1     M         0.786   0.797   0.835   1.177   1.182   1.175   0.800   0.816   0.873
2     P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
3     P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
4     K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
5     F         0.786   0.797   0.835   1.127   1.135   1.136   0.800   0.816   0.873
6     D         0.786   0.797   0.835   0.961   0.977   1.006   0.800   0.816   0.873
7     P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
8     N        -0.090  -0.065  -0.556   0.257   0.291  -0.499  -0.036  -0.006  -0.736
9     E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
10    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
11    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
12    Y        -3.038  -3.089  -2.546  -2.506  -2.669  -2.032  -2.440  -2.442  -1.873
13    L        -0.939  -0.805  -0.604  -1.313  -1.071  -0.758  -1.291  -1.083  -0.813
14    Y        -1.345  -1.493  -1.443  -0.747  -0.957  -1.029  -1.291  -1.448  -1.381
15    L        -0.544  -0.488  -0.563  -0.437  -0.362  -0.479  -0.663  -0.588  -0.749
16    R         0.786   0.797   0.835   0.984   0.992   1.024   0.800   0.816   0.873
17    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
18    V        -0.931  -1.237  -1.434  -0.749  -1.139  -1.321  -0.768  -1.136  -1.371
19    G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
20    G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
21    E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
22    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
23    G        -0.544  -0.488  -0.563  -0.690  -0.607  -0.785  -0.663  -0.588  -0.749
24    A        -0.544  -0.488  -0.563  -0.773  -0.687  -0.816  -0.663  -0.588  -0.749
25    S        -0.544  -0.488  -0.563  -0.567  -0.492  -0.671  -0.663  -0.588  -0.749
26    A        -0.812  -0.611  -0.582  -1.098  -0.734  -0.760  -1.081  -0.775  -0.778
27    A        -0.544  -0.488  -0.563  -0.697  -0.617  -0.701  -0.663  -0.588  -0.749
28    L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
29    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
30    P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
31    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
32    I         0.786   0.797   0.835   0.742   0.770   0.836   0.800   0.816   0.873
33    G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
34    P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
35    L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
36    G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
37    L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
38    S         0.786   0.797   0.835   0.824   0.837   0.899   0.800   0.816   0.873
39    P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
40    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
41    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
42    V        -0.090  -0.186  -0.562  -0.103  -0.226  -0.785  -0.036  -0.163  -0.746
43    G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
44    E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
45    D         0.786   0.797   0.835   0.961   0.977   1.006   0.800   0.816   0.873
46    I         0.786   0.797   0.835   0.742   0.770   0.836   0.800   0.816   0.873
47    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
48    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
49    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
50    T         0.786   0.797   0.835   0.994   0.998   1.032   0.800   0.816   0.873
51    K        -0.090  -0.323  -0.565  -0.274  -0.568  -0.914  -0.036  -0.350  -0.752
52    E        -1.345  -1.288  -1.437  -1.162  -1.065  -1.449  -1.291  -1.200  -1.374
53    F        -2.265  -2.234  -2.070  -1.604  -1.574  -1.353  -2.022  -1.984  -1.695
54    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
55    G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
56    I        -1.567  -1.639  -1.464  -1.750  -1.865  -1.595  -1.604  -1.679  -1.406
57    K        -0.939  -0.898  -0.619  -1.418  -1.299  -0.821  -1.291  -1.237  -0.839
58    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
59    T         0.786   0.797   0.835   0.994   0.998   1.032   0.800   0.816   0.873
60    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
61    Q        -0.812  -0.840  -0.617  -0.915  -1.032  -0.748  -1.081  -1.141  -0.835
62    L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
63    K        -1.878  -1.694  -1.461  -2.089  -1.737  -1.453  -1.918  -1.693  -1.402
64    I         0.786   0.797   0.835   0.742   0.770   0.836   0.800   0.816   0.873
65    Q         0.786   0.797   0.835   1.082   1.095   1.100   0.800   0.816   0.873
66    N         0.786   0.797   0.835   0.998   1.019   1.035   0.800   0.816   0.873
67    R         0.786   0.797   0.835   0.984   0.992   1.024   0.800   0.816   0.873
68    Q         0.786   0.797   0.835   1.082   1.095   1.100   0.800   0.816   0.873
69    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
70    A        -0.939  -0.862  -0.619  -1.305  -1.198  -0.769  -1.291  -1.178  -0.838
71    A        -0.939  -0.898  -0.619  -1.536  -1.476  -0.958  -1.291  -1.237  -0.839
72    S         0.786   0.797   0.835   0.824   0.837   0.899   0.800   0.816   0.873
73    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
74    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
75    P         0.786   0.797   0.835   0.834   0.849   0.907   0.800   0.816   0.873
76    S        -0.090  -0.323  -0.565   0.104  -0.192  -0.564  -0.036  -0.350  -0.752
77    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
78    S         0.786   0.797   0.835   0.824   0.837   0.899   0.800   0.816   0.873
79    S        -0.812  -0.840  -0.617  -1.098  -1.194  -0.842  -1.081  -1.141  -0.835
80    L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
81    V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
82    I         0.786   0.797   0.835   0.742   0.770   0.836   0.800   0.816   0.873
83    T        -2.099  -2.293  -2.068  -1.910  -2.222  -2.016  -1.813  -1.986  -1.694
84    A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
85    L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
86    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
87    E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
88    P        -0.090  -0.065  -0.556   0.066   0.097  -0.698  -0.036  -0.006  -0.736
89    P        -1.345  -1.216  -1.423  -1.336  -1.164  -1.559  -1.291  -1.146  -1.358
90    R         0.786   0.797   0.835   0.984   0.992   1.024   0.800   0.816   0.873
91    D         0.786   0.797   0.835   0.961   0.977   1.006   0.800   0.816   0.873
92    R         0.786   0.797   0.835   0.984   0.992   1.024   0.800   0.816   0.873
93    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
94    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
95    D        -0.812  -0.833  -0.622  -0.894  -0.965  -0.682  -1.081  -1.129  -0.843
96    K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
97    N         0.786   0.797   0.835   0.998   1.019   1.035   0.800   0.816   0.873
98    V        -0.090  -0.323  -0.565  -0.103  -0.413  -0.791  -0.036  -0.350  -0.752
99    K        -0.544  -0.488  -0.563  -0.941  -0.846  -0.963  -0.663  -0.588  -0.749
100   H         0.786   0.797   0.835   1.191   1.197   1.186   0.800   0.816   0.873
101   S        -0.544  -0.717  -0.616  -0.493  -0.776  -0.639  -0.663  -0.942  -0.833
102   G        -0.090  -0.323  -0.565  -0.052  -0.377  -0.846  -0.036  -0.350  -0.752
103   N        -0.090  -0.323  -0.565   0.257  -0.045  -0.517  -0.036  -0.350  -0.752
104   I        -1.637  -1.507  -1.451  -1.980  -1.817  -1.597  -1.709  -1.576  -1.392
105   Q        -2.506  -2.255  -2.067  -2.514  -2.211  -1.916  -2.231  -2.013  -1.693
106   L        -0.090  -0.323  -0.565   0.126  -0.153  -0.503  -0.036  -0.350  -0.752
107   D        -0.812  -0.782  -0.617  -0.894  -0.861  -0.668  -1.081  -1.046  -0.835
108   E        -0.090   0.028  -0.551   0.061   0.197  -0.580  -0.036   0.108  -0.729
109   I         0.786   0.797   0.835   0.742   0.770   0.836   0.800   0.816   0.873
110   I        -1.732  -1.835  -2.046  -1.368  -1.549  -1.756  -1.395  -1.519  -1.674
111   E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
112   I        -0.812  -0.726  -0.611  -1.159  -1.006  -0.863  -1.081  -0.955  -0.826
113   A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
114   R        -0.090   0.028  -0.551   0.202   0.338  -0.633  -0.036   0.108  -0.729
115   Q        -1.637  -1.493  -1.454  -1.542  -1.353  -1.378  -1.709  -1.542  -1.395
116   M         0.786   0.797   0.835   1.177   1.182   1.175   0.800   0.816   0.873
117   R        -0.931  -0.653  -1.408  -0.503  -0.176  -1.312  -0.768  -0.456  -1.341
118   D        -2.892  -2.732  -2.540  -2.470  -2.262  -1.991  -2.336  -2.190  -1.869
119   K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
120   S         0.786   0.797   0.835   0.824   0.837   0.899   0.800   0.816   0.873
121   F        -0.544  -0.488  -0.563  -0.245  -0.175  -0.424  -0.663  -0.588  -0.749
122   G        -1.713  -1.773  -1.463  -1.953  -2.088  -1.614  -1.709  -1.792  -1.404
123   R        -0.090   0.072  -0.550  -0.241  -0.047  -0.778  -0.036   0.161  -0.727
124   T        -1.878  -1.687  -1.465  -1.951  -1.681  -1.351  -1.918  -1.687  -1.406
125   L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
126   A        -1.567  -1.711  -1.463  -1.898  -2.122  -1.735  -1.604  -1.738  -1.405
127   S        -0.939  -0.898  -0.619  -1.309  -1.266  -0.793  -1.291  -1.237  -0.839
128   V        -0.939  -0.898  -0.619  -1.278  -1.194  -0.727  -1.291  -1.237  -0.839
129   T        -1.637  -1.493  -1.454  -1.791  -1.639  -1.480  -1.709  -1.542  -1.395
130   K        -0.090  -0.323  -0.565  -0.261  -0.547  -0.870  -0.036  -0.350  -0.752
131   E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
132   I        -0.090  -0.323  -0.565  -0.021  -0.327  -0.767  -0.036  -0.350  -0.752
133   L         0.786   0.797   0.835   0.829   0.848   0.903   0.800   0.816   0.873
134   G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
135   T         0.786   0.797   0.835   0.994   0.998   1.032   0.800   0.816   0.873
136   A         0.786   0.797   0.835   0.615   0.640   0.736   0.800   0.816   0.873
137   Q        -0.812  -0.840  -0.617  -0.633  -0.703  -0.422  -1.081  -1.141  -0.835
138   S         0.786   0.797   0.835   0.824   0.837   0.899   0.800   0.816   0.873
139   V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
140   G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
141   C        -0.090  -0.186  -0.562   0.478   0.341  -0.423  -0.036  -0.163  -0.746
142   R        -1.345  -1.493  -1.443  -1.002  -1.200  -1.181  -1.291  -1.448  -1.381
143   V         0.786   0.797   0.835   0.650   0.662   0.763   0.800   0.816   0.873
144   D        -1.345  -1.316  -1.443  -1.069  -1.040  -1.303  -1.291  -1.262  -1.382
145   F        -1.345  -1.031  -1.420  -1.172  -0.776  -1.189  -1.291  -0.905  -1.354
146   K         0.786   0.797   0.835   0.481   0.512   0.632   0.800   0.816   0.873
147   N        -0.931  -1.237  -1.434  -0.478  -0.898  -1.322  -0.768  -1.136  -1.371
148   P        -0.090  -0.186  -0.562   0.066  -0.059  -0.710  -0.036  -0.163  -0.746
149   H        -0.090  -0.323  -0.565   0.409   0.069  -0.522  -0.036  -0.350  -0.752
150   D        -0.931  -1.237  -1.434  -0.569  -1.020  -1.501  -0.768  -1.136  -1.371
151   I        -1.567  -1.639  -1.464  -1.750  -1.862  -1.462  -1.604  -1.679  -1.406
152   I        -0.812  -0.840  -0.617  -0.957  -0.998  -0.645  -1.081  -1.141  -0.835
153   E        -1.713  -1.663  -1.451  -1.899  -1.831  -1.547  -1.709  -1.652  -1.390
154   G        -1.345  -1.158  -1.419  -1.482  -1.236  -1.590  -1.291  -1.087  -1.354
155   I         0.786   0.797   0.835   0.742   0.770   0.836   0.800   0.816   0.873
156   N        -1.345  -1.493  -1.443  -0.981  -1.156  -1.143  -1.291  -1.448  -1.381
157   A        -1.567  -1.529  -1.451  -1.713  -1.656  -1.437  -1.604  -1.564  -1.392
158   G         0.786   0.797   0.835   0.733   0.751   0.828   0.800   0.816   0.873
159   E         0.786   0.797   0.835   0.786   0.803   0.869   0.800   0.816   0.873
160   I        -0.090  -0.186  -0.562   0.034  -0.065  -0.575  -0.036  -0.163  -0.746
161   E        -0.939  -0.899  -0.619  -1.192  -1.120  -0.675  -1.291  -1.239  -0.839
162   I        -1.345  -1.400  -1.449  -1.402  -1.528  -1.627  -1.291  -1.379  -1.389
163   P        -0.090  -0.065  -0.556   0.137   0.166  -0.465  -0.036  -0.006  -0.736
164   E        -2.099  -2.111  -2.049  -1.849  -1.867  -1.791  -1.813  -1.812  -1.677
165   N        -1.567  -1.555  -1.457  -1.516  -1.546  -1.394  -1.604  -1.603  -1.398
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -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/P0CX53
Output conservation file - output/P0CX53
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
