1     M         1.451   1.454   1.493   1.633   1.634   1.691   1.562   1.568   1.622
2     V         0.485   0.447   0.326   0.461   0.405   0.262   0.430   0.367   0.154
3     V         1.451   1.454   1.493   1.301   1.298   1.367   1.562   1.568   1.622
4     L         0.152   0.187   0.208   0.031   0.072   0.119  -0.137  -0.076  -0.056
5     N         1.451   1.454   1.493   1.445   1.450   1.508   1.562   1.568   1.622
6     P         1.451   1.454   1.493   1.605   1.610   1.665   1.562   1.568   1.622
7     N         1.451   1.454   1.493   1.445   1.450   1.508   1.562   1.568   1.622
8     N         1.451   1.454   1.493   1.445   1.450   1.508   1.562   1.568   1.622
9     W         1.451   1.454   1.493   1.653   1.657   1.711   1.562   1.568   1.622
10    H         1.451   1.454   1.493   1.612   1.616   1.671   1.562   1.568   1.622
11    W         1.451   1.454   1.493   1.653   1.657   1.711   1.562   1.568   1.622
12    V         0.152   0.156   0.187  -0.092  -0.090  -0.033  -0.137  -0.131  -0.094
13    D         1.451   1.454   1.493   1.242   1.252   1.310   1.562   1.568   1.622
14    K         1.451   1.454   1.493   1.345   1.351   1.410   1.562   1.568   1.622
15    N         1.451   1.454   1.493   1.445   1.450   1.508   1.562   1.568   1.622
16    T         0.152   0.187   0.208   0.227   0.293   0.310  -0.137  -0.076  -0.056
17    L         1.451   1.454   1.493   1.359   1.354   1.424   1.562   1.568   1.622
18    P         0.485   0.441   0.322   0.739   0.677   0.498   0.430   0.358   0.146
19    W         1.451   1.454   1.493   1.653   1.657   1.711   1.562   1.568   1.622
20    S         0.485   0.441   0.322   0.525   0.477   0.294   0.430   0.358   0.146
21    K         0.485   0.441   0.322   0.447   0.386   0.201   0.430   0.358   0.146
22    D         0.485   0.447   0.326   0.325   0.272   0.081   0.430   0.367   0.154
23    Y         1.451   1.454   1.493   1.626   1.630   1.685   1.562   1.568   1.622
24    L         0.152   0.156   0.187  -0.014  -0.017   0.044  -0.137  -0.132  -0.094
25    N        -0.383  -0.302  -0.494  -0.297  -0.177  -0.476  -0.420  -0.313  -0.563
26    G        -1.655  -1.646  -1.571  -1.360  -1.332  -1.236  -1.269  -1.263  -1.162
27    K        -1.120  -1.091  -1.113  -1.060  -1.009  -1.034  -0.986  -0.957  -0.956
28    L        -0.585  -0.575  -0.567  -0.575  -0.555  -0.549  -0.703  -0.691  -0.660
29    T        -0.585  -0.599  -0.569  -0.599  -0.604  -0.591  -0.703  -0.717  -0.663
30    S        -1.120  -1.112  -1.096  -1.170  -1.150  -1.151  -0.986  -0.979  -0.938
31    L        -0.585  -0.601  -0.573  -0.545  -0.566  -0.504  -0.703  -0.720  -0.668
32    S        -1.120  -1.115  -1.096  -0.784  -0.771  -0.763  -0.986  -0.982  -0.939
33    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    S        -1.655  -1.646  -1.571  -1.374  -1.372  -1.249  -1.269  -1.263  -1.162
36    S        -0.585  -0.599  -0.569  -0.650  -0.651  -0.585  -0.703  -0.717  -0.663
37    D        -0.585  -0.602  -0.554  -0.839  -0.861  -0.786  -0.703  -0.721  -0.647
38    G        -0.383  -0.412  -0.501  -0.390  -0.424  -0.520  -0.420  -0.460  -0.572
39    K        -0.585  -0.575  -0.567  -0.769  -0.749  -0.738  -0.703  -0.691  -0.660
40    S        -1.655  -1.646  -1.571  -1.470  -1.454  -1.344  -1.269  -1.263  -1.162
41    K        -0.383  -0.379  -0.477  -0.356  -0.363  -0.486  -0.420  -0.417  -0.541
42    I        -0.585  -0.553  -0.558  -0.678  -0.648  -0.617  -0.703  -0.669  -0.651
43    E        -1.120  -1.115  -1.096  -1.158  -1.143  -1.113  -0.986  -0.983  -0.939
44    L        -0.585  -0.602  -0.555  -0.844  -0.883  -0.790  -0.703  -0.721  -0.648
45    T        -1.120  -1.136  -1.097  -1.111  -1.136  -1.109  -0.986  -1.004  -0.940
46    Q        -1.120  -1.112  -1.096  -0.995  -0.990  -0.942  -0.986  -0.979  -0.938
47    V        -0.383  -0.449  -0.506  -0.481  -0.594  -0.682  -0.420  -0.509  -0.579
48    S        -1.120  -1.157  -1.130  -1.337  -1.396  -1.350  -0.986  -1.026  -0.973
49    S         0.485   0.447   0.326   0.461   0.409   0.198   0.430   0.367   0.154
50    I        -0.585  -0.604  -0.555  -0.629  -0.651  -0.560  -0.703  -0.724  -0.648
51    T        -0.585  -0.602  -0.555  -0.629  -0.642  -0.585  -0.703  -0.721  -0.648
52    G         1.451   1.454   1.493   1.592   1.594   1.651   1.562   1.568   1.622
53    D         1.451   1.454   1.493   1.242   1.252   1.310   1.562   1.568   1.622
54    S         0.152   0.187   0.208   0.093   0.148   0.180  -0.137  -0.076  -0.056
55    N         0.152   0.187   0.208  -0.109  -0.032  -0.022  -0.137  -0.076  -0.056
56    V         1.451   1.454   1.493   1.301   1.298   1.367   1.562   1.568   1.622
57    S         0.152   0.187   0.208   0.029   0.098   0.116  -0.137  -0.076  -0.056
58    Q         1.451   1.454   1.493   1.550   1.553   1.611   1.562   1.568   1.622
59    R         1.451   1.454   1.493   1.646   1.648   1.705   1.562   1.568   1.622
60    K         1.451   1.454   1.493   1.345   1.351   1.410   1.562   1.568   1.622
61    G         1.451   1.454   1.493   1.592   1.594   1.651   1.562   1.568   1.622
62    K         1.451   1.454   1.493   1.345   1.351   1.410   1.562   1.568   1.622
63    P        -0.585  -0.557  -0.559  -0.545  -0.517  -0.491  -0.703  -0.674  -0.652
64    I         0.152   0.187   0.208  -0.006   0.064   0.080  -0.137  -0.076  -0.056
65    C         1.451   1.454   1.493   1.667   1.671   1.725   1.562   1.568   1.622
66    Y         0.152   0.187   0.208   0.185   0.254   0.267  -0.137  -0.076  -0.056
67    F         0.152   0.143   0.184   0.212   0.191   0.247  -0.137  -0.156  -0.099
68    D         1.451   1.454   1.493   1.242   1.252   1.310   1.562   1.568   1.622
69    L         0.152   0.187   0.208   0.043   0.081   0.131  -0.137  -0.076  -0.056
70    Q        -1.120  -1.065  -1.104  -0.810  -0.726  -0.797  -0.986  -0.928  -0.947
71    L         1.451   1.454   1.493   1.359   1.354   1.424   1.562   1.568   1.622
72    S        -1.120  -1.157  -1.130  -0.949  -1.006  -0.988  -0.986  -1.026  -0.973
73    M         0.152   0.144   0.187   0.190   0.175   0.243  -0.137  -0.154  -0.093
74    N        -0.585  -0.575  -0.567  -0.822  -0.806  -0.782  -0.703  -0.691  -0.660
75    V        -1.120  -1.091  -1.113  -1.072  -1.029  -1.038  -0.986  -0.957  -0.956
76    K        -1.655  -1.646  -1.571  -1.712  -1.715  -1.581  -1.269  -1.263  -1.162
77    V        -0.585  -0.575  -0.567  -0.645  -0.655  -0.638  -0.703  -0.691  -0.660
78    T        -0.556  -0.479  -0.556  -0.465  -0.328  -0.474  -0.650  -0.550  -0.644
79    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    K        -0.669  -0.646  -0.598  -0.852  -0.821  -0.739  -0.797  -0.768  -0.698
85    D         0.366   0.326   0.268   0.199   0.133   0.009   0.235   0.166   0.052
86    D        -0.556  -0.539  -0.542  -0.726  -0.705  -0.719  -0.650  -0.631  -0.627
87    E         0.366   0.317   0.264   0.353   0.282   0.204   0.235   0.151   0.044
88    D         0.152   0.155   0.186  -0.216  -0.210  -0.162  -0.137  -0.134  -0.096
89    D         0.485   0.490   0.330   0.418   0.424   0.154   0.430   0.436   0.160
90    D        -0.585  -0.601  -0.573  -0.753  -0.783  -0.751  -0.703  -0.720  -0.668
91    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    A        -1.655  -1.646  -1.571  -1.217  -1.198  -1.096  -1.269  -1.263  -1.162
95    D        -1.655  -1.646  -1.571  -1.541  -1.520  -1.413  -1.269  -1.263  -1.162
96    G         0.485   0.537   0.347   0.744   0.808   0.553   0.430   0.510   0.189
97    K        -0.383  -0.412  -0.501  -0.239  -0.271  -0.460  -0.420  -0.460  -0.572
98    L        -0.383  -0.412  -0.501  -0.331  -0.381  -0.555  -0.420  -0.460  -0.572
99    E        -0.585  -0.601  -0.573  -0.758  -0.771  -0.704  -0.703  -0.720  -0.668
100   I         0.152   0.154   0.185  -0.038  -0.036  -0.006  -0.137  -0.135  -0.097
101   P         1.451   1.454   1.493   1.605   1.610   1.665   1.562   1.568   1.622
102   E         1.451   1.454   1.493   1.367   1.370   1.431   1.562   1.568   1.622
103   F         1.451   1.454   1.493   1.536   1.542   1.597   1.562   1.568   1.622
104   M         0.152   0.187   0.208   0.089   0.159   0.171  -0.137  -0.076  -0.056
105   H         1.451   1.454   1.493   1.612   1.616   1.671   1.562   1.568   1.622
106   D         1.451   1.454   1.493   1.242   1.252   1.310   1.562   1.568   1.622
107   E        -0.585  -0.599  -0.569  -0.690  -0.725  -0.690  -0.703  -0.717  -0.663
108   S        -0.585  -0.599  -0.569  -0.750  -0.743  -0.676  -0.703  -0.717  -0.663
109   D        -0.383  -0.302  -0.494  -0.554  -0.425  -0.735  -0.420  -0.313  -0.563
110   I        -0.585  -0.575  -0.567  -0.701  -0.661  -0.638  -0.703  -0.691  -0.660
111   P         0.485   0.490   0.330   0.509   0.513   0.300   0.430   0.436   0.160
112   I        -0.585  -0.601  -0.573  -0.531  -0.564  -0.535  -0.703  -0.720  -0.668
113   L        -1.655  -1.646  -1.571  -1.659  -1.651  -1.528  -1.269  -1.263  -1.162
114   S        -1.120  -1.157  -1.130  -0.932  -0.995  -0.962  -0.986  -1.026  -0.973
115   Q        -0.585  -0.575  -0.567  -0.657  -0.638  -0.601  -0.703  -0.691  -0.660
116   G        -1.120  -1.157  -1.130  -0.865  -0.911  -0.867  -0.986  -1.026  -0.973
117   F        -1.120  -1.088  -1.108  -1.090  -1.024  -1.104  -0.986  -0.953  -0.951
118   D        -0.585  -0.601  -0.573  -0.766  -0.778  -0.715  -0.703  -0.720  -0.668
119   A        -0.383  -0.380  -0.479  -0.129  -0.123  -0.316  -0.420  -0.418  -0.543
120   -        -0.669  -0.642  -0.598  -0.822  -0.798  -0.710  -0.797  -0.764  -0.698
121   F        -1.655  -1.646  -1.571  -1.292  -1.289  -1.170  -1.269  -1.263  -1.162
122   D        -0.383  -0.412  -0.501  -0.392  -0.429  -0.571  -0.420  -0.460  -0.572
123   G        -1.655  -1.646  -1.571  -1.533  -1.521  -1.405  -1.269  -1.263  -1.162
124   L        -1.120  -1.157  -1.130  -1.148  -1.219  -1.166  -0.986  -1.026  -0.973
125   V        -0.585  -0.599  -0.569  -0.742  -0.777  -0.723  -0.703  -0.717  -0.663
126   R         0.485   0.447   0.326   0.744   0.685   0.486   0.430   0.367   0.154
127   S        -0.383  -0.416  -0.501  -0.477  -0.529  -0.689  -0.420  -0.465  -0.573
128   E        -1.120  -1.065  -1.104  -1.066  -1.006  -1.021  -0.986  -0.928  -0.947
129   F         0.485   0.441   0.322   0.602   0.532   0.321   0.430   0.358   0.146
130   V        -0.585  -0.604  -0.554  -0.742  -0.773  -0.690  -0.703  -0.724  -0.647
131   P         0.485   0.441   0.322   0.685   0.618   0.410   0.430   0.358   0.146
132   K        -0.585  -0.601  -0.573  -0.607  -0.623  -0.559  -0.703  -0.720  -0.668
133   V        -0.383  -0.416  -0.501  -0.397  -0.457  -0.585  -0.420  -0.465  -0.573
134   V        -0.585  -0.599  -0.569  -0.745  -0.762  -0.681  -0.703  -0.717  -0.663
135   E         0.485   0.441   0.322   0.456   0.392   0.201   0.430   0.358   0.146
136   T        -1.120  -1.157  -1.130  -1.189  -1.253  -1.208  -0.986  -1.026  -0.973
137   L         0.485   0.447   0.326   0.509   0.448   0.300   0.430   0.367   0.154
138   L        -0.585  -0.599  -0.569  -0.514  -0.550  -0.483  -0.703  -0.717  -0.663
139   K        -1.120  -1.136  -1.097  -1.090  -1.108  -1.048  -0.986  -1.004  -0.940
140   Y         0.152   0.187   0.208   0.212   0.275   0.293  -0.137  -0.076  -0.056
141   Q         1.451   1.454   1.493   1.550   1.553   1.611   1.562   1.568   1.622
142   D        -1.655  -1.646  -1.571  -1.441  -1.442  -1.315  -1.269  -1.263  -1.162
143   D         0.485   0.441   0.322   0.325   0.264   0.073   0.430   0.358   0.146
144   L         1.451   1.454   1.493   1.359   1.354   1.424   1.562   1.568   1.622
145   I        -0.585  -0.557  -0.558  -0.721  -0.682  -0.684  -0.703  -0.674  -0.651
146   K        -1.120  -1.115  -1.096  -1.228  -1.229  -1.201  -0.986  -0.983  -0.939
147   E        -0.585  -0.601  -0.573  -0.553  -0.587  -0.549  -0.703  -0.720  -0.668
148   H         1.451   1.454   1.493   1.612   1.616   1.671   1.562   1.568   1.622
149   S        -0.383  -0.302  -0.494  -0.299  -0.178  -0.456  -0.420  -0.313  -0.563
150   K        -0.383  -0.449  -0.506  -0.295  -0.383  -0.443  -0.420  -0.509  -0.579
151   D         1.451   1.454   1.493   1.242   1.252   1.310   1.562   1.568   1.622
152   I        -0.585  -0.575  -0.567  -0.790  -0.781  -0.734  -0.703  -0.691  -0.660
153   Q         1.451   1.454   1.493   1.550   1.553   1.611   1.562   1.568   1.622
154   V        -1.120  -1.157  -1.130  -0.832  -0.894  -0.867  -0.986  -1.026  -0.973
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -         0.222   0.283   0.229   0.208   0.307   0.214  -0.011   0.093  -0.017
157   -        -0.669  -0.642  -0.598  -0.800  -0.744  -0.688  -0.797  -0.764  -0.698
* 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/P53834
Output conservation file - output/P53834
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
