1     M         1.851   1.872   1.940   2.089   2.123   2.228   2.052   2.083   2.187
2     N         0.129   0.070  -0.024   0.325   0.228   0.090   0.082  -0.009  -0.145
3     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     F        -0.157  -0.092  -0.138  -0.281  -0.199  -0.223  -0.356  -0.260  -0.313
7     G        -0.788  -0.814  -0.772  -0.844  -0.878  -0.833  -0.793  -0.812  -0.741
8     K        -0.788  -0.743  -0.744  -1.028  -0.979  -0.966  -0.793  -0.739  -0.713
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    Q        -0.035   0.041  -0.099  -0.009   0.105  -0.110  -0.154  -0.044  -0.253
11    L        -0.035  -0.021  -0.093  -0.185  -0.156  -0.266  -0.154  -0.135  -0.244
12    A        -0.243  -0.215  -0.200  -0.320  -0.281  -0.250  -0.469  -0.432  -0.401
13    F        -0.793  -0.816  -0.781  -0.589  -0.628  -0.593  -0.785  -0.805  -0.749
14    H        -1.705  -1.683  -1.605  -1.394  -1.361  -1.243  -1.231  -1.205  -1.101
15    K        -1.247  -1.188  -1.183  -1.367  -1.299  -1.253  -1.012  -0.948  -0.915
16    I        -0.788  -0.796  -0.763  -0.692  -0.709  -0.648  -0.793  -0.797  -0.732
17    V        -0.788  -0.753  -0.737  -0.798  -0.725  -0.701  -0.793  -0.751  -0.707
18    P        -1.705  -1.683  -1.605  -1.591  -1.541  -1.439  -1.231  -1.205  -1.101
19    T        -0.788  -0.807  -0.735  -0.776  -0.799  -0.687  -0.793  -0.807  -0.705
20    T        -0.157  -0.099  -0.115  -0.175  -0.089  -0.099  -0.356  -0.269  -0.281
21    A        -0.788  -0.750  -0.749  -0.858  -0.827  -0.775  -0.793  -0.746  -0.717
22    I        -1.705  -1.683  -1.605  -1.224  -1.192  -1.074  -1.231  -1.205  -1.101
23    G         0.129   0.090  -0.023   0.296   0.227   0.056   0.082   0.018  -0.143
24    -        -0.213  -0.208  -0.173  -0.168  -0.156  -0.115  -0.410  -0.406  -0.359
25    -        -0.213  -0.208  -0.173  -0.418  -0.414  -0.348  -0.410  -0.406  -0.359
26    -         1.851   1.872   1.940   1.859   1.895   1.999   2.052   2.083   2.187
27    -         0.735   0.685   0.694   0.708   0.630   0.630   0.574   0.477   0.458
28    W        -0.788  -0.814  -0.772  -0.757  -0.811  -0.732  -0.793  -0.812  -0.741
29    L        -1.247  -1.227  -1.217  -1.177  -1.144  -1.143  -1.012  -0.990  -0.946
30    V        -0.788  -0.721  -0.735  -0.726  -0.637  -0.635  -0.793  -0.720  -0.705
31    P        -0.330  -0.309  -0.225  -0.413  -0.380  -0.248  -0.574  -0.546  -0.431
32    L        -1.247  -1.164  -1.188  -1.134  -0.991  -1.058  -1.012  -0.924  -0.919
33    G        -1.247  -1.227  -1.217  -1.122  -1.123  -1.102  -1.012  -0.990  -0.946
34    N        -1.247  -1.227  -1.217  -1.124  -1.105  -1.073  -1.012  -0.990  -0.946
35    P        -1.247  -1.188  -1.183  -1.148  -1.063  -1.056  -1.012  -0.948  -0.915
36    S        -1.247  -1.164  -1.188  -1.073  -0.944  -0.985  -1.012  -0.924  -0.919
37    L         0.957   0.990   0.824   0.851   0.899   0.675   0.957   1.009   0.701
38    Q        -0.788  -0.815  -0.735  -0.835  -0.898  -0.760  -0.793  -0.813  -0.705
39    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    Q        -1.247  -1.269  -1.225  -0.966  -1.000  -0.925  -1.012  -1.027  -0.953
43    K        -1.247  -1.269  -1.225  -1.381  -1.391  -1.295  -1.012  -1.027  -0.953
44    Q        -0.157  -0.113  -0.122  -0.375  -0.310  -0.304  -0.356  -0.291  -0.295
45    L        -0.615  -0.673  -0.696  -0.661  -0.736  -0.755  -0.574  -0.643  -0.654
46    G        -0.615  -0.540  -0.637  -0.423  -0.300  -0.459  -0.574  -0.480  -0.586
47    S        -1.247  -1.247  -1.192  -1.169  -1.159  -1.098  -1.012  -1.008  -0.923
48    I        -0.788  -0.743  -0.735  -0.805  -0.736  -0.731  -0.793  -0.742  -0.705
49    H        -0.793  -0.737  -0.736  -0.674  -0.573  -0.590  -0.785  -0.714  -0.700
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    R        -0.213  -0.200  -0.168  -0.424  -0.418  -0.374  -0.410  -0.393  -0.352
53    W        -0.213  -0.262  -0.199  -0.199  -0.267  -0.165  -0.410  -0.480  -0.396
54    L         1.851   1.872   1.940   1.677   1.706   1.818   2.052   2.083   2.187
55    R        -0.793  -0.813  -0.772  -0.858  -0.889  -0.864  -0.785  -0.804  -0.740
56    E        -0.035  -0.068  -0.098   0.041  -0.004  -0.065  -0.154  -0.204  -0.251
57    K        -0.243  -0.268  -0.201  -0.783  -0.818  -0.701  -0.469  -0.494  -0.402
58    L        -0.788  -0.796  -0.763  -1.220  -1.219  -1.145  -0.793  -0.797  -0.732
59    Q        -1.247  -1.227  -1.217  -1.216  -1.182  -1.181  -1.012  -0.990  -0.946
60    Q        -0.615  -0.673  -0.696  -0.551  -0.648  -0.732  -0.574  -0.643  -0.654
61    D        -0.788  -0.796  -0.763  -0.692  -0.701  -0.653  -0.793  -0.797  -0.732
62    H        -0.615  -0.642  -0.681  -0.446  -0.479  -0.536  -0.574  -0.608  -0.637
63    K        -0.788  -0.818  -0.751  -1.110  -1.150  -1.017  -0.793  -0.816  -0.719
64    D        -1.247  -1.250  -1.188  -1.055  -1.066  -0.969  -1.012  -1.010  -0.920
65    T        -1.705  -1.683  -1.605  -1.556  -1.506  -1.404  -1.231  -1.205  -1.101
66    E        -0.788  -0.796  -0.763  -0.760  -0.750  -0.705  -0.793  -0.797  -0.732
67    D        -0.615  -0.614  -0.678  -0.594  -0.620  -0.721  -0.574  -0.575  -0.634
68    K        -0.615  -0.642  -0.681  -0.538  -0.578  -0.665  -0.574  -0.608  -0.637
69    D        -0.788  -0.814  -0.772  -0.759  -0.799  -0.732  -0.793  -0.812  -0.741
70    F         0.129   0.090  -0.023   0.467   0.395   0.239   0.082   0.018  -0.143
71    F        -0.157  -0.224  -0.176   0.059  -0.029   0.047  -0.356  -0.435  -0.369
72    S        -0.213  -0.187  -0.199  -0.193  -0.159  -0.184  -0.410  -0.373  -0.396
73    N         0.587   0.655   0.672   0.582   0.696   0.711   0.301   0.421   0.416
74    N         0.957   0.844   0.793   1.196   1.046   0.962   0.957   0.762   0.645
75    G         1.851   1.872   1.940   1.939   1.972   2.079   2.052   2.083   2.187
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    I         1.851   1.872   1.940   1.999   2.036   2.139   2.052   2.083   2.187
78    L         0.957   0.844   0.793   0.841   0.681   0.609   0.957   0.762   0.645
79    L        -0.615  -0.679  -0.722  -0.795  -0.883  -0.975  -0.574  -0.650  -0.684
80    A         1.851   1.872   1.940   1.909   1.931   2.049   2.052   2.083   2.187
81    V         0.957   0.999   0.819   1.122   1.177   0.915   0.957   1.025   0.692
82    P         1.851   1.872   1.940   1.909   1.937   2.049   2.052   2.083   2.187
83    K         1.851   1.872   1.940   1.573   1.601   1.714   2.052   2.083   2.187
84    K         1.851   1.872   1.940   1.573   1.601   1.714   2.052   2.083   2.187
85    K         1.851   1.872   1.940   1.573   1.601   1.714   2.052   2.083   2.187
86    V         0.129   0.154  -0.033   0.253   0.284  -0.039   0.082   0.119  -0.157
87    S         1.851   1.872   1.940   1.954   1.988   2.094   2.052   2.083   2.187
88    H        -0.157  -0.170  -0.170  -0.048  -0.072  -0.075  -0.356  -0.379  -0.365
89    Q        -0.615  -0.679  -0.722  -0.454  -0.557  -0.647  -0.574  -0.650  -0.684
90    K        -0.157  -0.224  -0.176  -0.524  -0.605  -0.518  -0.356  -0.435  -0.369
91    K         0.129   0.154  -0.033  -0.065  -0.030  -0.297   0.082   0.119  -0.157
92    R         1.851   1.872   1.940   1.868   1.900   2.008   2.052   2.083   2.187
93    Q         0.587   0.549   0.594   0.375   0.270   0.300   0.301   0.219   0.265
94    K         0.587   0.558   0.596   0.144   0.088   0.147   0.301   0.237   0.269
95    L         0.957   0.844   0.793   0.864   0.712   0.650   0.957   0.762   0.645
96    Y         0.587   0.558   0.596   0.516   0.432   0.452   0.301   0.237   0.269
97    G         0.957   1.018   0.837   1.073   1.151   0.902   0.957   1.055   0.726
98    P         1.851   1.872   1.940   1.914   1.944   2.054   2.052   2.083   2.187
99    G         0.957   0.844   0.793   1.110   0.952   0.870   0.957   0.762   0.645
100   K        -0.788  -0.826  -0.750  -0.920  -0.958  -0.823  -0.793  -0.824  -0.719
101   K         1.851   1.872   1.940   1.573   1.601   1.714   2.052   2.083   2.187
102   Q         0.129   0.054  -0.046   0.339   0.223   0.071   0.082  -0.030  -0.176
103   L        -0.157  -0.127  -0.151  -0.372  -0.333  -0.334  -0.356  -0.314  -0.339
104   K         0.129   0.162  -0.009  -0.014   0.034  -0.188   0.082   0.131  -0.123
105   M        -0.157  -0.160  -0.171  -0.045  -0.073  -0.080  -0.356  -0.369  -0.366
106   I        -0.157  -0.151  -0.152  -0.232  -0.256  -0.238  -0.356  -0.358  -0.342
107   H        -0.615  -0.648  -0.667  -0.325  -0.376  -0.406  -0.574  -0.615  -0.621
108   H         0.475   0.498   0.575   0.422   0.463   0.577   0.082   0.117   0.226
109   L         0.957   0.971   0.824   0.848   0.871   0.669   0.957   0.978   0.701
110   N         0.129   0.154  -0.033   0.378   0.421   0.122   0.082   0.119  -0.157
111   K         0.587   0.655   0.672   0.283   0.419   0.408   0.301   0.421   0.416
112   C         1.851   1.872   1.940   2.108   2.139   2.247   2.052   2.083   2.187
113   P         0.957   0.971   0.824   1.076   1.096   0.884   0.957   0.978   0.701
114   S         0.475   0.498   0.575   0.288   0.317   0.443   0.082   0.117   0.226
115   C         1.851   1.872   1.940   2.108   2.139   2.247   2.052   2.083   2.187
116   G         1.851   1.872   1.940   1.939   1.972   2.079   2.052   2.083   2.187
117   H         0.957   0.971   0.824   1.200   1.226   1.004   0.957   0.978   0.701
118   Y         0.475   0.498   0.575   0.411   0.436   0.562   0.082   0.117   0.226
119   K         1.851   1.872   1.940   1.573   1.601   1.714   2.052   2.083   2.187
120   R         0.957   1.042   0.836   0.961   1.090   0.746   0.957   1.093   0.724
121   A        -0.157  -0.224  -0.176  -0.153  -0.241  -0.157  -0.356  -0.435  -0.369
122   N         0.587   0.635   0.642   0.636   0.721   0.709   0.301   0.383   0.358
123   T         0.587   0.609   0.634   0.623   0.655   0.687   0.301   0.334   0.344
124   L        -0.157  -0.123  -0.149  -0.298  -0.250  -0.261  -0.356  -0.310  -0.331
125   C         1.851   1.872   1.940   2.108   2.139   2.247   2.052   2.083   2.187
126   M         1.851   1.872   1.940   2.089   2.123   2.228   2.052   2.083   2.187
127   Y         0.129   0.179   0.016   0.439   0.514   0.279   0.082   0.154  -0.086
128   C         1.851   1.872   1.940   2.108   2.139   2.247   2.052   2.083   2.187
129   V         0.587   0.655   0.672   0.650   0.763   0.777   0.301   0.421   0.416
130   G        -0.788  -0.814  -0.772  -0.738  -0.761  -0.696  -0.793  -0.812  -0.741
131   Q         0.129   0.204   0.001   0.265   0.388   0.080   0.082   0.190  -0.108
132   I         0.129   0.054  -0.046   0.301   0.167  -0.010   0.082  -0.030  -0.176
133   S        -0.157  -0.109  -0.131  -0.440  -0.366  -0.381  -0.356  -0.294  -0.307
134   H        -0.788  -0.759  -0.747  -0.607  -0.566  -0.532  -0.793  -0.756  -0.715
135   I        -0.157  -0.092  -0.138  -0.105   0.011  -0.095  -0.356  -0.260  -0.313
136   W        -0.157  -0.224  -0.176  -0.081  -0.179  -0.123  -0.356  -0.435  -0.369
137   K         0.957   0.844   0.793   0.732   0.567   0.495   0.957   0.762   0.645
138   T        -1.247  -1.232  -1.190  -1.134  -1.157  -1.056  -1.012  -0.994  -0.921
139   H        -0.788  -0.759  -0.747  -0.970  -0.964  -0.931  -0.793  -0.756  -0.715
140   T         0.587   0.609   0.634   0.399   0.435   0.432   0.301   0.334   0.344
141   A        -1.247  -1.164  -1.188  -1.245  -1.113  -1.163  -1.012  -0.924  -0.919
142   K        -1.247  -1.240  -1.185  -1.381  -1.364  -1.268  -1.012  -1.001  -0.916
143   E        -1.247  -1.269  -1.225  -1.075  -1.101  -1.028  -1.012  -1.027  -0.953
144   E        -0.793  -0.750  -0.734  -0.785  -0.707  -0.697  -0.785  -0.733  -0.698
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   I        -0.788  -0.757  -0.732  -0.807  -0.763  -0.729  -0.793  -0.756  -0.702
148   K        -0.157  -0.085  -0.144  -0.282  -0.146  -0.293  -0.356  -0.253  -0.326
149   P         0.129   0.031  -0.051   0.195   0.014  -0.128   0.082  -0.062  -0.183
150   R        -0.788  -0.806  -0.762  -0.828  -0.892  -0.819  -0.793  -0.806  -0.732
151   Q         0.129   0.154  -0.033   0.327   0.375   0.074   0.082   0.119  -0.157
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   E        -0.157  -0.224  -0.176  -0.223  -0.309  -0.248  -0.356  -0.435  -0.369
155   E        -1.247  -1.261  -1.209  -1.096  -1.121  -1.050  -1.012  -1.020  -0.939
156   E        -0.788  -0.826  -0.752  -0.703  -0.734  -0.624  -0.793  -0.823  -0.720
157   L         1.851   1.872   1.940   1.670   1.700   1.811   2.052   2.083   2.187
158   S        -1.247  -1.269  -1.225  -1.013  -1.051  -0.977  -1.012  -1.027  -0.953
159   E        -0.788  -0.814  -0.772  -0.802  -0.835  -0.761  -0.793  -0.812  -0.741
160   L         0.129   0.046  -0.040   0.077  -0.036  -0.148   0.082  -0.041  -0.167
161   D         1.851   1.872   1.940   1.974   2.003   2.114   2.052   2.083   2.187
162   Q        -0.157  -0.085  -0.144  -0.428  -0.279  -0.403  -0.356  -0.253  -0.326
163   R         0.129   0.046  -0.040   0.135   0.002  -0.176   0.082  -0.041  -0.167
164   V        -0.157  -0.208  -0.141  -0.087  -0.147  -0.048  -0.356  -0.410  -0.324
165   L        -0.157  -0.160  -0.171  -0.362  -0.357  -0.340  -0.356  -0.369  -0.366
166   Y         1.851   1.872   1.940   2.069   2.098   2.208   2.052   2.083   2.187
167   P         0.957   0.844   0.793   1.002   0.813   0.704   0.957   0.762   0.645
168   G         0.957   0.844   0.793   1.118   0.964   0.884   0.957   0.762   0.645
169   R         0.587   0.655   0.672   0.144   0.254   0.274   0.301   0.421   0.416
170   R        -1.705  -1.683  -1.605  -1.457  -1.393  -1.306  -1.231  -1.205  -1.101
171   D         0.475   0.493   0.569   0.281   0.319   0.430   0.082   0.108   0.216
172   T         0.129   0.046  -0.040   0.335   0.202   0.059   0.082  -0.041  -0.167
173   K        -1.247  -1.257  -1.196  -1.254  -1.260  -1.188  -1.012  -1.017  -0.927
174   Y         0.587   0.549   0.594   0.676   0.600   0.658   0.301   0.219   0.265
175   T        -0.157  -0.200  -0.142  -0.164  -0.197  -0.117  -0.356  -0.397  -0.320
176   K        -0.788  -0.814  -0.772  -1.055  -1.061  -0.993  -0.793  -0.812  -0.741
177   D        -0.615  -0.564  -0.658  -0.791  -0.719  -0.838  -0.574  -0.509  -0.610
178   L         1.851   1.872   1.940   1.670   1.700   1.811   2.052   2.083   2.187
179   K         1.851   1.872   1.940   1.573   1.601   1.714   2.052   2.083   2.187
180   D         0.129   0.154  -0.033   0.240   0.276  -0.064   0.082   0.119  -0.157
181   K         0.957   0.844   0.793   0.750   0.593   0.526   0.957   0.762   0.645
182   D         0.129   0.031  -0.051   0.312   0.156   0.013   0.082  -0.062  -0.183
183   N        -0.213  -0.108  -0.163  -0.180  -0.010  -0.110  -0.410  -0.259  -0.344
184   Y         0.587   0.609   0.634   0.742   0.775   0.810   0.301   0.334   0.344
185   L        -0.157  -0.160  -0.171  -0.372  -0.375  -0.350  -0.356  -0.369  -0.366
186   E        -0.788  -0.814  -0.772  -0.887  -0.943  -0.872  -0.793  -0.812  -0.741
187   R        -0.157  -0.160  -0.171  -0.437  -0.486  -0.490  -0.356  -0.369  -0.366
188   R         0.957   0.844   0.793   1.059   0.907   0.836   0.957   0.762   0.645
189   V        -0.788  -0.806  -0.762  -0.682  -0.710  -0.635  -0.793  -0.806  -0.732
190   R        -0.157  -0.115  -0.140  -0.463  -0.376  -0.455  -0.356  -0.294  -0.324
191   T        -0.157  -0.224  -0.176  -0.149  -0.248  -0.179  -0.356  -0.435  -0.369
192   L         0.129   0.031  -0.051   0.082  -0.057  -0.156   0.082  -0.062  -0.183
193   -        -0.035  -0.052  -0.088   0.055   0.021  -0.025  -0.154  -0.182  -0.237
194   -        -0.793  -0.751  -0.739  -0.694  -0.630  -0.630  -0.785  -0.731  -0.703
195   -        -0.793  -0.780  -0.763  -0.878  -0.876  -0.844  -0.785  -0.767  -0.730
196   -        -1.343  -1.326  -1.244  -1.402  -1.405  -1.251  -1.100  -1.077  -0.969
197   -        -1.343  -1.326  -1.244  -1.425  -1.425  -1.274  -1.100  -1.077  -0.969
198   -        -0.793  -0.816  -0.772  -0.839  -0.875  -0.847  -0.785  -0.807  -0.740
199   K        -0.157  -0.127  -0.151  -0.554  -0.516  -0.538  -0.356  -0.314  -0.339
200   K        -0.615  -0.673  -0.696  -0.828  -0.905  -0.936  -0.574  -0.643  -0.654
201   D        -1.705  -1.683  -1.605  -1.424  -1.387  -1.273  -1.231  -1.205  -1.101
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
206   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
207   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
208   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
209   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
210   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
211   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
212   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -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/P25348
Output conservation file - output/P25348
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
