1     M         1.996   2.030   2.107   2.265   2.308   2.441   2.201   2.252   2.370
2     I        -0.330  -0.230  -0.474  -0.203  -0.045  -0.417  -0.284  -0.155  -0.453
3     P        -0.685  -0.696  -0.600  -0.762  -0.784  -0.620  -0.731  -0.735  -0.610
4     S        -1.150  -1.158  -1.063  -1.198  -1.200  -1.059  -0.956  -0.956  -0.835
5     R        -0.690  -0.732  -0.646  -0.958  -1.052  -0.925  -0.722  -0.765  -0.654
6     I        -1.248  -1.219  -1.117  -1.327  -1.282  -1.129  -1.046  -1.011  -0.883
7     S        -0.690  -0.682  -0.610  -0.855  -0.855  -0.752  -0.722  -0.711  -0.614
8     H        -0.799  -0.778  -0.670  -0.732  -0.698  -0.538  -0.843  -0.815  -0.680
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    K        -0.799  -0.778  -0.670  -0.996  -0.957  -0.801  -0.843  -0.815  -0.680
16    F        -0.690  -0.594  -0.599  -0.826  -0.639  -0.705  -0.722  -0.605  -0.601
17    P         0.391   0.546   0.214   0.670   0.889   0.385   0.379   0.600   0.108
18    L        -0.978  -1.030  -1.008  -0.800  -0.866  -0.834  -0.781  -0.833  -0.782
19    F        -0.509  -0.559  -0.596  -0.357  -0.438  -0.510  -0.505  -0.566  -0.598
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    L        -0.690  -0.666  -0.607  -0.643  -0.601  -0.521  -0.722  -0.689  -0.611
23    R        -0.690  -0.681  -0.638  -0.694  -0.673  -0.585  -0.722  -0.706  -0.645
24    S        -1.248  -1.234  -1.117  -1.169  -1.141  -0.973  -1.046  -1.023  -0.883
25    S        -0.131  -0.113  -0.050  -0.306  -0.277  -0.218  -0.397  -0.372  -0.283
26    L        -0.690  -0.665  -0.610  -0.694  -0.659  -0.562  -0.722  -0.688  -0.614
27    A         0.080   0.101   0.037   0.087   0.123  -0.023  -0.072  -0.043  -0.153
28    A         0.080   0.101   0.037   0.193   0.228   0.117  -0.072  -0.043  -0.153
29    P         0.080   0.133   0.026   0.269   0.354   0.163  -0.072   0.004  -0.169
30    K        -0.690  -0.676  -0.639  -1.011  -0.985  -0.904  -0.722  -0.701  -0.646
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    A        -1.528  -1.526  -1.435  -1.137  -1.142  -0.993  -1.113  -1.104  -0.983
45    A        -1.128  -1.166  -1.088  -1.065  -1.118  -1.009  -0.947  -0.968  -0.859
46    Y        -1.528  -1.402  -1.431  -1.032  -0.802  -0.905  -1.113  -0.992  -0.980
47    R        -0.330  -0.314  -0.499  -0.276  -0.254  -0.501  -0.284  -0.262  -0.484
48    F        -0.978  -1.010  -1.015  -1.126  -1.137  -1.146  -0.781  -0.814  -0.789
49    S         0.391   0.316   0.162   0.579   0.471   0.241   0.379   0.263   0.031
50    S        -0.578  -0.450  -0.537  -0.535  -0.343  -0.457  -0.616  -0.466  -0.534
51    T         0.069   0.101   0.067  -0.044   0.060  -0.015  -0.119  -0.055  -0.116
52    I        -0.685  -0.661  -0.620  -0.642  -0.593  -0.528  -0.731  -0.697  -0.629
53    P        -0.043  -0.013  -0.005  -0.006   0.063   0.057  -0.280  -0.228  -0.220
54    K        -1.150  -1.106  -1.057  -1.308  -1.218  -1.187  -0.956  -0.904  -0.829
55    P         0.069   0.065   0.031   0.198   0.209   0.138  -0.119  -0.113  -0.168
56    S        -0.029  -0.092  -0.014  -0.478  -0.590  -0.466  -0.284  -0.346  -0.241
57    D        -0.978  -1.010  -1.015  -0.701  -0.751  -0.737  -0.781  -0.814  -0.789
58    Q        -1.128  -1.123  -1.070  -0.961  -0.944  -0.859  -0.947  -0.934  -0.844
59    V        -0.029  -0.044  -0.004  -0.026  -0.042   0.033  -0.284  -0.293  -0.230
60    P        -0.578  -0.670  -0.608  -0.302  -0.431  -0.356  -0.616  -0.702  -0.616
61    D         0.391   0.224   0.139   0.696   0.458   0.315   0.379   0.135  -0.002
62    V        -0.578  -0.670  -0.608  -0.516  -0.640  -0.568  -0.616  -0.702  -0.616
63    D        -0.578  -0.550  -0.549  -0.513  -0.470  -0.451  -0.616  -0.587  -0.555
64    A        -0.179  -0.179  -0.084  -0.240  -0.228  -0.089  -0.450  -0.452  -0.328
65    F         1.996   2.030   2.107   2.066   2.102   2.242   2.201   2.252   2.370
66    L         0.790   0.759   0.774   0.654   0.602   0.603   0.544   0.472   0.449
67    N        -0.330  -0.221  -0.439  -0.481  -0.331  -0.615  -0.284  -0.144  -0.411
68    K        -0.729  -0.673  -0.628  -1.210  -1.137  -1.051  -0.781  -0.724  -0.640
69    I         1.996   2.030   2.107   2.079   2.118   2.255   2.201   2.252   2.370
70    G         1.996   2.030   2.107   2.092   2.129   2.268   2.201   2.252   2.370
71    R         1.996   2.030   2.107   1.845   1.880   2.023   2.201   2.252   2.370
72    N         0.069   0.160   0.057   0.109   0.260   0.052  -0.119   0.007  -0.138
73    C         0.069   0.027   0.017   0.328   0.219   0.204  -0.119  -0.199  -0.197
74    N        -1.528  -1.514  -1.463  -1.196  -1.171  -1.097  -1.113  -1.094  -1.005
75    E         1.169   1.134   0.989   1.201   1.153   0.895   1.207   1.144   0.860
76    L        -0.978  -0.978  -1.019  -0.810  -0.850  -0.861  -0.781  -0.780  -0.792
77    K        -1.128  -1.163  -1.065  -1.284  -1.299  -1.182  -0.947  -0.966  -0.840
78    D         0.069  -0.018   0.021   0.166   0.047   0.077  -0.119  -0.228  -0.188
79    T        -0.978  -1.049  -1.051  -0.890  -1.019  -1.067  -0.781  -0.851  -0.824
80    F         0.391   0.331   0.167   0.570   0.441   0.220   0.379   0.283   0.039
81    E         1.169   1.044   0.983   1.268   1.103   1.013   1.207   0.992   0.850
82    N        -0.509  -0.574  -0.596  -0.348  -0.460  -0.499  -0.505  -0.589  -0.598
83    N        -1.128  -1.166  -1.088  -1.201  -1.224  -1.110  -0.947  -0.968  -0.859
84    W         0.790   0.847   0.831   0.932   1.034   0.962   0.544   0.638   0.561
85    N        -0.578  -0.459  -0.545  -0.385  -0.201  -0.326  -0.616  -0.477  -0.550
86    N        -0.578  -0.670  -0.608  -0.714  -0.836  -0.761  -0.616  -0.702  -0.616
87    L         0.790   0.847   0.831   0.654   0.752   0.705   0.544   0.638   0.561
88    F         0.069   0.065   0.031  -0.042  -0.046  -0.154  -0.119  -0.113  -0.168
89    Q        -1.927  -1.893  -1.791  -1.879  -1.827  -1.678  -1.278  -1.243  -1.116
90    W        -0.578  -0.670  -0.608  -0.440  -0.617  -0.553  -0.616  -0.702  -0.616
91    D        -0.729  -0.679  -0.627  -0.699  -0.639  -0.542  -0.781  -0.726  -0.639
92    S         0.391   0.331   0.167   0.562   0.468   0.241   0.379   0.283   0.039
93    K        -0.330  -0.306  -0.459  -0.467  -0.436  -0.621  -0.284  -0.252  -0.435
94    I        -1.128  -1.066  -1.048  -0.856  -0.767  -0.721  -0.947  -0.884  -0.825
95    L         0.619   0.630   0.721   0.478   0.510   0.650   0.213   0.218   0.341
96    K         1.996   2.030   2.107   1.656   1.696   1.836   2.201   2.252   2.370
97    E        -0.578  -0.585  -0.577  -0.660  -0.697  -0.686  -0.616  -0.617  -0.580
98    K         0.069  -0.002   0.019  -0.190  -0.282  -0.226  -0.119  -0.202  -0.186
99    G         1.996   2.030   2.107   2.092   2.129   2.268   2.201   2.252   2.370
100   V         0.790   0.884   0.837   0.800   0.945   0.863   0.544   0.708   0.573
101   N        -0.978  -0.881  -1.009  -0.630  -0.481  -0.694  -0.781  -0.674  -0.783
102   I        -0.578  -0.568  -0.555  -0.434  -0.400  -0.389  -0.616  -0.589  -0.557
103   Q        -0.029   0.039   0.022  -0.155  -0.085  -0.088  -0.284  -0.197  -0.192
104   Q        -0.578  -0.612  -0.593  -0.368  -0.415  -0.395  -0.616  -0.650  -0.603
105   R         1.996   2.030   2.107   1.845   1.880   2.023   2.201   2.252   2.370
106   K         0.790   0.756   0.768   0.390   0.294   0.262   0.544   0.467   0.436
107   Y         1.996   2.030   2.107   2.272   2.310   2.447   2.201   2.252   2.370
108   I         0.391   0.468   0.170   0.637   0.740   0.328   0.379   0.489   0.044
109   L         0.391   0.224   0.139   0.537   0.326   0.206   0.379   0.135  -0.002
110   K        -1.528  -1.514  -1.463  -1.517  -1.500  -1.400  -1.113  -1.094  -1.005
111   Q         0.790   0.847   0.831   0.972   1.068   1.030   0.544   0.638   0.561
112   V        -1.128  -1.073  -1.050  -1.109  -1.053  -1.000  -0.947  -0.888  -0.826
113   H        -0.978  -0.999  -1.018  -0.433  -0.463  -0.506  -0.781  -0.804  -0.791
114   N         0.069   0.053   0.017  -0.384  -0.448  -0.454  -0.119  -0.170  -0.197
115   Y         0.069   0.129   0.034   0.169   0.249   0.121  -0.119  -0.045  -0.172
116   R        -0.578  -0.558  -0.594  -0.915  -0.939  -0.937  -0.616  -0.601  -0.604
117   N         0.391   0.331   0.167   0.536   0.452   0.148   0.379   0.283   0.039
118   N         0.069   0.149   0.051   0.172   0.288   0.157  -0.119  -0.006  -0.139
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   R         0.391   0.316   0.162   0.504   0.402   0.144   0.379   0.263   0.031
121   P        -0.330  -0.426  -0.496  -0.079  -0.242  -0.399  -0.284  -0.407  -0.480
122   I        -0.179  -0.163  -0.071  -0.295  -0.260  -0.126  -0.450  -0.429  -0.310
123   H        -0.029   0.020  -0.004  -0.492  -0.440  -0.388  -0.284  -0.227  -0.230
124   E         1.169   1.044   0.983   1.288   1.133   1.051   1.207   0.992   0.850
125   I        -0.578  -0.585  -0.577  -0.250  -0.250  -0.202  -0.616  -0.617  -0.580
126   K         0.790   0.715   0.763   0.419   0.307   0.399   0.544   0.386   0.427
127   L        -0.729  -0.758  -0.628  -1.176  -1.162  -0.976  -0.781  -0.796  -0.640
128   G         1.169   1.044   0.983   1.387   1.223   1.159   1.207   0.992   0.850
129   K         1.169   1.044   0.983   0.931   0.766   0.699   1.207   0.992   0.850
130   K         1.996   2.030   2.107   1.656   1.696   1.836   2.201   2.252   2.370
131   S        -0.578  -0.612  -0.593  -0.836  -0.927  -0.918  -0.616  -0.650  -0.603
132   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   F        -0.029  -0.037  -0.011  -0.018  -0.008   0.063  -0.284  -0.282  -0.236
134   G         1.996   2.030   2.107   2.092   2.129   2.268   2.201   2.252   2.370
135   G         1.996   2.030   2.107   2.092   2.129   2.268   2.201   2.252   2.370
136   E         1.996   2.030   2.107   2.006   2.055   2.183   2.201   2.252   2.370
137   R         1.996   2.030   2.107   1.845   1.880   2.023   2.201   2.252   2.370
138   K         0.069   0.028   0.046  -0.322  -0.388  -0.349  -0.119  -0.156  -0.155
139   R         0.069  -0.002   0.019  -0.195  -0.326  -0.311  -0.119  -0.202  -0.186
140   K         0.391   0.224   0.139   0.154  -0.098  -0.221   0.379   0.135  -0.002
141   A        -0.685  -0.701  -0.637  -0.766  -0.803  -0.707  -0.731  -0.741  -0.646
142   F        -0.043   0.026  -0.014  -0.025   0.098   0.024  -0.280  -0.179  -0.232
143   T        -1.150  -1.139  -1.061  -0.957  -0.920  -0.828  -0.956  -0.939  -0.833
144   A         1.996   2.030   2.107   2.044   2.078   2.221   2.201   2.252   2.370
145   K         1.088   0.978   0.929   0.794   0.628   0.546   1.073   0.877   0.750
146   W        -0.043  -0.103  -0.040  -0.002  -0.091  -0.021  -0.280  -0.350  -0.270
147   K        -0.685  -0.647  -0.619  -1.037  -0.988  -0.906  -0.731  -0.683  -0.628
148   A         1.996   2.030   2.107   2.044   2.078   2.221   2.201   2.252   2.370
149   E        -0.043  -0.103  -0.040  -0.229  -0.306  -0.213  -0.280  -0.350  -0.270
150   N        -0.509  -0.452  -0.571  -0.380  -0.273  -0.552  -0.505  -0.430  -0.569
151   K         0.987   1.010   0.885   0.783   0.814   0.561   0.902   0.933   0.666
152   -         0.599   0.624   0.718   0.343   0.373   0.530   0.171   0.206   0.337
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   Q        -1.128  -1.092  -1.067  -1.220  -1.183  -1.111  -0.947  -0.906  -0.841
* 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/P38783
Output conservation file - output/P38783
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
