1     M         1.035   1.064   1.123   1.459   1.478   1.526   1.064   1.116   1.198
2     A         0.045  -0.199  -0.249   0.160  -0.232  -0.367   0.042  -0.331  -0.441
3     K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
4     Q        -2.151  -2.001  -1.721  -1.889  -1.773  -1.361  -1.936  -1.758  -1.394
5     S         0.126  -0.068  -0.217   0.000  -0.221  -0.358   0.151  -0.131  -0.390
6     L        -2.569  -2.591  -2.194  -2.163  -2.124  -1.632  -2.066  -2.032  -1.579
7     D         0.126  -0.068  -0.217   0.403   0.100  -0.249   0.151  -0.131  -0.390
8     V         1.035   1.064   1.123   0.905   0.945   1.075   1.064   1.116   1.198
9     S         0.126   0.056  -0.211   0.000  -0.066  -0.349   0.151   0.050  -0.378
10    S         1.035   1.064   1.123   0.734   0.793   0.936   1.064   1.116   1.198
11    D        -0.561  -0.273  -0.247  -0.971  -0.544  -0.456  -0.893  -0.448  -0.438
12    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
13    R        -0.322  -0.080  -0.242  -0.623  -0.256  -0.556  -0.501  -0.148  -0.429
14    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
15    A        -0.740  -0.937  -1.081  -0.477  -0.772  -1.054  -0.632  -0.882  -1.044
16    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
17    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
18    A         1.035   1.064   1.123   1.078   1.121   1.216   1.064   1.116   1.198
19    Y        -0.637  -0.439  -0.272  -0.422  -0.127   0.059  -1.023  -0.719  -0.480
20    F         1.035   1.064   1.123   1.428   1.454   1.501   1.064   1.116   1.198
21    T        -1.315  -1.263  -1.102  -1.322  -1.365  -1.076  -1.414  -1.325  -1.070
22    A         0.126   0.290  -0.193   0.253   0.458  -0.311   0.151   0.365  -0.350
23    P        -0.637  -0.523  -0.308  -0.967  -0.776  -0.442  -1.023  -0.863  -0.539
24    S         1.035   1.064   1.123   0.734   0.793   0.936   1.064   1.116   1.198
25    S        -1.137  -1.051  -1.090  -1.456  -1.302  -1.347  -1.153  -1.025  -1.055
26    E        -0.322  -0.429  -0.300  -0.257  -0.519  -0.386  -0.501  -0.702  -0.527
27    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
28    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
29    V        -1.555  -1.694  -1.697  -1.305  -1.517  -1.470  -1.284  -1.451  -1.371
30    L         0.126  -0.068  -0.217   0.213   0.003  -0.255   0.151  -0.131  -0.390
31    L        -0.637  -0.439  -0.272  -0.693  -0.283  -0.110  -1.023  -0.719  -0.480
32    S         1.035   1.064   1.123   0.734   0.793   0.936   1.064   1.116   1.198
33    A         1.035   1.064   1.123   1.078   1.121   1.216   1.064   1.116   1.198
34    P         1.035   1.064   1.123   1.316   1.348   1.409   1.064   1.116   1.198
35    L         1.035   1.064   1.123   0.972   1.060   1.130   1.064   1.116   1.198
36    S         1.035   1.064   1.123   0.734   0.793   0.936   1.064   1.116   1.198
37    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
38    E         1.035   1.064   1.123   1.207   1.252   1.321   1.064   1.116   1.198
39    L         1.035   1.064   1.123   0.972   1.060   1.130   1.064   1.116   1.198
40    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
41    A        -1.137  -0.696  -1.048  -0.884  -0.290  -0.793  -1.153  -0.611  -1.004
42    Q        -0.322  -0.450  -0.304  -0.214  -0.542  -0.459  -0.501  -0.739  -0.533
43    Y         1.035   1.064   1.123   1.397   1.426   1.476   1.064   1.116   1.198
44    G        -1.576  -1.323  -1.118  -1.770  -1.466  -1.122  -1.675  -1.389  -1.090
45    I        -0.561  -0.465  -0.303  -0.736  -0.621  -0.403  -0.893  -0.764  -0.532
46    K        -0.561  -0.522  -0.298  -1.252  -1.164  -0.739  -0.893  -0.861  -0.523
47    A        -0.561  -0.273  -0.247  -1.056  -0.597  -0.526  -0.893  -0.448  -0.438
48    L        -0.322  -0.339  -0.294  -0.393  -0.405  -0.373  -0.501  -0.554  -0.516
49    P         1.035   1.064   1.123   1.316   1.348   1.409   1.064   1.116   1.198
50    I         0.126   0.056  -0.211   0.394   0.284  -0.193   0.151   0.050  -0.378
51    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
52    R        -1.576  -1.336  -1.121  -2.056  -1.746  -1.341  -1.675  -1.397  -1.093
53    D        -1.137  -0.704  -1.064  -0.786  -0.256  -0.742  -1.153  -0.633  -1.024
54    D         1.035   1.064   1.123   1.227   1.261   1.337   1.064   1.116   1.198
55    E        -0.740  -0.937  -1.081  -0.248  -0.501  -0.734  -0.632  -0.882  -1.044
56    V         0.126   0.056  -0.211   0.146   0.055  -0.293   0.151   0.050  -0.378
57    L        -0.561  -0.522  -0.298  -0.690  -0.573  -0.244  -0.893  -0.861  -0.523
58    V         0.126  -0.068  -0.217   0.146  -0.110  -0.304   0.151  -0.131  -0.390
59    V        -1.555  -1.570  -1.687  -1.305  -1.393  -1.460  -1.284  -1.317  -1.362
60    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
61    G         1.035   1.064   1.123   1.227   1.274   1.337   1.064   1.116   1.198
62    S         0.126  -0.007  -0.219  -0.044  -0.203  -0.482   0.151  -0.040  -0.392
63    K        -1.137  -1.298  -1.125  -1.294  -1.403  -1.041  -1.153  -1.359  -1.097
64    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
65    G         0.126  -0.068  -0.217   0.471   0.220  -0.058   0.151  -0.131  -0.390
66    Q        -2.151  -2.057  -1.725  -2.328  -2.324  -1.882  -1.936  -1.808  -1.397
67    E         1.035   1.064   1.123   1.207   1.252   1.321   1.064   1.116   1.198
68    G         1.035   1.064   1.123   1.227   1.274   1.337   1.064   1.116   1.198
69    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
70    I        -0.561  -0.426  -0.299  -0.839  -0.651  -0.422  -0.893  -0.697  -0.524
71    S        -1.137  -1.039  -1.107  -1.210  -1.123  -1.018  -1.153  -1.109  -1.078
72    S         0.126  -0.007  -0.219  -0.004  -0.139  -0.370   0.151  -0.040  -0.392
73    V         1.035   1.064   1.123   0.905   0.945   1.075   1.064   1.116   1.198
74    Y         1.035   1.064   1.123   1.397   1.426   1.476   1.064   1.116   1.198
75    R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
76    L         0.126   0.056  -0.211   0.133   0.075  -0.467   0.151   0.050  -0.378
77    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
78    F         0.126  -0.068  -0.217   0.694   0.434   0.152   0.151  -0.131  -0.390
79    A        -1.994  -1.992  -1.702  -2.265  -2.305  -1.853  -1.806  -1.750  -1.377
80    V        -1.315  -1.253  -1.106  -1.413  -1.319  -1.129  -1.414  -1.312  -1.077
81    Q        -1.137  -1.225  -1.109  -0.786  -0.880  -0.846  -1.153  -1.248  -1.080
82    V        -0.740  -0.674  -1.052  -0.636  -0.565  -1.091  -0.632  -0.567  -1.009
83    D        -1.315  -1.303  -1.106  -1.127  -1.098  -0.816  -1.414  -1.366  -1.075
84    K        -1.137  -1.298  -1.125  -1.633  -1.925  -1.615  -1.153  -1.359  -1.097
85    V        -0.561  -0.305  -0.266  -0.961  -0.525  -0.486  -0.893  -0.498  -0.470
86    T        -1.137  -1.051  -1.090  -0.755  -0.683  -0.873  -1.153  -1.025  -1.055
87    K        -0.322  -0.429  -0.300  -0.826  -1.015  -0.774  -0.501  -0.702  -0.527
88    E        -0.322  -0.450  -0.304  -0.156  -0.406  -0.222  -0.501  -0.739  -0.533
89    K         1.035   1.064   1.123   0.636   0.730   0.856   1.064   1.116   1.198
90    V        -1.315  -1.039  -1.103  -1.709  -1.272  -1.305  -1.414  -1.125  -1.073
91    N        -0.740  -1.041  -1.089  -0.193  -0.672  -0.874  -0.632  -1.013  -1.054
92    G         1.035   1.064   1.123   1.227   1.274   1.337   1.064   1.116   1.198
93    A         1.035   1.064   1.123   1.078   1.121   1.216   1.064   1.116   1.198
94    S         0.126  -0.007  -0.219  -0.044  -0.203  -0.482   0.151  -0.040  -0.392
95    V         0.126   0.056  -0.211   0.128   0.034  -0.341   0.151   0.050  -0.378
96    P         1.035   1.064   1.123   1.316   1.348   1.409   1.064   1.116   1.198
97    I        -1.315  -1.032  -1.103  -1.332  -1.087  -1.005  -1.414  -1.120  -1.073
98    N        -1.137  -1.055  -1.109  -0.736  -0.742  -0.837  -1.153  -1.124  -1.080
99    L        -1.137  -1.011  -1.078  -0.916  -0.689  -0.855  -1.153  -0.974  -1.041
100   H        -0.740  -0.937  -1.081  -0.051  -0.340  -0.638  -0.632  -0.882  -1.044
101   P        -0.322  -0.402  -0.299  -0.099  -0.296  -0.222  -0.501  -0.657  -0.525
102   S         1.035   1.064   1.123   0.734   0.793   0.936   1.064   1.116   1.198
103   K         0.126  -0.068  -0.217  -0.098  -0.284  -0.428   0.151  -0.131  -0.390
104   L        -0.322  -0.261  -0.287  -0.532  -0.451  -0.525  -0.501  -0.427  -0.505
105   V         0.126  -0.007  -0.219   0.113  -0.064  -0.399   0.151  -0.040  -0.392
106   I         1.035   1.064   1.123   1.194   1.229   1.311   1.064   1.116   1.198
107   T         1.035   1.064   1.123   1.360   1.377   1.445   1.064   1.116   1.198
108   K         0.126  -0.007  -0.219  -0.195  -0.341  -0.707   0.151  -0.040  -0.392
109   L         1.035   1.064   1.123   0.972   1.060   1.130   1.064   1.116   1.198
110   H        -0.740  -1.041  -1.089  -0.140  -0.632  -0.865  -0.632  -1.013  -1.054
111   L         1.035   1.064   1.123   0.972   1.060   1.130   1.064   1.116   1.198
112   D         1.035   1.064   1.123   1.227   1.261   1.337   1.064   1.116   1.198
113   K         0.126  -0.007  -0.219  -0.143  -0.266  -0.555   0.151  -0.040  -0.392
114   D         1.035   1.064   1.123   1.227   1.261   1.337   1.064   1.116   1.198
115   R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
116   K         0.126  -0.068  -0.217  -0.122  -0.318  -0.496   0.151  -0.131  -0.390
117   A        -1.555  -1.331  -1.661  -1.195  -0.942  -1.431  -1.284  -1.057  -1.337
118   L         0.126  -0.068  -0.217   0.213   0.003  -0.255   0.151  -0.131  -0.390
119   I         0.126  -0.068  -0.217   0.403   0.129  -0.181   0.151  -0.131  -0.390
120   Q        -1.555  -1.859  -1.719  -1.052  -1.592  -1.606  -1.284  -1.607  -1.392
121   R         1.035   1.064   1.123   0.891   0.925   1.064   1.064   1.116   1.198
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   K         0.126   0.334  -0.192  -0.171   0.128  -0.590   0.151   0.421  -0.348
131   G        -0.740  -1.041  -1.089  -0.332  -0.781  -0.978  -0.632  -1.013  -1.054
132   G         0.126  -0.068  -0.217   0.490   0.248  -0.005   0.151  -0.131  -0.390
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   K        -1.555  -1.694  -1.697  -1.602  -1.821  -1.682  -1.284  -1.451  -1.371
135   L        -2.569  -2.591  -2.194  -2.474  -2.528  -1.977  -2.066  -2.032  -1.579
136   E         0.126  -0.068  -0.217   0.431   0.166  -0.130   0.151  -0.131  -0.390
* 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/P53221
Output conservation file - output/P53221
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
