1     M         0.971   0.999   1.039   1.325   1.335   1.373   1.004   1.041   1.100
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    S        -1.154  -1.117  -1.079  -1.339  -1.320  -1.302  -1.227  -1.173  -1.081
42    E        -0.142  -0.164  -0.275   0.078   0.026  -0.132  -0.245  -0.286  -0.492
43    V        -1.991  -1.888  -1.666  -2.013  -1.843  -1.539  -1.807  -1.671  -1.385
44    I        -1.142  -1.274  -1.101  -1.183  -1.410  -1.130  -1.182  -1.338  -1.105
45    E        -0.526  -0.470  -0.307  -0.760  -0.733  -0.456  -0.870  -0.788  -0.545
46    G        -0.279  -0.438  -0.310  -0.704  -0.881  -0.613  -0.460  -0.732  -0.550
47    N        -1.341  -1.226  -1.103  -1.536  -1.352  -1.275  -1.436  -1.297  -1.107
48    V        -0.031  -0.084  -0.261  -0.016  -0.084  -0.389  -0.080  -0.163  -0.467
49    K        -1.869  -1.715  -1.630  -1.673  -1.401  -1.364  -1.705  -1.488  -1.353
50    I        -1.154  -1.150  -1.080  -1.268  -1.252  -1.160  -1.227  -1.198  -1.081
51    D        -2.475  -2.241  -2.087  -2.281  -1.908  -1.746  -2.023  -1.767  -1.540
52    R        -1.869  -1.833  -1.650  -1.698  -1.673  -1.429  -1.705  -1.619  -1.371
53    I        -1.154  -1.202  -1.078  -1.316  -1.363  -1.200  -1.227  -1.247  -1.079
54    S        -0.548  -0.477  -0.310  -0.613  -0.477  -0.244  -0.908  -0.800  -0.550
55    P        -1.154  -1.194  -1.084  -1.234  -1.268  -1.080  -1.227  -1.262  -1.087
56    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
57    D         0.059   0.023  -0.230   0.241   0.202  -0.185   0.048  -0.005  -0.417
58    G        -0.800  -0.773  -1.040  -1.057  -0.994  -1.254  -0.749  -0.740  -1.031
59    A        -1.869  -1.697  -1.637  -1.773  -1.565  -1.394  -1.705  -1.513  -1.360
60    T        -0.800  -0.636  -1.026  -0.625  -0.436  -0.955  -0.749  -0.553  -1.015
61    F         0.059   0.050  -0.229   0.365   0.356  -0.065   0.048   0.034  -0.414
62    P         0.059  -0.128  -0.241   0.098  -0.127  -0.291   0.048  -0.230  -0.435
63    K         0.971   0.999   1.039   0.998   1.024   1.103   1.004   1.041   1.100
64    T        -1.594  -1.211  -1.598  -1.474  -0.968  -1.476  -1.386  -0.965  -1.322
65    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
66    D         0.971   0.999   1.039   1.038   1.074   1.136   1.004   1.041   1.100
67    L        -1.594  -1.758  -1.644  -1.406  -1.635  -1.445  -1.386  -1.535  -1.365
68    V         0.059   0.023  -0.230   0.104   0.069  -0.344   0.048  -0.005  -0.417
69    T         0.971   0.999   1.039   0.966   0.986   1.076   1.004   1.041   1.100
70    I         0.059   0.023  -0.230   0.190   0.159  -0.173   0.048  -0.005  -0.417
71    H         0.971   0.999   1.039   1.340   1.352   1.386   1.004   1.041   1.100
72    Y         0.971   0.999   1.039   1.249   1.270   1.310   1.004   1.041   1.100
73    T        -0.800  -0.981  -1.055  -0.669  -0.945  -1.090  -0.749  -0.972  -1.050
74    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
75    T         0.059  -0.128  -0.241   0.143  -0.135  -0.323   0.048  -0.230  -0.435
76    L         0.971   0.999   1.039   0.910   0.952   1.029   1.004   1.041   1.100
77    E        -0.359  -0.431  -0.313  -0.366  -0.551  -0.383  -0.589  -0.720  -0.555
78    N         0.971   0.999   1.039   1.156   1.179   1.233   1.004   1.041   1.100
79    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
80    Q        -0.548  -0.475  -0.308  -0.632  -0.558  -0.302  -0.908  -0.796  -0.546
81    K         0.059  -0.128  -0.241   0.193  -0.070  -0.252   0.048  -0.230  -0.435
82    F         0.971   0.999   1.039   1.148   1.178   1.227   1.004   1.041   1.100
83    D         0.971   0.999   1.039   1.038   1.074   1.136   1.004   1.041   1.100
84    S         0.971   0.999   1.039   1.078   1.118   1.169   1.004   1.041   1.100
85    S         0.971   0.999   1.039   1.078   1.118   1.169   1.004   1.041   1.100
86    V        -0.548  -0.477  -0.310  -0.748  -0.593  -0.342  -0.908  -0.800  -0.550
87    D         0.059  -0.128  -0.241   0.214  -0.049  -0.270   0.048  -0.230  -0.435
88    R         0.971   0.999   1.039   1.187   1.212   1.259   1.004   1.041   1.100
89    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
90    S        -1.154  -1.177  -1.084  -1.104  -1.163  -1.021  -1.227  -1.245  -1.086
91    P         0.971   0.999   1.039   0.885   0.933   1.009   1.004   1.041   1.100
92    F         0.971   0.999   1.039   1.148   1.178   1.227   1.004   1.041   1.100
93    Q        -1.594  -1.758  -1.644  -1.223  -1.529  -1.459  -1.386  -1.535  -1.365
94    C         0.059   0.050  -0.229   0.524   0.491  -0.024   0.048   0.034  -0.414
95    N        -0.548  -0.301  -0.263  -0.741  -0.352  -0.290  -0.908  -0.504  -0.471
96    I         0.059  -0.128  -0.241   0.124  -0.138  -0.357   0.048  -0.230  -0.435
97    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
98    V         0.971   0.999   1.039   0.934   0.978   1.050   1.004   1.041   1.100
99    G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
100   Q         0.059   0.050  -0.229   0.399   0.383  -0.097   0.048   0.034  -0.414
101   V         0.059   0.023  -0.230   0.096   0.060  -0.364   0.048  -0.005  -0.417
102   I         0.971   0.999   1.039   0.958   0.997   1.070   1.004   1.041   1.100
103   K        -1.154  -1.117  -1.079  -1.129  -1.076  -1.028  -1.227  -1.173  -1.081
104   G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
105   W         0.971   0.999   1.039   1.347   1.360   1.392   1.004   1.041   1.100
106   D         0.971   0.999   1.039   1.038   1.074   1.136   1.004   1.041   1.100
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   V        -1.869  -1.658  -1.641  -1.666  -1.394  -1.409  -1.705  -1.480  -1.364
119   G        -0.800  -0.773  -1.040  -1.027  -0.975  -1.196  -0.749  -0.740  -1.031
120   I        -1.154  -1.265  -1.086  -1.288  -1.462  -1.208  -1.227  -1.330  -1.088
121   P         0.971   0.999   1.039   0.885   0.933   1.009   1.004   1.041   1.100
122   K         0.971   0.999   1.039   0.998   1.024   1.103   1.004   1.041   1.100
123   L        -0.800  -1.003  -1.058  -0.661  -0.937  -0.998  -0.749  -0.998  -1.054
124   S         0.971   0.999   1.039   1.078   1.118   1.169   1.004   1.041   1.100
125   V        -1.154  -1.265  -1.086  -1.301  -1.464  -1.198  -1.227  -1.330  -1.088
126   G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
127   E        -0.800  -0.941  -1.053  -0.514  -0.752  -0.962  -0.749  -0.925  -1.047
128   K        -0.359  -0.327  -0.295  -0.387  -0.345  -0.302  -0.589  -0.546  -0.524
129   A         0.059   0.050  -0.229   0.398   0.384  -0.087   0.048   0.034  -0.414
130   R        -1.869  -1.893  -1.651  -1.747  -1.826  -1.512  -1.705  -1.674  -1.372
131   L         0.971   0.999   1.039   0.910   0.952   1.029   1.004   1.041   1.100
132   T         0.059   0.099  -0.220   0.156   0.201  -0.253   0.048   0.103  -0.400
133   I         0.971   0.999   1.039   0.958   0.997   1.070   1.004   1.041   1.100
134   P        -0.800  -0.854  -1.047  -0.735  -0.793  -1.100  -0.749  -0.807  -1.040
135   G        -0.359  -0.431  -0.313  -0.963  -1.050  -0.806  -0.589  -0.720  -0.555
136   P        -1.869  -1.872  -1.653  -1.805  -1.733  -1.389  -1.705  -1.657  -1.374
137   Y        -0.800  -0.941  -1.053  -0.382  -0.623  -0.880  -0.749  -0.925  -1.047
138   A        -0.359  -0.361  -0.303  -0.428  -0.477  -0.516  -0.589  -0.602  -0.538
139   Y         0.971   0.999   1.039   1.249   1.270   1.310   1.004   1.041   1.100
140   G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
141   P        -0.800  -0.788  -1.036  -0.714  -0.678  -1.042  -0.749  -0.725  -1.026
142   R         0.971   0.999   1.039   1.187   1.212   1.259   1.004   1.041   1.100
143   G         0.971   0.999   1.039   0.524   0.595   0.710   1.004   1.041   1.100
144   F         0.059  -0.128  -0.241   0.317   0.045  -0.205   0.048  -0.230  -0.435
145   P         0.971   0.999   1.039   0.885   0.933   1.009   1.004   1.041   1.100
146   G         0.059  -0.128  -0.241  -0.323  -0.550  -0.708   0.048  -0.230  -0.435
147   L         0.059  -0.128  -0.241   0.079  -0.176  -0.382   0.048  -0.230  -0.435
148   I         0.971   0.999   1.039   0.958   0.997   1.070   1.004   1.041   1.100
149   P         0.059  -0.128  -0.241  -0.016  -0.306  -0.587   0.048  -0.230  -0.435
150   P         0.971   0.999   1.039   0.885   0.933   1.009   1.004   1.041   1.100
151   N         0.971   0.999   1.039   1.156   1.179   1.233   1.004   1.041   1.100
152   S        -1.154  -1.202  -1.078  -0.951  -1.008  -0.892  -1.227  -1.247  -1.079
153   T         0.971   0.999   1.039   0.966   0.986   1.076   1.004   1.041   1.100
154   L         0.971   0.999   1.039   0.910   0.952   1.029   1.004   1.041   1.100
155   V        -1.154  -0.931  -1.062  -1.311  -1.008  -1.175  -1.227  -0.982  -1.061
156   F         0.971   0.999   1.039   1.148   1.178   1.227   1.004   1.041   1.100
157   D         0.059  -0.128  -0.241   0.233  -0.021  -0.223   0.048  -0.230  -0.435
158   V         0.971   0.999   1.039   0.934   0.978   1.050   1.004   1.041   1.100
159   E         0.971   0.999   1.039   1.109   1.124   1.195   1.004   1.041   1.100
160   L         0.971   0.999   1.039   0.910   0.952   1.029   1.004   1.041   1.100
161   L         0.971   0.999   1.039   0.910   0.952   1.029   1.004   1.041   1.100
162   K        -1.869  -1.807  -1.642  -2.030  -1.998  -1.662  -1.705  -1.597  -1.364
163   V        -0.548  -0.464  -0.314  -0.892  -0.737  -0.499  -0.908  -0.776  -0.557
164   N         0.971   0.999   1.039   1.156   1.179   1.233   1.004   1.041   1.100
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -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/P20081
Output conservation file - output/P20081
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
