1     M         1.259   1.290   1.340   1.448   1.493   1.567   1.362   1.406   1.480
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    S        -0.244  -0.333  -0.334  -0.347  -0.461  -0.509  -0.394  -0.495  -0.507
38    A        -0.766  -0.804  -0.815  -0.838  -0.872  -0.928  -0.807  -0.834  -0.824
39    S        -0.965  -0.952  -0.873  -1.066  -1.025  -0.950  -1.018  -0.998  -0.884
40    A        -0.327  -0.384  -0.383  -0.554  -0.638  -0.633  -0.489  -0.577  -0.575
41    F        -1.328  -1.249  -1.239  -1.375  -1.286  -1.239  -1.202  -1.114  -1.053
42    N        -0.873  -0.905  -0.856  -0.659  -0.690  -0.654  -0.932  -0.948  -0.866
43    F        -0.337  -0.409  -0.373  -0.561  -0.641  -0.571  -0.527  -0.605  -0.564
44    A         0.119   0.131   0.223  -0.250  -0.258  -0.106  -0.257  -0.245  -0.110
45    -        -0.327  -0.371  -0.378  -0.335  -0.402  -0.441  -0.489  -0.550  -0.567
46    F         1.259   1.290   1.340   1.243   1.292   1.371   1.362   1.406   1.480
47    R        -0.946  -0.845  -0.858  -0.972  -0.818  -0.829  -1.014  -0.885  -0.870
48    R         1.259   1.290   1.340   1.314   1.348   1.439   1.362   1.406   1.480
49    F        -0.244  -0.235  -0.354  -0.146  -0.114  -0.267  -0.394  -0.363  -0.539
50    W        -0.368  -0.268  -0.362  -0.393  -0.242  -0.342  -0.601  -0.466  -0.555
51    N         0.031   0.117  -0.282   0.297   0.412  -0.119   0.019   0.142  -0.431
52    S         0.630   0.477   0.382   0.722   0.544   0.414   0.639   0.389   0.194
53    E         0.320   0.222   0.270   0.425   0.251   0.308   0.122  -0.069  -0.018
54    T         0.031  -0.161  -0.292   0.109  -0.175  -0.408   0.019  -0.250  -0.444
55    G         1.259   1.290   1.340   1.243   1.296   1.371   1.362   1.406   1.480
56    P         0.630   0.597   0.372   0.791   0.758   0.410   0.639   0.585   0.176
57    K         0.320   0.395   0.277   0.279   0.394   0.190   0.122   0.248  -0.003
58    T         1.259   1.290   1.340   1.221   1.273   1.350   1.362   1.406   1.480
59    V         1.259   1.290   1.340   1.212   1.253   1.341   1.362   1.406   1.480
60    H         1.259   1.290   1.340   1.460   1.508   1.579   1.362   1.406   1.480
61    F         1.259   1.290   1.340   1.243   1.292   1.371   1.362   1.406   1.480
62    W         1.259   1.290   1.340   1.375   1.417   1.497   1.362   1.406   1.480
63    A         1.259   1.290   1.340   1.019   1.055   1.157   1.362   1.406   1.480
64    P         1.259   1.290   1.340   1.336   1.383   1.460   1.362   1.406   1.480
65    T        -0.368  -0.441  -0.372  -0.571  -0.683  -0.590  -0.601  -0.661  -0.566
66    L        -0.368  -0.331  -0.377  -0.437  -0.366  -0.415  -0.601  -0.562  -0.574
67    K         1.259   1.290   1.340   1.243   1.291   1.371   1.362   1.406   1.480
68    W         1.259   1.290   1.340   1.375   1.417   1.497   1.362   1.406   1.480
69    G        -0.766  -0.816  -0.820  -0.784  -0.841  -0.852  -0.807  -0.846  -0.829
70    L         1.259   1.290   1.340   1.144   1.190   1.277   1.362   1.406   1.480
71    V         1.259   1.290   1.340   1.212   1.253   1.341   1.362   1.406   1.480
72    F        -0.946  -0.915  -0.873  -1.113  -1.088  -1.031  -1.014  -0.975  -0.886
73    A         0.630   0.477   0.382   0.473   0.264   0.134   0.639   0.389   0.194
74    G         1.259   1.290   1.340   1.243   1.296   1.371   1.362   1.406   1.480
75    L        -0.548  -0.490  -0.426  -0.779  -0.670  -0.592  -0.807  -0.724  -0.635
76    N        -0.368  -0.448  -0.366  -0.440  -0.531  -0.416  -0.601  -0.673  -0.559
77    D         1.259   1.290   1.340   1.452   1.503   1.571   1.362   1.406   1.480
78    I        -1.344  -1.346  -1.232  -1.341  -1.305  -1.157  -1.221  -1.203  -1.048
79    K        -0.946  -0.849  -0.867  -1.121  -1.004  -0.965  -1.014  -0.890  -0.879
80    R         1.259   1.290   1.340   1.314   1.348   1.439   1.362   1.406   1.480
81    P         0.630   0.477   0.382   0.790   0.590   0.425   0.639   0.389   0.194
82    V        -0.533  -0.681  -0.788  -0.415  -0.639  -0.825  -0.497  -0.677  -0.788
83    E         0.320   0.412   0.289   0.462   0.598   0.397   0.122   0.278   0.019
84    K         0.031  -0.065  -0.275   0.187   0.070  -0.236   0.019  -0.125  -0.421
85    V         0.320   0.391   0.269   0.150   0.261   0.039   0.122   0.242  -0.019
86    S         1.259   1.290   1.340   1.234   1.283   1.363   1.362   1.406   1.480
87    G         0.031  -0.161  -0.292   0.151  -0.107  -0.342   0.019  -0.250  -0.444
88    A         0.031  -0.063  -0.276   0.114  -0.010  -0.368   0.019  -0.122  -0.423
89    Q         1.259   1.290   1.340   1.344   1.382   1.468   1.362   1.406   1.480
90    N        -0.244  -0.333  -0.334  -0.103  -0.203  -0.218  -0.394  -0.495  -0.507
91    L        -0.837  -0.761  -0.845  -1.119  -1.029  -1.085  -0.911  -0.816  -0.857
92    S         0.154   0.229   0.243  -0.244  -0.129  -0.099  -0.188  -0.055  -0.070
93    L         1.259   1.290   1.340   1.144   1.190   1.277   1.362   1.406   1.480
94    L        -0.837  -0.937  -0.847  -0.889  -0.968  -0.838  -0.911  -0.987  -0.859
95    A         1.259   1.290   1.340   1.019   1.055   1.157   1.362   1.406   1.480
96    T         1.259   1.290   1.340   1.221   1.273   1.350   1.362   1.406   1.480
97    A         0.154   0.229   0.243  -0.158  -0.005  -0.042  -0.188  -0.055  -0.070
98    L        -0.368  -0.325  -0.365  -0.712  -0.682  -0.682  -0.601  -0.554  -0.560
99    I         1.259   1.290   1.340   1.283   1.329   1.409   1.362   1.406   1.480
100   W         1.259   1.290   1.340   1.375   1.417   1.497   1.362   1.406   1.480
101   T         1.259   1.290   1.340   1.221   1.273   1.350   1.362   1.406   1.480
102   R         1.259   1.290   1.340   1.314   1.348   1.439   1.362   1.406   1.480
103   W         1.259   1.290   1.340   1.375   1.417   1.497   1.362   1.406   1.480
104   S        -0.477  -0.434  -0.400  -0.595  -0.517  -0.486  -0.704  -0.639  -0.598
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   F         0.154   0.137   0.227  -0.092  -0.147  -0.006  -0.188  -0.232  -0.100
107   V         0.154   0.137   0.227  -0.046  -0.089   0.059  -0.188  -0.232  -0.100
108   I         0.630   0.477   0.382   0.734   0.529   0.369   0.639   0.389   0.194
109   K         0.031  -0.085  -0.279   0.190   0.032  -0.237   0.019  -0.150  -0.426
110   P         1.259   1.290   1.340   1.336   1.383   1.460   1.362   1.406   1.480
111   K         0.320   0.387   0.298   0.279   0.381   0.227   0.122   0.234   0.037
112   N         1.259   1.290   1.340   1.327   1.377   1.451   1.362   1.406   1.480
113   Y         0.320   0.387   0.298   0.493   0.591   0.440   0.122   0.234   0.037
114   L         0.630   0.477   0.382   0.600   0.401   0.253   0.639   0.389   0.194
115   L         0.630   0.477   0.382   0.612   0.421   0.284   0.639   0.389   0.194
116   A         1.259   1.290   1.340   1.019   1.055   1.157   1.362   1.406   1.480
117   S         0.031  -0.161  -0.292   0.112  -0.164  -0.420   0.019  -0.250  -0.444
118   V         1.259   1.290   1.340   1.212   1.253   1.341   1.362   1.406   1.480
119   N         1.259   1.290   1.340   1.327   1.377   1.451   1.362   1.406   1.480
120   F         1.259   1.290   1.340   1.243   1.292   1.371   1.362   1.406   1.480
121   F         1.259   1.290   1.340   1.243   1.292   1.371   1.362   1.406   1.480
122   L         1.259   1.290   1.340   1.144   1.190   1.277   1.362   1.406   1.480
123   G         0.630   0.477   0.382   0.668   0.452   0.265   0.639   0.389   0.194
124   C        -0.477  -0.498  -0.405  -0.370  -0.430  -0.309  -0.704  -0.734  -0.605
125   T         0.102   0.140   0.222  -0.184  -0.120   0.008  -0.291  -0.227  -0.111
126   A         0.320   0.222   0.270   0.038  -0.136  -0.050   0.122  -0.069  -0.018
127   G        -0.533  -0.664  -0.803  -0.419  -0.642  -0.896  -0.497  -0.658  -0.805
128   Y         0.102   0.138   0.224  -0.035   0.001   0.146  -0.291  -0.231  -0.106
129   H         0.630   0.709   0.379   0.831   0.923   0.508   0.639   0.756   0.189
130   L        -0.548  -0.554  -0.424  -0.794  -0.810  -0.608  -0.807  -0.806  -0.632
131   T        -1.235  -1.112  -1.214  -1.172  -0.971  -1.136  -1.117  -0.974  -1.031
132   R         1.259   1.290   1.340   1.314   1.348   1.439   1.362   1.406   1.480
133   I         0.320   0.385   0.263   0.264   0.369   0.109   0.122   0.230  -0.030
134   A        -1.344  -1.269  -1.232  -1.474  -1.375  -1.273  -1.221  -1.136  -1.049
135   N        -1.235  -1.254  -1.216  -0.954  -0.993  -0.928  -1.117  -1.124  -1.034
136   F         0.031   0.046  -0.285   0.359   0.383  -0.109   0.019   0.041  -0.434
137   R         0.154   0.137   0.227   0.076   0.021   0.174  -0.188  -0.232  -0.100
138   I        -1.634  -1.583  -1.522  -1.479  -1.397  -1.332  -1.324  -1.262  -1.153
139   R        -1.923  -1.872  -1.788  -1.547  -1.481  -1.348  -1.427  -1.372  -1.242
140   N        -1.055  -1.007  -0.896  -1.053  -0.971  -0.825  -1.117  -1.052  -0.908
141   G         0.320   0.222   0.270   0.257   0.085   0.140   0.122  -0.069  -0.018
142   D        -0.533  -0.664  -0.803  -0.152  -0.338  -0.605  -0.497  -0.658  -0.805
143   S        -0.766  -0.875  -0.841  -0.748  -0.887  -0.864  -0.807  -0.908  -0.852
144   F        -1.235  -1.098  -1.215  -1.151  -0.942  -1.125  -1.117  -0.966  -1.032
145   K        -0.873  -0.812  -0.842  -0.975  -0.957  -0.918  -0.932  -0.871  -0.854
146   Q         1.259   1.290   1.340   1.352   1.388   1.475   1.362   1.406   1.480
147   V        -0.429  -0.394  -0.398  -0.669  -0.644  -0.631  -0.658  -0.616  -0.599
148   I        -0.575  -0.553  -0.431  -0.770  -0.734  -0.550  -0.842  -0.805  -0.640
149   H        -1.346  -1.343  -1.239  -1.178  -1.169  -1.020  -1.209  -1.189  -1.052
150   Y         0.507   0.449   0.318   0.705   0.619   0.367   0.444   0.341   0.076
151   I        -0.337  -0.356  -0.385  -0.416  -0.477  -0.534  -0.527  -0.564  -0.583
152   I        -1.328  -1.337  -1.233  -1.321  -1.322  -1.187  -1.202  -1.190  -1.048
153   K        -1.659  -1.658  -1.535  -1.514  -1.560  -1.364  -1.337  -1.317  -1.162
154   G         0.574   0.442   0.353   0.586   0.392   0.205   0.552   0.329   0.140
155   E        -1.203  -1.116  -1.203  -1.194  -1.080  -1.151  -1.067  -0.959  -1.020
156   T        -1.328  -1.280  -1.222  -1.286  -1.194  -1.147  -1.202  -1.140  -1.039
157   P        -1.328  -1.251  -1.222  -1.338  -1.205  -1.165  -1.202  -1.116  -1.039
158   A        -1.659  -1.649  -1.534  -1.703  -1.697  -1.496  -1.337  -1.311  -1.162
159   A        -1.203  -1.230  -1.218  -1.146  -1.203  -1.199  -1.067  -1.084  -1.034
160   V        -1.328  -1.313  -1.226  -1.166  -1.147  -1.007  -1.202  -1.170  -1.042
161   A        -1.328  -1.306  -1.223  -1.256  -1.200  -1.064  -1.202  -1.162  -1.040
162   A        -1.346  -1.341  -1.233  -1.488  -1.462  -1.299  -1.209  -1.189  -1.047
163   K        -0.815  -0.816  -0.833  -0.786  -0.787  -0.828  -0.842  -0.838  -0.839
164   Q        -1.732  -1.701  -1.551  -1.466  -1.431  -1.219  -1.393  -1.347  -1.173
165   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   G        -0.946  -0.846  -0.868  -1.023  -0.831  -0.926  -1.014  -0.888  -0.881
177   T        -1.525  -1.556  -1.516  -1.439  -1.516  -1.481  -1.221  -1.237  -1.148
178   N        -1.235  -1.295  -1.215  -1.060  -1.191  -1.052  -1.117  -1.154  -1.033
179   P        -1.634  -1.610  -1.528  -1.403  -1.374  -1.260  -1.324  -1.288  -1.158
180   P        -1.923  -1.907  -1.785  -1.693  -1.682  -1.528  -1.427  -1.397  -1.240
181   I        -1.634  -1.579  -1.518  -1.685  -1.604  -1.472  -1.324  -1.259  -1.151
182   T        -0.837  -0.884  -0.841  -0.938  -1.026  -0.948  -0.911  -0.941  -0.854
183   H        -1.055  -0.892  -1.169  -0.993  -0.789  -1.094  -0.911  -0.719  -0.988
* 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/P53311
Output conservation file - output/P53311
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
