1     M         1.940   1.951   2.004   2.242   2.258   2.346   2.162   2.179   2.264
2     S        -0.375  -0.364  -0.309  -0.521  -0.506  -0.414  -0.570  -0.555  -0.477
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -         1.940   1.951   2.004   1.802   1.826   1.905   2.162   2.179   2.264
18    -         0.599   0.656   0.621   0.590   0.683   0.612   0.341   0.443   0.356
19    -        -0.375  -0.353  -0.309  -0.561  -0.502  -0.454  -0.570  -0.540  -0.477
20    -         0.599   0.648   0.619   0.447   0.539   0.457   0.341   0.429   0.352
21    -        -0.375  -0.353  -0.309  -0.535  -0.483  -0.429  -0.570  -0.540  -0.477
22    -         0.599   0.541   0.582   0.304   0.221   0.285   0.341   0.227   0.281
23    K         0.522   0.567   0.599   0.262   0.357   0.395   0.195   0.277   0.314
24    A        -0.867  -0.831  -0.863  -0.755  -0.682  -0.760  -0.788  -0.747  -0.765
25    T        -0.062  -0.126  -0.163   0.140   0.038  -0.014  -0.133  -0.223  -0.274
26    C         1.940   1.951   2.004   2.084   2.097   2.187   2.162   2.179   2.264
27    S        -0.062  -0.089  -0.169   0.056   0.012  -0.123  -0.133  -0.171  -0.283
28    F         0.886   0.838   0.766   1.108   1.041   0.942   0.851   0.767   0.624
29    E        -1.451  -1.439  -1.385  -1.279  -1.270  -1.171  -1.116  -1.101  -1.026
30    G        -0.867  -0.886  -0.848  -0.839  -0.857  -0.803  -0.788  -0.807  -0.749
31    C         1.940   1.951   2.004   2.084   2.097   2.187   2.162   2.179   2.264
32    H        -0.867  -0.907  -0.883  -0.656  -0.711  -0.662  -0.788  -0.830  -0.787
33    S         0.522   0.567   0.599   0.216   0.284   0.341   0.195   0.277   0.314
34    A        -0.062  -0.089  -0.169   0.059   0.014  -0.133  -0.133  -0.171  -0.283
35    V        -0.283  -0.288  -0.260  -0.572  -0.567  -0.517  -0.461  -0.462  -0.415
36    I         0.886   0.838   0.766   0.798   0.738   0.615   0.851   0.767   0.624
37    T        -1.451  -1.439  -1.385  -1.270  -1.271  -1.163  -1.116  -1.101  -1.026
38    I        -1.451  -1.439  -1.385  -1.335  -1.327  -1.228  -1.116  -1.101  -1.026
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    N        -0.375  -0.364  -0.309  -0.454  -0.444  -0.347  -0.570  -0.554  -0.477
80    D        -0.283  -0.288  -0.260  -0.518  -0.515  -0.462  -0.461  -0.462  -0.415
81    D        -0.062   0.035  -0.125  -0.116   0.033  -0.214  -0.133   0.005  -0.221
82    N        -0.867  -0.907  -0.883  -0.741  -0.805  -0.755  -0.788  -0.830  -0.787
83    I        -0.062  -0.126  -0.163  -0.133  -0.238  -0.308  -0.133  -0.223  -0.274
84    I        -0.062  -0.070  -0.133  -0.145  -0.142  -0.250  -0.133  -0.144  -0.232
85    N        -0.981  -0.974  -0.915  -1.002  -1.005  -0.895  -0.911  -0.900  -0.820
86    L        -0.981  -0.974  -0.915  -1.014  -1.002  -0.906  -0.911  -0.900  -0.820
87    P        -0.867  -0.831  -0.863  -0.783  -0.742  -0.782  -0.788  -0.747  -0.765
88    E        -0.283  -0.273  -0.252  -0.461  -0.445  -0.390  -0.461  -0.445  -0.405
89    Q        -0.867  -0.873  -0.842  -0.680  -0.690  -0.649  -0.788  -0.793  -0.742
90    V        -0.062  -0.126  -0.163  -0.225  -0.323  -0.403  -0.133  -0.223  -0.274
91    H        -0.867  -0.873  -0.842  -0.475  -0.495  -0.433  -0.788  -0.793  -0.742
92    S        -0.867  -0.907  -0.883  -0.945  -1.023  -1.004  -0.788  -0.830  -0.787
93    E        -0.867  -0.820  -0.848  -0.883  -0.817  -0.859  -0.788  -0.734  -0.749
94    F        -0.867  -0.907  -0.883  -0.629  -0.690  -0.637  -0.788  -0.830  -0.787
95    K        -0.867  -0.831  -0.863  -0.825  -0.779  -0.820  -0.788  -0.747  -0.765
96    L        -0.867  -0.863  -0.855  -0.731  -0.737  -0.718  -0.788  -0.782  -0.756
97    L        -1.451  -1.439  -1.385  -1.305  -1.274  -1.197  -1.116  -1.101  -1.026
98    E        -0.062   0.035  -0.125   0.043   0.177  -0.036  -0.133   0.005  -0.221
99    N        -0.251  -0.234  -0.242  -0.227  -0.201  -0.215  -0.399  -0.375  -0.386
100   R         0.599   0.573   0.604   0.595   0.544   0.585   0.341   0.289   0.322
101   T        -0.375  -0.364  -0.309  -0.446  -0.415  -0.339  -0.570  -0.554  -0.477
102   M        -0.867  -0.863  -0.855  -0.769  -0.755  -0.741  -0.788  -0.782  -0.756
103   R        -0.867  -0.820  -0.848  -0.758  -0.680  -0.736  -0.788  -0.734  -0.749
104   D         0.886   0.838   0.766   0.865   0.795   0.692   0.851   0.767   0.624
105   A        -0.283  -0.299  -0.269  -0.261  -0.281  -0.223  -0.461  -0.475  -0.426
106   T        -0.867  -0.855  -0.843  -0.751  -0.726  -0.715  -0.788  -0.774  -0.743
107   P         0.755   0.800   0.719   0.756   0.833   0.681   0.625   0.701   0.539
108   S        -0.867  -0.855  -0.843  -1.072  -1.059  -1.030  -0.788  -0.774  -0.743
109   E        -0.867  -0.831  -0.863  -0.983  -0.932  -0.988  -0.788  -0.747  -0.765
110   S        -0.867  -0.873  -0.842  -0.908  -0.917  -0.852  -0.788  -0.793  -0.742
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   N        -0.867  -0.873  -0.842  -0.865  -0.863  -0.831  -0.788  -0.793  -0.742
116   F         1.940   1.951   2.004   2.084   2.098   2.187   2.162   2.179   2.264
117   L        -0.062   0.035  -0.125   0.013   0.147  -0.063  -0.133   0.005  -0.221
118   V        -0.867  -0.831  -0.863  -0.734  -0.696  -0.714  -0.788  -0.747  -0.765
119   V        -0.867  -0.831  -0.863  -0.905  -0.838  -0.905  -0.788  -0.747  -0.765
120   P        -0.867  -0.831  -0.863  -0.731  -0.660  -0.723  -0.788  -0.747  -0.765
121   D         0.886   0.886   0.777   0.833   0.833   0.663   0.851   0.850   0.644
122   V        -0.062  -0.106  -0.164   0.032  -0.042  -0.118  -0.133  -0.194  -0.276
123   W         0.886   0.838   0.766   1.262   1.191   1.078   0.851   0.767   0.624
124   D         1.940   1.951   2.004   1.868   1.884   1.972   2.162   2.179   2.264
125   F         1.940   1.951   2.004   2.084   2.098   2.187   2.162   2.179   2.264
126   D         1.940   1.951   2.004   1.868   1.884   1.972   2.162   2.179   2.264
127   N         1.940   1.951   2.004   2.016   2.040   2.119   2.162   2.179   2.264
128   V         0.886   0.859   0.773   0.798   0.770   0.626   0.851   0.803   0.637
129   G         0.886   0.838   0.766   0.985   0.906   0.774   0.851   0.767   0.624
130   V         1.940   1.951   2.004   1.964   1.971   2.068   2.162   2.179   2.264
131   S         0.886   0.838   0.766   0.778   0.710   0.608   0.851   0.767   0.624
132   R         0.886   0.838   0.766   1.052   0.980   0.865   0.851   0.767   0.624
133   E        -0.062  -0.089  -0.169   0.002  -0.043  -0.195  -0.133  -0.171  -0.283
134   I        -0.867  -0.907  -0.883  -1.119  -1.180  -1.144  -0.788  -0.830  -0.787
135   P        -0.867  -0.907  -0.883  -0.886  -0.930  -0.871  -0.788  -0.830  -0.787
136   S        -0.867  -0.863  -0.855  -0.919  -0.918  -0.902  -0.788  -0.782  -0.756
137   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   L        -0.867  -0.907  -0.883  -0.960  -1.013  -0.969  -0.788  -0.830  -0.787
140   G        -0.867  -0.806  -0.836  -0.814  -0.708  -0.770  -0.788  -0.716  -0.735
141   D        -0.062  -0.089  -0.169   0.138   0.087  -0.069  -0.133  -0.171  -0.283
142   L        -0.251  -0.250  -0.235  -0.475  -0.476  -0.455  -0.399  -0.398  -0.375
143   S        -0.062  -0.089  -0.169   0.021  -0.023  -0.170  -0.133  -0.171  -0.283
144   D         0.599   0.573   0.604   0.296   0.241   0.281   0.341   0.289   0.322
145   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   V        -0.867  -0.907  -0.883  -1.006  -1.065  -1.023  -0.788  -0.830  -0.787
150   F         0.522   0.518   0.562   0.269   0.274   0.339   0.195   0.184   0.242
151   E         0.522   0.533   0.570   0.183   0.199   0.250   0.195   0.213   0.258
152   Y        -1.451  -1.439  -1.385  -1.121  -1.116  -1.014  -1.116  -1.101  -1.026
153   G        -0.062  -0.053  -0.134  -0.074  -0.059  -0.177  -0.133  -0.120  -0.234
154   N         0.522   0.513   0.556   0.418   0.404   0.466   0.195   0.174   0.230
155   S        -0.867  -0.845  -0.843  -0.825  -0.796  -0.788  -0.788  -0.762  -0.744
156   S        -0.283  -0.255  -0.248  -0.483  -0.442  -0.422  -0.461  -0.426  -0.403
157   W         0.599   0.573   0.604   0.677   0.616   0.648   0.341   0.288   0.322
158   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   I        -0.867  -0.863  -0.855  -0.854  -0.854  -0.850  -0.788  -0.782  -0.756
160   K        -0.062  -0.126  -0.163  -0.156  -0.248  -0.312  -0.133  -0.223  -0.274
161   K        -0.283  -0.302  -0.248  -0.279  -0.322  -0.230  -0.461  -0.480  -0.403
162   C         0.522   0.518   0.562   0.269   0.274   0.339   0.195   0.184   0.242
163   L        -0.062  -0.089  -0.169  -0.014  -0.062  -0.174  -0.133  -0.171  -0.283
164   K         0.886   0.859   0.773   1.052   1.012   0.877   0.851   0.803   0.637
165   Y         0.522   0.518   0.562   0.388   0.383   0.460   0.195   0.184   0.242
166   L         0.886   0.967   0.805   0.833   0.957   0.701   0.851   0.985   0.696
167   I        -0.283  -0.237  -0.249  -0.427  -0.354  -0.367  -0.461  -0.407  -0.403
168   C         1.940   1.951   2.004   2.084   2.097   2.187   2.162   2.179   2.264
169   A         0.522   0.567   0.599   0.327   0.420   0.462   0.195   0.277   0.314
170   D         0.886   0.859   0.773   0.878   0.833   0.694   0.851   0.803   0.637
171   C         1.940   1.951   2.004   2.084   2.097   2.187   2.162   2.179   2.264
172   D         1.940   1.951   2.004   1.868   1.884   1.972   2.162   2.179   2.264
173   K         0.522   0.530   0.562   0.430   0.440   0.484   0.195   0.207   0.243
174   G         1.940   1.951   2.004   2.058   2.073   2.162   2.162   2.179   2.264
175   P         1.940   1.951   2.004   2.041   2.060   2.145   2.162   2.179   2.264
176   I        -0.062  -0.042  -0.131  -0.147  -0.100  -0.250  -0.133  -0.107  -0.229
177   G         1.940   1.951   2.004   2.058   2.073   2.162   2.162   2.179   2.264
178   I        -0.867  -0.907  -0.883  -0.854  -0.934  -0.913  -0.788  -0.830  -0.787
179   I        -0.283  -0.273  -0.252  -0.451  -0.445  -0.416  -0.461  -0.445  -0.405
180   C         0.522   0.518   0.562   0.468   0.455   0.527   0.195   0.184   0.242
181   K        -0.867  -0.806  -0.836  -0.949  -0.838  -0.908  -0.788  -0.716  -0.735
182   V         0.755   0.761   0.716   0.723   0.730   0.659   0.625   0.634   0.534
183   Q        -0.867  -0.831  -0.863  -0.751  -0.697  -0.772  -0.788  -0.747  -0.765
184   D        -0.283  -0.299  -0.269  -0.402  -0.427  -0.372  -0.461  -0.475  -0.426
185   Q        -1.451  -1.439  -1.385  -1.236  -1.223  -1.129  -1.116  -1.101  -1.026
186   T        -1.451  -1.439  -1.385  -1.353  -1.324  -1.246  -1.116  -1.101  -1.026
187   K        -0.062  -0.089  -0.169   0.037  -0.019  -0.155  -0.133  -0.171  -0.283
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   N        -0.867  -0.907  -0.883  -0.964  -1.022  -0.985  -0.788  -0.830  -0.787
193   E        -0.867  -0.863  -0.855  -0.738  -0.740  -0.746  -0.788  -0.782  -0.756
194   E        -0.867  -0.907  -0.883  -0.861  -0.945  -0.896  -0.788  -0.830  -0.787
195   R        -0.283  -0.299  -0.269  -0.296  -0.312  -0.264  -0.461  -0.475  -0.426
196   V        -0.867  -0.907  -0.883  -0.894  -0.958  -0.910  -0.788  -0.830  -0.787
197   L        -0.867  -0.863  -0.855  -0.945  -0.949  -0.937  -0.788  -0.782  -0.756
198   H        -0.062  -0.089  -0.169   0.291   0.252   0.134  -0.133  -0.171  -0.283
199   L         0.522   0.567   0.599   0.329   0.400   0.455   0.195   0.277   0.314
200   L         1.940   1.951   2.004   1.894   1.909   1.998   2.162   2.179   2.264
201   S         0.886   0.838   0.766   0.782   0.718   0.614   0.851   0.767   0.624
202   L        -1.451  -1.439  -1.385  -1.358  -1.341  -1.250  -1.116  -1.101  -1.026
203   R        -1.451  -1.439  -1.385  -1.449  -1.419  -1.341  -1.116  -1.101  -1.026
204   S         1.940   1.951   2.004   1.779   1.798   1.883   2.162   2.179   2.264
205   L         0.886   0.859   0.773   0.919   0.868   0.737   0.851   0.803   0.637
206   Q        -1.451  -1.439  -1.385  -1.454  -1.416  -1.346  -1.116  -1.101  -1.026
207   I        -0.867  -0.907  -0.883  -0.693  -0.773  -0.748  -0.788  -0.830  -0.787
208   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
209   G        -0.251  -0.294  -0.273  -0.337  -0.403  -0.355  -0.399  -0.459  -0.428
210   R        -0.375  -0.368  -0.309  -0.536  -0.523  -0.429  -0.570  -0.559  -0.477
211   N        -0.867  -0.869  -0.846  -0.807  -0.829  -0.773  -0.788  -0.789  -0.746
* 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/P32601
Output conservation file - output/P32601
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
