1     M         0.867   0.912   0.945   1.137   1.181   1.221   0.911   0.967   1.015
2     A         0.046  -0.082  -0.326   0.144   0.001  -0.349   0.062  -0.120  -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        -1.337  -1.249  -1.181  -1.348  -1.271  -1.138  -1.460  -1.330  -1.196
15    L        -0.575  -0.557  -0.403  -0.743  -0.701  -0.458  -0.908  -0.887  -0.651
16    K        -2.012  -1.967  -1.749  -2.098  -1.967  -1.643  -1.878  -1.763  -1.486
17    D         0.046  -0.231  -0.336   0.341  -0.000  -0.200   0.062  -0.346  -0.538
18    V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
19    V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
20    T         0.046  -0.082  -0.326   0.299   0.111  -0.322   0.062  -0.120  -0.521
21    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
22    E         0.046  -0.231  -0.336   0.101  -0.222  -0.430   0.062  -0.346  -0.538
23    Y         0.867   0.912   0.945   1.163   1.200   1.243   0.911   0.967   1.015
24    T         0.867   0.912   0.945   1.025   1.074   1.124   0.911   0.967   1.015
25    I         0.867   0.912   0.945   1.051   1.100   1.147   0.911   0.967   1.015
26    N        -0.575  -0.557  -0.403  -0.540  -0.545  -0.309  -0.908  -0.887  -0.651
27    L        -0.644  -0.528  -0.403  -0.781  -0.561  -0.399  -1.029  -0.836  -0.650
28    H         0.867   0.912   0.945   1.104   1.155   1.192   0.911   0.967   1.015
29    K         0.867   0.912   0.945   0.594   0.672   0.756   0.911   0.967   1.015
30    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
31    L        -0.736  -0.778  -1.125  -0.577  -0.603  -1.191  -0.665  -0.712  -1.128
32    H        -0.736  -0.910  -1.138  -0.240  -0.508  -0.821  -0.665  -0.896  -1.144
33    G         0.867   0.912   0.945   1.031   1.107   1.130   0.911   0.967   1.015
34    V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
35    S        -2.155  -2.021  -2.162  -1.505  -1.384  -1.575  -1.756  -1.591  -1.638
36    F         0.867   0.912   0.945   1.131   1.199   1.215   0.911   0.967   1.015
37    K         0.867   0.912   0.945   0.594   0.672   0.756   0.911   0.967   1.015
38    K         0.867   0.912   0.945   0.594   0.672   0.756   0.911   0.967   1.015
39    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
40    A         0.867   0.912   0.945   0.827   0.903   0.956   0.911   0.967   1.015
41    P         0.867   0.912   0.945   1.098   1.156   1.187   0.911   0.967   1.015
42    R        -1.257  -1.010  -1.147  -1.679  -1.261  -1.384  -1.393  -1.040  -1.157
43    A         0.867   0.912   0.945   0.827   0.903   0.956   0.911   0.967   1.015
44    V        -0.359  -0.523  -0.405  -0.649  -0.913  -0.647  -0.544  -0.826  -0.655
45    K         0.867   0.912   0.945   0.594   0.672   0.756   0.911   0.967   1.015
46    E         0.867   0.912   0.945   0.800   0.906   0.932   0.911   0.967   1.015
47    I         0.867   0.912   0.945   1.051   1.100   1.147   0.911   0.967   1.015
48    K         0.046  -0.231  -0.336  -0.169  -0.593  -0.789   0.062  -0.346  -0.538
49    K        -0.736  -1.115  -1.158  -0.860  -1.410  -1.481  -0.665  -1.130  -1.168
50    F         0.867   0.912   0.945   1.131   1.199   1.215   0.911   0.967   1.015
51    A         0.867   0.912   0.945   0.827   0.903   0.956   0.911   0.967   1.015
52    K        -1.777  -1.940  -1.743  -1.793  -1.928  -1.562  -1.635  -1.734  -1.481
53    L        -0.359  -0.523  -0.405  -0.538  -0.908  -0.752  -0.544  -0.826  -0.655
54    H         0.046  -0.082  -0.326   0.378   0.191  -0.261   0.062  -0.120  -0.521
55    M         0.867   0.912   0.945   1.137   1.181   1.221   0.911   0.967   1.015
56    G         0.046  -0.231  -0.336   0.354   0.001  -0.190   0.062  -0.346  -0.538
57    T         0.867   0.912   0.945   1.025   1.074   1.124   0.911   0.967   1.015
58    D        -2.532  -2.415  -2.180  -2.440  -2.342  -1.960  -2.120  -1.945  -1.652
59    D         0.046  -0.231  -0.336   0.288  -0.087  -0.360   0.062  -0.346  -0.538
60    V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
61    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
62    L        -0.736  -1.115  -1.158  -0.592  -1.179  -1.288  -0.665  -1.130  -1.168
63    A        -0.359  -0.072  -0.330  -0.305   0.157  -0.335  -0.544  -0.105  -0.527
64    P         0.867   0.912   0.945   1.098   1.156   1.187   0.911   0.967   1.015
65    E        -2.390  -2.393  -2.184  -2.475  -2.340  -2.033  -1.999  -1.927  -1.655
66    L         0.867   0.912   0.945   0.855   0.949   0.979   0.911   0.967   1.015
67    N         0.867   0.912   0.945   1.058   1.118   1.153   0.911   0.967   1.015
68    Q        -1.870  -1.576  -1.722  -1.935  -1.633  -1.768  -1.756  -1.397  -1.461
69    A        -1.777  -1.653  -1.720  -1.833  -1.634  -1.749  -1.635  -1.446  -1.460
70    I        -1.399  -1.357  -1.196  -1.550  -1.654  -1.370  -1.514  -1.440  -1.214
71    W         0.867   0.912   0.945   1.248   1.300   1.315   0.911   0.967   1.015
72    K         0.046  -0.082  -0.326  -0.137  -0.289  -0.671   0.062  -0.120  -0.521
73    R         0.046  -0.082  -0.326   0.048  -0.119  -0.404   0.062  -0.120  -0.521
74    G         0.867   0.912   0.945   1.031   1.107   1.130   0.911   0.967   1.015
75    V        -0.575  -0.539  -0.407  -0.977  -0.931  -0.644  -0.908  -0.855  -0.657
76    K        -1.095  -1.201  -1.159  -1.283  -1.479  -1.337  -1.150  -1.236  -1.170
77    G         0.046  -0.231  -0.336   0.338  -0.025  -0.239   0.062  -0.346  -0.538
78    V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
79    E        -1.492  -1.373  -1.192  -1.665  -1.436  -1.217  -1.635  -1.453  -1.209
80    Y        -2.155  -1.967  -1.750  -1.831  -1.601  -1.305  -1.999  -1.763  -1.487
81    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
82    L        -0.575  -0.432  -0.393  -0.697  -0.465  -0.414  -0.908  -0.671  -0.633
83    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
84    L         0.046  -0.082  -0.326   0.095  -0.066  -0.556   0.062  -0.120  -0.521
85    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
86    I         0.046  -0.231  -0.336   0.329  -0.080  -0.311   0.062  -0.346  -0.538
87    S         0.867   0.912   0.945   1.117   1.172   1.204   0.911   0.967   1.015
88    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
89    K        -0.359  -0.320  -0.389  -0.755  -0.707  -0.824  -0.544  -0.487  -0.627
90    R         0.867   0.912   0.945   0.723   0.773   0.866   0.911   0.967   1.015
91    N         0.046  -0.231  -0.336   0.373   0.001  -0.193   0.062  -0.346  -0.538
92    E        -0.575  -0.313  -0.355  -0.732  -0.226  -0.400  -0.908  -0.477  -0.570
93    E         0.867   0.912   0.945   0.800   0.906   0.932   0.911   0.967   1.015
94    E         0.046  -0.231  -0.336   0.101  -0.222  -0.430   0.062  -0.346  -0.538
95    D        -1.257  -1.241  -1.161  -1.151  -1.075  -0.994  -1.393  -1.303  -1.175
96    A         0.867   0.912   0.945   0.833   0.912   0.960   0.911   0.967   1.015
97    K         0.867   0.912   0.945   0.584   0.649   0.747   0.911   0.967   1.015
98    N        -1.257  -1.282  -1.158  -1.414  -1.459  -1.306  -1.393  -1.340  -1.169
99    P        -1.257  -1.282  -1.158  -1.508  -1.556  -1.326  -1.393  -1.340  -1.169
100   L         0.867   0.912   0.945   0.855   0.949   0.979   0.911   0.967   1.015
101   F        -0.359  -0.523  -0.405  -0.092  -0.393  -0.237  -0.544  -0.826  -0.655
102   S        -1.095  -1.201  -1.159  -0.864  -1.019  -1.033  -1.150  -1.236  -1.170
103   Y         0.046   0.167  -0.313   0.441   0.572  -0.177   0.062   0.227  -0.499
104   V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
105   E        -0.575  -0.557  -0.403  -0.726  -0.646  -0.410  -0.908  -0.887  -0.651
106   P        -0.575  -0.557  -0.403  -0.647  -0.704  -0.465  -0.908  -0.887  -0.651
107   V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
108   L        -3.288  -2.948  -2.839  -2.811  -2.347  -2.265  -2.363  -2.065  -1.848
109   V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
110   A        -1.095  -1.087  -1.154  -1.115  -1.115  -1.253  -1.150  -1.093  -1.165
111   S        -0.359  -0.523  -0.405  -0.138  -0.461  -0.305  -0.544  -0.826  -0.655
112   A        -1.095  -1.106  -1.173  -1.034  -1.085  -1.099  -1.150  -1.204  -1.188
113   K         0.867   0.912   0.945   0.594   0.672   0.756   0.911   0.967   1.015
114   G         0.867   0.912   0.945   1.011   1.067   1.112   0.911   0.967   1.015
115   L         0.046  -0.231  -0.336   0.174  -0.158  -0.335   0.062  -0.346  -0.538
116   Q        -1.492  -1.403  -1.192  -1.428  -1.359  -1.051  -1.635  -1.490  -1.208
117   T         0.867   0.912   0.945   1.025   1.074   1.124   0.911   0.967   1.015
118   V        -0.575  -0.538  -0.406  -0.992  -0.948  -0.662  -0.908  -0.854  -0.656
119   V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
120   V         0.867   0.912   0.945   0.587   0.644   0.750   0.911   0.967   1.015
121   E        -0.359  -0.154  -0.360  -0.455  -0.110  -0.468  -0.544  -0.227  -0.578
122   E        -0.736  -0.514  -1.108  -0.654  -0.325  -1.252  -0.665  -0.379  -1.107
123   D         0.867   0.912   0.945   1.016   1.076   1.117   0.911   0.967   1.015
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   A        -0.224  -0.353  -0.389  -0.284  -0.512  -0.624  -0.331  -0.542  -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/P0C2H8
Output conservation file - output/P0C2H8
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
