1     M         1.784   1.801   1.846   1.959   1.990   2.059   1.965   1.986   2.056
2     R        -0.837  -0.741  -0.767  -0.773  -0.654  -0.658  -0.826  -0.724  -0.722
3     V        -1.292  -1.254  -1.203  -1.332  -1.287  -1.206  -1.041  -0.997  -0.923
4     F        -0.837  -0.871  -0.779  -1.025  -1.077  -0.937  -0.826  -0.847  -0.732
5     T        -0.665  -0.586  -0.678  -0.511  -0.400  -0.532  -0.612  -0.517  -0.616
6     L         0.074   0.112  -0.064   0.009   0.077  -0.208   0.033   0.082  -0.173
7     I        -0.842  -0.775  -0.764  -1.023  -0.922  -0.903  -0.818  -0.741  -0.713
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    A        -1.292  -1.177  -1.214  -1.217  -1.014  -1.105  -1.041  -0.922  -0.932
13    I        -0.837  -0.865  -0.779  -1.003  -1.033  -0.908  -0.826  -0.841  -0.732
14    L         0.074   0.096  -0.061   0.097   0.148  -0.077   0.033   0.059  -0.168
15    F        -0.837  -0.809  -0.759  -1.019  -0.978  -0.895  -0.826  -0.790  -0.715
16    S        -1.292  -1.311  -1.240  -1.323  -1.353  -1.267  -1.041  -1.049  -0.955
17    S        -0.665  -0.577  -0.679  -0.771  -0.621  -0.807  -0.612  -0.507  -0.617
18    S         0.418   0.457   0.524   0.049   0.135   0.243   0.033   0.101   0.194
19    L        -0.837  -0.796  -0.789  -1.051  -0.979  -0.947  -0.826  -0.773  -0.742
20    L        -1.292  -1.254  -1.203  -1.284  -1.246  -1.147  -1.041  -0.997  -0.923
21    T        -0.665  -0.586  -0.682  -0.556  -0.466  -0.576  -0.612  -0.518  -0.621
22    H        -0.381  -0.345  -0.264  -0.508  -0.486  -0.354  -0.612  -0.561  -0.454
23    A         1.784   1.801   1.846   1.770   1.793   1.875   1.965   1.986   2.056
24    F        -0.837  -0.735  -0.767  -0.922  -0.777  -0.815  -0.826  -0.719  -0.722
25    S        -0.209  -0.264  -0.230  -0.457  -0.536  -0.473  -0.397  -0.464  -0.413
26    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    V        -0.381  -0.347  -0.264  -0.717  -0.666  -0.528  -0.612  -0.563  -0.455
32    G        -0.837  -0.792  -0.787  -0.814  -0.755  -0.715  -0.826  -0.770  -0.741
33    I        -0.665  -0.777  -0.779  -0.582  -0.757  -0.767  -0.612  -0.737  -0.729
34    S         0.418   0.457   0.524   0.046   0.132   0.240   0.033   0.101   0.194
35    L         0.896   0.842   0.735   0.814   0.754   0.577   0.891   0.798   0.590
36    P        -0.665  -0.777  -0.779  -0.395  -0.606  -0.659  -0.612  -0.737  -0.729
37    A         0.074  -0.037  -0.109   0.239   0.089  -0.002   0.033  -0.124  -0.236
38    F        -0.209  -0.251  -0.228  -0.218  -0.279  -0.215  -0.397  -0.450  -0.411
39    T        -0.209  -0.077  -0.185  -0.434  -0.209  -0.379  -0.397  -0.212  -0.350
40    K         0.896   0.842   0.735   0.915   0.837   0.661   0.891   0.798   0.590
41    E        -0.209  -0.251  -0.228  -0.283  -0.346  -0.290  -0.397  -0.450  -0.411
42    C         1.784   1.801   1.846   2.060   2.088   2.157   1.965   1.986   2.056
43    L        -0.209  -0.264  -0.230  -0.394  -0.457  -0.383  -0.397  -0.464  -0.413
44    Y         0.074  -0.015  -0.106   0.337   0.208   0.048   0.033  -0.093  -0.232
45    Y        -0.837  -0.801  -0.789  -0.741  -0.722  -0.670  -0.826  -0.779  -0.743
46    D         0.074  -0.015  -0.106   0.290   0.161   0.010   0.033  -0.093  -0.232
47    L        -1.292  -1.316  -1.244  -1.347  -1.396  -1.265  -1.041  -1.053  -0.959
48    S        -1.747  -1.703  -1.612  -1.594  -1.535  -1.400  -1.256  -1.208  -1.099
49    S        -1.292  -1.316  -1.244  -1.151  -1.157  -1.040  -1.041  -1.053  -0.959
50    D        -0.665  -0.588  -0.687  -0.609  -0.502  -0.660  -0.612  -0.521  -0.627
51    K        -1.292  -1.177  -1.214  -1.124  -0.928  -1.023  -1.041  -0.922  -0.932
52    D        -0.209  -0.258  -0.230  -0.221  -0.311  -0.256  -0.397  -0.458  -0.413
53    V        -0.665  -0.469  -0.706  -0.626  -0.334  -0.710  -0.612  -0.371  -0.648
54    L        -0.209  -0.264  -0.230  -0.444  -0.508  -0.455  -0.397  -0.464  -0.413
55    V        -0.837  -0.865  -0.777  -0.928  -0.940  -0.807  -0.826  -0.841  -0.730
56    V         0.418   0.457   0.524   0.108   0.176   0.293   0.033   0.101   0.194
57    S        -0.837  -0.798  -0.787  -0.758  -0.687  -0.700  -0.826  -0.777  -0.741
58    Y         0.896   0.857   0.737   1.110   1.058   0.866   0.891   0.823   0.593
59    Q         0.418   0.457   0.524   0.249   0.294   0.411   0.033   0.101   0.194
60    V         1.784   1.801   1.846   1.726   1.751   1.832   1.965   1.986   2.056
61    L         0.418   0.457   0.524   0.163   0.262   0.366   0.033   0.101   0.194
62    T        -0.209  -0.258  -0.230  -0.398  -0.495  -0.447  -0.397  -0.458  -0.413
63    G         1.784   1.801   1.846   1.883   1.914   1.985   1.965   1.986   2.056
64    G         1.784   1.801   1.846   1.883   1.914   1.985   1.965   1.986   2.056
65    N         0.418   0.457   0.524   0.153   0.209   0.309   0.033   0.101   0.194
66    F         1.784   1.801   1.846   1.770   1.791   1.875   1.965   1.986   2.056
67    E         0.418   0.457   0.524   0.201   0.288   0.392   0.033   0.101   0.194
68    I         0.896   0.830   0.730   0.925   0.841   0.674   0.891   0.777   0.581
69    D         0.896   0.842   0.735   1.079   1.013   0.852   0.891   0.798   0.590
70    F        -0.837  -0.797  -0.788  -0.839  -0.758  -0.771  -0.826  -0.774  -0.742
71    D        -1.292  -1.260  -1.206  -1.060  -1.020  -0.926  -1.041  -1.004  -0.926
72    I         0.529   0.498   0.540   0.329   0.267   0.320   0.247   0.179   0.225
73    T        -0.209  -0.170  -0.197  -0.341  -0.310  -0.325  -0.397  -0.360  -0.371
74    A        -0.837  -0.809  -0.759  -0.874  -0.833  -0.761  -0.826  -0.790  -0.715
75    P         1.784   1.801   1.846   2.031   2.061   2.129   1.965   1.986   2.056
76    D         0.529   0.489   0.535   0.406   0.315   0.363   0.247   0.162   0.215
77    G         0.896   0.830   0.730   1.083   0.999   0.851   0.891   0.777   0.581
78    S        -1.292  -1.316  -1.244  -1.203  -1.222  -1.099  -1.041  -1.053  -0.959
79    V         0.798   0.703   0.663   0.797   0.648   0.576   0.728   0.557   0.458
80    I         0.074   0.085  -0.066   0.092   0.115  -0.149   0.033   0.043  -0.175
81    V        -1.292  -1.248  -1.203  -1.259  -1.191  -1.134  -1.041  -0.992  -0.923
82    T        -1.747  -1.703  -1.612  -1.672  -1.581  -1.475  -1.256  -1.208  -1.099
83    E        -0.209  -0.258  -0.230  -0.270  -0.331  -0.271  -0.397  -0.458  -0.413
84    R         0.074   0.119  -0.053   0.203   0.256   0.029   0.033   0.092  -0.157
85    Q        -0.837  -0.797  -0.788  -0.811  -0.778  -0.748  -0.826  -0.774  -0.742
86    K        -0.665  -0.777  -0.779  -0.588  -0.775  -0.778  -0.612  -0.737  -0.729
87    K         0.529   0.494   0.538   0.412   0.342   0.417   0.247   0.171   0.221
88    H        -0.837  -0.792  -0.787  -0.547  -0.495  -0.454  -0.826  -0.770  -0.741
89    S        -0.837  -0.871  -0.776  -0.883  -0.907  -0.758  -0.826  -0.847  -0.729
90    D         0.896   0.842   0.735   1.049   0.978   0.801   0.891   0.798   0.590
91    F         0.074  -0.037  -0.109   0.172   0.001  -0.106   0.033  -0.124  -0.236
92    L        -0.209  -0.264  -0.230  -0.470  -0.549  -0.487  -0.397  -0.464  -0.413
93    L        -0.209  -0.258  -0.230  -0.387  -0.442  -0.374  -0.397  -0.458  -0.413
94    K         0.418   0.457   0.524   0.150   0.217   0.332   0.033   0.101   0.194
95    S         0.074  -0.025  -0.110   0.017  -0.121  -0.269   0.033  -0.107  -0.239
96    F        -0.665  -0.777  -0.779  -0.589  -0.778  -0.783  -0.612  -0.737  -0.729
97    G        -0.209  -0.264  -0.230  -0.172  -0.265  -0.212  -0.397  -0.464  -0.413
98    I        -0.665  -0.696  -0.716  -0.601  -0.647  -0.694  -0.612  -0.647  -0.660
99    G         1.784   1.801   1.846   1.883   1.914   1.985   1.965   1.986   2.056
100   K        -0.837  -0.785  -0.783  -0.798  -0.741  -0.720  -0.826  -0.763  -0.737
101   Y         1.784   1.801   1.846   1.938   1.969   2.039   1.965   1.986   2.056
102   T        -0.837  -0.734  -0.766  -0.980  -0.835  -0.873  -0.826  -0.717  -0.722
103   F         1.784   1.801   1.846   1.770   1.791   1.875   1.965   1.986   2.056
104   C         1.784   1.801   1.846   2.060   2.088   2.157   1.965   1.986   2.056
105   L         0.896   1.001   0.761   0.919   1.063   0.711   0.891   1.054   0.637
106   S        -0.837  -0.801  -0.789  -0.859  -0.765  -0.757  -0.826  -0.779  -0.743
107   N         1.784   1.801   1.846   1.909   1.944   2.010   1.965   1.986   2.056
108   N        -1.292  -1.177  -1.214  -1.034  -0.838  -0.952  -1.041  -0.922  -0.932
109   Y        -0.209  -0.080  -0.181  -0.013   0.182   0.056  -0.397  -0.214  -0.343
110   G         0.418   0.457   0.524   0.134   0.189   0.293   0.033   0.101   0.194
111   T         1.784   1.801   1.846   1.788   1.812   1.892   1.965   1.986   2.056
112   S        -0.209  -0.077  -0.185  -0.376  -0.163  -0.340  -0.397  -0.212  -0.350
113   P        -1.292  -1.311  -1.240  -1.200  -1.227  -1.093  -1.041  -1.049  -0.955
114   K        -0.209  -0.264  -0.230  -0.330  -0.420  -0.350  -0.397  -0.464  -0.413
115   K         1.784   1.801   1.846   1.766   1.790   1.871   1.965   1.986   2.056
116   V        -0.665  -0.777  -0.779  -0.652  -0.841  -0.848  -0.612  -0.737  -0.729
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   E         1.784   1.801   1.846   1.739   1.765   1.845   1.965   1.986   2.056
121   I         0.529   0.555   0.547   0.294   0.351   0.291   0.247   0.287   0.238
122   T         0.074  -0.015  -0.106   0.157   0.014  -0.136   0.033  -0.093  -0.232
123   L        -0.209  -0.231  -0.197  -0.345  -0.361  -0.304  -0.397  -0.419  -0.372
124   E         1.784   1.801   1.846   1.739   1.765   1.845   1.965   1.986   2.056
125   K        -1.292  -1.314  -1.245  -1.098  -1.094  -1.015  -1.041  -1.052  -0.960
126   E         1.784   1.801   1.846   1.739   1.765   1.845   1.965   1.986   2.056
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   K        -0.837  -0.790  -0.785  -0.964  -0.902  -0.871  -0.826  -0.767  -0.738
129   E        -0.665  -0.588  -0.687  -0.500  -0.400  -0.564  -0.612  -0.521  -0.627
130   I        -1.747  -1.703  -1.612  -1.839  -1.772  -1.638  -1.256  -1.208  -1.099
131   V        -1.747  -1.703  -1.612  -1.493  -1.423  -1.301  -1.256  -1.208  -1.099
132   S        -1.292  -1.253  -1.204  -1.374  -1.304  -1.242  -1.041  -0.996  -0.923
133   S        -0.837  -0.803  -0.789  -0.818  -0.731  -0.729  -0.826  -0.781  -0.743
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -0.265  -0.208  -0.203  -0.244  -0.152  -0.159  -0.451  -0.369  -0.370
137   -        -0.842  -0.820  -0.764  -0.721  -0.690  -0.596  -0.818  -0.786  -0.713
138   H        -1.292  -1.254  -1.206  -1.144  -1.126  -1.017  -1.041  -0.998  -0.925
139   E        -0.665  -0.686  -0.718  -0.683  -0.736  -0.795  -0.612  -0.636  -0.662
140   S        -1.292  -1.314  -1.245  -1.105  -1.105  -0.988  -1.041  -1.052  -0.960
141   K        -0.837  -0.810  -0.760  -0.701  -0.656  -0.586  -0.826  -0.792  -0.716
142   E         0.074  -0.025  -0.110   0.146  -0.005  -0.129   0.033  -0.107  -0.239
143   D        -0.665  -0.777  -0.779  -0.417  -0.589  -0.601  -0.612  -0.737  -0.729
144   I        -1.292  -1.253  -1.204  -1.291  -1.231  -1.169  -1.041  -0.996  -0.923
145   I        -0.209  -0.251  -0.228  -0.419  -0.495  -0.462  -0.397  -0.450  -0.411
146   A        -1.292  -1.314  -1.245  -1.232  -1.264  -1.170  -1.041  -1.052  -0.960
147   N        -0.209  -0.264  -0.230  -0.199  -0.295  -0.239  -0.397  -0.464  -0.413
148   N        -0.665  -0.686  -0.718  -0.443  -0.499  -0.549  -0.612  -0.636  -0.662
149   A        -0.209  -0.264  -0.230  -0.407  -0.509  -0.450  -0.397  -0.464  -0.413
150   I        -0.209  -0.264  -0.230  -0.430  -0.520  -0.480  -0.397  -0.464  -0.413
151   E        -0.665  -0.777  -0.779  -0.636  -0.817  -0.832  -0.612  -0.737  -0.729
152   E         0.529   0.498   0.540   0.327   0.258   0.324   0.247   0.179   0.225
153   I         1.784   1.801   1.846   1.761   1.799   1.866   1.965   1.986   2.056
154   D         0.418   0.457   0.524   0.134   0.190   0.293   0.033   0.101   0.194
155   R        -0.665  -0.777  -0.779  -0.356  -0.524  -0.522  -0.612  -0.737  -0.729
156   N        -0.665  -0.777  -0.779  -0.441  -0.629  -0.652  -0.612  -0.737  -0.729
157   L         0.896   0.842   0.735   0.814   0.754   0.577   0.891   0.798   0.590
158   N        -0.209  -0.258  -0.230  -0.259  -0.350  -0.313  -0.397  -0.458  -0.413
159   K        -0.665  -0.777  -0.779  -0.661  -0.863  -0.886  -0.612  -0.737  -0.729
160   I         0.074   0.108  -0.057   0.168   0.216  -0.024   0.033   0.078  -0.163
161   T        -0.665  -0.693  -0.719  -0.559  -0.618  -0.654  -0.612  -0.644  -0.663
162   K        -0.209  -0.258  -0.230  -0.307  -0.387  -0.342  -0.397  -0.458  -0.413
163   T        -1.747  -1.703  -1.612  -1.554  -1.503  -1.360  -1.256  -1.208  -1.099
164   M         0.529   0.494   0.538   0.597   0.524   0.586   0.247   0.171   0.221
165   D        -0.837  -0.860  -0.776  -0.703  -0.731  -0.610  -0.826  -0.836  -0.729
166   Y         1.784   1.801   1.846   1.938   1.969   2.039   1.965   1.986   2.056
167   L         0.529   0.494   0.538   0.247   0.186   0.249   0.247   0.171   0.221
168   R         0.529   0.489   0.535   0.471   0.375   0.442   0.247   0.162   0.215
169   A        -0.209  -0.258  -0.230  -0.343  -0.435  -0.380  -0.397  -0.458  -0.413
170   R         1.784   1.801   1.846   1.896   1.919   1.997   1.965   1.986   2.056
171   E         1.784   1.801   1.846   1.739   1.765   1.845   1.965   1.986   2.056
172   W        -0.665  -0.777  -0.779  -0.196  -0.371  -0.405  -0.612  -0.737  -0.729
173   R         1.784   1.801   1.846   1.896   1.919   1.997   1.965   1.986   2.056
174   N         1.784   1.801   1.846   1.909   1.944   2.010   1.965   1.986   2.056
175   M        -0.665  -0.777  -0.779  -0.389  -0.576  -0.606  -0.612  -0.737  -0.729
176   Y         0.074   0.106  -0.057   0.061   0.104  -0.119   0.033   0.073  -0.162
177   T         1.784   1.801   1.846   1.788   1.812   1.892   1.965   1.986   2.056
178   V         1.784   1.801   1.846   1.726   1.751   1.832   1.965   1.986   2.056
179   S        -1.292  -1.253  -1.204  -1.230  -1.181  -1.101  -1.041  -0.996  -0.923
180   S         1.784   1.801   1.846   1.646   1.683   1.754   1.965   1.986   2.056
181   T         1.784   1.801   1.846   1.788   1.812   1.892   1.965   1.986   2.056
182   E         0.896   0.830   0.730   0.942   0.853   0.718   0.891   0.777   0.581
183   S         0.074  -0.025  -0.110   0.017  -0.127  -0.269   0.033  -0.107  -0.239
184   R         1.784   1.801   1.846   1.896   1.919   1.997   1.965   1.986   2.056
185   L         0.529   0.624   0.619   0.294   0.484   0.442   0.247   0.416   0.377
186   T        -0.837  -0.871  -0.779  -0.876  -0.924  -0.773  -0.826  -0.847  -0.732
187   W         0.896   0.857   0.737   1.288   1.243   1.053   0.891   0.823   0.593
188   L         0.418   0.457   0.524   0.052   0.139   0.246   0.033   0.101   0.194
189   S         1.784   1.801   1.846   1.646   1.683   1.754   1.965   1.986   2.056
190   L         0.074   0.099  -0.065   0.009   0.054  -0.209   0.033   0.063  -0.174
191   L         0.074  -0.025  -0.110   0.020  -0.115  -0.267   0.033  -0.107  -0.239
192   I        -0.837  -0.788  -0.785  -0.886  -0.812  -0.789  -0.826  -0.765  -0.739
193   M        -0.209  -0.264  -0.230  -0.218  -0.324  -0.299  -0.397  -0.464  -0.413
194   G        -0.665  -0.777  -0.779  -0.560  -0.758  -0.811  -0.612  -0.737  -0.729
195   V        -0.837  -0.801  -0.789  -0.968  -0.896  -0.868  -0.826  -0.779  -0.743
196   M         0.529   0.494   0.538   0.512   0.428   0.479   0.247   0.171   0.221
197   V         0.074   0.112  -0.064   0.095   0.144  -0.122   0.033   0.082  -0.173
198   G        -0.209  -0.132  -0.175  -0.311  -0.198  -0.260  -0.397  -0.300  -0.343
199   I         0.074  -0.025  -0.110   0.150   0.014  -0.136   0.033  -0.107  -0.239
200   S         0.896   0.857   0.737   0.842   0.803   0.630   0.891   0.823   0.593
201   I        -0.837  -0.734  -0.767  -0.945  -0.806  -0.835  -0.826  -0.718  -0.723
202   V         0.074   0.106  -0.057   0.086   0.153  -0.086   0.033   0.073  -0.162
203   Q         1.784   1.801   1.846   1.917   1.937   2.018   1.965   1.986   2.056
204   A         0.418   0.457   0.524   0.108   0.169   0.285   0.033   0.101   0.194
205   L        -0.381  -0.347  -0.264  -0.678  -0.612  -0.479  -0.612  -0.563  -0.455
206   I         0.074   0.228  -0.036   0.092   0.331  -0.096   0.033   0.249  -0.132
207   I         0.529   0.624   0.619   0.313   0.478   0.460   0.247   0.416   0.377
208   Q        -0.665  -0.684  -0.721  -0.355  -0.414  -0.444  -0.612  -0.633  -0.665
209   F         0.074  -0.037  -0.109   0.134  -0.046  -0.165   0.033  -0.124  -0.236
210   F         0.074   0.228  -0.036   0.159   0.372  -0.008   0.033   0.249  -0.132
211   F         1.784   1.801   1.846   1.770   1.791   1.875   1.965   1.986   2.056
212   T        -1.292  -1.250  -1.202  -1.200  -1.132  -1.069  -1.041  -0.993  -0.921
213   S        -0.837  -0.801  -0.789  -0.839  -0.757  -0.729  -0.826  -0.779  -0.743
214   R        -0.209  -0.251  -0.228  -0.302  -0.401  -0.368  -0.397  -0.450  -0.411
215   Q        -0.209  -0.264  -0.230  -0.117  -0.211  -0.147  -0.397  -0.464  -0.413
216   K         0.529   0.542   0.541   0.412   0.424   0.423   0.247   0.263   0.227
217   N        -0.665  -0.777  -0.779  -0.370  -0.537  -0.549  -0.612  -0.737  -0.729
218   Y        -0.665  -0.696  -0.716  -0.458  -0.516  -0.577  -0.612  -0.647  -0.660
219   V         1.784   1.801   1.846   1.726   1.751   1.832   1.965   1.986   2.056
* 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/Q12450
Output conservation file - output/Q12450
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
