1     M         0.809   0.813   0.861   1.107   1.104   1.135   0.838   0.844   0.911
2     S        -0.652  -0.660  -0.539  -0.855  -0.895  -0.738  -0.915  -0.934  -0.766
3     D        -0.564  -0.639  -0.544  -0.533  -0.684  -0.618  -0.772  -0.898  -0.775
4     T        -2.243  -2.245  -1.953  -2.130  -2.110  -1.645  -2.010  -2.004  -1.622
5     E         0.809   0.813   0.861   0.657   0.678   0.759   0.838   0.844   0.911
6     A        -1.512  -1.641  -1.367  -1.899  -2.118  -1.661  -1.572  -1.705  -1.338
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     P        -2.248  -2.243  -1.954  -1.982  -1.972  -1.638  -2.001  -1.998  -1.623
10    V        -0.340  -0.345  -0.518  -0.415  -0.416  -0.592  -0.424  -0.435  -0.731
11    E        -1.512  -1.641  -1.367  -1.696  -1.913  -1.485  -1.572  -1.705  -1.338
12    V        -2.042  -2.116  -1.950  -2.162  -2.335  -2.029  -1.791  -1.882  -1.620
13    Q        -1.512  -1.641  -1.367  -1.629  -1.856  -1.479  -1.572  -1.705  -1.338
14    E        -1.512  -1.641  -1.367  -1.622  -1.785  -1.359  -1.572  -1.705  -1.338
15    D        -1.512  -1.318  -1.357  -1.436  -1.129  -1.264  -1.572  -1.332  -1.328
16    F        -1.512  -1.641  -1.367  -1.179  -1.340  -0.990  -1.572  -1.705  -1.338
17    E        -0.652  -0.575  -0.531  -1.020  -0.865  -0.839  -0.915  -0.794  -0.753
18    V         0.809   0.813   0.861   0.586   0.604   0.700   0.838   0.844   0.911
19    V        -0.736  -0.741  -0.546  -1.096  -1.104  -0.753  -1.055  -1.070  -0.778
20    E        -0.340  -0.319  -0.527  -0.427  -0.398  -0.691  -0.424  -0.396  -0.747
21    E         0.809   0.813   0.861   0.670   0.694   0.770   0.838   0.844   0.911
22    F        -1.512  -1.624  -1.367  -1.346  -1.521  -1.188  -1.572  -1.685  -1.338
23    T        -2.243  -2.242  -1.953  -2.236  -2.275  -1.899  -2.010  -2.001  -1.622
24    P        -1.182  -1.104  -1.350  -0.905  -0.801  -1.316  -1.134  -1.039  -1.319
25    V         0.809   0.813   0.861   0.594   0.613   0.706   0.838   0.844   0.911
26    V        -2.042  -2.026  -1.942  -2.104  -2.123  -2.006  -1.791  -1.792  -1.613
27    L         0.809   0.813   0.861   0.778   0.770   0.860   0.838   0.844   0.911
28    A        -0.056  -0.151  -0.495  -0.124  -0.235  -0.680  -0.024  -0.155  -0.693
29    T        -1.257  -1.348  -1.349  -1.087  -1.239  -1.272  -1.257  -1.374  -1.318
30    P        -2.620  -2.676  -2.397  -2.176  -2.258  -1.931  -2.120  -2.145  -1.785
31    I        -0.652  -0.698  -0.544  -0.876  -0.971  -0.722  -0.915  -0.998  -0.775
32    P         0.008  -0.037  -0.486   0.353   0.300  -0.366   0.059  -0.001  -0.678
33    E        -3.040  -2.890  -2.763  -2.825  -2.577  -2.479  -2.278  -2.150  -1.897
34    E        -1.139  -1.147  -1.335  -1.019  -1.014  -1.236  -1.109  -1.110  -1.303
35    V        -0.407  -0.359  -0.528  -0.572  -0.493  -0.775  -0.525  -0.456  -0.748
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    Q        -1.341  -1.370  -1.353  -1.271  -1.342  -1.311  -1.402  -1.444  -1.324
38    Q        -2.686  -2.565  -2.396  -2.574  -2.422  -2.155  -2.181  -2.074  -1.785
39    A        -1.406  -1.325  -1.350  -1.686  -1.557  -1.457  -1.499  -1.406  -1.321
40    Q        -2.466  -2.559  -2.392  -2.040  -2.183  -2.010  -1.986  -2.051  -1.782
41    T        -2.113  -1.944  -1.938  -1.838  -1.596  -1.638  -1.888  -1.708  -1.610
42    E        -1.341  -1.370  -1.349  -1.351  -1.396  -1.224  -1.402  -1.444  -1.320
43    I        -0.768  -0.750  -0.546  -1.172  -1.145  -0.799  -1.109  -1.086  -0.777
44    K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
45    L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
46    F         0.809   0.813   0.861   1.037   1.039   1.077   0.838   0.844   0.911
47    N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
48    K         0.008  -0.136  -0.490   0.137  -0.036  -0.592   0.059  -0.134  -0.686
49    W        -0.407  -0.435  -0.512   0.041  -0.008  -0.215  -0.525  -0.572  -0.722
50    S        -1.139  -1.168  -1.329  -0.891  -0.942  -1.148  -1.109  -1.150  -1.295
51    F        -0.407  -0.492  -0.529  -0.073  -0.201  -0.306  -0.525  -0.662  -0.750
52    E         0.008   0.002  -0.488   0.086   0.090  -0.541   0.059   0.051  -0.682
53    E        -1.139  -1.088  -1.335  -0.829  -0.785  -1.187  -1.109  -1.067  -1.301
54    V         0.809   0.813   0.861   0.633   0.649   0.739   0.838   0.844   0.911
55    E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
56    V         0.008  -0.136  -0.490  -0.021  -0.185  -0.709   0.059  -0.134  -0.686
57    K         0.008  -0.136  -0.490   0.137  -0.036  -0.592   0.059  -0.134  -0.686
58    D         0.809   0.813   0.861   0.955   0.957   1.008   0.838   0.844   0.911
59    A        -2.113  -1.944  -1.939  -2.217  -1.943  -1.917  -1.888  -1.708  -1.610
60    S         0.809   0.813   0.861   0.837   0.835   0.910   0.838   0.844   0.911
61    L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
62    V        -0.407  -0.492  -0.529  -0.524  -0.640  -0.685  -0.525  -0.662  -0.750
63    D         0.809   0.813   0.861   0.955   0.957   1.008   0.838   0.844   0.911
64    Y         0.809   0.813   0.861   1.101   1.098   1.130   0.838   0.844   0.911
65    V        -0.652  -0.594  -0.538  -0.933  -0.829  -0.780  -0.915  -0.826  -0.764
66    Q        -0.407  -0.435  -0.512  -0.233  -0.269  -0.452  -0.525  -0.572  -0.722
67    V         0.008   0.096  -0.485   0.061   0.163  -0.672   0.059   0.169  -0.677
68    R        -1.475  -1.455  -1.347  -1.483  -1.465  -1.298  -1.499  -1.475  -1.316
69    Q        -1.979  -1.997  -1.933  -1.727  -1.752  -1.658  -1.791  -1.799  -1.606
70    P        -0.407  -0.435  -0.512  -0.173  -0.221  -0.402  -0.525  -0.572  -0.722
71    I        -1.626  -1.583  -1.358  -1.859  -1.775  -1.415  -1.694  -1.636  -1.328
72    F        -1.626  -1.624  -1.357  -1.311  -1.317  -0.974  -1.694  -1.689  -1.328
73    V        -1.341  -1.370  -1.353  -1.538  -1.586  -1.489  -1.402  -1.444  -1.324
74    A        -1.341  -1.217  -1.342  -1.294  -1.088  -1.289  -1.402  -1.245  -1.311
75    H         0.809   0.813   0.861   1.118   1.117   1.145   0.838   0.844   0.911
76    T         0.008  -0.136  -0.490   0.254   0.087  -0.465   0.059  -0.134  -0.686
77    A         0.008   0.070  -0.487  -0.066   0.002  -0.695   0.059   0.136  -0.681
78    G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
79    R        -0.407  -0.323  -0.511  -0.462  -0.344  -0.645  -0.525  -0.402  -0.719
80    Y        -0.407  -0.435  -0.512  -0.030  -0.080  -0.266  -0.525  -0.572  -0.722
81    A        -0.407  -0.435  -0.512  -0.570  -0.608  -0.684  -0.525  -0.572  -0.722
82    N        -1.828  -1.904  -1.932  -1.548  -1.683  -1.768  -1.596  -1.675  -1.604
83    K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
84    R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
85    F         0.809   0.813   0.861   1.037   1.039   1.077   0.838   0.844   0.911
86    R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
87    K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
88    A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
89    Q        -1.139  -1.282  -1.341  -0.891  -1.085  -1.237  -1.109  -1.274  -1.308
90    C         0.809   0.813   0.861   1.139   1.136   1.163   0.838   0.844   0.911
91    P        -0.407  -0.435  -0.512  -0.140  -0.184  -0.345  -0.525  -0.572  -0.722
92    I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
93    I        -1.341  -1.278  -1.342  -1.549  -1.469  -1.478  -1.402  -1.340  -1.312
94    E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
95    R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
96    L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
97    T         0.809   0.813   0.861   0.893   0.903   0.957   0.838   0.844   0.911
98    N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
99    S        -0.407  -0.366  -0.527  -0.412  -0.360  -0.708  -0.525  -0.467  -0.746
100   L         0.008   0.070  -0.487   0.150   0.212  -0.438   0.059   0.136  -0.681
101   M         0.809   0.813   0.861   1.107   1.104   1.135   0.838   0.844   0.911
102   M         0.809   0.813   0.861   1.107   1.104   1.135   0.838   0.844   0.911
103   N         0.008  -0.136  -0.490   0.252   0.093  -0.365   0.059  -0.134  -0.686
104   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
105   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
106   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
107   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
108   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
109   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
110   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
111   L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
112   K        -1.139  -1.282  -1.341  -0.976  -1.154  -1.202  -1.109  -1.274  -1.308
113   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
114   V        -0.407  -0.435  -0.512  -0.524  -0.554  -0.662  -0.525  -0.572  -0.722
115   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
116   I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
117   I        -0.652  -0.565  -0.534  -0.977  -0.822  -0.785  -0.915  -0.777  -0.758
118   K        -1.492  -1.562  -1.917  -1.155  -1.267  -1.823  -1.207  -1.287  -1.591
119   H         0.809   0.813   0.861   1.118   1.117   1.145   0.838   0.844   0.911
120   T        -0.652  -0.560  -0.528  -0.951  -0.809  -0.724  -0.915  -0.770  -0.748
121   L        -0.652  -0.698  -0.542  -0.717  -0.791  -0.537  -0.915  -0.998  -0.770
122   D         0.008   0.096  -0.485   0.086   0.190  -0.537   0.059   0.169  -0.677
123   I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
124   I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
125   N        -1.475  -1.411  -1.347  -1.241  -1.164  -1.192  -1.499  -1.422  -1.315
126   V        -1.406  -1.325  -1.350  -1.645  -1.517  -1.481  -1.499  -1.406  -1.321
127   L         0.008  -0.136  -0.490   0.150  -0.010  -0.442   0.059  -0.134  -0.686
128   T         0.008   0.079  -0.487   0.254   0.335  -0.459   0.059   0.148  -0.680
129   D        -0.652  -0.575  -0.537  -0.684  -0.548  -0.579  -0.915  -0.793  -0.762
130   Q         0.008   0.002  -0.488   0.281   0.281  -0.471   0.059   0.051  -0.682
131   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
132   P         0.809   0.813   0.861   0.985   0.989   1.034   0.838   0.844   0.911
133   I        -0.768  -0.742  -0.546  -1.087  -1.050  -0.725  -1.109  -1.072  -0.778
134   Q         0.809   0.813   0.861   0.930   0.943   0.988   0.838   0.844   0.911
135   V         0.008  -0.136  -0.490  -0.021  -0.185  -0.709   0.059  -0.134  -0.686
136   V        -1.139  -1.282  -1.341  -1.219  -1.422  -1.545  -1.109  -1.274  -1.308
137   V         0.809   0.813   0.861   0.633   0.649   0.739   0.838   0.844   0.911
138   D         0.809   0.813   0.861   0.955   0.957   1.008   0.838   0.844   0.911
139   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
140   I        -0.407  -0.435  -0.512  -0.506  -0.552  -0.726  -0.525  -0.572  -0.722
141   T        -2.333  -2.265  -1.945  -2.564  -2.474  -1.969  -2.083  -2.011  -1.616
142   N        -0.407  -0.435  -0.512  -0.393  -0.448  -0.659  -0.525  -0.572  -0.722
143   T        -1.626  -1.511  -1.359  -1.413  -1.227  -1.090  -1.694  -1.553  -1.330
144   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
145   P         0.008   0.070  -0.487   0.315   0.385  -0.506   0.059   0.137  -0.681
146   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
147   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
148   D         0.809   0.813   0.861   0.955   0.957   1.008   0.838   0.844   0.911
149   T        -0.652  -0.560  -0.528  -0.710  -0.568  -0.544  -0.915  -0.770  -0.748
150   T         0.809   0.813   0.861   0.893   0.903   0.957   0.838   0.844   0.911
151   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
152   V        -0.652  -0.560  -0.528  -0.933  -0.767  -0.759  -0.915  -0.770  -0.748
153   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
154   G        -0.652  -0.560  -0.528  -0.699  -0.563  -0.532  -0.915  -0.770  -0.748
155   G        -1.712  -1.658  -1.368  -1.914  -1.872  -1.396  -1.791  -1.724  -1.340
156   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
157   A        -0.768  -0.720  -0.545  -1.070  -0.968  -0.721  -1.109  -1.034  -0.776
158   A        -0.652  -0.560  -0.528  -1.049  -0.876  -0.857  -0.915  -0.770  -0.748
159   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
160   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
161   Q         0.809   0.813   0.861   0.930   0.943   0.988   0.838   0.844   0.911
162   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
163   V         0.809   0.813   0.861   0.633   0.649   0.739   0.838   0.844   0.911
164   D         0.809   0.813   0.861   0.955   0.957   1.008   0.838   0.844   0.911
165   V         0.809   0.813   0.861   0.633   0.649   0.739   0.838   0.844   0.911
166   S         0.809   0.813   0.861   0.837   0.835   0.910   0.838   0.844   0.911
167   P         0.809   0.813   0.861   0.985   0.989   1.034   0.838   0.844   0.911
168   L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
169   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
170   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
171   V         0.809   0.813   0.861   0.633   0.649   0.739   0.838   0.844   0.911
172   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
173   Q         0.809   0.813   0.861   0.930   0.943   0.988   0.838   0.844   0.911
174   A         0.008   0.091  -0.485  -0.066   0.024  -0.692   0.059   0.162  -0.677
175   I        -1.139  -1.103  -1.337  -1.116  -1.086  -1.448  -1.109  -1.082  -1.304
176   A        -0.407  -0.366  -0.527  -0.598  -0.544  -0.753  -0.525  -0.467  -0.746
177   L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
178   L        -0.652  -0.638  -0.543  -0.863  -0.848  -0.719  -0.915  -0.896  -0.773
179   T         0.809   0.813   0.861   0.893   0.903   0.957   0.838   0.844   0.911
180   I         0.008  -0.136  -0.490   0.094  -0.071  -0.562   0.059  -0.134  -0.686
181   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
182   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
183   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
184   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
185   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
186   A        -0.407  -0.458  -0.533  -0.598  -0.679  -0.761  -0.525  -0.608  -0.756
187   F         0.809   0.813   0.861   1.037   1.039   1.077   0.838   0.844   0.911
188   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
189   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
190   I        -0.652  -0.698  -0.542  -0.933  -1.033  -0.789  -0.915  -0.998  -0.770
191   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
192   T        -0.652  -0.698  -0.542  -0.684  -0.780  -0.562  -0.915  -0.998  -0.770
193   I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
194   A        -0.407  -0.435  -0.512  -0.598  -0.644  -0.733  -0.525  -0.572  -0.722
195   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
196   T        -0.652  -0.560  -0.528  -0.436  -0.288  -0.340  -0.915  -0.770  -0.748
197   L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
198   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
199   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
200   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
201   L        -0.407  -0.435  -0.512  -0.451  -0.501  -0.659  -0.525  -0.572  -0.722
202   I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
203   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
204   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
205   A         0.008   0.002  -0.488  -0.055  -0.061  -0.658   0.059   0.051  -0.682
206   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
207   G         0.809   0.813   0.861   0.918   0.918   0.977   0.838   0.844   0.911
208   S         0.809   0.813   0.861   0.837   0.835   0.910   0.838   0.844   0.911
209   S         0.809   0.813   0.861   0.837   0.835   0.910   0.838   0.844   0.911
210   T        -0.768  -0.756  -0.547  -0.891  -0.880  -0.562  -1.109  -1.095  -0.779
211   S         0.809   0.813   0.861   0.837   0.835   0.910   0.838   0.844   0.911
212   Y         0.809   0.813   0.861   1.101   1.098   1.130   0.838   0.844   0.911
213   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
214   I         0.809   0.813   0.861   0.726   0.732   0.817   0.838   0.844   0.911
215   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
216   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
217   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
218   D         0.809   0.813   0.861   0.955   0.957   1.008   0.838   0.844   0.911
219   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
220   L         0.809   0.813   0.861   0.755   0.758   0.841   0.838   0.844   0.911
221   E         0.809   0.813   0.861   0.710   0.726   0.803   0.838   0.844   0.911
222   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
223   V         0.809   0.813   0.861   0.633   0.649   0.739   0.838   0.844   0.911
224   A         0.809   0.813   0.861   0.574   0.580   0.689   0.838   0.844   0.911
225   K         0.809   0.813   0.861   0.790   0.798   0.870   0.838   0.844   0.911
226   S         0.809   0.813   0.861   0.837   0.835   0.910   0.838   0.844   0.911
227   N         0.809   0.813   0.861   0.856   0.859   0.925   0.838   0.844   0.911
228   R         0.809   0.813   0.861   0.726   0.729   0.817   0.838   0.844   0.911
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/P26783
Output conservation file - output/P26783
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
