1     M         1.397   1.477   1.515   1.610   1.704   1.783   1.514   1.624   1.689
2     G         0.214   0.436   0.221   0.295   0.622   0.257   0.058   0.407   0.030
3     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     N        -1.521  -1.335  -1.271  -1.524  -1.199  -1.167  -1.399  -1.158  -1.067
7     F        -0.062   0.060   0.132  -0.418  -0.176  -0.087  -0.428  -0.232  -0.131
8     K        -0.792  -0.727  -0.685  -0.896  -0.794  -0.802  -0.914  -0.820  -0.752
9     F         0.214   0.108   0.140   0.302   0.119   0.166   0.058  -0.146  -0.116
10    K        -0.062   0.068   0.133  -0.508  -0.235  -0.169  -0.428  -0.218  -0.129
11    Y         0.214   0.108   0.140   0.414   0.198   0.222   0.058  -0.146  -0.116
12    T         1.397   1.477   1.515   1.550   1.648   1.726   1.514   1.624   1.689
13    R         0.344   0.145   0.186   0.389   0.071   0.155   0.271  -0.081  -0.033
14    A        -0.603  -0.730  -0.675  -0.501  -0.767  -0.689  -0.661  -0.819  -0.740
15    Q         0.344   0.145   0.186   0.654   0.320   0.402   0.271  -0.081  -0.033
16    L         1.397   1.477   1.515   1.151   1.275   1.350   1.514   1.624   1.689
17    E         1.397   1.477   1.515   1.058   1.191   1.264   1.514   1.624   1.689
18    I        -0.824  -0.701  -0.651  -0.668  -0.449  -0.401  -0.972  -0.779  -0.709
19    F         0.344   0.381   0.202   0.446   0.487   0.208   0.271   0.319  -0.005
20    R        -0.019   0.049   0.134  -0.362  -0.256  -0.167  -0.350  -0.252  -0.128
21    F         1.397   1.477   1.515   1.429   1.518   1.612   1.514   1.624   1.689
22    S        -0.019   0.204   0.171   0.055   0.373   0.333  -0.350   0.022  -0.060
23    F         0.057   0.037   0.123   0.108   0.143   0.193  -0.212  -0.275  -0.148
24    C        -0.062   0.125   0.165   0.105   0.370   0.421  -0.428  -0.116  -0.070
25    L         1.397   1.477   1.515   1.142   1.272   1.343   1.514   1.624   1.689
26    L         0.057   0.037   0.123  -0.198  -0.161  -0.037  -0.212  -0.275  -0.148
27    A        -0.732  -0.794  -0.660  -0.620  -0.641  -0.477  -0.860  -0.896  -0.722
28    P         1.397   1.477   1.515   1.446   1.529   1.628   1.514   1.624   1.689
29    V        -0.062   0.125   0.165  -0.085   0.187   0.244  -0.428  -0.116  -0.070
30    A        -1.218  -1.320  -1.256  -0.976  -1.096  -1.035  -1.076  -1.150  -1.053
31    V         0.057   0.037   0.123   0.163   0.069   0.191  -0.212  -0.275  -0.148
32    M         1.397   1.477   1.515   1.600   1.769   1.774   1.514   1.624   1.689
33    Y        -0.279  -0.573  -0.634   0.090  -0.272  -0.540  -0.230  -0.610  -0.687
34    Y         1.397   1.477   1.515   1.592   1.727   1.766   1.514   1.624   1.689
35    I        -0.615  -0.697  -0.624  -0.439  -0.428  -0.440  -0.706  -0.768  -0.674
36    G         1.397   1.477   1.515   1.543   1.704   1.720   1.514   1.624   1.689
37    T        -0.615  -0.564  -0.629  -0.523  -0.334  -0.580  -0.706  -0.598  -0.681
38    D         0.534   0.293   0.239   0.812   0.438   0.419   0.563   0.173   0.062
39    T        -0.279  -0.409  -0.565   0.101  -0.098  -0.361  -0.230  -0.416  -0.595
40    D         1.397   1.477   1.515   1.519   1.563   1.697   1.514   1.624   1.689
41    K        -0.279  -0.409  -0.565  -0.176  -0.314  -0.497  -0.230  -0.416  -0.595
42    K         0.534   0.293   0.239   0.456   0.115   0.023   0.563   0.173   0.062
43    L        -0.040   0.035   0.122  -0.373  -0.096  -0.091  -0.388  -0.278  -0.148
44    N        -0.279  -0.573  -0.634   0.219  -0.179  -0.290  -0.230  -0.610  -0.687
45    V         0.138   0.304   0.214   0.196   0.534   0.250  -0.071   0.193   0.017
46    P         1.397   1.477   1.515   1.428   1.548   1.611   1.514   1.624   1.689
47    G         0.534   0.293   0.239   0.818   0.524   0.395   0.563   0.173   0.062
48    F         1.397   1.477   1.515   1.494   1.721   1.674   1.514   1.624   1.689
49    W         1.397   1.477   1.515   1.721   1.824   1.887   1.514   1.624   1.689
50    P         1.397   1.477   1.515   1.428   1.548   1.611   1.514   1.624   1.689
51    D         0.534   0.293   0.239   0.745   0.316   0.247   0.563   0.173   0.062
52    P         1.397   1.477   1.515   1.428   1.548   1.611   1.514   1.624   1.689
53    A        -0.717  -0.567  -0.630  -0.955  -0.821  -0.747  -0.864  -0.661  -0.690
54    T        -1.032  -1.158  -1.231  -0.521  -0.712  -0.830  -0.864  -0.994  -1.029
55    L         0.534   0.293   0.239   0.421   0.167   0.022   0.563   0.173   0.062
56    N         1.397   1.477   1.515   1.625   1.708   1.797   1.514   1.624   1.689
57    Q        -0.615  -0.677  -0.648  -0.489  -0.660  -0.666  -0.706  -0.762  -0.710
58    I         0.534   0.293   0.239   0.727   0.484   0.342   0.563   0.173   0.062
59    P         1.397   1.477   1.515   1.428   1.548   1.611   1.514   1.624   1.689
60    K         0.534   0.293   0.239   0.504   0.231   0.146   0.563   0.173   0.062
61    E         0.534   0.293   0.239   0.332  -0.091  -0.025   0.563   0.173   0.062
62    P         0.534   0.293   0.239   0.670   0.319   0.210   0.563   0.173   0.062
63    Y        -1.291  -1.374  -1.258  -0.821  -0.948  -0.803  -1.181  -1.200  -1.055
64    E         1.397   1.477   1.515   1.055   1.070   1.261   1.514   1.624   1.689
65    I         1.397   1.477   1.515   1.436   1.591   1.619   1.514   1.624   1.689
66    K        -1.291  -1.374  -1.258  -1.065  -1.037  -0.884  -1.181  -1.200  -1.055
67    A        -0.279  -0.573  -0.634  -0.137  -0.673  -0.809  -0.230  -0.610  -0.687
68    E         1.397   1.477   1.515   1.055   1.070   1.261   1.514   1.624   1.689
69    L         0.138   0.304   0.214  -0.130   0.195  -0.010  -0.071   0.193   0.017
70    A         0.138   0.050   0.122  -0.027  -0.338  -0.216  -0.071  -0.251  -0.148
71    R         1.397   1.477   1.515   1.318   1.395   1.508   1.514   1.624   1.689
72    M        -0.615  -0.697  -0.624  -0.441  -0.518  -0.532  -0.706  -0.768  -0.674
73    K        -0.040   0.053   0.134  -0.444  -0.302  -0.150  -0.388  -0.246  -0.127
74    K        -1.291  -1.374  -1.258  -1.335  -1.374  -1.199  -1.181  -1.200  -1.055
75    E        -1.291  -1.300  -1.234  -1.386  -1.380  -1.191  -1.181  -1.144  -1.033
76    R         1.397   1.477   1.515   1.318   1.395   1.508   1.514   1.624   1.689
77    L        -0.279  -0.244  -0.574  -0.300  -0.168  -0.696  -0.230  -0.177  -0.608
78    E        -0.279  -0.573  -0.634  -0.373  -0.797  -0.782  -0.230  -0.610  -0.687
79    K         0.534   0.293   0.239   0.430   0.094  -0.047   0.563   0.173   0.062
80    R         1.397   1.477   1.515   1.318   1.395   1.508   1.514   1.624   1.689
81    L        -0.874  -0.751  -0.674  -1.474  -1.359  -1.186  -1.023  -0.841  -0.738
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    R         0.534   0.743   0.286   0.543   0.786   0.156   0.563   0.861   0.143
84    L         1.397   1.477   1.515   1.162   1.334   1.361   1.514   1.624   1.689
85    E        -0.279  -0.573  -0.634  -0.377  -0.819  -0.790  -0.230  -0.610  -0.687
86    K        -1.291  -1.300  -1.234  -1.484  -1.486  -1.343  -1.181  -1.144  -1.033
87    K        -0.615  -0.748  -0.654  -0.882  -1.210  -0.993  -0.706  -0.836  -0.716
88    I        -0.792  -0.715  -0.685  -0.884  -0.820  -0.810  -0.914  -0.807  -0.752
89    Q        -1.218  -1.107  -1.241  -0.975  -0.771  -1.016  -1.076  -0.939  -1.039
90    E        -0.732  -0.781  -0.681  -1.116  -1.202  -0.976  -0.860  -0.880  -0.746
91    E         0.449   0.278   0.181   0.143  -0.215  -0.311   0.435   0.149  -0.043
92    F        -0.062   0.084   0.134  -0.365  -0.032  -0.079  -0.428  -0.190  -0.126
93    G         0.449   0.278   0.181   0.759   0.551   0.377   0.435   0.149  -0.043
94    L        -0.732  -0.725  -0.669  -0.849  -0.760  -0.736  -0.860  -0.805  -0.732
95    D        -0.429  -0.520  -0.648  -0.168  -0.464  -0.588  -0.428  -0.549  -0.705
96    L        -1.888  -1.675  -1.716  -1.945  -1.678  -1.613  -1.507  -1.269  -1.248
97    E         0.449   0.278   0.181   0.145  -0.248  -0.306   0.435   0.149  -0.043
98    E        -0.824  -0.740  -0.661  -1.088  -1.021  -0.831  -0.972  -0.827  -0.722
99    E         0.344   0.322   0.207   0.077   0.049  -0.086   0.271   0.221   0.005
100   K        -0.603  -0.739  -0.675  -0.992  -1.324  -1.234  -0.661  -0.825  -0.740
101   E        -0.603  -0.583  -0.641  -0.957  -1.028  -1.023  -0.661  -0.641  -0.696
102   K         0.344   0.322   0.207   0.060   0.010  -0.228   0.271   0.221   0.005
103   I        -0.603  -0.492  -0.623  -0.364  -0.214  -0.378  -0.661  -0.507  -0.673
104   K        -1.407  -1.330  -1.264  -1.496  -1.357  -1.325  -1.283  -1.165  -1.061
105   R        -0.824  -0.612  -0.658  -1.000  -0.745  -0.769  -0.972  -0.701  -0.720
106   D        -0.603  -0.545  -0.646  -0.743  -0.705  -0.709  -0.661  -0.598  -0.701
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   L        -0.603  -0.742  -0.675  -0.838  -1.042  -0.953  -0.661  -0.831  -0.740
144   A        -1.991  -1.756  -1.719  -1.561  -1.229  -1.201  -1.594  -1.330  -1.251
145   L        -1.407  -1.331  -1.265  -1.394  -1.102  -1.113  -1.283  -1.165  -1.062
146   -        -1.521  -1.381  -1.271  -1.316  -1.123  -0.971  -1.399  -1.205  -1.067
147   -        -1.521  -1.381  -1.271  -1.515  -1.338  -1.158  -1.399  -1.205  -1.067
148   K        -1.888  -1.791  -1.714  -1.793  -1.631  -1.509  -1.507  -1.363  -1.247
149   K        -2.699  -2.439  -2.395  -2.148  -1.687  -1.754  -1.816  -1.561  -1.461
150   G        -1.708  -1.472  -1.657  -1.620  -1.446  -1.468  -1.340  -1.069  -1.200
* 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/P38958
Output conservation file - output/P38958
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
