1     M         1.385   1.412   1.482   1.468   1.511   1.618   1.477   1.515   1.617
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S         1.385   1.412   1.482   1.300   1.337   1.457   1.477   1.515   1.617
4     L        -0.419  -0.461  -0.373  -0.607  -0.632  -0.498  -0.648  -0.676  -0.548
5     Q        -0.046  -0.097  -0.281   0.237   0.183  -0.089  -0.081  -0.158  -0.414
6     S         0.158   0.233   0.299  -0.108   0.028   0.117  -0.223  -0.093  -0.016
7     N        -0.910  -0.937  -0.871  -0.932  -0.977  -0.844  -0.931  -0.951  -0.840
8     S        -1.044  -0.980  -0.905  -1.192  -1.149  -0.988  -1.073  -0.999  -0.874
9     V        -1.265  -1.346  -1.273  -1.215  -1.327  -1.187  -1.073  -1.143  -1.025
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -0.046  -0.097  -0.281   0.047  -0.017  -0.296  -0.081  -0.158  -0.414
12    P        -1.400  -1.393  -1.288  -1.373  -1.354  -1.212  -1.214  -1.190  -1.039
13    T        -1.756  -1.678  -1.610  -1.682  -1.572  -1.482  -1.356  -1.281  -1.157
14    E        -0.419  -0.387  -0.369  -0.449  -0.405  -0.342  -0.648  -0.602  -0.545
15    I        -0.332  -0.344  -0.364  -0.441  -0.524  -0.534  -0.506  -0.546  -0.537
16    P         0.648   0.543   0.436   0.673   0.532   0.368   0.627   0.455   0.241
17    L         0.648   0.543   0.436   0.554   0.409   0.275   0.627   0.455   0.241
18    S        -0.046  -0.008  -0.256   0.018   0.049  -0.277  -0.081  -0.038  -0.379
19    E         0.310   0.383   0.340   0.222   0.339   0.257   0.060   0.182   0.064
20    I        -0.046  -0.221  -0.293   0.062  -0.204  -0.361  -0.081  -0.322  -0.430
21    R        -1.400  -1.345  -1.279  -1.325  -1.257  -1.144  -1.214  -1.152  -1.032
22    R         1.385   1.412   1.482   1.364   1.407   1.519   1.477   1.515   1.617
23    P         1.385   1.412   1.482   1.329   1.368   1.485   1.477   1.515   1.617
24    L         0.648   0.698   0.459   0.715   0.790   0.405   0.627   0.701   0.281
25    A        -0.688  -0.572  -0.799  -0.591  -0.423  -0.768  -0.648  -0.503  -0.754
26    P         1.385   1.412   1.482   1.329   1.368   1.485   1.477   1.515   1.617
27    V         1.385   1.412   1.482   1.370   1.418   1.524   1.477   1.515   1.617
28    L         1.385   1.412   1.482   1.198   1.227   1.359   1.477   1.515   1.617
29    D         1.385   1.412   1.482   1.399   1.442   1.552   1.477   1.515   1.617
30    P        -1.400  -1.435  -1.285  -1.152  -1.210  -1.008  -1.214  -1.225  -1.037
31    Q        -0.688  -0.824  -0.844  -0.434  -0.627  -0.707  -0.648  -0.805  -0.804
32    K         1.385   1.412   1.482   1.335   1.377   1.491   1.477   1.515   1.617
33    I         0.648   0.543   0.436   0.743   0.608   0.426   0.627   0.455   0.241
34    D        -0.046  -0.221  -0.293   0.109  -0.136  -0.263  -0.081  -0.322  -0.430
35    A        -0.046  -0.221  -0.293  -0.025  -0.279  -0.422  -0.081  -0.322  -0.430
36    M         1.385   1.412   1.482   1.468   1.511   1.618   1.477   1.515   1.617
37    V        -0.910  -0.944  -0.881  -0.937  -0.976  -0.903  -0.931  -0.961  -0.849
38    A        -0.332  -0.359  -0.367  -0.486  -0.559  -0.555  -0.506  -0.562  -0.541
39    T         1.385   1.412   1.482   1.393   1.429   1.547   1.477   1.515   1.617
40    M        -0.419  -0.387  -0.369  -0.580  -0.533  -0.458  -0.648  -0.602  -0.545
41    K        -0.046  -0.037  -0.269   0.054   0.052  -0.264  -0.081  -0.082  -0.396
42    G         0.648   0.575   0.447   0.715   0.621   0.406   0.627   0.508   0.260
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    I        -1.265  -1.205  -1.243  -1.064  -0.969  -1.044  -1.073  -1.004  -0.997
45    P         0.648   0.575   0.447   0.664   0.566   0.367   0.627   0.508   0.260
46    T        -1.265  -1.346  -1.273  -1.013  -1.147  -1.058  -1.073  -1.143  -1.025
47    A        -0.046  -0.069  -0.274  -0.015  -0.044  -0.372  -0.081  -0.116  -0.404
48    S         1.385   1.412   1.482   1.300   1.337   1.457   1.477   1.515   1.617
49    K        -1.400  -1.439  -1.296  -1.411  -1.441  -1.239  -1.214  -1.229  -1.046
50    T        -0.046  -0.221  -0.293   0.083  -0.176  -0.308  -0.081  -0.322  -0.430
51    C        -0.688  -0.824  -0.844  -0.426  -0.675  -0.744  -0.648  -0.805  -0.804
52    S        -1.400  -1.333  -1.280  -1.355  -1.272  -1.162  -1.214  -1.144  -1.033
53    L        -1.419  -1.399  -1.300  -1.532  -1.521  -1.349  -1.222  -1.194  -1.048
54    E         0.575   0.588   0.417   0.579   0.603   0.317   0.513   0.529   0.206
55    Q        -0.432  -0.363  -0.377  -0.488  -0.381  -0.403  -0.644  -0.554  -0.551
56    A        -0.847  -0.839  -0.868  -0.898  -0.920  -0.944  -0.837  -0.830  -0.831
57    E        -1.004  -0.928  -0.892  -1.094  -0.987  -0.933  -1.030  -0.943  -0.859
58    A         0.241   0.286   0.311  -0.018   0.059   0.075  -0.066   0.006   0.007
59    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    A        -1.106  -1.065  -0.929  -1.160  -1.109  -0.901  -1.126  -1.072  -0.895
67    G        -0.046  -0.101  -0.278   0.087   0.008  -0.267  -0.081  -0.159  -0.409
68    E        -0.688  -0.669  -0.816  -0.576  -0.559  -0.783  -0.648  -0.624  -0.774
69    L         1.385   1.412   1.482   1.198   1.227   1.359   1.477   1.515   1.617
70    P         1.385   1.412   1.482   1.329   1.368   1.485   1.477   1.515   1.617
71    P         1.385   1.412   1.482   1.329   1.368   1.485   1.477   1.515   1.617
72    V        -0.332  -0.331  -0.344  -0.389  -0.365  -0.417  -0.506  -0.483  -0.508
73    D         1.385   1.412   1.482   1.399   1.442   1.552   1.477   1.515   1.617
74    V         1.385   1.412   1.482   1.370   1.418   1.524   1.477   1.515   1.617
75    L        -0.910  -0.776  -0.851  -0.988  -0.820  -0.886  -0.931  -0.767  -0.815
76    G        -1.756  -1.755  -1.622  -1.608  -1.619  -1.414  -1.356  -1.341  -1.166
77    V        -0.332  -0.423  -0.364  -0.347  -0.463  -0.381  -0.506  -0.618  -0.535
78    R         0.648   0.543   0.436   0.697   0.556   0.376   0.627   0.455   0.241
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    V        -0.688  -0.813  -0.841  -0.597  -0.796  -0.859  -0.648  -0.793  -0.802
82    K        -1.265  -1.226  -1.251  -1.026  -0.994  -1.071  -1.073  -1.029  -1.005
83    G         1.385   1.412   1.482   1.388   1.430   1.541   1.477   1.515   1.617
84    Q        -0.332  -0.251  -0.335  -0.412  -0.280  -0.402  -0.506  -0.387  -0.493
85    T        -0.910  -0.879  -0.863  -0.920  -0.869  -0.835  -0.931  -0.878  -0.829
86    L        -1.265  -1.251  -1.250  -0.981  -0.954  -0.992  -1.073  -1.049  -1.004
87    Y         1.385   1.412   1.482   1.497   1.543   1.646   1.477   1.515   1.617
88    Y         0.648   0.698   0.459   0.872   0.945   0.606   0.627   0.701   0.281
89    A         1.385   1.412   1.482   1.306   1.354   1.462   1.477   1.515   1.617
90    F         1.385   1.412   1.482   1.514   1.558   1.662   1.477   1.515   1.617
91    G         1.385   1.412   1.482   1.388   1.430   1.541   1.477   1.515   1.617
92    G         1.385   1.412   1.482   1.388   1.430   1.541   1.477   1.515   1.617
93    C         1.385   1.412   1.482   1.548   1.587   1.694   1.477   1.515   1.617
94    H         1.385   1.412   1.482   1.570   1.608   1.716   1.477   1.515   1.617
95    R         1.385   1.412   1.482   1.364   1.407   1.519   1.477   1.515   1.617
96    L         0.158   0.171   0.277  -0.069  -0.078   0.084  -0.223  -0.210  -0.057
97    Q         0.648   0.543   0.436   0.822   0.693   0.496   0.627   0.455   0.241
98    A         1.385   1.412   1.482   1.306   1.354   1.462   1.477   1.515   1.617
99    Y         0.648   0.543   0.436   0.867   0.742   0.581   0.627   0.455   0.241
100   D         1.385   1.412   1.482   1.399   1.442   1.552   1.477   1.515   1.617
101   R        -0.046  -0.130  -0.289   0.043  -0.078  -0.346  -0.081  -0.200  -0.425
102   R        -0.910  -0.906  -0.867  -1.083  -1.084  -1.008  -0.931  -0.907  -0.833
103   A        -0.910  -0.921  -0.873  -0.953  -0.955  -0.879  -0.931  -0.935  -0.841
104   R        -1.400  -1.347  -1.279  -1.395  -1.318  -1.205  -1.214  -1.155  -1.033
105   E        -0.046  -0.221  -0.293   0.036  -0.218  -0.348  -0.081  -0.322  -0.430
106   T        -1.400  -1.269  -1.276  -1.365  -1.194  -1.180  -1.214  -1.087  -1.030
107   Q        -0.510  -0.487  -0.405  -0.513  -0.482  -0.372  -0.744  -0.705  -0.587
108   N        -1.009  -0.996  -0.914  -1.008  -0.987  -0.867  -1.022  -1.000  -0.880
109   A        -1.009  -0.996  -0.914  -1.072  -1.046  -0.939  -1.022  -1.000  -0.880
110   A        -1.507  -1.471  -1.317  -1.452  -1.415  -1.181  -1.299  -1.253  -1.063
111   F        -1.009  -0.967  -0.906  -1.001  -0.927  -0.860  -1.022  -0.967  -0.872
112   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   V         0.648   0.575   0.447   0.715   0.629   0.425   0.627   0.508   0.260
114   R        -0.332  -0.318  -0.340  -0.456  -0.420  -0.497  -0.506  -0.463  -0.499
115   C        -0.046   0.096  -0.245   0.210   0.407  -0.135  -0.081   0.114  -0.363
116   R         0.158   0.191   0.282  -0.111  -0.055   0.079  -0.223  -0.172  -0.047
117   V        -0.554  -0.449  -0.400  -0.860  -0.708  -0.621  -0.790  -0.642  -0.578
118   L        -0.688  -0.824  -0.844  -0.699  -0.905  -0.908  -0.648  -0.805  -0.804
119   P         0.648   0.543   0.436   0.696   0.563   0.419   0.627   0.455   0.241
120   A        -0.332  -0.370  -0.369  -0.349  -0.399  -0.368  -0.506  -0.574  -0.543
121   T         0.648   0.543   0.436   0.720   0.569   0.389   0.627   0.455   0.241
122   P        -0.419  -0.438  -0.368  -0.598  -0.610  -0.499  -0.648  -0.649  -0.543
123   R        -1.400  -1.413  -1.284  -1.272  -1.280  -1.075  -1.214  -1.209  -1.036
124   Q        -0.332  -0.286  -0.350  -0.296  -0.228  -0.357  -0.506  -0.451  -0.517
125   I         0.648   0.698   0.459   0.542   0.601   0.286   0.627   0.701   0.281
126   R         0.158   0.174   0.277  -0.117  -0.095   0.066  -0.223  -0.204  -0.057
127   M        -0.046   0.042  -0.256  -0.083   0.026  -0.365  -0.081   0.041  -0.379
128   Y         1.385   1.412   1.482   1.497   1.543   1.646   1.477   1.515   1.617
129   L         0.310   0.383   0.340   0.035   0.143   0.072   0.060   0.182   0.064
130   G         1.385   1.412   1.482   1.388   1.430   1.541   1.477   1.515   1.617
131   S        -0.910  -0.844  -0.865  -1.033  -0.948  -0.962  -0.931  -0.861  -0.833
132   S         1.385   1.412   1.482   1.300   1.337   1.457   1.477   1.515   1.617
133   L        -1.044  -0.986  -0.906  -1.289  -1.189  -1.064  -1.073  -0.998  -0.873
134   D        -0.046  -0.221  -0.293   0.118  -0.123  -0.246  -0.081  -0.322  -0.430
135   I        -1.419  -1.352  -1.285  -1.399  -1.297  -1.222  -1.222  -1.149  -1.036
136   -        -0.510  -0.525  -0.404  -0.699  -0.725  -0.526  -0.744  -0.751  -0.585
137   -         0.176   0.170   0.277  -0.042  -0.104   0.065  -0.189  -0.213  -0.057
138   -        -0.510  -0.426  -0.393  -0.742  -0.613  -0.563  -0.744  -0.642  -0.573
139   -        -1.009  -0.946  -0.889  -1.150  -1.055  -0.975  -1.022  -0.946  -0.853
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   E        -1.756  -1.731  -1.617  -1.720  -1.671  -1.524  -1.356  -1.324  -1.162
* 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/P36077
Output conservation file - output/P36077
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
