1     M         1.151   1.170   1.221   1.355   1.373   1.446   1.228   1.255   1.335
2     A         0.397   0.370   0.150   0.549   0.520   0.207   0.388   0.345  -0.032
3     R        -1.333  -1.227  -1.188  -1.267  -1.093  -1.035  -1.292  -1.178  -1.084
4     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    S        -1.196  -1.179  -1.155  -0.840  -0.823  -0.758  -1.152  -1.128  -1.053
15    N         0.118   0.052   0.034   0.342   0.219   0.111  -0.058  -0.178  -0.240
16    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    V        -2.141  -2.059  -1.913  -2.305  -2.169  -1.991  -1.630  -1.549  -1.369
19    E        -0.694  -0.703  -0.647  -0.536  -0.526  -0.443  -0.872  -0.857  -0.765
20    K        -0.969  -1.001  -1.138  -0.869  -0.914  -1.035  -0.872  -0.914  -1.032
21    L        -0.605  -0.607  -0.637  -0.782  -0.798  -0.913  -0.732  -0.722  -0.750
22    V        -1.697  -1.698  -1.569  -1.501  -1.481  -1.270  -1.432  -1.409  -1.242
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    E        -1.196  -1.253  -1.164  -0.856  -0.921  -0.787  -1.152  -1.191  -1.062
25    A        -1.196  -1.125  -1.148  -1.278  -1.205  -1.206  -1.152  -1.054  -1.043
26    P         1.151   1.170   1.221   1.265   1.286   1.361   1.228   1.255   1.335
27    V        -1.697  -1.672  -1.568  -1.640  -1.634  -1.440  -1.432  -1.394  -1.241
28    E         0.397   0.297   0.133   0.590   0.480   0.246   0.388   0.232  -0.062
29    F         1.151   1.170   1.221   1.225   1.240   1.323   1.228   1.255   1.335
30    V        -1.560  -1.649  -1.575  -1.528  -1.655  -1.551  -1.292  -1.363  -1.246
31    R        -0.312  -0.244  -0.566  -0.289  -0.201  -0.574  -0.312  -0.225  -0.651
32    E         0.052   0.043   0.039   0.119   0.103   0.078  -0.172  -0.194  -0.231
33    G         1.151   1.170   1.221   1.132   1.158   1.236   1.228   1.255   1.335
34    T        -1.196  -1.164  -1.147  -0.793  -0.794  -0.780  -1.152  -1.106  -1.044
35    Q        -0.605  -0.674  -0.644  -0.347  -0.443  -0.417  -0.732  -0.807  -0.759
36    F         1.151   1.170   1.221   1.225   1.240   1.323   1.228   1.255   1.335
37    L        -0.605  -0.620  -0.657  -0.782  -0.885  -0.960  -0.732  -0.769  -0.776
38    A        -1.560  -1.358  -1.529  -1.312  -1.079  -1.213  -1.292  -1.085  -1.206
39    K         0.397   0.297   0.133   0.297   0.192  -0.020   0.388   0.232  -0.062
40    C         1.151   1.170   1.221   1.414   1.435   1.501   1.228   1.255   1.335
41    K        -1.196  -1.263  -1.175  -1.189  -1.250  -1.102  -1.152  -1.203  -1.072
42    K         1.151   1.170   1.221   0.908   0.949   1.026   1.228   1.255   1.335
43    P         1.151   1.170   1.221   1.265   1.286   1.361   1.228   1.255   1.335
44    D         0.397   0.491   0.157   0.719   0.809   0.395   0.388   0.525  -0.019
45    L        -1.196  -1.020  -1.142  -1.011  -0.724  -0.985  -1.152  -0.939  -1.037
46    K         0.397   0.326   0.144   0.297   0.228  -0.005   0.388   0.277  -0.043
47    E         1.151   1.170   1.221   1.194   1.230   1.294   1.228   1.255   1.335
48    Y         0.052  -0.020   0.026   0.195   0.058   0.091  -0.172  -0.307  -0.256
49    T        -0.694  -0.712  -0.651  -0.651  -0.712  -0.647  -0.872  -0.872  -0.770
50    K         0.397   0.297   0.133   0.307   0.205   0.002   0.388   0.232  -0.062
51    I         1.151   1.170   1.221   0.853   0.883   0.975   1.228   1.255   1.335
52    V        -0.832  -0.806  -0.697  -1.101  -1.002  -0.889  -1.012  -0.976  -0.824
53    K        -0.832  -0.809  -0.696  -0.903  -0.862  -0.677  -1.012  -0.977  -0.822
54    A         1.151   1.170   1.221   1.173   1.202   1.275   1.228   1.255   1.335
55    V         1.151   1.170   1.221   0.941   0.980   1.057   1.228   1.255   1.335
56    G         0.397   0.297   0.133   0.492   0.364   0.107   0.388   0.232  -0.062
57    I        -0.605  -0.675  -0.662  -0.777  -0.841  -0.826  -0.732  -0.828  -0.781
58    G         1.151   1.170   1.221   1.132   1.158   1.236   1.228   1.255   1.335
59    F         1.151   1.170   1.221   1.225   1.240   1.323   1.228   1.255   1.335
60    I        -0.832  -0.794  -0.694  -1.258  -1.183  -1.051  -1.012  -0.960  -0.820
61    A        -1.560  -1.649  -1.575  -1.380  -1.585  -1.510  -1.292  -1.363  -1.246
62    V        -0.104  -0.005   0.043  -0.220  -0.007   0.012  -0.452  -0.279  -0.224
63    G         1.151   1.170   1.221   1.132   1.158   1.236   1.228   1.255   1.335
64    I        -1.196  -1.192  -1.163  -1.362  -1.332  -1.332  -1.152  -1.145  -1.061
65    I         0.052   0.043   0.039  -0.360  -0.380  -0.417  -0.172  -0.194  -0.231
66    G         1.151   1.170   1.221   1.132   1.158   1.236   1.228   1.255   1.335
67    Y         1.151   1.170   1.221   1.315   1.345   1.408   1.228   1.255   1.335
68    A        -0.694  -0.703  -0.647  -0.942  -0.969  -0.870  -0.872  -0.857  -0.765
69    I        -0.104  -0.089   0.009  -0.655  -0.629  -0.472  -0.452  -0.434  -0.287
70    K         1.151   1.170   1.221   0.908   0.949   1.026   1.228   1.255   1.335
71    L         1.151   1.170   1.221   1.122   1.135   1.226   1.228   1.255   1.335
72    I         0.052   0.066   0.049  -0.360  -0.338  -0.398  -0.172  -0.153  -0.213
73    H         1.151   1.170   1.221   1.395   1.411   1.483   1.228   1.255   1.335
74    I         1.151   1.170   1.221   0.853   0.883   0.975   1.228   1.255   1.335
75    P         1.151   1.170   1.221   1.265   1.286   1.361   1.228   1.255   1.335
76    I         0.397   0.326   0.144   0.204   0.113  -0.144   0.388   0.277  -0.043
77    R         0.052  -0.020   0.026   0.272   0.140   0.197  -0.172  -0.307  -0.256
78    Y        -0.969  -1.130  -1.151  -0.531  -0.777  -0.850  -0.872  -1.047  -1.046
79    V         0.052   0.131   0.060  -0.201  -0.074  -0.205  -0.172  -0.041  -0.194
80    I         0.052  -0.020   0.026  -0.286  -0.413  -0.328  -0.172  -0.307  -0.256
81    V         0.397   0.370   0.150   0.301   0.282  -0.034   0.388   0.345  -0.032
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P35179
Output conservation file - output/P35179
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
