1     M         1.599   1.608   1.625   1.874   1.887   1.911   1.698   1.708   1.729
2     S        -0.078  -0.017  -0.098   0.040   0.146   0.001  -0.179  -0.084  -0.207
3     -        -0.227  -0.220  -0.195  -0.219  -0.210  -0.164  -0.414  -0.401  -0.361
4     -        -0.227  -0.220  -0.195  -0.353  -0.345  -0.297  -0.414  -0.401  -0.361
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    L        -0.078  -0.055  -0.113  -0.388  -0.364  -0.435  -0.179  -0.142  -0.231
11    R        -1.296  -1.282  -1.260  -1.212  -1.204  -1.148  -1.118  -1.095  -1.058
12    P        -0.078  -0.129  -0.135   0.144   0.056   0.053  -0.179  -0.256  -0.266
13    C        -0.078  -0.129  -0.135   0.110  -0.007  -0.035  -0.179  -0.256  -0.266
14    F         1.599   1.608   1.625   1.644   1.659   1.683   1.698   1.708   1.729
15    V        -0.078  -0.055  -0.113  -0.213  -0.172  -0.282  -0.179  -0.142  -0.231
16    S         1.599   1.608   1.625   1.566   1.605   1.606   1.698   1.708   1.729
17    L        -0.078  -0.055  -0.113  -0.458  -0.429  -0.516  -0.179  -0.142  -0.231
18    I        -0.078  -0.129  -0.135  -0.403  -0.505  -0.519  -0.179  -0.256  -0.266
19    D        -0.078  -0.055  -0.113  -0.088  -0.032  -0.150  -0.179  -0.142  -0.231
20    E        -0.078  -0.129  -0.135  -0.228  -0.310  -0.322  -0.179  -0.256  -0.266
21    S        -1.296  -1.282  -1.260  -1.145  -1.118  -1.082  -1.118  -1.095  -1.058
22    D        -0.078  -0.055  -0.113  -0.045  -0.002  -0.100  -0.179  -0.142  -0.231
23    K        -1.296  -1.282  -1.260  -1.164  -1.113  -1.100  -1.118  -1.095  -1.058
24    P         1.599   1.608   1.625   1.783   1.799   1.821   1.698   1.708   1.729
25    I        -0.078  -0.129  -0.135  -0.403  -0.505  -0.519  -0.179  -0.256  -0.266
26    L        -0.078  -0.055  -0.113  -0.458  -0.429  -0.516  -0.179  -0.142  -0.231
27    I        -1.296  -1.282  -1.260  -1.290  -1.269  -1.226  -1.118  -1.095  -1.058
28    Y        -0.078  -0.129  -0.135   0.246   0.167   0.172  -0.179  -0.256  -0.266
29    V        -1.296  -1.282  -1.260  -0.889  -0.856  -0.827  -1.118  -1.095  -1.058
30    P        -0.078  -0.129  -0.135   0.192   0.112   0.110  -0.179  -0.256  -0.266
31    N        -1.296  -1.282  -1.260  -1.098  -1.080  -1.035  -1.118  -1.095  -1.058
32    E        -1.296  -1.282  -1.260  -1.079  -1.049  -1.016  -1.118  -1.095  -1.058
33    A        -1.296  -1.282  -1.260  -1.033  -1.038  -0.970  -1.118  -1.095  -1.058
34    E        -1.296  -1.282  -1.260  -1.202  -1.164  -1.139  -1.118  -1.095  -1.058
35    N        -1.296  -1.282  -1.260  -1.145  -1.126  -1.082  -1.118  -1.095  -1.058
36    E        -0.078  -0.129  -0.135  -0.081  -0.145  -0.145  -0.179  -0.256  -0.266
37    M        -0.078  -0.129  -0.135   0.026  -0.096  -0.114  -0.179  -0.256  -0.266
38    N        -0.078  -0.017  -0.098  -0.176  -0.076  -0.201  -0.179  -0.084  -0.207
39    D        -0.227  -0.220  -0.195   0.018   0.021   0.071  -0.414  -0.401  -0.361
40    V        -0.227  -0.220  -0.195  -0.585  -0.581  -0.526  -0.414  -0.401  -0.361
41    L        -0.078  -0.129  -0.135  -0.458  -0.556  -0.555  -0.179  -0.256  -0.266
42    K         1.599   1.608   1.625   1.550   1.565   1.590   1.698   1.708   1.729
43    Y        -0.078  -0.055  -0.113   0.068   0.110  -0.001  -0.179  -0.142  -0.231
44    N         1.599   1.608   1.625   1.660   1.673   1.699   1.698   1.708   1.729
45    V         1.599   1.608   1.625   1.566   1.581   1.606   1.698   1.708   1.729
46    L         1.599   1.608   1.625   1.307   1.312   1.350   1.698   1.708   1.729
47    S        -0.078  -0.055  -0.113   0.005   0.057  -0.032  -0.179  -0.142  -0.231
48    N         1.599   1.608   1.625   1.660   1.673   1.699   1.698   1.708   1.729
49    I        -0.078  -0.129  -0.135  -0.403  -0.505  -0.519  -0.179  -0.256  -0.266
50    S        -0.078  -0.129  -0.135   0.005  -0.045  -0.061  -0.179  -0.256  -0.266
51    L         1.599   1.608   1.625   1.307   1.312   1.350   1.698   1.708   1.729
52    D         1.599   1.608   1.625   1.628   1.655   1.668   1.698   1.708   1.729
53    Y         1.599   1.608   1.625   1.798   1.809   1.836   1.698   1.708   1.729
54    F         1.599   1.608   1.625   1.644   1.659   1.683   1.698   1.708   1.729
55    E        -0.078  -0.129  -0.135  -0.095  -0.162  -0.162  -0.179  -0.256  -0.266
56    S        -0.078  -0.129  -0.135  -0.183  -0.253  -0.289  -0.179  -0.256  -0.266
57    A        -1.296  -1.282  -1.260  -0.951  -0.945  -0.889  -1.118  -1.095  -1.058
58    L        -0.078  -0.129  -0.135  -0.288  -0.371  -0.349  -0.179  -0.256  -0.266
59    V        -0.227  -0.220  -0.195  -0.210  -0.197  -0.155  -0.414  -0.401  -0.361
60    E        -0.227  -0.220  -0.195  -0.534  -0.511  -0.476  -0.414  -0.401  -0.361
61    W         1.599   1.608   1.625   2.008   2.024   2.044   1.698   1.708   1.729
62    -         1.599   1.608   1.625   1.558   1.573   1.598   1.698   1.708   1.729
63    H        -1.296  -1.282  -1.260  -0.759  -0.754  -0.699  -1.118  -1.095  -1.058
64    S        -1.296  -1.282  -1.260  -1.145  -1.118  -1.082  -1.118  -1.095  -1.058
65    L        -1.296  -1.282  -1.260  -1.290  -1.233  -1.226  -1.118  -1.095  -1.058
66    D         1.599   1.608   1.625   1.628   1.655   1.668   1.698   1.708   1.729
67    S        -1.296  -1.282  -1.260  -0.969  -0.926  -0.907  -1.118  -1.095  -1.058
68    K        -1.296  -1.282  -1.260  -1.164  -1.128  -1.100  -1.118  -1.095  -1.058
69    P        -0.078  -0.055  -0.113   0.054   0.091  -0.014  -0.179  -0.142  -0.231
70    L        -1.296  -1.282  -1.260  -1.310  -1.289  -1.246  -1.118  -1.095  -1.058
71    L        -1.296  -1.282  -1.260  -1.433  -1.388  -1.367  -1.118  -1.095  -1.058
72    K         1.599   1.608   1.625   1.583   1.588   1.623   1.698   1.708   1.729
73    S        -0.227  -0.220  -0.195  -0.401  -0.393  -0.344  -0.414  -0.401  -0.361
74    I        -0.078  -0.017  -0.098  -0.458  -0.364  -0.489  -0.179  -0.084  -0.207
75    F         1.599   1.608   1.625   1.644   1.659   1.683   1.698   1.708   1.729
76    Q        -0.078  -0.129  -0.135   0.089  -0.012  -0.033  -0.179  -0.256  -0.266
77    L        -1.296  -1.282  -1.260  -1.381  -1.330  -1.316  -1.118  -1.095  -1.058
78    E        -0.078  -0.129  -0.135  -0.031  -0.089  -0.085  -0.179  -0.256  -0.266
79    G        -0.078  -0.017  -0.098  -0.095  -0.004  -0.112  -0.179  -0.084  -0.207
80    V        -0.078  -0.129  -0.135  -0.213  -0.308  -0.325  -0.179  -0.256  -0.266
81    S        -0.078  -0.129  -0.135  -0.146  -0.216  -0.244  -0.179  -0.256  -0.266
82    V         1.599   1.608   1.625   1.566   1.581   1.606   1.698   1.708   1.729
83    F        -0.078  -0.129  -0.135   0.033  -0.049  -0.047  -0.179  -0.256  -0.266
84    A        -0.078  -0.017  -0.098   0.240   0.327   0.214  -0.179  -0.084  -0.207
85    M        -0.078  -0.129  -0.135   0.103   0.000  -0.020  -0.179  -0.256  -0.266
86    L        -0.078  -0.129  -0.135  -0.273  -0.353  -0.331  -0.179  -0.256  -0.266
87    I        -1.296  -1.282  -1.260  -1.592  -1.588  -1.525  -1.118  -1.095  -1.058
88    K        -1.296  -1.282  -1.260  -1.330  -1.300  -1.266  -1.118  -1.095  -1.058
89    Q        -0.078  -0.055  -0.113   0.124   0.169   0.052  -0.179  -0.142  -0.231
90    T        -0.078  -0.129  -0.135   0.033  -0.071  -0.078  -0.179  -0.256  -0.266
91    G        -0.078  -0.055  -0.113   0.137   0.169   0.073  -0.179  -0.142  -0.231
92    L         1.599   1.608   1.625   1.307   1.312   1.350   1.698   1.708   1.729
93    K         1.599   1.608   1.625   1.550   1.565   1.590   1.698   1.708   1.729
94    I         1.599   1.608   1.625   1.422   1.445   1.463   1.698   1.708   1.729
95    V         1.599   1.608   1.625   1.566   1.581   1.606   1.698   1.708   1.729
96    I        -0.078  -0.055  -0.113  -0.403  -0.362  -0.474  -0.179  -0.142  -0.231
97    G         1.599   1.608   1.625   1.828   1.841   1.866   1.698   1.708   1.729
98    F         1.599   1.608   1.625   1.644   1.659   1.683   1.698   1.708   1.729
99    E        -1.296  -1.282  -1.260  -1.183  -1.157  -1.119  -1.118  -1.095  -1.058
100   Q        -0.227  -0.220  -0.195  -0.006  -0.001   0.048  -0.414  -0.401  -0.361
101   K        -0.227  -0.220  -0.195  -0.196  -0.195  -0.141  -0.414  -0.401  -0.361
102   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   A        -0.227  -0.220  -0.195  -0.163  -0.149  -0.109  -0.414  -0.401  -0.361
107   D         1.599   1.608   1.625   1.713   1.722   1.752   1.698   1.708   1.729
108   D        -0.227  -0.220  -0.195  -0.226  -0.229  -0.170  -0.414  -0.401  -0.361
109   E        -0.227  -0.220  -0.195  -0.619  -0.581  -0.560  -0.414  -0.401  -0.361
110   F         1.599   1.608   1.625   1.670   1.678   1.709   1.698   1.708   1.729
111   E        -0.078  -0.055  -0.113  -0.191  -0.144  -0.242  -0.179  -0.142  -0.231
112   -         1.599   1.608   1.625   1.604   1.643   1.644   1.698   1.708   1.729
113   -        -0.227  -0.220  -0.195  -0.457  -0.432  -0.399  -0.414  -0.401  -0.361
114   A        -0.078  -0.055  -0.113   0.117   0.159   0.039  -0.179  -0.142  -0.231
115   I         1.599   1.608   1.625   1.422   1.445   1.463   1.698   1.708   1.729
116   N        -1.296  -1.282  -1.260  -1.281  -1.271  -1.216  -1.118  -1.095  -1.058
117   Q        -1.296  -1.282  -1.260  -0.853  -0.842  -0.793  -1.118  -1.095  -1.058
118   I        -0.078  -0.129  -0.135  -0.243  -0.318  -0.324  -0.179  -0.256  -0.266
119   F         1.599   1.608   1.625   1.644   1.659   1.683   1.698   1.708   1.729
120   E        -1.296  -1.282  -1.260  -1.154  -1.106  -1.091  -1.118  -1.095  -1.058
121   T        -1.296  -1.282  -1.260  -1.051  -1.056  -0.989  -1.118  -1.095  -1.058
122   V        -0.078  -0.055  -0.113  -0.213  -0.172  -0.282  -0.179  -0.142  -0.231
123   R        -0.078  -0.129  -0.135   0.103   0.005  -0.013  -0.179  -0.256  -0.266
124   K        -0.078  -0.129  -0.135  -0.280  -0.393  -0.403  -0.179  -0.256  -0.266
125   I        -1.296  -1.282  -1.260  -1.271  -1.230  -1.206  -1.118  -1.095  -1.058
126   Y         1.599   1.608   1.625   1.798   1.809   1.836   1.698   1.708   1.729
127   I        -1.296  -1.282  -1.260  -1.453  -1.457  -1.387  -1.118  -1.095  -1.058
128   R        -0.078  -0.129  -0.135   0.103   0.005  -0.013  -0.179  -0.256  -0.266
129   V        -0.078  -0.129  -0.135  -0.146  -0.225  -0.244  -0.179  -0.256  -0.266
130   K        -0.078  -0.129  -0.135  -0.161  -0.252  -0.258  -0.179  -0.256  -0.266
131   C        -0.078  -0.129  -0.135   0.158   0.056   0.024  -0.179  -0.256  -0.266
132   N         1.599   1.608   1.625   1.660   1.673   1.699   1.698   1.708   1.729
133   P         1.599   1.608   1.625   1.783   1.799   1.821   1.698   1.708   1.729
134   L        -0.078  -0.017  -0.098  -0.191  -0.083  -0.238  -0.179  -0.084  -0.207
135   L        -0.227  -0.220  -0.195  -0.706  -0.705  -0.646  -0.414  -0.401  -0.361
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   V        -0.227  -0.220  -0.195  -0.585  -0.581  -0.526  -0.414  -0.401  -0.361
140   S        -0.227  -0.220  -0.195  -0.619  -0.581  -0.560  -0.414  -0.401  -0.361
141   G        -0.227  -0.220  -0.195  -0.117  -0.118  -0.063  -0.414  -0.401  -0.361
142   D        -0.227  -0.220  -0.195  -0.057  -0.055  -0.003  -0.414  -0.401  -0.361
143   E        -0.078  -0.129  -0.135  -0.176  -0.253  -0.259  -0.179  -0.256  -0.266
144   K        -1.296  -1.282  -1.260  -1.351  -1.315  -1.286  -1.118  -1.095  -1.058
145   S        -1.296  -1.282  -1.260  -1.340  -1.292  -1.275  -1.118  -1.095  -1.058
146   I        -1.296  -1.282  -1.260  -1.145  -1.088  -1.082  -1.118  -1.095  -1.058
147   I        -0.078  -0.055  -0.113  -0.280  -0.228  -0.333  -0.179  -0.142  -0.231
148   K        -1.296  -1.282  -1.260  -1.107  -1.089  -1.044  -1.118  -1.095  -1.058
149   S        -1.296  -1.282  -1.260  -1.300  -1.253  -1.236  -1.118  -1.095  -1.058
150   L        -0.078  -0.129  -0.135  -0.458  -0.556  -0.555  -0.179  -0.256  -0.266
151   E        -0.078  -0.129  -0.135  -0.088  -0.151  -0.154  -0.179  -0.256  -0.266
152   R        -1.296  -1.282  -1.260  -0.960  -0.927  -0.898  -1.118  -1.095  -1.058
153   K         1.599   1.608   1.625   1.550   1.565   1.590   1.698   1.708   1.729
154   F        -0.078  -0.017  -0.098  -0.349  -0.269  -0.368  -0.179  -0.084  -0.207
155   D        -0.078  -0.055  -0.113  -0.045  -0.002  -0.100  -0.179  -0.142  -0.231
156   E        -0.078  -0.129  -0.135  -0.125  -0.197  -0.197  -0.179  -0.256  -0.266
157   L        -0.078  -0.055  -0.113  -0.458  -0.429  -0.516  -0.179  -0.142  -0.231
158   F        -0.078  -0.129  -0.135   0.061  -0.016  -0.013  -0.179  -0.256  -0.266
159   I        -1.296  -1.282  -1.260  -1.453  -1.457  -1.387  -1.118  -1.095  -1.058
160   S        -0.227  -0.220  -0.195  -0.412  -0.416  -0.355  -0.414  -0.401  -0.361
161   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   L        -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/P32613
Output conservation file - output/P32613
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
