1     M         1.301   1.330   1.404   1.535   1.580   1.685   1.413   1.453   1.572
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     N        -0.762  -0.767  -0.636  -1.079  -1.086  -0.868  -0.952  -0.944  -0.759
4     S        -0.557  -0.568  -0.599  -0.588  -0.617  -0.712  -0.657  -0.665  -0.708
5     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    E        -0.762  -0.677  -0.631  -1.091  -0.945  -0.890  -0.952  -0.837  -0.753
21    E        -0.395  -0.493  -0.571  -0.349  -0.489  -0.640  -0.435  -0.564  -0.671
22    P         1.301   1.330   1.404   1.442   1.485   1.598   1.413   1.453   1.572
23    L         1.301   1.330   1.404   1.180   1.214   1.350   1.413   1.453   1.572
24    T         0.420   0.474   0.236   0.369   0.439   0.086   0.386   0.469   0.047
25    S         0.420   0.474   0.236   0.489   0.571   0.167   0.386   0.469   0.047
26    N        -0.677  -0.638  -0.612  -0.894  -0.832  -0.755  -0.846  -0.781  -0.730
27    A        -0.677  -0.732  -0.617  -0.708  -0.810  -0.657  -0.846  -0.896  -0.736
28    R         1.301   1.330   1.404   1.417   1.464   1.574   1.413   1.453   1.572
29    P         1.301   1.330   1.404   1.442   1.485   1.598   1.413   1.453   1.572
30    L        -0.677  -0.740  -0.629  -0.855  -0.962  -0.776  -0.846  -0.907  -0.750
31    K         0.499   0.623   0.282   0.436   0.586   0.105   0.508   0.690   0.130
32    N        -1.196  -1.299  -1.163  -1.218  -1.304  -1.087  -1.151  -1.234  -1.047
33    S        -0.663  -0.610  -0.593  -0.686  -0.599  -0.564  -0.850  -0.770  -0.708
34    V        -1.343  -1.297  -1.170  -1.568  -1.522  -1.310  -1.302  -1.239  -1.055
35    I        -0.034  -0.028   0.105  -0.369  -0.397  -0.165  -0.397  -0.393  -0.193
36    T         1.301   1.330   1.404   1.174   1.202   1.345   1.413   1.453   1.572
37    I         0.131   0.217   0.157   0.024   0.170   0.030  -0.095   0.049  -0.096
38    R         1.301   1.330   1.404   1.414   1.461   1.571   1.413   1.453   1.572
39    V         0.131   0.179   0.154   0.024   0.106   0.023  -0.095  -0.016  -0.102
40    I         0.131   0.143   0.139   0.018   0.029  -0.008  -0.095  -0.080  -0.129
41    K         0.499   0.316   0.256   0.486   0.250   0.158   0.508   0.217   0.083
42    S         0.499   0.316   0.256   0.615   0.364   0.220   0.508   0.217   0.083
43    F         0.499   0.482   0.270   0.702   0.685   0.320   0.508   0.481   0.107
44    P        -0.256  -0.452  -0.539   0.042  -0.243  -0.413  -0.246  -0.510  -0.627
45    Y         1.301   1.330   1.404   1.419   1.462   1.576   1.413   1.453   1.572
46    R         1.301   1.330   1.404   1.414   1.461   1.571   1.413   1.453   1.572
47    N        -0.256  -0.452  -0.539  -0.247  -0.536  -0.692  -0.246  -0.510  -0.627
48    V        -0.256  -0.452  -0.539  -0.150  -0.454  -0.626  -0.246  -0.510  -0.627
49    K         1.301   1.330   1.404   1.186   1.233   1.356   1.413   1.453   1.572
50    N         1.301   1.330   1.404   1.192   1.248   1.361   1.413   1.453   1.572
51    I        -1.730  -1.714  -1.585  -1.557  -1.530  -1.358  -1.453  -1.421  -1.231
52    V        -0.034   0.012   0.110  -0.288  -0.205  -0.065  -0.397  -0.317  -0.184
53    L        -0.568  -0.476  -0.577  -0.551  -0.389  -0.605  -0.699  -0.561  -0.684
54    H        -1.584  -1.520  -1.557  -1.201  -1.096  -1.225  -1.302  -1.221  -1.206
55    D         0.131   0.143   0.139  -0.023  -0.001  -0.031  -0.095  -0.080  -0.129
56    Y        -0.663  -0.604  -0.595  -0.727  -0.647  -0.616  -0.850  -0.759  -0.709
57    D         0.499   0.543   0.277   0.489   0.557   0.146   0.508   0.573   0.121
58    L         1.301   1.330   1.404   1.174   1.207   1.345   1.413   1.453   1.572
59    A        -1.196  -1.163  -1.135  -1.212  -1.195  -1.088  -1.151  -1.113  -1.021
60    D        -1.730  -1.622  -1.586  -1.884  -1.713  -1.653  -1.453  -1.336  -1.232
61    K        -0.034   0.052   0.132  -0.460  -0.310  -0.182  -0.397  -0.244  -0.143
62    T         1.301   1.330   1.404   1.174   1.202   1.345   1.413   1.453   1.572
63    A        -0.568  -0.681  -0.595  -0.450  -0.624  -0.508  -0.699  -0.822  -0.707
64    K        -1.584  -1.630  -1.565  -1.497  -1.592  -1.461  -1.302  -1.338  -1.213
65    D        -0.034  -0.028   0.105  -0.195  -0.173   0.048  -0.397  -0.393  -0.194
66    L         0.499   0.316   0.256   0.480   0.232   0.159   0.508   0.217   0.083
67    F        -1.584  -1.569  -1.548  -1.517  -1.549  -1.460  -1.302  -1.281  -1.198
68    N        -1.196  -1.087  -1.126  -1.300  -1.168  -1.197  -1.151  -1.046  -1.013
69    D        -1.584  -1.671  -1.585  -1.459  -1.588  -1.458  -1.302  -1.373  -1.230
70    V        -1.343  -1.250  -1.176  -1.328  -1.233  -1.093  -1.302  -1.197  -1.060
71    L        -2.117  -2.114  -1.945  -1.796  -1.837  -1.609  -1.604  -1.581  -1.365
72    N        -1.196  -1.028  -1.125  -1.298  -1.023  -1.185  -1.151  -0.954  -1.009
73    K        -1.343  -1.322  -1.173  -1.449  -1.385  -1.178  -1.302  -1.259  -1.057
74    I         0.499   0.482   0.270   0.571   0.549   0.230   0.508   0.481   0.107
75    Q        -1.196  -1.126  -1.136  -1.091  -0.984  -1.037  -1.151  -1.062  -1.020
76    N         0.499   0.623   0.282   0.437   0.588   0.107   0.508   0.690   0.130
77    E        -1.196  -1.267  -1.142  -1.391  -1.501  -1.315  -1.151  -1.197  -1.024
78    G         0.499   0.316   0.256   0.812   0.570   0.455   0.508   0.217   0.083
79    S        -0.809  -0.768  -0.650  -0.799  -0.732  -0.559  -1.001  -0.937  -0.775
80    F        -0.034  -0.028   0.105  -0.241  -0.267  -0.055  -0.397  -0.392  -0.194
81    R         0.499   0.316   0.256   0.676   0.413   0.273   0.508   0.217   0.083
82    P        -0.256  -0.452  -0.539   0.046  -0.243  -0.407  -0.246  -0.510  -0.627
83    F        -0.663  -0.646  -0.599  -0.565  -0.524  -0.431  -0.850  -0.804  -0.714
84    R         1.301   1.330   1.404   1.414   1.461   1.571   1.413   1.453   1.572
85    N         0.131   0.040   0.128  -0.125  -0.308  -0.184  -0.095  -0.266  -0.151
86    V         0.499   0.316   0.256   0.561   0.296   0.168   0.508   0.217   0.083
87    K        -2.117  -2.124  -1.948  -2.083  -2.038  -1.828  -1.604  -1.587  -1.366
88    F        -0.809  -0.800  -0.651  -0.900  -0.884  -0.678  -1.001  -0.980  -0.777
89    D         0.131   0.147   0.143  -0.085  -0.057  -0.114  -0.095  -0.072  -0.123
90    T        -0.568  -0.516  -0.575  -0.672  -0.614  -0.656  -0.699  -0.623  -0.682
91    L        -0.256  -0.147  -0.488  -0.203  -0.069  -0.507  -0.246  -0.094  -0.557
92    K         1.301   1.330   1.404   1.186   1.233   1.356   1.413   1.453   1.572
93    I         0.499   0.626   0.286   0.571   0.732   0.257   0.508   0.695   0.136
94    Y         1.301   1.330   1.404   1.419   1.462   1.576   1.413   1.453   1.572
95    T         0.499   0.316   0.256   0.455   0.188   0.103   0.508   0.217   0.083
96    H        -0.034   0.052   0.132  -0.238  -0.112   0.021  -0.397  -0.244  -0.143
97    A         1.301   1.330   1.404   1.414   1.442   1.571   1.413   1.453   1.572
98    H         0.499   0.316   0.256   0.836   0.594   0.495   0.508   0.217   0.083
99    G         0.499   0.316   0.256   0.825   0.585   0.485   0.508   0.217   0.083
100   S         0.499   0.316   0.256   0.669   0.447   0.345   0.508   0.217   0.083
101   K         1.301   1.330   1.404   1.186   1.233   1.356   1.413   1.453   1.572
102   T         0.131   0.179   0.154  -0.073  -0.007  -0.049  -0.095  -0.016  -0.102
103   V        -0.663  -0.747  -0.608  -0.580  -0.648  -0.443  -0.850  -0.919  -0.725
104   N         0.499   0.543   0.277   0.513   0.585   0.243   0.508   0.573   0.121
105   L         1.301   1.330   1.404   1.174   1.207   1.345   1.413   1.453   1.572
106   V         0.131   0.040   0.128   0.072  -0.090   0.043  -0.095  -0.266  -0.151
107   I         1.301   1.330   1.404   1.290   1.327   1.454   1.413   1.453   1.572
108   N         1.301   1.330   1.404   1.192   1.248   1.361   1.413   1.453   1.572
109   F        -0.034  -0.028   0.105  -0.241  -0.276  -0.060  -0.397  -0.393  -0.193
110   D         1.301   1.330   1.404   1.227   1.272   1.394   1.413   1.453   1.572
111   H         0.131   0.147   0.143   0.195   0.219   0.127  -0.095  -0.072  -0.123
112   D         0.499   0.482   0.270   0.534   0.523   0.231   0.508   0.481   0.107
113   D        -0.015   0.007   0.110  -0.379  -0.343  -0.180  -0.361  -0.328  -0.184
114   D        -0.256  -0.210  -0.500  -0.225  -0.152  -0.620  -0.246  -0.181  -0.573
115   W         1.301   1.330   1.404   1.551   1.595   1.701   1.413   1.453   1.572
116   T        -1.196  -1.220  -1.139  -1.117  -1.159  -1.044  -1.151  -1.163  -1.024
117   L         0.499   0.593   0.282   0.496   0.606   0.235   0.508   0.648   0.130
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   D         0.420   0.434   0.233   0.375   0.409   0.095   0.386   0.407   0.043
122   I        -1.299  -1.329  -1.168  -1.404  -1.426  -1.190  -1.256  -1.264  -1.052
123   E        -0.955  -0.760  -1.066  -0.938  -0.637  -1.129  -0.850  -0.610  -0.940
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   N        -1.196  -1.031  -1.123  -1.172  -0.938  -1.065  -1.151  -0.965  -1.007
129   D        -0.955  -0.961  -1.089  -0.839  -0.832  -1.037  -0.850  -0.862  -0.966
130   K        -1.129  -1.148  -1.118  -1.065  -1.095  -1.021  -1.051  -1.067  -0.998
131   K        -0.256  -0.117  -0.482  -0.166   0.016  -0.444  -0.246  -0.055  -0.549
132   K        -0.809  -0.807  -0.655  -1.131  -1.144  -0.891  -1.001  -0.989  -0.782
133   L         1.301   1.330   1.404   1.174   1.207   1.345   1.413   1.453   1.572
134   F        -2.505  -2.441  -2.245  -1.992  -1.934  -1.646  -1.755  -1.687  -1.456
135   E        -0.256  -0.393  -0.519  -0.191  -0.406  -0.640  -0.246  -0.437  -0.600
136   Y        -0.568  -0.681  -0.595  -0.496  -0.629  -0.528  -0.699  -0.822  -0.707
137   G        -0.256  -0.193  -0.509   0.061   0.156  -0.383  -0.246  -0.154  -0.586
138   I        -0.034   0.030   0.120  -0.290  -0.178  -0.047  -0.397  -0.285  -0.166
139   E        -0.256  -0.147  -0.488  -0.151   0.014  -0.507  -0.246  -0.094  -0.557
140   N         1.301   1.330   1.404   1.192   1.248   1.361   1.413   1.453   1.572
141   E         1.301   1.330   1.404   1.273   1.326   1.438   1.413   1.453   1.572
142   T         1.301   1.330   1.404   1.174   1.202   1.345   1.413   1.453   1.572
143   E         1.301   1.330   1.404   1.273   1.326   1.438   1.413   1.453   1.572
144   I        -0.034  -0.028   0.105  -0.369  -0.396  -0.165  -0.397  -0.393  -0.194
145   S         1.301   1.330   1.404   1.352   1.408   1.513   1.413   1.453   1.572
146   L        -1.584  -1.649  -1.569  -1.348  -1.424  -1.264  -1.302  -1.353  -1.217
147   F         1.301   1.330   1.404   1.442   1.489   1.597   1.413   1.453   1.572
148   N         0.499   0.316   0.256   0.468   0.227   0.107   0.508   0.217   0.083
149   K        -1.730  -1.577  -1.582  -1.530  -1.370  -1.319  -1.453  -1.304  -1.230
150   E        -1.196  -1.179  -1.158  -1.178  -1.145  -1.115  -1.151  -1.128  -1.043
151   D        -0.256  -0.358  -0.517  -0.180  -0.325  -0.561  -0.246  -0.393  -0.597
152   Y         1.301   1.330   1.404   1.419   1.462   1.576   1.413   1.453   1.572
153   L        -1.584  -1.632  -1.568  -1.450  -1.556  -1.467  -1.302  -1.339  -1.216
154   R        -1.196  -1.074  -1.125  -1.088  -0.928  -0.982  -1.151  -1.017  -1.010
155   F        -0.034  -0.024   0.106  -0.094  -0.082   0.111  -0.397  -0.384  -0.192
156   K        -0.256  -0.452  -0.539  -0.166  -0.423  -0.522  -0.246  -0.510  -0.627
157   E        -1.196  -1.158  -1.138  -1.099  -1.038  -1.017  -1.151  -1.085  -1.023
158   N         1.301   1.330   1.404   1.192   1.248   1.361   1.413   1.453   1.572
159   P         1.301   1.330   1.404   1.453   1.503   1.608   1.413   1.453   1.572
160   E         0.131   0.063   0.129   0.001  -0.116  -0.043  -0.095  -0.224  -0.149
161   E         0.131   0.040   0.128   0.092  -0.049   0.091  -0.095  -0.266  -0.151
162   K         1.301   1.330   1.404   1.186   1.233   1.356   1.413   1.453   1.572
163   W         1.301   1.330   1.404   1.551   1.595   1.701   1.413   1.453   1.572
164   -        -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/P36154
Output conservation file - output/P36154
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
