 0.99 = = = = = 1 1 = = = = 1 = = = = = = 0.96 = = = 1 = 1 0.96 0.96 1 0.87 = 1 = = = = = 1 1 = = = = = = = = = 0.97 = = = = 1 = = = = = = 1 0.58 = = = = = = = = 1 = = 1 0.96 0.73 0.91 = = = 1 1 = 1 = = 1 = = 1 = = 1 1 = = = 1 1 = = = = = 1 1 = = = = = = = = 0.51 = = = = = = 0.51 = = 1 1 = = 0.87 = = = = = = = = = = = = 1 = = = = = = = = = = 1 = = = = 0.51 = = = 1 0.53 = = = = 0.53 = 0.51 = = = = 1 1 = = 0.53 = 1 = = 1 1 = = = = = 0.53 1 = 1 0.54 0.85 1 0.82 = 1 = = = = 0.52 1 1 = = = = = = = = = = = = 0.55 = 1 = = = = = = 1 = = 0.92 = = 0.85 = = = = 0.87 = = 0.92 0.53 0.79 = = = 1 1 = = = 1 1 = = = = = = 1 1 = = = 1 = = = = = 1 = 1 = = = 1 = = = 0.9 = = = = = = = = = = = = = = = = 1 = 1 1 = 1 = = 1 = = = 1 = = 1 = 1 = 1 = = = = = = = = = = = 0.64 = = = = 0.57 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.69 = 0.79 = = = = = = = = = = = = = = = = 0.94 = 0.94 = = 1 = = 1 = = = 1 = = = = = 1 = = = = = 1 1 1 1 = = = 1 1 = 1 1 = = = = 1 = 1 = 1 = 1 = 1 0.97 = = 1 = 1 = = = 1 1 1 = = 0.7 = = = = 1 = = = = = = = 1 1 = = = = = 1 = 1 = 1 = 0.79 = 0.8 0.72 = 0.99 = = = = = = 1 0.79 = = = 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.69 0.8 = 0.65 = = = = = 0.64 = = = 0.69 = 0.64 = 0.98 = = = = = = 0.8 1 = = = = = = = = = = 0.64 = 1 = = = = = 0.94 = = = 1 = = = = = 0.97 0.98 = 0.99 = = = = = 0.92 = = = = 1 = 1 0.97 = = = = = = 0.91 = = = 0.97 = = 1 = = = = = 1 = 1 = = = = = = = = = = 1 1 = = = = 1 = = = = = = = = = = 1 = 1 = = 1 = = 1 = 1 = 0.99 = 1 1 1 = = = = = = = = = = = = = 1 = = = = 1 = 1 = = = = = 1 = = = = = = 1 = = = 1 = = = = = = = = = = = 1 1 1 1 = = = 1 1 = 1 1 = = = = 1 = 1 = 1 = = = = = = = 1 = 1 = 1 = 1 = = = 1 = = 1 = = = = = = = = = = = 1 = = = = = = 1 1 1 = = 0.89 = 0.99 0.99 = 0.9 = = = = = = 0.99 0.83 = = = = = 1 = = 1 = = 1 = 1 = = = 0.97 0.97 = = 0.99 = = 1 = = 0.99 = 1 = = = = 1 = = 1 = = = = 0.97 1 = = 0.99 = = = = = = = 1 = 1 = = = = = = = = 1 = 1 = = = = = 1 = = = 0.6 = = = = = = = = 0.7 = = 0.99 = = 0.75 1 = = = 1 0.99 = = = = = 1 1 = = = = = 0.96 = 0.97 0.66 = = = = = = 1 = = = = = 1 = = 0.85 = = = = = = = = = = = = = = = = = 0.97 = = = = = = = = = = 0.98 = 1 = = = = 1 = = = = = = = 1 1 = = = 1 1 = = 1 1 = = = = = = 1 1 1 = 0.94 1 0.95 = 1 = = 1 = = 1 1 = = = 0.93 = = = = = = = = = = 1 1 = 1 = = = = 0.91 = = = = = = = = = 0.64 = = = = = 0.7 = = = = = = = = 0.78 = = = = = = 0.98 0.76 = 0.56 = 0.97 0.56 0.56 = = = 0.98 = = 0.55 = = = 0.62 = 0.62 0.58 = = = = = = = = = 0.77 0.78 0.52 = = = = = = 0.67 = = = = = = = 0.78 = = 0.57 = = = 0.74 = = = 0.76 = = = = 0.89 = = = 1 = = = = = = = = = = = = 1 1 = = = = 1 = = 1 1 = = = = = = 1 = 1 = 0.98 1 0.98 = 1 = = 0.95 = = = 1 = = = = = = = = = = = = = = 1 0.95 = 0.95 = = = 1 = = = = = = = = =