1     M         1.534   1.553   1.624   1.768   1.798   1.905   1.704   1.734   1.852
2     S        -1.258  -1.262  -1.167  -1.211  -1.206  -1.066  -1.106  -1.103  -0.974
3     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    G        -1.238  -1.224  -1.157  -1.214  -1.199  -1.118  -1.098  -1.076  -0.968
27    D        -1.592  -1.603  -1.490  -1.341  -1.366  -1.191  -1.245  -1.245  -1.100
28    E        -1.238  -1.146  -1.154  -1.181  -1.067  -1.057  -1.098  -1.007  -0.965
29    R        -0.688  -0.695  -0.751  -0.687  -0.703  -0.823  -0.704  -0.711  -0.762
30    L        -1.258  -1.230  -1.175  -1.271  -1.229  -1.170  -1.106  -1.072  -0.982
31    L        -1.258  -1.230  -1.175  -1.116  -1.068  -1.001  -1.106  -1.072  -0.982
32    F        -1.258  -1.227  -1.173  -1.094  -1.047  -0.994  -1.106  -1.070  -0.980
33    L        -0.688  -0.695  -0.751  -0.736  -0.748  -0.841  -0.704  -0.711  -0.762
34    R        -1.258  -1.230  -1.175  -1.437  -1.393  -1.297  -1.106  -1.072  -0.982
35    S        -1.258  -1.227  -1.163  -1.138  -1.092  -0.991  -1.106  -1.068  -0.970
36    V         0.728   0.697   0.574   0.817   0.781   0.574   0.701   0.645   0.394
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    G        -1.592  -1.520  -1.482  -1.331  -1.231  -1.165  -1.245  -1.177  -1.094
39    E        -0.750  -0.773  -0.727  -0.721  -0.757  -0.686  -0.803  -0.820  -0.740
40    R        -1.238  -1.251  -1.173  -1.208  -1.234  -1.127  -1.098  -1.099  -0.982
41    N         0.464   0.452   0.457   0.377   0.349   0.348   0.230   0.199   0.166
42    E        -1.258  -1.273  -1.186  -1.283  -1.304  -1.160  -1.106  -1.114  -0.992
43    I        -1.258  -1.273  -1.186  -1.083  -1.141  -1.028  -1.106  -1.114  -0.992
44    G        -1.258  -1.273  -1.186  -1.216  -1.272  -1.131  -1.106  -1.114  -0.992
45    F        -0.688  -0.661  -0.735  -0.616  -0.571  -0.650  -0.704  -0.668  -0.743
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    P        -0.530  -0.567  -0.667  -0.463  -0.521  -0.674  -0.508  -0.556  -0.663
53    S        -1.238  -1.251  -1.173  -1.255  -1.289  -1.193  -1.098  -1.099  -0.982
54    R        -1.238  -1.253  -1.171  -1.334  -1.376  -1.235  -1.098  -1.101  -0.980
55    F         1.534   1.553   1.624   1.724   1.755   1.862   1.704   1.734   1.852
56    K         0.464   0.401   0.438   0.189   0.081   0.122   0.230   0.101   0.128
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    S        -0.530  -0.426  -0.672  -0.440  -0.289  -0.676  -0.508  -0.376  -0.669
59    A        -0.530  -0.454  -0.665  -0.476  -0.375  -0.690  -0.508  -0.413  -0.661
60    H        -1.238  -1.222  -1.164  -1.030  -1.028  -0.921  -1.098  -1.071  -0.973
61    Y        -0.884  -0.834  -0.777  -0.790  -0.705  -0.609  -0.950  -0.896  -0.795
62    K         0.800   0.791   0.617   0.743   0.748   0.518   0.819   0.803   0.475
63    K        -0.750  -0.663  -0.729  -0.866  -0.719  -0.827  -0.803  -0.699  -0.742
64    P        -0.750  -0.727  -0.725  -0.745  -0.708  -0.675  -0.803  -0.779  -0.739
65    T        -1.592  -1.541  -1.490  -1.619  -1.561  -1.471  -1.245  -1.193  -1.100
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    R        -0.175  -0.192  -0.211  -0.347  -0.361  -0.423  -0.360  -0.373  -0.401
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    R         1.534   1.553   1.624   1.528   1.551   1.670   1.704   1.734   1.852
70    H        -0.396  -0.313  -0.258  -0.481  -0.358  -0.271  -0.655  -0.535  -0.463
71    K         0.800   0.708   0.609   0.702   0.586   0.424   0.819   0.663   0.460
72    S        -0.396  -0.313  -0.258  -0.679  -0.530  -0.457  -0.655  -0.535  -0.463
73    A        -1.238  -1.267  -1.159  -1.102  -1.169  -1.002  -1.098  -1.111  -0.970
74    R         0.464   0.481   0.456   0.277   0.302   0.203   0.230   0.254   0.163
75    Q         0.800   0.756   0.602   0.945   0.887   0.647   0.819   0.745   0.448
76    L         0.312   0.316   0.409   0.003   0.004   0.160  -0.065  -0.068   0.070
77    I         0.800   0.884   0.628   0.896   1.005   0.625   0.819   0.951   0.496
78    S        -0.530  -0.596  -0.688  -0.409  -0.514  -0.642  -0.508  -0.592  -0.689
79    D         0.110  -0.025  -0.133   0.332   0.130  -0.053   0.082  -0.113  -0.280
80    E         0.800   0.708   0.609   0.965   0.845   0.694   0.819   0.663   0.460
81    N        -1.592  -1.560  -1.486  -1.409  -1.359  -1.262  -1.245  -1.210  -1.098
82    K         0.728   0.665   0.565   0.578   0.494   0.329   0.701   0.590   0.377
83    R         0.395   0.433   0.457   0.262   0.326   0.346   0.099   0.163   0.167
84    I        -0.175  -0.187  -0.192  -0.318  -0.317  -0.327  -0.360  -0.355  -0.371
85    N        -0.750  -0.752  -0.748  -0.723  -0.703  -0.709  -0.803  -0.787  -0.762
86    A        -1.104  -1.024  -1.114  -0.978  -0.862  -0.996  -0.950  -0.861  -0.924
87    L        -0.750  -0.717  -0.742  -0.902  -0.837  -0.862  -0.803  -0.767  -0.759
88    L        -0.946  -0.915  -0.808  -1.109  -1.078  -0.900  -1.005  -0.966  -0.825
89    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    K        -0.849  -0.816  -0.777  -1.149  -1.093  -1.026  -0.897  -0.853  -0.792
91    A        -0.018  -0.006  -0.159   0.030   0.044  -0.199  -0.102  -0.088  -0.319
92    N        -1.258  -1.198  -1.164  -1.237  -1.149  -1.088  -1.106  -1.041  -0.972
93    K         0.395   0.359   0.422   0.102   0.049   0.153   0.099   0.018   0.095
94    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   V        -1.104  -1.184  -1.134  -0.927  -1.061  -0.991  -0.950  -1.026  -0.943
106   P        -0.750  -0.781  -0.750  -0.730  -0.763  -0.730  -0.803  -0.819  -0.764
107   K        -0.750  -0.766  -0.741  -0.857  -0.863  -0.816  -0.803  -0.806  -0.753
108   A        -1.592  -1.590  -1.508  -1.506  -1.485  -1.368  -1.245  -1.235  -1.114
109   T         0.464   0.415   0.453   0.439   0.339   0.368   0.230   0.128   0.158
110   Y         1.534   1.553   1.624   1.602   1.631   1.742   1.704   1.734   1.852
111   F        -0.530  -0.529  -0.687  -0.238  -0.248  -0.522  -0.508  -0.509  -0.687
112   S         0.312   0.326   0.412   0.021   0.035   0.173  -0.065  -0.048   0.075
113   V         0.312   0.351   0.424   0.133   0.203   0.308  -0.065   0.002   0.101
114   E        -1.104  -1.087  -1.126  -0.840  -0.812  -0.876  -0.950  -0.927  -0.936
115   A         0.800   0.846   0.615   0.885   0.946   0.602   0.819   0.891   0.471
116   P         0.800   0.791   0.617   0.815   0.805   0.557   0.819   0.803   0.475
117   P         1.534   1.553   1.624   1.476   1.501   1.620   1.704   1.734   1.852
118   S         1.534   1.553   1.624   1.505   1.528   1.648   1.704   1.734   1.852
119   I        -0.530  -0.562  -0.674  -0.479  -0.528  -0.682  -0.508  -0.550  -0.671
120   R        -0.530  -0.588  -0.677  -0.609  -0.700  -0.848  -0.508  -0.583  -0.675
121   P         1.534   1.553   1.624   1.476   1.501   1.620   1.704   1.734   1.852
122   A        -0.750  -0.765  -0.754  -0.730  -0.757  -0.729  -0.803  -0.815  -0.770
123   K         0.110   0.053  -0.119   0.081   0.004  -0.234   0.082  -0.004  -0.259
124   K         0.110   0.126  -0.115   0.096   0.125  -0.201   0.082   0.103  -0.253
125   Y         1.534   1.553   1.624   1.602   1.631   1.742   1.704   1.734   1.852
126   C         1.534   1.553   1.624   1.801   1.831   1.936   1.704   1.734   1.852
127   D         1.534   1.553   1.624   1.652   1.673   1.792   1.704   1.734   1.852
128   V         0.312   0.320   0.412   0.133   0.143   0.284  -0.065  -0.060   0.075
129   T         1.534   1.553   1.624   1.647   1.676   1.786   1.704   1.734   1.852
130   G         1.534   1.553   1.624   1.663   1.694   1.803   1.704   1.734   1.852
131   L         1.534   1.553   1.624   1.435   1.459   1.580   1.704   1.734   1.852
132   K        -1.104  -1.134  -1.149  -1.223  -1.268  -1.306  -0.950  -0.978  -0.958
133   G        -0.262  -0.226  -0.225  -0.298  -0.246  -0.217  -0.508  -0.460  -0.430
134   F        -1.238  -1.238  -1.159  -1.231  -1.223  -1.071  -1.098  -1.088  -0.969
135   Y         1.534   1.553   1.624   1.602   1.631   1.742   1.704   1.734   1.852
136   K        -0.175  -0.242  -0.213  -0.388  -0.464  -0.425  -0.360  -0.442  -0.407
137   S        -0.530  -0.596  -0.669  -0.365  -0.465  -0.547  -0.508  -0.589  -0.665
138   P         1.534   1.553   1.624   1.476   1.501   1.620   1.704   1.734   1.852
139   T        -1.238  -1.239  -1.164  -1.269  -1.294  -1.180  -1.098  -1.088  -0.974
140   N         0.312   0.313   0.408   0.113   0.116   0.269  -0.065  -0.075   0.067
141   N        -1.104  -1.115  -1.125  -0.996  -1.018  -1.036  -0.950  -0.958  -0.935
142   I         0.464   0.556   0.502   0.268   0.414   0.319   0.230   0.395   0.256
143   R         1.534   1.553   1.624   1.528   1.551   1.670   1.704   1.734   1.852
144   Y         0.312   0.332   0.417   0.250   0.286   0.405  -0.065  -0.035   0.086
145   H         0.312   0.334   0.415   0.277   0.318   0.425  -0.065  -0.032   0.081
146   N         0.800   0.880   0.620   0.869   0.969   0.623   0.819   0.944   0.481
147   A        -1.238  -1.252  -1.161  -1.285  -1.316  -1.171  -1.098  -1.100  -0.971
148   E         1.534   1.553   1.624   1.619   1.648   1.759   1.704   1.734   1.852
149   I         0.464   0.438   0.443   0.415   0.364   0.344   0.230   0.172   0.138
150   Y         0.800   0.756   0.602   0.933   0.878   0.637   0.819   0.745   0.448
151   Q         0.110   0.005  -0.115   0.299   0.154  -0.045   0.082  -0.070  -0.253
152   L         0.330   0.345   0.421   0.056   0.079   0.201  -0.030  -0.011   0.094
153   I        -0.175  -0.226  -0.210  -0.208  -0.277  -0.285  -0.360  -0.417  -0.401
154   V         0.312   0.343   0.416   0.133   0.187   0.291  -0.065  -0.015   0.083
155   K         0.312   0.316   0.409  -0.083  -0.071   0.076  -0.065  -0.068   0.070
156   P        -0.750  -0.813  -0.761  -0.820  -0.893  -0.801  -0.803  -0.857  -0.776
157   M         0.110  -0.025  -0.133   0.423   0.218   0.007   0.082  -0.113  -0.280
158   A         0.312   0.351   0.424   0.022   0.086   0.200  -0.065   0.002   0.101
159   P        -0.175  -0.206  -0.199  -0.313  -0.350  -0.353  -0.360  -0.385  -0.387
160   G         1.534   1.553   1.624   1.663   1.694   1.803   1.704   1.734   1.852
161   V         0.464   0.415   0.453   0.412   0.326   0.355   0.230   0.128   0.158
162   D         0.800   0.791   0.617   0.993   0.979   0.727   0.819   0.803   0.475
163   Q         1.534   1.553   1.624   1.613   1.640   1.753   1.704   1.734   1.852
164   E         0.110   0.047  -0.126   0.305   0.222  -0.057   0.082  -0.007  -0.269
165   Y         1.534   1.553   1.624   1.602   1.631   1.742   1.704   1.734   1.852
166   L         1.534   1.553   1.624   1.435   1.459   1.580   1.704   1.734   1.852
167   K        -0.175  -0.139  -0.219  -0.352  -0.290  -0.392  -0.360  -0.313  -0.414
168   L         1.534   1.553   1.624   1.435   1.459   1.580   1.704   1.734   1.852
169   R         1.534   1.553   1.624   1.528   1.551   1.670   1.704   1.734   1.852
170   G         0.800   0.708   0.609   0.986   0.859   0.686   0.819   0.663   0.460
171   A         0.110   0.005  -0.115   0.246   0.092  -0.094   0.082  -0.070  -0.253
172   N         0.110   0.005  -0.115   0.258   0.116  -0.041   0.082  -0.070  -0.253
173   F        -0.262  -0.280  -0.247  -0.245  -0.257  -0.210  -0.508  -0.518  -0.456
174   V         0.312   0.334   0.415   0.135   0.175   0.291  -0.065  -0.032   0.081
175   L         1.534   1.553   1.624   1.435   1.459   1.580   1.704   1.734   1.852
176   K         0.800   0.756   0.602   0.702   0.655   0.413   0.819   0.745   0.448
* 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/P32617
Output conservation file - output/P32617
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
