1     M         0.887   0.892   0.958   0.871   0.878   0.986   0.939   0.946   1.036
2     A        -0.864  -0.866  -1.013  -0.712  -0.720  -0.969  -0.910  -0.912  -1.076
3     S         0.887   0.892   0.958   0.964   0.971   1.069   0.939   0.946   1.036
4     V        -0.864  -0.905  -1.018  -0.899  -0.966  -1.148  -0.910  -0.962  -1.082
5     L        -0.320  -0.327  -0.301  -0.448  -0.462  -0.466  -0.571  -0.582  -0.565
6     L         0.887   0.892   0.958   0.803   0.810   0.927   0.939   0.946   1.036
7     P         0.059   0.011  -0.229   0.316   0.256  -0.135   0.033  -0.038  -0.439
8     Q        -0.720  -0.750  -0.995  -0.391  -0.436  -0.825  -0.722  -0.759  -1.053
9     L         0.887   0.892   0.958   0.803   0.810   0.927   0.939   0.946   1.036
10    R        -1.441  -1.497  -1.554  -1.130  -1.219  -1.385  -1.325  -1.383  -1.374
11    T        -0.491  -0.481  -0.319  -0.573  -0.555  -0.317  -0.873  -0.854  -0.596
12    G         0.059   0.007  -0.231   0.213   0.150  -0.203   0.033  -0.043  -0.443
13    W         0.887   0.892   0.958   1.149   1.155   1.232   0.939   0.946   1.036
14    H         0.887   0.892   0.958   1.031   1.038   1.128   0.939   0.946   1.036
15    V         0.887   0.892   0.958   0.769   0.775   0.897   0.939   0.946   1.036
16    D         0.887   0.892   0.958   0.705   0.716   0.841   0.939   0.946   1.036
17    Q         0.887   0.892   0.958   1.074   1.080   1.166   0.939   0.946   1.036
18    A         0.887   0.892   0.958   1.014   1.021   1.113   0.939   0.946   1.036
19    I         0.887   0.892   0.958   0.786   0.798   0.912   0.939   0.946   1.036
20    V        -0.491  -0.471  -0.315  -0.870  -0.835  -0.573  -0.873  -0.837  -0.590
21    T        -0.491  -0.471  -0.315  -0.577  -0.542  -0.312  -0.873  -0.837  -0.590
22    E         0.887   0.892   0.958   0.825   0.833   0.947   0.939   0.946   1.036
23    T        -2.240  -2.177  -1.996  -2.226  -2.138  -1.817  -1.929  -1.870  -1.570
24    K        -1.042  -1.057  -1.035  -1.220  -1.267  -1.223  -1.175  -1.201  -1.105
25    R         0.887   0.892   0.958   0.898   0.906   1.011   0.939   0.946   1.036
26    L         0.059   0.007  -0.231   0.049  -0.022  -0.406   0.033  -0.043  -0.443
27    V         0.887   0.892   0.958   0.769   0.775   0.897   0.939   0.946   1.036
28    V         0.059   0.145  -0.222   0.018   0.127  -0.410   0.033   0.156  -0.428
29    I        -0.320  -0.303  -0.297  -0.553  -0.521  -0.548  -0.571  -0.541  -0.558
30    R         0.887   0.892   0.958   0.898   0.906   1.011   0.939   0.946   1.036
31    F         0.887   0.892   0.958   0.882   0.891   0.996   0.939   0.946   1.036
32    G         0.887   0.892   0.958   0.926   0.936   1.036   0.939   0.946   1.036
33    R         0.059   0.175  -0.218   0.184   0.323  -0.208   0.033   0.198  -0.420
34    K        -1.441  -1.507  -1.553  -1.430  -1.522  -1.575  -1.325  -1.395  -1.373
35    N        -2.240  -2.229  -2.001  -2.025  -2.005  -1.689  -1.929  -1.909  -1.573
36    D        -1.042  -0.939  -1.026  -1.270  -1.131  -1.213  -1.175  -1.053  -1.093
37    R        -2.240  -2.257  -2.002  -2.184  -2.197  -1.835  -1.929  -1.928  -1.574
38    Q        -1.042  -0.988  -1.033  -1.080  -1.009  -1.072  -1.175  -1.117  -1.103
39    C         0.887   0.892   0.958   1.090   1.099   1.180   0.939   0.946   1.036
40    M         0.059   0.051  -0.225   0.120   0.110  -0.333   0.033   0.021  -0.433
41    I        -1.290  -1.279  -1.063  -1.601  -1.582  -1.239  -1.476  -1.457  -1.138
42    M        -0.720  -0.654  -0.987  -0.521  -0.438  -0.874  -0.722  -0.635  -1.043
43    D         0.887   0.892   0.958   0.705   0.716   0.841   0.939   0.946   1.036
44    E         0.059   0.025  -0.224   0.061   0.015  -0.401   0.033  -0.017  -0.432
45    L        -2.240  -2.254  -1.999  -2.288  -2.296  -1.899  -1.929  -1.927  -1.572
46    L         0.887   0.892   0.958   0.803   0.810   0.927   0.939   0.946   1.036
47    S        -1.690  -1.699  -1.574  -1.559  -1.567  -1.372  -1.627  -1.627  -1.395
48    S        -0.720  -0.654  -0.987  -0.462  -0.376  -0.894  -0.722  -0.635  -1.043
49    I        -0.320  -0.359  -0.304  -0.553  -0.624  -0.562  -0.571  -0.638  -0.570
50    A         0.059   0.007  -0.231   0.295   0.228  -0.148   0.033  -0.043  -0.443
51    E         0.887   0.892   0.958   0.825   0.833   0.947   0.939   0.946   1.036
52    R         0.059   0.078  -0.227   0.110   0.136  -0.311   0.033   0.062  -0.435
53    V        -0.320  -0.361  -0.302  -0.563  -0.638  -0.561  -0.571  -0.641  -0.566
54    R        -1.140  -1.132  -1.039  -1.309  -1.292  -1.139  -1.325  -1.307  -1.111
55    N         0.887   0.892   0.958   0.871   0.879   0.986   0.939   0.946   1.036
56    F         0.059   0.051  -0.225   0.145   0.136  -0.289   0.033   0.021  -0.433
57    A         0.059   0.011  -0.229   0.261   0.193  -0.229   0.033  -0.038  -0.439
58    V        -1.140  -1.077  -1.035  -1.220  -1.151  -1.020  -1.325  -1.257  -1.106
59    I        -0.320  -0.361  -0.302  -0.553  -0.627  -0.558  -0.571  -0.641  -0.566
60    Y         0.887   0.892   0.958   0.948   0.957   1.055   0.939   0.946   1.036
61    L         0.059   0.025  -0.224   0.049   0.003  -0.393   0.033  -0.017  -0.432
62    C        -0.320  -0.349  -0.302  -0.262  -0.321  -0.333  -0.571  -0.620  -0.566
63    D         0.059   0.007  -0.231  -0.031  -0.096  -0.441   0.033  -0.043  -0.443
64    I         0.059   0.007  -0.231   0.038  -0.028  -0.405   0.033  -0.043  -0.443
65    D         0.059   0.175  -0.218  -0.036   0.111  -0.430   0.033   0.198  -0.420
66    E        -0.720  -0.800  -0.999  -0.597  -0.705  -0.987  -0.722  -0.823  -1.058
67    V         0.887   0.892   0.958   0.769   0.775   0.897   0.939   0.946   1.036
68    S         0.059   0.078  -0.227   0.322   0.348  -0.119   0.033   0.062  -0.435
69    D         0.059   0.025  -0.224  -0.039  -0.081  -0.449   0.033  -0.017  -0.432
70    F         0.887   0.892   0.958   0.882   0.891   0.996   0.939   0.946   1.036
71    D         0.059   0.078  -0.227   0.107   0.133  -0.368   0.033   0.062  -0.435
72    E        -2.240  -2.212  -2.000  -2.108  -2.064  -1.786  -1.929  -1.894  -1.573
73    M         0.887   0.892   0.958   0.871   0.878   0.986   0.939   0.946   1.036
74    Y         0.887   0.892   0.958   0.948   0.957   1.055   0.939   0.946   1.036
75    E         0.887   0.892   0.958   0.825   0.833   0.947   0.939   0.946   1.036
76    L         0.887   0.892   0.958   0.803   0.810   0.927   0.939   0.946   1.036
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    T        -1.441  -1.507  -1.553  -1.193  -1.296  -1.411  -1.325  -1.395  -1.373
82    D         0.059   0.007  -0.231  -0.039  -0.105  -0.460   0.033  -0.043  -0.443
83    P        -0.720  -0.774  -0.993  -0.414  -0.490  -0.882  -0.722  -0.790  -1.050
84    M        -2.090  -2.096  -1.994  -1.852  -1.879  -1.724  -1.778  -1.779  -1.568
85    T        -0.720  -0.797  -0.994  -0.393  -0.491  -0.793  -0.722  -0.819  -1.051
86    V        -1.140  -1.159  -1.042  -1.439  -1.460  -1.248  -1.325  -1.335  -1.114
87    M         0.887   0.892   0.958   0.871   0.878   0.986   0.939   0.946   1.036
88    F         0.887   0.892   0.958   0.882   0.891   0.996   0.939   0.946   1.036
89    F         0.887   0.892   0.958   0.882   0.891   0.996   0.939   0.946   1.036
90    Y         0.887   0.892   0.958   0.948   0.957   1.055   0.939   0.946   1.036
91    H        -1.441  -1.378  -1.552  -1.176  -1.106  -1.335  -1.325  -1.254  -1.372
92    N         0.887   0.892   0.958   0.871   0.879   0.986   0.939   0.946   1.036
93    K         0.887   0.892   0.958   0.842   0.851   0.962   0.939   0.946   1.036
94    H         0.887   0.892   0.958   1.031   1.038   1.128   0.939   0.946   1.036
95    M         0.059   0.025  -0.224   0.120   0.075  -0.331   0.033  -0.017  -0.432
96    M         0.887   0.892   0.958   0.871   0.878   0.986   0.939   0.946   1.036
97    C         0.059   0.051  -0.225   0.339   0.329  -0.155   0.033   0.021  -0.433
98    D         0.887   0.892   0.958   0.705   0.716   0.841   0.939   0.946   1.036
99    F         0.059   0.051  -0.225   0.134   0.124  -0.317   0.033   0.021  -0.433
100   G         0.887   0.892   0.958   0.926   0.936   1.036   0.939   0.946   1.036
101   T         0.887   0.892   0.958   1.003   1.013   1.104   0.939   0.946   1.036
102   G         0.887   0.892   0.958   0.926   0.936   1.036   0.939   0.946   1.036
103   N         0.059   0.025  -0.224   0.107   0.061  -0.364   0.033  -0.017  -0.432
104   N         0.887   0.892   0.958   0.871   0.879   0.986   0.939   0.946   1.036
105   N         0.887   0.892   0.958   0.871   0.879   0.986   0.939   0.946   1.036
106   K         0.887   0.892   0.958   0.842   0.851   0.962   0.939   0.946   1.036
107   L        -1.042  -1.025  -1.023  -1.178  -1.148  -1.153  -1.175  -1.144  -1.090
108   N         0.887   0.892   0.958   0.871   0.879   0.986   0.939   0.946   1.036
109   F        -0.320  -0.340  -0.298  -0.315  -0.344  -0.275  -0.571  -0.605  -0.559
110   I        -2.240  -2.246  -1.996  -2.278  -2.280  -1.890  -1.929  -1.921  -1.570
111   V        -1.841  -1.842  -1.590  -2.036  -2.022  -1.612  -1.778  -1.766  -1.409
112   D        -1.690  -1.675  -1.580  -1.792  -1.780  -1.547  -1.627  -1.610  -1.400
113   D         0.887   0.892   0.958   0.705   0.716   0.841   0.939   0.946   1.036
114   K         0.887   0.892   0.958   0.842   0.851   0.962   0.939   0.946   1.036
115   Q         0.887   0.892   0.958   1.074   1.080   1.166   0.939   0.946   1.036
116   E         0.887   0.892   0.958   0.825   0.833   0.947   0.939   0.946   1.036
117   M        -0.320  -0.359  -0.304  -0.459  -0.533  -0.481  -0.571  -0.638  -0.570
118   I         0.887   0.892   0.958   0.786   0.798   0.912   0.939   0.946   1.036
119   D         0.887   0.892   0.958   0.705   0.716   0.841   0.939   0.946   1.036
120   I         0.887   0.892   0.958   0.786   0.798   0.912   0.939   0.946   1.036
121   L        -1.042  -1.026  -1.031  -1.206  -1.160  -1.177  -1.175  -1.135  -1.099
122   E         0.887   0.892   0.958   0.825   0.833   0.947   0.939   0.946   1.036
123   T         0.887   0.892   0.958   1.003   1.013   1.104   0.939   0.946   1.036
124   I        -0.320  -0.361  -0.302  -0.553  -0.627  -0.558  -0.571  -0.641  -0.566
125   F        -0.491  -0.485  -0.320  -0.692  -0.682  -0.418  -0.873  -0.862  -0.598
126   R         0.887   0.892   0.958   0.898   0.906   1.011   0.939   0.946   1.036
127   G         0.887   0.892   0.958   0.926   0.936   1.036   0.939   0.946   1.036
128   A         0.887   0.892   0.958   1.014   1.021   1.113   0.939   0.946   1.036
129   R         0.059   0.025  -0.224   0.180   0.138  -0.228   0.033  -0.017  -0.432
130   K         0.887   0.892   0.958   0.842   0.851   0.962   0.939   0.946   1.036
131   N        -0.491  -0.471  -0.315  -0.703  -0.666  -0.427  -0.873  -0.837  -0.590
132   K         0.887   0.892   0.958   0.842   0.851   0.962   0.939   0.946   1.036
133   G         0.887   0.892   0.958   0.926   0.936   1.036   0.939   0.946   1.036
134   L         0.059   0.011  -0.229   0.052  -0.013  -0.394   0.033  -0.038  -0.439
135   V         0.887   0.892   0.958   0.769   0.775   0.897   0.939   0.946   1.036
136   V        -1.042  -1.052  -1.031  -1.229  -1.233  -1.198  -1.175  -1.174  -1.100
137   S         0.887   0.892   0.958   0.981   0.990   1.084   0.939   0.946   1.036
138   P         0.887   0.892   0.958   1.042   1.050   1.137   0.939   0.946   1.036
139   Y        -0.491  -0.471  -0.315  -0.724  -0.690  -0.439  -0.873  -0.837  -0.590
140   D         0.887   0.892   0.958   0.705   0.716   0.841   0.939   0.946   1.036
141   Y         0.887   0.892   0.958   0.948   0.957   1.055   0.939   0.946   1.036
142   N        -0.320  -0.334  -0.294  -0.328  -0.355  -0.341  -0.571  -0.595  -0.552
143   H        -2.240  -2.167  -1.999  -2.004  -1.897  -1.701  -1.929  -1.863  -1.572
144   K        -1.290  -1.251  -1.061  -1.434  -1.373  -1.082  -1.476  -1.421  -1.135
145   R        -1.042  -1.096  -1.038  -0.966  -1.041  -0.936  -1.175  -1.238  -1.108
146   V        -2.240  -2.190  -2.000  -2.195  -2.118  -1.847  -1.929  -1.880  -1.573
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   S        -2.640  -2.629  -2.344  -2.498  -2.492  -2.043  -2.080  -2.061  -1.688
* 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/Q06819
Output conservation file - output/Q06819
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
