1     M         1.309   1.332   1.437   1.526   1.556   1.701   1.400   1.433   1.597
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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    A        -0.795  -0.862  -1.038  -0.842  -0.924  -1.182  -0.674  -0.756  -0.923
22    A        -0.729  -0.704  -0.599  -1.154  -1.084  -0.945  -0.904  -0.871  -0.729
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -         0.328   0.230   0.216  -0.078  -0.238  -0.314   0.220   0.049  -0.024
28    S        -0.806  -0.758  -0.606  -1.249  -1.161  -0.934  -1.008  -0.943  -0.738
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    V        -1.280  -1.276  -1.129  -1.298  -1.321  -1.126  -1.250  -1.236  -1.024
33    P        -0.812  -0.774  -0.614  -1.087  -1.050  -0.784  -1.019  -0.969  -0.748
34    P         1.309   1.332   1.437   1.419   1.440   1.601   1.400   1.433   1.597
35    G         1.309   1.332   1.437   1.236   1.267   1.429   1.400   1.433   1.597
36    G         1.309   1.332   1.437   1.236   1.267   1.429   1.400   1.433   1.597
37    Q        -1.748  -1.690  -1.549  -1.547  -1.441  -1.248  -1.480  -1.414  -1.205
38    R        -0.133  -0.283  -0.473   0.098  -0.114  -0.457  -0.098  -0.300  -0.559
39    I        -1.152  -1.145  -1.100  -1.312  -1.287  -1.203  -1.135  -1.113  -0.995
40    L        -0.812  -0.804  -0.618  -1.128  -1.088  -0.793  -1.019  -1.003  -0.754
41    Q        -1.620  -1.513  -1.533  -1.316  -1.172  -1.236  -1.365  -1.271  -1.193
42    K         0.012   0.000   0.141  -0.101  -0.141   0.072  -0.328  -0.362  -0.164
43    R         1.309   1.332   1.437   1.369   1.397   1.553   1.400   1.433   1.597
44    R         0.571   0.680   0.331   0.751   0.878   0.417   0.594   0.748   0.181
45    Q        -1.748  -1.631  -1.548  -1.498  -1.402  -1.209  -1.480  -1.380  -1.205
46    A        -0.133  -0.055  -0.435  -0.114  -0.027  -0.451  -0.098   0.002  -0.507
47    Q        -0.601  -0.665  -0.554  -0.733  -0.815  -0.672  -0.789  -0.839  -0.678
48    S        -2.088  -2.053  -1.885  -1.710  -1.673  -1.508  -1.596  -1.550  -1.323
49    I        -1.620  -1.616  -1.534  -1.344  -1.347  -1.223  -1.365  -1.340  -1.193
50    K        -0.133  -0.283  -0.473   0.165  -0.017  -0.256  -0.098  -0.300  -0.559
51    E        -0.456  -0.468  -0.506  -0.237  -0.221  -0.356  -0.558  -0.549  -0.605
52    K        -0.456  -0.353  -0.487  -0.376  -0.227  -0.469  -0.558  -0.401  -0.579
53    Q        -1.748  -1.732  -1.552  -1.619  -1.523  -1.260  -1.480  -1.449  -1.208
54    A        -0.601  -0.609  -0.558  -1.038  -1.024  -0.894  -0.789  -0.787  -0.681
55    K        -0.795  -0.847  -1.042  -0.292  -0.369  -0.766  -0.674  -0.730  -0.927
56    Q        -0.601  -0.642  -0.554  -0.774  -0.795  -0.730  -0.789  -0.803  -0.675
57    T        -1.069  -1.066  -1.084  -0.843  -0.877  -0.861  -1.019  -1.016  -0.976
58    P         1.309   1.332   1.437   1.419   1.440   1.601   1.400   1.433   1.597
59    T        -1.280  -1.190  -1.104  -1.331  -1.228  -1.049  -1.250  -1.152  -0.998
60    S         0.571   0.429   0.304   0.382   0.236   0.018   0.594   0.377   0.134
61    T        -0.456  -0.470  -0.542  -0.418  -0.525  -0.610  -0.558  -0.611  -0.661
62    R         1.309   1.332   1.437   1.369   1.397   1.553   1.400   1.433   1.597
63    Q        -0.812  -0.761  -0.599  -1.279  -1.185  -0.927  -1.019  -0.950  -0.730
64    A         0.571   0.566   0.318   0.426   0.414   0.076   0.594   0.585   0.159
65    G         1.309   1.332   1.437   1.236   1.267   1.429   1.400   1.433   1.597
66    Y        -0.456  -0.438  -0.530  -0.530  -0.511  -0.541  -0.558  -0.532  -0.640
67    G         0.571   0.429   0.304   0.632   0.456   0.288   0.594   0.377   0.134
68    G         1.309   1.332   1.437   1.236   1.267   1.429   1.400   1.433   1.597
69    S         1.309   1.332   1.437   1.015   1.084   1.222   1.400   1.433   1.597
70    S         0.571   0.429   0.304   0.401   0.264   0.068   0.594   0.377   0.134
71    S        -0.133  -0.158  -0.450  -0.245  -0.241  -0.693  -0.098  -0.147  -0.527
72    S         0.012   0.037   0.159  -0.260  -0.214  -0.078  -0.328  -0.295  -0.131
73    I        -0.601  -0.683  -0.567  -0.422  -0.544  -0.395  -0.789  -0.866  -0.693
74    L         0.207   0.350   0.271   0.171   0.365   0.268   0.018   0.249   0.075
75    K         0.571   0.648   0.327   0.720   0.810   0.391   0.594   0.703   0.175
76    L         0.571   0.542   0.311   0.620   0.590   0.294   0.594   0.550   0.146
77    Y         0.012   0.078   0.168   0.177   0.284   0.370  -0.328  -0.219  -0.114
78    T         1.309   1.332   1.437   1.362   1.389   1.547   1.400   1.433   1.597
79    D         1.309   1.332   1.437   1.533   1.564   1.708   1.400   1.433   1.597
80    E         1.309   1.332   1.437   1.561   1.586   1.734   1.400   1.433   1.597
81    A         0.207   0.245   0.207  -0.158  -0.097  -0.219   0.018   0.074  -0.041
82    N        -1.620  -1.661  -1.539  -1.193  -1.283  -1.110  -1.365  -1.387  -1.197
83    G         1.309   1.332   1.437   1.236   1.267   1.429   1.400   1.433   1.597
84    F         0.207   0.133   0.166   0.130   0.010   0.050   0.018  -0.120  -0.117
85    R         0.012   0.004   0.144  -0.088  -0.125   0.079  -0.328  -0.355  -0.159
86    V         1.309   1.332   1.437   1.214   1.237   1.408   1.400   1.433   1.597
87    D         1.309   1.332   1.437   1.533   1.564   1.708   1.400   1.433   1.597
88    S         0.571   0.579   0.319   0.758   0.764   0.335   0.594   0.604   0.161
89    L         0.012   0.004   0.144  -0.283  -0.322  -0.106  -0.328  -0.355  -0.159
90    V         1.309   1.332   1.437   1.214   1.237   1.408   1.400   1.433   1.597
91    V         1.309   1.332   1.437   1.214   1.237   1.408   1.400   1.433   1.597
92    L         0.207   0.128   0.172   0.171   0.052   0.127   0.018  -0.130  -0.107
93    F         0.012   0.004   0.144  -0.118  -0.165   0.031  -0.328  -0.355  -0.159
94    L         1.309   1.332   1.437   1.221   1.253   1.415   1.400   1.433   1.597
95    S        -0.050  -0.012   0.146  -0.685  -0.601  -0.362  -0.443  -0.385  -0.155
96    V        -0.456  -0.461  -0.526  -0.571  -0.592  -0.733  -0.558  -0.557  -0.636
97    G        -0.133   0.002  -0.425  -0.055   0.116  -0.530  -0.098   0.079  -0.493
98    F         1.309   1.332   1.437   1.405   1.437   1.587   1.400   1.433   1.597
99    I         0.571   0.659   0.331   0.807   0.914   0.443   0.594   0.719   0.182
100   F         0.571   0.429   0.304   0.750   0.553   0.308   0.594   0.377   0.134
101   S         0.571   0.542   0.311   0.401   0.408   0.079   0.594   0.550   0.146
102   V         1.309   1.332   1.437   1.214   1.237   1.408   1.400   1.433   1.597
103   I        -1.152  -1.232  -1.103  -1.004  -1.098  -0.879  -1.135  -1.190  -0.998
104   A        -1.069  -1.116  -1.080  -1.209  -1.291  -1.263  -1.019  -1.045  -0.969
105   L         0.571   0.542   0.311   0.633   0.605   0.326   0.594   0.550   0.146
106   H         1.309   1.332   1.437   1.603   1.631   1.773   1.400   1.433   1.597
107   L        -1.152  -1.143  -1.098  -1.077  -1.034  -0.969  -1.135  -1.104  -0.993
108   L        -1.280  -1.173  -1.103  -1.310  -1.187  -1.038  -1.250  -1.131  -0.997
109   T         0.571   0.579   0.319   0.448   0.454   0.134   0.594   0.604   0.161
110   K         0.571   0.429   0.304   0.720   0.540   0.354   0.594   0.377   0.134
111   F        -1.069  -1.076  -1.094  -0.803  -0.809  -0.843  -1.019  -1.014  -0.988
112   T        -0.456  -0.546  -0.539  -0.474  -0.597  -0.689  -0.558  -0.661  -0.654
113   -        -0.952  -1.003  -1.085  -0.778  -0.869  -0.972  -0.857  -0.918  -0.974
114   H        -0.133  -0.170  -0.461   0.167   0.121  -0.234  -0.098  -0.146  -0.542
115   I        -1.069  -1.080  -1.095  -0.845  -0.866  -0.934  -1.019  -1.017  -0.987
116   I        -2.088  -2.079  -1.895  -2.059  -2.049  -1.784  -1.596  -1.571  -1.329
117   -         0.328   0.275   0.222  -0.014  -0.085  -0.181   0.220   0.126  -0.015
118   -        -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/P52871
Output conservation file - output/P52871
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
