1     M         1.828   1.838   1.889   2.167   2.181   2.264   1.996   2.007   2.083
2     Y        -0.678  -0.667  -0.628  -0.906  -0.888  -0.822  -0.756  -0.738  -0.677
3     K        -0.678  -0.667  -0.628  -1.197  -1.168  -1.115  -0.756  -0.738  -0.677
4     T        -0.678  -0.667  -0.628  -0.648  -0.631  -0.564  -0.756  -0.738  -0.677
5     W         0.376   0.405   0.386   0.142   0.180   0.177   0.161   0.209   0.165
6     R         0.545   0.585   0.480   0.573   0.636   0.460   0.448   0.512   0.327
7     L        -0.544  -0.558  -0.556  -0.701  -0.726  -0.744  -0.584  -0.601  -0.586
8     C        -1.335  -1.322  -1.287  -1.057  -1.043  -0.974  -1.100  -1.081  -1.022
9     R        -1.335  -1.322  -1.287  -1.048  -1.025  -0.965  -1.100  -1.081  -1.022
10    T        -0.544  -0.558  -0.556  -0.503  -0.530  -0.521  -0.584  -0.601  -0.586
11    H        -0.544  -0.566  -0.565  -0.283  -0.327  -0.335  -0.584  -0.612  -0.598
12    T        -1.335  -1.322  -1.287  -1.359  -1.358  -1.277  -1.100  -1.081  -1.022
13    V         0.247   0.258   0.304   0.146   0.165   0.236  -0.068  -0.049   0.019
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    S        -0.678  -0.670  -0.628  -0.713  -0.697  -0.628  -0.756  -0.742  -0.677
30    T        -0.678  -0.670  -0.628  -0.741  -0.731  -0.657  -0.756  -0.742  -0.677
31    G        -0.544  -0.499  -0.542  -0.491  -0.416  -0.493  -0.584  -0.522  -0.569
32    G        -0.544  -0.566  -0.565  -0.495  -0.531  -0.533  -0.584  -0.612  -0.598
33    A         0.247   0.258   0.304   0.087   0.102   0.176  -0.068  -0.049   0.019
34    K        -0.544  -0.558  -0.556  -0.569  -0.589  -0.604  -0.584  -0.601  -0.586
35    I        -0.544  -0.566  -0.565  -0.487  -0.526  -0.519  -0.584  -0.612  -0.598
36    G         0.545   0.472   0.443   0.688   0.590   0.538   0.448   0.324   0.264
37    K        -0.544  -0.577  -0.572  -0.676  -0.727  -0.704  -0.584  -0.625  -0.606
38    K        -0.544  -0.566  -0.565  -0.628  -0.661  -0.640  -0.584  -0.612  -0.598
39    F         0.545   0.472   0.443   0.679   0.539   0.460   0.448   0.324   0.264
40    E        -1.335  -1.322  -1.287  -1.401  -1.388  -1.319  -1.100  -1.081  -1.022
41    N        -0.544  -0.577  -0.572  -0.503  -0.567  -0.553  -0.584  -0.625  -0.606
42    M        -1.335  -1.322  -1.287  -1.006  -0.992  -0.923  -1.100  -1.081  -1.022
43    N        -1.335  -1.322  -1.287  -1.369  -1.347  -1.288  -1.100  -1.081  -1.022
44    Q         0.545   0.599   0.488   0.567   0.649   0.488   0.448   0.535   0.342
45    I         0.247   0.256   0.302   0.146   0.161   0.234  -0.068  -0.054   0.015
46    R        -0.544  -0.508  -0.535  -0.656  -0.585  -0.653  -0.584  -0.534  -0.560
47    D        -1.335  -1.322  -1.287  -1.189  -1.171  -1.107  -1.100  -1.081  -1.022
48    Y         0.247   0.258   0.304   0.401   0.422   0.493  -0.068  -0.049   0.019
49    L         1.828   1.838   1.889   1.557   1.567   1.651   1.996   2.007   2.083
50    S         0.247   0.257   0.303   0.087   0.111   0.182  -0.068  -0.052   0.016
51    R        -0.544  -0.558  -0.556  -0.746  -0.766  -0.761  -0.584  -0.601  -0.586
52    P        -0.544  -0.486  -0.542  -0.457  -0.379  -0.440  -0.584  -0.505  -0.568
53    V         0.545   0.599   0.488   0.682   0.763   0.595   0.448   0.535   0.342
54    W         1.828   1.838   1.889   2.192   2.210   2.290   1.996   2.007   2.083
55    S         0.545   0.566   0.478   0.559   0.583   0.455   0.448   0.481   0.325
56    V         0.247   0.257   0.303   0.146   0.162   0.234  -0.068  -0.052   0.016
57    H        -1.335  -1.322  -1.287  -1.075  -1.063  -0.992  -1.100  -1.081  -1.022
58    E         1.828   1.838   1.889   1.807   1.821   1.902   1.996   2.007   2.083
59    Y        -0.544  -0.566  -0.565  -0.430  -0.493  -0.504  -0.584  -0.612  -0.598
60    L         0.545   0.566   0.478   0.310   0.340   0.217   0.448   0.481   0.325
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    G        -0.544  -0.577  -0.572  -0.526  -0.588  -0.580  -0.584  -0.625  -0.606
63    I        -0.544  -0.486  -0.542  -0.612  -0.523  -0.611  -0.584  -0.505  -0.568
64    N        -1.335  -1.322  -1.287  -1.174  -1.152  -1.092  -1.100  -1.081  -1.022
65    T         0.545   0.566   0.478   0.682   0.714   0.579   0.448   0.481   0.325
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    K        -0.544  -0.577  -0.572  -0.709  -0.762  -0.742  -0.584  -0.625  -0.606
68    E        -0.544  -0.566  -0.565  -0.588  -0.629  -0.620  -0.584  -0.612  -0.598
69    E        -1.335  -1.322  -1.287  -1.308  -1.260  -1.226  -1.100  -1.081  -1.022
70    K        -0.544  -0.577  -0.572  -0.788  -0.823  -0.835  -0.584  -0.625  -0.606
71    L        -1.335  -1.322  -1.287  -1.416  -1.391  -1.335  -1.100  -1.081  -1.022
72    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    P         0.545   0.472   0.443   0.766   0.651   0.600   0.448   0.324   0.264
75    S         0.545   0.585   0.480   0.559   0.610   0.457   0.448   0.512   0.327
76    A        -0.544  -0.558  -0.556  -0.499  -0.511  -0.503  -0.584  -0.601  -0.586
77    E         1.828   1.838   1.889   1.807   1.821   1.902   1.996   2.007   2.083
78    A        -1.335  -1.322  -1.287  -1.238  -1.212  -1.156  -1.100  -1.081  -1.022
79    V         1.828   1.838   1.889   1.977   1.995   2.073   1.996   2.007   2.083
80    K        -0.544  -0.508  -0.535  -0.668  -0.605  -0.645  -0.584  -0.534  -0.560
81    K         0.545   0.566   0.478   0.396   0.434   0.290   0.448   0.481   0.325
82    L         0.545   0.472   0.443   0.377   0.280   0.257   0.448   0.324   0.264
83    L         1.828   1.838   1.889   1.557   1.567   1.651   1.996   2.007   2.083
84    R        -0.544  -0.486  -0.542  -0.676  -0.577  -0.663  -0.584  -0.505  -0.568
85    L         0.545   0.566   0.478   0.279   0.308   0.177   0.448   0.481   0.325
86    S         0.545   0.585   0.480   0.654   0.702   0.579   0.448   0.512   0.327
87    G         0.545   0.585   0.480   0.651   0.726   0.549   0.448   0.512   0.327
88    L         0.545   0.585   0.480   0.344   0.398   0.262   0.448   0.512   0.327
89    P         0.545   0.472   0.443   0.747   0.624   0.573   0.448   0.324   0.264
90    L        -0.678  -0.670  -0.628  -0.897  -0.873  -0.813  -0.756  -0.742  -0.677
91    E        -0.544  -0.577  -0.572  -0.660  -0.706  -0.714  -0.584  -0.625  -0.606
92    G        -0.678  -0.664  -0.628  -0.860  -0.860  -0.776  -0.756  -0.735  -0.677
93    A         0.376   0.329   0.358   0.245   0.158   0.174   0.161   0.078   0.115
94    D         0.545   0.566   0.478   0.662   0.695   0.553   0.448   0.481   0.325
95    I        -0.544  -0.566  -0.565  -0.640  -0.671  -0.696  -0.584  -0.612  -0.598
96    K        -0.544  -0.499  -0.542  -0.472  -0.382  -0.482  -0.584  -0.522  -0.569
97    E        -1.335  -1.322  -1.287  -1.253  -1.241  -1.171  -1.100  -1.081  -1.022
98    I        -0.544  -0.566  -0.565  -0.510  -0.544  -0.545  -0.584  -0.612  -0.598
99    Q        -0.544  -0.566  -0.565  -0.472  -0.504  -0.527  -0.584  -0.612  -0.598
100   M        -1.335  -1.322  -1.287  -1.223  -1.224  -1.141  -1.100  -1.081  -1.022
101   R        -0.544  -0.566  -0.565  -0.499  -0.526  -0.530  -0.584  -0.612  -0.598
102   L         1.828   1.838   1.889   1.557   1.567   1.651   1.996   2.007   2.083
103   A        -0.544  -0.566  -0.565  -0.412  -0.444  -0.445  -0.584  -0.612  -0.598
104   K        -0.544  -0.577  -0.572  -0.843  -0.917  -0.900  -0.584  -0.625  -0.606
105   Q         1.828   1.838   1.889   2.020   2.037   2.117   1.996   2.007   2.083
106   L         0.545   0.472   0.443   0.377   0.280   0.257   0.448   0.324   0.264
107   S         0.545   0.472   0.443   0.634   0.525   0.500   0.448   0.324   0.264
108   F         1.828   1.838   1.889   2.073   2.086   2.169   1.996   2.007   2.083
109   I         1.828   1.838   1.889   1.888   1.901   1.984   1.996   2.007   2.083
110   N         1.828   1.838   1.889   1.915   1.922   2.010   1.996   2.007   2.083
111   K        -0.544  -0.577  -0.572  -0.584  -0.607  -0.598  -0.584  -0.625  -0.606
112   L         1.828   1.838   1.889   1.557   1.567   1.651   1.996   2.007   2.083
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   H         1.828   1.838   1.889   2.158   2.176   2.255   1.996   2.007   2.083
118   N         0.247   0.257   0.303   0.041   0.051   0.129  -0.068  -0.052   0.016
119   I        -0.544  -0.499  -0.542  -0.616  -0.537  -0.631  -0.584  -0.522  -0.569
120   P        -0.544  -0.566  -0.565  -0.389  -0.428  -0.433  -0.584  -0.612  -0.598
121   V         0.545   0.472   0.443   0.705   0.592   0.536   0.448   0.324   0.264
122   E        -0.678  -0.664  -0.628  -0.663  -0.627  -0.578  -0.756  -0.735  -0.677
123   G        -0.678  -0.664  -0.628  -0.670  -0.654  -0.586  -0.756  -0.735  -0.677
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   E        -0.544  -0.558  -0.556  -0.600  -0.634  -0.640  -0.584  -0.601  -0.586
126   K        -0.544  -0.577  -0.572  -0.746  -0.790  -0.786  -0.584  -0.625  -0.606
127   H         0.545   0.599   0.488   0.716   0.788   0.645   0.448   0.535   0.342
128   T        -1.335  -1.322  -1.287  -1.465  -1.443  -1.384  -1.100  -1.081  -1.022
129   K        -0.544  -0.486  -0.542  -0.565  -0.463  -0.570  -0.584  -0.505  -0.568
130   E        -0.544  -0.577  -0.572  -0.518  -0.574  -0.548  -0.584  -0.625  -0.606
131   Y        -0.544  -0.558  -0.556  -0.375  -0.402  -0.380  -0.584  -0.601  -0.586
132   D        -1.335  -1.322  -1.287  -0.948  -0.932  -0.865  -1.100  -1.081  -1.022
133   A         0.545   0.472   0.443   0.730   0.632   0.578   0.448   0.324   0.264
134   R         1.828   1.838   1.889   1.879   1.894   1.975   1.996   2.007   2.083
135   L         0.545   0.566   0.478   0.279   0.308   0.177   0.448   0.481   0.325
136   V        -0.544  -0.499  -0.542  -0.771  -0.708  -0.752  -0.584  -0.522  -0.569
137   Q        -1.335  -1.322  -1.287  -1.117  -1.091  -1.035  -1.100  -1.081  -1.022
138   R         0.545   0.472   0.443   0.573   0.450   0.394   0.448   0.324   0.264
139   N        -0.544  -0.566  -0.565  -0.419  -0.460  -0.445  -0.584  -0.612  -0.598
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   T        -1.335  -1.322  -1.287  -1.071  -1.047  -0.988  -1.100  -1.081  -1.022
144   K        -0.544  -0.577  -0.572  -0.684  -0.730  -0.714  -0.584  -0.625  -0.606
145   Q        -0.544  -0.486  -0.542  -0.316  -0.219  -0.310  -0.584  -0.505  -0.568
146   L         1.828   1.838   1.889   1.557   1.567   1.651   1.996   2.007   2.083
147   N        -1.335  -1.322  -1.287  -1.233  -1.223  -1.151  -1.100  -1.081  -1.022
148   Y         0.545   0.472   0.443   0.755   0.621   0.534   0.448   0.324   0.264
149   T        -1.335  -1.322  -1.287  -1.233  -1.215  -1.151  -1.100  -1.081  -1.022
150   K        -1.335  -1.322  -1.287  -1.318  -1.281  -1.236  -1.100  -1.081  -1.022
151   L         1.828   1.838   1.889   1.557   1.567   1.651   1.996   2.007   2.083
152   L         0.545   0.566   0.478   0.279   0.308   0.177   0.448   0.481   0.325
153   E         0.545   0.599   0.488   0.371   0.462   0.276   0.448   0.535   0.342
154   G        -0.544  -0.566  -0.565  -0.530  -0.544  -0.573  -0.584  -0.612  -0.598
155   I         1.828   1.838   1.889   1.888   1.901   1.984   1.996   2.007   2.083
156   S        -1.335  -1.322  -1.287  -1.213  -1.190  -1.131  -1.100  -1.081  -1.022
157   H        -1.335  -1.322  -1.287  -1.174  -1.166  -1.092  -1.100  -1.081  -1.022
158   Q        -0.544  -0.566  -0.565  -0.545  -0.609  -0.612  -0.584  -0.612  -0.598
159   K         0.545   0.566   0.478   0.444   0.482   0.352   0.448   0.481   0.325
160   Q        -0.544  -0.577  -0.572  -0.434  -0.482  -0.496  -0.584  -0.625  -0.606
161   D         0.545   0.566   0.478   0.634   0.666   0.516   0.448   0.481   0.325
162   A        -1.335  -1.322  -1.287  -1.160  -1.123  -1.078  -1.100  -1.081  -1.022
163   E        -0.544  -0.486  -0.542  -0.580  -0.488  -0.576  -0.584  -0.505  -0.568
164   L        -0.544  -0.566  -0.565  -0.886  -0.933  -0.913  -0.584  -0.612  -0.598
165   G         1.828   1.838   1.889   1.915   1.939   2.010   1.996   2.007   2.083
166   E         1.828   1.838   1.889   1.807   1.821   1.902   1.996   2.007   2.083
167   V        -0.544  -0.508  -0.535  -0.386  -0.325  -0.369  -0.584  -0.534  -0.560
168   S        -0.544  -0.566  -0.565  -0.530  -0.571  -0.555  -0.584  -0.612  -0.598
169   G         0.545   0.472   0.443   0.688   0.590   0.538   0.448   0.324   0.264
170   S         0.545   0.472   0.443   0.559   0.436   0.396   0.448   0.324   0.264
171   W         1.828   1.838   1.889   2.180   2.196   2.277   1.996   2.007   2.083
172   K         0.376   0.413   0.373   0.256   0.326   0.223   0.161   0.223   0.142
173   A        -0.678  -0.670  -0.628  -0.649  -0.632  -0.565  -0.756  -0.742  -0.677
174   T         1.828   1.838   1.889   1.965   1.981   2.061   1.996   2.007   2.083
175   G         0.376   0.363   0.358   0.190   0.166   0.125   0.161   0.138   0.115
176   L        -0.544  -0.577  -0.572  -0.788  -0.836  -0.807  -0.584  -0.625  -0.606
177   A         0.545   0.472   0.443   0.651   0.536   0.469   0.448   0.324   0.264
178   A        -0.544  -0.566  -0.565  -0.526  -0.547  -0.577  -0.584  -0.612  -0.598
179   E        -1.335  -1.322  -1.287  -1.277  -1.285  -1.196  -1.100  -1.081  -1.022
180   S        -1.335  -1.322  -1.287  -1.343  -1.304  -1.262  -1.100  -1.081  -1.022
181   K         0.247   0.258   0.304  -0.079  -0.045   0.022  -0.068  -0.049   0.019
182   N         0.545   0.599   0.488   0.662   0.746   0.570   0.448   0.535   0.342
183   A        -1.335  -1.322  -1.287  -1.228  -1.212  -1.146  -1.100  -1.081  -1.022
184   Y         0.247   0.258   0.304   0.401   0.422   0.493  -0.068  -0.049   0.019
185   F         0.545   0.472   0.443   0.808   0.693   0.640   0.448   0.324   0.264
186   V         0.545   0.599   0.488   0.631   0.713   0.545   0.448   0.535   0.342
187   V        -0.544  -0.577  -0.572  -0.573  -0.631  -0.649  -0.584  -0.625  -0.606
188   K         0.376   0.413   0.373   0.201   0.273   0.169   0.161   0.223   0.142
189   E         0.376   0.377   0.364   0.315   0.321   0.298   0.161   0.161   0.126
190   G         1.828   1.838   1.889   1.861   1.877   1.956   1.996   2.007   2.083
191   L         1.828   1.838   1.889   1.584   1.600   1.678   1.996   2.007   2.083
192   L         1.828   1.838   1.889   1.584   1.600   1.678   1.996   2.007   2.083
193   K         1.828   1.838   1.889   1.678   1.698   1.773   1.996   2.007   2.083
194   N        -0.544  -0.577  -0.572  -0.491  -0.549  -0.540  -0.584  -0.625  -0.606
195   R         0.545   0.472   0.443   0.527   0.401   0.329   0.448   0.324   0.264
196   K        -0.544  -0.577  -0.572  -0.717  -0.766  -0.752  -0.584  -0.625  -0.606
* 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/P53260
Output conservation file - output/P53260
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
