1     M         1.491   1.504   1.553   1.729   1.747   1.824   1.621   1.640   1.712
2     K        -0.616  -0.561  -0.568  -0.773  -0.670  -0.704  -0.747  -0.680  -0.662
3     Y        -0.407  -0.387  -0.505  -0.396  -0.372  -0.562  -0.451  -0.422  -0.574
4     N        -1.724  -1.700  -1.618  -1.666  -1.618  -1.504  -1.340  -1.312  -1.197
5     I        -1.170  -1.183  -1.134  -1.048  -1.077  -0.995  -1.043  -1.055  -0.972
6     V        -1.170  -1.077  -1.127  -1.108  -0.962  -1.049  -1.043  -0.937  -0.965
7     H        -1.278  -1.251  -1.178  -1.244  -1.186  -1.090  -1.155  -1.122  -1.015
8     G        -1.278  -1.251  -1.178  -1.230  -1.167  -1.077  -1.155  -1.122  -1.015
9     I        -0.407  -0.426  -0.499  -0.280  -0.336  -0.419  -0.451  -0.481  -0.566
10    C        -1.724  -1.700  -1.618  -1.645  -1.632  -1.483  -1.340  -1.312  -1.197
11    L         0.146   0.197   0.227  -0.155  -0.085  -0.023  -0.155  -0.067  -0.033
12    L        -0.407  -0.426  -0.499  -0.498  -0.513  -0.610  -0.451  -0.481  -0.566
13    F        -0.407  -0.387  -0.505  -0.506  -0.478  -0.629  -0.451  -0.422  -0.574
14    A        -1.170  -1.201  -1.162  -1.139  -1.204  -1.109  -1.043  -1.072  -1.000
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    I        -0.407  -0.455  -0.519  -0.555  -0.640  -0.717  -0.451  -0.518  -0.592
17    T        -1.170  -1.171  -1.132  -1.239  -1.216  -1.158  -1.043  -1.041  -0.969
18    Q         0.491   0.394   0.328   0.626   0.486   0.382   0.437   0.276   0.146
19    A        -1.170  -1.130  -1.123  -1.254  -1.204  -1.165  -1.043  -0.995  -0.960
20    V        -1.170  -1.171  -1.132  -1.148  -1.139  -1.091  -1.043  -1.041  -0.969
21    G        -0.407  -0.455  -0.519  -0.251  -0.325  -0.418  -0.451  -0.518  -0.592
22    A        -0.407  -0.446  -0.503  -0.154  -0.207  -0.285  -0.451  -0.506  -0.572
23    V        -0.407  -0.455  -0.519  -0.498  -0.555  -0.636  -0.451  -0.518  -0.592
24    H         1.491   1.504   1.553   1.662   1.685   1.757   1.621   1.640   1.712
25    F        -0.407  -0.495  -0.524  -0.329  -0.468  -0.525  -0.451  -0.569  -0.599
26    Y         1.491   1.504   1.553   1.637   1.654   1.733   1.621   1.640   1.712
27    A        -0.616  -0.586  -0.565  -0.889  -0.855  -0.789  -0.747  -0.709  -0.659
28    K         1.491   1.504   1.553   1.397   1.419   1.498   1.621   1.640   1.712
29    S         0.146   0.197   0.227  -0.065   0.028   0.066  -0.155  -0.067  -0.033
30    G         1.491   1.504   1.553   1.603   1.625   1.700   1.621   1.640   1.712
31    E         1.491   1.504   1.553   1.458   1.479   1.558   1.621   1.640   1.712
32    T        -0.407  -0.495  -0.524  -0.279  -0.413  -0.435  -0.451  -0.569  -0.599
33    K         0.491   0.549   0.362   0.478   0.558   0.297   0.437   0.527   0.205
34    C         1.491   1.504   1.553   1.715   1.733   1.809   1.621   1.640   1.712
35    F         0.491   0.394   0.328   0.596   0.464   0.364   0.437   0.276   0.146
36    Y         0.491   0.549   0.362   0.694   0.774   0.488   0.437   0.527   0.205
37    E         0.491   0.482   0.350   0.492   0.480   0.261   0.437   0.421   0.186
38    H        -0.616  -0.609  -0.576  -0.585  -0.553  -0.503  -0.747  -0.732  -0.670
39    L         1.491   1.504   1.553   1.272   1.286   1.375   1.621   1.640   1.712
40    S        -1.170  -1.183  -1.134  -1.076  -1.113  -1.016  -1.043  -1.055  -0.972
41    R        -1.170  -1.077  -1.127  -1.133  -0.996  -1.058  -1.043  -0.937  -0.965
42    G        -0.407  -0.302  -0.498  -0.225  -0.062  -0.383  -0.451  -0.307  -0.565
43    N        -1.170  -1.201  -1.162  -1.124  -1.179  -1.115  -1.043  -1.072  -1.000
44    L         0.491   0.482   0.350   0.306   0.289   0.087   0.437   0.421   0.186
45    L         0.146   0.197   0.227  -0.264  -0.179  -0.131  -0.155  -0.067  -0.033
46    I        -0.616  -0.653  -0.588  -0.718  -0.758  -0.648  -0.747  -0.782  -0.684
47    G         0.491   0.394   0.328   0.678   0.540   0.429   0.437   0.276   0.146
48    D        -0.616  -0.653  -0.588  -0.755  -0.794  -0.689  -0.747  -0.782  -0.684
49    L        -0.616  -0.653  -0.588  -0.834  -0.893  -0.778  -0.747  -0.782  -0.684
50    D         1.491   1.504   1.553   1.483   1.502   1.582   1.621   1.640   1.712
51    L        -0.616  -0.578  -0.573  -0.726  -0.673  -0.680  -0.747  -0.697  -0.666
52    Y        -1.170  -1.195  -1.136  -0.995  -1.054  -0.963  -1.043  -1.067  -0.973
53    V         0.146   0.197   0.227  -0.119  -0.025   0.012  -0.155  -0.067  -0.033
54    E        -0.616  -0.579  -0.569  -0.866  -0.802  -0.797  -0.747  -0.701  -0.663
55    -         0.219   0.293   0.249   0.149   0.279   0.179  -0.024   0.104   0.006
56    K        -0.616  -0.588  -0.563  -0.708  -0.664  -0.625  -0.747  -0.711  -0.657
57    D        -0.616  -0.566  -0.567  -0.614  -0.552  -0.520  -0.747  -0.688  -0.661
58    G         0.491   0.574   0.367   0.648   0.770   0.447   0.437   0.567   0.215
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    L        -1.724  -1.700  -1.618  -1.738  -1.700  -1.575  -1.340  -1.312  -1.197
61    F         0.146   0.136   0.193   0.113   0.085   0.165  -0.155  -0.177  -0.096
62    E        -1.170  -1.152  -1.149  -1.141  -1.106  -1.112  -1.043  -1.022  -0.987
63    E         0.146   0.161   0.208  -0.119  -0.093  -0.023  -0.155  -0.132  -0.069
64    D         0.146   0.197   0.227  -0.004   0.084   0.125  -0.155  -0.067  -0.033
65    P        -0.407  -0.446  -0.503  -0.068  -0.141  -0.234  -0.451  -0.506  -0.572
66    E        -1.170  -1.201  -1.162  -1.139  -1.216  -1.154  -1.043  -1.072  -1.000
67    S        -0.616  -0.578  -0.573  -0.938  -0.865  -0.841  -0.747  -0.697  -0.666
68    S        -1.170  -1.171  -1.132  -1.184  -1.188  -1.121  -1.043  -1.041  -0.969
69    L         0.146   0.173   0.206  -0.264  -0.223  -0.168  -0.155  -0.111  -0.072
70    T        -0.616  -0.578  -0.573  -0.690  -0.637  -0.622  -0.747  -0.697  -0.666
71    I         0.491   0.482   0.350   0.542   0.523   0.308   0.437   0.421   0.186
72    T        -0.407  -0.356  -0.477  -0.367  -0.293  -0.483  -0.451  -0.382  -0.536
73    V         0.146   0.127   0.191  -0.089  -0.124  -0.019  -0.155  -0.194  -0.100
74    D        -0.616  -0.609  -0.576  -0.693  -0.676  -0.609  -0.747  -0.732  -0.670
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    E         1.491   1.504   1.553   1.458   1.479   1.558   1.621   1.640   1.712
79    T         1.491   1.504   1.553   1.468   1.488   1.568   1.621   1.640   1.712
80    F         1.491   1.504   1.553   1.503   1.527   1.602   1.621   1.640   1.712
81    D         1.491   1.504   1.553   1.483   1.502   1.582   1.621   1.640   1.712
82    N         0.491   0.482   0.350   0.582   0.572   0.361   0.437   0.421   0.186
83    D         0.146   0.144   0.195  -0.004  -0.011   0.067  -0.155  -0.164  -0.093
84    H         1.491   1.504   1.553   1.662   1.685   1.757   1.621   1.640   1.712
85    R        -0.616  -0.609  -0.576  -0.690  -0.666  -0.604  -0.747  -0.732  -0.670
86    V         1.491   1.504   1.553   1.397   1.422   1.498   1.621   1.640   1.712
87    L        -0.407  -0.302  -0.498  -0.550  -0.401  -0.679  -0.451  -0.307  -0.565
88    N        -0.407  -0.446  -0.503  -0.279  -0.337  -0.433  -0.451  -0.506  -0.572
89    Q         1.491   1.504   1.553   1.548   1.567   1.646   1.621   1.640   1.712
90    K         1.491   1.504   1.553   1.397   1.419   1.498   1.621   1.640   1.712
91    N        -0.616  -0.653  -0.588  -0.665  -0.703  -0.599  -0.747  -0.782  -0.684
92    S        -1.724  -1.700  -1.618  -1.477  -1.450  -1.319  -1.340  -1.312  -1.197
93    H        -0.407  -0.387  -0.505  -0.023   0.006  -0.175  -0.451  -0.422  -0.574
94    T        -1.170  -1.152  -1.149  -1.087  -1.059  -1.051  -1.043  -1.022  -0.987
95    G         1.491   1.504   1.553   1.603   1.625   1.700   1.621   1.640   1.712
96    D        -0.407  -0.446  -0.503  -0.299  -0.345  -0.440  -0.451  -0.506  -0.572
97    V         0.491   0.536   0.354   0.537   0.608   0.310   0.437   0.507   0.192
98    T        -0.407  -0.426  -0.499  -0.345  -0.386  -0.489  -0.451  -0.481  -0.566
99    F         1.491   1.504   1.553   1.503   1.527   1.602   1.621   1.640   1.712
100   T         0.491   0.394   0.328   0.515   0.370   0.254   0.437   0.276   0.146
101   A         0.146   0.197   0.227   0.035   0.130   0.163  -0.155  -0.067  -0.033
102   L         0.491   0.394   0.328   0.306   0.154   0.048   0.437   0.276   0.146
103   D         0.491   0.394   0.328   0.532   0.384   0.270   0.437   0.276   0.146
104   T        -1.170  -1.201  -1.162  -1.169  -1.224  -1.164  -1.043  -1.072  -1.000
105   G         1.491   1.504   1.553   1.603   1.625   1.700   1.621   1.640   1.712
106   E         1.491   1.504   1.553   1.458   1.479   1.558   1.621   1.640   1.712
107   H         1.491   1.504   1.553   1.662   1.685   1.757   1.621   1.640   1.712
108   R         0.146   0.139   0.194   0.008  -0.019   0.057  -0.155  -0.173  -0.095
109   F         0.146   0.127   0.191   0.002  -0.040   0.062  -0.155  -0.194  -0.100
110   C         1.491   1.504   1.553   1.715   1.733   1.809   1.621   1.640   1.712
111   F        -0.407  -0.387  -0.505  -0.576  -0.549  -0.724  -0.451  -0.422  -0.574
112   T        -0.407  -0.495  -0.524  -0.383  -0.525  -0.584  -0.451  -0.569  -0.599
113   P         1.491   1.504   1.553   1.729   1.748   1.824   1.621   1.640   1.712
114   F        -1.724  -1.700  -1.618  -1.623  -1.557  -1.462  -1.340  -1.312  -1.197
115   Y         1.491   1.504   1.553   1.637   1.654   1.733   1.621   1.640   1.712
116   S         0.146   0.127   0.191   0.087   0.069   0.174  -0.155  -0.194  -0.100
117   K         0.491   0.536   0.354   0.517   0.582   0.291   0.437   0.507   0.192
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   K        -0.407  -0.312  -0.468  -0.393  -0.246  -0.495  -0.451  -0.321  -0.524
121   S        -0.407  -0.455  -0.519  -0.323  -0.402  -0.520  -0.451  -0.518  -0.592
122   A        -1.170  -1.201  -1.162  -1.120  -1.159  -1.086  -1.043  -1.072  -1.000
123   T        -1.724  -1.700  -1.618  -1.443  -1.392  -1.286  -1.340  -1.312  -1.197
124   L        -0.616  -0.578  -0.573  -0.637  -0.589  -0.599  -0.747  -0.697  -0.666
125   R         0.491   0.394   0.328   0.615   0.462   0.337   0.437   0.276   0.146
126   V        -0.616  -0.653  -0.588  -0.829  -0.904  -0.803  -0.747  -0.782  -0.684
127   F         0.146   0.127   0.191   0.076   0.048   0.149  -0.155  -0.194  -0.100
128   I        -1.170  -1.201  -1.162  -1.103  -1.145  -1.102  -1.043  -1.072  -1.000
129   E        -0.407  -0.455  -0.519  -0.329  -0.402  -0.506  -0.451  -0.518  -0.592
130   L        -0.616  -0.653  -0.588  -0.916  -0.965  -0.849  -0.747  -0.782  -0.684
131   E        -0.616  -0.653  -0.588  -0.659  -0.716  -0.614  -0.747  -0.782  -0.684
132   I        -0.407  -0.302  -0.498  -0.312  -0.161  -0.460  -0.451  -0.307  -0.565
133   G         0.491   0.482   0.350   0.648   0.639   0.418   0.437   0.421   0.186
134   N         0.146   0.161   0.208  -0.030  -0.004   0.066  -0.155  -0.132  -0.069
135   V        -1.170  -1.130  -1.123  -1.079  -1.010  -1.021  -1.043  -0.995  -0.960
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   E        -0.407  -0.446  -0.503  -0.367  -0.432  -0.522  -0.451  -0.506  -0.572
138   A        -0.616  -0.653  -0.588  -0.545  -0.608  -0.510  -0.747  -0.782  -0.684
139   L        -0.407  -0.302  -0.498  -0.574  -0.421  -0.712  -0.451  -0.307  -0.565
140   D         0.491   0.394   0.328   0.554   0.412   0.308   0.437   0.276   0.146
141   S         0.491   0.482   0.350   0.504   0.494   0.285   0.437   0.421   0.186
142   K         0.491   0.394   0.328   0.478   0.342   0.244   0.437   0.276   0.146
143   K        -1.170  -1.201  -1.162  -1.089  -1.123  -1.067  -1.043  -1.072  -1.000
144   K        -0.616  -0.653  -0.588  -0.766  -0.809  -0.705  -0.747  -0.782  -0.684
145   E        -1.724  -1.700  -1.618  -1.470  -1.447  -1.312  -1.340  -1.312  -1.197
146   D        -1.724  -1.700  -1.618  -1.374  -1.350  -1.218  -1.340  -1.312  -1.197
147   M        -0.616  -0.609  -0.576  -0.602  -0.566  -0.519  -0.747  -0.732  -0.670
148   N        -1.170  -1.201  -1.162  -1.097  -1.155  -1.087  -1.043  -1.072  -1.000
149   S        -1.170  -1.108  -1.131  -1.079  -0.986  -1.014  -1.043  -0.972  -0.969
150   L         1.491   1.504   1.553   1.272   1.286   1.375   1.621   1.640   1.712
151   K        -0.616  -0.609  -0.576  -0.745  -0.732  -0.663  -0.747  -0.732  -0.670
152   G        -1.170  -1.195  -1.136  -1.141  -1.190  -1.122  -1.043  -1.067  -0.973
153   R         0.146   0.197   0.227   0.008   0.107   0.136  -0.155  -0.067  -0.033
154   V         0.491   0.394   0.328   0.459   0.320   0.212   0.437   0.276   0.146
155   G        -1.724  -1.700  -1.618  -1.424  -1.382  -1.267  -1.340  -1.312  -1.197
156   Q         0.491   0.549   0.362   0.613   0.694   0.416   0.437   0.527   0.205
157   L         1.491   1.504   1.553   1.272   1.286   1.375   1.621   1.640   1.712
158   T        -0.407  -0.312  -0.468  -0.265  -0.126  -0.357  -0.451  -0.321  -0.524
159   Q        -1.170  -1.152  -1.149  -1.112  -1.088  -1.101  -1.043  -1.022  -0.987
160   R         0.146   0.197   0.227   0.008   0.107   0.136  -0.155  -0.067  -0.033
161   L         1.491   1.504   1.553   1.272   1.286   1.375   1.621   1.640   1.712
162   S        -1.724  -1.700  -1.618  -1.735  -1.721  -1.572  -1.340  -1.312  -1.197
163   S        -1.170  -1.108  -1.131  -1.173  -1.067  -1.119  -1.043  -0.972  -0.969
164   I         1.491   1.504   1.553   1.508   1.521   1.607   1.621   1.640   1.712
165   R        -0.616  -0.653  -0.588  -0.544  -0.608  -0.517  -0.747  -0.782  -0.684
166   K        -1.170  -1.201  -1.162  -0.801  -0.858  -0.826  -1.043  -1.072  -1.000
167   E         1.491   1.504   1.553   1.458   1.479   1.558   1.621   1.640   1.712
168   Q         1.491   1.504   1.553   1.548   1.567   1.646   1.621   1.640   1.712
169   D         0.146   0.197   0.227  -0.044   0.048   0.085  -0.155  -0.067  -0.033
170   A        -1.170  -1.201  -1.162  -0.969  -1.033  -0.993  -1.043  -1.072  -1.000
171   I         0.146   0.197   0.227   0.133   0.201   0.259  -0.155  -0.067  -0.033
172   R         0.491   0.394   0.328   0.615   0.462   0.337   0.437   0.276   0.146
173   E         0.146   0.139   0.194  -0.101  -0.121  -0.041  -0.155  -0.173  -0.095
174   K        -0.616  -0.609  -0.576  -0.683  -0.678  -0.618  -0.747  -0.732  -0.670
175   E         1.491   1.504   1.553   1.458   1.479   1.558   1.621   1.640   1.712
176   A         1.491   1.504   1.553   1.578   1.596   1.675   1.621   1.640   1.712
177   E        -1.724  -1.700  -1.618  -1.688  -1.659  -1.526  -1.340  -1.312  -1.197
178   F         1.491   1.504   1.553   1.503   1.527   1.602   1.621   1.640   1.712
179   R         1.491   1.504   1.553   1.583   1.600   1.680   1.621   1.640   1.712
180   N        -0.616  -0.653  -0.588  -0.686  -0.737  -0.637  -0.747  -0.782  -0.684
181   Q         0.491   0.394   0.328   0.663   0.531   0.443   0.437   0.276   0.146
182   S         0.491   0.394   0.328   0.504   0.361   0.247   0.437   0.276   0.146
183   E         1.491   1.504   1.553   1.458   1.479   1.558   1.621   1.640   1.712
184   S        -1.170  -1.195  -1.136  -1.148  -1.193  -1.097  -1.043  -1.067  -0.973
185   A         0.146   0.161   0.208   0.012   0.034   0.109  -0.155  -0.132  -0.069
186   N         1.491   1.504   1.553   1.528   1.550   1.627   1.621   1.640   1.712
187   S         0.491   0.394   0.328   0.502   0.358   0.242   0.437   0.276   0.146
188   K        -0.616  -0.653  -0.588  -0.709  -0.768  -0.667  -0.747  -0.782  -0.684
189   I         0.146   0.161   0.208  -0.089  -0.066   0.008  -0.155  -0.132  -0.069
190   M        -0.616  -0.578  -0.573  -0.691  -0.630  -0.581  -0.747  -0.697  -0.666
191   T        -1.724  -1.700  -1.618  -1.527  -1.473  -1.368  -1.340  -1.312  -1.197
192   W         1.491   1.504   1.553   1.777   1.798   1.871   1.621   1.640   1.712
193   S         0.491   0.482   0.350   0.504   0.494   0.285   0.437   0.421   0.186
194   V        -0.407  -0.387  -0.505  -0.420  -0.397  -0.622  -0.451  -0.422  -0.574
195   F        -1.170  -1.171  -1.132  -1.263  -1.289  -1.209  -1.043  -1.041  -0.969
196   Q         0.491   0.394   0.328   0.551   0.390   0.254   0.437   0.276   0.146
197   L        -0.407  -0.495  -0.524  -0.550  -0.692  -0.718  -0.451  -0.569  -0.599
198   L        -1.170  -1.183  -1.134  -1.318  -1.347  -1.249  -1.043  -1.055  -0.972
199   I         0.146   0.161   0.208  -0.089  -0.066   0.008  -0.155  -0.132  -0.069
200   L         1.491   1.504   1.553   1.272   1.286   1.375   1.621   1.640   1.712
201   L        -1.170  -1.130  -1.123  -1.230  -1.163  -1.158  -1.043  -0.995  -0.960
202   G         0.491   0.394   0.328   0.635   0.487   0.355   0.437   0.276   0.146
203   T         0.491   0.482   0.350   0.585   0.575   0.404   0.437   0.421   0.186
204   C         1.491   1.504   1.553   1.715   1.733   1.809   1.621   1.640   1.712
205   A        -1.170  -1.201  -1.162  -1.150  -1.192  -1.121  -1.043  -1.072  -1.000
206   F         0.146   0.197   0.227   0.076   0.159   0.203  -0.155  -0.067  -0.033
207   Q         1.491   1.504   1.553   1.548   1.567   1.646   1.621   1.640   1.712
208   L         0.491   0.482   0.350   0.306   0.289   0.087   0.437   0.421   0.186
209   R         0.491   0.482   0.350   0.629   0.614   0.399   0.437   0.421   0.186
210   Y         0.146   0.197   0.227   0.201   0.286   0.326  -0.155  -0.067  -0.033
211   L         1.491   1.504   1.553   1.272   1.286   1.375   1.621   1.640   1.712
212   K         1.491   1.504   1.553   1.397   1.419   1.498   1.621   1.640   1.712
213   N        -1.170  -1.152  -1.149  -1.052  -1.029  -1.026  -1.043  -1.022  -0.987
214   F         0.491   0.394   0.328   0.507   0.350   0.212   0.437   0.276   0.146
215   F         1.491   1.504   1.553   1.503   1.527   1.602   1.621   1.640   1.712
216   V         0.491   0.394   0.328   0.459   0.320   0.212   0.437   0.276   0.146
217   K         1.491   1.504   1.553   1.397   1.419   1.498   1.621   1.640   1.712
218   Q         1.491   1.504   1.553   1.548   1.567   1.646   1.621   1.640   1.712
219   K         1.491   1.504   1.553   1.397   1.419   1.498   1.621   1.640   1.712
220   V        -0.616  -0.653  -0.588  -0.729  -0.777  -0.669  -0.747  -0.782  -0.684
221   V        -0.407  -0.495  -0.524  -0.430  -0.566  -0.613  -0.451  -0.569  -0.599
* 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/P38819
Output conservation file - output/P38819
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
