1     M         1.295   1.309   1.379   1.492   1.509   1.609   1.393   1.413   1.515
2     S        -0.534  -0.600  -0.762  -0.285  -0.385  -0.666  -0.499  -0.584  -0.763
3     N        -1.758  -1.720  -1.544  -1.802  -1.748  -1.502  -1.410  -1.372  -1.164
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -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     N        -1.364  -1.359  -1.220  -1.160  -1.146  -0.959  -1.223  -1.214  -1.034
10    E        -0.881  -0.941  -0.853  -0.948  -1.015  -0.895  -0.941  -0.991  -0.866
11    I         0.337   0.329   0.308   0.291   0.279   0.206   0.132   0.111   0.025
12    V        -0.844  -0.905  -0.823  -0.895  -0.980  -0.864  -0.919  -0.967  -0.838
13    F         1.295   1.309   1.379   1.316   1.339   1.443   1.393   1.413   1.515
14    V         0.653   0.645   0.431   0.751   0.743   0.428   0.658   0.642   0.254
15    T         1.295   1.309   1.379   1.303   1.329   1.431   1.393   1.413   1.515
16    G         1.295   1.309   1.379   1.190   1.204   1.323   1.393   1.413   1.515
17    N         1.295   1.309   1.379   1.332   1.353   1.458   1.393   1.413   1.515
18    A         0.653   0.533   0.408   0.611   0.447   0.231   0.658   0.465   0.212
19    N         0.042  -0.082  -0.267   0.231   0.071  -0.226   0.027  -0.150  -0.423
20    K         1.295   1.309   1.379   1.170   1.193   1.305   1.393   1.413   1.515
21    L         1.295   1.309   1.379   1.176   1.194   1.311   1.393   1.413   1.515
22    K        -0.772  -0.864  -0.820  -0.822  -0.961  -0.892  -0.814  -0.911  -0.834
23    E         0.653   0.533   0.408   0.661   0.506   0.319   0.658   0.465   0.212
24    V         0.653   0.649   0.428   0.751   0.748   0.423   0.658   0.649   0.249
25    Q        -1.363  -1.331  -1.225  -1.328  -1.293  -1.131  -1.235  -1.196  -1.040
26    S        -1.251  -1.291  -1.211  -1.090  -1.141  -0.993  -1.130  -1.158  -1.028
27    I         0.653   0.695   0.437   0.727   0.788   0.390   0.658   0.719   0.264
28    L         1.295   1.309   1.379   1.176   1.194   1.311   1.393   1.413   1.515
29    T        -1.251  -1.215  -1.184  -1.353  -1.329  -1.252  -1.130  -1.098  -1.006
30    Q        -1.953  -1.894  -1.780  -1.681  -1.602  -1.475  -1.445  -1.396  -1.231
31    E        -1.658  -1.684  -1.533  -1.521  -1.542  -1.341  -1.340  -1.347  -1.156
32    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    N        -0.975  -0.945  -0.874  -1.112  -1.067  -1.004  -1.029  -0.992  -0.887
49    K        -0.324  -0.309  -0.364  -0.469  -0.448  -0.571  -0.491  -0.471  -0.560
50    T        -1.364  -1.365  -1.239  -1.434  -1.445  -1.237  -1.223  -1.218  -1.051
51    I        -0.365  -0.308  -0.343  -0.434  -0.368  -0.368  -0.604  -0.545  -0.543
52    H        -1.251  -1.216  -1.193  -1.122  -1.102  -1.013  -1.130  -1.101  -1.013
53    L        -0.365  -0.365  -0.354  -0.578  -0.574  -0.530  -0.604  -0.600  -0.555
54    I        -1.251  -1.246  -1.200  -1.286  -1.297  -1.239  -1.130  -1.123  -1.019
55    N         0.653   0.649   0.428   0.780   0.779   0.465   0.658   0.649   0.249
56    E        -0.956  -0.912  -0.859  -0.953  -0.885  -0.799  -1.025  -0.984  -0.875
57    A        -1.363  -1.383  -1.224  -1.346  -1.377  -1.167  -1.235  -1.238  -1.039
58    L         0.042   0.009  -0.255   0.089   0.042  -0.312   0.027  -0.032  -0.405
59    D         1.295   1.309   1.379   1.354   1.376   1.479   1.393   1.413   1.515
60    L         1.295   1.309   1.379   1.176   1.194   1.311   1.393   1.413   1.515
61    E        -0.844  -0.905  -0.823  -0.909  -0.987  -0.868  -0.919  -0.967  -0.838
62    E         1.295   1.309   1.379   1.216   1.234   1.348   1.393   1.413   1.515
63    L        -0.844  -0.785  -0.821  -0.966  -0.881  -0.898  -0.919  -0.858  -0.836
64    Q         1.295   1.309   1.379   1.439   1.461   1.559   1.393   1.413   1.515
65    D         0.337   0.382   0.340   0.192   0.256   0.181   0.132   0.207   0.084
66    T        -0.534  -0.600  -0.762  -0.361  -0.451  -0.733  -0.499  -0.584  -0.763
67    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    L        -0.365  -0.420  -0.354  -0.578  -0.639  -0.532  -0.604  -0.651  -0.555
69    N        -0.772  -0.770  -0.817  -0.841  -0.865  -0.901  -0.814  -0.822  -0.831
70    A        -0.239  -0.127  -0.287  -0.338  -0.188  -0.397  -0.394  -0.246  -0.455
71    I         0.168   0.200   0.275  -0.009   0.047   0.143  -0.184  -0.130  -0.040
72    A        -0.844  -0.905  -0.840  -0.938  -1.009  -0.893  -0.919  -0.968  -0.854
73    L         0.168   0.221   0.279  -0.130  -0.040   0.040  -0.184  -0.090  -0.032
74    A        -1.546  -1.510  -1.495  -1.403  -1.385  -1.327  -1.235  -1.202  -1.127
75    K         1.295   1.309   1.379   1.170   1.193   1.305   1.393   1.413   1.515
76    G        -0.844  -0.801  -0.809  -0.846  -0.759  -0.795  -0.919  -0.868  -0.824
77    K        -0.239  -0.200  -0.310  -0.276  -0.210  -0.340  -0.394  -0.329  -0.491
78    Q        -0.365  -0.355  -0.350  -0.443  -0.424  -0.369  -0.604  -0.583  -0.547
79    A         1.295   1.309   1.379   1.193   1.213   1.326   1.393   1.413   1.515
80    V         0.168   0.200   0.275  -0.112  -0.061   0.050  -0.184  -0.130  -0.040
81    A        -1.546  -1.555  -1.489  -1.459  -1.488  -1.381  -1.235  -1.240  -1.123
82    A        -1.251  -1.173  -1.188  -1.307  -1.187  -1.239  -1.130  -1.051  -1.007
83    L        -0.239  -0.225  -0.329  -0.356  -0.373  -0.493  -0.394  -0.410  -0.519
84    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    G        -1.251  -1.223  -1.209  -1.299  -1.276  -1.203  -1.130  -1.104  -1.027
87    K        -0.772  -0.729  -0.809  -0.859  -0.803  -0.896  -0.814  -0.763  -0.822
88    P         1.295   1.309   1.379   1.408   1.422   1.529   1.393   1.413   1.515
89    V         1.295   1.309   1.379   1.313   1.332   1.440   1.393   1.413   1.515
90    F         0.168   0.200   0.275  -0.125  -0.074   0.039  -0.184  -0.130  -0.040
91    V         1.295   1.309   1.379   1.313   1.332   1.440   1.393   1.413   1.515
92    E         1.295   1.309   1.379   1.216   1.234   1.348   1.393   1.413   1.515
93    D         1.295   1.309   1.379   1.354   1.376   1.479   1.393   1.413   1.515
94    T         1.295   1.309   1.379   1.303   1.329   1.431   1.393   1.413   1.515
95    A        -0.365  -0.421  -0.355  -0.376  -0.432  -0.304  -0.604  -0.652  -0.555
96    L         1.295   1.309   1.379   1.176   1.194   1.311   1.393   1.413   1.515
97    R        -1.067  -1.025  -1.163  -0.866  -0.814  -0.964  -0.919  -0.870  -0.982
98    F         0.653   0.533   0.408   0.777   0.632   0.447   0.658   0.465   0.212
99    D        -1.251  -1.263  -1.213  -1.222  -1.256  -1.231  -1.130  -1.134  -1.030
100   E         0.168   0.200   0.275  -0.165  -0.112  -0.005  -0.184  -0.130  -0.040
101   F        -0.239  -0.348  -0.339  -0.238  -0.390  -0.400  -0.394  -0.536  -0.530
102   N         0.337   0.329   0.308   0.271   0.252   0.159   0.132   0.111   0.025
103   G         0.042   0.197  -0.230   0.087   0.276  -0.294   0.027   0.237  -0.370
104   L         1.295   1.309   1.379   1.176   1.194   1.311   1.393   1.413   1.515
105   P         1.295   1.309   1.379   1.408   1.422   1.529   1.393   1.413   1.515
106   G         1.295   1.309   1.379   1.190   1.204   1.323   1.393   1.413   1.515
107   A        -0.365  -0.352  -0.352  -0.456  -0.431  -0.421  -0.604  -0.579  -0.550
108   Y         1.295   1.309   1.379   1.461   1.478   1.579   1.393   1.413   1.515
109   I         0.653   0.533   0.408   0.746   0.595   0.385   0.658   0.465   0.212
110   K         1.295   1.309   1.379   1.170   1.193   1.305   1.393   1.413   1.515
111   W         1.295   1.309   1.379   1.532   1.549   1.646   1.393   1.413   1.515
112   F         1.295   1.309   1.379   1.316   1.339   1.443   1.393   1.413   1.515
113   L        -0.772  -0.708  -0.786  -0.804  -0.698  -0.790  -0.814  -0.722  -0.793
114   K        -0.772  -0.759  -0.813  -0.802  -0.805  -0.825  -0.814  -0.818  -0.826
115   S         1.295   1.309   1.379   1.376   1.398   1.500   1.393   1.413   1.515
116   M        -0.956  -0.980  -0.861  -0.942  -0.979  -0.838  -1.025  -1.036  -0.875
117   G         0.653   0.695   0.437   0.638   0.686   0.349   0.658   0.719   0.264
118   L        -0.239  -0.348  -0.339  -0.259  -0.406  -0.364  -0.394  -0.536  -0.530
119   E        -1.067  -1.031  -1.165  -0.960  -0.921  -1.127  -0.919  -0.887  -0.983
120   K         0.168   0.200   0.275  -0.193  -0.140  -0.034  -0.184  -0.130  -0.040
121   I        -0.239  -0.193  -0.315  -0.357  -0.287  -0.469  -0.394  -0.325  -0.495
122   V        -0.239  -0.348  -0.339  -0.190  -0.338  -0.335  -0.394  -0.536  -0.530
123   K        -0.534  -0.590  -0.761  -0.433  -0.503  -0.731  -0.499  -0.575  -0.762
124   M         0.337   0.354   0.304   0.428   0.449   0.289   0.132   0.156   0.017
125   L         0.653   0.533   0.408   0.616   0.457   0.268   0.658   0.465   0.212
126   E        -1.658  -1.617  -1.525  -1.593  -1.543  -1.369  -1.340  -1.303  -1.151
127   P        -1.363  -1.304  -1.221  -1.455  -1.386  -1.258  -1.235  -1.179  -1.037
128   F         0.337   0.354   0.304   0.349   0.375   0.279   0.132   0.156   0.017
129   E         0.042  -0.041  -0.255   0.121   0.005  -0.295   0.027  -0.096  -0.406
130   N        -0.365  -0.434  -0.353  -0.423  -0.507  -0.393  -0.604  -0.674  -0.554
131   K         1.295   1.309   1.379   1.170   1.193   1.305   1.393   1.413   1.515
132   N        -0.844  -0.881  -0.820  -0.921  -0.978  -0.878  -0.919  -0.948  -0.835
133   A         1.295   1.309   1.379   1.193   1.213   1.326   1.393   1.413   1.515
134   E        -1.658  -1.656  -1.526  -1.595  -1.570  -1.367  -1.340  -1.329  -1.152
135   A         1.295   1.309   1.379   1.193   1.213   1.326   1.393   1.413   1.515
136   V        -0.772  -0.857  -0.816  -0.703  -0.832  -0.770  -0.814  -0.903  -0.830
137   T         0.168   0.200   0.275   0.181   0.239   0.315  -0.184  -0.130  -0.040
138   T         1.295   1.309   1.379   1.303   1.329   1.431   1.393   1.413   1.515
139   I         0.168   0.200   0.275  -0.006   0.053   0.145  -0.184  -0.130  -0.040
140   C        -0.365  -0.328  -0.348  -0.591  -0.549  -0.505  -0.604  -0.558  -0.549
141   F         0.653   0.693   0.433   0.900   0.949   0.569   0.658   0.716   0.258
142   A        -0.772  -0.850  -0.812  -0.564  -0.683  -0.669  -0.814  -0.893  -0.822
143   D        -1.251  -1.291  -1.218  -1.296  -1.363  -1.317  -1.130  -1.152  -1.033
144   S        -0.239  -0.185  -0.319  -0.336  -0.264  -0.465  -0.394  -0.320  -0.500
145   R        -0.534  -0.470  -0.759  -0.237  -0.156  -0.603  -0.499  -0.418  -0.759
146   G        -0.239  -0.136  -0.308  -0.322  -0.185  -0.419  -0.394  -0.255  -0.488
147   -        -0.975  -0.935  -0.854  -1.120  -1.059  -0.943  -1.029  -0.981  -0.866
148   E        -0.534  -0.636  -0.774  -0.383  -0.525  -0.703  -0.499  -0.627  -0.777
149   Y        -1.251  -1.299  -1.213  -1.099  -1.173  -1.064  -1.130  -1.165  -1.029
150   H        -0.772  -0.726  -0.799  -0.638  -0.539  -0.734  -0.814  -0.742  -0.807
151   F        -0.772  -0.689  -0.796  -0.847  -0.720  -0.874  -0.814  -0.706  -0.807
152   F         1.295   1.309   1.379   1.316   1.339   1.443   1.393   1.413   1.515
153   Q         0.653   0.533   0.408   0.865   0.702   0.471   0.658   0.465   0.212
154   G         1.295   1.309   1.379   1.190   1.204   1.323   1.393   1.413   1.515
155   I        -0.534  -0.473  -0.741  -0.377  -0.287  -0.729  -0.499  -0.424  -0.738
156   T         0.042  -0.082  -0.267   0.205   0.033  -0.245   0.027  -0.150  -0.423
157   R        -1.363  -1.319  -1.218  -1.344  -1.268  -1.098  -1.235  -1.188  -1.035
158   G         1.295   1.309   1.379   1.190   1.204   1.323   1.393   1.413   1.515
159   K        -0.772  -0.803  -0.810  -0.821  -0.854  -0.847  -0.814  -0.851  -0.824
160   I         0.653   0.533   0.408   0.746   0.595   0.385   0.658   0.465   0.212
161   V         1.295   1.309   1.379   1.313   1.332   1.440   1.393   1.413   1.515
162   P         0.114   0.140   0.253  -0.015   0.028   0.198  -0.289  -0.247  -0.083
163   S         0.168   0.146   0.252   0.100   0.049   0.206  -0.184  -0.235  -0.086
164   R         1.295   1.309   1.379   1.492   1.508   1.609   1.393   1.413   1.515
165   G         1.295   1.309   1.379   1.190   1.204   1.323   1.393   1.413   1.515
166   P        -0.534  -0.636  -0.774  -0.217  -0.372  -0.592  -0.499  -0.627  -0.777
167   T        -0.239  -0.308  -0.342  -0.209  -0.323  -0.369  -0.394  -0.503  -0.536
168   T        -0.534  -0.551  -0.754  -0.340  -0.385  -0.709  -0.499  -0.528  -0.753
169   F         1.295   1.309   1.379   1.316   1.339   1.443   1.393   1.413   1.515
170   G         1.295   1.309   1.379   1.190   1.204   1.323   1.393   1.413   1.515
171   W         1.295   1.309   1.379   1.532   1.549   1.646   1.393   1.413   1.515
172   D         0.337   0.269   0.285   0.344   0.224   0.209   0.132   0.000  -0.022
173   S         0.337   0.329   0.308   0.321   0.302   0.208   0.132   0.111   0.025
174   I         0.337   0.379   0.315   0.291   0.362   0.218   0.132   0.200   0.037
175   F         1.295   1.309   1.379   1.316   1.339   1.443   1.393   1.413   1.515
176   E         0.168   0.168   0.251  -0.023  -0.025   0.112  -0.184  -0.191  -0.086
177   P         0.653   0.645   0.431   0.868   0.854   0.564   0.658   0.642   0.254
178   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   D        -0.772  -0.773  -0.800  -0.823  -0.836  -0.873  -0.814  -0.820  -0.812
180   S         0.337   0.370   0.329   0.199   0.244   0.173   0.132   0.184   0.063
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   H        -1.346  -1.315  -1.213  -1.177  -1.106  -0.995  -1.216  -1.178  -1.029
183   G        -1.683  -1.662  -1.535  -1.741  -1.737  -1.534  -1.353  -1.331  -1.158
184   L        -1.251  -1.274  -1.204  -1.051  -1.085  -0.999  -1.130  -1.147  -1.023
185   T         1.295   1.309   1.379   1.303   1.329   1.431   1.393   1.413   1.515
186   Y         0.653   0.649   0.428   0.900   0.895   0.560   0.658   0.649   0.249
187   A         1.295   1.309   1.379   1.193   1.213   1.326   1.393   1.413   1.515
188   E         1.295   1.309   1.379   1.216   1.234   1.348   1.393   1.413   1.515
189   M         1.295   1.309   1.379   1.492   1.509   1.609   1.393   1.413   1.515
190   S        -1.251  -1.282  -1.205  -1.161  -1.209  -1.135  -1.130  -1.152  -1.023
191   K         0.042  -0.082  -0.267   0.047  -0.117  -0.412   0.027  -0.150  -0.423
192   D        -0.956  -0.897  -0.826  -1.170  -1.063  -0.976  -1.025  -0.947  -0.838
193   A        -1.953  -1.852  -1.774  -1.848  -1.702  -1.602  -1.445  -1.361  -1.227
194   K         0.653   0.533   0.408   0.636   0.494   0.329   0.658   0.465   0.212
195   N         1.295   1.309   1.379   1.332   1.353   1.458   1.393   1.413   1.515
196   A        -1.067  -1.043  -0.882  -1.285  -1.242  -1.015  -1.130  -1.099  -0.896
197   I         0.042  -0.041  -0.255   0.208   0.112  -0.224   0.027  -0.096  -0.406
198   S         1.295   1.309   1.379   1.376   1.398   1.500   1.393   1.413   1.515
199   H         0.653   0.674   0.427   0.963   0.984   0.639   0.658   0.686   0.248
200   R         1.295   1.309   1.379   1.492   1.508   1.609   1.393   1.413   1.515
201   G        -0.956  -0.953  -0.860  -1.055  -1.047  -0.901  -1.025  -1.015  -0.875
202   K        -0.239  -0.298  -0.330  -0.316  -0.402  -0.446  -0.394  -0.459  -0.519
203   A         1.295   1.309   1.379   1.193   1.213   1.326   1.393   1.413   1.515
204   F        -0.365  -0.431  -0.360  -0.598  -0.688  -0.581  -0.604  -0.669  -0.562
205   A        -1.251  -1.263  -1.197  -1.220  -1.219  -1.126  -1.130  -1.128  -1.014
206   Q        -0.239  -0.185  -0.319  -0.330  -0.251  -0.449  -0.394  -0.320  -0.500
207   F        -0.239  -0.127  -0.287  -0.354  -0.202  -0.420  -0.394  -0.246  -0.455
208   K        -0.365  -0.365  -0.354  -0.439  -0.432  -0.372  -0.604  -0.600  -0.555
209   E        -0.844  -0.821  -0.820  -0.934  -0.900  -0.901  -0.919  -0.891  -0.836
210   Y        -0.365  -0.345  -0.333  -0.324  -0.287  -0.238  -0.604  -0.565  -0.529
211   L         0.653   0.645   0.431   0.616   0.605   0.308   0.658   0.642   0.254
212   Y        -1.251  -1.225  -1.213  -1.176  -1.169  -1.193  -1.130  -1.108  -1.030
213   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
214   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
215   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
216   Q        -0.975  -0.958  -0.861  -1.016  -0.993  -0.838  -1.029  -1.008  -0.873
217   N        -1.448  -1.420  -1.246  -1.336  -1.312  -1.062  -1.298  -1.266  -1.057
218   D        -1.683  -1.681  -1.527  -1.588  -1.612  -1.401  -1.353  -1.344  -1.152
219   F        -1.658  -1.667  -1.520  -1.568  -1.593  -1.403  -1.340  -1.336  -1.147
* 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/P47119
Output conservation file - output/P47119
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
