chromosome 2

50400 bytes allocated in orders_morecore

3024000 bytes allocated in morecore

Option chosen: twopoint

Current values for parameters:

par_file = chr2.par
dat_file = chr2.dat
gen_file = chr2.gen
ord_file = chr2.ord
nb_our_alloc = 3000000    [# bytes reserved for our_alloc]
SEX_EQ = 1   [0 = sex specific analysis, 1 = sex equal]
TOL = 0.010000
PUK_NUM_ORDERS_TOL = 6
PK_NUM_ORDERS_TOL = 8
PUK_LIKE_TOL = 2.000
PK_LIKE_TOL = 2.000
use_ord_file = 0
write_ord_file = 0
use_haps = 1



Haplotyped system (distances forced to 0.0):

  0   CRYG1-5               2   CRYG1-5_2             4   CRYG1-5_3           


Haplotyped system (distances forced to 0.0):

  1   D2S54                 3   D2S54_2  

Haplotyped system (distances forced to 0.0):

 24   D2S38_2              23   D2S38    

Haplotyped system (distances forced to 0.0):

 40   D2S5_2               39   D2S5     

Haplotyped system (distances forced to 0.0):

 42   D2S1_2               41   D2S1     

Haplotyped system (distances forced to 0.0):

 44   TPO                  45   TPO_2    

Haplotyped system (distances forced to 0.0):

 54   APOB_2               53   APOB     

Haplotyped system (distances forced to 0.0):

 64   D2S61_2              63   D2S61    

Haplotyped system (distances forced to 0.0):

 75   TGFA_3               73   TGFA_2               72   TGFA     
 76   TGFA_4   

N.B. Only the first locus in each set is retained in the orders
objects, but the remaining loci are used in all likelihood calculations.



D2S51               D2S44               D2S54               D2S43               D2S62
D2S45               D2S5_2              D2S6                D2S48               APOB_2
D2S70               D2S47



AGAINST:



TPO                 D2S61_2             ACP1                D2S49               POMC
D2S46               TGFA_3              CPSI                D2S1_2              CD8A
D2S12               CALMOD              CEB1/HINF           CEB11/HINF          D2S25
D2S24               D2S22               D2S36               D2S35               D2S34
D2S21               D2S19               D2S20               D2S42               D2S41
D2S40               D2S39               D2S38_2             D2S37               D2S30
D2S32               D2S31               D2S27               D2S29               D2S28
IL1-RN/pcr          IL1A/pcr            IMR-6               D2S72               D2S65
LCT                 Prot_C/pcr          CRYG1-5             COL5A2              D2S16
D2S17               D2S53               D2S50               LCO                 D2S3
CRYGP1              D2S55               GYPC                D2S90


D2S51   D2S25  rec. fracs.=    0.10,   lods =    4.83
  -1.48   2.37   4.49   4.83   4.64   4.22   3.66   3.00   2.28   1.51   0.73   0.00

D2S51   LCT  rec. fracs.=    0.14,   lods =    2.53
  -2.69   0.24   2.00   2.46   2.52   2.41   2.19   1.88   1.51   1.07   0.57   0.00

D2S51   Prot_C/pcr  rec. fracs.=    0.13,   lods =    2.93
  -3.88   0.01   2.30   2.87   2.91   2.73   2.41   2.01   1.54   1.04   0.52   0.00

D2S51   LCO  rec. fracs.=    0.12,   lods =    3.74
  -2.98   0.90   3.18   3.71   3.69   3.44   3.03   2.51   1.91   1.26   0.59   0.00

D2S44   TGFA_3  rec. fracs.=    0.35,   lods =    2.77
 -125.40 -66.88 -27.84 -12.93  -5.52  -1.28   1.17   2.41   2.77   2.42   1.48   0.00

D2S44   CD8A  rec. fracs.=    0.27,   lods =    2.49
 -42.25 -20.51  -6.33  -1.25   1.01   2.08   2.47   2.42   2.05   1.45   0.73   0.00

D2S44   D2S25  rec. fracs.=    0.28,   lods =    4.90
 -71.61 -35.00 -10.93  -2.13   1.92   3.95   4.80   4.83   4.24   3.16   1.67   0.00

D2S44   D2S36  rec. fracs.=    0.02,   lods =    9.37
   8.42   9.25   9.19   8.50   7.65   6.70   5.69   4.62   3.50   2.32   1.14   0.00

D2S44   D2S21  rec. fracs.=    0.06,   lods =   25.97
  15.08  22.58  25.92  25.37  23.65  21.34  18.59  15.47  12.00   8.21   4.15   0.00

D2S44   D2S20  rec. fracs.=    0.13,   lods =   10.79
 -13.14   0.48   8.56  10.56  10.72  10.08   8.96   7.51   5.83   3.96   1.97   0.00

D2S44   D2S41  rec. fracs.=    0.18,   lods =    8.63
 -32.03 -10.45   3.04   7.19   8.49   8.54   7.87   6.72   5.23   3.51   1.68   0.00

D2S44   D2S40  rec. fracs.=    0.25,   lods =    3.80
 -38.64 -17.89  -4.34   0.49   2.60   3.54   3.80   3.60   3.04   2.22   1.19   0.00

D2S44   D2S39  rec. fracs.=    0.19,   lods =    4.76
 -21.56  -7.81   0.84   3.60   4.56   4.76   4.50   3.95   3.16   2.18   1.09   0.00

D2S44   D2S38_2  rec. fracs.=    0.32,   lods =    2.90
 -80.61 -41.95 -16.23  -6.50  -1.76   0.87   2.28   2.85   2.80   2.24   1.27   0.00

D2S44   LCT  rec. fracs.=    0.06,   lods =   13.01
   6.34  11.00  12.99  12.56  11.45  10.05   8.49   6.85   5.18   3.49   1.76   0.00

D2S44   Prot_C/pcr  rec. fracs.=    0.05,   lods =   31.90
  20.78  29.02  31.88  30.19  27.27  23.80  20.02  16.07  12.02   7.93   3.89   0.00

D2S44   LCO  rec. fracs.=    0.09,   lods =   26.21
   3.40  17.76  25.36  26.13  24.86  22.66  19.87  16.63  13.02   9.05   4.73   0.00

D2S44   GYPC  rec. fracs.=    0.09,   lods =   18.61
  -3.23  10.23  17.56  18.60  17.76  16.09  13.90  11.36   8.58   5.64   2.68   0.00

D2S54   D2S21  rec. fracs.=    0.00,   lods =   15.05
  15.03  14.82  13.89  12.67  11.38  10.01   8.56   7.01   5.36   3.62   1.81   0.00

D2S54   D2S41  rec. fracs.=    0.09,   lods =    6.41
   0.32   4.15   6.18   6.39   6.05   5.46   4.71   3.84   2.89   1.88   0.89   0.00

D2S54   LCT  rec. fracs.=    0.12,   lods =    2.35
  -4.19  -0.32   1.88   2.33   2.29   2.06   1.77   1.45   1.12   0.78   0.41   0.00

D2S54   Prot_C/pcr  rec. fracs.=    0.06,   lods =   14.03
   7.24  11.93  14.00  13.66  12.63  11.27   9.69   7.95   6.09   4.13   2.09   0.00

D2S54   LCO  rec. fracs.=    0.06,   lods =   11.99
   6.63  10.37  11.97  11.62  10.71   9.51   8.12   6.58   4.94   3.24   1.56   0.00

D2S54   GYPC  rec. fracs.=    0.01,   lods =   17.84
  17.14  17.83  17.14  15.63  13.91  12.05  10.07   7.99   5.83   3.67   1.64   0.00

D2S43   CD8A  rec. fracs.=    0.19,   lods =    3.42
 -17.37  -6.56   0.28   2.48   3.26   3.42   3.22   2.77   2.13   1.37   0.60   0.00

D2S43   D2S25  rec. fracs.=    0.13,   lods =    8.75
 -11.65   0.02   6.90   8.58   8.68   8.10   7.12   5.86   4.41   2.86   1.32   0.00

D2S43   D2S21  rec. fracs.=    0.14,   lods =    6.42
 -12.56  -1.85   4.54   6.18   6.40   6.00   5.27   4.34   3.31   2.22   1.08   0.00

D2S43   D2S41  rec. fracs.=    0.03,   lods =   11.48
   9.33  11.08  11.36  10.51   9.36   8.06   6.66   5.21   3.72   2.24   0.87   0.00

D2S43   D2S38_2  rec. fracs.=    0.15,   lods =    9.10
 -17.64  -2.98   6.00   8.54   9.10   8.79   7.93   6.69   5.16   3.42   1.61   0.00

D2S43   IL1-RN/pcr  rec. fracs.=    0.00,   lods =    6.62
   6.61   6.51   6.07   5.48   4.86   4.20   3.51   2.77   2.00   1.23   0.51   0.00

D2S43   IL1A/pcr  rec. fracs.=    0.00,   lods =    3.61
   3.61   3.55   3.28   2.93   2.55   2.16   1.75   1.32   0.88   0.47   0.13   0.00

D2S43   Prot_C/pcr  rec. fracs.=    0.18,   lods =    6.36
 -23.65  -7.93   1.99   5.14   6.19   6.34   5.92   5.11   4.01   2.70   1.30   0.00

D2S43   LCO  rec. fracs.=    0.08,   lods =   13.73
   0.35   8.93  13.34  13.62  12.69  11.24   9.50   7.59   5.57   3.50   1.52   0.00

D2S43   GYPC  rec. fracs.=    0.11,   lods =    8.30
  -6.26   2.43   7.34   8.28   8.06   7.35   6.36   5.18   3.87   2.48   1.11   0.00

D2S62   TGFA_3  rec. fracs.=    0.14,   lods =    4.26
  -6.28  -0.42   3.13   4.09   4.26   4.06   3.64   3.05   2.33   1.51   0.69   0.00

D2S62   CD8A  rec. fracs.=    0.00,   lods =    9.03
   9.02   8.89   8.30   7.52   6.70   5.83   4.91   3.93   2.91   1.85   0.85   0.00

D2S62   D2S25  rec. fracs.=    0.02,   lods =   14.01
  13.23  13.98  13.54  12.36  11.01   9.54   7.98   6.34   4.63   2.92   1.31   0.00

D2S62   D2S21  rec. fracs.=    0.29,   lods =    2.00
 -33.56 -16.73  -5.61  -1.50   0.43   1.44   1.90   2.00   1.81   1.39   0.78   0.00

D2S62   D2S41  rec. fracs.=    0.18,   lods =    4.18
 -14.37  -4.55   1.60   3.51   4.11   4.14   3.82   3.26   2.50   1.61   0.69   0.00

D2S62   D2S38_2  rec. fracs.=    0.01,   lods =   19.03
  18.34  19.02  18.27  16.70  14.91  12.99  10.95   8.79   6.55   4.26   2.05   0.00

D2S62   D2S30  rec. fracs.=    0.20,   lods =    4.80
 -29.35 -11.66  -0.46   3.16   4.47   4.80   4.58   3.98   3.12   2.11   1.03   0.00

D2S62   D2S31  rec. fracs.=    0.25,   lods =    2.29
 -23.97 -11.12  -2.75   0.23   1.53   2.12   2.29   2.18   1.85   1.36   0.73   0.00

D2S62   IL1-RN/pcr  rec. fracs.=    0.08,   lods =    2.12
   0.61   1.56   2.07   2.11   2.01   1.85   1.64   1.39   1.10   0.77   0.41   0.00

D2S62   Prot_C/pcr  rec. fracs.=    0.22,   lods =    3.45
 -31.15 -13.45  -2.19   1.52   2.95   3.42   3.37   2.99   2.40   1.67   0.86   0.00

D2S45   TGFA_3  rec. fracs.=    0.00,   lods =   18.66
  18.63  18.32  16.94  15.15  13.31  11.40   9.43   7.41   5.37   3.36   1.52   0.00

D2S45   CD8A  rec. fracs.=    0.00,   lods =    3.31
   3.31   3.25   3.00   2.67   2.33   1.96   1.58   1.19   0.80   0.42   0.12   0.00

D2S45   D2S38_2  rec. fracs.=    0.08,   lods =    3.86
   0.91   2.82   3.79   3.83   3.58   3.20   2.73   2.18   1.57   0.93   0.34   0.00

D2S45   D2S30  rec. fracs.=    0.07,   lods =    7.30
   1.52   5.32   7.19   7.19   6.65   5.85   4.89   3.82   2.70   1.60   0.64   0.00

D2S45   LCO  rec. fracs.=    0.26,   lods =    2.72
 -33.85 -16.07  -4.47  -0.32   1.53   2.40   2.70   2.64   2.29   1.72   0.95   0.00

D2S5_2   D2S34  rec. fracs.=    0.00,   lods =    9.63
   9.62   9.47   8.79   7.91   6.99   6.03   5.02   3.97   2.88   1.78   0.76   0.00

D2S5_2   D2S30  rec. fracs.=    0.15,   lods =    5.29
 -12.27  -2.51   3.40   5.00   5.29   5.01   4.39   3.56   2.61   1.61   0.68   0.00

D2S5_2   D2S31  rec. fracs.=    0.02,   lods =    8.44
   7.52   8.34   8.24   7.50   6.59   5.60   4.54   3.45   2.37   1.36   0.53   0.00

D2S5_2   D2S28  rec. fracs.=    0.08,   lods =    4.20
   1.21   3.12   4.11   4.17   3.95   3.60   3.15   2.63   2.04   1.40   0.72   0.00

D2S5_2   IMR-6  rec. fracs.=    0.02,   lods =    9.29
   8.42   9.22   9.01   8.16   7.15   6.06   4.93   3.77   2.63   1.56   0.66   0.00

D2S5_2   D2S17  rec. fracs.=    0.08,   lods =    3.00
   0.01   1.92   2.91   2.97   2.77   2.43   2.02   1.56   1.08   0.61   0.23   0.00

D2S6   POMC  rec. fracs.=    0.22,   lods =    3.01
 -24.26 -10.47  -1.65   1.34   2.53   2.97   2.97   2.68   2.17   1.52   0.78   0.00

D2S6   D2S46  rec. fracs.=    0.16,   lods =    7.87
 -26.04  -7.47   3.86   7.08   7.86   7.62   6.83   5.69   4.34   2.87   1.38   0.00

D2S6   CALMOD  rec. fracs.=    0.07,   lods =    9.92
   2.73   7.47   9.79   9.78   9.08   8.08   6.89   5.57   4.15   2.68   1.23   0.00

D2S6   D2S25  rec. fracs.=    0.30,   lods =    2.81
 -66.22 -33.56 -12.04  -4.12  -0.39   1.57   2.53   2.81   2.60   2.01   1.12   0.00

D2S6   D2S34  rec. fracs.=    0.24,   lods =    2.03
 -15.87  -6.99  -1.24   0.77   1.62   1.97   2.02   1.87   1.57   1.14   0.61   0.00

D2S6   D2S19  rec. fracs.=    0.04,   lods =   14.82
  11.43  14.11  14.73  13.73  12.29  10.63   8.83   6.94   5.01   3.10   1.32   0.00

D2S6   D2S38_2  rec. fracs.=    0.30,   lods =    2.28
 -62.03 -31.40 -11.34  -4.02  -0.59   1.19   2.04   2.28   2.09   1.57   0.84   0.00

D2S6   D2S30  rec. fracs.=    0.27,   lods =    3.58
 -65.35 -31.78  -9.95  -2.20   1.23   2.87   3.52   3.51   3.01   2.15   1.07   0.00

D2S6   D2S31  rec. fracs.=    0.13,   lods =    4.00
  -6.28  -0.44   3.03   3.89   3.97   3.72   3.28   2.73   2.10   1.42   0.69   0.00

D2S6   D2S27  rec. fracs.=    0.04,   lods =   14.72
  11.14  13.86  14.68  13.92  12.69  11.20   9.52   7.66   5.66   3.55   1.52   0.00

D2S6   D2S28  rec. fracs.=    0.14,   lods =    6.64
 -10.76  -1.01   4.86   6.40   6.63   6.27   5.57   4.62   3.52   2.30   1.08   0.00

D2S6   IMR-6  rec. fracs.=    0.07,   lods =    3.18
   0.31   2.20   3.13   3.12   2.85   2.47   2.04   1.60   1.17   0.76   0.36   0.00

D2S6   D2S16  rec. fracs.=    0.15,   lods =    4.91
 -11.07  -2.28   3.07   4.57   4.91   4.74   4.28   3.63   2.84   1.95   1.00   0.00

D2S6   D2S17  rec. fracs.=    0.18,   lods =    4.20
 -25.46  -9.76   0.04   3.07   4.05   4.18   3.83   3.19   2.37   1.49   0.65   0.00

D2S48   POMC  rec. fracs.=    0.00,   lods =    3.31
   3.31   3.25   3.02   2.72   2.40   2.06   1.72   1.36   1.01   0.65   0.32   0.00

D2S48   D2S46  rec. fracs.=    0.15,   lods =    6.51
 -16.16  -3.49   4.12   6.14   6.50   6.17   5.46   4.51   3.45   2.33   1.19   0.00

D2S48   D2S25  rec. fracs.=    0.25,   lods =    3.05
 -39.25 -18.51  -5.02  -0.24   1.85   2.78   3.05   2.87   2.37   1.64   0.80   0.00

D2S48   D2S34  rec. fracs.=    0.19,   lods =    3.01
 -11.97  -4.12   0.83   2.40   2.93   3.00   2.81   2.43   1.91   1.31   0.66   0.00

D2S48   D2S19  rec. fracs.=    0.15,   lods =    3.43
  -7.18  -1.32   2.25   3.24   3.43   3.26   2.88   2.34   1.70   1.02   0.40   0.00

D2S48   D2S27  rec. fracs.=    0.09,   lods =    6.23
   0.02   3.87   5.95   6.22   5.95   5.43   4.74   3.93   3.02   2.03   1.00   0.00

D2S48   D2S16  rec. fracs.=    0.17,   lods =    4.46
 -10.17  -2.33   2.55   4.02   4.43   4.38   4.04   3.48   2.75   1.88   0.94   0.00

APOB_2   POMC  rec. fracs.=    0.09,   lods =    4.92
  -1.18   2.65   4.68   4.91   4.60   4.06   3.40   2.67   1.92   1.18   0.48   0.00

APOB_2   D2S46  rec. fracs.=    0.10,   lods =    7.19
  -3.87   2.87   6.59   7.19   6.86   6.12   5.15   4.03   2.84   1.66   0.64   0.00

APOB_2   D2S19  rec. fracs.=    0.17,   lods =    3.22
 -13.30  -4.47   1.01   2.68   3.18   3.17   2.86   2.36   1.74   1.06   0.42   0.00

APOB_2   D2S27  rec. fracs.=    0.09,   lods =    6.09
   1.52   4.40   5.92   6.07   5.81   5.34   4.73   4.01   3.18   2.24   1.19   0.00

APOB_2   D2S16  rec. fracs.=    0.03,   lods =    6.75
   5.71   6.58   6.66   6.16   5.50   4.77   3.99   3.17   2.34   1.51   0.71   0.00

D2S70   POMC  rec. fracs.=    0.06,   lods =    2.86
   1.51   2.45   2.86   2.78   2.56   2.27   1.92   1.53   1.11   0.68   0.29   0.00

D2S70   D2S16  rec. fracs.=    0.02,   lods =    9.99
   9.02   9.86   9.83   9.17   8.34   7.40   6.36   5.25   4.04   2.76   1.41   0.00

D2S47   TPO  rec. fracs.=    0.03,   lods =   35.74
  30.39  34.76  35.41  33.20  30.17  26.67  22.79  18.56  14.00   9.15   4.23   0.00

D2S47   ACP1  rec. fracs.=    0.05,   lods =   23.14
  13.87  20.39  23.12  22.41  20.68  18.44  15.85  12.97   9.82   6.44   2.95   0.00

D2S47   D2S49  rec. fracs.=    0.01,   lods =   30.31
  29.76  30.30  28.90  26.46  23.73  20.78  17.61  14.22  10.60   6.82   3.09   0.00

D2S47   D2S1_2  rec. fracs.=    0.01,   lods =   33.02
  31.56  32.98  31.75  28.94  25.75  22.32  18.71  14.95  11.07   7.15   3.32   0.00

D2S47   D2S16  rec. fracs.=    0.29,   lods =    2.19
 -45.85 -23.08  -8.08  -2.54   0.05   1.40   2.04   2.19   1.99   1.53   0.86   0.00