1     M         1.250   1.251   1.262   1.519   1.518   1.534   1.304   1.305   1.318
2     D        -0.216  -0.217  -0.276  -0.076  -0.080  -0.163  -0.325  -0.327  -0.416
3     Q        -0.346  -0.346  -0.327  -0.137  -0.136  -0.108  -0.528  -0.528  -0.496
4     K        -0.346  -0.346  -0.327  -0.659  -0.659  -0.626  -0.528  -0.528  -0.496
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    K         1.250   1.251   1.262   0.952   0.953   0.972   1.304   1.305   1.318
11    D         1.250   1.251   1.262   1.284   1.285   1.301   1.304   1.305   1.318
12    P         1.250   1.251   1.262   1.263   1.263   1.280   1.304   1.305   1.318
13    S        -0.346  -0.346  -0.327  -0.659  -0.659  -0.626  -0.528  -0.528  -0.496
14    N        -0.346  -0.346  -0.327  -0.542  -0.541  -0.510  -0.528  -0.528  -0.496
15    N         1.250   1.251   1.262   1.088   1.088   1.106   1.304   1.305   1.318
16    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    T        -0.346  -0.346  -0.327  -0.241  -0.241  -0.212  -0.528  -0.528  -0.496
18    E         1.250   1.251   1.262   1.132   1.132   1.150   1.304   1.305   1.318
19    R        -0.346  -0.346  -0.327  -0.642  -0.642  -0.609  -0.528  -0.528  -0.496
20    R        -0.346  -0.346  -0.327  -0.412  -0.412  -0.381  -0.528  -0.528  -0.496
21    V         1.250   1.251   1.262   1.369   1.370   1.385   1.304   1.305   1.318
22    S        -0.346  -0.346  -0.327  -0.525  -0.525  -0.493  -0.528  -0.528  -0.496
23    K        -0.346  -0.346  -0.327  -0.396  -0.396  -0.365  -0.528  -0.528  -0.496
24    V        -0.346  -0.346  -0.327  -0.196  -0.196  -0.167  -0.528  -0.528  -0.496
25    Q        -0.346  -0.346  -0.327  -0.365  -0.364  -0.334  -0.528  -0.528  -0.496
26    R        -0.346  -0.346  -0.327  -0.542  -0.541  -0.510  -0.528  -0.528  -0.496
27    P        -0.346  -0.346  -0.327  -0.365  -0.364  -0.334  -0.528  -0.528  -0.496
28    N         1.250   1.251   1.262   1.088   1.088   1.106   1.304   1.305   1.318
29    K        -0.216  -0.217  -0.276  -0.501  -0.502  -0.585  -0.325  -0.327  -0.416
30    K        -0.216  -0.246  -0.265  -0.346  -0.380  -0.387  -0.325  -0.371  -0.399
31    K        -1.280  -1.278  -1.257  -1.461  -1.444  -1.421  -1.139  -1.136  -1.101
32    V        -1.280  -1.278  -1.257  -1.134  -1.136  -1.097  -1.139  -1.136  -1.101
33    R        -1.280  -1.278  -1.257  -1.303  -1.289  -1.264  -1.139  -1.136  -1.101
34    N        -1.280  -1.278  -1.257  -1.154  -1.136  -1.117  -1.139  -1.136  -1.101
35    Q        -0.216  -0.217  -0.276   0.026   0.025  -0.060  -0.325  -0.327  -0.416
36    V        -0.216  -0.217  -0.276  -0.076  -0.075  -0.193  -0.325  -0.327  -0.416
37    E        -0.216  -0.246  -0.265  -0.298  -0.345  -0.380  -0.325  -0.371  -0.399
38    S        -0.216  -0.180  -0.262  -0.099  -0.037  -0.184  -0.325  -0.270  -0.393
39    L         1.250   1.251   1.262   1.178   1.177   1.195   1.304   1.305   1.318
40    S        -0.216  -0.246  -0.265  -0.386  -0.445  -0.491  -0.325  -0.371  -0.399
41    R        -0.216  -0.217  -0.276  -0.251  -0.248  -0.354  -0.325  -0.327  -0.416
42    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    L         1.250   1.251   1.262   1.176   1.176   1.194   1.304   1.305   1.318
44    E         1.250   1.251   1.262   1.132   1.132   1.150   1.304   1.305   1.318
45    R        -1.280  -1.278  -1.257  -1.449  -1.452  -1.409  -1.139  -1.136  -1.101
46    N        -0.216  -0.217  -0.276  -0.275  -0.272  -0.374  -0.325  -0.327  -0.416
47    K        -0.216  -0.246  -0.265  -0.419  -0.460  -0.472  -0.325  -0.371  -0.399
48    E        -0.216  -0.217  -0.276  -0.213  -0.212  -0.294  -0.325  -0.327  -0.416
49    G        -1.280  -1.278  -1.257  -1.369  -1.368  -1.330  -1.139  -1.136  -1.101
50    Q        -1.280  -1.278  -1.257  -1.336  -1.340  -1.297  -1.139  -1.136  -1.101
51    L        -1.280  -1.278  -1.257  -1.369  -1.365  -1.330  -1.139  -1.136  -1.101
52    L         1.250   1.251   1.262   1.178   1.177   1.195   1.304   1.305   1.318
53    Q        -1.280  -1.278  -1.257  -1.314  -1.317  -1.275  -1.139  -1.136  -1.101
54    T        -1.280  -1.278  -1.257  -0.917  -0.917  -0.881  -1.139  -1.136  -1.101
55    V         1.250   1.251   1.262   1.392   1.395   1.408   1.304   1.305   1.318
56    S        -1.280  -1.278  -1.257  -1.144  -1.134  -1.107  -1.139  -1.136  -1.101
57    K        -0.216  -0.217  -0.276  -0.526  -0.529  -0.616  -0.325  -0.327  -0.416
58    G        -1.280  -1.278  -1.257  -1.154  -1.155  -1.117  -1.139  -1.136  -1.101
59    H        -1.280  -1.278  -1.257  -1.003  -1.009  -0.967  -1.139  -1.136  -1.101
60    L        -1.280  -1.278  -1.257  -0.994  -0.984  -0.958  -1.139  -1.136  -1.101
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    E        -0.346  -0.346  -0.327  -0.525  -0.525  -0.493  -0.528  -0.528  -0.496
66    A         1.250   1.251   1.262   1.432   1.433   1.448   1.304   1.305   1.318
67    D        -0.346  -0.346  -0.327  -0.476  -0.476  -0.445  -0.528  -0.528  -0.496
68    S        -0.346  -0.346  -0.327  -0.365  -0.364  -0.334  -0.528  -0.528  -0.496
69    G        -0.346  -0.346  -0.327  -0.241  -0.241  -0.212  -0.528  -0.528  -0.496
70    H        -0.346  -0.346  -0.327  -0.257  -0.256  -0.227  -0.528  -0.528  -0.496
71    S         1.250   1.251   1.262   1.176   1.176   1.194   1.304   1.305   1.318
72    L        -0.346  -0.346  -0.327  -0.303  -0.302  -0.272  -0.528  -0.528  -0.496
73    G         1.250   1.251   1.262   1.263   1.263   1.280   1.304   1.305   1.318
74    R        -1.280  -1.278  -1.257  -1.426  -1.431  -1.386  -1.139  -1.136  -1.101
75    E        -1.280  -1.278  -1.257  -1.392  -1.398  -1.353  -1.139  -1.136  -1.101
76    K        -0.216  -0.246  -0.265  -0.510  -0.559  -0.579  -0.325  -0.371  -0.399
77    E        -1.280  -1.278  -1.257  -1.013  -0.997  -0.977  -1.139  -1.136  -1.101
78    N        -1.280  -1.278  -1.257  -1.113  -1.104  -1.076  -1.139  -1.136  -1.101
79    G        -1.280  -1.278  -1.257  -1.043  -1.029  -1.007  -1.139  -1.136  -1.101
80    E         1.250   1.251   1.262   1.144   1.146   1.162   1.304   1.305   1.318
81    L         1.250   1.251   1.262   1.178   1.177   1.195   1.304   1.305   1.318
82    G         1.250   1.251   1.262   1.294   1.297   1.311   1.304   1.305   1.318
83    I        -0.216  -0.217  -0.276  -0.099  -0.106  -0.212  -0.325  -0.327  -0.416
84    R        -0.216  -0.180  -0.262  -0.501  -0.447  -0.564  -0.325  -0.270  -0.393
85    S         1.250   1.251   1.262   1.178   1.179   1.195   1.304   1.305   1.318
86    I         1.250   1.251   1.262   1.359   1.357   1.376   1.304   1.305   1.318
87    F         1.250   1.251   1.262   1.472   1.470   1.487   1.304   1.305   1.318
88    Y         1.250   1.251   1.262   1.456   1.456   1.471   1.304   1.305   1.318
89    D         1.250   1.251   1.262   1.277   1.274   1.294   1.304   1.305   1.318
90    K        -0.216  -0.180  -0.262  -0.386  -0.325  -0.483  -0.325  -0.270  -0.393
91    D         1.250   1.251   1.262   1.277   1.274   1.294   1.304   1.305   1.318
92    W         1.250   1.251   1.262   1.550   1.551   1.565   1.304   1.305   1.318
93    N         1.250   1.251   1.262   1.161   1.164   1.179   1.304   1.305   1.318
94    P         1.250   1.251   1.262   1.178   1.173   1.195   1.304   1.305   1.318
95    R        -1.280  -1.278  -1.257  -1.426  -1.419  -1.386  -1.139  -1.136  -1.101
96    G         1.250   1.251   1.262   1.294   1.297   1.311   1.304   1.305   1.318
97    T        -1.280  -1.278  -1.257  -1.281  -1.296  -1.243  -1.139  -1.136  -1.101
98    A         1.250   1.251   1.262   1.440   1.441   1.455   1.304   1.305   1.318
99    P         1.250   1.251   1.262   1.178   1.173   1.195   1.304   1.305   1.318
100   S        -1.280  -1.278  -1.257  -1.023  -1.010  -0.987  -1.139  -1.136  -1.101
101   H        -0.216  -0.180  -0.262  -0.010   0.041  -0.068  -0.325  -0.270  -0.393
102   Y        -1.280  -1.278  -1.257  -0.917  -0.923  -0.881  -1.139  -1.136  -1.101
103   R        -0.216  -0.246  -0.265  -0.370  -0.424  -0.476  -0.325  -0.371  -0.399
104   N         1.250   1.251   1.262   1.161   1.164   1.179   1.304   1.305   1.318
105   I        -0.216  -0.217  -0.276  -0.003  -0.006  -0.095  -0.325  -0.327  -0.416
106   P         1.250   1.251   1.262   1.178   1.173   1.195   1.304   1.305   1.318
107   Y         1.250   1.251   1.262   1.456   1.456   1.471   1.304   1.305   1.318
108   N         1.250   1.251   1.262   1.161   1.164   1.179   1.304   1.305   1.318
109   P         1.250   1.251   1.262   1.178   1.173   1.195   1.304   1.305   1.318
110   A        -1.280  -1.278  -1.257  -1.249  -1.251  -1.211  -1.139  -1.136  -1.101
111   T         1.250   1.251   1.262   1.440   1.442   1.455   1.304   1.305   1.318
112   F         1.250   1.251   1.262   1.472   1.470   1.487   1.304   1.305   1.318
113   K        -0.216  -0.246  -0.265  -0.501  -0.544  -0.569  -0.325  -0.371  -0.399
114   R         1.250   1.251   1.262   1.194   1.200   1.212   1.304   1.305   1.318
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   R        -1.280  -1.278  -1.257  -0.994  -0.984  -0.958  -1.139  -1.136  -1.101
117   T        -0.216  -0.217  -0.276  -0.032  -0.031  -0.152  -0.325  -0.327  -0.416
118   E        -1.280  -1.278  -1.257  -1.175  -1.171  -1.138  -1.139  -1.136  -1.101
119   V        -0.216  -0.180  -0.262  -0.003   0.049  -0.072  -0.325  -0.270  -0.393
120   Q        -0.216  -0.180  -0.262  -0.213  -0.160  -0.274  -0.325  -0.270  -0.393
121   A        -1.280  -1.278  -1.257  -1.123  -1.131  -1.086  -1.139  -1.136  -1.101
122   R        -0.216  -0.217  -0.276  -0.205  -0.204  -0.298  -0.325  -0.327  -0.416
123   L         1.250   1.251   1.262   1.178   1.177   1.195   1.304   1.305   1.318
124   G        -0.216  -0.246  -0.265  -0.167  -0.215  -0.257  -0.325  -0.371  -0.399
125   N        -1.280  -1.278  -1.257  -1.206  -1.193  -1.169  -1.139  -1.136  -1.101
126   L         1.250   1.251   1.262   1.178   1.177   1.195   1.304   1.305   1.318
127   E        -1.280  -1.278  -1.257  -1.461  -1.464  -1.421  -1.139  -1.136  -1.101
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   N        -1.280  -1.278  -1.257  -1.472  -1.466  -1.432  -1.139  -1.136  -1.101
130   I        -0.216  -0.217  -0.276  -0.099  -0.104  -0.212  -0.325  -0.327  -0.416
131   K        -0.216  -0.246  -0.265  -0.510  -0.559  -0.579  -0.325  -0.371  -0.399
132   I        -1.280  -1.278  -1.257  -0.984  -0.988  -0.948  -1.139  -1.136  -1.101
133   P         1.250   1.251   1.262   1.178   1.173   1.195   1.304   1.305   1.318
134   K        -0.216  -0.217  -0.276  -0.526  -0.529  -0.616  -0.325  -0.327  -0.416
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     *
* 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/P38305
Output conservation file - output/P38305
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
