1     M         0.787   0.801   0.839   1.035   1.049   1.079   0.817   0.836   0.889
2     S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
3     Q        -0.022  -0.276  -0.412   0.304  -0.049  -0.319  -0.017  -0.392  -0.639
4     S        -0.022  -0.276  -0.412   0.004  -0.338  -0.530  -0.017  -0.392  -0.639
5     L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
6     R        -0.420  -0.316  -0.426  -0.478  -0.325  -0.505  -0.613  -0.454  -0.663
7     P         0.787   0.801   0.839   1.008   1.030   1.057   0.817   0.836   0.889
8     Y         0.787   0.801   0.839   1.079   1.108   1.116   0.817   0.836   0.889
9     L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
10    T        -1.818  -1.795  -1.762  -1.624  -1.630  -1.606  -1.685  -1.669  -1.540
11    A         0.787   0.801   0.839   0.842   0.874   0.918   0.817   0.836   0.889
12    V         0.787   0.801   0.839   0.796   0.814   0.880   0.817   0.836   0.889
13    R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
14    Y        -1.909  -1.827  -1.761  -1.840  -1.749  -1.612  -1.804  -1.702  -1.539
15    S        -0.022  -0.276  -0.412   0.004  -0.338  -0.530  -0.017  -0.392  -0.639
16    L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
17    E        -1.146  -0.949  -1.198  -1.002  -0.714  -1.183  -1.209  -0.961  -1.236
18    A         0.787   0.801   0.839   0.842   0.874   0.918   0.817   0.836   0.889
19    A        -0.022  -0.276  -0.412   0.104  -0.259  -0.545  -0.017  -0.392  -0.639
20    L        -0.420  -0.316  -0.426  -0.766  -0.595  -0.777  -0.613  -0.454  -0.663
21    T        -1.818  -1.852  -1.765  -1.375  -1.450  -1.410  -1.685  -1.700  -1.542
22    L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
23    S        -0.701  -0.641  -0.472  -1.312  -1.225  -0.875  -1.089  -0.996  -0.740
24    N        -1.305  -1.413  -1.216  -1.274  -1.451  -1.206  -1.447  -1.532  -1.260
25    F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
26    S        -0.793  -0.719  -1.176  -0.668  -0.576  -1.152  -0.732  -0.641  -1.209
27    S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
28    Q        -0.793  -0.909  -1.185  -0.508  -0.746  -1.314  -0.732  -0.907  -1.220
29    E        -2.422  -2.435  -2.205  -2.781  -2.831  -2.337  -2.043  -2.030  -1.721
30    V        -1.146  -1.079  -1.203  -1.202  -1.104  -1.327  -1.209  -1.120  -1.244
31    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
32    R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
33    H        -0.022  -0.276  -0.412   0.391   0.047  -0.236  -0.017  -0.392  -0.639
34    N        -0.022  -0.276  -0.412   0.208  -0.163  -0.468  -0.017  -0.392  -0.639
35    R        -1.146  -1.302  -1.219  -1.162  -1.380  -1.246  -1.209  -1.382  -1.263
36    P         0.787   0.801   0.839   1.008   1.030   1.057   0.817   0.836   0.889
37    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
38    V        -0.420  -0.316  -0.426  -0.554  -0.387  -0.617  -0.613  -0.454  -0.663
39    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
40    V        -0.793  -0.719  -1.176  -0.653  -0.561  -1.274  -0.732  -0.641  -1.209
41    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    N        -2.050  -1.968  -1.777  -1.821  -1.689  -1.451  -1.923  -1.835  -1.553
43    T        -2.190  -2.220  -2.189  -1.822  -1.943  -1.935  -1.804  -1.840  -1.710
44    S        -0.022   0.007  -0.393  -0.001   0.036  -0.515  -0.017   0.021  -0.607
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    A        -0.701  -0.645  -0.472  -0.864  -0.754  -0.494  -1.089  -1.003  -0.741
50    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
51    L        -1.518  -1.656  -1.758  -1.581  -1.831  -1.932  -1.328  -1.491  -1.535
52    L        -0.420  -0.316  -0.426  -0.766  -0.595  -0.777  -0.613  -0.454  -0.663
53    L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
54    Q        -1.909  -1.954  -1.774  -1.704  -1.767  -1.496  -1.804  -1.821  -1.550
55    P         0.787   0.801   0.839   1.008   1.030   1.057   0.817   0.836   0.889
56    M        -0.420  -0.526  -0.464  -0.353  -0.597  -0.590  -0.613  -0.796  -0.727
57    H        -2.050  -2.081  -1.782  -1.973  -2.035  -1.631  -1.923  -1.921  -1.557
58    I        -0.022  -0.276  -0.412  -0.040  -0.396  -0.622  -0.017  -0.392  -0.639
59    S        -0.634  -0.623  -0.471  -0.921  -0.921  -0.675  -0.970  -0.964  -0.738
60    R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
61    N         0.787   0.801   0.839   0.946   0.971   1.005   0.817   0.836   0.889
62    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
63    N        -1.146  -1.262  -1.206  -0.909  -1.059  -1.000  -1.209  -1.330  -1.247
64    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
65    Q        -1.818  -1.684  -1.759  -1.544  -1.352  -1.501  -1.685  -1.527  -1.536
66    V        -1.146  -1.266  -1.208  -1.162  -1.283  -1.192  -1.209  -1.335  -1.249
67    L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
68    I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
69    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
70    P        -0.420  -0.538  -0.466  -0.341  -0.592  -0.553  -0.613  -0.818  -0.731
71    S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
72    V        -0.634  -0.582  -0.468  -0.972  -0.890  -0.709  -0.970  -0.893  -0.733
73    N         0.787   0.801   0.839   0.946   0.971   1.005   0.817   0.836   0.889
74    S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
75    V        -0.420  -0.363  -0.443  -0.554  -0.468  -0.654  -0.613  -0.529  -0.692
76    R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
77    M        -2.050  -2.081  -1.772  -2.151  -2.205  -1.722  -1.923  -1.921  -1.548
78    S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
79    L        -0.420  -0.259  -0.414  -0.697  -0.423  -0.723  -0.613  -0.366  -0.643
80    M        -1.146  -1.140  -1.213  -1.026  -1.109  -1.149  -1.209  -1.248  -1.256
81    V        -0.634  -0.523  -0.448  -1.012  -0.817  -0.686  -0.970  -0.792  -0.700
82    K         0.787   0.801   0.839   0.932   0.956   0.994   0.817   0.836   0.889
83    Q         0.787   0.801   0.839   1.008   1.024   1.057   0.817   0.836   0.889
84    A        -0.022  -0.276  -0.412   0.117  -0.235  -0.505  -0.017  -0.392  -0.639
85    D         0.787   0.801   0.839   1.030   1.069   1.075   0.817   0.836   0.889
86    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
87    I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
88    E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
89    Q        -1.818  -1.809  -1.766  -1.560  -1.632  -1.507  -1.685  -1.690  -1.544
90    I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
91    L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
92    V         0.787   0.801   0.839   0.796   0.814   0.880   0.817   0.836   0.889
93    H        -0.022  -0.276  -0.412   0.361  -0.007  -0.326  -0.017  -0.392  -0.639
94    K        -0.022   0.005  -0.397   0.238   0.274  -0.320  -0.017   0.017  -0.613
95    F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
96    T        -0.022  -0.276  -0.412   0.277  -0.063  -0.310  -0.017  -0.392  -0.639
97    R        -0.793  -0.989  -1.190  -0.629  -0.915  -1.232  -0.732  -0.996  -1.226
98    F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
99    L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
100   E        -1.305  -1.402  -1.222  -1.467  -1.543  -1.254  -1.447  -1.517  -1.267
101   Q        -1.446  -1.432  -1.232  -1.375  -1.355  -1.087  -1.566  -1.553  -1.278
102   R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
103   A         0.787   0.801   0.839   0.842   0.874   0.918   0.817   0.836   0.889
104   E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
105   A        -1.537  -1.405  -1.227  -1.786  -1.601  -1.299  -1.685  -1.525  -1.272
106   F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
107   Y        -0.701  -0.645  -0.472  -0.816  -0.738  -0.465  -1.089  -1.003  -0.741
108   I        -0.022   0.024  -0.395  -0.040   0.025  -0.590  -0.017   0.044  -0.610
109   L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
110   R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
111   R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
112   V        -1.305  -1.266  -1.219  -1.388  -1.326  -1.187  -1.447  -1.398  -1.263
113   P         0.787   0.801   0.839   1.008   1.030   1.057   0.817   0.836   0.889
114   I        -0.634  -0.648  -0.474  -1.012  -1.052  -0.726  -0.970  -1.007  -0.744
115   P        -1.305  -1.413  -1.224  -1.210  -1.331  -1.064  -1.447  -1.532  -1.269
116   G         0.787   0.801   0.839   1.157   1.163   1.181   0.817   0.836   0.889
117   Y         0.787   0.801   0.839   1.079   1.108   1.116   0.817   0.836   0.889
118   S        -0.701  -0.645  -0.472  -0.946  -0.818  -0.557  -1.089  -1.003  -0.741
119   I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
120   S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
121   F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
122   L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
123   I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
124   T         0.787   0.801   0.839   0.968   0.989   1.023   0.817   0.836   0.889
125   N         0.787   0.801   0.839   0.946   0.971   1.005   0.817   0.836   0.889
126   K        -1.305  -1.402  -1.222  -1.332  -1.414  -1.127  -1.447  -1.517  -1.267
127   H         0.787   0.801   0.839   1.087   1.109   1.123   0.817   0.836   0.889
128   T         0.787   0.801   0.839   0.968   0.989   1.023   0.817   0.836   0.889
129   E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
130   S        -2.190  -2.078  -1.780  -2.415  -2.299  -1.791  -2.043  -1.918  -1.555
131   M         0.787   0.801   0.839   1.035   1.049   1.079   0.817   0.836   0.889
132   K        -1.818  -1.656  -1.748  -2.010  -1.770  -1.874  -1.685  -1.488  -1.525
133   T        -0.634  -0.523  -0.448  -0.702  -0.514  -0.428  -0.970  -0.792  -0.700
134   G        -2.422  -2.171  -2.187  -2.009  -1.663  -1.752  -2.043  -1.803  -1.708
135   K         0.787   0.801   0.839   0.932   0.956   0.994   0.817   0.836   0.889
136   L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
137   V        -0.022   0.024  -0.395   0.056   0.113  -0.553  -0.017   0.044  -0.610
138   D        -0.022   0.024  -0.395   0.271   0.349  -0.431  -0.017   0.044  -0.610
139   F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
140   I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
141   I        -0.022   0.116  -0.388  -0.040   0.136  -0.577  -0.017   0.165  -0.598
142   E        -0.793  -0.701  -1.171  -0.821  -0.706  -1.238  -0.732  -0.619  -1.203
143   F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
144   M         0.787   0.801   0.839   1.035   1.049   1.079   0.817   0.836   0.889
145   E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
146   D        -1.305  -1.209  -1.208  -1.566  -1.433  -1.347  -1.447  -1.310  -1.251
147   V         0.787   0.801   0.839   0.796   0.814   0.880   0.817   0.836   0.889
148   D         0.787   0.801   0.839   1.030   1.069   1.075   0.817   0.836   0.889
149   K        -0.022  -0.276  -0.412   0.214  -0.140  -0.419  -0.017  -0.392  -0.639
150   E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
151   I         0.787   0.801   0.839   0.685   0.712   0.788   0.817   0.836   0.889
152   S         0.787   0.801   0.839   0.703   0.723   0.803   0.817   0.836   0.889
153   E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
154   I        -0.022   0.106  -0.390   0.295   0.451  -0.360  -0.017   0.152  -0.601
155   K         0.787   0.801   0.839   0.932   0.956   0.994   0.817   0.836   0.889
156   L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
157   F        -0.022   0.005  -0.397   0.113   0.146  -0.479  -0.017   0.017  -0.613
158   L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
159   N         0.787   0.801   0.839   0.946   0.971   1.005   0.817   0.836   0.889
160   A        -0.022  -0.276  -0.412   0.170  -0.144  -0.346  -0.017  -0.392  -0.639
161   R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
162   A         0.787   0.801   0.839   0.842   0.874   0.918   0.817   0.836   0.889
163   R         0.787   0.801   0.839   0.791   0.807   0.876   0.817   0.836   0.889
164   F        -1.518  -1.588  -1.750  -1.373  -1.562  -1.866  -1.328  -1.426  -1.528
165   V        -1.146  -1.025  -1.196  -1.232  -1.040  -1.328  -1.209  -1.047  -1.235
166   A         0.787   0.801   0.839   0.842   0.874   0.918   0.817   0.836   0.889
167   E         0.787   0.801   0.839   0.542   0.563   0.669   0.817   0.836   0.889
168   A        -1.305  -1.425  -1.222  -1.491  -1.631  -1.294  -1.447  -1.549  -1.267
169   Y        -0.420  -0.363  -0.443  -0.232  -0.139  -0.380  -0.613  -0.529  -0.692
170   L         0.787   0.801   0.839   0.581   0.604   0.701   0.817   0.836   0.889
171   D        -2.935  -2.782  -2.541  -2.919  -2.744  -2.379  -2.281  -2.140  -1.825
172   E        -2.422  -2.425  -2.200  -2.217  -2.151  -1.857  -2.043  -2.019  -1.718
173   F         0.787   0.801   0.839   0.837   0.857   0.915   0.817   0.836   0.889
174   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   Y        -0.679  -0.616  -0.466  -0.651  -0.554  -0.343  -1.051  -0.951  -0.730
* 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/P33204
Output conservation file - output/P33204
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
