1     M         1.177   1.230   1.271   1.363   1.442   1.473   1.251   1.321   1.382
2     A         0.023  -0.034   0.034  -0.473  -0.556  -0.388  -0.226  -0.334  -0.256
3     R         1.177   1.230   1.271   1.228   1.307   1.350   1.251   1.321   1.382
4     S        -1.287  -1.332  -1.192  -1.312  -1.320  -1.139  -1.260  -1.253  -1.071
5     R         1.177   1.230   1.271   1.228   1.307   1.350   1.251   1.321   1.382
6     G        -0.905  -0.840  -0.691  -0.949  -0.906  -0.675  -1.112  -0.999  -0.808
7     S        -1.049  -1.137  -1.163  -0.946  -1.241  -1.210  -0.964  -1.049  -1.041
8     S         0.023   0.176   0.094  -0.519  -0.302  -0.389  -0.226   0.030  -0.148
9     R        -0.656  -0.739  -0.668  -0.599  -0.770  -0.776  -0.775  -0.875  -0.778
10    P         1.177   1.230   1.271   1.145   1.201   1.275   1.251   1.321   1.382
11    I        -1.669  -1.600  -1.576  -1.593  -1.538  -1.327  -1.407  -1.311  -1.227
12    S        -1.834  -1.751  -1.609  -1.772  -1.622  -1.487  -1.563  -1.435  -1.254
13    R         1.177   1.230   1.271   1.228   1.307   1.350   1.251   1.321   1.382
14    S        -1.287  -1.127  -1.170  -1.582  -1.490  -1.492  -1.260  -1.074  -1.052
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    R        -0.160  -0.070   0.039  -0.605  -0.528  -0.337  -0.558  -0.400  -0.247
20    P         1.177   1.230   1.271   1.124   1.184   1.256   1.251   1.321   1.382
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    Q         1.177   1.230   1.271   0.782   0.868   0.946   1.251   1.321   1.382
23    T        -0.761  -0.840  -0.664  -0.870  -1.099  -0.808  -0.964  -1.000  -0.776
24    R         1.177   1.230   1.271   1.228   1.307   1.350   1.251   1.321   1.382
25    S         1.177   1.230   1.271   1.041   1.087   1.181   1.251   1.321   1.382
26    A         1.177   1.230   1.271   0.648   0.727   0.824   1.251   1.321   1.382
27    S         0.023   0.150   0.097   0.007   0.152   0.115  -0.226  -0.013  -0.142
28    T         1.177   1.230   1.271   1.224   1.304   1.346   1.251   1.321   1.382
29    M        -0.667  -0.460  -0.622  -0.868  -0.633  -0.698  -0.817  -0.526  -0.721
30    A         0.386   0.476   0.175  -0.018   0.100  -0.268   0.365   0.499  -0.005
31    A        -0.359  -0.229  -0.565  -0.518  -0.355  -0.640  -0.374  -0.184  -0.643
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    P         1.177   1.230   1.271   1.128   1.185   1.259   1.251   1.321   1.382
35    V        -1.220  -1.224  -1.176  -1.454  -1.410  -1.307  -1.161  -1.143  -1.055
36    H        -1.393  -1.334  -1.199  -1.287  -1.165  -1.142  -1.354  -1.251  -1.078
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    P        -0.761  -0.659  -0.652  -1.034  -0.955  -0.813  -0.964  -0.798  -0.761
39    Q        -1.049  -0.796  -1.110  -0.864  -0.499  -1.065  -0.964  -0.640  -0.986
40    Q        -1.813  -1.659  -1.585  -1.544  -1.281  -1.175  -1.555  -1.353  -1.235
41    Q        -0.667  -0.769  -0.657  -0.724  -0.806  -0.645  -0.817  -0.903  -0.767
42    Q        -1.287  -1.332  -1.192  -1.583  -1.750  -1.488  -1.260  -1.253  -1.071
43    Q        -1.287  -1.038  -1.149  -1.396  -0.986  -1.194  -1.260  -0.946  -1.030
44    P        -0.359  -0.502  -0.611  -0.107  -0.370  -0.462  -0.374  -0.573  -0.703
45    N        -1.287  -1.264  -1.178  -1.400  -1.359  -1.189  -1.260  -1.189  -1.058
46    A        -0.359  -0.502  -0.611  -0.584  -0.733  -0.803  -0.374  -0.573  -0.703
47    Y        -1.393  -1.346  -1.208  -1.217  -1.218  -1.082  -1.354  -1.263  -1.086
48    S        -1.393  -1.346  -1.208  -1.378  -1.386  -1.134  -1.354  -1.263  -1.086
49    H        -0.667  -0.477  -0.608  -0.933  -0.708  -0.806  -0.817  -0.527  -0.702
50    P        -1.049  -0.830  -1.108  -0.724  -0.442  -0.842  -0.964  -0.677  -0.983
51    P         1.177   1.230   1.271   1.145   1.201   1.275   1.251   1.321   1.382
52    A        -1.669  -1.582  -1.583  -1.271  -1.181  -1.320  -1.407  -1.294  -1.232
53    A        -0.905  -0.831  -0.691  -1.384  -1.151  -1.013  -1.112  -0.990  -0.808
54    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    A        -0.667  -0.622  -0.657  -1.182  -1.130  -1.091  -0.817  -0.773  -0.769
57    Q        -1.049  -1.158  -1.161  -1.206  -1.342  -1.470  -0.964  -1.071  -1.039
58    T        -1.669  -1.614  -1.584  -1.415  -1.392  -1.395  -1.407  -1.322  -1.233
59    R        -0.667  -0.605  -0.652  -0.880  -0.804  -0.810  -0.817  -0.750  -0.763
60    Q        -0.359  -0.528  -0.615  -0.457  -0.669  -0.809  -0.374  -0.603  -0.709
61    P         1.177   1.230   1.271   1.145   1.201   1.275   1.251   1.321   1.382
62    G         1.177   1.230   1.271   1.108   1.178   1.241   1.251   1.321   1.382
63    M        -0.761  -0.844  -0.666  -0.385  -0.450  -0.255  -0.964  -1.005  -0.780
64    F         1.177   1.230   1.271   1.372   1.439   1.481   1.251   1.321   1.382
65    A        -0.141  -0.096   0.028  -0.712  -0.605  -0.387  -0.521  -0.448  -0.267
66    Q         0.386   0.144   0.132   0.242   0.026  -0.016   0.365  -0.024  -0.080
67    M         0.386   0.144   0.132   0.753   0.467   0.403   0.365  -0.024  -0.080
68    A         0.386   0.144   0.132   0.040  -0.223  -0.185   0.365  -0.024  -0.080
69    S         1.177   1.230   1.271   1.041   1.087   1.181   1.251   1.321   1.382
70    T         1.177   1.230   1.271   1.224   1.304   1.346   1.251   1.321   1.382
71    A         1.177   1.230   1.271   0.648   0.727   0.824   1.251   1.321   1.382
72    A         1.177   1.230   1.271   0.648   0.727   0.824   1.251   1.321   1.382
73    G         1.177   1.230   1.271   1.108   1.178   1.241   1.251   1.321   1.382
74    V         1.177   1.230   1.271   1.345   1.416   1.457   1.251   1.321   1.382
75    A         0.386   0.144   0.132  -0.006  -0.315  -0.300   0.365  -0.024  -0.080
76    V         0.386   0.144   0.132   0.743   0.452   0.406   0.365  -0.024  -0.080
77    G         1.177   1.230   1.271   1.108   1.178   1.241   1.251   1.321   1.382
78    S         1.177   1.230   1.271   1.041   1.087   1.181   1.251   1.321   1.382
79    T         0.386   0.144   0.132   0.504   0.114   0.010   0.365  -0.024  -0.080
80    I         1.177   1.230   1.271   1.394   1.462   1.501   1.251   1.321   1.382
81    G         1.177   1.230   1.271   1.108   1.178   1.241   1.251   1.321   1.382
82    H         1.177   1.230   1.271   1.390   1.470   1.497   1.251   1.321   1.382
83    T         1.177   1.230   1.271   1.224   1.304   1.346   1.251   1.321   1.382
84    L         0.386   0.144   0.132   0.739   0.451   0.391   0.365  -0.024  -0.080
85    G         1.177   1.230   1.271   1.108   1.178   1.241   1.251   1.321   1.382
86    A         0.386   0.144   0.132  -0.018  -0.350  -0.332   0.365  -0.024  -0.080
87    G         0.386   0.144   0.132   0.500   0.212   0.194   0.365  -0.024  -0.080
88    I         1.177   1.230   1.271   1.394   1.462   1.501   1.251   1.321   1.382
89    T         1.177   1.230   1.271   1.224   1.304   1.346   1.251   1.321   1.382
90    G         0.386   0.476   0.175   0.448   0.558   0.139   0.365   0.499  -0.005
91    M        -0.359  -0.479  -0.612   0.120  -0.082  -0.273  -0.374  -0.547  -0.705
92    F         1.177   1.230   1.271   1.372   1.439   1.481   1.251   1.321   1.382
93    S        -0.141  -0.051   0.041  -0.378  -0.272  -0.113  -0.521  -0.366  -0.243
94    G         1.177   1.230   1.271   1.108   1.178   1.241   1.251   1.321   1.382
95    S         0.386   0.454   0.174   0.393   0.455   0.105   0.365   0.466  -0.007
96    G        -0.141  -0.096   0.028  -0.378  -0.342  -0.130  -0.521  -0.448  -0.268
97    S         1.177   1.230   1.271   1.041   1.087   1.181   1.251   1.321   1.382
98    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    S        -0.497  -0.592  -0.631  -0.482  -0.608  -0.736  -0.558  -0.684  -0.730
100   A         0.386   0.508   0.178   0.047   0.197  -0.120   0.365   0.545   0.001
101   P         0.386   0.508   0.178   0.537   0.667   0.289   0.365   0.545   0.001
102   V        -0.761  -0.630  -0.643  -0.964  -0.870  -0.824  -0.964  -0.773  -0.751
103   E         0.023  -0.041   0.033   0.311   0.206   0.271  -0.226  -0.347  -0.257
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   Q        -1.049  -1.102  -1.164  -1.071  -1.064  -1.225  -0.964  -1.015  -1.042
106   Q        -1.049  -1.102  -1.164  -0.996  -1.073  -1.095  -0.964  -1.015  -1.042
107   Q        -0.359  -0.546  -0.618  -0.485  -0.648  -0.874  -0.374  -0.624  -0.712
108   Q        -0.359  -0.546  -0.618  -0.531  -0.746  -0.977  -0.374  -0.624  -0.712
109   N        -0.667  -0.487  -0.626  -0.795  -0.528  -0.672  -0.817  -0.563  -0.727
110   M        -1.813  -1.755  -1.601  -1.311  -1.288  -1.116  -1.555  -1.444  -1.247
111   A        -1.049  -1.079  -1.154  -1.297  -1.377  -1.399  -0.964  -0.992  -1.032
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   N        -1.287  -1.311  -1.184  -1.525  -1.571  -1.367  -1.260  -1.233  -1.064
128   T        -1.287  -1.143  -1.169  -1.406  -1.190  -1.105  -1.260  -1.087  -1.051
129   S        -2.577  -2.405  -2.221  -1.758  -1.534  -1.357  -1.850  -1.657  -1.448
130   G        -0.761  -0.599  -0.642  -1.375  -1.131  -1.138  -0.964  -0.741  -0.750
131   Q        -0.667  -0.748  -0.651  -1.129  -1.178  -1.134  -0.817  -0.876  -0.759
132   T        -2.577  -2.405  -2.221  -2.166  -1.950  -1.727  -1.850  -1.657  -1.448
133   Q        -0.359  -0.460  -0.607  -0.513  -0.708  -0.918  -0.374  -0.526  -0.699
134   T        -1.813  -1.745  -1.596  -1.426  -1.263  -1.088  -1.555  -1.437  -1.244
135   D        -0.829  -0.784  -0.684  -0.984  -0.933  -0.754  -1.011  -0.937  -0.798
136   Q        -0.359  -0.460  -0.607  -0.330  -0.391  -0.540  -0.374  -0.526  -0.699
137   Q        -0.141  -0.096   0.028  -0.361  -0.209  -0.060  -0.521  -0.448  -0.267
138   L        -0.359  -0.469  -0.608  -0.484  -0.692  -0.855  -0.374  -0.536  -0.699
139   G        -1.669  -1.641  -1.590  -1.578  -1.441  -1.304  -1.407  -1.345  -1.238
140   R        -1.669  -1.620  -1.583  -1.066  -1.008  -0.974  -1.407  -1.327  -1.232
141   T        -0.905  -0.831  -0.692  -0.918  -0.943  -0.741  -1.112  -0.990  -0.810
142   C         1.177   1.230   1.271   1.377   1.450   1.485   1.251   1.321   1.382
143   E        -0.667  -0.772  -0.657  -0.198  -0.301  -0.193  -0.817  -0.908  -0.767
144   I        -1.049  -1.033  -1.150  -1.117  -1.147  -1.098  -0.964  -0.946  -1.027
145   D         1.177   1.230   1.271   1.377   1.455   1.485   1.251   1.321   1.382
146   A         1.177   1.230   1.271   0.648   0.727   0.824   1.251   1.321   1.382
147   R         0.023  -0.041   0.033   0.200   0.117   0.209  -0.226  -0.347  -0.257
148   N        -0.359  -0.546  -0.618   0.033  -0.209  -0.452  -0.374  -0.624  -0.712
149   F         1.177   1.230   1.271   1.372   1.439   1.481   1.251   1.321   1.382
150   T         0.386   0.144   0.132   0.504   0.114   0.010   0.365  -0.024  -0.080
151   R        -0.359  -0.546  -0.618   0.059  -0.158  -0.239  -0.374  -0.624  -0.712
152   C         1.177   1.230   1.271   1.377   1.450   1.485   1.251   1.321   1.382
153   L         0.386   0.144   0.132   0.747   0.466   0.410   0.365  -0.024  -0.080
154   D        -0.761  -0.844  -0.669  -0.363  -0.437  -0.242  -0.964  -1.005  -0.783
155   E         0.023   0.198   0.092   0.311   0.551   0.364  -0.226   0.067  -0.151
156   N         0.386   0.144   0.132   0.751   0.466   0.412   0.365  -0.024  -0.080
157   N        -0.774  -0.704  -0.673  -0.579  -0.459  -0.499  -0.960  -0.832  -0.787
158   G         1.177   1.230   1.271   1.121   1.200   1.254   1.251   1.321   1.382
159   N         0.386   0.144   0.132   0.748   0.458   0.406   0.365  -0.024  -0.080
160   F        -0.141  -0.096   0.028   0.046   0.104   0.251  -0.521  -0.448  -0.268
161   Q         0.386   0.144   0.132   0.185  -0.096  -0.158   0.365  -0.024  -0.080
162   I        -0.359  -0.528  -0.615   0.079  -0.215  -0.402  -0.374  -0.603  -0.709
163   C         1.177   1.230   1.271   1.377   1.450   1.485   1.251   1.321   1.382
164   D        -0.359  -0.528  -0.615   0.126  -0.154  -0.282  -0.374  -0.603  -0.709
165   Y         0.386   0.454   0.174   0.794   0.891   0.531   0.365   0.466  -0.007
166   Y         1.177   1.230   1.271   1.381   1.462   1.489   1.251   1.321   1.382
167   L         1.177   1.230   1.271   1.350   1.431   1.461   1.251   1.321   1.382
168   Q         0.386   0.144   0.132   0.246   0.032  -0.006   0.365  -0.024  -0.080
169   Q         0.386   0.454   0.174   0.118   0.271  -0.245   0.365   0.466  -0.007
170   L         1.177   1.230   1.271   1.350   1.431   1.461   1.251   1.321   1.382
171   K         1.177   1.230   1.271   1.443   1.506   1.545   1.251   1.321   1.382
172   A         1.177   1.230   1.271   0.648   0.727   0.824   1.251   1.321   1.382
173   C         1.177   1.230   1.271   1.377   1.450   1.485   1.251   1.321   1.382
174   Q         1.177   1.230   1.271   0.847   0.978   1.004   1.251   1.321   1.382
175   E        -0.359  -0.546  -0.618  -0.043  -0.412  -0.650  -0.374  -0.624  -0.712
176   A         0.386   0.144   0.132   0.044  -0.212  -0.177   0.365  -0.024  -0.080
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   A         0.023  -0.034   0.034  -0.519  -0.627  -0.460  -0.226  -0.334  -0.256
179   R        -0.359  -0.546  -0.618  -0.023  -0.257  -0.405  -0.374  -0.624  -0.712
180   Q        -0.359  -0.258  -0.564  -0.449  -0.267  -0.719  -0.374  -0.222  -0.640
181   Y         0.386   0.144   0.132   0.692   0.345   0.223   0.365  -0.024  -0.080
* 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/Q03667
Output conservation file - output/Q03667
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
