1     M         1.008   1.029   1.079   1.163   1.192   1.257   1.053   1.081   1.158
2     I        -0.393  -0.393  -0.226  -0.528  -0.546  -0.290  -0.721  -0.734  -0.492
3     I         0.210   0.120  -0.118   0.363   0.257  -0.106   0.225   0.094  -0.307
4     Y        -0.393  -0.324  -0.216  -0.474  -0.372  -0.229  -0.721  -0.613  -0.474
5     K        -1.561  -1.485  -1.483  -1.533  -1.429  -1.424  -1.430  -1.330  -1.272
6     D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
7     I        -0.460  -0.405  -0.225  -0.843  -0.761  -0.460  -0.839  -0.756  -0.490
8     F        -0.183  -0.004  -0.146  -0.169   0.095  -0.145  -0.366  -0.090  -0.353
9     S         0.210   0.042  -0.129   0.412   0.196  -0.073   0.225  -0.020  -0.324
10    N        -0.183  -0.126  -0.196  -0.240  -0.145  -0.279  -0.366  -0.282  -0.439
11    D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
12    E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
13    L        -0.550  -0.760  -0.918  -0.236  -0.522  -0.784  -0.484  -0.751  -0.954
14    L        -1.265  -1.521  -1.494  -0.889  -1.269  -1.275  -1.076  -1.348  -1.281
15    S         1.008   1.029   1.079   1.073   1.097   1.180   1.053   1.081   1.158
16    D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
17    A         0.210   0.042  -0.129   0.310   0.097  -0.167   0.225  -0.020  -0.324
18    Y         0.210   0.159  -0.116   0.417   0.352  -0.056   0.225   0.151  -0.304
19    D         0.210   0.159  -0.116   0.074   0.024  -0.392   0.225   0.151  -0.304
20    A        -2.156  -1.936  -1.906  -1.988  -1.648  -1.641  -1.785  -1.562  -1.447
21    K         0.210   0.349  -0.104   0.219   0.379  -0.188   0.225   0.410  -0.283
22    L        -1.055  -1.062  -0.947  -1.204  -1.254  -1.079  -1.194  -1.180  -0.994
23    V         1.008   1.029   1.079   0.814   0.850   0.958   1.053   1.081   1.158
24    D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
25    D        -1.055  -1.048  -0.946  -1.311  -1.264  -1.089  -1.194  -1.158  -0.993
26    V        -0.898  -0.883  -0.947  -1.036  -1.064  -1.083  -0.957  -0.987  -0.994
27    I        -1.055  -1.068  -0.942  -1.294  -1.282  -1.081  -1.194  -1.157  -0.986
28    Y         1.008   1.029   1.079   1.082   1.107   1.188   1.053   1.081   1.158
29    E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
30    A        -0.183  -0.287  -0.213  -0.311  -0.525  -0.453  -0.366  -0.550  -0.470
31    D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
32    C         1.008   1.029   1.079   1.334   1.357   1.403   1.053   1.081   1.158
33    A        -1.265  -1.281  -1.462  -0.991  -1.001  -1.296  -1.076  -1.094  -1.250
34    M         1.008   1.029   1.079   1.163   1.192   1.257   1.053   1.081   1.158
35    V        -0.183  -0.287  -0.213  -0.401  -0.575  -0.447  -0.366  -0.550  -0.470
36    N        -2.295  -2.271  -1.939  -2.115  -2.076  -1.623  -1.903  -1.838  -1.473
37    V         0.210   0.042  -0.129   0.115  -0.108  -0.381   0.225  -0.020  -0.324
38    G        -1.265  -1.323  -1.465  -1.059  -1.153  -1.400  -1.076  -1.136  -1.254
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    G        -1.561  -1.623  -1.499  -1.497  -1.584  -1.448  -1.430  -1.460  -1.287
41    D        -1.055  -1.068  -0.942  -1.376  -1.327  -1.183  -1.194  -1.157  -0.986
42    N        -1.055  -1.068  -0.942  -1.209  -1.174  -0.946  -1.194  -1.157  -0.986
43    I        -0.460  -0.363  -0.210  -0.843  -0.702  -0.443  -0.839  -0.681  -0.464
44    D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
45    I         1.008   1.029   1.079   1.030   1.065   1.143   1.053   1.081   1.158
46    G         1.008   1.029   1.079   0.952   0.999   1.076   1.053   1.081   1.158
47    A         1.008   1.029   1.079   0.978   1.011   1.099   1.053   1.081   1.158
48    N         1.008   1.029   1.079   1.112   1.140   1.213   1.053   1.081   1.158
49    P         0.210   0.042  -0.129   0.535   0.313  -0.019   0.225  -0.020  -0.324
50    S         1.008   1.029   1.079   1.073   1.097   1.180   1.053   1.081   1.158
51    A         0.210   0.349  -0.104   0.317   0.482  -0.107   0.225   0.410  -0.283
52    E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
53    G        -0.898  -0.812  -0.937  -1.146  -1.059  -1.198  -0.957  -0.881  -0.981
54    G        -0.393  -0.407  -0.224  -0.653  -0.689  -0.400  -0.721  -0.758  -0.489
55    D        -1.194  -1.100  -0.974  -1.547  -1.411  -1.238  -1.312  -1.191  -1.023
56    D        -0.393  -0.232  -0.181  -0.840  -0.538  -0.483  -0.721  -0.457  -0.413
57    D        -1.561  -1.662  -1.502  -1.675  -1.799  -1.534  -1.430  -1.513  -1.291
58    V        -1.055  -1.084  -0.952  -1.260  -1.279  -1.051  -1.194  -1.200  -1.000
59    E        -0.183  -0.287  -0.213  -0.433  -0.645  -0.555  -0.366  -0.550  -0.470
60    E        -0.898  -0.921  -0.937  -1.121  -1.142  -1.150  -0.957  -0.973  -0.981
61    G         0.210   0.159  -0.116   0.241   0.191  -0.285   0.225   0.151  -0.304
62    A        -1.194  -1.127  -0.980  -1.287  -1.237  -1.051  -1.312  -1.233  -1.030
63    E        -0.550  -0.760  -0.918  -0.465  -0.759  -0.972  -0.484  -0.751  -0.954
64    M        -1.928  -1.745  -1.898  -1.533  -1.335  -1.620  -1.549  -1.374  -1.440
65    V         1.008   1.029   1.079   0.814   0.850   0.958   1.053   1.081   1.158
66    N         1.008   1.029   1.079   1.112   1.140   1.213   1.053   1.081   1.158
67    N         1.008   1.029   1.079   1.112   1.140   1.213   1.053   1.081   1.158
68    V         0.210   0.120  -0.118   0.147   0.043  -0.275   0.225   0.094  -0.307
69    V         1.008   1.029   1.079   0.814   0.850   0.958   1.053   1.081   1.158
70    H        -0.393  -0.336  -0.216  -0.279  -0.202  -0.081  -0.721  -0.635  -0.475
71    S         1.008   1.029   1.079   1.073   1.097   1.180   1.053   1.081   1.158
72    F         1.008   1.029   1.079   1.099   1.133   1.202   1.053   1.081   1.158
73    R         1.008   1.029   1.079   1.284   1.310   1.360   1.053   1.081   1.158
74    L         1.008   1.029   1.079   1.082   1.110   1.188   1.053   1.081   1.158
75    Q         0.210   0.120  -0.118   0.606   0.488   0.081   0.225   0.094  -0.307
76    Q        -1.284  -1.242  -0.988  -1.111  -1.088  -0.744  -1.430  -1.366  -1.040
77    T         1.008   1.029   1.079   1.125   1.161   1.224   1.053   1.081   1.158
78    A        -2.295  -2.205  -1.933  -2.097  -1.948  -1.573  -1.903  -1.796  -1.469
79    F         1.008   1.029   1.079   1.099   1.133   1.202   1.053   1.081   1.158
80    D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
81    K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
82    K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
83    S         0.210   0.042  -0.129   0.388   0.161  -0.141   0.225  -0.020  -0.324
84    F        -0.393  -0.407  -0.224  -0.468  -0.521  -0.244  -0.721  -0.758  -0.489
85    L        -0.898  -0.784  -0.934  -0.703  -0.580  -0.771  -0.957  -0.834  -0.977
86    T        -0.550  -0.794  -0.914  -0.243  -0.596  -0.867  -0.484  -0.792  -0.949
87    Y         1.008   1.029   1.079   1.082   1.107   1.188   1.053   1.081   1.158
88    I        -0.898  -0.909  -0.950  -0.775  -0.841  -0.853  -0.957  -1.005  -0.996
89    K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
90    G         1.008   1.029   1.079   0.952   0.999   1.076   1.053   1.081   1.158
91    Y         1.008   1.029   1.079   1.082   1.107   1.188   1.053   1.081   1.158
92    M         1.008   1.029   1.079   1.163   1.192   1.257   1.053   1.081   1.158
93    K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
94    A        -1.789  -1.645  -1.512  -1.688  -1.526  -1.328  -1.667  -1.521  -1.300
95    V        -0.460  -0.407  -0.226  -0.843  -0.756  -0.456  -0.839  -0.758  -0.492
96    K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
97    A        -0.898  -0.868  -0.947  -0.852  -0.858  -0.945  -0.957  -0.965  -0.993
98    K        -2.295  -2.227  -1.935  -1.994  -1.908  -1.496  -1.903  -1.810  -1.470
99    L         1.008   1.029   1.079   1.082   1.110   1.188   1.053   1.081   1.158
100   Q        -1.055  -1.118  -0.957  -0.963  -1.062  -0.879  -1.194  -1.229  -1.005
101   E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   T        -1.789  -1.642  -1.504  -1.785  -1.618  -1.358  -1.667  -1.514  -1.294
105   N        -1.265  -1.345  -1.477  -0.947  -1.087  -1.405  -1.076  -1.169  -1.265
106   P         0.210   0.042  -0.129   0.508   0.274  -0.097   0.225  -0.020  -0.324
107   E        -0.393  -0.237  -0.193  -0.840  -0.548  -0.510  -0.721  -0.466  -0.434
108   E        -1.561  -1.435  -1.475  -1.516  -1.329  -1.339  -1.430  -1.275  -1.265
109   V        -0.393  -0.361  -0.224  -0.747  -0.699  -0.459  -0.721  -0.678  -0.488
110   P        -1.651  -1.613  -1.496  -1.586  -1.568  -1.377  -1.549  -1.491  -1.286
111   K        -2.662  -2.557  -2.280  -2.655  -2.557  -2.129  -2.022  -1.910  -1.582
112   F         1.008   1.029   1.079   1.099   1.133   1.202   1.053   1.081   1.158
113   E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
114   K        -0.550  -0.629  -0.900  -0.428  -0.539  -0.882  -0.484  -0.596  -0.932
115   G        -0.550  -0.794  -0.914  -0.398  -0.727  -0.949  -0.484  -0.792  -0.949
116   A         1.008   1.029   1.079   0.978   1.011   1.099   1.053   1.081   1.158
117   Q        -1.928  -1.950  -1.915  -1.353  -1.441  -1.501  -1.549  -1.566  -1.454
118   T        -1.561  -1.432  -1.475  -1.485  -1.295  -1.415  -1.430  -1.270  -1.265
119   Y        -0.183  -0.303  -0.217  -0.119  -0.335  -0.232  -0.366  -0.577  -0.476
120   V        -0.898  -0.909  -0.950  -1.032  -1.095  -1.069  -0.957  -1.005  -0.996
121   K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
122   K         0.210   0.042  -0.129   0.219   0.008  -0.226   0.225  -0.020  -0.324
123   V        -0.183  -0.250  -0.206  -0.401  -0.514  -0.437  -0.366  -0.487  -0.456
124   I        -1.194  -1.151  -0.983  -1.325  -1.274  -1.061  -1.312  -1.251  -1.034
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   G        -1.055  -0.959  -0.948  -1.192  -1.062  -0.986  -1.194  -1.082  -0.995
127   S        -0.898  -1.079  -0.960  -0.775  -1.077  -0.933  -0.957  -1.173  -1.009
128   F         1.008   1.029   1.079   1.099   1.133   1.202   1.053   1.081   1.158
129   K         0.210   0.308  -0.107   0.195   0.316  -0.255   0.225   0.356  -0.288
130   D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
131   W        -0.550  -0.693  -0.903  -0.007  -0.202  -0.601  -0.484  -0.662  -0.934
132   E        -0.393  -0.380  -0.225  -0.840  -0.840  -0.583  -0.721  -0.710  -0.489
133   F         1.008   1.029   1.079   1.099   1.133   1.202   1.053   1.081   1.158
134   F        -0.393  -0.232  -0.181  -0.474  -0.215  -0.166  -0.721  -0.457  -0.413
135   T         0.210   0.120  -0.118   0.450   0.343  -0.052   0.225   0.094  -0.307
136   G         1.008   1.029   1.079   0.952   0.999   1.076   1.053   1.081   1.158
137   E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
138   S         1.008   1.029   1.079   1.073   1.097   1.180   1.053   1.081   1.158
139   M         1.008   1.029   1.079   1.163   1.192   1.257   1.053   1.081   1.158
140   D         0.210   0.042  -0.129   0.111  -0.082  -0.310   0.225  -0.020  -0.324
141   P         1.008   1.029   1.079   1.218   1.249   1.304   1.053   1.081   1.158
142   D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
143   A        -0.460  -0.400  -0.223  -0.781  -0.675  -0.399  -0.839  -0.745  -0.487
144   M         1.008   1.029   1.079   1.163   1.192   1.257   1.053   1.081   1.158
145   V         0.210   0.360  -0.104   0.147   0.327  -0.253   0.225   0.425  -0.283
146   V         0.210   0.159  -0.116   0.131   0.074  -0.314   0.225   0.151  -0.304
147   M        -0.183  -0.004  -0.146  -0.099   0.153  -0.079  -0.366  -0.090  -0.353
148   L         0.210   0.120  -0.118   0.426   0.316  -0.034   0.225   0.094  -0.307
149   N         1.008   1.029   1.079   1.112   1.140   1.213   1.053   1.081   1.158
150   Y         1.008   1.029   1.079   1.082   1.107   1.188   1.053   1.081   1.158
151   R         1.008   1.029   1.079   1.284   1.310   1.360   1.053   1.081   1.158
152   E         1.008   1.029   1.079   0.868   0.899   1.004   1.053   1.081   1.158
153   D         1.008   1.029   1.079   0.773   0.820   0.924   1.053   1.081   1.158
154   G         1.008   1.029   1.079   0.952   0.999   1.076   1.053   1.081   1.158
155   T         0.210   0.120  -0.118   0.450   0.343  -0.052   0.225   0.094  -0.307
156   T         1.008   1.029   1.079   1.125   1.161   1.224   1.053   1.081   1.158
157   P         1.008   1.029   1.079   1.218   1.249   1.304   1.053   1.081   1.158
158   F        -0.393  -0.232  -0.181  -0.474  -0.215  -0.166  -0.721  -0.457  -0.413
159   V        -0.550  -0.693  -0.903  -0.493  -0.668  -0.928  -0.484  -0.662  -0.934
160   A        -0.898  -1.079  -0.960  -0.910  -1.210  -1.064  -0.957  -1.173  -1.009
161   I        -0.898  -1.079  -0.960  -0.833  -1.127  -0.992  -0.957  -1.173  -1.009
162   W         0.210   0.120  -0.118   0.651   0.537   0.123   0.225   0.094  -0.307
163   K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
164   H         0.210   0.120  -0.118   0.607   0.481   0.004   0.225   0.094  -0.307
165   G         1.008   1.029   1.079   0.952   0.999   1.076   1.053   1.081   1.158
166   I        -1.284  -1.244  -0.989  -1.537  -1.452  -1.071  -1.430  -1.368  -1.041
167   V        -1.561  -1.377  -1.474  -1.704  -1.459  -1.606  -1.430  -1.235  -1.265
168   E        -0.550  -0.512  -0.888  -0.473  -0.435  -0.946  -0.484  -0.446  -0.916
169   E        -1.265  -1.226  -1.463  -1.135  -1.096  -1.438  -1.076  -1.042  -1.252
170   K         1.008   1.029   1.079   0.881   0.911   1.016   1.053   1.081   1.158
171   I        -0.550  -0.794  -0.914  -0.333  -0.680  -0.924  -0.484  -0.792  -0.949
* 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/P35691
Output conservation file - output/P35691
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
