1     M         1.469   1.477   1.561   1.739   1.752   1.881   1.596   1.607   1.743
2     H        -0.299  -0.297  -0.323  -0.220  -0.216  -0.240  -0.458  -0.459  -0.483
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    Q        -1.398  -1.352  -1.301  -1.369  -1.301  -1.231  -1.192  -1.146  -1.045
40    Q        -1.259  -1.155  -1.252  -1.141  -1.001  -1.159  -1.045  -0.938  -0.998
41    H        -0.893  -0.888  -0.879  -0.783  -0.785  -0.709  -0.898  -0.896  -0.843
42    S        -1.259  -1.194  -1.254  -1.180  -1.094  -1.212  -1.045  -0.976  -1.000
43    K        -1.418  -1.340  -1.302  -1.383  -1.269  -1.214  -1.200  -1.120  -1.044
44    S        -0.289  -0.239  -0.305  -0.302  -0.211  -0.343  -0.417  -0.349  -0.448
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    E        -0.893  -0.885  -0.886  -0.941  -0.939  -0.937  -0.898  -0.893  -0.850
53    N        -1.398  -1.420  -1.316  -1.344  -1.370  -1.221  -1.192  -1.199  -1.057
54    K        -1.764  -1.780  -1.658  -1.673  -1.707  -1.528  -1.339  -1.341  -1.186
55    P        -0.527  -0.514  -0.413  -0.621  -0.589  -0.453  -0.752  -0.734  -0.599
56    Q        -0.527  -0.464  -0.386  -0.720  -0.627  -0.512  -0.752  -0.667  -0.564
57    Q        -0.893  -0.937  -0.895  -0.920  -0.999  -0.960  -0.898  -0.937  -0.858
58    Q         0.206   0.246   0.341   0.029   0.094   0.247  -0.165  -0.093   0.038
59    R        -0.299  -0.281  -0.344  -0.323  -0.293  -0.427  -0.458  -0.434  -0.510
60    K        -0.004   0.059  -0.214   0.093   0.165  -0.199  -0.018   0.064  -0.319
61    K         0.206   0.246   0.341  -0.018   0.046   0.199  -0.165  -0.093   0.038
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    F        -0.829  -0.863  -0.868  -0.602  -0.687  -0.755  -0.801  -0.840  -0.825
64    E         0.710   0.803   0.534   0.713   0.829   0.456   0.716   0.855   0.397
65    G        -0.665  -0.744  -0.830  -0.489  -0.598  -0.700  -0.605  -0.701  -0.784
66    P         1.469   1.477   1.561   1.629   1.644   1.775   1.596   1.607   1.743
67    K         0.710   0.685   0.516   0.735   0.703   0.448   0.716   0.674   0.364
68    R         0.710   0.685   0.516   0.797   0.775   0.492   0.716   0.674   0.364
69    E         1.469   1.477   1.561   1.415   1.420   1.568   1.596   1.607   1.743
70    A        -0.299  -0.378  -0.342  -0.117  -0.237  -0.206  -0.458  -0.559  -0.509
71    I         1.469   1.477   1.561   1.510   1.527   1.659   1.596   1.607   1.743
72    L        -0.004   0.014  -0.236  -0.082  -0.053  -0.435  -0.018   0.006  -0.350
73    D         0.710   0.711   0.514   0.807   0.826   0.526   0.716   0.715   0.362
74    L         1.469   1.477   1.561   1.312   1.327   1.468   1.596   1.607   1.743
75    A        -1.031  -0.987  -0.909  -0.972  -0.897  -0.795  -1.045  -0.994  -0.873
76    K        -0.893  -0.853  -0.863  -0.981  -0.935  -0.921  -0.898  -0.865  -0.827
77    Y         0.710   0.613   0.497   1.103   0.977   0.804   0.716   0.558   0.331
78    K        -0.004  -0.117  -0.258   0.032  -0.148  -0.382  -0.018  -0.177  -0.382
79    D         0.710   0.613   0.497   0.807   0.692   0.497   0.716   0.558   0.331
80    S        -1.031  -1.010  -0.913  -1.122  -1.098  -0.931  -1.045  -1.017  -0.877
81    K        -0.893  -0.853  -0.863  -1.027  -0.985  -0.983  -0.898  -0.865  -0.827
82    I         0.206   0.208   0.313  -0.049  -0.047   0.112  -0.165  -0.168  -0.018
83    R        -0.665  -0.744  -0.830  -0.526  -0.647  -0.805  -0.605  -0.701  -0.784
84    V         0.710   0.685   0.516   0.817   0.795   0.563   0.716   0.674   0.364
85    K         0.710   0.685   0.516   0.752   0.720   0.483   0.716   0.674   0.364
86    L        -0.299  -0.358  -0.342  -0.227  -0.320  -0.360  -0.458  -0.528  -0.506
87    M        -0.527  -0.528  -0.413  -0.565  -0.562  -0.383  -0.752  -0.753  -0.598
88    G         1.469   1.477   1.561   1.462   1.472   1.613   1.596   1.607   1.743
89    G         1.469   1.477   1.561   1.449   1.458   1.601   1.596   1.607   1.743
90    K         0.710   0.721   0.516   0.797   0.824   0.493   0.716   0.730   0.365
91    L        -1.398  -1.367  -1.305  -1.609  -1.585  -1.469  -1.192  -1.160  -1.048
92    V         0.362   0.307   0.344   0.244   0.145   0.173   0.129   0.021   0.043
93    I        -0.893  -0.860  -0.852  -0.890  -0.843  -0.850  -0.898  -0.858  -0.815
94    G         1.469   1.477   1.561   1.449   1.458   1.601   1.596   1.607   1.743
95    V        -0.299  -0.333  -0.324  -0.352  -0.380  -0.393  -0.458  -0.489  -0.484
96    L         1.469   1.477   1.561   1.312   1.327   1.468   1.596   1.607   1.743
97    K         1.469   1.477   1.561   1.436   1.447   1.588   1.596   1.607   1.743
98    G         1.469   1.477   1.561   1.449   1.458   1.601   1.596   1.607   1.743
99    Y        -0.389  -0.431  -0.366  -0.110  -0.147  -0.037  -0.605  -0.642  -0.542
100   D         1.469   1.477   1.561   1.497   1.523   1.646   1.596   1.607   1.743
101   Q         0.710   0.711   0.514   0.807   0.799   0.496   0.716   0.715   0.362
102   L         1.469   1.477   1.561   1.312   1.327   1.468   1.596   1.607   1.743
103   M         1.469   1.477   1.561   1.739   1.752   1.881   1.596   1.607   1.743
104   N         1.469   1.477   1.561   1.577   1.602   1.724   1.596   1.607   1.743
105   L         1.469   1.477   1.561   1.312   1.327   1.468   1.596   1.607   1.743
106   V         0.710   0.613   0.497   0.783   0.655   0.460   0.716   0.558   0.331
107   L         1.469   1.477   1.561   1.312   1.327   1.468   1.596   1.607   1.743
108   D         0.206   0.260   0.336  -0.102   0.016   0.113  -0.165  -0.068   0.027
109   D        -0.299  -0.209  -0.311  -0.403  -0.270  -0.427  -0.458  -0.349  -0.465
110   T         0.206   0.222   0.317   0.008   0.040   0.186  -0.165  -0.141  -0.010
111   V        -1.031  -0.969  -0.908  -1.257  -1.186  -1.051  -1.045  -0.985  -0.873
112   E         1.469   1.477   1.561   1.415   1.420   1.568   1.596   1.607   1.743
113   Y        -0.893  -0.845  -0.852  -0.697  -0.634  -0.639  -0.898  -0.847  -0.813
114   M        -0.893  -0.887  -0.864  -0.981  -0.966  -0.872  -0.898  -0.889  -0.827
115   S        -0.665  -0.718  -0.830  -0.478  -0.538  -0.727  -0.605  -0.670  -0.784
116   N        -0.893  -0.932  -0.879  -0.907  -0.963  -0.880  -0.898  -0.935  -0.843
117   P        -0.004  -0.074  -0.255   0.219   0.114  -0.216  -0.018  -0.119  -0.378
118   D        -0.004   0.022  -0.246   0.020   0.052  -0.365  -0.018   0.018  -0.365
119   D         0.362   0.327   0.347   0.221   0.156   0.138   0.129   0.059   0.049
120   E        -1.398  -1.411  -1.313  -1.448  -1.464  -1.305  -1.192  -1.191  -1.055
121   N        -1.398  -1.383  -1.288  -1.446  -1.434  -1.285  -1.192  -1.169  -1.035
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   E        -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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   L        -1.845  -1.802  -1.666  -1.779  -1.724  -1.519  -1.400  -1.357  -1.192
130   I        -1.259  -1.297  -1.299  -1.233  -1.296  -1.239  -1.045  -1.080  -1.041
131   S        -1.259  -1.297  -1.299  -1.096  -1.186  -1.225  -1.045  -1.080  -1.041
132   K        -0.893  -0.888  -0.879  -1.004  -1.015  -0.997  -0.898  -0.896  -0.843
133   N        -1.259  -1.257  -1.277  -1.153  -1.149  -1.174  -1.045  -1.038  -1.022
134   A        -0.893  -0.955  -0.882  -0.752  -0.846  -0.752  -0.898  -0.956  -0.846
135   R         0.710   0.711   0.514   0.797   0.811   0.490   0.716   0.715   0.362
136   K        -0.893  -0.883  -0.860  -1.035  -1.017  -0.984  -0.898  -0.871  -0.819
137   L         0.206   0.214   0.316  -0.197  -0.180  -0.011  -0.165  -0.155  -0.011
138   G         1.469   1.477   1.561   1.449   1.458   1.601   1.596   1.607   1.743
139   L         0.710   0.803   0.534   0.655   0.771   0.449   0.716   0.855   0.397
140   T        -0.299  -0.358  -0.342  -0.294  -0.360  -0.331  -0.458  -0.528  -0.506
141   V         1.469   1.477   1.561   1.483   1.503   1.633   1.596   1.607   1.743
142   I         0.206   0.246   0.341  -0.049   0.035   0.175  -0.165  -0.093   0.038
143   R         1.469   1.477   1.561   1.510   1.535   1.659   1.596   1.607   1.743
144   G         0.710   0.812   0.527   0.807   0.924   0.595   0.716   0.868   0.385
145   T         0.362   0.356   0.360   0.409   0.399   0.374   0.129   0.112   0.074
146   I        -1.398  -1.420  -1.316  -1.236  -1.255  -1.094  -1.192  -1.199  -1.057
147   L         1.469   1.477   1.561   1.312   1.327   1.468   1.596   1.607   1.743
148   V        -0.299  -0.285  -0.337  -0.560  -0.541  -0.610  -0.458  -0.445  -0.503
149   S        -0.299  -0.236  -0.300  -0.288  -0.175  -0.320  -0.458  -0.355  -0.445
150   L         0.206   0.222   0.317  -0.155  -0.126   0.009  -0.165  -0.141  -0.010
151   S        -0.665  -0.761  -0.824  -0.277  -0.400  -0.461  -0.605  -0.720  -0.777
152   S         0.362   0.370   0.371   0.413   0.426   0.391   0.129   0.138   0.095
153   A        -0.893  -0.847  -0.850  -0.996  -0.909  -0.865  -0.898  -0.831  -0.808
154   E         0.362   0.370   0.371   0.221   0.240   0.189   0.129   0.138   0.095
155   G         1.469   1.477   1.561   1.449   1.458   1.601   1.596   1.607   1.743
156   S        -0.004  -0.094  -0.251   0.230   0.095  -0.151  -0.018  -0.147  -0.372
157   D         0.710   0.721   0.516   0.713   0.723   0.425   0.716   0.730   0.365
158   V        -0.893  -0.951  -0.886  -1.000  -1.099  -1.014  -0.898  -0.951  -0.849
159   L        -0.299  -0.358  -0.342  -0.460  -0.547  -0.562  -0.458  -0.528  -0.506
160   -        -0.454  -0.507  -0.405  -0.661  -0.761  -0.604  -0.651  -0.725  -0.588
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -         0.429   0.337   0.363   0.316   0.156   0.153   0.248   0.077   0.079
163   -         1.469   1.477   1.561   1.565   1.581   1.712   1.596   1.607   1.743
164   Y        -0.402  -0.449  -0.384  -0.204  -0.286  -0.212  -0.601  -0.655  -0.562
165   M        -1.418  -1.414  -1.308  -1.204  -1.201  -1.035  -1.200  -1.192  -1.049
166   -        -0.289  -0.264  -0.325  -0.386  -0.368  -0.483  -0.417  -0.389  -0.476
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   Q        -1.398  -1.379  -1.304  -1.312  -1.260  -1.140  -1.192  -1.163  -1.047
169   K        -1.764  -1.736  -1.644  -1.733  -1.705  -1.551  -1.339  -1.310  -1.176
* 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/P53905
Output conservation file - output/P53905
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
