1     M         0.972   0.981   1.031   1.267   1.269   1.321   1.031   1.044   1.111
2     T        -0.725  -0.615  -0.891  -0.518  -0.366  -0.738  -0.757  -0.609  -0.950
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     T        -0.128  -0.066  -0.177  -0.124  -0.014  -0.302  -0.310  -0.208  -0.412
9     S        -1.634  -1.658  -1.489  -1.371  -1.390  -1.135  -1.544  -1.562  -1.315
10    F         0.091  -0.045  -0.150   0.170  -0.019  -0.184   0.038  -0.175  -0.366
11    Y         0.972   0.981   1.031   1.111   1.118   1.182   1.031   1.044   1.111
12    D        -0.725  -0.641  -0.890  -0.535  -0.412  -0.822  -0.757  -0.642  -0.949
13    L         0.091  -0.045  -0.150  -0.002  -0.197  -0.359   0.038  -0.175  -0.366
14    E        -1.629  -1.646  -1.484  -1.653  -1.701  -1.459  -1.552  -1.556  -1.311
15    C        -0.273  -0.210  -0.203  -0.216  -0.123  -0.119  -0.559  -0.449  -0.458
16    K        -0.384  -0.366  -0.233  -0.979  -0.924  -0.686  -0.757  -0.726  -0.511
17    D         0.972   0.981   1.031   1.073   1.083   1.148   1.031   1.044   1.111
18    K         0.091   0.143  -0.126  -0.104  -0.017  -0.356   0.038   0.117  -0.324
19    K        -1.007  -0.976  -0.939  -1.300  -1.233  -1.117  -1.155  -1.104  -1.012
20    G         0.091   0.143  -0.126   0.077   0.149  -0.226   0.038   0.117  -0.324
21    E        -1.459  -1.513  -1.464  -1.472  -1.554  -1.518  -1.354  -1.410  -1.291
22    S        -1.459  -1.464  -1.463  -1.233  -1.269  -1.269  -1.354  -1.359  -1.290
23    F         0.091  -0.045  -0.150   0.117  -0.091  -0.302   0.038  -0.175  -0.366
24    K        -0.273  -0.210  -0.203  -0.461  -0.330  -0.398  -0.559  -0.449  -0.458
25    F         0.091  -0.045  -0.150   0.117  -0.091  -0.302   0.038  -0.175  -0.366
26    D        -1.629  -1.566  -1.476  -1.702  -1.587  -1.497  -1.552  -1.479  -1.304
27    Q        -1.629  -1.589  -1.476  -1.498  -1.426  -1.276  -1.552  -1.502  -1.304
28    L         0.091  -0.045  -0.150   0.028  -0.156  -0.293   0.038  -0.175  -0.366
29    K        -0.725  -0.807  -0.910  -0.920  -1.015  -1.145  -0.757  -0.868  -0.974
30    G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
31    K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
32    V         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
33    V         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
34    L         0.972   0.981   1.031   0.819   0.829   0.921   1.031   1.044   1.111
35    I        -0.273  -0.246  -0.210  -0.322  -0.281  -0.257  -0.559  -0.512  -0.470
36    V         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
37    N         0.972   0.981   1.031   1.040   1.047   1.118   1.031   1.044   1.111
38    V         0.091   0.094  -0.135   0.183   0.188  -0.134   0.038   0.044  -0.339
39    A         0.972   0.981   1.031   1.170   1.178   1.235   1.031   1.044   1.111
40    S         0.972   0.981   1.031   1.006   1.020   1.088   1.031   1.044   1.111
41    K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
42    C         0.972   0.981   1.031   1.224   1.231   1.283   1.031   1.044   1.111
43    G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
44    F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
45    T         0.972   0.981   1.031   1.149   1.153   1.216   1.031   1.044   1.111
46    P         0.972   0.981   1.031   1.078   1.080   1.152   1.031   1.044   1.111
47    Q         0.972   0.981   1.031   1.051   1.066   1.128   1.031   1.044   1.111
48    Y         0.972   0.981   1.031   1.111   1.118   1.182   1.031   1.044   1.111
49    K         0.091  -0.045  -0.150  -0.099  -0.257  -0.379   0.038  -0.175  -0.366
50    E        -1.007  -0.927  -0.933  -1.187  -1.060  -1.029  -1.155  -1.045  -1.005
51    L         0.972   0.981   1.031   0.819   0.829   0.921   1.031   1.044   1.111
52    E         0.972   0.981   1.031   0.945   0.947   1.033   1.031   1.044   1.111
53    E        -1.459  -1.510  -1.466  -1.429  -1.543  -1.461  -1.354  -1.407  -1.293
54    L        -0.273  -0.310  -0.228  -0.572  -0.636  -0.489  -0.559  -0.624  -0.501
55    Y         0.091   0.143  -0.126   0.303   0.371  -0.048   0.038   0.117  -0.324
56    K        -0.384  -0.368  -0.234  -0.797  -0.760  -0.533  -0.757  -0.729  -0.512
57    K         0.091  -0.045  -0.150  -0.148  -0.326  -0.486   0.038  -0.175  -0.366
58    Y        -0.725  -0.796  -0.910  -0.403  -0.517  -0.665  -0.757  -0.855  -0.974
59    Q        -0.273  -0.213  -0.205  -0.662  -0.543  -0.514  -0.559  -0.454  -0.461
60    D         0.091  -0.045  -0.150   0.246   0.045  -0.162   0.038  -0.175  -0.366
61    K        -1.459  -1.391  -1.450  -1.551  -1.432  -1.446  -1.354  -1.271  -1.277
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    G         0.091  -0.045  -0.150   0.077  -0.109  -0.264   0.038  -0.175  -0.366
66    F        -0.273  -0.220  -0.209  -0.502  -0.401  -0.427  -0.559  -0.467  -0.468
67    V        -2.081  -2.085  -1.897  -1.895  -1.915  -1.610  -1.751  -1.744  -1.480
68    I         0.972   0.981   1.031   1.089   1.091   1.162   1.031   1.044   1.111
69    L        -0.273  -0.226  -0.205  -0.513  -0.440  -0.386  -0.559  -0.478  -0.462
70    G         0.091  -0.045  -0.150   0.098  -0.081  -0.220   0.038  -0.175  -0.366
71    F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
72    P         0.972   0.981   1.031   1.078   1.080   1.152   1.031   1.044   1.111
73    C         0.972   0.981   1.031   1.224   1.231   1.283   1.031   1.044   1.111
74    N         0.972   0.981   1.031   1.040   1.047   1.118   1.031   1.044   1.111
75    Q         0.972   0.981   1.031   1.051   1.066   1.128   1.031   1.044   1.111
76    F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
77    G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
78    K        -0.725  -0.664  -0.891  -0.792  -0.687  -1.082  -0.757  -0.673  -0.949
79    Q         0.972   0.981   1.031   1.051   1.066   1.128   1.031   1.044   1.111
80    E         0.972   0.981   1.031   0.945   0.947   1.033   1.031   1.044   1.111
81    P         0.972   0.981   1.031   1.078   1.080   1.152   1.031   1.044   1.111
82    G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
83    S         0.091  -0.045  -0.150   0.221   0.040  -0.127   0.038  -0.175  -0.366
84    D        -2.081  -2.064  -1.892  -1.837  -1.825  -1.572  -1.751  -1.726  -1.476
85    E         0.091   0.136  -0.132   0.145   0.198  -0.180   0.038   0.106  -0.334
86    Q         0.091   0.165  -0.128   0.140   0.232  -0.182   0.038   0.149  -0.328
87    I         0.972   0.981   1.031   1.089   1.091   1.162   1.031   1.044   1.111
88    T        -2.081  -2.054  -1.893  -1.796  -1.754  -1.556  -1.751  -1.718  -1.477
89    E        -1.459  -1.370  -1.452  -1.319  -1.177  -1.325  -1.354  -1.248  -1.279
90    F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
91    C         0.972   0.981   1.031   1.224   1.231   1.283   1.031   1.044   1.111
92    Q         0.091   0.143  -0.126   0.236   0.315  -0.110   0.038   0.117  -0.324
93    L         0.091   0.094  -0.135  -0.060  -0.051  -0.457   0.038   0.044  -0.339
94    N         0.972   0.981   1.031   1.040   1.047   1.118   1.031   1.044   1.111
95    Y         0.972   0.981   1.031   1.111   1.118   1.182   1.031   1.044   1.111
96    G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
97    V         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
98    T        -0.273  -0.307  -0.224  -0.250  -0.323  -0.223  -0.559  -0.620  -0.495
99    F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
100   P         0.972   0.981   1.031   1.078   1.080   1.152   1.031   1.044   1.111
101   I        -0.384  -0.368  -0.233  -0.560  -0.534  -0.312  -0.757  -0.730  -0.511
102   M        -0.384  -0.368  -0.233  -0.532  -0.496  -0.281  -0.757  -0.730  -0.511
103   K        -1.459  -1.391  -1.450  -1.465  -1.356  -1.336  -1.354  -1.271  -1.277
104   K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
105   I        -0.273  -0.307  -0.224  -0.322  -0.400  -0.288  -0.559  -0.620  -0.495
106   D        -1.177  -1.153  -0.973  -1.301  -1.270  -0.981  -1.354  -1.316  -1.053
107   V         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
108   N         0.972   0.981   1.031   1.040   1.047   1.118   1.031   1.044   1.111
109   G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
110   S        -0.725  -0.627  -0.890  -0.520  -0.377  -0.797  -0.757  -0.624  -0.949
111   N        -0.725  -0.646  -0.889  -0.621  -0.496  -0.936  -0.757  -0.649  -0.947
112   A        -1.007  -0.972  -0.936  -0.857  -0.796  -0.772  -1.155  -1.098  -1.009
113   D         0.972   0.981   1.031   1.073   1.083   1.148   1.031   1.044   1.111
114   S         0.091   0.165  -0.128   0.264   0.356  -0.091   0.038   0.149  -0.328
115   V         0.091  -0.045  -0.150   0.117  -0.092  -0.302   0.038  -0.175  -0.366
116   Y         0.972   0.981   1.031   1.111   1.118   1.182   1.031   1.044   1.111
117   N        -2.533  -2.491  -2.239  -2.479  -2.400  -2.035  -1.950  -1.904  -1.595
118   Y        -1.007  -1.076  -0.949  -0.916  -0.989  -0.797  -1.155  -1.223  -1.024
119   L         0.091  -0.045  -0.150   0.061  -0.111  -0.222   0.038  -0.175  -0.366
120   K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
121   S        -1.459  -1.487  -1.464  -1.373  -1.413  -1.418  -1.354  -1.383  -1.291
122   Q        -0.273  -0.307  -0.224  -0.368  -0.437  -0.329  -0.559  -0.620  -0.495
123   K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
124   A        -2.081  -2.080  -1.894  -1.985  -1.979  -1.765  -1.751  -1.740  -1.477
125   G         0.972   0.981   1.031   0.869   0.878   0.965   1.031   1.044   1.111
126   L         0.091   0.094  -0.135   0.016   0.023  -0.296   0.038   0.044  -0.339
127   L         0.091  -0.045  -0.150   0.061  -0.111  -0.222   0.038  -0.175  -0.366
128   G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
129   F        -0.273  -0.216  -0.209  -0.572  -0.473  -0.459  -0.559  -0.460  -0.468
130   K        -1.629  -1.594  -1.475  -1.746  -1.707  -1.456  -1.552  -1.506  -1.303
131   G        -0.273  -0.216  -0.209  -0.204  -0.097  -0.171  -0.559  -0.460  -0.468
132   I         0.091   0.149  -0.132   0.267   0.339  -0.105   0.038   0.126  -0.334
133   K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
134   W         0.972   0.981   1.031   1.288   1.290   1.340   1.031   1.044   1.111
135   N         0.972   0.981   1.031   1.040   1.047   1.118   1.031   1.044   1.111
136   F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
137   E         0.972   0.981   1.031   0.945   0.947   1.033   1.031   1.044   1.111
138   K         0.972   0.981   1.031   0.679   0.708   0.794   1.031   1.044   1.111
139   F         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
140   L         0.972   0.981   1.031   0.819   0.829   0.921   1.031   1.044   1.111
141   V        -0.273  -0.307  -0.224  -0.378  -0.440  -0.305  -0.559  -0.620  -0.495
142   D        -0.725  -0.841  -0.914  -0.551  -0.738  -0.892  -0.757  -0.910  -0.979
143   S        -0.725  -0.664  -0.891  -0.847  -0.739  -0.996  -0.757  -0.673  -0.949
144   N        -1.629  -1.666  -1.480  -1.365  -1.410  -1.158  -1.552  -1.573  -1.307
145   G         0.972   0.981   1.031   0.877   0.887   0.972   1.031   1.044   1.111
146   K        -0.725  -0.689  -0.894  -0.895  -0.820  -1.080  -0.757  -0.706  -0.953
147   V         0.972   0.981   1.031   0.967   0.977   1.053   1.031   1.044   1.111
148   V        -1.629  -1.644  -1.481  -1.593  -1.648  -1.364  -1.552  -1.554  -1.309
149   Q        -1.629  -1.649  -1.484  -1.649  -1.689  -1.419  -1.552  -1.558  -1.310
150   R         0.972   0.981   1.031   1.261   1.266   1.317   1.031   1.044   1.111
151   F        -0.725  -0.783  -0.905  -0.433  -0.507  -0.708  -0.757  -0.839  -0.968
152   S        -0.273  -0.310  -0.228  -0.305  -0.359  -0.234  -0.559  -0.624  -0.501
153   S         0.972   0.981   1.031   1.006   1.020   1.088   1.031   1.044   1.111
154   L        -0.725  -0.841  -0.914  -0.718  -0.875  -0.935  -0.757  -0.910  -0.979
155   T        -0.725  -0.689  -0.894  -0.530  -0.469  -0.888  -0.757  -0.706  -0.953
156   K         0.091   0.136  -0.132  -0.104  -0.026  -0.364   0.038   0.106  -0.334
157   P         0.972   0.981   1.031   1.078   1.080   1.152   1.031   1.044   1.111
158   S        -1.629  -1.552  -1.476  -1.457  -1.372  -1.214  -1.552  -1.468  -1.303
159   S        -0.725  -0.689  -0.894  -0.552  -0.490  -0.799  -0.757  -0.706  -0.953
160   L         0.091   0.149  -0.132   0.024   0.099  -0.275   0.038   0.126  -0.334
161   D        -1.459  -1.468  -1.459  -1.521  -1.574  -1.579  -1.354  -1.363  -1.286
162   Q        -2.081  -2.071  -1.896  -1.914  -1.909  -1.641  -1.751  -1.733  -1.479
163   E        -1.629  -1.637  -1.483  -1.441  -1.439  -1.226  -1.552  -1.549  -1.310
164   I         0.972   0.981   1.031   1.089   1.091   1.162   1.031   1.044   1.111
165   Q        -1.459  -1.464  -1.463  -1.529  -1.557  -1.598  -1.354  -1.359  -1.290
166   S        -2.081  -2.064  -1.892  -2.024  -2.032  -1.753  -1.751  -1.726  -1.476
167   L        -0.725  -0.841  -0.914  -0.802  -0.981  -1.083  -0.757  -0.910  -0.979
168   L         0.972   0.981   1.031   0.819   0.829   0.921   1.031   1.044   1.111
169   S        -1.634  -1.624  -1.487  -1.881  -1.875  -1.579  -1.544  -1.528  -1.313
170   K        -0.887  -0.942  -0.937  -1.171  -1.261  -1.185  -0.972  -1.045  -1.008
171   -        -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/P38143
Output conservation file - output/P38143
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
