1     M         1.881   1.945   2.082   2.156   2.245   2.478   2.113   2.212   2.460
2     V         1.881   1.945   2.082   1.955   2.037   2.271   2.113   2.212   2.460
3     E        -0.490  -0.547  -0.478  -0.595  -0.650  -0.540  -0.636  -0.679  -0.575
4     L         1.881   1.945   2.082   1.731   1.837   2.040   2.113   2.212   2.460
5     T         1.169   1.112   1.036   1.228   1.143   1.016   1.238   1.132   0.954
6     E         0.181   0.296   0.163  -0.043   0.117  -0.095  -0.011   0.176  -0.046
7     I         0.181   0.122   0.103   0.229   0.101   0.058  -0.011  -0.138  -0.150
8     K        -1.391  -1.443  -1.331  -1.302  -1.398  -1.217  -1.136  -1.156  -1.014
9     D         0.819   0.917   0.877   0.563   0.725   0.589   0.613   0.778   0.633
10    D         0.819   0.960   0.906   0.506   0.716   0.598   0.613   0.859   0.692
11    V        -0.940  -0.933  -0.901  -0.797  -0.738  -0.694  -0.886  -0.862  -0.795
12    V        -1.718  -1.724  -1.639  -1.559  -1.577  -1.474  -1.261  -1.247  -1.124
13    Q        -0.146  -0.112  -0.329   0.133   0.176  -0.140  -0.136  -0.091  -0.369
14    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    D        -1.045  -1.006  -0.962  -0.900  -0.817  -0.724  -0.988  -0.932  -0.853
16    E        -1.391  -1.338  -1.305  -1.153  -1.055  -1.040  -1.136  -1.072  -0.993
17    P        -0.530  -0.488  -0.490  -0.503  -0.458  -0.468  -0.661  -0.607  -0.586
18    Q        -0.940  -0.805  -0.888  -0.840  -0.623  -0.745  -0.886  -0.727  -0.781
19    F        -1.267  -1.240  -1.266  -1.088  -1.069  -1.139  -1.011  -0.974  -0.956
20    S        -0.940  -0.903  -0.898  -0.799  -0.733  -0.726  -0.886  -0.825  -0.792
21    R        -0.940  -0.836  -0.899  -0.787  -0.651  -0.738  -0.886  -0.778  -0.795
22    N        -1.267  -1.297  -1.286  -1.220  -1.325  -1.237  -1.011  -1.030  -0.974
23    Q        -1.045  -1.036  -0.964  -1.338  -1.367  -1.216  -0.988  -0.965  -0.855
24    A        -0.904  -0.877  -0.908  -0.841  -0.808  -0.819  -0.825  -0.789  -0.795
25    I        -0.904  -0.794  -0.889  -0.790  -0.634  -0.751  -0.825  -0.688  -0.775
26    V        -1.045  -1.064  -0.971  -0.931  -0.959  -0.775  -0.988  -0.988  -0.861
27    E        -0.297  -0.307  -0.413  -0.318  -0.317  -0.492  -0.335  -0.350  -0.480
28    E        -0.671  -0.615  -0.545  -0.836  -0.770  -0.646  -0.825  -0.756  -0.650
29    K        -1.045  -1.060  -0.963  -1.094  -1.078  -0.997  -0.988  -0.985  -0.854
30    A        -0.530  -0.445  -0.469  -0.860  -0.736  -0.763  -0.661  -0.544  -0.556
31    S        -1.419  -1.418  -1.325  -1.691  -1.682  -1.584  -1.151  -1.134  -1.008
32    A        -1.419  -1.366  -1.318  -1.306  -1.268  -1.177  -1.151  -1.089  -1.002
33    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    V        -0.613  -0.575  -0.526  -0.860  -0.859  -0.748  -0.761  -0.714  -0.629
39    D         0.041   0.091   0.098  -0.383  -0.315  -0.325  -0.261  -0.194  -0.170
40    D        -0.409  -0.348  -0.450  -0.594  -0.497  -0.697  -0.511  -0.434  -0.540
41    E         0.492   0.435   0.245   0.429   0.334   0.065   0.489   0.402   0.093
42    D        -0.409  -0.301  -0.419  -0.640  -0.488  -0.721  -0.511  -0.394  -0.501
43    D         0.492   0.459   0.288   0.531   0.504   0.249   0.489   0.423   0.161
44    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    D         0.819   0.814   0.825   0.563   0.535   0.476   0.613   0.578   0.523
46    S        -0.409  -0.449  -0.435  -0.618  -0.680  -0.707  -0.511  -0.551  -0.520
47    D         1.169   1.242   1.061   1.110   1.220   0.940   1.238   1.351   1.003
48    F        -0.409  -0.372  -0.441  -0.375  -0.342  -0.509  -0.511  -0.472  -0.528
49    -        -0.029   0.100   0.074  -0.484  -0.289  -0.353  -0.331  -0.150  -0.193
50    -        -1.066  -1.020  -0.956  -1.154  -1.058  -1.030  -0.997  -0.937  -0.845
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    E         0.076   0.206   0.125  -0.266  -0.036  -0.230  -0.172   0.030  -0.106
54    D         0.377   0.252   0.186   0.286   0.082  -0.073   0.318   0.116  -0.003
55    E         0.751   0.819   0.815   0.430   0.535   0.453   0.481   0.588   0.502
56    F         0.377   0.252   0.186   0.662   0.495   0.367   0.318   0.116  -0.003
57    D         0.377   0.252   0.186   0.372   0.162   0.090   0.318   0.116  -0.003
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    E         0.492   0.379   0.272   0.428   0.251   0.106   0.489   0.312   0.135
60    N        -0.409  -0.558  -0.470  -0.289  -0.527  -0.459  -0.511  -0.671  -0.563
61    E         1.881   1.945   2.082   1.683   1.757   1.990   2.113   2.212   2.460
62    T         1.169   1.242   1.061   1.288   1.386   1.183   1.238   1.351   1.003
63    L         0.041  -0.044   0.078  -0.154  -0.218  -0.049  -0.261  -0.358  -0.198
64    L        -0.409  -0.558  -0.470  -0.389  -0.574  -0.431  -0.511  -0.671  -0.563
65    D         0.632   0.699   0.776   0.186   0.297   0.360   0.239   0.346   0.417
66    R         1.881   1.945   2.082   2.139   2.227   2.460   2.113   2.212   2.460
67    I        -0.082  -0.076   0.008  -0.223  -0.237  -0.141  -0.386  -0.384  -0.282
68    V        -0.737  -0.840  -0.865  -0.419  -0.581  -0.607  -0.636  -0.750  -0.748
69    A         1.881   1.945   2.082   1.712   1.791   2.020   2.113   2.212   2.460
70    L         1.881   1.945   2.082   1.731   1.837   2.040   2.113   2.212   2.460
71    K         1.169   1.049   1.051   1.429   1.296   1.314   1.238   1.022   0.984
72    D         1.169   1.112   1.036   1.110   1.038   0.896   1.238   1.132   0.954
73    I         0.492   0.459   0.288   0.772   0.740   0.522   0.489   0.423   0.161
74    V         0.632   0.730   0.796   0.506   0.663   0.744   0.239   0.410   0.461
75    P         1.169   1.049   1.051   1.443   1.283   1.278   1.238   1.022   0.984
76    P         1.169   1.112   1.036   1.465   1.400   1.298   1.238   1.132   0.954
77    G        -0.409  -0.357  -0.447  -0.354  -0.343  -0.450  -0.511  -0.481  -0.537
78    K        -0.940  -1.008  -0.921  -0.474  -0.562  -0.433  -0.886  -0.934  -0.814
79    R         1.169   1.290   1.058   1.527   1.685   1.406   1.238   1.429   0.997
80    Q        -1.718  -1.632  -1.616  -1.413  -1.285  -1.265  -1.261  -1.177  -1.107
81    T        -1.718  -1.709  -1.629  -1.271  -1.210  -1.110  -1.261  -1.236  -1.118
82    I         0.492   0.379   0.272   0.716   0.574   0.392   0.489   0.312   0.135
83    S        -0.940  -0.909  -0.909  -0.754  -0.727  -0.667  -0.886  -0.852  -0.805
84    N        -1.718  -1.721  -1.622  -1.329  -1.288  -1.204  -1.261  -1.245  -1.112
85    F        -1.391  -1.399  -1.306  -1.403  -1.381  -1.241  -1.136  -1.126  -0.995
86    F        -1.064  -0.969  -0.955  -0.931  -0.816  -0.771  -1.011  -0.914  -0.850
87    G        -0.737  -0.645  -0.810  -0.589  -0.445  -0.693  -0.636  -0.525  -0.689
88    F         0.492   0.635   0.302   0.681   0.864   0.447   0.489   0.701   0.183
89    T        -0.490  -0.477  -0.470  -0.573  -0.567  -0.569  -0.636  -0.609  -0.568
90    S        -1.718  -1.560  -1.607  -1.266  -1.064  -1.085  -1.261  -1.110  -1.101
91    S        -0.490  -0.604  -0.490  -0.668  -0.770  -0.624  -0.636  -0.735  -0.589
92    F        -1.391  -1.346  -1.296  -1.156  -1.059  -0.991  -1.136  -1.081  -0.987
93    V        -1.064  -1.013  -0.951  -1.097  -1.030  -0.940  -1.011  -0.951  -0.847
94    R        -0.490  -0.354  -0.439  -0.400  -0.248  -0.269  -0.636  -0.491  -0.536
95    N        -0.146  -0.129  -0.346  -0.028   0.000  -0.314  -0.136  -0.113  -0.392
96    A        -1.391  -1.425  -1.322  -1.452  -1.516  -1.362  -1.136  -1.143  -1.007
97    F        -0.146  -0.290  -0.370   0.143  -0.110  -0.265  -0.136  -0.329  -0.424
98    T        -0.082  -0.009   0.041  -0.300  -0.183  -0.129  -0.386  -0.280  -0.232
99    K        -0.490  -0.365  -0.449  -0.243  -0.069  -0.128  -0.636  -0.485  -0.544
100   S         0.041  -0.008   0.101  -0.110  -0.175  -0.029  -0.261  -0.297  -0.161
101   G         1.169   1.290   1.058   1.358   1.511   1.204   1.238   1.429   0.997
102   N        -0.490  -0.507  -0.462  -0.236  -0.234  -0.154  -0.636  -0.640  -0.559
103   L        -0.409  -0.465  -0.462  -0.618  -0.740  -0.724  -0.511  -0.587  -0.556
104   A        -0.490  -0.516  -0.473  -0.725  -0.724  -0.642  -0.636  -0.645  -0.571
105   W         1.169   1.224   1.053   1.623   1.703   1.519   1.238   1.322   0.988
106   T        -0.409  -0.499  -0.468  -0.455  -0.634  -0.578  -0.511  -0.620  -0.562
107   L        -0.082  -0.129  -0.012  -0.327  -0.385  -0.224  -0.386  -0.460  -0.313
108   T         0.819   0.723   0.810   0.716   0.512   0.613   0.613   0.396   0.490
109   T         0.041  -0.017   0.086  -0.156  -0.214  -0.072  -0.261  -0.313  -0.181
110   T         1.169   1.311   1.067   1.168   1.358   1.038   1.238   1.462   1.014
111   A         0.181   0.107   0.142  -0.027  -0.123  -0.097  -0.011  -0.103  -0.085
112   L         1.881   1.945   2.082   1.731   1.837   2.040   2.113   2.212   2.460
113   L         1.881   1.945   2.082   1.731   1.837   2.040   2.113   2.212   2.460
114   L         1.169   1.049   1.051   1.113   0.979   0.971   1.238   1.022   0.984
115   G         1.881   1.945   2.082   2.001   2.079   2.317   2.113   2.212   2.460
116   V         1.881   1.945   2.082   1.955   2.037   2.271   2.113   2.212   2.460
117   P         1.881   1.945   2.082   2.086   2.180   2.405   2.113   2.212   2.460
118   L         0.819   0.723   0.810   0.652   0.509   0.620   0.613   0.396   0.490
119   S         0.041  -0.008   0.080  -0.240  -0.305  -0.156  -0.261  -0.317  -0.194
120   L         0.492   0.281   0.237   0.540   0.288   0.224   0.489   0.169   0.078
121   S         0.632   0.664   0.777   0.228   0.259   0.409   0.239   0.273   0.421
122   I         0.492   0.281   0.237   0.719   0.436   0.338   0.489   0.169   0.078
123   L        -0.146  -0.335  -0.387  -0.153  -0.456  -0.549  -0.136  -0.381  -0.445
124   A        -0.082  -0.104  -0.006  -0.548  -0.646  -0.502  -0.386  -0.429  -0.304
125   E         1.169   1.049   1.051   1.035   0.855   0.860   1.238   1.022   0.984
126   Q         0.181   0.201   0.153   0.199   0.239   0.118  -0.011   0.042  -0.062
127   Q         1.169   1.049   1.051   1.370   1.226   1.250   1.238   1.022   0.984
128   L         1.169   1.049   1.051   1.147   1.026   1.040   1.238   1.022   0.984
129   I        -0.940  -1.029  -0.944  -0.797  -0.949  -0.814  -0.886  -0.950  -0.836
130   E         1.169   1.049   1.051   1.027   0.838   0.842   1.238   1.022   0.984
131   M         0.492   0.435   0.245   0.949   0.884   0.621   0.489   0.402   0.093
132   E         1.881   1.945   2.082   1.683   1.757   1.990   2.113   2.212   2.460
133   K        -0.146  -0.203  -0.333   0.189   0.104  -0.090  -0.136  -0.215  -0.375
134   T        -0.940  -0.895  -0.902  -1.068  -1.010  -0.999  -0.886  -0.816  -0.792
135   F        -0.490  -0.604  -0.490  -0.277  -0.457  -0.285  -0.636  -0.735  -0.589
136   D        -0.613  -0.658  -0.536  -0.738  -0.729  -0.577  -0.761  -0.791  -0.639
137   L         0.492   0.281   0.237   0.506   0.247   0.155   0.489   0.169   0.078
138   Q        -0.146  -0.203  -0.333   0.082   0.008  -0.233  -0.136  -0.215  -0.375
139   S        -0.940  -0.995  -0.919  -0.774  -0.866  -0.760  -0.886  -0.924  -0.812
140   D        -0.613  -0.658  -0.536  -0.861  -0.910  -0.752  -0.761  -0.791  -0.639
141   A         0.492   0.379   0.272   0.463   0.303   0.146   0.489   0.312   0.135
142   N         0.181   0.150   0.160   0.372   0.349   0.319  -0.011  -0.033  -0.052
143   N         0.492   0.514   0.274   0.520   0.541   0.206   0.489   0.513   0.138
144   I         0.572   0.624   0.754   0.390   0.462   0.660   0.114   0.189   0.369
145   L         0.492   0.435   0.245   0.504   0.451   0.166   0.489   0.402   0.093
146   A         1.169   1.049   1.051   1.082   0.913   0.926   1.238   1.022   0.984
147   Q        -0.082  -0.043   0.025  -0.123  -0.097  -0.028  -0.386  -0.337  -0.259
148   G         1.881   1.945   2.082   2.001   2.079   2.317   2.113   2.212   2.460
149   E        -1.064  -1.057  -0.966  -1.437  -1.409  -1.295  -1.011  -0.986  -0.859
150   K        -0.409  -0.341  -0.440  -0.538  -0.482  -0.557  -0.511  -0.439  -0.526
151   D        -1.718  -1.698  -1.617  -1.822  -1.766  -1.687  -1.261  -1.229  -1.109
152   A        -0.737  -0.840  -0.865  -0.658  -0.816  -0.826  -0.636  -0.750  -0.748
153   A        -0.940  -0.823  -0.889  -0.895  -0.749  -0.801  -0.886  -0.739  -0.780
154   A        -0.940  -0.909  -0.909  -0.991  -0.972  -0.928  -0.886  -0.852  -0.805
155   T        -1.064  -0.987  -0.955  -1.040  -0.912  -0.874  -1.011  -0.929  -0.850
156   -        -0.634  -0.523  -0.514  -0.922  -0.755  -0.755  -0.766  -0.620  -0.607
157   -        -0.634  -0.577  -0.521  -0.841  -0.773  -0.679  -0.766  -0.687  -0.616
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   A        -0.015   0.049   0.062  -0.297  -0.233  -0.163  -0.335  -0.250  -0.217
172   N        -1.267  -1.302  -1.272  -1.171  -1.253  -1.156  -1.011  -1.034  -0.962
* 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/P49334
Output conservation file - output/P49334
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
