1     M         1.538   1.587   1.665   1.760   1.816   1.952   1.659   1.736   1.873
2     A         0.286   0.347   0.418   0.113   0.202   0.294  -0.075   0.017   0.087
3     E        -1.618  -1.699  -1.584  -1.478  -1.603  -1.397  -1.231  -1.281  -1.141
4     E        -1.396  -1.355  -1.228  -1.336  -1.252  -1.078  -1.210  -1.148  -0.998
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    T        -1.618  -1.362  -1.507  -1.200  -0.834  -1.121  -1.231  -0.986  -1.080
12    D        -0.166  -0.133  -0.241  -0.164  -0.137  -0.293  -0.306  -0.314  -0.424
13    F        -1.290  -1.399  -1.247  -1.146  -1.334  -1.173  -1.116  -1.183  -1.015
14    S        -1.742  -1.574  -1.548  -1.792  -1.564  -1.534  -1.347  -1.202  -1.116
15    Q        -0.962  -0.801  -0.805  -1.074  -0.912  -0.895  -1.000  -0.835  -0.795
16    F        -1.618  -1.699  -1.584  -1.274  -1.451  -1.345  -1.231  -1.281  -1.141
17    E        -0.306  -0.178  -0.248  -0.531  -0.375  -0.432  -0.538  -0.391  -0.438
18    E         0.825   0.718   0.602   0.714   0.580   0.398   0.850   0.678   0.440
19    E        -0.962  -0.878  -0.823  -1.278  -1.153  -1.099  -1.000  -0.904  -0.814
20    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    N        -0.839  -0.783  -0.784  -0.814  -0.763  -0.747  -0.885  -0.817  -0.775
25    D        -0.758  -0.858  -0.802  -0.828  -0.960  -0.915  -0.769  -0.855  -0.789
26    Q        -1.290  -1.160  -1.196  -1.146  -0.996  -1.045  -1.116  -0.990  -0.972
27    Y         0.825   0.718   0.602   1.011   0.875   0.674   0.850   0.678   0.440
28    K        -1.086  -1.156  -1.197  -1.051  -1.152  -1.189  -0.885  -0.951  -0.969
29    V        -0.166  -0.304  -0.272  -0.214  -0.447  -0.398  -0.306  -0.505  -0.465
30    S         0.286   0.375   0.447   0.099   0.224   0.328  -0.075   0.071   0.145
31    A         0.145   0.213  -0.111   0.165   0.247  -0.157   0.156   0.236  -0.227
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    K         1.538   1.587   1.665   1.273   1.376   1.485   1.659   1.736   1.873
34    K         0.825   0.758   0.611   0.688   0.648   0.439   0.850   0.743   0.456
35    T         0.286   0.279   0.406   0.108   0.056   0.246  -0.075  -0.114   0.064
36    V        -0.430  -0.423  -0.317  -0.620  -0.634  -0.492  -0.653  -0.651  -0.523
37    D        -0.962  -0.974  -0.825  -1.086  -1.052  -0.882  -1.000  -0.987  -0.816
38    E         1.538   1.587   1.665   1.336   1.409   1.544   1.659   1.736   1.873
39    Y         1.538   1.587   1.665   1.631   1.706   1.828   1.659   1.736   1.873
40    K        -1.086  -1.252  -1.212  -0.983  -1.161  -1.090  -0.885  -1.045  -0.982
41    N         0.226   0.285   0.409  -0.121  -0.034   0.137  -0.191  -0.103   0.069
42    L         0.473   0.387   0.441   0.451   0.322   0.400   0.272   0.093   0.134
43    D         1.538   1.587   1.665   1.461   1.538   1.665   1.659   1.736   1.873
44    A         0.825   0.758   0.611   0.968   0.884   0.624   0.850   0.743   0.456
45    E         0.145   0.192  -0.118   0.131   0.195  -0.234   0.156   0.211  -0.236
46    D         1.538   1.587   1.665   1.461   1.538   1.665   1.659   1.736   1.873
47    E         1.538   1.587   1.665   1.336   1.409   1.544   1.659   1.736   1.873
48    S         0.825   0.987   0.634   0.908   1.107   0.658   0.850   1.090   0.498
49    L         1.538   1.587   1.665   1.477   1.561   1.681   1.659   1.736   1.873
50    A        -0.758  -0.885  -0.794  -0.570  -0.758  -0.667  -0.769  -0.890  -0.784
51    K         0.825   0.758   0.611   0.685   0.644   0.434   0.850   0.743   0.456
52    W         0.825   0.758   0.611   1.205   1.131   0.899   0.850   0.743   0.456
53    K         1.538   1.587   1.665   1.273   1.376   1.485   1.659   1.736   1.873
54    E        -0.306  -0.184  -0.250  -0.531  -0.377  -0.434  -0.538  -0.402  -0.440
55    S         0.825   0.761   0.602   0.908   0.837   0.608   0.850   0.747   0.441
56    L         1.538   1.587   1.665   1.477   1.561   1.681   1.659   1.736   1.873
57    G         1.538   1.587   1.665   1.550   1.603   1.750   1.659   1.736   1.873
58    L         0.473   0.388   0.436   0.375   0.229   0.263   0.272   0.095   0.124
59    S        -0.511  -0.431  -0.317  -0.673  -0.557  -0.399  -0.769  -0.658  -0.522
60    S        -0.839  -0.728  -0.766  -0.840  -0.707  -0.730  -0.885  -0.754  -0.755
61    D        -0.758  -0.900  -0.802  -0.684  -0.882  -0.743  -0.769  -0.909  -0.792
62    V        -0.646  -0.710  -0.791  -0.490  -0.584  -0.728  -0.606  -0.686  -0.775
63    L        -0.814  -0.913  -0.845  -0.814  -0.953  -0.926  -0.808  -0.919  -0.834
64    P        -0.758  -0.819  -0.799  -0.608  -0.761  -0.720  -0.769  -0.842  -0.789
65    L        -0.306  -0.337  -0.271  -0.350  -0.363  -0.255  -0.538  -0.559  -0.467
66    E        -0.962  -0.964  -0.834  -1.118  -1.097  -0.897  -1.000  -0.979  -0.823
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    F        -1.414  -1.322  -1.227  -1.395  -1.282  -1.116  -1.231  -1.126  -0.997
70    P         0.145   0.087  -0.142   0.401   0.309  -0.033   0.156   0.069  -0.271
71    G         0.286   0.279   0.406   0.173   0.135   0.340  -0.075  -0.114   0.064
72    D         0.877   0.661   0.643   0.920   0.653   0.610   0.928   0.583   0.516
73    K        -1.455  -1.483  -1.492  -1.351  -1.368  -1.403  -1.082  -1.116  -1.068
74    R         0.877   0.661   0.643   1.105   0.799   0.736   0.928   0.583   0.516
75    K        -1.163  -1.323  -1.198  -1.172  -1.377  -1.182  -0.990  -1.114  -0.974
76    V         0.877   0.851   0.636   0.947   0.924   0.689   0.928   0.888   0.503
77    V         0.244  -0.017  -0.103   0.337  -0.045  -0.183   0.289  -0.076  -0.214
78    V         0.535   0.718   0.511   0.507   0.786   0.417   0.380   0.677   0.270
79    Q        -1.636  -1.553  -1.546  -1.208  -1.151  -1.131  -1.264  -1.173  -1.113
80    K        -0.289  -0.268  -0.257  -0.751  -0.670  -0.655  -0.533  -0.479  -0.450
81    I        -1.235  -1.221  -1.184  -1.068  -1.048  -0.950  -1.082  -1.038  -0.958
82    Q        -0.943  -0.854  -0.795  -0.803  -0.709  -0.610  -0.990  -0.887  -0.782
83    L        -0.069  -0.202  -0.202   0.002  -0.194  -0.164  -0.168  -0.368  -0.361
84    L        -1.345  -1.223  -1.214  -1.315  -1.165  -1.137  -1.173  -1.062  -0.989
85    V        -0.872  -0.895  -0.808  -0.891  -0.949  -0.811  -0.899  -0.912  -0.796
86    N        -0.943  -0.832  -0.803  -0.945  -0.847  -0.730  -0.990  -0.886  -0.794
87    T        -1.345  -1.262  -1.235  -1.279  -1.209  -1.155  -1.173  -1.088  -1.005
88    E        -0.872  -0.819  -0.815  -0.898  -0.826  -0.787  -0.899  -0.837  -0.805
89    P         0.591   0.748   0.486   0.621   0.857   0.335   0.475   0.727   0.222
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    N        -1.345  -1.263  -1.184  -1.272  -1.187  -1.051  -1.173  -1.089  -0.963
93    P         1.538   1.587   1.665   1.597   1.660   1.796   1.659   1.736   1.873
94    I         0.535   0.477   0.456   0.507   0.401   0.306   0.380   0.259   0.162
95    T        -0.762  -0.641  -0.736  -0.759  -0.577  -0.687  -0.808  -0.623  -0.714
96    F        -0.943  -0.947  -0.811  -1.027  -1.086  -0.887  -0.990  -0.964  -0.799
97    D         0.333   0.370   0.416   0.191   0.251   0.303   0.015   0.061   0.084
98    L         0.535   0.382   0.447   0.541   0.316   0.408   0.380   0.084   0.144
99    T        -0.289  -0.284  -0.241  -0.519  -0.501  -0.433  -0.533  -0.505  -0.427
100   N        -0.236  -0.096  -0.179  -0.267  -0.028  -0.162  -0.442  -0.198  -0.327
101   E        -0.943  -0.813  -0.806  -1.043  -0.804  -0.797  -0.990  -0.832  -0.795
102   K        -1.455  -1.347  -1.525  -1.327  -1.182  -1.400  -1.082  -0.972  -1.095
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   T        -0.069  -0.316  -0.231   0.016  -0.378  -0.284  -0.168  -0.500  -0.408
106   I        -0.236  -0.306  -0.235  -0.328  -0.440  -0.349  -0.442  -0.527  -0.425
107   K        -0.762  -0.514  -0.731  -1.076  -0.637  -0.954  -0.808  -0.481  -0.709
108   E        -0.762  -0.752  -0.731  -0.870  -0.848  -0.773  -0.808  -0.781  -0.717
109   L         0.762   0.699   0.565   0.792   0.732   0.503   0.753   0.646   0.372
110   A        -0.236  -0.129  -0.192  -0.461  -0.252  -0.339  -0.442  -0.240  -0.346
111   S        -1.345  -1.369  -1.235  -1.477  -1.500  -1.337  -1.173  -1.166  -1.005
112   K        -0.346  -0.348  -0.265  -0.636  -0.638  -0.527  -0.533  -0.548  -0.448
113   R        -1.345  -1.364  -1.248  -1.243  -1.281  -1.153  -1.173  -1.157  -1.015
114   Y        -0.470  -0.400  -0.266  -0.463  -0.364  -0.183  -0.716  -0.616  -0.450
115   K        -0.637  -0.580  -0.781  -0.723  -0.654  -0.876  -0.625  -0.581  -0.769
116   I         0.535   0.490   0.483   0.507   0.426   0.362   0.380   0.284   0.215
117   K         1.538   1.587   1.665   1.265   1.363   1.476   1.659   1.736   1.873
118   E         1.538   1.587   1.665   1.335   1.412   1.544   1.659   1.736   1.873
119   N        -0.069   0.021  -0.215  -0.231  -0.152  -0.410  -0.168  -0.102  -0.386
120   S        -0.360  -0.566  -0.693  -0.091  -0.380  -0.574  -0.259  -0.518  -0.662
121   I        -0.762  -0.745  -0.780  -0.955  -0.975  -1.043  -0.808  -0.771  -0.770
122   Y         0.535   0.477   0.456   0.645   0.543   0.482   0.380   0.259   0.162
123   K        -1.345  -1.261  -1.221  -1.270  -1.153  -1.056  -1.173  -1.086  -0.993
124   L        -1.455  -1.609  -1.548  -1.067  -1.280  -1.194  -1.082  -1.211  -1.114
125   K        -1.345  -1.265  -1.219  -1.586  -1.509  -1.360  -1.173  -1.091  -0.991
126   I        -0.637  -0.847  -0.760  -0.456  -0.715  -0.625  -0.625  -0.850  -0.747
127   V        -0.637  -0.370  -0.691  -0.730  -0.335  -0.781  -0.625  -0.284  -0.661
128   F         1.538   1.587   1.665   1.663   1.738   1.859   1.659   1.736   1.873
129   K         0.226   0.293   0.416  -0.097   0.055   0.223  -0.191  -0.086   0.083
130   V         1.538   1.587   1.665   1.454   1.517   1.658   1.659   1.736   1.873
131   Q         0.877   0.661   0.643   1.139   0.850   0.802   0.928   0.583   0.516
132   H         1.538   1.587   1.665   1.748   1.819   1.941   1.659   1.736   1.873
133   E         0.877   0.661   0.643   0.796   0.535   0.513   0.928   0.583   0.516
134   I         0.244  -0.051  -0.114   0.445   0.058  -0.067   0.289  -0.121  -0.230
135   I        -0.069  -0.202  -0.202  -0.026  -0.256  -0.266  -0.168  -0.368  -0.361
136   T        -0.069  -0.316  -0.231  -0.014  -0.427  -0.348  -0.168  -0.500  -0.408
137   G         1.538   1.587   1.665   1.546   1.599   1.746   1.659   1.736   1.873
138   L         1.538   1.587   1.665   1.482   1.567   1.685   1.659   1.736   1.873
139   R        -0.872  -0.895  -0.808  -0.821  -0.884  -0.762  -0.899  -0.912  -0.796
140   Y         1.538   1.587   1.665   1.618   1.685   1.816   1.659   1.736   1.873
141   V        -0.637  -0.712  -0.743  -0.603  -0.747  -0.779  -0.625  -0.697  -0.723
142   Q         0.535   0.651   0.528   0.743   0.905   0.709   0.380   0.566   0.301
143   Y        -0.943  -0.854  -0.790  -0.923  -0.823  -0.733  -0.990  -0.885  -0.780
144   I        -0.236  -0.111  -0.238  -0.323  -0.199  -0.333  -0.442  -0.319  -0.427
145   K        -0.069  -0.233  -0.210  -0.238  -0.454  -0.406  -0.168  -0.405  -0.372
146   K         0.238   0.392   0.448  -0.042   0.299   0.315  -0.168   0.102   0.146
147   A        -1.345  -1.326  -1.233  -1.046  -1.017  -0.899  -1.173  -1.133  -1.003
148   G         0.877   0.851   0.636   0.966   0.923   0.593   0.928   0.888   0.503
149   I        -0.069  -0.233  -0.210   0.003  -0.259  -0.215  -0.168  -0.405  -0.372
150   A        -0.943  -0.947  -0.811  -0.824  -0.843  -0.654  -0.990  -0.964  -0.799
151   V         0.535   0.554   0.472   0.449   0.465   0.309   0.380   0.399   0.193
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   D        -0.236  -0.278  -0.244  -0.450  -0.538  -0.466  -0.442  -0.495  -0.432
155   K         0.535   0.438   0.521   0.271   0.137   0.241   0.380   0.189   0.289
156   I        -1.345  -1.262  -1.235  -1.199  -1.077  -1.077  -1.173  -1.088  -1.005
157   D        -1.053  -1.005  -0.848  -1.410  -1.354  -1.142  -1.082  -1.017  -0.837
158   D        -0.943  -0.947  -0.811  -1.077  -1.027  -0.867  -0.990  -0.964  -0.799
159   H        -1.053  -1.005  -0.848  -0.868  -0.865  -0.619  -1.082  -1.017  -0.837
160   L        -0.346  -0.449  -0.308  -0.355  -0.502  -0.322  -0.533  -0.681  -0.510
161   G         1.538   1.587   1.665   1.546   1.599   1.746   1.659   1.736   1.873
162   S         0.877   0.661   0.643   0.960   0.680   0.639   0.928   0.583   0.516
163   Y         1.538   1.587   1.665   1.618   1.685   1.816   1.659   1.736   1.873
164   A        -0.360  -0.597  -0.703  -0.041  -0.423  -0.594  -0.259  -0.554  -0.673
165   P         1.538   1.587   1.665   1.597   1.660   1.796   1.659   1.736   1.873
166   N         0.877   0.811   0.625   1.119   1.053   0.765   0.928   0.827   0.483
167   T         0.877   0.811   0.625   0.993   0.916   0.612   0.928   0.827   0.483
168   K        -1.345  -1.312  -1.220  -1.437  -1.331  -1.232  -1.173  -1.122  -0.994
169   T        -1.636  -1.413  -1.527  -1.687  -1.394  -1.520  -1.264  -1.063  -1.100
170   K         0.226   0.316   0.419  -0.127   0.100   0.208  -0.191  -0.042   0.090
171   P         1.538   1.587   1.665   1.598   1.658   1.796   1.659   1.736   1.873
172   F         0.145   0.096  -0.178   0.506   0.448   0.057   0.156   0.083  -0.323
173   Y         1.538   1.587   1.665   1.618   1.685   1.816   1.659   1.736   1.873
174   E        -0.929  -1.173  -1.184  -0.836  -1.194  -1.238  -0.716  -0.971  -0.956
175   V        -0.762  -0.641  -0.736  -0.945  -0.724  -0.818  -0.808  -0.623  -0.714
176   E        -0.943  -0.845  -0.812  -1.320  -1.141  -1.091  -0.990  -0.873  -0.802
177   L        -0.236  -0.129  -0.192  -0.205   0.030  -0.116  -0.442  -0.240  -0.346
178   P        -1.345  -1.372  -1.221  -1.297  -1.391  -1.181  -1.173  -1.171  -0.994
179   E        -0.360  -0.597  -0.703  -0.287  -0.611  -0.773  -0.259  -0.554  -0.673
180   S        -1.345  -1.364  -1.248  -1.298  -1.301  -1.214  -1.173  -1.157  -1.015
181   E         1.538   1.587   1.665   1.335   1.412   1.544   1.659   1.736   1.873
182   A         1.538   1.587   1.665   1.603   1.675   1.801   1.659   1.736   1.873
183   P         1.538   1.587   1.665   1.597   1.660   1.796   1.659   1.736   1.873
184   S         0.535   0.477   0.456   0.517   0.415   0.346   0.380   0.259   0.162
185   G         1.538   1.587   1.665   1.546   1.599   1.746   1.659   1.736   1.873
186   F         0.238   0.282   0.409   0.250   0.302   0.501  -0.168  -0.108   0.069
187   L         0.877   0.983   0.647   0.935   1.083   0.634   0.928   1.083   0.522
188   A         0.333   0.336   0.434   0.215   0.181   0.316   0.015  -0.003   0.120
189   R         1.538   1.587   1.665   1.684   1.752   1.879   1.659   1.736   1.873
190   G         1.538   1.587   1.665   1.546   1.599   1.746   1.659   1.736   1.873
191   N        -1.163  -1.174  -1.204  -0.917  -1.009  -1.006  -0.990  -1.004  -0.976
192   Y         1.538   1.587   1.665   1.618   1.685   1.816   1.659   1.736   1.873
193   S        -0.637  -0.809  -0.784  -0.549  -0.832  -0.810  -0.625  -0.821  -0.770
194   A         0.244   0.074  -0.113   0.559   0.356   0.101   0.289   0.039  -0.230
195   V        -1.163  -1.174  -1.204  -0.940  -0.952  -0.983  -0.990  -1.004  -0.976
196   S         0.244   0.233  -0.113   0.432   0.417  -0.067   0.289   0.272  -0.230
197   K         0.877   0.851   0.636   0.737   0.746   0.464   0.928   0.888   0.503
198   F         0.535   0.438   0.521   0.676   0.508   0.617   0.380   0.189   0.289
199   I         0.333   0.339   0.410   0.153   0.139   0.206   0.015   0.003   0.072
200   D         1.538   1.587   1.665   1.469   1.553   1.673   1.659   1.736   1.873
201   D         0.877   0.661   0.643   0.931   0.674   0.638   0.928   0.583   0.516
202   D         1.538   1.587   1.665   1.469   1.553   1.673   1.659   1.736   1.873
203   K        -0.236  -0.195  -0.243  -0.534  -0.478  -0.514  -0.442  -0.420  -0.432
204   T        -0.943  -0.933  -0.816  -0.962  -0.970  -0.838  -0.990  -0.953  -0.808
205   N        -0.346  -0.115  -0.240  -0.404  -0.088  -0.280  -0.533  -0.211  -0.417
206   H         1.538   1.587   1.665   1.748   1.819   1.941   1.659   1.736   1.873
207   L        -0.069  -0.233  -0.210   0.013  -0.212  -0.163  -0.168  -0.405  -0.372
208   T        -0.289  -0.137  -0.236  -0.519  -0.320  -0.427  -0.533  -0.315  -0.419
209   L        -0.943  -0.854  -0.795  -0.907  -0.759  -0.684  -0.990  -0.887  -0.782
210   N        -0.762  -0.737  -0.769  -0.651  -0.606  -0.711  -0.808  -0.723  -0.751
211   W         0.244   0.074  -0.113   0.743   0.515   0.240   0.289   0.039  -0.230
212   G        -0.762  -0.761  -0.780  -0.689  -0.698  -0.679  -0.808  -0.785  -0.770
213   V        -0.236  -0.249  -0.174  -0.225  -0.176  -0.106  -0.442  -0.399  -0.320
214   E        -0.637  -0.580  -0.781  -0.688  -0.647  -0.872  -0.625  -0.581  -0.769
215   I         0.877   0.811   0.625   0.980   0.915   0.624   0.928   0.827   0.483
216   V        -0.470  -0.378  -0.296  -0.609  -0.444  -0.352  -0.716  -0.583  -0.494
217   K         1.538   1.587   1.665   1.265   1.363   1.476   1.659   1.736   1.873
218   K        -0.646  -0.624  -0.776  -0.718  -0.704  -0.905  -0.606  -0.586  -0.757
219   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
220   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q12434
Output conservation file - output/Q12434
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
