1     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    T        -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    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    M         1.391   1.413   1.487   1.606   1.632   1.741   1.527   1.561   1.676
38    V        -0.607  -0.717  -0.747  -0.498  -0.681  -0.716  -0.613  -0.752  -0.767
39    S         0.739   0.768   0.536   0.796   0.832   0.529   0.762   0.806   0.387
40    Q        -1.496  -1.506  -1.461  -1.308  -1.353  -1.299  -1.204  -1.207  -1.108
41    E        -1.609  -1.508  -1.474  -1.409  -1.285  -1.212  -1.313  -1.221  -1.120
42    T        -0.709  -0.733  -0.751  -0.643  -0.703  -0.739  -0.767  -0.801  -0.778
43    V        -1.309  -1.284  -1.176  -1.294  -1.220  -1.096  -1.204  -1.170  -1.010
44    A        -1.293  -1.289  -1.175  -1.288  -1.313  -1.135  -1.184  -1.167  -1.008
45    H        -1.163  -1.132  -1.156  -1.025  -0.984  -0.953  -1.041  -0.999  -0.988
46    V         0.117   0.084  -0.155   0.200   0.149  -0.205   0.107   0.060  -0.296
47    K        -0.709  -0.683  -0.737  -0.825  -0.795  -0.840  -0.767  -0.731  -0.763
48    D        -1.496  -1.493  -1.467  -1.249  -1.268  -1.231  -1.204  -1.193  -1.113
49    L        -0.468  -0.548  -0.694  -0.315  -0.407  -0.577  -0.439  -0.542  -0.705
50    I         0.739   0.612   0.523   0.764   0.603   0.459   0.762   0.553   0.364
51    G        -1.009  -0.965  -0.827  -1.197  -1.125  -0.915  -1.095  -1.038  -0.858
52    Q        -1.309  -1.246  -1.179  -1.306  -1.218  -1.141  -1.204  -1.131  -1.012
53    K        -0.709  -0.724  -0.761  -0.801  -0.832  -0.843  -0.767  -0.799  -0.790
54    E        -1.196  -1.217  -1.150  -1.167  -1.211  -1.096  -1.095  -1.097  -0.983
55    V         0.417   0.462   0.411   0.302   0.364   0.259   0.216   0.290   0.149
56    F         0.417   0.328   0.368   0.536   0.355   0.379   0.216   0.039   0.066
57    V         0.417   0.536   0.452   0.302   0.478   0.333   0.216   0.422   0.229
58    A         0.417   0.328   0.368   0.369   0.229   0.297   0.216   0.039   0.066
59    A         0.417   0.380   0.380   0.319   0.244   0.211   0.216   0.138   0.088
60    K         1.391   1.413   1.487   1.172   1.200   1.325   1.527   1.561   1.676
61    T         0.417   0.485   0.415   0.356   0.456   0.331   0.216   0.332   0.158
62    Y         1.391   1.413   1.487   1.535   1.558   1.673   1.527   1.561   1.676
63    C         1.391   1.413   1.487   1.585   1.611   1.720   1.527   1.561   1.676
64    P         1.391   1.413   1.487   1.541   1.571   1.678   1.527   1.561   1.676
65    Y         1.391   1.413   1.487   1.535   1.558   1.673   1.527   1.561   1.676
66    C         1.391   1.413   1.487   1.585   1.611   1.720   1.527   1.561   1.676
67    K        -1.496  -1.527  -1.461  -1.321  -1.338  -1.227  -1.204  -1.224  -1.108
68    A        -0.468  -0.446  -0.669  -0.357  -0.332  -0.677  -0.439  -0.411  -0.675
69    T         0.739   0.775   0.534   0.860   0.910   0.565   0.762   0.817   0.385
70    L        -0.168  -0.229  -0.246  -0.390  -0.441  -0.502  -0.330  -0.397  -0.436
71    S        -0.896  -0.822  -0.790  -1.042  -0.965  -0.884  -0.985  -0.903  -0.822
72    T        -0.468  -0.610  -0.709  -0.260  -0.467  -0.680  -0.439  -0.618  -0.723
73    L         0.246   0.266   0.345  -0.078  -0.020   0.066  -0.112  -0.084   0.018
74    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    N        -1.609  -1.587  -1.486  -1.602  -1.595  -1.405  -1.313  -1.283  -1.129
79    V        -1.496  -1.488  -1.473  -1.343  -1.352  -1.343  -1.204  -1.192  -1.117
80    P        -1.609  -1.629  -1.495  -1.415  -1.466  -1.275  -1.313  -1.310  -1.135
81    K        -0.709  -0.660  -0.719  -0.729  -0.652  -0.683  -0.767  -0.686  -0.736
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    S        -1.196  -1.217  -1.159  -1.324  -1.360  -1.248  -1.095  -1.108  -0.994
84    K        -0.168  -0.041  -0.204  -0.367  -0.173  -0.424  -0.330  -0.135  -0.372
85    A         0.117   0.084  -0.155   0.263   0.222  -0.065   0.107   0.060  -0.296
86    L        -1.609  -1.613  -1.491  -1.432  -1.458  -1.307  -1.313  -1.299  -1.132
87    V        -0.296  -0.289  -0.274  -0.447  -0.413  -0.379  -0.548  -0.515  -0.480
88    L        -0.168  -0.188  -0.258  -0.223  -0.237  -0.334  -0.330  -0.393  -0.457
89    E         0.417   0.368   0.378   0.397   0.312   0.288   0.216   0.115   0.085
90    L         0.739   0.612   0.523   0.676   0.544   0.380   0.762   0.553   0.364
91    D         0.417   0.415   0.385   0.395   0.376   0.318   0.216   0.203   0.099
92    E        -0.168  -0.282  -0.265  -0.148  -0.313  -0.339  -0.330  -0.481  -0.466
93    M        -1.309  -1.288  -1.176  -1.234  -1.149  -1.032  -1.204  -1.167  -1.009
94    S        -0.896  -0.927  -0.796  -0.899  -0.931  -0.751  -0.985  -0.999  -0.828
95    N        -0.168  -0.182  -0.255  -0.113  -0.157  -0.245  -0.330  -0.364  -0.452
96    G         1.391   1.413   1.487   1.377   1.405   1.521   1.527   1.561   1.676
97    S        -0.168  -0.215  -0.236  -0.201  -0.254  -0.315  -0.330  -0.375  -0.422
98    E         0.246   0.261   0.339   0.100   0.121   0.220  -0.112  -0.093   0.006
99    I         0.117   0.084  -0.155   0.193   0.159  -0.226   0.107   0.060  -0.296
100   Q         1.391   1.413   1.487   1.360   1.383   1.505   1.527   1.561   1.676
101   D        -1.196  -1.199  -1.148  -1.096  -1.104  -1.043  -1.095  -1.079  -0.981
102   A         0.739   0.612   0.523   0.778   0.621   0.516   0.762   0.553   0.364
103   L         1.391   1.413   1.487   1.237   1.297   1.388   1.527   1.561   1.676
104   E        -0.783  -0.689  -0.745  -0.878  -0.748  -0.776  -0.876  -0.774  -0.776
105   E         0.417   0.328   0.368   0.338   0.162   0.171   0.216   0.039   0.066
106   I        -0.168  -0.270  -0.256  -0.285  -0.431  -0.479  -0.330  -0.461  -0.454
107   S         0.117   0.202  -0.145   0.328   0.438  -0.048   0.107   0.226  -0.282
108   G         1.391   1.413   1.487   1.377   1.405   1.521   1.527   1.561   1.676
109   Q         1.391   1.413   1.487   1.360   1.383   1.505   1.527   1.561   1.676
110   K        -0.296  -0.236  -0.265  -0.267  -0.149  -0.210  -0.548  -0.457  -0.472
111   T         1.391   1.413   1.487   1.423   1.455   1.565   1.527   1.561   1.676
112   V         1.391   1.413   1.487   1.319   1.341   1.466   1.527   1.561   1.676
113   P         1.391   1.413   1.487   1.541   1.571   1.678   1.527   1.561   1.676
114   N         1.391   1.413   1.487   1.440   1.456   1.581   1.527   1.561   1.676
115   V         0.191   0.229   0.331  -0.112  -0.049   0.105  -0.221  -0.157  -0.009
116   Y         0.417   0.478   0.408   0.602   0.683   0.558   0.216   0.319   0.144
117   I         1.391   1.413   1.487   1.325   1.360   1.472   1.527   1.561   1.676
118   N        -0.709  -0.749  -0.753  -0.553  -0.591  -0.591  -0.767  -0.799  -0.780
119   G         0.117  -0.055  -0.178   0.241  -0.003  -0.227   0.107  -0.140  -0.330
120   K        -0.296  -0.241  -0.269  -0.512  -0.462  -0.454  -0.548  -0.488  -0.479
121   H         1.391   1.413   1.487   1.601   1.624   1.736   1.527   1.561   1.676
122   I         0.739   0.612   0.523   0.764   0.603   0.459   0.762   0.553   0.364
123   G         1.391   1.413   1.487   1.377   1.405   1.521   1.527   1.561   1.676
124   G         1.391   1.413   1.487   1.377   1.405   1.521   1.527   1.561   1.676
125   N         1.391   1.413   1.487   1.440   1.456   1.581   1.527   1.561   1.676
126   S         1.391   1.413   1.487   1.343   1.369   1.488   1.527   1.561   1.676
127   D         1.391   1.413   1.487   1.377   1.399   1.521   1.527   1.561   1.676
128   L        -0.168  -0.188  -0.222  -0.261  -0.224  -0.302  -0.330  -0.334  -0.397
129   E         0.417   0.429   0.386   0.367   0.379   0.288   0.216   0.230   0.102
130   T        -1.196  -1.106  -1.130  -1.182  -1.050  -1.102  -1.095  -0.991  -0.968
131   L         0.739   0.694   0.532   0.675   0.650   0.392   0.762   0.688   0.380
132   K        -1.496  -1.530  -1.457  -1.414  -1.451  -1.341  -1.204  -1.227  -1.105
133   K        -0.896  -0.806  -0.778  -1.092  -0.972  -0.895  -0.985  -0.872  -0.807
134   N        -1.309  -1.243  -1.170  -1.344  -1.278  -1.135  -1.204  -1.133  -1.005
135   G         0.246   0.319   0.364   0.075   0.196   0.246  -0.112   0.021   0.057
136   K        -0.168  -0.189  -0.256  -0.327  -0.371  -0.439  -0.330  -0.381  -0.455
137   L         0.739   0.694   0.532   0.693   0.670   0.432   0.762   0.688   0.380
138   A        -1.196  -1.153  -1.131  -1.114  -1.055  -1.023  -1.095  -1.039  -0.969
139   E        -1.309  -1.250  -1.172  -1.337  -1.268  -1.117  -1.204  -1.140  -1.007
140   I        -0.296  -0.248  -0.276  -0.652  -0.574  -0.594  -0.548  -0.498  -0.489
141   L        -0.296  -0.359  -0.284  -0.467  -0.495  -0.393  -0.548  -0.606  -0.495
142   K        -0.709  -0.784  -0.759  -0.833  -0.939  -0.880  -0.767  -0.849  -0.788
143   P        -1.496  -1.530  -1.480  -1.313  -1.367  -1.306  -1.204  -1.226  -1.123
144   V        -0.483  -0.462  -0.346  -0.787  -0.751  -0.591  -0.767  -0.735  -0.575
145   F         0.611   0.622   0.472   0.555   0.587   0.381   0.556   0.571   0.267
146   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -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/P17695
Output conservation file - output/P17695
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
