1     M         1.691   1.707   1.784   1.932   1.948   2.067   1.855   1.877   2.000
2     A        -0.244  -0.200  -0.229  -0.165  -0.096  -0.163  -0.442  -0.380  -0.409
3     L        -1.389  -1.368  -1.281  -1.188  -1.120  -1.027  -1.152  -1.125  -1.010
4     K        -0.858  -0.848  -0.808  -0.996  -0.953  -0.920  -0.851  -0.837  -0.771
5     K        -0.858  -0.842  -0.816  -1.040  -0.995  -0.938  -0.851  -0.830  -0.779
6     N        -0.858  -0.885  -0.827  -1.020  -1.025  -0.920  -0.851  -0.877  -0.791
7     T        -0.858  -0.879  -0.811  -1.113  -1.170  -1.057  -0.851  -0.870  -0.774
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     H        -1.389  -1.379  -1.281  -1.417  -1.398  -1.254  -1.152  -1.134  -1.010
10    N        -0.858  -0.852  -0.811  -0.702  -0.696  -0.646  -0.851  -0.839  -0.774
11    K        -0.328  -0.309  -0.271  -0.749  -0.717  -0.662  -0.550  -0.525  -0.462
12    S        -0.858  -0.852  -0.811  -0.797  -0.788  -0.723  -0.851  -0.839  -0.774
13    T        -0.687  -0.590  -0.731  -0.403  -0.263  -0.475  -0.651  -0.531  -0.683
14    K         0.829   0.715   0.663   0.524   0.362   0.256   0.811   0.617   0.498
15    R         0.473   0.497   0.527   0.444   0.475   0.502   0.184   0.225   0.241
16    V         0.365   0.382   0.468   0.074   0.099   0.233  -0.024   0.003   0.126
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    T        -0.299  -0.324  -0.275  -0.492  -0.540  -0.481  -0.494  -0.529  -0.463
23    K         1.691   1.707   1.784   1.323   1.348   1.463   1.855   1.877   2.000
24    H         1.691   1.707   1.784   1.924   1.944   2.059   1.855   1.877   2.000
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    P         1.691   1.707   1.784   1.945   1.961   2.080   1.855   1.877   2.000
27    S        -0.328  -0.305  -0.279  -0.502  -0.470  -0.430  -0.550  -0.520  -0.471
28    L        -0.328  -0.309  -0.271  -0.617  -0.586  -0.543  -0.550  -0.525  -0.462
29    K        -0.687  -0.720  -0.770  -1.022  -1.063  -1.161  -0.651  -0.691  -0.728
30    T        -0.244  -0.301  -0.247  -0.284  -0.352  -0.256  -0.442  -0.504  -0.430
31    L        -0.244  -0.214  -0.221  -0.169  -0.125  -0.110  -0.442  -0.397  -0.399
32    T        -1.296  -1.282  -1.252  -1.268  -1.247  -1.211  -1.068  -1.051  -0.986
33    H        -0.687  -0.720  -0.770  -0.435  -0.481  -0.630  -0.651  -0.691  -0.728
34    K        -0.687  -0.626  -0.740  -0.991  -0.886  -1.074  -0.651  -0.574  -0.694
35    Q        -0.854  -0.876  -0.811  -0.924  -0.952  -0.822  -0.859  -0.875  -0.778
36    I        -0.687  -0.720  -0.770  -0.499  -0.560  -0.603  -0.651  -0.691  -0.728
37    H        -1.296  -1.282  -1.252  -1.243  -1.216  -1.111  -1.068  -1.051  -0.986
38    T        -0.244  -0.306  -0.233  -0.472  -0.550  -0.446  -0.442  -0.511  -0.413
39    T         0.031  -0.044  -0.142   0.117   0.038  -0.079  -0.024  -0.134  -0.274
40    I        -0.244  -0.203  -0.229  -0.114  -0.042  -0.082  -0.442  -0.379  -0.407
41    F        -0.244  -0.171  -0.220  -0.112   0.002  -0.060  -0.442  -0.344  -0.392
42    V         0.829   0.868   0.683   0.829   0.880   0.606   0.811   0.872   0.535
43    K         0.829   0.715   0.663   0.549   0.393   0.302   0.811   0.617   0.498
44    S         1.691   1.707   1.784   1.679   1.698   1.816   1.855   1.877   2.000
45    T        -0.687  -0.709  -0.746  -0.737  -0.804  -0.881  -0.651  -0.678  -0.701
46    T         0.031  -0.054  -0.136   0.038  -0.066  -0.192  -0.024  -0.148  -0.265
47    P         0.829   0.715   0.663   1.173   1.011   0.931   0.811   0.617   0.498
48    Y         0.473   0.438   0.491   0.619   0.551   0.622   0.184   0.112   0.172
49    V        -0.244  -0.212  -0.219  -0.509  -0.452  -0.498  -0.442  -0.394  -0.395
50    S         1.691   1.707   1.784   1.679   1.698   1.816   1.855   1.877   2.000
51    A         0.829   0.856   0.686   1.054   1.086   0.820   0.811   0.853   0.540
52    L        -0.687  -0.641  -0.727  -0.686  -0.604  -0.783  -0.651  -0.591  -0.679
53    K         1.691   1.707   1.784   1.357   1.384   1.496   1.855   1.877   2.000
54    R         0.031  -0.044  -0.142   0.210   0.052  -0.103  -0.024  -0.134  -0.274
55    I         0.031  -0.054  -0.136   0.056  -0.081  -0.243  -0.024  -0.148  -0.265
56    N        -0.854  -0.818  -0.801  -0.799  -0.759  -0.714  -0.859  -0.816  -0.768
57    K         0.829   0.856   0.686   0.582   0.623   0.395   0.811   0.853   0.540
58    F        -0.854  -0.811  -0.800  -0.881  -0.816  -0.830  -0.859  -0.810  -0.766
59    L         1.691   1.707   1.784   1.692   1.716   1.829   1.855   1.877   2.000
60    D        -1.296  -1.288  -1.235  -1.154  -1.183  -1.090  -1.068  -1.056  -0.970
61    S        -1.296  -1.296  -1.255  -1.265  -1.224  -1.134  -1.068  -1.064  -0.988
62    V        -1.296  -1.296  -1.255  -0.977  -0.992  -0.937  -1.068  -1.064  -0.988
63    H        -1.296  -1.304  -1.245  -0.938  -0.958  -0.879  -1.068  -1.070  -0.979
64    K         0.473   0.497   0.527   0.075   0.112   0.161   0.184   0.225   0.241
65    Q        -0.328  -0.326  -0.268  -0.329  -0.320  -0.222  -0.550  -0.542  -0.457
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    G        -0.858  -0.848  -0.808  -1.124  -1.091  -1.025  -0.851  -0.837  -0.771
82    S        -0.858  -0.842  -0.816  -0.891  -0.862  -0.833  -0.851  -0.830  -0.779
83    S        -0.858  -0.885  -0.827  -1.078  -1.081  -0.987  -0.851  -0.877  -0.791
84    Y         1.691   1.707   1.784   1.914   1.933   2.049   1.855   1.877   2.000
85    V         0.473   0.520   0.536   0.287   0.368   0.365   0.184   0.267   0.259
86    A         0.031  -0.013  -0.133   0.060  -0.003  -0.155  -0.024  -0.093  -0.261
87    V         0.031  -0.054  -0.136   0.112  -0.001  -0.123  -0.024  -0.148  -0.265
88    L        -0.244  -0.301  -0.247  -0.476  -0.522  -0.463  -0.442  -0.504  -0.430
89    G         1.691   1.707   1.784   1.833   1.850   1.968   1.855   1.877   2.000
90    M         1.691   1.707   1.784   1.932   1.948   2.067   1.855   1.877   2.000
91    G         1.691   1.707   1.784   1.833   1.850   1.968   1.855   1.877   2.000
92    K         0.829   0.855   0.701   0.605   0.648   0.456   0.811   0.851   0.567
93    A        -0.687  -0.734  -0.746  -0.395  -0.452  -0.506  -0.651  -0.706  -0.701
94    V         0.473   0.512   0.521   0.263   0.326   0.318   0.184   0.252   0.231
95    E        -0.687  -0.741  -0.757  -0.528  -0.621  -0.655  -0.651  -0.714  -0.714
96    K         0.829   0.875   0.685   0.594   0.664   0.414   0.811   0.884   0.538
97    T         0.829   0.868   0.683   0.745   0.807   0.517   0.811   0.872   0.535
98    L         0.031  -0.044  -0.142   0.152   0.036  -0.108  -0.024  -0.134  -0.274
99    A         0.473   0.520   0.536   0.391   0.460   0.481   0.184   0.267   0.259
100   L        -0.244  -0.241  -0.233  -0.381  -0.382  -0.373  -0.442  -0.442  -0.414
101   G         0.365   0.379   0.466   0.340   0.355   0.490  -0.024  -0.003   0.122
102   C        -0.854  -0.805  -0.795  -0.823  -0.759  -0.701  -0.859  -0.806  -0.762
103   H        -0.687  -0.729  -0.744  -0.495  -0.556  -0.658  -0.651  -0.700  -0.699
104   F         0.829   0.855   0.701   1.145   1.177   0.971   0.811   0.851   0.567
105   Q         0.829   0.856   0.686   1.115   1.142   0.914   0.811   0.853   0.540
106   D        -0.854  -0.826  -0.799  -1.168  -1.141  -1.085  -0.859  -0.823  -0.766
107   Q        -0.858  -0.780  -0.798  -0.812  -0.692  -0.729  -0.851  -0.756  -0.760
108   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   N        -0.854  -0.885  -0.800  -0.721  -0.754  -0.640  -0.859  -0.883  -0.767
110   K         0.031   0.108  -0.090   0.307   0.431   0.090  -0.024   0.086  -0.200
111   K         1.691   1.707   1.784   1.357   1.384   1.496   1.855   1.877   2.000
112   I         0.829   0.906   0.693   0.829   0.930   0.621   0.811   0.932   0.552
113   E         0.031   0.108  -0.090   0.197   0.301   0.026  -0.024   0.086  -0.200
114   V         0.365   0.381   0.467   0.061   0.088   0.219  -0.024   0.002   0.124
115   Y        -0.687  -0.709  -0.746  -0.414  -0.442  -0.465  -0.651  -0.678  -0.701
116   T         1.691   1.707   1.784   1.561   1.588   1.699   1.855   1.877   2.000
117   K         0.365   0.381   0.466  -0.027   0.021   0.145  -0.024   0.000   0.123
118   T        -0.244  -0.301  -0.247  -0.422  -0.480  -0.395  -0.442  -0.504  -0.430
119   I        -0.854  -0.818  -0.804  -1.040  -0.983  -0.967  -0.859  -0.816  -0.771
120   E        -0.244  -0.247  -0.236  -0.370  -0.395  -0.376  -0.442  -0.451  -0.419
121   V         0.829   0.715   0.663   0.830   0.664   0.574   0.811   0.617   0.498
122   L         0.829   0.715   0.663   0.932   0.785   0.709   0.811   0.617   0.498
123   D         1.691   1.707   1.784   1.718   1.736   1.855   1.855   1.877   2.000
124   E         1.691   1.707   1.784   1.756   1.773   1.893   1.855   1.877   2.000
125   V        -0.244  -0.301  -0.247  -0.286  -0.371  -0.282  -0.442  -0.504  -0.430
126   I        -1.738  -1.715  -1.628  -1.566  -1.589  -1.402  -1.277  -1.250  -1.136
127   T        -1.738  -1.715  -1.628  -1.516  -1.490  -1.352  -1.277  -1.250  -1.136
128   E        -1.296  -1.282  -1.252  -1.086  -1.061  -1.013  -1.068  -1.051  -0.986
129   G        -1.296  -1.291  -1.239  -1.170  -1.136  -1.062  -1.068  -1.059  -0.974
130   Q        -1.296  -1.222  -1.229  -1.006  -0.905  -0.901  -1.068  -0.990  -0.965
131   A        -1.738  -1.715  -1.628  -1.645  -1.630  -1.480  -1.277  -1.250  -1.136
132   D        -0.687  -0.734  -0.746  -0.546  -0.634  -0.644  -0.651  -0.706  -0.701
133   I        -0.127  -0.038  -0.149  -0.051   0.086  -0.104  -0.250  -0.121  -0.284
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   D         1.691   1.707   1.784   1.718   1.736   1.855   1.855   1.877   2.000
142   M        -0.328  -0.290  -0.262  -0.387  -0.340  -0.272  -0.550  -0.503  -0.451
143   E        -0.244  -0.241  -0.233  -0.260  -0.266  -0.233  -0.442  -0.442  -0.414
144   S        -0.244  -0.203  -0.229  -0.253  -0.189  -0.222  -0.442  -0.382  -0.408
145   D         0.829   0.856   0.686   0.927   0.962   0.716   0.811   0.853   0.540
146   V        -1.296  -1.304  -1.245  -1.212  -1.234  -1.128  -1.068  -1.070  -0.979
147   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   D         0.733   0.800   0.658   0.807   0.899   0.695   0.652   0.762   0.489
151   K        -0.858  -0.885  -0.827  -0.946  -0.981  -0.923  -0.851  -0.877  -0.791
152   E         1.691   1.707   1.784   1.756   1.773   1.893   1.855   1.877   2.000
153   T         0.829   0.715   0.663   0.756   0.599   0.502   0.811   0.617   0.498
154   Q        -1.738  -1.715  -1.628  -1.742  -1.720  -1.576  -1.277  -1.250  -1.136
155   L        -0.687  -0.720  -0.770  -0.586  -0.674  -0.724  -0.651  -0.691  -0.728
156   K         0.031  -0.054  -0.136  -0.208  -0.313  -0.447  -0.024  -0.148  -0.265
157   K         0.829   0.715   0.663   0.594   0.450   0.384   0.811   0.617   0.498
158   R         1.691   1.707   1.784   1.826   1.834   1.962   1.855   1.877   2.000
159   A        -1.296  -1.288  -1.233  -1.193  -1.191  -1.082  -1.068  -1.056  -0.968
160   V        -0.244  -0.309  -0.239  -0.411  -0.503  -0.402  -0.442  -0.515  -0.419
161   S         1.691   1.707   1.784   1.679   1.698   1.816   1.855   1.877   2.000
162   G        -0.687  -0.720  -0.770  -0.468  -0.545  -0.628  -0.651  -0.691  -0.728
163   V         0.365   0.381   0.466   0.061   0.086   0.218  -0.024   0.000   0.123
164   E         1.691   1.707   1.784   1.756   1.773   1.893   1.855   1.877   2.000
165   L        -0.687  -0.590  -0.731  -0.724  -0.568  -0.819  -0.651  -0.531  -0.683
166   R         1.691   1.707   1.784   1.826   1.834   1.962   1.855   1.877   2.000
167   I         0.829   0.715   0.663   0.871   0.700   0.603   0.811   0.617   0.498
168   Y        -0.854  -0.829  -0.807  -0.467  -0.436  -0.408  -0.859  -0.828  -0.773
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   -        -0.858  -0.884  -0.827  -0.834  -0.893  -0.818  -0.851  -0.876  -0.791
172   V        -0.687  -0.720  -0.770  -0.590  -0.637  -0.703  -0.651  -0.691  -0.728
* 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/P38291
Output conservation file - output/P38291
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
