1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    M        -0.077  -0.251  -0.557   0.340   0.092  -0.552  -0.032  -0.268  -0.752
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    S        -0.077   0.019  -0.548   0.315   0.411  -0.352  -0.032   0.090  -0.738
27    L        -0.077  -0.251  -0.557  -0.185  -0.384  -0.726  -0.032  -0.268  -0.752
28    V        -0.077  -0.251  -0.557   0.079  -0.119  -0.535  -0.032  -0.268  -0.752
29    V        -0.888  -1.065  -1.413  -0.614  -0.828  -1.310  -0.755  -0.969  -1.370
30    Q        -3.295  -3.310  -2.900  -2.757  -2.790  -2.327  -2.512  -2.495  -1.999
31    E        -0.515  -0.520  -0.565  -0.385  -0.402  -0.549  -0.652  -0.664  -0.765
32    Q        -1.161  -1.361  -1.435  -0.969  -1.294  -1.592  -1.084  -1.330  -1.396
33    G        -1.161  -1.361  -1.435  -1.043  -1.348  -1.521  -1.084  -1.330  -1.396
34    S        -1.570  -1.613  -1.441  -1.539  -1.577  -1.344  -1.686  -1.681  -1.405
35    F        -0.077  -0.251  -0.557   0.381   0.166  -0.340  -0.032  -0.268  -0.752
36    Q        -0.144  -0.203  -0.568   0.082   0.012  -0.586  -0.120  -0.201  -0.770
37    H         0.768   0.779   0.826   0.988   1.005   1.036   0.795   0.810   0.875
38    I         0.768   0.779   0.826   0.791   0.804   0.877   0.795   0.810   0.875
39    L        -0.077  -0.251  -0.557  -0.187  -0.388  -0.733  -0.032  -0.268  -0.752
40    R        -0.077  -0.251  -0.557  -0.200  -0.396  -0.765  -0.032  -0.268  -0.752
41    L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
42    L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
43    N         0.768   0.779   0.826   0.815   0.834   0.896   0.795   0.810   0.875
44    T         0.768   0.779   0.826   0.805   0.818   0.888   0.795   0.810   0.875
45    N         0.768   0.779   0.826   0.815   0.834   0.896   0.795   0.810   0.875
46    V        -0.515  -0.568  -0.586  -0.553  -0.639  -0.717  -0.652  -0.738  -0.800
47    D         0.768   0.779   0.826   0.830   0.840   0.909   0.795   0.810   0.875
48    G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
49    N        -1.893  -1.794  -1.456  -2.429  -2.306  -1.734  -1.996  -1.872  -1.421
50    I        -1.288  -1.303  -1.422  -1.186  -1.213  -1.411  -1.272  -1.288  -1.382
51    K        -0.077   0.075  -0.548  -0.093   0.078  -0.736  -0.032   0.158  -0.738
52    I        -0.896  -0.838  -0.609  -1.220  -1.120  -0.759  -1.272  -1.181  -0.838
53    V        -0.896  -0.790  -0.610  -0.976  -0.765  -0.568  -1.272  -1.099  -0.839
54    Y        -0.515  -0.520  -0.565  -0.192  -0.214  -0.357  -0.652  -0.664  -0.765
55    A        -0.077  -0.085  -0.555   0.224   0.230  -0.466  -0.032  -0.042  -0.749
56    L        -0.774  -0.791  -0.612  -1.086  -1.106  -0.759  -1.065  -1.101  -0.842
57    T        -0.077  -0.170  -0.558   0.145   0.041  -0.465  -0.032  -0.156  -0.755
58    T        -1.802  -1.675  -1.434  -2.085  -1.885  -1.513  -1.892  -1.722  -1.395
59    I         0.768   0.779   0.826   0.789   0.803   0.875   0.795   0.810   0.875
60    K        -0.774  -0.747  -0.603  -1.260  -1.222  -1.004  -1.065  -1.027  -0.828
61    G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
62    V         0.768   0.779   0.826   0.748   0.766   0.842   0.795   0.810   0.875
63    G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
64    R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
65    R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
66    Y         0.768   0.779   0.826   1.043   1.047   1.080   0.795   0.810   0.875
67    S        -0.774  -0.766  -0.612  -0.755  -0.742  -0.560  -1.065  -1.059  -0.843
68    N         0.768   0.779   0.826   0.815   0.834   0.896   0.795   0.810   0.875
69    L        -0.515  -0.520  -0.565  -0.809  -0.821  -0.864  -0.652  -0.664  -0.765
70    V         0.768   0.779   0.826   0.748   0.766   0.842   0.795   0.810   0.875
71    C         0.768   0.779   0.826   1.156   1.161   1.172   0.795   0.810   0.875
72    K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
73    K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
74    A         0.768   0.779   0.826   0.907   0.935   0.971   0.795   0.810   0.875
75    D         0.768   0.779   0.826   0.830   0.840   0.909   0.795   0.810   0.875
76    V        -0.515  -0.520  -0.565  -0.553  -0.562  -0.679  -0.652  -0.664  -0.765
77    D        -0.077   0.019  -0.548   0.139   0.243  -0.540  -0.032   0.090  -0.738
78    L        -0.515  -0.520  -0.565  -0.721  -0.729  -0.724  -0.652  -0.664  -0.765
79    H        -2.689  -2.496  -2.504  -2.231  -1.989  -2.121  -2.202  -2.003  -1.872
80    K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
81    R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
82    A         0.768   0.779   0.826   0.907   0.935   0.971   0.795   0.810   0.875
83    G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
84    E         0.768   0.779   0.826   0.907   0.920   0.971   0.795   0.810   0.875
85    L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
86    T         0.768   0.779   0.826   0.805   0.818   0.888   0.795   0.810   0.875
87    Q        -2.016  -2.096  -2.043  -1.729  -1.847  -1.816  -1.789  -1.857  -1.700
88    E         0.768   0.779   0.826   0.907   0.920   0.971   0.795   0.810   0.875
89    E         0.768   0.779   0.826   0.907   0.920   0.971   0.795   0.810   0.875
90    L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
91    E         0.768   0.779   0.826   0.907   0.920   0.971   0.795   0.810   0.875
92    R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
93    I        -0.077   0.076  -0.549   0.077   0.251  -0.639  -0.032   0.160  -0.740
94    V         0.768   0.779   0.826   0.748   0.766   0.842   0.795   0.810   0.875
95    Q        -0.774  -0.568  -0.584  -0.899  -0.560  -0.635  -1.065  -0.738  -0.796
96    I         0.768   0.779   0.826   0.789   0.803   0.875   0.795   0.810   0.875
97    M        -0.774  -0.791  -0.612  -0.683  -0.749  -0.553  -1.065  -1.101  -0.842
98    Q         0.768   0.779   0.826   0.871   0.891   0.942   0.795   0.810   0.875
99    N         0.768   0.779   0.826   0.815   0.834   0.896   0.795   0.810   0.875
100   P         0.768   0.779   0.826   1.102   1.109   1.129   0.795   0.810   0.875
101   T        -1.288  -1.374  -1.425  -1.113  -1.234  -1.354  -1.272  -1.366  -1.385
102   H        -2.316  -2.207  -2.041  -2.106  -1.953  -1.745  -2.099  -1.973  -1.697
103   Y        -0.515  -0.520  -0.565  -0.192  -0.214  -0.357  -0.652  -0.664  -0.765
104   K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
105   I         0.768   0.779   0.826   0.789   0.803   0.875   0.795   0.810   0.875
106   P         0.768   0.779   0.826   1.102   1.109   1.129   0.795   0.810   0.875
107   A        -1.288  -1.374  -1.425  -1.016  -1.125  -1.292  -1.272  -1.366  -1.385
108   W         0.768   0.779   0.826   1.127   1.133   1.148   0.795   0.810   0.875
109   F         0.768   0.779   0.826   1.058   1.064   1.093   0.795   0.810   0.875
110   L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
111   N         0.768   0.779   0.826   0.815   0.834   0.896   0.795   0.810   0.875
112   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
113   Q         0.768   0.779   0.826   0.871   0.891   0.942   0.795   0.810   0.875
114   N        -1.502  -1.325  -1.435  -1.889  -1.676  -1.710  -1.582  -1.405  -1.398
115   D         0.768   0.779   0.826   0.830   0.840   0.909   0.795   0.810   0.875
116   I        -2.016  -2.009  -2.036  -1.766  -1.773  -1.794  -1.789  -1.792  -1.694
117   T        -2.407  -2.256  -2.048  -2.439  -2.246  -1.895  -2.202  -2.057  -1.705
118   D         0.768   0.779   0.826   0.830   0.840   0.909   0.795   0.810   0.875
119   G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
120   K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
121   D        -0.515  -0.520  -0.565  -0.417  -0.435  -0.535  -0.652  -0.664  -0.765
122   Y        -1.642  -1.677  -1.447  -1.312  -1.388  -1.131  -1.686  -1.725  -1.411
123   H        -0.896  -0.868  -0.616  -0.975  -0.937  -0.583  -1.272  -1.231  -0.849
124   T        -2.922  -2.739  -2.516  -3.024  -2.806  -2.350  -2.409  -2.239  -1.881
125   L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
126   A        -0.077  -0.170  -0.558   0.195   0.094  -0.572  -0.032  -0.156  -0.755
127   N         0.768   0.779   0.826   0.815   0.834   0.896   0.795   0.810   0.875
128   N        -1.288  -1.273  -1.434  -1.140  -1.112  -1.406  -1.272  -1.247  -1.396
129   V        -0.896  -0.866  -0.617  -1.416  -1.384  -0.952  -1.272  -1.228  -0.851
130   E        -0.896  -0.868  -0.616  -1.065  -1.036  -0.653  -1.272  -1.231  -0.849
131   S        -0.077  -0.170  -0.558   0.271   0.147  -0.519  -0.032  -0.156  -0.755
132   K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
133   L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
134   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
135   D        -0.515  -0.520  -0.565  -0.439  -0.456  -0.569  -0.652  -0.664  -0.765
136   D         0.768   0.779   0.826   0.830   0.840   0.909   0.795   0.810   0.875
137   L        -0.077  -0.170  -0.558  -0.221  -0.332  -0.853  -0.032  -0.156  -0.755
138   E         0.768   0.779   0.826   0.907   0.920   0.971   0.795   0.810   0.875
139   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
140   L         0.768   0.779   0.826   0.487   0.503   0.631   0.795   0.810   0.875
141   K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
142   K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
143   I         0.768   0.779   0.826   0.789   0.803   0.875   0.795   0.810   0.875
144   R        -0.515  -0.520  -0.565  -0.790  -0.789  -0.829  -0.652  -0.664  -0.765
145   A        -1.642  -1.525  -1.428  -1.519  -1.346  -1.274  -1.686  -1.539  -1.389
146   H         0.768   0.779   0.826   0.988   1.006   1.036   0.795   0.810   0.875
147   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
148   G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
149   I        -0.896  -0.868  -0.616  -1.381  -1.365  -0.930  -1.272  -1.231  -0.849
150   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
151   H         0.768   0.779   0.826   0.988   1.006   1.036   0.795   0.810   0.875
152   F        -1.642  -1.677  -1.447  -1.330  -1.399  -1.152  -1.686  -1.725  -1.411
153   W        -0.515  -0.520  -0.565  -0.261  -0.290  -0.540  -0.652  -0.664  -0.765
154   G        -0.515  -0.520  -0.565  -0.531  -0.540  -0.653  -0.652  -0.664  -0.765
155   L        -0.077  -0.170  -0.558  -0.187  -0.290  -0.735  -0.032  -0.156  -0.755
156   R        -0.774  -0.811  -0.614  -1.322  -1.402  -1.040  -1.065  -1.135  -0.846
157   V         0.768   0.779   0.826   0.748   0.766   0.842   0.795   0.810   0.875
158   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
159   G         0.768   0.779   0.826   0.758   0.778   0.850   0.795   0.810   0.875
160   Q         0.768   0.779   0.826   0.871   0.891   0.942   0.795   0.810   0.875
161   H         0.768   0.779   0.826   0.988   1.006   1.036   0.795   0.810   0.875
162   T         0.768   0.779   0.826   0.805   0.818   0.888   0.795   0.810   0.875
163   K         0.768   0.779   0.826   0.611   0.625   0.731   0.795   0.810   0.875
164   T         0.768   0.779   0.826   0.805   0.818   0.888   0.795   0.810   0.875
165   T         0.768   0.779   0.826   0.805   0.818   0.888   0.795   0.810   0.875
166   G        -1.288  -1.414  -1.433  -1.151  -1.323  -1.369  -1.272  -1.420  -1.394
167   R         0.768   0.779   0.826   0.481   0.506   0.626   0.795   0.810   0.875
168   R        -1.288  -1.414  -1.433  -1.529  -1.710  -1.728  -1.272  -1.420  -1.394
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   R        -1.288  -1.303  -1.422  -1.554  -1.575  -1.718  -1.272  -1.288  -1.382
180   A        -2.326  -2.399  -2.057  -2.322  -2.452  -1.985  -2.110  -2.152  -1.712
* 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/P0CX55
Output conservation file - output/P0CX55
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
