1     M         1.889   1.925   2.043   1.954   2.004   2.198   2.091   2.149   2.355
2     S        -0.210  -0.401  -0.499  -0.272  -0.547  -0.684  -0.147  -0.390  -0.508
3     S         1.152   1.241   0.980   0.981   1.090   0.762   1.221   1.357   0.895
4     R         0.451   0.623   0.217   0.644   0.873   0.327   0.475   0.718   0.118
5     F         0.554   0.566   0.686   0.484   0.490   0.658   0.143   0.145   0.312
6     A         0.534   0.571   0.688   0.102   0.164   0.343   0.102   0.155   0.316
7     G        -1.162  -1.147  -1.081  -0.964  -0.917  -0.834  -1.003  -0.984  -0.891
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    G         0.719   0.744   0.735   0.511   0.535   0.438   0.467   0.498   0.414
11    N        -1.528  -1.506  -1.453  -1.510  -1.514  -1.435  -1.156  -1.133  -1.043
12    A        -0.074  -0.156  -0.022  -0.322  -0.441  -0.241  -0.344  -0.430  -0.259
13    Y        -0.482  -0.488  -0.530  -0.104  -0.110  -0.188  -0.519  -0.516  -0.550
14    Q         1.152   0.988   0.964   1.323   1.120   1.080   1.221   0.944   0.865
15    R         1.152   1.152   0.971   1.235   1.245   0.958   1.221   1.217   0.877
16    D         0.451   0.273   0.168   0.686   0.449   0.282   0.475   0.211   0.043
17    T        -1.160  -1.164  -1.058  -1.144  -1.133  -0.959  -1.017  -1.008  -0.873
18    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    R         0.451   0.273   0.168   0.588   0.343   0.139   0.475   0.211   0.043
20    T         0.129  -0.031   0.008  -0.015  -0.292  -0.310  -0.022  -0.242  -0.209
21    Q        -0.210  -0.401  -0.499   0.105  -0.140  -0.305  -0.147  -0.390  -0.508
22    L         1.152   1.152   0.971   1.063   1.065   0.832   1.221   1.217   0.877
23    F         0.789   0.698   0.756   0.827   0.692   0.760   0.599   0.409   0.456
24    G        -1.032  -1.072  -1.029  -0.983  -1.034  -1.001  -0.892  -0.919  -0.846
25    P        -1.032  -0.879  -0.986  -1.131  -0.943  -1.032  -0.892  -0.737  -0.807
26    A        -1.032  -1.062  -1.035  -0.726  -0.744  -0.719  -0.892  -0.909  -0.849
27    D        -0.565  -0.506  -0.557  -0.740  -0.683  -0.713  -0.644  -0.569  -0.590
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    G        -0.710  -0.676  -0.621  -0.885  -0.847  -0.776  -0.782  -0.737  -0.656
32    S         1.008   1.108   0.922   0.798   0.935   0.674   0.986   1.147   0.785
33    -        -0.715  -0.747  -0.657  -0.779  -0.864  -0.760  -0.773  -0.807  -0.695
34    -         0.031   0.112   0.042  -0.007   0.122  -0.027  -0.137  -0.023  -0.148
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    -        -0.259  -0.224  -0.106  -0.404  -0.332  -0.181  -0.561  -0.516  -0.368
42    N        -0.608  -0.630  -0.595  -0.604  -0.629  -0.582  -0.669  -0.691  -0.631
43    S        -0.608  -0.526  -0.588  -0.690  -0.588  -0.727  -0.669  -0.585  -0.624
44    L        -0.608  -0.482  -0.563  -0.575  -0.363  -0.522  -0.669  -0.519  -0.596
45    D        -0.608  -0.681  -0.619  -0.729  -0.827  -0.748  -0.669  -0.737  -0.654
46    D         0.644   0.720   0.766   0.476   0.589   0.649   0.323   0.451   0.476
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    N        -1.528  -1.397  -1.430  -1.373  -1.153  -1.253  -1.156  -1.030  -1.024
76    V        -1.528  -1.466  -1.422  -1.434  -1.340  -1.299  -1.156  -1.095  -1.018
77    S         0.332   0.181   0.074   0.202  -0.010  -0.184   0.305   0.082  -0.098
78    S         0.332   0.291   0.108   0.570   0.509   0.171   0.305   0.238  -0.047
79    A         0.021   0.057  -0.000   0.140   0.176   0.077  -0.182  -0.147  -0.224
80    L        -0.540  -0.616  -0.590  -0.452  -0.583  -0.582  -0.561  -0.652  -0.618
81    G        -0.540  -0.446  -0.540  -0.354  -0.203  -0.391  -0.561  -0.443  -0.557
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    S         0.451   0.613   0.198   0.755   0.977   0.355   0.475   0.705   0.089
89    T        -1.141  -1.055  -1.045  -1.149  -1.005  -1.021  -0.994  -0.909  -0.861
90    D        -1.528  -1.397  -1.430  -1.507  -1.346  -1.338  -1.156  -1.030  -1.024
91    K        -1.528  -1.519  -1.451  -1.380  -1.344  -1.277  -1.156  -1.140  -1.041
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    L        -1.141  -1.158  -1.089  -1.186  -1.213  -1.089  -0.994  -0.999  -0.898
94    D        -0.220  -0.207  -0.095  -0.375  -0.354  -0.200  -0.507  -0.493  -0.352
95    Y         1.889   1.925   2.043   2.091   2.144   2.336   2.091   2.149   2.355
96    S         0.719   0.790   0.798   0.379   0.491   0.485   0.467   0.586   0.541
97    Q        -0.608  -0.681  -0.619  -0.558  -0.653  -0.577  -0.669  -0.737  -0.654
98    S         0.129   0.009   0.026  -0.104  -0.262  -0.237  -0.022  -0.179  -0.186
99    T        -1.371  -1.421  -1.415  -1.033  -1.062  -1.080  -1.017  -1.060  -1.012
100   L         1.889   1.925   2.043   1.702   1.746   1.944   2.091   2.149   2.355
101   A        -1.160  -1.162  -1.058  -1.322  -1.311  -1.186  -1.017  -1.007  -0.874
102   S        -0.482  -0.417  -0.527  -0.588  -0.511  -0.591  -0.519  -0.439  -0.552
103   L         1.889   1.925   2.043   1.702   1.746   1.944   2.091   2.149   2.355
104   E         1.889   1.925   2.043   1.978   2.020   2.223   2.091   2.149   2.355
105   S         1.152   0.988   0.964   0.983   0.762   0.740   1.221   0.944   0.865
106   Q         1.152   0.988   0.964   1.323   1.120   1.080   1.221   0.944   0.865
107   S         0.595   0.692   0.743   0.272   0.465   0.489   0.226   0.398   0.430
108   E        -0.144  -0.010  -0.001  -0.195   0.025   0.015  -0.395  -0.203  -0.212
109   E         1.152   1.245   0.985   1.340   1.451   1.127   1.221   1.363   0.904
110   Q         0.129   0.053   0.062   0.210   0.125   0.107  -0.022  -0.110  -0.121
111   M         0.129   0.005   0.029   0.230   0.062   0.077  -0.022  -0.185  -0.183
112   G        -1.160  -1.154  -1.076  -1.156  -1.193  -1.053  -1.017  -0.999  -0.888
113   A        -1.032  -1.037  -1.034  -0.917  -0.939  -0.907  -0.892  -0.900  -0.851
114   M         0.129   0.025   0.005   0.117  -0.100  -0.136  -0.022  -0.192  -0.218
115   G        -0.693  -0.690  -0.608  -0.984  -0.961  -0.833  -0.768  -0.756  -0.648
116   Q        -0.693  -0.682  -0.622  -0.682  -0.671  -0.574  -0.768  -0.750  -0.662
117   R         1.152   1.245   0.983   1.259   1.378   1.036   1.221   1.363   0.900
118   I         0.595   0.692   0.743   0.515   0.680   0.737   0.226   0.398   0.430
119   K        -1.032  -0.907  -0.988  -0.910  -0.717  -0.837  -0.892  -0.754  -0.807
120   A        -1.032  -1.092  -1.039  -1.068  -1.217  -1.134  -0.892  -0.942  -0.856
121   L         1.889   1.925   2.043   1.702   1.746   1.944   2.091   2.149   2.355
122   K         1.889   1.925   2.043   1.904   1.952   2.148   2.091   2.149   2.355
123   S        -0.693  -0.746  -0.624  -0.843  -0.888  -0.726  -0.768  -0.808  -0.662
124   L         0.451   0.407   0.154   0.444   0.386   0.047   0.475   0.412   0.023
125   S        -0.227  -0.147  -0.070  -0.635  -0.464  -0.381  -0.519  -0.412  -0.318
126   L        -1.498  -1.449  -1.407  -1.499  -1.419  -1.347  -1.141  -1.088  -1.008
127   K        -0.565  -0.659  -0.549  -0.579  -0.686  -0.527  -0.644  -0.724  -0.585
128   M         0.595   0.573   0.690   0.468   0.412   0.588   0.226   0.160   0.320
129   G         1.889   1.925   2.043   1.909   1.957   2.153   2.091   2.149   2.355
130   D        -0.144  -0.157  -0.085  -0.199  -0.225  -0.138  -0.395  -0.421  -0.336
131   E         1.889   1.925   2.043   1.978   2.020   2.223   2.091   2.149   2.355
132   I         1.889   1.925   2.043   1.983   2.036   2.228   2.091   2.149   2.355
133   R         0.129   0.053   0.062   0.150   0.067   0.046  -0.022  -0.110  -0.121
134   G        -0.693  -0.751  -0.632  -0.818  -0.934  -0.759  -0.768  -0.814  -0.670
135   S         1.889   1.925   2.043   1.624   1.666   1.865   2.091   2.149   2.355
136   N        -1.032  -1.051  -1.046  -1.034  -1.104  -1.064  -0.892  -0.912  -0.861
137   Q        -0.482  -0.464  -0.526  -0.340  -0.287  -0.365  -0.519  -0.478  -0.547
138   T         0.595   0.692   0.743   0.203   0.365   0.423   0.226   0.398   0.430
139   I        -1.032  -1.073  -1.031  -1.058  -1.108  -1.020  -0.892  -0.921  -0.844
140   D         0.129   0.031   0.007   0.216   0.047   0.018  -0.022  -0.187  -0.213
141   Q        -1.371  -1.421  -1.415  -1.148  -1.290  -1.269  -1.017  -1.060  -1.012
142   L        -0.144  -0.147  -0.064  -0.408  -0.420  -0.288  -0.395  -0.411  -0.307
143   G        -1.160  -1.088  -1.070  -1.101  -0.982  -0.949  -1.017  -0.941  -0.883
144   D        -0.016   0.014   0.007  -0.060   0.013   0.002  -0.271  -0.210  -0.219
145   T        -0.482  -0.441  -0.536  -0.545  -0.564  -0.650  -0.519  -0.503  -0.563
146   F         1.152   1.245   0.985   1.295   1.427   1.082   1.221   1.363   0.904
147   H        -0.482  -0.429  -0.546  -0.277  -0.253  -0.345  -0.519  -0.491  -0.575
148   N        -1.160  -1.155  -1.058  -1.191  -1.221  -1.054  -1.017  -1.002  -0.873
149   T         0.129   0.187   0.079   0.143   0.260   0.077  -0.022   0.074  -0.095
150   S        -0.565  -0.513  -0.565  -0.811  -0.724  -0.786  -0.644  -0.584  -0.602
151   V        -1.498  -1.524  -1.446  -1.412  -1.525  -1.403  -1.141  -1.147  -1.038
152   K        -0.693  -0.737  -0.616  -0.828  -0.902  -0.735  -0.768  -0.797  -0.654
153   L         1.889   1.925   2.043   1.702   1.746   1.944   2.091   2.149   2.355
154   K         0.451   0.261   0.141   0.576   0.279   0.071   0.475   0.194   0.003
155   R        -0.693  -0.545  -0.598  -0.738  -0.509  -0.586  -0.768  -0.594  -0.632
156   T         1.889   1.925   2.043   1.904   1.970   2.148   2.091   2.149   2.355
157   F        -0.482  -0.448  -0.562  -0.300  -0.285  -0.376  -0.519  -0.510  -0.593
158   G        -0.482  -0.535  -0.526  -0.407  -0.485  -0.482  -0.519  -0.578  -0.551
159   N        -0.144  -0.010  -0.001  -0.269  -0.042  -0.060  -0.395  -0.203  -0.212
160   M         1.152   0.988   0.964   1.279   1.043   0.991   1.221   0.944   0.865
161   M        -0.482  -0.579  -0.559  -0.408  -0.552  -0.557  -0.519  -0.615  -0.584
162   E        -1.032  -1.037  -1.034  -0.793  -0.821  -0.792  -0.892  -0.900  -0.851
163   M         1.152   0.988   0.964   1.322   1.111   1.084   1.221   0.944   0.865
164   A         0.595   0.601   0.707   0.290   0.265   0.408   0.226   0.217   0.355
165   R        -0.482  -0.481  -0.532  -0.381  -0.389  -0.469  -0.519  -0.530  -0.563
166   R        -0.016  -0.034  -0.001  -0.115  -0.134  -0.077  -0.271  -0.294  -0.235
167   S        -0.482  -0.579  -0.559  -0.674  -0.802  -0.765  -0.519  -0.615  -0.584
168   G         0.129   0.194   0.083   0.144   0.262   0.076  -0.022   0.090  -0.093
169   I         1.152   1.138   0.963   1.351   1.342   1.111   1.221   1.195   0.863
170   S        -0.482  -0.393  -0.521  -0.659  -0.559  -0.681  -0.519  -0.428  -0.545
171   I        -0.016   0.052   0.005   0.043   0.131   0.059  -0.271  -0.199  -0.226
172   K        -0.016  -0.118   0.000  -0.095  -0.201  -0.032  -0.271  -0.384  -0.234
173   T        -0.693  -0.606  -0.616  -0.669  -0.536  -0.539  -0.768  -0.672  -0.653
174   W         1.889   1.925   2.043   2.123   2.178   2.369   2.091   2.149   2.355
175   L         0.129   0.270   0.056  -0.051   0.155  -0.159  -0.022   0.185  -0.139
176   I        -1.160  -1.097  -1.061  -1.186  -1.067  -1.039  -1.017  -0.947  -0.877
177   I        -0.821  -0.767  -0.663  -0.956  -0.868  -0.742  -0.892  -0.828  -0.702
178   F         1.889   1.925   2.043   1.934   1.997   2.178   2.091   2.149   2.355
179   F        -1.160  -1.158  -1.067  -1.070  -1.004  -0.919  -1.017  -1.002  -0.881
180   M        -1.498  -1.499  -1.412  -1.303  -1.344  -1.186  -1.141  -1.130  -1.013
181   V        -0.016   0.084   0.032  -0.051   0.098   0.017  -0.271  -0.141  -0.191
182   G        -1.032  -1.070  -1.005  -0.894  -0.919  -0.844  -0.892  -0.918  -0.823
183   V        -0.210  -0.122  -0.408  -0.162  -0.050  -0.424  -0.147  -0.035  -0.393
184   L        -0.482  -0.569  -0.539  -0.429  -0.531  -0.440  -0.519  -0.605  -0.559
185   F         1.152   0.988   0.964   1.259   1.036   0.972   1.221   0.944   0.865
186   F         1.152   0.988   0.964   1.302   1.104   1.065   1.221   0.944   0.865
187   W        -0.482  -0.568  -0.512  -0.205  -0.344  -0.269  -0.519  -0.604  -0.536
188   V         1.889   1.925   2.043   2.007   2.055   2.252   2.091   2.149   2.355
189   W         0.789   0.692   0.753   0.946   0.764   0.821   0.599   0.398   0.450
190   I        -1.032  -1.121  -1.057  -0.915  -1.017  -0.916  -0.892  -0.962  -0.870
191   T        -0.754  -0.764  -0.643  -0.915  -0.933  -0.769  -0.831  -0.829  -0.681
* 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/P22804
Output conservation file - output/P22804
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
