1     M         1.598   1.603   1.623   1.913   1.915   1.951   1.696   1.701   1.726
2     I        -0.128  -0.125  -0.103  -0.025  -0.021   0.019  -0.334  -0.328  -0.292
3     T        -0.128  -0.125  -0.103  -0.176  -0.175  -0.132  -0.334  -0.328  -0.292
4     P        -0.128  -0.125  -0.103   0.041   0.045   0.085  -0.334  -0.328  -0.292
5     K        -0.128  -0.125  -0.103  -0.008  -0.004   0.036  -0.334  -0.328  -0.292
6     G        -0.128  -0.125  -0.103  -0.176  -0.175  -0.132  -0.334  -0.328  -0.292
7     T        -0.128  -0.125  -0.103  -0.176  -0.175  -0.132  -0.334  -0.328  -0.292
8     H        -0.128  -0.125  -0.103  -0.125  -0.106  -0.081  -0.334  -0.328  -0.292
9     D        -0.128  -0.125  -0.103  -0.351  -0.334  -0.307  -0.334  -0.328  -0.292
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    A        -1.138  -1.133  -1.112  -0.916  -0.904  -0.870  -1.010  -1.001  -0.964
26    V         0.013  -0.017  -0.038   0.107   0.062   0.028  -0.108  -0.154  -0.188
27    A        -1.138  -1.133  -1.112  -1.040  -1.022  -0.993  -1.010  -1.001  -0.964
28    K        -1.138  -1.133  -1.112  -1.213  -1.210  -1.166  -1.010  -1.001  -0.964
29    F         1.598   1.603   1.623   1.863   1.872   1.901   1.696   1.701   1.726
30    Q         1.598   1.603   1.623   1.447   1.450   1.487   1.696   1.701   1.726
31    K        -1.138  -1.133  -1.112  -1.008  -0.993  -0.962  -1.010  -1.001  -0.964
32    T        -1.138  -1.133  -1.112  -1.158  -1.160  -1.111  -1.010  -1.001  -0.964
33    D        -1.138  -1.133  -1.112  -0.977  -0.958  -0.931  -1.010  -1.001  -0.964
34    L        -1.138  -1.133  -1.112  -1.224  -1.211  -1.177  -1.010  -1.001  -0.964
35    H         0.013   0.011  -0.030   0.099   0.100   0.052  -0.108  -0.110  -0.174
36    Q         0.013   0.011  -0.030  -0.150  -0.153  -0.238  -0.108  -0.110  -0.174
37    D         0.013   0.011  -0.030   0.099   0.096   0.016  -0.108  -0.110  -0.174
38    L        -1.138  -1.133  -1.112  -1.158  -1.149  -1.111  -1.010  -1.001  -0.964
39    D         1.598   1.603   1.623   1.606   1.619   1.645   1.696   1.701   1.726
40    Y         1.598   1.603   1.623   1.795   1.804   1.834   1.696   1.701   1.726
41    I        -1.138  -1.133  -1.112  -0.988  -0.973  -0.941  -1.010  -1.001  -0.964
42    V         1.598   1.603   1.623   1.693   1.702   1.732   1.696   1.701   1.726
43    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
44    Q         0.013   0.058  -0.009  -0.117  -0.053  -0.142  -0.108  -0.037  -0.142
45    Q         1.598   1.603   1.623   1.447   1.450   1.487   1.696   1.701   1.726
46    R         0.013  -0.017  -0.038   0.138   0.098   0.057  -0.108  -0.154  -0.188
47    R         0.013  -0.017  -0.038  -0.019  -0.074  -0.131  -0.108  -0.154  -0.188
48    T         0.013   0.058  -0.009   0.107   0.181   0.070  -0.108  -0.037  -0.142
49    Q        -1.138  -1.133  -1.112  -0.916  -0.907  -0.870  -1.010  -1.001  -0.964
50    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
51    E         0.013  -0.017  -0.038  -0.019  -0.067  -0.100  -0.108  -0.154  -0.188
52    T        -1.138  -1.133  -1.112  -0.988  -0.979  -0.941  -1.010  -1.001  -0.964
53    L        -1.138  -1.133  -1.112  -1.292  -1.291  -1.245  -1.010  -1.001  -0.964
54    I         0.013   0.011  -0.030  -0.336  -0.336  -0.373  -0.108  -0.110  -0.174
55    N        -1.138  -1.133  -1.112  -1.008  -1.002  -0.962  -1.010  -1.001  -0.964
56    E         0.013  -0.017  -0.038  -0.276  -0.341  -0.407  -0.108  -0.154  -0.188
57    R        -1.138  -1.133  -1.112  -1.125  -1.101  -1.078  -1.010  -1.001  -0.964
58    E         0.013   0.011  -0.030  -0.217  -0.222  -0.288  -0.108  -0.110  -0.174
59    S        -1.138  -1.133  -1.112  -0.767  -0.753  -0.721  -1.010  -1.001  -0.964
60    F         0.013   0.011  -0.030  -0.336  -0.335  -0.373  -0.108  -0.110  -0.174
61    V        -1.138  -1.133  -1.112  -1.542  -1.543  -1.494  -1.010  -1.001  -0.964
62    K         1.598   1.603   1.623   1.779   1.784   1.817   1.696   1.701   1.726
63    N         0.013   0.011  -0.030  -0.150  -0.157  -0.210  -0.108  -0.110  -0.174
64    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
65    C        -1.138  -1.133  -1.112  -0.967  -0.950  -0.921  -1.010  -1.001  -0.964
66    S        -1.138  -1.133  -1.112  -1.315  -1.326  -1.267  -1.010  -1.001  -0.964
67    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
68    F         0.013   0.011  -0.030   0.230   0.231   0.165  -0.108  -0.110  -0.174
69    H        -1.138  -1.133  -1.112  -0.757  -0.746  -0.711  -1.010  -1.001  -0.964
70    K        -1.138  -1.133  -1.112  -1.480  -1.460  -1.433  -1.010  -1.001  -0.964
71    I         0.013   0.011  -0.030  -0.336  -0.336  -0.373  -0.108  -0.110  -0.174
72    Q         0.013   0.011  -0.030  -0.133  -0.134  -0.223  -0.108  -0.110  -0.174
73    N        -1.138  -1.133  -1.112  -1.040  -1.039  -0.993  -1.010  -1.001  -0.964
74    T         0.013  -0.017  -0.038   0.245   0.202   0.184  -0.108  -0.154  -0.188
75    K         0.013   0.011  -0.030   0.130   0.134   0.062  -0.108  -0.110  -0.174
76    N         1.598   1.603   1.623   1.727   1.731   1.766   1.696   1.701   1.726
77    Y         0.013  -0.017  -0.038   0.253   0.207   0.178  -0.108  -0.154  -0.188
78    Q         1.598   1.603   1.623   1.447   1.450   1.487   1.696   1.701   1.726
79    E         1.598   1.603   1.623   1.589   1.599   1.628   1.696   1.701   1.726
80    F         0.013  -0.017  -0.038  -0.011  -0.080  -0.154  -0.108  -0.154  -0.188
81    V        -1.138  -1.133  -1.112  -0.896  -0.885  -0.849  -1.010  -1.001  -0.964
82    D         1.598   1.603   1.623   1.606   1.619   1.645   1.696   1.701   1.726
83    V         0.013   0.058  -0.009   0.076   0.149   0.040  -0.108  -0.037  -0.142
84    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
85    A         0.013   0.011  -0.030   0.305   0.300   0.230  -0.108  -0.110  -0.174
86    E        -1.138  -1.133  -1.112  -1.072  -1.066  -1.025  -1.010  -1.001  -0.964
87    N         0.013  -0.017  -0.038  -0.019  -0.084  -0.131  -0.108  -0.154  -0.188
88    R         0.013   0.058  -0.009  -0.019   0.071  -0.071  -0.108  -0.037  -0.142
89    D        -1.138  -1.133  -1.112  -1.235  -1.239  -1.188  -1.010  -1.001  -0.964
90    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
91    L         1.598   1.603   1.623   1.171   1.179   1.212   1.696   1.701   1.726
92    R         0.013  -0.017  -0.038  -0.019  -0.074  -0.131  -0.108  -0.154  -0.188
93    E         0.013  -0.017  -0.038   0.005  -0.040  -0.071  -0.108  -0.154  -0.188
94    I         0.013   0.058  -0.009   0.215   0.294   0.172  -0.108  -0.037  -0.142
95    F         1.598   1.603   1.623   1.863   1.872   1.901   1.696   1.701   1.726
96    T         1.598   1.603   1.623   1.727   1.730   1.766   1.696   1.701   1.726
97    V         0.013   0.011  -0.030  -0.424  -0.424  -0.474  -0.108  -0.110  -0.174
98    E         1.598   1.603   1.623   1.589   1.599   1.628   1.696   1.701   1.726
99    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   G         1.598   1.603   1.623   1.908   1.915   1.946   1.696   1.701   1.726
101   F        -0.128  -0.125  -0.103   0.100   0.105   0.143  -0.334  -0.328  -0.292
102   Q        -0.128  -0.125  -0.103  -0.688  -0.684  -0.642  -0.334  -0.328  -0.292
103   K        -0.128  -0.125  -0.103  -0.152  -0.147  -0.108  -0.334  -0.328  -0.292
104   Q        -1.138  -1.133  -1.112  -1.125  -1.115  -1.078  -1.010  -1.001  -0.964
105   K        -1.138  -1.133  -1.112  -0.926  -0.923  -0.880  -1.010  -1.001  -0.964
106   W        -1.138  -1.133  -1.112  -0.836  -0.826  -0.790  -1.010  -1.001  -0.964
107   I        -1.138  -1.133  -1.112  -0.786  -0.775  -0.741  -1.010  -1.001  -0.964
108   S        -1.138  -1.133  -1.112  -1.147  -1.130  -1.100  -1.010  -1.001  -0.964
109   N        -1.138  -1.133  -1.112  -0.977  -0.968  -0.931  -1.010  -1.001  -0.964
110   D         0.013  -0.017  -0.038  -0.133  -0.189  -0.240  -0.108  -0.154  -0.188
111   D        -1.138  -1.133  -1.112  -1.061  -1.060  -1.014  -1.010  -1.001  -0.964
112   I        -1.138  -1.133  -1.112  -1.029  -1.007  -0.983  -1.010  -1.001  -0.964
113   P         1.598   1.603   1.623   1.995   2.001   2.033   1.696   1.701   1.726
114   Q        -1.138  -1.133  -1.112  -1.235  -1.225  -1.188  -1.010  -1.001  -0.964
115   I         0.013  -0.017  -0.038   0.215   0.163   0.118  -0.108  -0.154  -0.188
116   D         0.013  -0.017  -0.038   0.020  -0.022  -0.056  -0.108  -0.154  -0.188
117   W         1.598   1.603   1.623   2.012   2.019   2.049   1.696   1.701   1.726
118   D         0.013   0.011  -0.030   0.099   0.096   0.016  -0.108  -0.110  -0.174
119   K         1.598   1.603   1.623   1.779   1.784   1.817   1.696   1.701   1.726
120   F         0.013   0.011  -0.030   0.230   0.231   0.165  -0.108  -0.110  -0.174
121   A         0.013   0.011  -0.030   0.260   0.258   0.187  -0.108  -0.110  -0.174
122   L         0.013   0.058  -0.009  -0.424  -0.356  -0.447  -0.108  -0.037  -0.142
123   D         1.598   1.603   1.623   1.606   1.619   1.645   1.696   1.701   1.726
124   I        -1.138  -1.133  -1.112  -1.258  -1.224  -1.211  -1.010  -1.001  -0.964
125   N        -1.138  -1.133  -1.112  -1.029  -1.028  -0.983  -1.010  -1.001  -0.964
126   A        -1.138  -1.133  -1.112  -1.202  -1.197  -1.155  -1.010  -1.001  -0.964
127   Y         1.598   1.603   1.623   1.795   1.804   1.834   1.696   1.701   1.726
128   I         0.013  -0.017  -0.038  -0.011  -0.082  -0.154  -0.108  -0.154  -0.188
129   A         0.013  -0.017  -0.038   0.154   0.104   0.060  -0.108  -0.154  -0.188
130   E         0.013   0.058  -0.009   0.005   0.076  -0.026  -0.108  -0.037  -0.142
131   N        -1.138  -1.133  -1.112  -1.061  -1.049  -1.014  -1.010  -1.001  -0.964
132   D        -1.138  -1.133  -1.112  -0.946  -0.935  -0.900  -1.010  -1.001  -0.964
133   Q         0.013   0.011  -0.030  -0.019  -0.018  -0.113  -0.108  -0.110  -0.174
134   L         0.013  -0.017  -0.038  -0.371  -0.408  -0.423  -0.108  -0.154  -0.188
135   L         0.013  -0.017  -0.038  -0.468  -0.510  -0.539  -0.108  -0.154  -0.188
136   A         0.013  -0.017  -0.038  -0.076  -0.144  -0.216  -0.108  -0.154  -0.188
137   L         0.013  -0.017  -0.038  -0.424  -0.464  -0.485  -0.108  -0.154  -0.188
138   Y         0.013  -0.017  -0.038   0.107   0.054   0.005  -0.108  -0.154  -0.188
139   E        -1.138  -1.133  -1.112  -1.072  -1.059  -1.025  -1.010  -1.001  -0.964
140   D         0.013  -0.017  -0.038   0.020  -0.022  -0.056  -0.108  -0.154  -0.188
141   G         1.598   1.603   1.623   1.863   1.868   1.901   1.696   1.701   1.726
142   L        -1.138  -1.133  -1.112  -1.082  -1.085  -1.036  -1.010  -1.001  -0.964
143   L         0.013  -0.017  -0.038  -0.267  -0.298  -0.300  -0.108  -0.154  -0.188
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -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/P25649
Output conservation file - output/P25649
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
