1     M         1.045   1.052   1.111   1.239   1.252   1.316   1.111   1.120   1.210
2     G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
3     A        -0.665  -0.533  -0.703  -0.777  -0.596  -0.767  -0.787  -0.607  -0.816
4     K        -1.340  -1.321  -1.241  -1.522  -1.471  -1.267  -1.345  -1.310  -1.150
5     T        -1.588  -1.526  -1.279  -1.538  -1.448  -1.096  -1.568  -1.491  -1.186
6     S         1.045   1.052   1.111   1.022   1.038   1.128   1.111   1.120   1.210
7     K         0.329   0.412   0.055   0.251   0.354  -0.107   0.330   0.446  -0.137
8     L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
9     S         0.329   0.357   0.049   0.377   0.420  -0.050   0.330   0.368  -0.146
10    K        -0.353  -0.302  -0.667  -0.347  -0.283  -0.742  -0.340  -0.272  -0.767
11    D        -0.353  -0.207  -0.650  -0.363  -0.173  -0.761  -0.340  -0.150  -0.744
12    D        -0.994  -0.877  -1.198  -1.021  -0.855  -1.336  -0.898  -0.757  -1.103
13    L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
14    T        -1.259  -1.330  -1.244  -1.105  -1.208  -1.103  -1.233  -1.304  -1.154
15    C        -1.793  -1.770  -1.633  -1.766  -1.714  -1.496  -1.568  -1.528  -1.321
16    L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
17    K        -1.259  -1.272  -1.249  -1.364  -1.383  -1.295  -1.233  -1.258  -1.158
18    Q        -0.665  -0.582  -0.717  -0.611  -0.480  -0.726  -0.787  -0.667  -0.834
19    S        -0.272  -0.241  -0.081  -0.489  -0.420  -0.171  -0.675  -0.621  -0.381
20    T         1.045   1.052   1.111   1.147   1.165   1.237   1.111   1.120   1.210
21    Y        -0.353  -0.302  -0.667  -0.037   0.021  -0.473  -0.340  -0.272  -0.767
22    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
23    D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
24    R        -0.272  -0.235  -0.078  -0.607  -0.570  -0.292  -0.675  -0.610  -0.376
25    R        -0.212  -0.161  -0.063  -0.429  -0.331  -0.215  -0.563  -0.475  -0.348
26    E         1.045   1.052   1.111   1.001   1.021   1.110   1.111   1.120   1.210
27    I        -0.212  -0.141  -0.047  -0.554  -0.432  -0.271  -0.563  -0.438  -0.320
28    Q         1.045   1.052   1.111   1.190   1.192   1.274   1.111   1.120   1.210
29    Q         1.045   1.052   1.111   1.190   1.192   1.274   1.111   1.120   1.210
30    W         1.045   1.052   1.111   1.342   1.349   1.406   1.111   1.120   1.210
31    H        -0.212  -0.141  -0.047  -0.197  -0.089   0.041  -0.563  -0.438  -0.320
32    K         1.045   1.052   1.111   0.876   0.886   1.001   1.111   1.120   1.210
33    G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
34    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
35    L         0.329   0.362   0.049   0.246   0.288  -0.162   0.330   0.376  -0.148
36    R        -0.212  -0.161  -0.063  -0.429  -0.331  -0.215  -0.563  -0.475  -0.348
37    D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
38    C         1.045   1.052   1.111   1.338   1.344   1.403   1.111   1.120   1.210
39    P         1.045   1.052   1.111   1.245   1.253   1.322   1.111   1.120   1.210
40    S        -0.665  -0.673  -0.703  -0.690  -0.693  -0.769  -0.787  -0.772  -0.816
41    G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
42    Q        -0.994  -0.885  -1.182  -0.585  -0.451  -0.853  -0.898  -0.766  -1.085
43    L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
44    A        -1.464  -1.422  -1.260  -1.417  -1.379  -1.108  -1.456  -1.407  -1.168
45    R        -1.011  -1.010  -0.783  -1.325  -1.333  -0.967  -1.233  -1.222  -0.919
46    E        -0.994  -0.885  -1.182  -0.895  -0.729  -1.208  -0.898  -0.766  -1.085
47    D        -0.023   0.053  -0.002  -0.209  -0.068  -0.212  -0.229  -0.102  -0.238
48    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
49    V        -1.464  -1.478  -1.262  -1.428  -1.447  -1.151  -1.456  -1.448  -1.171
50    K         0.329   0.409   0.058   0.256   0.353  -0.091   0.330   0.442  -0.132
51    I        -0.023  -0.126  -0.054  -0.012  -0.188  -0.106  -0.229  -0.412  -0.331
52    Y         0.329   0.225   0.042   0.514   0.368   0.045   0.330   0.173  -0.160
53    K        -0.353  -0.250  -0.658  -0.346  -0.218  -0.726  -0.340  -0.206  -0.754
54    Q         1.045   1.052   1.111   1.190   1.192   1.274   1.111   1.120   1.210
55    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
56    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
57    P         1.045   1.052   1.111   1.245   1.253   1.322   1.111   1.120   1.210
58    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
59    G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
60    S        -0.212  -0.141  -0.047  -0.617  -0.484  -0.329  -0.563  -0.438  -0.320
61    P         1.045   1.052   1.111   1.245   1.253   1.322   1.111   1.120   1.210
62    E        -1.259  -1.225  -1.226  -1.337  -1.253  -1.297  -1.233  -1.180  -1.133
63    D        -1.793  -1.654  -1.623  -1.872  -1.666  -1.553  -1.568  -1.419  -1.313
64    F        -0.023  -0.126  -0.054  -0.132  -0.304  -0.191  -0.229  -0.412  -0.331
65    A        -0.665  -0.678  -0.735  -0.464  -0.508  -0.601  -0.787  -0.838  -0.859
66    N        -2.247  -2.116  -1.969  -1.996  -1.761  -1.631  -1.791  -1.672  -1.446
67    H        -0.023   0.053  -0.002   0.098   0.204   0.110  -0.229  -0.102  -0.238
68    L        -0.272  -0.242  -0.082  -0.625  -0.587  -0.308  -0.675  -0.623  -0.384
69    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
70    T        -1.464  -1.413  -1.268  -1.393  -1.318  -1.113  -1.456  -1.398  -1.176
71    V         1.045   1.052   1.111   1.137   1.151   1.228   1.111   1.120   1.210
72    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
73    D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
74    K        -1.588  -1.690  -1.634  -1.561  -1.726  -1.594  -1.345  -1.439  -1.321
75    D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
76    N        -0.212  -0.161  -0.063  -0.382  -0.277  -0.175  -0.563  -0.475  -0.348
77    N        -0.272  -0.241  -0.081  -0.463  -0.419  -0.165  -0.675  -0.621  -0.381
78    G        -0.023  -0.126  -0.054  -0.126  -0.329  -0.261  -0.229  -0.412  -0.331
79    F        -1.259  -1.118  -1.204  -1.149  -0.935  -1.107  -1.233  -1.065  -1.111
80    I         0.329   0.418   0.055   0.493   0.607   0.089   0.330   0.455  -0.136
81    H         0.329   0.378   0.055   0.290   0.353  -0.024   0.330   0.399  -0.137
82    F         0.329   0.418   0.055   0.364   0.475  -0.011   0.330   0.455  -0.136
83    E         0.329   0.378   0.055   0.230   0.295  -0.162   0.330   0.399  -0.137
84    E         1.045   1.052   1.111   1.001   1.021   1.110   1.111   1.120   1.210
85    F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
86    I         1.045   1.052   1.111   1.119   1.134   1.213   1.111   1.120   1.210
87    T        -1.011  -1.010  -0.783  -0.985  -0.990  -0.667  -1.233  -1.222  -0.919
88    V        -0.023   0.053  -0.002   0.062   0.182   0.048  -0.229  -0.102  -0.238
89    L         0.329   0.418   0.055   0.266   0.374  -0.101   0.330   0.455  -0.136
90    S         1.045   1.052   1.111   1.022   1.038   1.128   1.111   1.120   1.210
91    T        -1.011  -1.010  -0.783  -1.118  -1.111  -0.777  -1.233  -1.222  -0.919
92    T         1.045   1.052   1.111   1.147   1.165   1.237   1.111   1.120   1.210
93    S         1.045   1.052   1.111   1.022   1.038   1.128   1.111   1.120   1.210
94    R         1.045   1.052   1.111   1.179   1.184   1.265   1.111   1.120   1.210
95    G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
96    T        -1.259  -1.227  -1.224  -1.247  -1.200  -1.262  -1.233  -1.195  -1.134
97    L        -0.353  -0.428  -0.673  -0.350  -0.457  -0.784  -0.340  -0.441  -0.774
98    E         0.329   0.362   0.049   0.389   0.441   0.016   0.330   0.376  -0.148
99    E        -0.930  -0.957  -0.775  -1.174  -1.205  -0.936  -1.121  -1.156  -0.909
100   K         1.045   1.052   1.111   0.876   0.886   1.001   1.111   1.120   1.210
101   L         0.329   0.225   0.040   0.266   0.132  -0.126   0.330   0.173  -0.163
102   S        -2.247  -2.129  -1.970  -2.093  -1.886  -1.752  -1.791  -1.680  -1.447
103   W         1.045   1.052   1.111   1.342   1.349   1.406   1.111   1.120   1.210
104   A        -0.023  -0.126  -0.054   0.026  -0.171  -0.106  -0.229  -0.412  -0.331
105   F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
106   E        -0.665  -0.709  -0.735  -0.645  -0.788  -0.837  -0.787  -0.871  -0.859
107   L         0.329   0.225   0.040   0.284   0.156  -0.080   0.330   0.173  -0.163
108   Y         1.045   1.052   1.111   1.162   1.166   1.250   1.111   1.120   1.210
109   D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
110   L        -1.259  -1.357  -1.246  -1.373  -1.504  -1.309  -1.233  -1.315  -1.154
111   N        -1.259  -1.375  -1.250  -1.190  -1.377  -1.253  -1.233  -1.337  -1.158
112   H        -1.793  -1.849  -1.653  -1.488  -1.590  -1.362  -1.568  -1.595  -1.338
113   D        -0.994  -1.140  -1.221  -0.915  -1.107  -1.166  -0.898  -1.066  -1.128
114   G         0.329   0.225   0.042   0.442   0.311  -0.010   0.330   0.173  -0.160
115   Y        -2.122  -2.038  -1.947  -2.118  -1.997  -1.843  -1.680  -1.596  -1.431
116   I         0.329   0.225   0.042   0.459   0.318  -0.022   0.330   0.173  -0.160
117   T        -0.806  -0.843  -0.734  -0.930  -0.955  -0.783  -1.010  -1.027  -0.861
118   F        -0.023   0.053  -0.002  -0.019   0.103  -0.041  -0.229  -0.102  -0.238
119   D        -0.994  -1.101  -1.216  -1.012  -1.170  -1.346  -0.898  -1.025  -1.122
120   E         0.329   0.225   0.042   0.339   0.204  -0.125   0.330   0.173  -0.160
121   M        -0.353  -0.544  -0.700  -0.007  -0.266  -0.569  -0.340  -0.593  -0.810
122   L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
123   T        -1.588  -1.561  -1.619  -1.270  -1.230  -1.361  -1.345  -1.312  -1.309
124   I         1.045   1.052   1.111   1.119   1.134   1.213   1.111   1.120   1.210
125   V         0.329   0.225   0.042   0.508   0.378   0.073   0.330   0.173  -0.160
126   A        -2.247  -2.118  -1.971  -2.079  -1.883  -1.742  -1.791  -1.674  -1.448
127   S        -0.212  -0.141  -0.047  -0.338  -0.199  -0.092  -0.563  -0.438  -0.320
128   V        -0.930  -0.935  -0.764  -0.983  -0.992  -0.749  -1.121  -1.129  -0.895
129   Y         1.045   1.052   1.111   1.162   1.166   1.250   1.111   1.120   1.210
130   K         1.045   1.052   1.111   0.876   0.886   1.001   1.111   1.120   1.210
131   M         1.045   1.052   1.111   1.239   1.252   1.316   1.111   1.120   1.210
132   M        -0.930  -0.886  -0.758  -0.937  -0.867  -0.701  -1.121  -1.059  -0.889
133   G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
134   S        -0.994  -1.101  -1.216  -0.760  -0.903  -1.033  -0.898  -1.025  -1.122
135   M         1.045   1.052   1.111   1.239   1.252   1.316   1.111   1.120   1.210
136   V         1.045   1.052   1.111   1.137   1.151   1.228   1.111   1.120   1.210
137   T        -0.994  -1.127  -1.216  -0.971  -1.160  -1.256  -0.898  -1.052  -1.122
138   L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
139   N        -0.994  -0.824  -1.189  -0.647  -0.411  -1.031  -0.898  -0.695  -1.093
140   E         0.329   0.412   0.055   0.339   0.457  -0.100   0.330   0.446  -0.137
141   D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
142   E         0.329   0.225   0.040   0.383   0.261  -0.013   0.330   0.173  -0.163
143   A        -1.793  -1.829  -1.653  -1.692  -1.741  -1.496  -1.568  -1.583  -1.338
144   T         1.045   1.052   1.111   1.147   1.165   1.237   1.111   1.120   1.210
145   P         1.045   1.052   1.111   1.245   1.253   1.322   1.111   1.120   1.210
146   E         1.045   1.052   1.111   1.001   1.021   1.110   1.111   1.120   1.210
147   M        -1.793  -1.831  -1.649  -1.890  -1.907  -1.560  -1.568  -1.579  -1.334
148   R         1.045   1.052   1.111   1.179   1.184   1.265   1.111   1.120   1.210
149   V         0.329   0.225   0.042   0.512   0.384   0.083   0.330   0.173  -0.160
150   K        -2.122  -1.961  -1.943  -2.130  -1.888  -1.858  -1.680  -1.523  -1.428
151   K         0.329   0.225   0.040   0.256   0.125  -0.118   0.330   0.173  -0.163
152   I        -0.994  -1.103  -1.212  -0.760  -0.935  -1.140  -0.898  -1.027  -1.117
153   F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
154   K        -1.259  -1.261  -1.218  -1.160  -1.143  -1.085  -1.233  -1.215  -1.125
155   L        -1.793  -1.732  -1.629  -1.724  -1.649  -1.440  -1.568  -1.501  -1.318
156   M        -0.023  -0.126  -0.054   0.028  -0.183  -0.137  -0.229  -0.412  -0.331
157   D        -0.353  -0.544  -0.700  -0.348  -0.596  -0.800  -0.340  -0.593  -0.810
158   K         1.045   1.052   1.111   0.876   0.886   1.001   1.111   1.120   1.210
159   N        -0.023   0.025  -0.042  -0.208  -0.130  -0.214  -0.229  -0.149  -0.310
160   E        -1.011  -0.989  -0.778  -1.367  -1.326  -0.970  -1.233  -1.196  -0.914
161   D        -0.212  -0.202  -0.077  -0.501  -0.480  -0.255  -0.563  -0.549  -0.374
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   G        -0.023  -0.126  -0.054  -0.124  -0.324  -0.257  -0.229  -0.412  -0.331
164   Y        -2.576  -2.536  -2.244  -2.278  -2.261  -1.849  -1.903  -1.855  -1.528
165   I        -0.272  -0.249  -0.084  -0.639  -0.602  -0.319  -0.675  -0.637  -0.387
166   T        -0.665  -0.782  -0.742  -0.639  -0.819  -0.799  -0.787  -0.933  -0.870
167   L        -0.353  -0.427  -0.669  -0.372  -0.488  -0.825  -0.340  -0.441  -0.770
168   D        -1.340  -1.359  -1.237  -1.592  -1.589  -1.378  -1.345  -1.342  -1.147
169   E        -0.023  -0.126  -0.054  -0.209  -0.403  -0.323  -0.229  -0.412  -0.331
170   F         1.045   1.052   1.111   0.986   1.000   1.097   1.111   1.120   1.210
171   R        -0.806  -0.783  -0.744  -0.913  -0.930  -0.772  -1.010  -0.984  -0.874
172   E        -0.665  -0.683  -0.735  -0.851  -0.932  -1.020  -0.787  -0.844  -0.859
173   G        -0.023  -0.126  -0.054  -0.120  -0.322  -0.252  -0.229  -0.412  -0.331
174   S        -0.353  -0.544  -0.700  -0.247  -0.514  -0.788  -0.340  -0.593  -0.810
175   K        -0.023  -0.065  -0.056  -0.229  -0.298  -0.260  -0.229  -0.304  -0.335
176   V        -1.259  -1.375  -1.250  -1.184  -1.375  -1.239  -1.233  -1.337  -1.158
177   D         1.045   1.052   1.111   0.883   0.897   1.007   1.111   1.120   1.210
178   P        -0.994  -1.144  -1.222  -0.632  -0.857  -1.064  -0.898  -1.070  -1.128
179   S        -1.340  -1.428  -1.261  -1.340  -1.427  -1.174  -1.345  -1.403  -1.169
180   I         1.045   1.052   1.111   1.119   1.134   1.213   1.111   1.120   1.210
181   I        -0.665  -0.690  -0.704  -0.569  -0.577  -0.629  -0.787  -0.797  -0.817
182   G        -1.259  -1.352  -1.239  -1.206  -1.301  -1.128  -1.233  -1.309  -1.147
183   A         1.045   1.052   1.111   1.197   1.204   1.280   1.111   1.120   1.210
184   L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
185   N        -0.023   0.013  -0.025   0.060   0.120  -0.017  -0.229  -0.170  -0.278
186   L        -0.665  -0.685  -0.732  -0.851  -0.924  -0.920  -0.787  -0.846  -0.855
187   Y         1.045   1.052   1.111   1.162   1.166   1.250   1.111   1.120   1.210
188   D        -0.353  -0.544  -0.700  -0.400  -0.666  -0.923  -0.340  -0.593  -0.810
189   G         1.045   1.052   1.111   1.087   1.105   1.185   1.111   1.120   1.210
190   L         1.045   1.052   1.111   0.894   0.903   1.017   1.111   1.120   1.210
191   I         0.329   0.378   0.055   0.508   0.575   0.095   0.330   0.399  -0.137
* 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/Q06389
Output conservation file - output/Q06389
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
