1     M         1.072   1.098   1.156   1.259   1.289   1.371   1.150   1.184   1.263
2     S         1.072   1.098   1.156   1.222   1.250   1.338   1.150   1.184   1.263
3     D         1.072   1.098   1.156   0.901   0.957   1.053   1.150   1.184   1.263
4     Y        -0.287  -0.124  -0.592   0.045   0.240  -0.411  -0.285  -0.067  -0.693
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    E         0.033  -0.054  -0.009  -0.402  -0.563  -0.480  -0.174  -0.338  -0.297
17    E        -0.287  -0.095  -0.592  -0.488  -0.235  -0.916  -0.285  -0.028  -0.693
18    -        -1.901  -1.811  -1.583  -2.047  -1.947  -1.570  -1.675  -1.564  -1.278
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    A         1.072   1.098   1.156   1.032   1.058   1.169   1.150   1.184   1.263
21    F         0.376   0.444   0.102   0.653   0.754   0.258   0.377   0.475  -0.097
22    N        -0.287  -0.502  -0.639  -0.037  -0.354  -0.645  -0.285  -0.572  -0.757
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    D        -0.150  -0.133  -0.022  -0.685  -0.663  -0.492  -0.505  -0.484  -0.322
25    G        -1.489  -1.524  -1.549  -1.281  -1.361  -1.420  -1.277  -1.301  -1.250
26    N        -1.247  -1.153  -1.150  -1.207  -1.093  -1.002  -1.277  -1.165  -1.070
27    E        -0.287  -0.502  -0.639  -0.477  -0.777  -0.964  -0.285  -0.572  -0.757
28    N        -0.287  -0.502  -0.639  -0.031  -0.358  -0.629  -0.285  -0.572  -0.757
29    F        -1.169  -1.259  -1.165  -0.990  -1.156  -1.080  -1.167  -1.245  -1.083
30    E         0.033  -0.054  -0.009  -0.289  -0.420  -0.285  -0.174  -0.338  -0.297
31    D        -0.150  -0.164  -0.023  -0.685  -0.755  -0.501  -0.505  -0.543  -0.324
32    F        -0.911  -1.132  -1.151  -0.591  -0.925  -1.069  -0.836  -1.085  -1.066
33    D         0.033  -0.054  -0.009  -0.299  -0.477  -0.452  -0.174  -0.338  -0.297
34    V        -2.129  -2.125  -1.881  -1.912  -1.933  -1.601  -1.719  -1.672  -1.375
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    E        -0.591  -0.587  -0.651  -0.979  -0.942  -1.027  -0.726  -0.695  -0.774
37    H        -0.287  -0.502  -0.639   0.109  -0.215  -0.562  -0.285  -0.572  -0.757
38    F        -0.911  -1.132  -1.151  -0.514  -0.826  -0.910  -0.836  -1.085  -1.066
39    S        -0.287  -0.502  -0.639  -0.001  -0.320  -0.604  -0.285  -0.572  -0.757
40    D         0.376   0.444   0.102   0.248   0.361  -0.203   0.377   0.475  -0.097
41    E        -1.688  -1.594  -1.550  -1.902  -1.783  -1.570  -1.498  -1.396  -1.252
42    E        -1.247  -1.331  -1.166  -1.609  -1.659  -1.358  -1.277  -1.319  -1.084
43    T        -2.449  -2.322  -2.144  -2.197  -2.078  -1.782  -1.829  -1.705  -1.453
44    Y        -1.791  -1.720  -1.569  -1.611  -1.529  -1.327  -1.588  -1.497  -1.267
45    E        -0.797  -0.825  -0.692  -1.317  -1.331  -1.082  -1.008  -1.021  -0.828
46    E        -0.797  -0.696  -0.691  -1.221  -1.066  -1.021  -1.008  -0.880  -0.826
47    -        -1.901  -1.822  -1.583  -1.979  -1.907  -1.509  -1.675  -1.573  -1.278
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    K        -0.171  -0.140  -0.023  -0.560  -0.511  -0.363  -0.545  -0.497  -0.323
50    P        -1.389  -1.288  -1.188  -1.351  -1.195  -1.063  -1.392  -1.265  -1.104
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    Q        -1.791  -1.701  -1.568  -1.649  -1.507  -1.379  -1.588  -1.485  -1.266
55    F        -2.157  -2.104  -1.889  -1.822  -1.767  -1.490  -1.732  -1.658  -1.381
56    K        -1.059  -0.913  -1.133  -0.855  -0.657  -0.954  -1.012  -0.840  -1.047
57    D        -0.399  -0.360  -0.623  -0.434  -0.363  -0.719  -0.435  -0.390  -0.735
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    G        -1.059  -1.105  -1.164  -0.995  -1.121  -1.236  -1.012  -1.064  -1.080
61    E        -1.287  -1.171  -1.172  -1.538  -1.315  -1.288  -1.300  -1.176  -1.090
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    T        -2.129  -1.961  -1.869  -1.904  -1.683  -1.533  -1.719  -1.555  -1.368
64    T        -1.688  -1.753  -1.560  -1.627  -1.763  -1.479  -1.498  -1.514  -1.260
65    D        -1.247  -1.183  -1.158  -1.433  -1.292  -1.224  -1.277  -1.176  -1.075
66    A        -0.591  -0.391  -0.635  -0.905  -0.630  -0.917  -0.726  -0.459  -0.752
67    N        -1.247  -1.186  -1.162  -1.383  -1.269  -1.256  -1.277  -1.195  -1.081
68    G        -0.287  -0.502  -0.639  -0.127  -0.425  -0.671  -0.285  -0.572  -0.757
69    K        -1.169  -1.138  -1.159  -1.035  -1.009  -1.017  -1.167  -1.133  -1.078
70    T        -0.287  -0.462  -0.626  -0.065  -0.286  -0.521  -0.285  -0.520  -0.739
71    I         0.376   0.300   0.084   0.529   0.441   0.105   0.377   0.260  -0.129
72    V        -0.150  -0.114  -0.017  -0.267  -0.204  -0.075  -0.505  -0.449  -0.312
73    T        -0.728  -0.603  -0.662  -0.766  -0.599  -0.650  -0.947  -0.792  -0.792
74    G         0.314   0.126   0.049   0.425   0.186   0.054   0.285  -0.022  -0.191
75    G         0.314   0.283   0.074   0.344   0.309  -0.107   0.285   0.233  -0.147
76    N        -1.389  -1.314  -1.188  -1.233  -1.140  -0.962  -1.392  -1.293  -1.104
77    G         0.314   0.126   0.049   0.366   0.087  -0.102   0.285  -0.022  -0.191
78    P         0.314   0.283   0.074   0.448   0.398   0.088   0.285   0.233  -0.147
79    E        -0.591  -0.642  -0.662  -0.950  -0.983  -0.984  -0.726  -0.767  -0.789
80    D        -1.169  -1.232  -1.160  -1.425  -1.475  -1.380  -1.167  -1.203  -1.077
81    F        -1.368  -1.282  -1.182  -1.268  -1.179  -1.006  -1.388  -1.293  -1.101
82    Q        -1.223  -1.255  -1.176  -1.115  -1.239  -1.172  -1.204  -1.237  -1.092
83    Q        -1.384  -1.334  -1.181  -1.270  -1.209  -1.003  -1.400  -1.317  -1.097
84    H        -1.389  -1.119  -1.176  -1.232  -0.888  -0.913  -1.392  -1.068  -1.092
85    E        -0.171  -0.163  -0.021  -0.673  -0.603  -0.364  -0.545  -0.541  -0.320
86    Q        -1.247  -1.210  -1.161  -1.179  -1.141  -1.036  -1.277  -1.215  -1.079
87    I        -2.449  -2.354  -2.151  -2.005  -1.906  -1.602  -1.829  -1.728  -1.457
88    R        -0.287  -0.502  -0.639  -0.058  -0.335  -0.539  -0.285  -0.572  -0.757
89    R        -1.169  -1.225  -1.168  -1.144  -1.279  -1.198  -1.167  -1.212  -1.086
90    K        -0.287  -0.259  -0.612  -0.078  -0.048  -0.571  -0.285  -0.253  -0.721
91    T        -0.591  -0.697  -0.671  -0.523  -0.684  -0.648  -0.726  -0.860  -0.804
92    L        -2.008  -2.056  -1.883  -1.671  -1.684  -1.477  -1.608  -1.620  -1.377
93    K        -0.591  -0.648  -0.653  -0.510  -0.582  -0.598  -0.726  -0.786  -0.779
94    E        -0.287  -0.502  -0.639  -0.488  -0.794  -0.992  -0.285  -0.572  -0.757
95    K        -0.150  -0.101  -0.010  -0.319  -0.236  -0.114  -0.505  -0.424  -0.300
96    A         0.376   0.232   0.073   0.433   0.238   0.002   0.377   0.152  -0.147
97    I         0.033   0.026   0.002   0.048   0.036  -0.041  -0.174  -0.194  -0.277
98    P         0.033   0.056   0.008   0.010   0.025  -0.088  -0.174  -0.143  -0.266
99    K        -0.287  -0.462  -0.626  -0.062  -0.294  -0.554  -0.285  -0.520  -0.739
100   D         0.033   0.024  -0.007  -0.402  -0.422  -0.477  -0.174  -0.199  -0.294
101   Q        -1.169  -1.141  -1.155  -1.274  -1.227  -1.239  -1.167  -1.128  -1.073
102   R         1.072   1.098   1.156   1.100   1.141   1.230   1.150   1.184   1.263
103   A        -0.287  -0.298  -0.623  -0.093  -0.113  -0.584  -0.285  -0.317  -0.736
104   T         1.072   1.098   1.156   1.092   1.131   1.222   1.150   1.184   1.263
105   T         1.072   1.098   1.156   1.092   1.131   1.222   1.150   1.184   1.263
106   P         1.072   1.098   1.156   1.121   1.145   1.249   1.150   1.184   1.263
107   Y         1.072   1.098   1.156   1.222   1.249   1.338   1.150   1.184   1.263
108   M         1.072   1.098   1.156   1.259   1.289   1.371   1.150   1.184   1.263
109   T         1.072   1.098   1.156   1.092   1.131   1.222   1.150   1.184   1.263
110   K         1.072   1.098   1.156   1.117   1.152   1.245   1.150   1.184   1.263
111   Y         1.072   1.098   1.156   1.222   1.249   1.338   1.150   1.184   1.263
112   E         1.072   1.098   1.156   0.748   0.784   0.916   1.150   1.184   1.263
113   R         0.376   0.232   0.073   0.501   0.319   0.058   0.377   0.152  -0.147
114   A         1.072   1.098   1.156   1.032   1.058   1.169   1.150   1.184   1.263
115   R         1.072   1.098   1.156   1.100   1.141   1.230   1.150   1.184   1.263
116   I         0.033   0.053   0.018   0.048   0.080  -0.013  -0.174  -0.147  -0.249
117   L         1.072   1.098   1.156   1.062   1.106   1.196   1.150   1.184   1.263
118   G         1.072   1.098   1.156   1.079   1.121   1.211   1.150   1.184   1.263
119   T         1.072   1.098   1.156   1.092   1.131   1.222   1.150   1.184   1.263
120   R         1.072   1.098   1.156   1.100   1.141   1.230   1.150   1.184   1.263
121   A         1.072   1.098   1.156   1.032   1.058   1.169   1.150   1.184   1.263
122   L         1.072   1.098   1.156   1.062   1.106   1.196   1.150   1.184   1.263
123   Q         1.072   1.098   1.156   1.234   1.278   1.349   1.150   1.184   1.263
124   I         1.072   1.098   1.156   1.126   1.163   1.253   1.150   1.184   1.263
125   S         1.072   1.098   1.156   1.222   1.250   1.338   1.150   1.184   1.263
126   M         0.033   0.130   0.035   0.152   0.301   0.088  -0.174  -0.017  -0.217
127   N         1.072   1.098   1.156   1.193   1.225   1.312   1.150   1.184   1.263
128   A         1.072   1.098   1.156   1.032   1.058   1.169   1.150   1.184   1.263
129   P         1.072   1.098   1.156   1.121   1.145   1.249   1.150   1.184   1.263
130   V         0.376   0.346   0.103   0.540   0.518   0.143   0.377   0.330  -0.095
131   F        -0.150   0.001   0.019  -0.274  -0.020  -0.010  -0.505  -0.240  -0.246
132   V         1.072   1.098   1.156   1.138   1.184   1.264   1.150   1.184   1.263
133   D         1.072   1.098   1.156   0.901   0.957   1.053   1.150   1.184   1.263
134   L        -0.150  -0.101  -0.010  -0.334  -0.247  -0.118  -0.505  -0.424  -0.300
135   E         1.072   1.098   1.156   0.748   0.784   0.916   1.150   1.184   1.263
136   G         0.376   0.346   0.103   0.491   0.465   0.119   0.377   0.330  -0.095
137   E         0.376   0.346   0.103   0.135   0.098  -0.221   0.377   0.330  -0.095
138   T         1.072   1.098   1.156   1.092   1.131   1.222   1.150   1.184   1.263
139   D         1.072   1.098   1.156   0.901   0.957   1.053   1.150   1.184   1.263
140   P         1.072   1.098   1.156   1.121   1.145   1.249   1.150   1.184   1.263
141   L         1.072   1.098   1.156   1.062   1.106   1.196   1.150   1.184   1.263
142   R        -0.150   0.001   0.019  -0.196   0.083   0.054  -0.505  -0.240  -0.246
143   I         1.072   1.098   1.156   1.126   1.163   1.253   1.150   1.184   1.263
144   A         1.072   1.098   1.156   1.032   1.058   1.169   1.150   1.184   1.263
145   M         0.376   0.232   0.073   0.660   0.468   0.190   0.377   0.152  -0.147
146   K         1.072   1.098   1.156   1.117   1.152   1.245   1.150   1.184   1.263
147   E         1.072   1.098   1.156   0.748   0.784   0.916   1.150   1.184   1.263
148   L         1.072   1.098   1.156   1.062   1.106   1.196   1.150   1.184   1.263
149   A        -0.287  -0.462  -0.626  -0.139  -0.379  -0.601  -0.285  -0.520  -0.739
150   E        -0.209  -0.162  -0.023  -0.581  -0.481  -0.261  -0.616  -0.539  -0.325
151   K         0.033   0.130   0.035   0.028   0.177  -0.006  -0.174  -0.017  -0.217
152   K         1.072   1.098   1.156   1.117   1.152   1.245   1.150   1.184   1.263
153   I         1.072   1.098   1.156   1.126   1.163   1.253   1.150   1.184   1.263
154   P         1.072   1.098   1.156   1.121   1.145   1.249   1.150   1.184   1.263
155   L         1.072   1.098   1.156   1.062   1.106   1.196   1.150   1.184   1.263
156   V        -0.287  -0.502  -0.639  -0.058  -0.343  -0.603  -0.285  -0.572  -0.757
157   I        -0.150  -0.158  -0.023  -0.272  -0.294  -0.088  -0.505  -0.532  -0.324
158   R         1.072   1.098   1.156   1.100   1.141   1.230   1.150   1.184   1.263
159   R         1.072   1.098   1.156   1.100   1.141   1.230   1.150   1.184   1.263
160   Y         1.072   1.098   1.156   1.222   1.249   1.338   1.150   1.184   1.263
161   L         0.376   0.232   0.073   0.484   0.316   0.085   0.377   0.152  -0.147
162   P         1.072   1.098   1.156   1.121   1.145   1.249   1.150   1.184   1.263
163   D         1.072   1.098   1.156   0.901   0.957   1.053   1.150   1.184   1.263
164   G         1.072   1.098   1.156   1.079   1.121   1.211   1.150   1.184   1.263
165   S         0.376   0.232   0.073   0.637   0.447   0.198   0.377   0.152  -0.147
166   F        -0.150  -0.155  -0.023  -0.130  -0.149   0.036  -0.505  -0.527  -0.324
167   E         1.072   1.098   1.156   0.748   0.784   0.916   1.150   1.184   1.263
168   D         1.072   1.098   1.156   0.901   0.957   1.053   1.150   1.184   1.263
169   W         1.072   1.098   1.156   1.369   1.400   1.469   1.150   1.184   1.263
170   S        -0.728  -0.793  -0.681  -0.717  -0.799  -0.641  -0.947  -0.992  -0.816
171   V        -0.209  -0.155  -0.019  -0.196  -0.091   0.095  -0.616  -0.527  -0.317
172   E        -0.728  -0.750  -0.673  -1.248  -1.253  -1.076  -0.947  -0.944  -0.806
173   E         1.072   1.098   1.156   0.748   0.784   0.916   1.150   1.184   1.263
174   L         1.072   1.098   1.156   1.062   1.106   1.196   1.150   1.184   1.263
175   I        -0.287  -0.309  -0.620  -0.069  -0.114  -0.574  -0.285  -0.329  -0.731
176   V         0.239   0.233   0.039   0.370   0.354   0.034   0.169   0.154  -0.209
177   D         1.072   1.098   1.156   0.908   0.953   1.059   1.150   1.184   1.263
178   L        -0.783  -0.698  -0.672  -0.737  -0.571  -0.504  -1.012  -0.879  -0.803
179   -        -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/P20435
Output conservation file - output/P20435
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
