1     M         0.869   0.913   0.945   1.139   1.183   1.220   0.912   0.967   1.016
2     A         0.045  -0.083  -0.326   0.143  -0.000  -0.348   0.061  -0.121  -0.521
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    G        -1.343  -1.252  -1.181  -1.352  -1.273  -1.137  -1.464  -1.331  -1.196
15    L        -0.578  -0.560  -0.403  -0.746  -0.704  -0.458  -0.911  -0.889  -0.651
16    K        -2.020  -1.973  -1.749  -2.106  -1.972  -1.642  -1.883  -1.766  -1.486
17    D         0.045  -0.233  -0.336   0.347   0.003  -0.195   0.061  -0.348  -0.538
18    V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
19    V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
20    T         0.045  -0.083  -0.326   0.299   0.111  -0.322   0.061  -0.121  -0.521
21    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
22    E         0.045  -0.233  -0.336   0.095  -0.227  -0.432   0.061  -0.348  -0.538
23    Y         0.869   0.913   0.945   1.166   1.201   1.243   0.912   0.967   1.016
24    T         0.869   0.913   0.945   1.026   1.075   1.124   0.912   0.967   1.016
25    I         0.869   0.913   0.945   1.053   1.101   1.147   0.912   0.967   1.016
26    N        -0.578  -0.560  -0.403  -0.543  -0.547  -0.309  -0.911  -0.889  -0.651
27    L        -0.647  -0.530  -0.402  -0.784  -0.561  -0.398  -1.032  -0.837  -0.649
28    H         0.869   0.913   0.945   1.106   1.156   1.192   0.912   0.967   1.016
29    K         0.869   0.913   0.945   0.595   0.672   0.756   0.912   0.967   1.016
30    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
31    L        -0.740  -0.779  -1.125  -0.580  -0.602  -1.191  -0.668  -0.711  -1.128
32    H        -0.740  -0.912  -1.139  -0.242  -0.507  -0.820  -0.668  -0.895  -1.144
33    G         0.869   0.913   0.945   1.033   1.108   1.130   0.912   0.967   1.016
34    V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
35    S        -2.163  -2.025  -2.163  -1.510  -1.385  -1.575  -1.761  -1.592  -1.638
36    F         0.869   0.913   0.945   1.133   1.201   1.215   0.912   0.967   1.016
37    K         0.869   0.913   0.945   0.595   0.672   0.756   0.912   0.967   1.016
38    K         0.869   0.913   0.945   0.595   0.672   0.756   0.912   0.967   1.016
39    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
40    A         0.869   0.913   0.945   0.829   0.904   0.955   0.912   0.967   1.016
41    P         0.869   0.913   0.945   1.100   1.158   1.187   0.912   0.967   1.016
42    R        -1.262  -1.015  -1.149  -1.685  -1.267  -1.386  -1.397  -1.045  -1.159
43    A         0.869   0.913   0.945   0.829   0.904   0.955   0.912   0.967   1.016
44    V        -0.361  -0.525  -0.405  -0.652  -0.915  -0.647  -0.546  -0.828  -0.655
45    K         0.869   0.913   0.945   0.595   0.672   0.756   0.912   0.967   1.016
46    E         0.869   0.913   0.945   0.794   0.903   0.926   0.912   0.967   1.016
47    I         0.869   0.913   0.945   1.053   1.101   1.147   0.912   0.967   1.016
48    K         0.045  -0.233  -0.336  -0.170  -0.595  -0.789   0.061  -0.348  -0.538
49    K        -0.740  -1.119  -1.158  -0.865  -1.415  -1.483  -0.668  -1.132  -1.168
50    F         0.869   0.913   0.945   1.133   1.201   1.215   0.912   0.967   1.016
51    A         0.869   0.913   0.945   0.829   0.904   0.955   0.912   0.967   1.016
52    K        -1.784  -1.945  -1.743  -1.799  -1.932  -1.562  -1.640  -1.737  -1.481
53    L        -0.361  -0.525  -0.405  -0.541  -0.910  -0.752  -0.546  -0.828  -0.655
54    H         0.045  -0.083  -0.326   0.378   0.191  -0.260   0.061  -0.121  -0.521
55    M         0.869   0.913   0.945   1.139   1.183   1.220   0.912   0.967   1.016
56    G         0.045  -0.233  -0.336   0.354   0.000  -0.190   0.061  -0.348  -0.538
57    T         0.869   0.913   0.945   1.026   1.075   1.124   0.912   0.967   1.016
58    E        -2.399  -2.311  -2.175  -2.293  -2.256  -1.960  -2.004  -1.879  -1.648
59    D         0.045  -0.233  -0.336   0.294  -0.085  -0.357   0.061  -0.348  -0.538
60    V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
61    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
62    L        -0.740  -1.119  -1.158  -0.595  -1.182  -1.288  -0.668  -1.132  -1.168
63    A        -0.361  -0.070  -0.328  -0.301   0.166  -0.325  -0.546  -0.101  -0.523
64    P         0.869   0.913   0.945   1.100   1.158   1.187   0.912   0.967   1.016
65    E        -2.399  -2.398  -2.184  -2.487  -2.344  -2.035  -2.004  -1.928  -1.655
66    L         0.869   0.913   0.945   0.856   0.950   0.979   0.912   0.967   1.016
67    N         0.869   0.913   0.945   1.060   1.120   1.153   0.912   0.967   1.016
68    Q        -1.877  -1.582  -1.722  -1.942  -1.638  -1.768  -1.761  -1.401  -1.462
69    A        -1.784  -1.657  -1.720  -1.846  -1.640  -1.753  -1.640  -1.447  -1.460
70    I        -1.405  -1.360  -1.196  -1.556  -1.657  -1.370  -1.518  -1.442  -1.214
71    W         0.869   0.913   0.945   1.250   1.302   1.315   0.912   0.967   1.016
72    K         0.045  -0.083  -0.326  -0.140  -0.291  -0.674   0.061  -0.121  -0.521
73    R         0.045  -0.083  -0.326   0.047  -0.120  -0.404   0.061  -0.121  -0.521
74    G         0.869   0.913   0.945   1.033   1.108   1.130   0.912   0.967   1.016
75    V        -0.578  -0.542  -0.407  -0.981  -0.934  -0.643  -0.911  -0.858  -0.657
76    K        -1.100  -1.205  -1.160  -1.288  -1.482  -1.337  -1.154  -1.239  -1.171
77    G         0.045  -0.233  -0.336   0.338  -0.026  -0.238   0.061  -0.348  -0.538
78    V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
79    E        -1.498  -1.377  -1.192  -1.676  -1.440  -1.220  -1.640  -1.455  -1.209
80    Y        -2.163  -1.974  -1.751  -1.838  -1.606  -1.305  -2.004  -1.766  -1.487
81    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
82    L        -0.578  -0.433  -0.393  -0.700  -0.465  -0.414  -0.911  -0.672  -0.633
83    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
84    L         0.045  -0.083  -0.326   0.095  -0.067  -0.556   0.061  -0.121  -0.521
85    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
86    I         0.045  -0.233  -0.336   0.329  -0.081  -0.310   0.061  -0.348  -0.538
87    S         0.869   0.913   0.945   1.120   1.173   1.204   0.912   0.967   1.016
88    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
89    K        -0.361  -0.325  -0.390  -0.759  -0.715  -0.825  -0.546  -0.494  -0.628
90    R         0.869   0.913   0.945   0.724   0.773   0.866   0.912   0.967   1.016
91    N         0.045  -0.233  -0.336   0.373   0.001  -0.193   0.061  -0.348  -0.538
92    E        -0.578  -0.316  -0.356  -0.733  -0.226  -0.398  -0.911  -0.480  -0.570
93    E         0.869   0.913   0.945   0.794   0.903   0.926   0.912   0.967   1.016
94    E         0.045  -0.233  -0.336   0.095  -0.227  -0.432   0.061  -0.348  -0.538
95    D        -1.262  -1.244  -1.160  -1.150  -1.072  -0.988  -1.397  -1.304  -1.174
96    A         0.869   0.913   0.945   0.834   0.913   0.960   0.912   0.967   1.016
97    K         0.869   0.913   0.945   0.584   0.650   0.747   0.912   0.967   1.016
98    N        -1.262  -1.287  -1.158  -1.425  -1.468  -1.310  -1.397  -1.343  -1.169
99    P        -1.262  -1.287  -1.158  -1.514  -1.560  -1.325  -1.397  -1.343  -1.169
100   L         0.869   0.913   0.945   0.856   0.950   0.979   0.912   0.967   1.016
101   F        -0.361  -0.525  -0.405  -0.093  -0.394  -0.236  -0.546  -0.828  -0.655
102   S        -1.100  -1.205  -1.160  -0.868  -1.022  -1.032  -1.154  -1.239  -1.171
103   Y         0.045   0.166  -0.313   0.441   0.572  -0.177   0.061   0.227  -0.499
104   V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
105   E        -0.578  -0.560  -0.403  -0.736  -0.651  -0.413  -0.911  -0.889  -0.651
106   P        -0.578  -0.560  -0.403  -0.650  -0.706  -0.464  -0.911  -0.889  -0.651
107   V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
108   L        -3.299  -2.958  -2.840  -2.817  -2.352  -2.262  -2.369  -2.069  -1.848
109   V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
110   A        -1.100  -1.090  -1.154  -1.119  -1.116  -1.253  -1.154  -1.093  -1.165
111   S        -0.361  -0.525  -0.405  -0.139  -0.463  -0.305  -0.546  -0.828  -0.655
112   A        -1.100  -1.110  -1.173  -1.038  -1.088  -1.099  -1.154  -1.206  -1.188
113   K         0.869   0.913   0.945   0.595   0.672   0.756   0.912   0.967   1.016
114   G         0.869   0.913   0.945   1.013   1.068   1.112   0.912   0.967   1.016
115   L         0.045  -0.233  -0.336   0.174  -0.159  -0.335   0.061  -0.348  -0.538
116   Q        -1.498  -1.406  -1.191  -1.436  -1.363  -1.054  -1.640  -1.491  -1.208
117   T         0.869   0.913   0.945   1.026   1.075   1.124   0.912   0.967   1.016
118   V        -0.578  -0.540  -0.406  -0.996  -0.950  -0.662  -0.911  -0.854  -0.656
119   V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
120   V         0.869   0.913   0.945   0.588   0.645   0.750   0.912   0.967   1.016
121   E        -0.361  -0.160  -0.361  -0.462  -0.121  -0.472  -0.546  -0.236  -0.580
122   E        -0.740  -0.514  -1.108  -0.663  -0.327  -1.254  -0.668  -0.377  -1.107
123   D         0.869   0.913   0.945   1.027   1.083   1.125   0.912   0.967   1.016
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   A        -0.226  -0.352  -0.389  -0.288  -0.511  -0.629  -0.333  -0.538  -0.627
* 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/P0C2H9
Output conservation file - output/P0C2H9
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
