1     M         1.930   1.937   1.997   2.303   2.315   2.420   2.119   2.130   2.222
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S         0.840   0.769   0.696   0.850   0.760   0.663   0.802   0.684   0.541
4     V        -0.141  -0.208  -0.267  -0.100  -0.218  -0.381  -0.186  -0.278  -0.356
5     K        -0.369  -0.398  -0.348  -0.840  -0.831  -0.752  -0.516  -0.545  -0.472
6     P        -0.369  -0.368  -0.344  -0.173  -0.175  -0.139  -0.516  -0.511  -0.467
7     I         0.463   0.451   0.501   0.463   0.436   0.510   0.143   0.118   0.184
8     D         1.930   1.937   1.997   2.175   2.184   2.292   2.119   2.130   2.222
9     N        -0.141  -0.105  -0.217  -0.114  -0.061  -0.257  -0.186  -0.137  -0.287
10    Y         0.840   0.900   0.732   1.299   1.378   1.162   0.802   0.900   0.605
11    I         1.930   1.937   1.997   2.081   2.097   2.197   2.119   2.130   2.222
12    T        -0.974  -0.994  -0.968  -0.649  -0.680  -0.623  -0.845  -0.866  -0.817
13    N        -0.974  -1.006  -0.981  -0.606  -0.641  -0.593  -0.845  -0.878  -0.831
14    S         1.930   1.937   1.997   1.827   1.845   1.941   2.119   2.130   2.222
15    V        -0.974  -1.006  -0.981  -0.788  -0.851  -0.822  -0.845  -0.878  -0.831
16    R        -0.974  -0.985  -0.971  -1.247  -1.270  -1.193  -0.845  -0.857  -0.820
17    L         0.840   0.769   0.696   1.058   0.954   0.848   0.802   0.684   0.541
18    F         0.463   0.499   0.526   0.565   0.613   0.663   0.143   0.208   0.232
19    E         1.930   1.937   1.997   2.146   2.149   2.263   2.119   2.130   2.222
20    V        -0.141  -0.082  -0.203   0.083   0.163  -0.026  -0.186  -0.105  -0.269
21    N        -0.141  -0.208  -0.267   0.124   0.039  -0.032  -0.186  -0.278  -0.356
22    P         0.840   0.857   0.730   1.129   1.149   0.972   0.802   0.830   0.601
23    S         0.840   0.769   0.696   0.847   0.756   0.657   0.802   0.684   0.541
24    Q        -0.369  -0.341  -0.341  -0.208  -0.187  -0.163  -0.516  -0.481  -0.464
25    T         0.840   0.882   0.725   0.871   0.934   0.681   0.802   0.871   0.592
26    L        -1.578  -1.566  -1.510  -1.688  -1.655  -1.600  -1.174  -1.161  -1.081
27    F        -0.369  -0.332  -0.341  -0.185  -0.147  -0.129  -0.516  -0.472  -0.464
28    S        -0.141  -0.097  -0.211  -0.076  -0.011  -0.167  -0.186  -0.125  -0.279
29    I        -0.141  -0.186  -0.239   0.198   0.126   0.064  -0.186  -0.249  -0.318
30    S        -0.369  -0.352  -0.344  -0.782  -0.743  -0.787  -0.516  -0.493  -0.467
31    Y         1.930   1.937   1.997   2.268   2.280   2.385   2.119   2.130   2.222
32    K        -0.974  -0.952  -0.951  -1.081  -1.075  -1.007  -0.845  -0.820  -0.799
33    P        -0.974  -0.994  -0.968  -0.539  -0.565  -0.532  -0.845  -0.866  -0.817
34    P        -0.974  -0.929  -0.954  -0.497  -0.438  -0.478  -0.845  -0.794  -0.803
35    T        -1.578  -1.566  -1.510  -1.380  -1.366  -1.289  -1.174  -1.161  -1.081
36    Q        -0.974  -0.971  -0.957  -1.081  -1.080  -1.008  -0.845  -0.842  -0.806
37    K        -0.141  -0.097  -0.211  -0.511  -0.455  -0.580  -0.186  -0.125  -0.279
38    T        -1.091  -1.083  -1.024  -0.850  -0.837  -0.756  -0.968  -0.957  -0.875
39    D        -0.336  -0.317  -0.316  -0.131  -0.115  -0.111  -0.454  -0.428  -0.423
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    T        -1.578  -1.566  -1.510  -1.337  -1.316  -1.247  -1.174  -1.161  -1.081
63    K        -0.974  -0.994  -0.968  -1.352  -1.366  -1.309  -0.845  -0.866  -0.817
64    V         0.840   0.769   0.696   1.047   0.942   0.835   0.802   0.684   0.541
65    S        -0.974  -0.958  -0.962  -0.810  -0.776  -0.795  -0.845  -0.828  -0.811
66    F         0.840   0.769   0.696   1.254   1.149   1.038   0.802   0.684   0.541
67    R         0.463   0.445   0.493   0.178   0.094   0.129   0.143   0.107   0.170
68    T         0.840   0.828   0.704   1.011   0.996   0.857   0.802   0.783   0.556
69    H        -0.974  -1.006  -0.981  -0.581  -0.630  -0.638  -0.845  -0.878  -0.831
70    N        -0.141  -0.208  -0.267   0.081  -0.009  -0.091  -0.186  -0.278  -0.356
71    S        -0.141  -0.082  -0.203   0.140   0.227   0.029  -0.186  -0.105  -0.269
72    H        -0.974  -1.006  -0.981  -0.617  -0.681  -0.682  -0.845  -0.878  -0.831
73    L        -0.369  -0.352  -0.344  -0.435  -0.426  -0.400  -0.516  -0.493  -0.467
74    S         0.463   0.499   0.526   0.386   0.465   0.478   0.143   0.208   0.232
75    L        -0.974  -0.994  -0.968  -1.027  -1.080  -1.073  -0.845  -0.866  -0.817
76    N        -0.369  -0.332  -0.341  -0.163  -0.093  -0.117  -0.516  -0.472  -0.464
77    Y        -0.141  -0.208  -0.267   0.361   0.261   0.168  -0.186  -0.278  -0.356
78    K         0.840   0.769   0.696   0.398   0.311   0.225   0.802   0.684   0.541
79    F        -0.141  -0.152  -0.232   0.361   0.332   0.224  -0.186  -0.204  -0.308
80    T        -0.974  -0.929  -0.954  -1.376  -1.331  -1.327  -0.845  -0.794  -0.803
81    T         0.840   0.769   0.696   0.934   0.834   0.728   0.802   0.684   0.541
82    N        -1.578  -1.566  -1.510  -1.547  -1.511  -1.458  -1.174  -1.161  -1.081
83    K        -0.974  -0.980  -0.957  -0.977  -0.982  -0.896  -0.845  -0.851  -0.806
84    S        -0.974  -0.994  -0.968  -0.916  -0.935  -0.903  -0.845  -0.866  -0.817
85    K         1.930   1.937   1.997   1.371   1.388   1.482   2.119   2.130   2.222
86    D        -0.141  -0.152  -0.232   0.268   0.238   0.144  -0.186  -0.204  -0.308
87    V         0.463   0.499   0.526   0.446   0.504   0.542   0.143   0.208   0.232
88    S         0.840   0.769   0.696   0.794   0.699   0.575   0.802   0.684   0.541
89    R         1.930   1.937   1.997   2.189   2.196   2.306   2.119   2.130   2.222
90    L        -0.141  -0.097  -0.211   0.133   0.191   0.028  -0.186  -0.125  -0.279
91    L         1.930   1.937   1.997   2.066   2.075   2.182   2.119   2.130   2.222
92    S        -0.141  -0.120  -0.225  -0.188  -0.152  -0.330  -0.186  -0.157  -0.299
93    A         0.840   0.828   0.704   1.118   1.100   0.945   0.802   0.783   0.556
94    L         0.463   0.468   0.509   0.459   0.461   0.522   0.143   0.149   0.199
95    G         1.930   1.937   1.997   2.146   2.160   2.263   2.119   2.130   2.222
96    P         1.930   1.937   1.997   2.139   2.148   2.255   2.119   2.130   2.222
97    R         0.840   0.857   0.730   1.145   1.163   0.972   0.802   0.830   0.601
98    G         1.930   1.937   1.997   2.146   2.160   2.263   2.119   2.130   2.222
99    V         1.930   1.937   1.997   2.059   2.069   2.175   2.119   2.130   2.222
100   S        -0.141  -0.186  -0.239  -0.119  -0.179  -0.262  -0.186  -0.249  -0.318
101   I        -0.974  -0.952  -0.951  -0.589  -0.569  -0.555  -0.845  -0.820  -0.799
102   T        -0.974  -0.952  -0.951  -0.862  -0.833  -0.837  -0.845  -0.820  -0.799
103   P         0.543   0.506   0.536   0.598   0.519   0.542   0.290   0.220   0.250
104   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   I         0.543   0.509   0.536   0.625   0.567   0.598   0.290   0.226   0.250
107   E        -0.464  -0.454  -0.397  -0.403  -0.388  -0.305  -0.625  -0.612  -0.530
108   K         1.930   1.937   1.997   1.352   1.370   1.462   2.119   2.130   2.222
109   I         0.419   0.430   0.490   0.371   0.383   0.477   0.061   0.078   0.164
110   A        -0.974  -1.006  -0.981  -0.794  -0.870  -0.834  -0.845  -0.878  -0.831
111   Q         0.840   0.900   0.732   0.411   0.492   0.291   0.802   0.900   0.605
112   S        -0.336  -0.269  -0.320  -0.828  -0.731  -0.793  -0.454  -0.361  -0.428
113   K         0.419   0.426   0.487  -0.007  -0.004   0.087   0.061   0.070   0.158
114   K        -1.091  -1.078  -1.024  -1.195  -1.126  -1.103  -0.968  -0.953  -0.875
115   -        -0.464  -0.458  -0.397  -0.333  -0.325  -0.235  -0.625  -0.616  -0.530
116   -        -0.464  -0.458  -0.397  -0.458  -0.452  -0.361  -0.625  -0.616  -0.530
117   -         0.543   0.538   0.561   0.368   0.349   0.342   0.290   0.279   0.296
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -         0.543   0.571   0.577   0.769   0.815   0.815   0.290   0.338   0.326
125   -        -0.464  -0.458  -0.397  -0.230  -0.227  -0.131  -0.625  -0.616  -0.530
126   K        -1.091  -1.078  -1.024  -1.239  -1.182  -1.148  -0.968  -0.953  -0.875
127   N        -0.336  -0.378  -0.349  -0.538  -0.606  -0.609  -0.454  -0.511  -0.467
128   N        -0.336  -0.329  -0.323  -0.448  -0.426  -0.432  -0.454  -0.446  -0.432
129   K        -0.974  -1.006  -0.981  -1.185  -1.206  -1.124  -0.845  -0.878  -0.831
130   I        -0.974  -1.006  -0.981  -0.583  -0.626  -0.590  -0.845  -0.878  -0.831
131   K        -0.974  -0.980  -0.957  -1.251  -1.245  -1.192  -0.845  -0.851  -0.806
132   E        -0.141  -0.152  -0.232  -0.486  -0.503  -0.572  -0.186  -0.204  -0.308
133   S        -0.369  -0.371  -0.340  -1.010  -0.995  -0.948  -0.516  -0.515  -0.462
134   S        -0.369  -0.344  -0.337  -0.881  -0.850  -0.804  -0.516  -0.486  -0.460
135   K        -0.974  -0.942  -0.941  -1.064  -0.991  -1.053  -0.845  -0.809  -0.789
136   K        -0.141  -0.208  -0.267  -0.500  -0.585  -0.625  -0.186  -0.278  -0.356
137   I        -1.091  -1.078  -1.024  -0.936  -0.937  -0.843  -0.968  -0.953  -0.875
138   K        -0.336  -0.329  -0.323  -0.434  -0.394  -0.456  -0.454  -0.446  -0.432
139   G        -1.091  -1.078  -1.024  -0.787  -0.781  -0.693  -0.968  -0.953  -0.875
140   K        -0.336  -0.378  -0.349  -0.786  -0.841  -0.770  -0.454  -0.511  -0.467
141   S        -0.464  -0.451  -0.397  -0.508  -0.480  -0.411  -0.625  -0.606  -0.530
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   I         0.543   0.496   0.536   0.585   0.501   0.556   0.290   0.201   0.250
147   Q         0.543   0.589   0.577   0.656   0.723   0.709   0.290   0.371   0.326
148   D        -0.974  -0.994  -0.968  -0.495  -0.525  -0.488  -0.845  -0.866  -0.817
149   I        -0.974  -0.971  -0.957  -0.755  -0.761  -0.728  -0.845  -0.842  -0.806
150   V        -1.578  -1.566  -1.510  -1.555  -1.591  -1.466  -1.174  -1.161  -1.081
151   G         1.930   1.937   1.997   2.146   2.160   2.263   2.119   2.130   2.222
152   L        -0.974  -0.980  -0.957  -0.514  -0.525  -0.480  -0.845  -0.851  -0.806
153   A        -0.141  -0.097  -0.211   0.111   0.168  -0.004  -0.186  -0.125  -0.279
154   T        -0.974  -0.994  -0.968  -1.193  -1.218  -1.240  -0.845  -0.866  -0.817
155   L        -0.141  -0.208  -0.267   0.076  -0.038  -0.138  -0.186  -0.278  -0.356
156   I        -0.369  -0.352  -0.344  -0.093  -0.060  -0.046  -0.516  -0.493  -0.467
157   V        -0.369  -0.341  -0.341  -0.432  -0.408  -0.388  -0.516  -0.481  -0.464
158   N         1.930   1.937   1.997   1.970   1.995   2.085   2.119   2.130   2.222
159   T        -0.974  -0.952  -0.951  -0.696  -0.681  -0.656  -0.845  -0.820  -0.799
160   D        -0.369  -0.398  -0.348  -0.635  -0.693  -0.608  -0.516  -0.545  -0.472
161   V        -0.974  -0.994  -0.968  -0.533  -0.558  -0.513  -0.845  -0.866  -0.817
162   E        -1.091  -1.078  -1.024  -1.146  -1.122  -1.054  -0.968  -0.953  -0.875
163   K        -0.336  -0.296  -0.306  -0.504  -0.417  -0.494  -0.454  -0.400  -0.409
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   S         1.930   1.937   1.997   1.742   1.747   1.855   2.119   2.130   2.222
171   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   A        -0.464  -0.454  -0.397  -0.347  -0.336  -0.249  -0.625  -0.611  -0.530
175   K        -0.464  -0.454  -0.397  -1.209  -1.190  -1.118  -0.625  -0.611  -0.530
176   K         1.930   1.937   1.997   1.363   1.378   1.474   2.119   2.130   2.222
177   T        -1.091  -1.082  -1.024  -1.259  -1.224  -1.168  -0.968  -0.956  -0.875
178   A        -1.091  -1.082  -1.024  -0.739  -0.723  -0.644  -0.968  -0.956  -0.875
179   T        -0.336  -0.318  -0.323  -0.603  -0.565  -0.626  -0.454  -0.428  -0.433
180   E        -0.336  -0.349  -0.334   0.029   0.000   0.030  -0.454  -0.471  -0.448
181   P         0.705   0.735   0.638   0.746   0.804   0.557   0.575   0.627   0.438
182   K        -0.141  -0.140  -0.227  -0.555  -0.554  -0.655  -0.186  -0.184  -0.302
183   Q        -0.974  -0.913  -0.954  -0.865  -0.770  -0.873  -0.845  -0.776  -0.803
184   K        -0.369  -0.352  -0.344  -0.740  -0.678  -0.668  -0.516  -0.493  -0.467
185   A        -1.091  -1.078  -1.024  -1.415  -1.407  -1.325  -0.968  -0.953  -0.875
186   N        -0.336  -0.378  -0.349  -0.267  -0.332  -0.286  -0.454  -0.511  -0.467
187   A         0.463   0.484   0.521   0.076   0.127   0.144   0.143   0.180   0.222
188   V        -0.141  -0.166  -0.237   0.160   0.113   0.026  -0.186  -0.223  -0.315
189   Q        -0.974  -0.985  -0.971  -0.675  -0.692  -0.636  -0.845  -0.857  -0.820
190   N        -0.141  -0.061  -0.219   0.056   0.175  -0.087  -0.186  -0.076  -0.291
191   -         0.705   0.713   0.655   0.883   0.892   0.794   0.575   0.589   0.469
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   N        -0.141  -0.186  -0.239  -0.235  -0.331  -0.469  -0.186  -0.249  -0.318
195   N        -0.369  -0.332  -0.341  -0.330  -0.276  -0.286  -0.516  -0.472  -0.464
196   G        -1.578  -1.566  -1.510  -1.307  -1.293  -1.216  -1.174  -1.161  -1.081
197   N         0.840   0.900   0.732   1.045   1.130   0.882   0.802   0.900   0.605
198   S        -0.974  -0.994  -0.968  -0.909  -0.921  -0.896  -0.845  -0.866  -0.817
199   A        -0.369  -0.398  -0.348  -0.294  -0.332  -0.254  -0.516  -0.545  -0.472
200   A        -1.578  -1.566  -1.510  -1.651  -1.702  -1.563  -1.174  -1.161  -1.081
201   S        -0.141  -0.186  -0.239  -0.340  -0.441  -0.555  -0.186  -0.249  -0.318
202   K        -0.141  -0.186  -0.239  -0.617  -0.673  -0.750  -0.186  -0.249  -0.318
203   K        -0.369  -0.371  -0.340  -0.728  -0.743  -0.704  -0.516  -0.515  -0.462
204   K         1.930   1.937   1.997   1.371   1.388   1.482   2.119   2.130   2.222
205   K        -0.369  -0.399  -0.343  -0.788  -0.807  -0.740  -0.516  -0.547  -0.466
206   N        -0.369  -0.334  -0.337  -0.728  -0.656  -0.676  -0.516  -0.475  -0.460
207   K         1.930   1.937   1.997   1.371   1.388   1.482   2.119   2.130   2.222
208   N         0.463   0.499   0.526  -0.213  -0.157  -0.119   0.143   0.208   0.232
209   K         1.930   1.937   1.997   1.371   1.388   1.482   2.119   2.130   2.222
210   G         0.463   0.484   0.521   0.465   0.510   0.547   0.143   0.180   0.222
211   K         1.930   1.937   1.997   1.352   1.370   1.462   2.119   2.130   2.222
212   K         1.930   1.937   1.997   1.352   1.370   1.462   2.119   2.130   2.222
213   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
214   K         0.840   0.769   0.696   0.398   0.311   0.225   0.802   0.684   0.541
215   R         0.463   0.499   0.526  -0.066  -0.034   0.031   0.143   0.208   0.232
* 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/P32342
Output conservation file - output/P32342
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
