1     M         2.346   2.397   2.513   2.588   2.671   2.869   2.743   2.836   3.070
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     F         0.179   0.534   0.268   0.066   0.613   0.202  -0.028   0.510   0.112
6     L        -0.270  -0.051  -0.342  -0.152   0.108  -0.238  -0.226   0.038  -0.319
7     -         1.071   1.105   1.124   0.792   0.854   0.887   0.925   0.966   0.957
8     -        -0.797  -0.724  -0.625  -0.963  -0.864  -0.711  -0.894  -0.803  -0.679
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    R        -0.669  -0.683  -0.555  -0.858  -0.875  -0.687  -0.759  -0.756  -0.600
15    T        -1.716  -1.562  -1.543  -1.704  -1.437  -1.458  -1.298  -1.153  -1.096
16    Q         0.379   0.182   0.189   0.464   0.127   0.095   0.318   0.000  -0.007
17    A        -1.168  -1.116  -1.042  -1.242  -1.159  -1.060  -1.018  -0.953  -0.849
18    R         2.346   2.397   2.513   2.211   2.277   2.489   2.743   2.836   3.070
19    F        -0.998  -0.704  -0.960  -1.023  -0.637  -0.966  -0.820  -0.498  -0.753
20    F         2.346   2.397   2.513   2.389   2.481   2.669   2.743   2.836   3.070
21    H         0.179   0.342   0.304   0.032   0.252   0.219  -0.028   0.247   0.174
22    A         0.798   0.986   1.064   0.283   0.601   0.722   0.368   0.726   0.829
23    T         0.989   0.953   0.992   0.724   0.633   0.640   0.764   0.658   0.675
24    T         0.179   0.136   0.168  -0.016  -0.079  -0.075  -0.028  -0.088  -0.063
25    K        -1.168  -1.048  -1.068  -1.327  -1.167  -1.178  -1.018  -0.882  -0.871
26    K         0.069   0.250   0.161  -0.171   0.069  -0.025  -0.226   0.011  -0.076
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    M        -1.192  -0.911  -1.062  -1.224  -0.844  -1.040  -1.029  -0.724  -0.862
29    D         0.541   0.449   0.319   0.771   0.644   0.440   0.566   0.417   0.202
30    F         0.541   0.348   0.287   0.761   0.503   0.396   0.566   0.261   0.149
31    S         0.179   0.273   0.273  -0.021   0.204   0.171  -0.028   0.143   0.126
32    K         0.989   0.918   0.986   0.859   0.698   0.774   0.764   0.585   0.663
33    M        -0.270  -0.465  -0.474   0.114  -0.217  -0.265  -0.226  -0.483  -0.493
34    S        -0.549  -0.604  -0.549  -0.729  -0.754  -0.669  -0.622  -0.676  -0.594
35    I         0.798   0.836   0.945   0.618   0.658   0.817   0.368   0.409   0.573
36    V        -1.168  -1.165  -1.073  -1.058  -1.029  -0.902  -1.018  -0.989  -0.875
37    G         2.346   2.397   2.513   2.382   2.463   2.662   2.743   2.836   3.070
38    R         0.179   0.128   0.129  -0.023  -0.116  -0.113  -0.028  -0.131  -0.121
39    I        -0.100  -0.073   0.032  -0.240  -0.248  -0.091  -0.424  -0.392  -0.254
40    G         0.541   0.348   0.287   0.711   0.433   0.311   0.566   0.261   0.149
41    S        -0.270  -0.465  -0.474  -0.289  -0.568  -0.578  -0.226  -0.483  -0.493
42    E         0.191   0.004   0.071   0.141  -0.169  -0.094   0.027  -0.277  -0.195
43    F        -0.549  -0.362  -0.468  -0.465  -0.193  -0.293  -0.622  -0.370  -0.487
44    T        -1.168  -1.031  -1.064  -1.230  -1.016  -1.068  -1.018  -0.859  -0.866
45    E        -0.998  -1.135  -1.096  -1.005  -1.279  -1.230  -0.820  -0.958  -0.896
46    H        -0.998  -0.704  -0.960  -0.854  -0.489  -0.787  -0.820  -0.498  -0.753
47    T        -0.549  -0.643  -0.569  -0.648  -0.759  -0.672  -0.622  -0.716  -0.617
48    S         0.798   0.850   0.948   0.283   0.361   0.514   0.368   0.440   0.578
49    A        -0.998  -1.135  -1.096  -0.935  -1.162  -1.131  -0.820  -0.958  -0.896
50    N        -0.998  -1.135  -1.096  -0.892  -1.113  -1.094  -0.820  -0.958  -0.896
51    N         0.179   0.521   0.297   0.167   0.700   0.387  -0.028   0.501   0.163
52    N        -1.168  -1.079  -1.037  -1.125  -1.027  -0.926  -1.018  -0.921  -0.845
53    R        -0.549  -0.565  -0.553  -0.677  -0.688  -0.648  -0.622  -0.634  -0.599
54    Y         0.541   0.449   0.319   0.903   0.804   0.611   0.566   0.417   0.202
55    L        -0.549  -0.619  -0.558  -0.443  -0.498  -0.402  -0.622  -0.692  -0.605
56    K        -0.549  -0.550  -0.507  -0.620  -0.614  -0.582  -0.622  -0.612  -0.550
57    Y         2.346   2.397   2.513   2.496   2.585   2.777   2.743   2.836   3.070
58    S         0.541   0.348   0.287   0.441   0.155   0.055   0.566   0.261   0.149
59    I         0.069   0.168   0.175  -0.024   0.110   0.143  -0.226  -0.058  -0.040
60    A         2.346   2.397   2.513   2.280   2.372   2.559   2.743   2.836   3.070
61    S         0.989   0.993   1.028   0.632   0.602   0.664   0.764   0.739   0.754
62    Q         0.798   0.986   1.064   0.546   0.892   0.984   0.368   0.726   0.829
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    P         0.179   0.090   0.130   0.290   0.129   0.162  -0.028  -0.162  -0.115
69    R         0.179   0.090   0.130  -0.096  -0.265  -0.200  -0.028  -0.162  -0.115
70    R        -0.998  -0.966  -0.995  -0.875  -0.850  -0.921  -0.820  -0.787  -0.792
71    D         0.989   0.993   1.028   0.962   0.952   0.991   0.764   0.739   0.754
72    G        -1.617  -1.601  -1.537  -1.565  -1.582  -1.509  -1.216  -1.183  -1.092
73    Q        -1.617  -1.601  -1.537  -1.460  -1.473  -1.394  -1.216  -1.183  -1.092
74    T         0.989   0.940   0.998   0.899   0.831   0.913   0.764   0.631   0.688
75    N        -0.549  -0.593  -0.557  -0.651  -0.725  -0.688  -0.622  -0.664  -0.604
76    W         1.416   1.313   1.265   1.839   1.709   1.645   1.556   1.363   1.244
77    Y         0.179   0.119   0.159   0.344   0.291   0.324  -0.028  -0.112  -0.073
78    N         0.541   0.398   0.303   0.604   0.392   0.199   0.566   0.337   0.175
79    I         0.798   0.843   0.945   0.605   0.655   0.809   0.368   0.424   0.572
80    T        -0.270  -0.403  -0.471  -0.179  -0.373  -0.517  -0.226  -0.403  -0.489
81    V         0.541   0.420   0.327   0.590   0.381   0.240   0.566   0.372   0.214
82    F         2.346   2.397   2.513   2.389   2.481   2.669   2.743   2.836   3.070
83    N         0.179   0.078   0.128   0.129  -0.023   0.044  -0.028  -0.189  -0.121
84    E        -0.270  -0.275  -0.397  -0.178  -0.208  -0.384  -0.226  -0.248  -0.393
85    P        -1.617  -1.601  -1.537  -1.269  -1.292  -1.213  -1.216  -1.183  -1.092
86    Q        -0.549  -0.623  -0.529  -0.334  -0.420  -0.288  -0.622  -0.690  -0.574
87    I         0.541   0.348   0.287   0.837   0.576   0.448   0.566   0.261   0.149
88    N        -0.998  -1.135  -1.096  -0.950  -1.199  -1.185  -0.820  -0.958  -0.896
89    F         0.179   0.078   0.128   0.124  -0.062   0.010  -0.028  -0.189  -0.121
90    L         0.179   0.286   0.176   0.175   0.290   0.192  -0.028   0.080  -0.048
91    T        -0.998  -1.135  -1.096  -0.892  -1.085  -1.065  -0.820  -0.958  -0.896
92    E        -1.617  -1.590  -1.527  -1.436  -1.401  -1.343  -1.216  -1.176  -1.084
93    Y        -0.270  -0.465  -0.474   0.072  -0.215  -0.268  -0.226  -0.483  -0.493
94    V         0.798   0.986   1.064   0.460   0.794   0.916   0.368   0.726   0.829
95    R         0.069   0.058   0.144  -0.099  -0.077   0.066  -0.226  -0.223  -0.104
96    K         0.541   0.500   0.330   0.771   0.729   0.486   0.566   0.498   0.219
97    G         2.346   2.397   2.513   2.382   2.463   2.662   2.743   2.836   3.070
98    A        -0.549  -0.565  -0.553  -0.638  -0.654  -0.635  -0.622  -0.634  -0.599
99    L        -0.270  -0.442  -0.474  -0.144  -0.423  -0.490  -0.226  -0.455  -0.492
100   V         1.416   1.432   1.287   1.457   1.468   1.295   1.556   1.576   1.288
101   Y         0.541   0.420   0.327   0.910   0.765   0.634   0.566   0.372   0.214
102   V         1.416   1.608   1.324   1.487   1.713   1.403   1.556   1.872   1.360
103   E         1.416   1.398   1.291   1.448   1.441   1.307   1.556   1.516   1.296
104   A         0.541   0.449   0.319   0.717   0.616   0.454   0.566   0.417   0.202
105   D         1.416   1.398   1.291   1.580   1.565   1.419   1.556   1.516   1.296
106   A        -0.270  -0.385  -0.447  -0.107  -0.259  -0.364  -0.226  -0.380  -0.458
107   A        -0.719  -0.672  -0.572  -1.105  -1.056  -0.893  -0.820  -0.747  -0.622
108   N        -0.549  -0.643  -0.569  -0.447  -0.518  -0.421  -0.622  -0.716  -0.617
109   Y         0.179   0.534   0.268   0.085   0.576   0.241  -0.028   0.510   0.112
110   V        -1.617  -1.590  -1.527  -1.635  -1.638  -1.535  -1.216  -1.176  -1.084
111   F        -0.998  -1.135  -1.096  -0.620  -0.802  -0.732  -0.820  -0.958  -0.896
112   E         0.179   0.074   0.128   0.001  -0.175  -0.093  -0.028  -0.189  -0.121
113   R         0.069   0.086   0.157  -0.141  -0.054   0.059  -0.226  -0.168  -0.069
114   D        -0.998  -0.844  -0.969  -0.759  -0.561  -0.699  -0.820  -0.661  -0.763
115   D        -0.100  -0.077   0.035  -0.302  -0.289  -0.142  -0.424  -0.398  -0.251
116   G         0.541   0.398   0.303   0.708   0.502   0.335   0.566   0.337   0.175
117   S        -1.617  -1.587  -1.526  -1.603  -1.535  -1.442  -1.216  -1.173  -1.083
118   K        -0.998  -1.030  -1.037  -0.812  -0.889  -0.912  -0.820  -0.856  -0.836
119   G        -0.998  -1.135  -1.096  -0.802  -1.047  -0.999  -0.820  -0.958  -0.896
120   T        -0.549  -0.594  -0.528  -0.502  -0.533  -0.437  -0.622  -0.662  -0.573
121   T        -0.549  -0.630  -0.525  -0.747  -0.849  -0.731  -0.622  -0.698  -0.570
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   L        -0.998  -1.135  -1.096  -0.759  -0.943  -0.889  -0.820  -0.958  -0.896
124   S         1.416   1.339   1.274   1.277   1.174   1.099   1.556   1.410   1.264
125   L         1.416   1.339   1.274   1.507   1.424   1.350   1.556   1.410   1.264
126   V        -0.998  -1.135  -1.096  -0.856  -1.100  -1.020  -0.820  -0.958  -0.896
127   Q         1.416   1.313   1.265   1.637   1.534   1.481   1.556   1.363   1.244
128   K        -1.168  -1.165  -1.073  -1.161  -1.168  -1.025  -1.018  -0.989  -0.875
129   D        -0.549  -0.608  -0.551  -0.611  -0.753  -0.668  -0.622  -0.680  -0.596
130   I        -0.549  -0.575  -0.512  -0.385  -0.399  -0.332  -0.622  -0.636  -0.554
131   N         0.069   0.103   0.152  -0.065   0.045   0.104  -0.226  -0.145  -0.077
132   L         0.069   0.144   0.174  -0.109   0.027   0.109  -0.226  -0.090  -0.043
133   L         0.541   0.500   0.330   0.646   0.591   0.326   0.566   0.498   0.219
134   K        -0.549  -0.535  -0.466  -0.697  -0.671  -0.573  -0.622  -0.576  -0.488
135   N        -0.549  -0.593  -0.557  -0.512  -0.541  -0.505  -0.622  -0.664  -0.604
136   G        -0.549  -0.446  -0.444  -0.400  -0.212  -0.228  -0.622  -0.463  -0.456
137   K         0.541   0.348   0.287   0.740   0.475   0.364   0.566   0.261   0.149
138   K        -0.549  -0.566  -0.489  -0.582  -0.552  -0.481  -0.622  -0.613  -0.517
139   L        -1.617  -1.432  -1.497  -1.409  -1.150  -1.233  -1.216  -1.046  -1.058
140   E         0.541   0.348   0.287   0.662   0.412   0.321   0.566   0.261   0.149
141   D        -1.168  -1.048  -1.068  -1.170  -0.991  -1.018  -1.018  -0.882  -0.871
142   A        -0.270  -0.051  -0.342  -0.102   0.177  -0.192  -0.226   0.038  -0.319
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   E         1.324   1.225   1.196   1.346   1.222   1.208   1.396   1.199   1.105
150   G        -0.471  -0.495  -0.521  -0.377  -0.427  -0.481  -0.490  -0.536  -0.553
151   Q         0.820   0.959   1.039   0.521   0.750   0.868   0.415   0.671   0.777
152   E        -0.797  -0.725  -0.625  -1.132  -1.015  -0.881  -0.894  -0.804  -0.679
153   N        -0.797  -0.725  -0.625  -1.040  -0.927  -0.788  -0.894  -0.804  -0.679
154   A         1.071   1.147   1.155   0.884   1.006   0.997   0.925   1.048   1.022
155   A        -0.797  -0.725  -0.625  -0.689  -0.581  -0.435  -0.894  -0.804  -0.679
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   S        -0.674  -0.622  -0.554  -0.939  -0.855  -0.757  -0.749  -0.682  -0.595
160   S        -0.100  -0.059   0.035  -0.492  -0.427  -0.276  -0.424  -0.372  -0.250
161   E        -0.998  -0.901  -0.978  -0.941  -0.779  -0.938  -0.820  -0.725  -0.773
* 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/P32445
Output conservation file - output/P32445
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
