1     M         1.587   1.634   1.664   1.837   1.911   1.960   1.736   1.803   1.856
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    I        -1.296  -1.279  -1.208  -1.287  -1.259  -1.147  -1.102  -1.067  -0.983
14    E        -1.296  -1.279  -1.208  -1.330  -1.301  -1.189  -1.102  -1.067  -0.983
15    T        -0.799  -0.765  -0.767  -0.741  -0.684  -0.694  -0.818  -0.765  -0.759
16    A        -1.296  -1.279  -1.208  -1.254  -1.245  -1.114  -1.102  -1.067  -0.983
17    I        -0.303  -0.315  -0.269  -0.491  -0.501  -0.429  -0.534  -0.537  -0.475
18    Y        -0.115  -0.113  -0.201  -0.210  -0.209  -0.367  -0.250  -0.243  -0.376
19    G         1.587   1.634   1.664   1.749   1.824   1.872   1.736   1.803   1.856
20    K         0.381   0.404   0.441   0.202   0.228   0.299   0.033   0.061   0.108
21    T         0.691   0.780   0.592   0.667   0.802   0.510   0.601   0.745   0.398
22    V         1.587   1.634   1.664   1.703   1.775   1.827   1.736   1.803   1.856
23    D         1.587   1.634   1.664   1.657   1.733   1.780   1.736   1.803   1.856
24    D        -0.799  -0.733  -0.764  -0.904  -0.803  -0.849  -0.818  -0.728  -0.757
25    Q        -0.303  -0.282  -0.258  -0.364  -0.332  -0.293  -0.534  -0.500  -0.462
26    S         0.381   0.453   0.463   0.263   0.384   0.393   0.033   0.156   0.152
27    R         1.587   1.634   1.664   1.767   1.850   1.891   1.736   1.803   1.856
28    C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
29    V        -1.623  -1.575  -1.533  -1.479  -1.464  -1.337  -1.220  -1.163  -1.101
30    H         1.587   1.634   1.664   1.659   1.732   1.783   1.736   1.803   1.856
31    W        -0.225  -0.267  -0.215  -0.220  -0.272  -0.196  -0.432  -0.463  -0.401
32    H         0.780   0.619   0.624   0.885   0.630   0.645   0.751   0.465   0.457
33    L        -1.209  -1.154  -1.163  -1.135  -1.074  -1.066  -1.023  -0.962  -0.944
34    P        -0.381  -0.333  -0.289  -0.574  -0.486  -0.426  -0.629  -0.558  -0.500
35    K        -0.639  -0.684  -0.715  -0.623  -0.668  -0.740  -0.629  -0.683  -0.702
36    D         1.587   1.634   1.664   1.657   1.733   1.780   1.736   1.803   1.856
37    V         0.381   0.404   0.441   0.247   0.282   0.331   0.033   0.061   0.108
38    I         0.447   0.398   0.443   0.383   0.309   0.353   0.160   0.050   0.112
39    A         0.780   0.619   0.624   0.931   0.688   0.689   0.751   0.465   0.457
40    I         0.447   0.516   0.480   0.314   0.475   0.345   0.160   0.276   0.186
41    R         0.447   0.501   0.488   0.365   0.438   0.409   0.160   0.248   0.200
42    F         0.033  -0.120  -0.150   0.130  -0.153  -0.201  -0.038  -0.259  -0.302
43    K         0.033  -0.120  -0.150   0.105  -0.134  -0.155  -0.038  -0.259  -0.302
44    C         0.780   0.796   0.643   0.692   0.708   0.504   0.751   0.771   0.492
45    C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
46    D        -0.795  -0.849  -0.765  -0.886  -0.957  -0.822  -0.826  -0.863  -0.761
47    K        -0.639  -0.506  -0.671  -0.618  -0.425  -0.664  -0.629  -0.456  -0.650
48    Y         0.033  -0.120  -0.150   0.151  -0.054  -0.104  -0.038  -0.259  -0.302
49    Y         0.780   0.833   0.657   0.841   0.929   0.660   0.751   0.833   0.518
50    A        -0.225  -0.311  -0.235  -0.274  -0.399  -0.293  -0.432  -0.529  -0.431
51    C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
52    F        -0.225  -0.295  -0.221  -0.300  -0.390  -0.293  -0.432  -0.504  -0.414
53    E        -0.381  -0.327  -0.289  -0.565  -0.460  -0.406  -0.629  -0.550  -0.500
54    C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
55    H         1.587   1.634   1.664   1.659   1.732   1.783   1.736   1.803   1.856
56    Q        -0.639  -0.741  -0.729  -0.512  -0.696  -0.696  -0.629  -0.743  -0.717
57    E         1.587   1.634   1.664   1.643   1.717   1.767   1.736   1.803   1.856
58    L         0.033  -0.077  -0.132   0.068  -0.086  -0.185  -0.038  -0.202  -0.276
59    S        -1.209  -1.078  -1.153  -1.147  -0.954  -1.057  -1.023  -0.877  -0.934
60    S        -1.209  -1.209  -1.171  -1.150  -1.177  -1.097  -1.023  -1.010  -0.951
61    H         1.587   1.634   1.664   1.659   1.732   1.783   1.736   1.803   1.856
62    P        -0.639  -0.506  -0.671  -0.538  -0.300  -0.597  -0.629  -0.456  -0.650
63    L        -1.209  -1.130  -1.156  -1.178  -1.032  -1.088  -1.023  -0.929  -0.937
64    E        -1.209  -1.243  -1.189  -1.184  -1.215  -1.153  -1.023  -1.037  -0.967
65    K        -0.225  -0.239  -0.229  -0.291  -0.350  -0.310  -0.432  -0.449  -0.426
66    Y        -0.303  -0.274  -0.259  -0.320  -0.245  -0.227  -0.534  -0.486  -0.462
67    D        -0.303  -0.319  -0.259  -0.461  -0.476  -0.377  -0.534  -0.543  -0.463
68    L        -0.115   0.007  -0.175  -0.207  -0.013  -0.320  -0.250  -0.070  -0.339
69    L        -0.303  -0.319  -0.260  -0.545  -0.564  -0.463  -0.534  -0.542  -0.464
70    D         0.691   0.645   0.565   0.725   0.648   0.494   0.601   0.512   0.347
71    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    A        -1.623  -1.575  -1.533  -1.550  -1.498  -1.408  -1.220  -1.163  -1.101
73    N        -0.639  -0.545  -0.673  -0.545  -0.421  -0.609  -0.629  -0.505  -0.652
74    K        -1.209  -1.078  -1.153  -1.163  -0.954  -1.074  -1.023  -0.877  -0.934
75    H        -0.795  -0.797  -0.766  -0.823  -0.795  -0.753  -0.826  -0.818  -0.762
76    L        -1.209  -1.243  -1.189  -1.255  -1.307  -1.218  -1.023  -1.037  -0.967
77    I        -0.225  -0.295  -0.224  -0.237  -0.320  -0.233  -0.432  -0.504  -0.418
78    I        -0.225  -0.311  -0.235  -0.333  -0.424  -0.346  -0.432  -0.529  -0.431
79    C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
80    G         0.780   0.619   0.624   0.979   0.723   0.717   0.751   0.465   0.457
81    V        -1.209  -1.243  -1.189  -1.132  -1.218  -1.115  -1.023  -1.037  -0.967
82    C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
83    R        -0.795  -0.751  -0.753  -0.818  -0.760  -0.735  -0.826  -0.764  -0.749
84    H        -0.639  -0.599  -0.697  -0.668  -0.635  -0.781  -0.629  -0.589  -0.681
85    E        -0.639  -0.741  -0.729  -0.589  -0.747  -0.743  -0.629  -0.743  -0.717
86    M        -0.225  -0.267  -0.215  -0.274  -0.324  -0.245  -0.432  -0.463  -0.401
87    T        -0.639  -0.661  -0.700  -0.526  -0.603  -0.631  -0.629  -0.657  -0.684
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    F        -0.795  -0.830  -0.769  -0.815  -0.872  -0.780  -0.826  -0.844  -0.765
91    A        -0.795  -0.756  -0.755  -0.768  -0.720  -0.694  -0.826  -0.762  -0.750
92    E         0.033  -0.016  -0.116   0.114   0.008  -0.125  -0.038  -0.125  -0.253
93    Y         0.780   0.619   0.624   0.841   0.603   0.605   0.751   0.465   0.457
94    Y        -1.209  -1.209  -1.171  -1.175  -1.188  -1.124  -1.023  -1.010  -0.951
95    D        -1.209  -1.243  -1.189  -1.188  -1.246  -1.153  -1.023  -1.037  -0.967
96    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    S        -0.896  -0.868  -0.809  -1.087  -1.023  -0.948  -0.924  -0.879  -0.805
99    N        -1.209  -1.078  -1.153  -1.141  -0.953  -1.049  -1.023  -0.877  -0.934
100   L        -1.209  -1.243  -1.189  -1.229  -1.243  -1.188  -1.023  -1.037  -0.967
101   I        -1.623  -1.575  -1.533  -1.479  -1.423  -1.337  -1.220  -1.163  -1.101
102   C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
103   P        -0.639  -0.600  -0.701  -0.584  -0.497  -0.708  -0.629  -0.569  -0.685
104   N         0.447   0.586   0.519   0.263   0.521   0.377   0.160   0.406   0.261
105   C         1.587   1.634   1.664   1.449   1.506   1.574   1.736   1.803   1.856
106   R        -1.209  -1.243  -1.189  -1.080  -1.167  -1.058  -1.023  -1.037  -0.967
107   S        -0.639  -0.731  -0.727  -0.524  -0.693  -0.673  -0.629  -0.733  -0.715
108   P        -0.795  -0.836  -0.764  -0.784  -0.839  -0.738  -0.826  -0.851  -0.760
109   F         1.587   1.634   1.664   1.706   1.766   1.830   1.736   1.803   1.856
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   N         0.780   0.619   0.624   0.837   0.588   0.599   0.751   0.465   0.457
116   P         1.587   1.634   1.664   1.690   1.796   1.814   1.736   1.803   1.856
117   G        -0.639  -0.741  -0.729  -0.510  -0.699  -0.696  -0.629  -0.743  -0.717
118   C         0.780   0.619   0.624   0.676   0.411   0.445   0.751   0.465   0.457
119   K         0.447   0.501   0.488   0.271   0.339   0.328   0.160   0.248   0.200
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   L         0.780   0.796   0.643   0.790   0.841   0.574   0.751   0.771   0.492
142   H         0.780   0.619   0.624   0.872   0.616   0.622   0.751   0.465   0.457
143   Y         0.033  -0.120  -0.150   0.099  -0.135  -0.186  -0.038  -0.259  -0.302
144   H        -1.209  -1.154  -1.163  -1.065  -0.978  -1.003  -1.023  -0.962  -0.944
145   L        -0.795  -0.764  -0.753  -0.792  -0.693  -0.714  -0.826  -0.776  -0.749
146   Y         0.780   0.619   0.624   0.867   0.650   0.652   0.751   0.465   0.457
147   F         0.780   0.619   0.624   0.940   0.683   0.706   0.751   0.465   0.457
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   Q        -0.795  -0.691  -0.752  -0.864  -0.712  -0.784  -0.826  -0.702  -0.749
151   N         0.381   0.449   0.459   0.149   0.261   0.272   0.033   0.149   0.144
152   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   C        -0.799  -0.677  -0.748  -0.860  -0.643  -0.788  -0.818  -0.662  -0.739
* 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/P36078
Output conservation file - output/P36078
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
