1     M         1.953   1.956   2.025   2.128   2.137   2.236   2.136   2.141   2.244
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -0.295  -0.305  -0.296  -0.162  -0.175  -0.172  -0.424  -0.437  -0.422
41    Y        -0.328  -0.323  -0.310  -0.321  -0.303  -0.264  -0.485  -0.477  -0.445
42    T        -0.927  -0.924  -0.898  -0.739  -0.712  -0.702  -0.813  -0.808  -0.760
43    K        -0.927  -0.948  -0.925  -0.597  -0.630  -0.594  -0.813  -0.834  -0.788
44    E         0.871   0.876   0.759   1.024   1.067   0.878   0.826   0.833   0.617
45    Y         1.953   1.956   2.025   1.893   1.901   2.002   2.136   2.141   2.244
46    Y        -0.328  -0.323  -0.310  -0.285  -0.251  -0.239  -0.485  -0.477  -0.445
47    W         0.498   0.518   0.557   0.509   0.551   0.600   0.170   0.207   0.249
48    F         0.871   0.826   0.750   1.045   0.981   0.874   0.826   0.750   0.601
49    S        -0.102  -0.143  -0.216   0.040  -0.006  -0.131  -0.158  -0.214  -0.312
50    Q        -0.927  -0.951  -0.933  -0.889  -0.965  -0.955  -0.813  -0.837  -0.796
51    Y         1.953   1.956   2.025   1.893   1.901   2.002   2.136   2.141   2.244
52    M        -0.102  -0.131  -0.187  -0.081  -0.143  -0.216  -0.158  -0.198  -0.273
53    I        -0.927  -0.922  -0.899  -1.087  -1.063  -1.042  -0.813  -0.807  -0.761
54    I        -0.927  -0.919  -0.911  -0.900  -0.876  -0.880  -0.813  -0.804  -0.773
55    T        -0.102  -0.143  -0.216   0.035  -0.009  -0.121  -0.158  -0.214  -0.312
56    S        -1.527  -1.522  -1.459  -1.636  -1.637  -1.525  -1.141  -1.135  -1.046
57    T        -0.927  -0.951  -0.933  -0.845  -0.879  -0.846  -0.813  -0.837  -0.796
58    L        -0.102  -0.135  -0.186  -0.343  -0.421  -0.458  -0.158  -0.204  -0.271
59    V        -0.927  -0.948  -0.925  -0.982  -1.044  -1.008  -0.813  -0.834  -0.788
60    L        -0.927  -0.948  -0.925  -1.040  -1.100  -1.075  -0.813  -0.834  -0.788
61    T        -1.527  -1.522  -1.459  -1.328  -1.325  -1.216  -1.141  -1.135  -1.046
62    I        -0.328  -0.348  -0.303  -0.546  -0.582  -0.485  -0.485  -0.506  -0.437
63    I        -1.527  -1.522  -1.459  -1.611  -1.637  -1.499  -1.141  -1.135  -1.046
64    W         1.953   1.956   2.025   2.154   2.150   2.262   2.136   2.141   2.244
65    S        -0.328  -0.323  -0.290  -0.388  -0.360  -0.317  -0.485  -0.479  -0.423
66    I        -0.102  -0.092  -0.176  -0.383  -0.393  -0.494  -0.158  -0.143  -0.258
67    L        -0.102  -0.143  -0.216  -0.398  -0.477  -0.575  -0.158  -0.214  -0.312
68    P         1.953   1.956   2.025   2.085   2.082   2.194   2.136   2.141   2.244
69    S        -0.927  -0.948  -0.925  -0.681  -0.699  -0.693  -0.813  -0.834  -0.788
70    S        -1.527  -1.522  -1.459  -1.591  -1.588  -1.479  -1.141  -1.135  -1.046
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    L        -0.328  -0.323  -0.290  -0.765  -0.795  -0.704  -0.485  -0.479  -0.423
78    G        -0.102  -0.053  -0.190  -0.346  -0.290  -0.468  -0.158  -0.090  -0.278
79    E        -1.527  -1.522  -1.459  -0.984  -0.941  -0.873  -1.141  -1.135  -1.046
80    A        -1.527  -1.522  -1.459  -1.310  -1.294  -1.199  -1.141  -1.135  -1.046
81    A        -1.044  -1.040  -0.976  -1.197  -1.211  -1.086  -0.936  -0.930  -0.840
82    P        -0.295  -0.323  -0.304  -0.124  -0.156  -0.134  -0.424  -0.462  -0.433
83    K        -0.295  -0.257  -0.296  -0.368  -0.315  -0.353  -0.424  -0.371  -0.422
84    Q        -0.328  -0.299  -0.302  -0.300  -0.253  -0.248  -0.485  -0.452  -0.437
85    F        -0.328  -0.323  -0.310  -0.400  -0.396  -0.357  -0.485  -0.477  -0.445
86    I         0.577   0.620   0.593   0.252   0.307   0.270   0.316   0.393   0.316
87    N        -0.422  -0.416  -0.353  -0.270  -0.255  -0.160  -0.594  -0.585  -0.498
88    T        -0.422  -0.416  -0.353  -0.538  -0.504  -0.427  -0.594  -0.585  -0.498
89    L        -0.422  -0.416  -0.353  -0.911  -0.918  -0.800  -0.594  -0.585  -0.498
90    L        -0.422  -0.416  -0.353  -0.709  -0.696  -0.598  -0.594  -0.585  -0.498
91    D         0.577   0.582   0.582   0.538   0.557   0.525   0.316   0.325   0.296
92    I         1.953   1.956   2.025   1.747   1.740   1.856   2.136   2.141   2.244
93    F        -0.927  -0.902  -0.900  -1.052  -1.011  -1.030  -0.813  -0.784  -0.762
94    P         1.953   1.956   2.025   2.085   2.082   2.194   2.136   2.141   2.244
95    Q        -0.102  -0.143  -0.216   0.205   0.147   0.005  -0.158  -0.214  -0.312
96    R         0.871   0.866   0.744   1.187   1.181   1.010   0.826   0.817   0.591
97    R        -0.927  -0.919  -0.911  -0.739  -0.719  -0.689  -0.813  -0.804  -0.773
98    W         1.953   1.956   2.025   2.154   2.150   2.262   2.136   2.141   2.244
99    I        -0.328  -0.323  -0.310  -0.588  -0.590  -0.576  -0.485  -0.477  -0.445
100   I         0.498   0.485   0.542  -0.010  -0.064   0.034   0.170   0.146   0.220
101   T        -0.102  -0.053  -0.190   0.019   0.092  -0.140  -0.158  -0.090  -0.278
102   L        -0.102  -0.053  -0.190  -0.262  -0.202  -0.423  -0.158  -0.090  -0.278
103   E        -0.328  -0.323  -0.310  -0.243  -0.211  -0.189  -0.485  -0.477  -0.445
104   S         0.498   0.517   0.558   0.521   0.566   0.618   0.170   0.204   0.252
105   I        -1.527  -1.522  -1.459  -1.581  -1.582  -1.469  -1.141  -1.135  -1.046
106   M        -0.927  -0.924  -0.898  -1.119  -1.132  -1.055  -0.813  -0.808  -0.760
107   L         0.871   0.826   0.750   0.567   0.472   0.370   0.826   0.750   0.601
108   M         0.871   0.826   0.750   1.112   1.050   0.931   0.826   0.750   0.601
109   G        -0.927  -0.951  -0.933  -0.892  -0.931  -0.928  -0.813  -0.837  -0.796
110   M         0.871   0.826   0.750   1.108   1.048   0.924   0.826   0.750   0.601
111   L        -0.102  -0.143  -0.216  -0.426  -0.523  -0.613  -0.158  -0.214  -0.312
112   C        -0.328  -0.328  -0.302  -0.182  -0.185  -0.153  -0.485  -0.483  -0.436
113   T         0.871   0.866   0.744   0.908   0.908   0.706   0.826   0.817   0.591
114   Y         1.953   1.956   2.025   1.893   1.901   2.002   2.136   2.141   2.244
115   I         0.498   0.488   0.543   0.157   0.123   0.221   0.170   0.150   0.222
116   G        -0.102  -0.143  -0.216   0.113   0.058  -0.065  -0.158  -0.214  -0.312
117   L         0.871   0.876   0.759   0.648   0.633   0.504   0.826   0.833   0.617
118   L        -0.927  -0.927  -0.915  -1.017  -1.041  -0.960  -0.813  -0.812  -0.777
119   M        -0.927  -0.894  -0.925  -1.044  -1.012  -0.999  -0.813  -0.775  -0.789
120   Y         0.871   0.924   0.762   0.878   0.955   0.721   0.826   0.911   0.623
121   N         1.953   1.956   2.025   2.154   2.175   2.262   2.136   2.141   2.244
122   E        -0.328  -0.328  -0.302  -0.520  -0.498  -0.475  -0.485  -0.483  -0.436
123   D         0.498   0.485   0.542   0.348   0.347   0.408   0.170   0.146   0.220
124   T        -0.927  -0.894  -0.925  -0.922  -0.870  -0.915  -0.813  -0.775  -0.789
125   L         0.871   0.826   0.750   0.648   0.566   0.491   0.826   0.750   0.601
126   T         1.953   1.956   2.025   1.955   1.968   2.064   2.136   2.141   2.244
127   P        -0.927  -0.951  -0.933  -0.971  -1.036  -1.022  -0.813  -0.837  -0.796
128   P         1.953   1.956   2.025   2.085   2.082   2.194   2.136   2.141   2.244
129   L         0.871   0.924   0.762   0.567   0.619   0.391   0.826   0.911   0.623
130   D         1.953   1.956   2.025   1.990   1.994   2.099   2.136   2.141   2.244
131   S        -0.102  -0.131  -0.187   0.054   0.021  -0.066  -0.158  -0.198  -0.273
132   L        -0.102  -0.104  -0.186  -0.352  -0.378  -0.470  -0.158  -0.160  -0.272
133   S        -0.102  -0.131  -0.187   0.168   0.138   0.023  -0.158  -0.198  -0.273
134   T        -0.102  -0.143  -0.216  -0.009  -0.061  -0.180  -0.158  -0.214  -0.312
135   V        -0.102  -0.099  -0.185  -0.172  -0.178  -0.297  -0.158  -0.154  -0.270
136   T         0.498   0.485   0.542   0.273   0.248   0.329   0.170   0.146   0.220
137   D         1.953   1.956   2.025   1.990   1.994   2.099   2.136   2.141   2.244
138   A        -0.927  -0.894  -0.925  -0.813  -0.721  -0.807  -0.813  -0.775  -0.789
139   G        -0.927  -0.894  -0.925  -0.414  -0.344  -0.410  -0.813  -0.775  -0.789
140   G        -0.328  -0.329  -0.292  -0.282  -0.274  -0.219  -0.485  -0.486  -0.424
141   Q        -0.927  -0.899  -0.909  -0.567  -0.524  -0.535  -0.813  -0.781  -0.771
142   L        -0.328  -0.348  -0.295  -0.804  -0.861  -0.747  -0.485  -0.506  -0.428
143   V        -1.044  -1.040  -0.976  -1.155  -1.159  -1.044  -0.936  -0.930  -0.840
144   I        -0.328  -0.320  -0.307  -0.441  -0.423  -0.412  -0.485  -0.475  -0.442
145   E        -0.927  -0.927  -0.915  -0.806  -0.753  -0.782  -0.813  -0.812  -0.777
146   D        -0.295  -0.339  -0.304  -0.353  -0.419  -0.384  -0.424  -0.485  -0.433
147   D        -1.044  -1.032  -0.976  -0.852  -0.817  -0.741  -0.936  -0.922  -0.840
148   P        -0.295  -0.331  -0.296  -0.230  -0.298  -0.254  -0.424  -0.474  -0.422
149   D         0.737   0.744   0.682   0.783   0.800   0.690   0.600   0.611   0.480
150   V        -1.044  -1.032  -0.976  -1.053  -1.013  -0.942  -0.936  -0.922  -0.840
151   F        -0.295  -0.339  -0.304  -0.349  -0.428  -0.392  -0.424  -0.485  -0.433
152   V        -1.044  -1.032  -0.976  -1.299  -1.285  -1.188  -0.936  -0.922  -0.840
153   K        -0.295  -0.279  -0.276  -0.077  -0.042  -0.051  -0.424  -0.401  -0.395
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   K        -0.927  -0.894  -0.925  -0.617  -0.535  -0.586  -0.813  -0.775  -0.789
160   W         0.871   0.881   0.754   0.906   0.924   0.749   0.826   0.842   0.608
161   A        -0.927  -0.951  -0.933  -0.971  -1.034  -1.015  -0.813  -0.837  -0.796
162   F        -0.328  -0.323  -0.310  -0.255  -0.244  -0.223  -0.485  -0.477  -0.445
163   K        -0.102  -0.135  -0.186   0.238   0.210   0.106  -0.158  -0.204  -0.271
164   E        -0.102  -0.143  -0.216   0.027   0.002  -0.149  -0.158  -0.214  -0.312
165   T        -0.102  -0.065  -0.175  -0.006   0.063  -0.114  -0.158  -0.107  -0.257
166   S         0.871   0.826   0.750   0.969   0.922   0.783   0.826   0.750   0.601
167   G         1.953   1.956   2.025   2.077   2.092   2.185   2.136   2.141   2.244
168   I         0.498   0.518   0.557   0.185   0.212   0.271   0.170   0.207   0.249
169   Y        -0.927  -0.894  -0.925  -0.742  -0.692  -0.756  -0.813  -0.775  -0.789
170   D         1.953   1.956   2.025   1.990   1.994   2.099   2.136   2.141   2.244
171   L         1.953   1.956   2.025   1.638   1.618   1.747   2.136   2.141   2.244
172   S         0.871   0.881   0.754   1.056   1.069   0.875   0.826   0.842   0.608
173   L        -0.328  -0.328  -0.295  -0.804  -0.836  -0.747  -0.485  -0.484  -0.428
174   M        -0.927  -0.951  -0.933  -0.701  -0.731  -0.717  -0.813  -0.837  -0.796
175   D        -0.102  -0.104  -0.186  -0.112  -0.109  -0.277  -0.158  -0.160  -0.272
176   A         0.871   0.881   0.754   0.908   0.907   0.740   0.826   0.842   0.608
177   C        -0.328  -0.328  -0.302  -0.125  -0.108  -0.079  -0.485  -0.483  -0.436
178   Q        -1.527  -1.522  -1.459  -0.996  -0.958  -0.885  -1.141  -1.135  -1.046
179   L        -0.102  -0.053  -0.190  -0.239  -0.178  -0.427  -0.158  -0.090  -0.278
180   L         1.953   1.956   2.025   1.638   1.618   1.747   2.136   2.141   2.244
181   Y         1.953   1.956   2.025   1.893   1.901   2.002   2.136   2.141   2.244
182   L        -0.328  -0.299  -0.302  -0.501  -0.463  -0.439  -0.485  -0.452  -0.437
183   Y        -0.927  -0.944  -0.907  -0.777  -0.769  -0.739  -0.813  -0.830  -0.769
184   D        -0.328  -0.299  -0.291  -0.330  -0.262  -0.257  -0.485  -0.453  -0.424
185   N        -1.044  -1.040  -0.976  -0.977  -0.945  -0.866  -0.936  -0.930  -0.840
186   D        -1.044  -1.040  -0.976  -0.858  -0.839  -0.747  -0.936  -0.930  -0.840
187   H        -0.422  -0.411  -0.353  -0.278  -0.276  -0.168  -0.594  -0.579  -0.498
188   T         0.577   0.602   0.601   0.468   0.507   0.490   0.316   0.360   0.331
189   S         0.577   0.625   0.608   0.422   0.506   0.457   0.316   0.402   0.345
190   T        -0.422  -0.411  -0.353  -0.400  -0.376  -0.290  -0.594  -0.579  -0.498
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q04082
Output conservation file - output/Q04082
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
