1     M         0.732   0.737   0.752   0.968   0.966   0.972   0.760   0.765   0.786
2     S        -0.394  -0.481  -0.649  -0.183  -0.312  -0.599  -0.456  -0.582  -0.854
3     A        -2.266  -2.188  -2.125  -2.160  -2.032  -1.984  -1.976  -1.885  -1.772
4     N        -2.266  -2.188  -2.125  -2.188  -2.064  -1.938  -1.976  -1.885  -1.772
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     D        -0.394  -0.477  -0.650  -0.460  -0.577  -0.858  -0.456  -0.575  -0.856
9     K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
10    Q        -0.783  -0.806  -0.694  -0.744  -0.775  -0.598  -1.064  -1.099  -0.928
11    Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
12    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
13    S         0.732   0.737   0.752   0.859   0.858   0.875   0.760   0.765   0.786
14    Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
15    N         0.732   0.737   0.752   0.853   0.858   0.871   0.760   0.765   0.786
16    N         0.732   0.737   0.752   0.853   0.858   0.871   0.760   0.765   0.786
17    V        -0.394  -0.477  -0.650  -0.389  -0.512  -0.836  -0.456  -0.575  -0.856
18    H         0.732   0.737   0.752   0.957   0.959   0.962   0.760   0.765   0.786
19    Q         0.732   0.737   0.752   0.815   0.818   0.836   0.760   0.765   0.786
20    L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
21    C         0.732   0.737   0.752   1.037   1.039   1.033   0.760   0.765   0.786
22    Q         0.732   0.737   0.752   0.815   0.818   0.836   0.760   0.765   0.786
23    V        -1.407  -1.234  -1.504  -1.462  -1.196  -1.626  -1.368  -1.147  -1.458
24    S        -2.266  -2.287  -2.136  -2.134  -2.201  -1.981  -1.976  -1.979  -1.781
25    A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
26    E        -1.407  -1.532  -1.527  -1.405  -1.595  -1.576  -1.368  -1.510  -1.484
27    R        -0.783  -0.806  -0.694  -0.908  -0.976  -0.797  -1.064  -1.099  -0.928
28    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
29    K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
30    N        -1.642  -1.574  -1.534  -1.731  -1.635  -1.568  -1.672  -1.579  -1.493
31    F         0.732   0.737   0.752   0.870   0.876   0.885   0.760   0.765   0.786
32    K        -0.394  -0.481  -0.649  -0.435  -0.544  -0.769  -0.456  -0.582  -0.854
33    P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
34    D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
35    L        -0.394  -0.336  -0.644  -0.435  -0.340  -0.860  -0.456  -0.369  -0.846
36    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
37    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
38    A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
39    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
40    G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
41    G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
42    G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
43    G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
44    F         0.732   0.737   0.752   0.870   0.876   0.885   0.760   0.765   0.786
45    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
46    P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
47    A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
48    R         0.732   0.737   0.752   0.875   0.880   0.890   0.760   0.765   0.786
49    I        -0.783  -0.806  -0.694  -0.975  -0.981  -0.774  -1.064  -1.099  -0.928
50    L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
51    R         0.732   0.737   0.752   0.875   0.880   0.890   0.760   0.765   0.786
52    T        -0.783  -0.806  -0.694  -0.796  -0.836  -0.659  -1.064  -1.099  -0.928
53    F         0.732   0.737   0.752   0.870   0.876   0.885   0.760   0.765   0.786
54    L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
55    K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
56    E         0.732   0.737   0.752   0.640   0.644   0.682   0.760   0.765   0.786
57    P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
58    G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
59    V        -1.642  -1.574  -1.534  -1.727  -1.594  -1.566  -1.672  -1.579  -1.493
60    P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
61    T        -0.783  -0.806  -0.694  -0.800  -0.836  -0.662  -1.064  -1.099  -0.928
62    I        -0.783  -0.806  -0.694  -1.131  -1.158  -0.944  -1.064  -1.099  -0.928
63    R         0.732   0.737   0.752   0.875   0.880   0.890   0.760   0.765   0.786
64    I        -0.394  -0.481  -0.649  -0.518  -0.641  -0.880  -0.456  -0.582  -0.854
65    F        -0.783  -0.806  -0.694  -0.699  -0.731  -0.563  -1.064  -1.099  -0.928
66    A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
67    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
68    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
69    L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
70    S         0.732   0.737   0.752   0.859   0.858   0.875   0.760   0.765   0.786
71    L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
72    Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
73    E         0.732   0.737   0.752   0.640   0.644   0.682   0.760   0.765   0.786
74    D        -1.407  -1.532  -1.527  -1.456  -1.645  -1.632  -1.368  -1.510  -1.484
75    L        -1.407  -1.532  -1.527  -1.440  -1.635  -1.652  -1.368  -1.510  -1.484
76    N        -2.890  -2.834  -2.607  -2.562  -2.515  -2.153  -2.280  -2.213  -1.957
77    S        -0.700  -0.641  -0.687  -0.655  -0.557  -0.639  -0.929  -0.828  -0.917
78    V        -0.700  -0.651  -0.688  -0.860  -0.769  -0.846  -0.929  -0.845  -0.918
79    G        -0.394  -0.477  -0.650  -0.244  -0.358  -0.623  -0.456  -0.575  -0.856
80    S        -1.407  -1.532  -1.527  -1.231  -1.444  -1.489  -1.368  -1.510  -1.484
81    E        -0.783  -0.806  -0.694  -0.956  -0.980  -0.782  -1.064  -1.099  -0.928
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    V        -2.266  -2.300  -2.138  -2.260  -2.334  -2.070  -1.976  -1.991  -1.783
84    E         0.732   0.737   0.752   0.640   0.644   0.682   0.760   0.765   0.786
85    E        -2.266  -2.205  -2.125  -2.209  -2.110  -2.025  -1.976  -1.901  -1.772
86    V        -1.407  -1.532  -1.527  -1.363  -1.559  -1.569  -1.368  -1.510  -1.484
87    G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
88    V        -0.783  -0.806  -0.694  -0.914  -0.940  -0.755  -1.064  -1.099  -0.928
89    K        -2.266  -2.300  -2.138  -2.243  -2.278  -1.997  -1.976  -1.991  -1.783
90    V         0.732   0.737   0.752   0.708   0.718   0.742   0.760   0.765   0.786
91    S        -2.266  -2.108  -2.133  -2.039  -1.812  -1.813  -1.976  -1.801  -1.779
92    R         0.732   0.737   0.752   0.875   0.880   0.890   0.760   0.765   0.786
93    T         0.732   0.737   0.752   0.826   0.833   0.846   0.760   0.765   0.786
94    Q         0.732   0.737   0.752   0.815   0.818   0.836   0.760   0.765   0.786
95    W         0.732   0.737   0.752   1.005   1.006   1.005   0.760   0.765   0.786
96    I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
97    D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
98    Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
99    E        -1.407  -1.532  -1.527  -1.292  -1.456  -1.399  -1.368  -1.510  -1.484
100   Q         0.732   0.737   0.752   0.815   0.818   0.836   0.760   0.765   0.786
101   C        -0.783  -0.806  -0.694  -0.619  -0.680  -0.522  -1.064  -1.099  -0.928
102   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
103   L        -0.783  -0.806  -0.694  -1.120  -1.175  -0.971  -1.064  -1.099  -0.928
104   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
105   L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
106   V         0.732   0.737   0.752   0.708   0.718   0.742   0.760   0.765   0.786
107   G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
108   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
109   N        -0.394  -0.481  -0.649  -0.235  -0.366  -0.697  -0.456  -0.582  -0.854
110   V        -0.394  -0.481  -0.649  -0.389  -0.519  -0.833  -0.456  -0.582  -0.854
111   L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
112   I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
113   V        -0.783  -0.806  -0.694  -1.080  -1.142  -0.939  -1.064  -1.099  -0.928
114   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
115   E         0.732   0.737   0.752   0.640   0.644   0.682   0.760   0.765   0.786
116   V         0.732   0.737   0.752   0.708   0.718   0.742   0.760   0.765   0.786
117   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
118   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
119   T         0.732   0.737   0.752   0.826   0.833   0.846   0.760   0.765   0.786
120   R         0.732   0.737   0.752   0.875   0.880   0.890   0.760   0.765   0.786
121   T         0.732   0.737   0.752   0.826   0.833   0.846   0.760   0.765   0.786
122   T         0.732   0.737   0.752   0.826   0.833   0.846   0.760   0.765   0.786
123   L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
124   H         0.732   0.737   0.752   0.957   0.959   0.962   0.760   0.765   0.786
125   Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
126   A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
127   L        -1.407  -1.532  -1.527  -1.440  -1.636  -1.652  -1.368  -1.510  -1.484
128   S        -0.783  -0.726  -0.681  -0.714  -0.624  -0.560  -1.064  -0.965  -0.907
129   E         0.732   0.737   0.752   0.640   0.644   0.682   0.760   0.765   0.786
130   L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
131   E        -0.783  -0.806  -0.694  -1.114  -1.164  -0.956  -1.064  -1.099  -0.928
132   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
133   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
134   A        -1.407  -1.532  -1.527  -1.429  -1.632  -1.644  -1.368  -1.510  -1.484
135   A        -0.783  -0.782  -0.693  -1.050  -1.049  -0.895  -1.064  -1.058  -0.927
136   E        -1.407  -1.287  -1.503  -1.403  -1.221  -1.538  -1.368  -1.212  -1.457
137   Q         0.732   0.737   0.752   0.815   0.818   0.836   0.760   0.765   0.786
138   A        -0.783  -0.806  -0.694  -0.924  -0.951  -0.756  -1.064  -1.099  -0.928
139   K        -0.394  -0.481  -0.649  -0.480  -0.599  -0.861  -0.456  -0.582  -0.854
140   A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
141   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
142   G        -0.783  -0.783  -0.693  -0.842  -0.839  -0.693  -1.064  -1.060  -0.926
143   I        -0.783  -0.806  -0.694  -1.151  -1.185  -0.967  -1.064  -1.099  -0.928
144   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
145   T        -1.642  -1.546  -1.533  -1.661  -1.503  -1.455  -1.672  -1.555  -1.492
146   E        -2.266  -2.300  -2.138  -2.294  -2.332  -2.080  -1.976  -1.991  -1.783
147   K         0.732   0.737   0.752   0.569   0.578   0.619   0.760   0.765   0.786
148   S        -1.741  -1.706  -1.541  -1.620  -1.561  -1.319  -1.773  -1.718  -1.500
149   P         0.732   0.737   0.752   0.820   0.824   0.841   0.760   0.765   0.786
150   E         0.732   0.737   0.752   0.663   0.668   0.702   0.760   0.765   0.786
151   M        -0.700  -0.651  -0.688  -0.526  -0.443  -0.560  -0.929  -0.845  -0.918
152   K        -1.642  -1.574  -1.534  -1.841  -1.720  -1.590  -1.672  -1.579  -1.493
153   T         0.732   0.737   0.752   0.826   0.833   0.846   0.760   0.765   0.786
154   N        -1.642  -1.656  -1.528  -1.685  -1.695  -1.479  -1.672  -1.665  -1.486
155   F         0.732   0.737   0.752   0.870   0.876   0.885   0.760   0.765   0.786
156   G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
157   I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
158   F         0.732   0.737   0.752   0.870   0.876   0.885   0.760   0.765   0.786
159   V         0.732   0.737   0.752   0.708   0.718   0.742   0.760   0.765   0.786
160   L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
161   H         0.732   0.737   0.752   0.957   0.959   0.962   0.760   0.765   0.786
162   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
163   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
164   Q        -2.266  -2.224  -2.124  -2.162  -2.094  -1.971  -1.976  -1.919  -1.771
165   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
166   P        -0.394  -0.477  -0.650  -0.222  -0.339  -0.620  -0.456  -0.575  -0.856
167   K         0.732   0.737   0.752   0.583   0.594   0.631   0.760   0.765   0.786
168   K        -0.394  -0.481  -0.649  -0.429  -0.537  -0.757  -0.456  -0.582  -0.854
169   A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
170   D        -0.783  -0.806  -0.694  -1.105  -1.147  -0.938  -1.064  -1.099  -0.928
171   L         0.732   0.737   0.752   0.663   0.677   0.702   0.760   0.765   0.786
172   P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
173   A        -1.407  -1.426  -1.513  -1.427  -1.457  -1.616  -1.368  -1.383  -1.469
174   E        -0.394  -0.477  -0.650  -0.439  -0.561  -0.851  -0.456  -0.575  -0.856
175   M        -1.407  -1.234  -1.504  -1.434  -1.196  -1.511  -1.368  -1.147  -1.458
176   L        -1.642  -1.574  -1.534  -1.589  -1.442  -1.415  -1.672  -1.579  -1.493
177   N        -0.394  -0.477  -0.650  -0.235  -0.359  -0.700  -0.456  -0.575  -0.856
178   D        -0.533  -0.735  -0.680  -0.604  -0.902  -0.803  -0.665  -0.980  -0.904
179   K        -2.266  -2.108  -2.133  -2.186  -1.918  -2.002  -1.976  -1.801  -1.779
180   N        -0.394  -0.336  -0.644  -0.228  -0.141  -0.674  -0.456  -0.369  -0.846
181   R         0.732   0.737   0.752   0.865   0.868   0.881   0.760   0.765   0.786
182   Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
183   F        -0.394  -0.336  -0.644  -0.229  -0.141  -0.697  -0.456  -0.369  -0.846
184   A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
185   A        -0.394  -0.336  -0.644  -0.364  -0.281  -0.732  -0.456  -0.369  -0.846
186   K        -0.394  -0.273  -0.639  -0.213  -0.037  -0.659  -0.456  -0.280  -0.838
187   T        -2.266  -2.222  -2.125  -2.052  -1.972  -1.856  -1.976  -1.917  -1.772
188   V         0.732   0.737   0.752   0.708   0.718   0.742   0.760   0.765   0.786
189   P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
190   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
191   K        -0.783  -0.806  -0.694  -1.001  -1.017  -0.815  -1.064  -1.099  -0.928
192   W         0.732   0.737   0.752   1.005   1.006   1.005   0.760   0.765   0.786
193   Y        -0.783  -0.806  -0.694  -0.938  -1.016  -0.829  -1.064  -1.099  -0.928
194   A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
195   Y         0.732   0.737   0.752   0.870   0.874   0.885   0.760   0.765   0.786
196   P         0.732   0.737   0.752   0.809   0.812   0.831   0.760   0.765   0.786
197   W         0.732   0.737   0.752   1.005   1.006   1.005   0.760   0.765   0.786
198   E         0.732   0.737   0.752   0.640   0.644   0.682   0.760   0.765   0.786
199   S        -0.394  -0.481  -0.649  -0.207  -0.341  -0.649  -0.456  -0.582  -0.854
200   T        -1.407  -1.405  -1.508  -1.322  -1.324  -1.562  -1.368  -1.360  -1.462
201   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
202   I         0.732   0.737   0.752   0.536   0.540   0.590   0.760   0.765   0.786
203   V         0.732   0.737   0.752   0.708   0.718   0.742   0.760   0.765   0.786
204   F        -1.642  -1.656  -1.528  -1.540  -1.556  -1.382  -1.672  -1.665  -1.486
205   H         0.732   0.737   0.752   0.957   0.959   0.962   0.760   0.765   0.786
206   T        -0.394  -0.477  -0.650  -0.206  -0.319  -0.607  -0.456  -0.575  -0.856
207   R        -1.407  -1.376  -1.507  -1.322  -1.270  -1.384  -1.368  -1.327  -1.461
208   M        -1.407  -1.532  -1.527  -1.085  -1.290  -1.349  -1.368  -1.510  -1.484
209   A         0.732   0.737   0.752   0.674   0.681   0.712   0.760   0.765   0.786
210   I        -2.266  -2.205  -2.125  -2.193  -2.096  -1.973  -1.976  -1.901  -1.772
211   E        -0.394  -0.305  -0.640  -0.388  -0.268  -0.732  -0.456  -0.324  -0.840
212   Q         0.732   0.737   0.752   0.815   0.818   0.836   0.760   0.765   0.786
213   G         0.732   0.737   0.752   0.776   0.780   0.802   0.760   0.765   0.786
214   N         0.732   0.737   0.752   0.853   0.858   0.871   0.760   0.765   0.786
215   D         0.732   0.737   0.752   0.612   0.621   0.657   0.760   0.765   0.786
216   I        -1.642  -1.656  -1.528  -1.743  -1.708  -1.466  -1.672  -1.665  -1.486
217   F         0.732   0.737   0.752   0.870   0.876   0.885   0.760   0.765   0.786
218   I        -1.407  -1.234  -1.504  -1.354  -1.093  -1.483  -1.368  -1.147  -1.458
219   P        -0.394  -0.305  -0.640  -0.271  -0.143  -0.701  -0.456  -0.324  -0.840
220   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
221   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
222   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
223   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
224   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
225   Q        -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/Q04178
Output conservation file - output/Q04178
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
