1     M         1.098   1.108   1.161   1.327   1.338   1.406   1.170   1.187   1.264
2     P        -1.827  -1.853  -1.760  -1.638  -1.678  -1.530  -1.444  -1.466  -1.317
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     R        -1.104  -1.084  -1.081  -1.239  -1.196  -1.141  -1.130  -1.106  -1.039
6     E        -1.235  -1.265  -1.114  -1.429  -1.487  -1.234  -1.246  -1.272  -1.070
7     F         0.307   0.217   0.104   0.338   0.202  -0.001   0.240   0.092  -0.141
8     K        -0.118  -0.106   0.020  -0.355  -0.334  -0.131  -0.503  -0.486  -0.296
9     S        -0.424  -0.491  -0.582  -0.499  -0.613  -0.768  -0.503  -0.599  -0.729
10    F        -0.676  -0.716  -0.628  -0.865  -0.917  -0.787  -0.875  -0.916  -0.791
11    G        -1.640  -1.645  -1.483  -1.650  -1.680  -1.456  -1.432  -1.436  -1.229
12    S        -0.753  -0.755  -0.642  -0.901  -0.893  -0.724  -0.971  -0.971  -0.809
13    T        -0.083  -0.081   0.029  -0.225  -0.230  -0.059  -0.436  -0.439  -0.280
14    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    L        -1.640  -1.640  -1.484  -1.549  -1.539  -1.301  -1.432  -1.431  -1.229
18    L        -0.579  -0.485  -0.581  -0.703  -0.564  -0.703  -0.742  -0.620  -0.730
19    S        -0.579  -0.567  -0.590  -0.694  -0.666  -0.691  -0.742  -0.717  -0.742
20    -        -1.640  -1.592  -1.472  -1.721  -1.648  -1.460  -1.432  -1.387  -1.219
21    K        -1.334  -1.221  -1.424  -1.162  -0.996  -1.333  -1.130  -1.010  -1.177
22    G        -1.942  -1.934  -1.782  -1.759  -1.767  -1.534  -1.548  -1.539  -1.332
23    H        -1.030  -1.052  -1.071  -0.863  -0.926  -0.961  -1.026  -1.061  -1.028
24    G        -0.481  -0.513  -0.578  -0.549  -0.621  -0.718  -0.608  -0.668  -0.728
25    E        -0.785  -0.714  -1.015  -0.590  -0.485  -1.017  -0.712  -0.626  -0.964
26    P        -0.481  -0.415  -0.572  -0.444  -0.337  -0.624  -0.608  -0.515  -0.716
27    S         0.437   0.315   0.146   0.465   0.304   0.047   0.438   0.251  -0.063
28    Y        -1.030  -1.017  -1.073  -0.969  -0.966  -1.005  -1.026  -1.023  -1.031
29    S        -1.638  -1.661  -1.474  -1.500  -1.516  -1.242  -1.444  -1.455  -1.221
30    E        -0.193  -0.277  -0.532  -0.143  -0.263  -0.621  -0.189  -0.310  -0.662
31    I        -0.481  -0.477  -0.580  -0.475  -0.477  -0.615  -0.608  -0.620  -0.732
32    Y         1.098   1.108   1.161   1.274   1.292   1.358   1.170   1.187   1.264
33    A        -0.726  -0.728  -0.630  -0.704  -0.709  -0.569  -0.921  -0.927  -0.795
34    E        -0.481  -0.525  -0.590  -0.595  -0.682  -0.754  -0.608  -0.682  -0.744
35    P         1.098   1.108   1.161   1.108   1.122   1.207   1.170   1.187   1.264
36    E         1.098   1.108   1.161   1.002   1.012   1.109   1.170   1.187   1.264
37    N         1.098   1.108   1.161   1.192   1.215   1.283   1.170   1.187   1.264
38    F         0.437   0.315   0.146   0.498   0.332   0.051   0.438   0.251  -0.063
39    L         1.098   1.108   1.161   1.032   1.044   1.137   1.170   1.187   1.264
40    E         1.098   1.108   1.161   1.002   1.012   1.109   1.170   1.187   1.264
41    I         1.098   1.108   1.161   1.066   1.082   1.168   1.170   1.187   1.264
42    E         0.437   0.315   0.146   0.432   0.273   0.037   0.438   0.251  -0.063
43    V         1.098   1.108   1.161   1.138   1.149   1.234   1.170   1.187   1.264
44    H        -1.334  -1.375  -1.427  -1.203  -1.281  -1.301  -1.130  -1.175  -1.180
45    N         0.437   0.451   0.162   0.596   0.623   0.158   0.438   0.459  -0.036
46    P         1.098   1.108   1.161   1.108   1.122   1.207   1.170   1.187   1.264
47    K        -1.104  -1.082  -1.074  -1.172  -1.125  -1.134  -1.130  -1.104  -1.031
48    T         1.098   1.108   1.161   1.159   1.175   1.253   1.170   1.187   1.264
49    H         1.098   1.108   1.161   1.278   1.292   1.362   1.170   1.187   1.264
50    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    G         1.098   1.108   1.161   1.162   1.179   1.256   1.170   1.187   1.264
54    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    D        -0.801  -0.771  -0.636  -0.899  -0.865  -0.648  -1.026  -0.989  -0.802
56    S        -1.030  -0.959  -1.064  -0.883  -0.778  -0.944  -1.026  -0.946  -1.021
57    K        -0.611  -0.578  -0.592  -0.876  -0.822  -0.814  -0.817  -0.769  -0.750
58    G        -1.523  -1.502  -1.458  -1.393  -1.359  -1.310  -1.339  -1.325  -1.209
59    M         0.111   0.152   0.097   0.232   0.295   0.139  -0.085  -0.018  -0.153
60    F        -0.118  -0.104   0.021  -0.278  -0.262  -0.062  -0.503  -0.483  -0.294
61    T         1.098   1.108   1.161   1.159   1.175   1.253   1.170   1.187   1.264
62    D         0.437   0.315   0.146   0.649   0.486   0.204   0.438   0.251  -0.063
63    Y         1.098   1.108   1.161   1.274   1.292   1.358   1.170   1.187   1.264
64    E         1.098   1.108   1.161   1.002   1.012   1.109   1.170   1.187   1.264
65    I         1.098   1.108   1.161   1.066   1.082   1.168   1.170   1.187   1.264
66    I        -0.118  -0.101   0.021  -0.397  -0.366  -0.166  -0.503  -0.477  -0.295
67    C         1.098   1.108   1.161   1.359   1.375   1.436   1.170   1.187   1.264
68    R         1.098   1.108   1.161   0.984   0.993   1.094   1.170   1.187   1.264
69    T         1.098   1.108   1.161   1.159   1.175   1.253   1.170   1.187   1.264
70    N         1.098   1.108   1.161   1.192   1.215   1.283   1.170   1.187   1.264
71    L        -0.611  -0.676  -0.609  -0.790  -0.851  -0.709  -0.817  -0.877  -0.769
72    P         1.098   1.108   1.161   1.108   1.122   1.207   1.170   1.187   1.264
73    S        -1.827  -1.830  -1.764  -1.436  -1.434  -1.414  -1.444  -1.447  -1.320
74    F         1.098   1.108   1.161   1.091   1.104   1.191   1.170   1.187   1.264
75    H        -1.030  -1.067  -1.077  -0.999  -1.056  -1.104  -1.026  -1.059  -1.032
76    K        -0.063  -0.081   0.028  -0.322  -0.364  -0.196  -0.399  -0.440  -0.281
77    R        -0.193  -0.299  -0.534  -0.155  -0.297  -0.624  -0.189  -0.338  -0.663
78    V        -1.942  -1.897  -1.762  -1.811  -1.741  -1.545  -1.548  -1.511  -1.319
79    S         1.098   1.108   1.161   1.045   1.058   1.149   1.170   1.187   1.264
80    K        -1.523  -1.514  -1.452  -1.625  -1.625  -1.489  -1.339  -1.334  -1.204
81    V         0.437   0.455   0.165   0.545   0.566   0.124   0.438   0.464  -0.031
82    R         0.437   0.455   0.165   0.409   0.427   0.036   0.438   0.464  -0.031
83    R         1.098   1.108   1.161   0.984   0.993   1.094   1.170   1.187   1.264
84    R         1.098   1.108   1.161   0.984   0.993   1.094   1.170   1.187   1.264
85    Y         1.098   1.108   1.161   1.274   1.292   1.358   1.170   1.187   1.264
86    S         1.098   1.108   1.161   1.045   1.058   1.149   1.170   1.187   1.264
87    D         0.437   0.315   0.146   0.627   0.454   0.146   0.438   0.251  -0.063
88    F         1.098   1.108   1.161   1.091   1.104   1.191   1.170   1.187   1.264
89    E         0.111   0.152   0.097  -0.049   0.009  -0.084  -0.085  -0.018  -0.153
90    F        -2.246  -2.240  -2.039  -1.951  -1.939  -1.652  -1.653  -1.645  -1.409
91    F         1.098   1.108   1.161   1.091   1.104   1.191   1.170   1.187   1.264
92    R         0.437   0.315   0.146   0.422   0.265   0.042   0.438   0.251  -0.063
93    K        -0.481  -0.526  -0.590  -0.487  -0.557  -0.674  -0.608  -0.682  -0.744
94    C        -1.219  -1.247  -1.098  -1.217  -1.232  -1.010  -1.235  -1.250  -1.055
95    L         1.098   1.108   1.161   1.032   1.044   1.137   1.170   1.187   1.264
96    I        -0.481  -0.408  -0.577  -0.639  -0.533  -0.800  -0.608  -0.511  -0.725
97    K        -0.801  -0.771  -0.636  -1.081  -1.041  -0.815  -1.026  -0.989  -0.802
98    E         1.098   1.108   1.161   1.002   1.012   1.109   1.170   1.187   1.264
99    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   H        -1.219  -1.155  -1.099  -1.247  -1.163  -1.041  -1.235  -1.167  -1.055
105   P        -1.104  -1.158  -1.085  -1.079  -1.141  -0.995  -1.130  -1.175  -1.042
106   K         0.111   0.149   0.080  -0.079  -0.021  -0.148  -0.085  -0.023  -0.185
107   V         1.098   1.108   1.161   1.138   1.149   1.234   1.170   1.187   1.264
108   M        -1.523  -1.457  -1.447  -1.495  -1.402  -1.338  -1.339  -1.273  -1.198
109   V        -0.063  -0.025   0.041  -0.296  -0.231  -0.134  -0.399  -0.334  -0.257
110   P         0.437   0.476   0.163   0.533   0.581   0.139   0.438   0.494  -0.034
111   H        -0.611  -0.581  -0.598  -0.662  -0.619  -0.637  -0.817  -0.772  -0.756
112   L         1.098   1.108   1.161   1.032   1.044   1.137   1.170   1.187   1.264
113   P         1.098   1.108   1.161   1.108   1.122   1.207   1.170   1.187   1.264
114   G         1.098   1.108   1.161   1.167   1.186   1.260   1.170   1.187   1.264
115   K         1.098   1.108   1.161   1.100   1.125   1.199   1.170   1.187   1.264
116   I         0.111   0.127   0.088   0.013   0.037  -0.047  -0.085  -0.061  -0.169
117   L        -0.611  -0.549  -0.595  -0.781  -0.690  -0.701  -0.817  -0.739  -0.754
118   L         1.098   1.108   1.161   1.004   1.016   1.111   1.170   1.187   1.264
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   S        -0.063  -0.081   0.028  -0.304  -0.342  -0.160  -0.399  -0.440  -0.281
121   N         0.437   0.315   0.146   0.616   0.466   0.183   0.438   0.251  -0.063
122   R         0.111   0.152   0.097  -0.079  -0.017  -0.116  -0.085  -0.018  -0.153
123   F         1.098   1.108   1.161   1.091   1.104   1.191   1.170   1.187   1.264
124   S        -0.481  -0.553  -0.579  -0.557  -0.662  -0.726  -0.608  -0.689  -0.726
125   N         0.437   0.467   0.163   0.653   0.690   0.244   0.438   0.481  -0.034
126   E        -1.219  -1.203  -1.095  -1.340  -1.315  -1.098  -1.235  -1.221  -1.051
127   V         0.111   0.152   0.097   0.100   0.162   0.052  -0.085  -0.018  -0.153
128   I         1.098   1.108   1.161   1.066   1.082   1.168   1.170   1.187   1.264
129   E         1.098   1.108   1.161   1.002   1.012   1.109   1.170   1.187   1.264
130   E        -1.030  -0.993  -1.063  -1.069  -1.008  -1.064  -1.026  -0.978  -1.018
131   R         1.098   1.108   1.161   0.984   0.993   1.094   1.170   1.187   1.264
132   R         1.098   1.108   1.161   0.984   0.993   1.094   1.170   1.187   1.264
133   Q        -0.193  -0.174  -0.521   0.035   0.063  -0.468  -0.189  -0.164  -0.646
134   G         1.098   1.108   1.161   1.167   1.186   1.260   1.170   1.187   1.264
135   L         1.098   1.108   1.161   1.032   1.044   1.137   1.170   1.187   1.264
136   N        -0.063  -0.025   0.041  -0.323  -0.261  -0.152  -0.399  -0.334  -0.257
137   T        -0.785  -0.828  -1.034  -0.633  -0.684  -1.036  -0.712  -0.770  -0.985
138   W        -0.063  -0.025   0.041  -0.144  -0.085   0.020  -0.399  -0.334  -0.257
139   M        -0.481  -0.400  -0.553  -0.500  -0.390  -0.601  -0.608  -0.498  -0.691
140   Q        -1.827  -1.836  -1.756  -1.627  -1.665  -1.587  -1.444  -1.452  -1.313
141   S        -1.523  -1.564  -1.450  -1.575  -1.644  -1.457  -1.339  -1.371  -1.201
142   V         1.098   1.108   1.161   1.138   1.149   1.234   1.170   1.187   1.264
143   A        -0.481  -0.441  -0.564  -0.340  -0.266  -0.510  -0.608  -0.549  -0.706
144   G         1.098   1.108   1.161   1.167   1.186   1.260   1.170   1.187   1.264
145   H         1.098   1.108   1.161   1.278   1.292   1.362   1.170   1.187   1.264
146   P         1.098   1.108   1.161   1.108   1.122   1.207   1.170   1.187   1.264
147   L         1.098   1.108   1.161   1.032   1.044   1.137   1.170   1.187   1.264
148   L         0.437   0.315   0.146   0.438   0.271  -0.000   0.438   0.251  -0.063
149   Q         1.098   1.108   1.161   1.188   1.205   1.279   1.170   1.187   1.264
150   S         0.111   0.160   0.096   0.073   0.154   0.003  -0.085  -0.005  -0.154
151   G         0.437   0.315   0.146   0.604   0.454   0.196   0.438   0.251  -0.063
152   S         1.098   1.108   1.161   1.045   1.058   1.149   1.170   1.187   1.264
153   K         0.437   0.315   0.146   0.495   0.335   0.028   0.438   0.251  -0.063
154   V        -0.481  -0.419  -0.573  -0.470  -0.372  -0.638  -0.608  -0.516  -0.722
155   L         1.098   1.108   1.161   1.032   1.044   1.137   1.170   1.187   1.264
156   V        -1.523  -1.565  -1.458  -1.414  -1.479  -1.273  -1.339  -1.372  -1.208
157   R        -1.219  -1.263  -1.106  -1.398  -1.459  -1.209  -1.235  -1.268  -1.062
158   F         1.098   1.108   1.161   1.091   1.104   1.191   1.170   1.187   1.264
159   I        -0.193  -0.298  -0.526  -0.109  -0.263  -0.627  -0.189  -0.336  -0.653
160   E         0.111   0.160   0.096   0.088   0.170   0.009  -0.085  -0.005  -0.154
161   A        -1.030  -1.032  -1.067  -0.884  -0.912  -0.949  -1.026  -1.038  -1.024
162   E        -0.726  -0.669  -0.633  -0.880  -0.792  -0.759  -0.921  -0.844  -0.798
163   K        -1.334  -1.387  -1.440  -1.158  -1.245  -1.343  -1.130  -1.187  -1.191
164   F        -0.118  -0.105   0.021  -0.201  -0.184   0.005  -0.503  -0.485  -0.295
165   V        -1.523  -1.526  -1.460  -1.396  -1.402  -1.338  -1.339  -1.338  -1.210
166   G        -1.104  -1.084  -1.081  -1.165  -1.133  -1.136  -1.130  -1.106  -1.039
167   -        -1.239  -1.244  -1.114  -1.317  -1.330  -1.166  -1.239  -1.246  -1.070
168   -        -1.239  -1.240  -1.100  -1.196  -1.222  -1.001  -1.239  -1.242  -1.056
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     *
* 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/Q08826
Output conservation file - output/Q08826
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
