1     M         1.195   1.198   1.211   1.489   1.492   1.509   1.245   1.247   1.262
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     L        -0.411  -0.408  -0.383  -0.504  -0.500  -0.455  -0.595  -0.591  -0.548
7     I        -0.411  -0.408  -0.383  -0.480  -0.476  -0.431  -0.595  -0.591  -0.548
8     N        -0.411  -0.408  -0.383  -0.397  -0.393  -0.350  -0.595  -0.591  -0.548
9     H        -0.411  -0.408  -0.383  -0.339  -0.335  -0.292  -0.595  -0.591  -0.548
10    L         1.195   1.198   1.211   0.997   1.000   1.024   1.245   1.247   1.262
11    S        -0.411  -0.408  -0.383  -0.444  -0.440  -0.396  -0.595  -0.591  -0.548
12    K         1.195   1.198   1.211   1.049   1.052   1.075   1.245   1.247   1.262
13    I        -0.279  -0.310  -0.342  -0.417  -0.477  -0.551  -0.391  -0.437  -0.483
14    R        -0.411  -0.408  -0.383  -0.598  -0.593  -0.547  -0.595  -0.591  -0.548
15    T        -1.350  -1.345  -1.316  -1.342  -1.344  -1.281  -1.208  -1.200  -1.152
16    V        -1.350  -1.345  -1.316  -1.335  -1.327  -1.274  -1.208  -1.200  -1.152
17    R         1.195   1.198   1.211   1.297   1.298   1.320   1.245   1.247   1.262
18    H        -1.350  -1.345  -1.316  -1.113  -1.108  -1.055  -1.208  -1.200  -1.152
19    F        -0.279  -0.273  -0.330  -0.439  -0.430  -0.546  -0.391  -0.380  -0.465
20    S        -1.350  -1.345  -1.316  -1.342  -1.328  -1.281  -1.208  -1.200  -1.152
21    N        -1.350  -1.345  -1.316  -1.222  -1.214  -1.163  -1.208  -1.200  -1.152
22    I        -1.350  -1.345  -1.316  -1.278  -1.270  -1.218  -1.208  -1.200  -1.152
23    K        -1.350  -1.345  -1.316  -1.437  -1.428  -1.374  -1.208  -1.200  -1.152
24    P        -0.279  -0.310  -0.342  -0.167  -0.219  -0.276  -0.391  -0.437  -0.483
25    V        -1.350  -1.345  -1.316  -1.551  -1.548  -1.487  -1.208  -1.200  -1.152
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    L        -1.350  -1.345  -1.316  -1.452  -1.440  -1.389  -1.208  -1.200  -1.152
30    S         1.195   1.198   1.211   1.169   1.169   1.194   1.245   1.247   1.262
31    K        -0.279  -0.310  -0.342  -0.412  -0.458  -0.500  -0.391  -0.437  -0.483
32    E        -0.279  -0.310  -0.342  -0.314  -0.357  -0.397  -0.391  -0.437  -0.483
33    V         1.195   1.198   1.211   1.193   1.201   1.217   1.245   1.247   1.262
34    S         1.195   1.198   1.211   1.169   1.169   1.194   1.245   1.247   1.262
35    R        -1.350  -1.345  -1.316  -1.271  -1.262  -1.211  -1.208  -1.200  -1.152
36    R        -0.279  -0.273  -0.330  -0.309  -0.297  -0.415  -0.391  -0.380  -0.465
37    V        -0.279  -0.273  -0.330  -0.341  -0.324  -0.427  -0.391  -0.380  -0.465
38    I         1.195   1.198   1.211   1.216   1.221   1.240   1.245   1.247   1.262
39    V        -0.279  -0.244  -0.322  -0.330  -0.266  -0.406  -0.391  -0.336  -0.453
40    A        -0.279  -0.244  -0.322  -0.125  -0.068  -0.193  -0.391  -0.336  -0.453
41    P         1.195   1.198   1.211   1.343   1.346   1.365   1.245   1.247   1.262
42    A        -0.279  -0.310  -0.342  -0.224  -0.281  -0.362  -0.391  -0.437  -0.483
43    S        -1.350  -1.345  -1.316  -1.174  -1.157  -1.115  -1.208  -1.200  -1.152
44    H        -0.279  -0.310  -0.342  -0.245  -0.308  -0.392  -0.391  -0.437  -0.483
45    F        -0.279  -0.310  -0.342  -0.287  -0.340  -0.381  -0.391  -0.437  -0.483
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    K        -1.350  -1.345  -1.316  -1.342  -1.325  -1.281  -1.208  -1.200  -1.152
53    T        -1.350  -1.345  -1.316  -1.306  -1.312  -1.246  -1.208  -1.200  -1.152
54    S        -1.350  -1.345  -1.316  -1.174  -1.156  -1.115  -1.208  -1.200  -1.152
55    S        -1.350  -1.345  -1.316  -1.335  -1.319  -1.274  -1.208  -1.200  -1.152
56    P        -0.279  -0.273  -0.330  -0.213  -0.199  -0.311  -0.391  -0.380  -0.465
57    N        -0.279  -0.244  -0.322  -0.156  -0.102  -0.227  -0.391  -0.336  -0.453
58    V        -1.350  -1.345  -1.316  -1.613  -1.607  -1.548  -1.208  -1.200  -1.152
59    K         1.195   1.198   1.211   1.074   1.080   1.101   1.245   1.247   1.262
60    S         1.195   1.198   1.211   1.169   1.169   1.194   1.245   1.247   1.262
61    N         1.195   1.198   1.211   1.333   1.336   1.355   1.245   1.247   1.262
62    I         1.195   1.198   1.211   1.217   1.221   1.242   1.245   1.247   1.262
63    P        -0.279  -0.310  -0.342  -0.298  -0.360  -0.441  -0.391  -0.437  -0.483
64    I        -1.350  -1.345  -1.316  -1.154  -1.144  -1.095  -1.208  -1.200  -1.152
65    H        -0.279  -0.310  -0.342  -0.172  -0.230  -0.300  -0.391  -0.437  -0.483
66    E         1.195   1.198   1.211   1.134   1.138   1.159   1.245   1.247   1.262
67    Y         1.195   1.198   1.211   1.343   1.346   1.365   1.245   1.247   1.262
68    K        -0.279  -0.273  -0.330  -0.412  -0.400  -0.482  -0.391  -0.380  -0.465
69    Q         1.195   1.198   1.211   1.343   1.343   1.365   1.245   1.247   1.262
70    L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
71    P         1.195   1.198   1.211   1.343   1.346   1.365   1.245   1.247   1.262
72    E        -0.279  -0.273  -0.330  -0.390  -0.378  -0.471  -0.391  -0.380  -0.465
73    D        -0.279  -0.310  -0.342  -0.250  -0.298  -0.346  -0.391  -0.437  -0.483
74    S         1.195   1.198   1.211   1.169   1.169   1.194   1.245   1.247   1.262
75    N         1.195   1.198   1.211   1.343   1.347   1.365   1.245   1.247   1.262
76    Y        -0.279  -0.310  -0.342  -0.213  -0.271  -0.335  -0.391  -0.437  -0.483
77    I         1.195   1.198   1.211   1.216   1.221   1.240   1.245   1.247   1.262
78    E        -0.279  -0.310  -0.342  -0.390  -0.440  -0.491  -0.391  -0.437  -0.483
79    K         1.195   1.198   1.211   1.074   1.080   1.101   1.245   1.247   1.262
80    H        -1.350  -1.345  -1.316  -1.195  -1.195  -1.135  -1.208  -1.200  -1.152
81    Y         1.195   1.198   1.211   1.343   1.346   1.365   1.245   1.247   1.262
82    K        -1.350  -1.345  -1.316  -1.278  -1.260  -1.218  -1.208  -1.200  -1.152
83    E         1.195   1.198   1.211   1.134   1.138   1.159   1.245   1.247   1.262
84    L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
85    Q        -0.279  -0.273  -0.330  -0.198  -0.189  -0.293  -0.391  -0.380  -0.465
86    V        -0.279  -0.310  -0.342  -0.406  -0.458  -0.529  -0.391  -0.437  -0.483
87    F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
88    L        -0.279  -0.310  -0.342  -0.428  -0.469  -0.499  -0.391  -0.437  -0.483
89    N        -0.411  -0.408  -0.383  -0.464  -0.460  -0.415  -0.595  -0.591  -0.548
90    E        -0.279  -0.273  -0.330  -0.335  -0.325  -0.406  -0.391  -0.380  -0.465
91    F        -0.279  -0.273  -0.330  -0.282  -0.274  -0.356  -0.391  -0.380  -0.465
92    L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
93    I        -1.350  -1.345  -1.316  -1.306  -1.296  -1.246  -1.208  -1.200  -1.152
94    K        -1.350  -1.345  -1.316  -1.306  -1.288  -1.246  -1.208  -1.200  -1.152
95    K        -1.350  -1.345  -1.316  -1.328  -1.313  -1.267  -1.208  -1.200  -1.152
96    L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
97    N        -0.279  -0.273  -0.330  -0.120  -0.108  -0.200  -0.391  -0.380  -0.465
98    K         1.195   1.198   1.211   1.074   1.080   1.101   1.245   1.247   1.262
99    T        -1.350  -1.345  -1.316  -1.215  -1.206  -1.156  -1.208  -1.200  -1.152
100   Y         1.195   1.198   1.211   1.343   1.346   1.365   1.245   1.247   1.262
101   A        -1.350  -1.345  -1.316  -1.208  -1.199  -1.149  -1.208  -1.200  -1.152
102   D         1.195   1.198   1.211   1.228   1.231   1.252   1.245   1.247   1.262
103   F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
104   E        -0.279  -0.310  -0.342  -0.390  -0.440  -0.491  -0.391  -0.437  -0.483
105   G        -1.350  -1.345  -1.316  -1.222  -1.222  -1.163  -1.208  -1.200  -1.152
106   D        -0.279  -0.310  -0.342  -0.250  -0.298  -0.346  -0.391  -0.437  -0.483
107   P         1.195   1.198   1.211   1.343   1.346   1.365   1.245   1.247   1.262
108   D         1.195   1.198   1.211   1.228   1.231   1.252   1.245   1.247   1.262
109   E        -0.279  -0.310  -0.342  -0.390  -0.440  -0.491  -0.391  -0.437  -0.483
110   L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
111   V         1.195   1.198   1.211   1.193   1.201   1.217   1.245   1.247   1.262
112   F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
113   Q        -0.279  -0.310  -0.342  -0.240  -0.300  -0.367  -0.391  -0.437  -0.483
114   L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
115   E         1.195   1.198   1.211   1.134   1.138   1.159   1.245   1.247   1.262
116   K         1.195   1.198   1.211   1.074   1.080   1.101   1.245   1.247   1.262
117   F        -0.279  -0.244  -0.322  -0.213  -0.153  -0.296  -0.391  -0.336  -0.453
118   I         1.195   1.198   1.211   1.216   1.221   1.240   1.245   1.247   1.262
119   E         1.195   1.198   1.211   1.134   1.138   1.159   1.245   1.247   1.262
120   L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
121   E        -1.350  -1.345  -1.316  -1.229  -1.211  -1.169  -1.208  -1.200  -1.152
122   V        -0.279  -0.310  -0.342  -0.341  -0.388  -0.448  -0.391  -0.437  -0.483
123   T        -1.350  -1.345  -1.316  -1.250  -1.248  -1.190  -1.208  -1.200  -1.152
124   P        -0.279  -0.273  -0.330  -0.224  -0.213  -0.324  -0.391  -0.380  -0.465
125   R        -1.350  -1.345  -1.316  -1.271  -1.270  -1.211  -1.208  -1.200  -1.152
126   Y        -0.279  -0.310  -0.342  -0.120  -0.168  -0.219  -0.391  -0.437  -0.483
127   T        -1.350  -1.345  -1.316  -1.321  -1.322  -1.260  -1.208  -1.200  -1.152
128   N        -1.350  -1.345  -1.316  -1.201  -1.193  -1.142  -1.208  -1.200  -1.152
129   H        -1.350  -1.345  -1.316  -1.133  -1.128  -1.075  -1.208  -1.200  -1.152
130   S        -1.350  -1.345  -1.316  -1.415  -1.402  -1.353  -1.208  -1.200  -1.152
131   A        -0.279  -0.310  -0.342  -0.105  -0.155  -0.213  -0.391  -0.437  -0.483
132   P        -0.411  -0.408  -0.383  -0.548  -0.544  -0.499  -0.595  -0.591  -0.548
133   D        -0.411  -0.408  -0.383  -0.598  -0.593  -0.547  -0.595  -0.591  -0.548
134   G        -0.411  -0.408  -0.383  -0.381  -0.377  -0.334  -0.595  -0.591  -0.548
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     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   C         1.195   1.198   1.211   1.544   1.547   1.564   1.245   1.247   1.262
148   E         1.195   1.198   1.211   1.136   1.140   1.162   1.245   1.247   1.262
149   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   S        -0.411  -0.408  -0.383  -0.536  -0.532  -0.486  -0.595  -0.591  -0.548
154   I        -0.411  -0.408  -0.383  -0.711  -0.707  -0.658  -0.595  -0.591  -0.548
155   G         1.195   1.198   1.211   1.411   1.415   1.432   1.245   1.247   1.262
156   D        -0.279  -0.273  -0.330  -0.346  -0.334  -0.442  -0.391  -0.380  -0.465
157   R        -0.279  -0.244  -0.322  -0.412  -0.356  -0.471  -0.391  -0.336  -0.453
158   I        -1.350  -1.345  -1.316  -1.328  -1.305  -1.267  -1.208  -1.200  -1.152
159   V         1.195   1.198   1.211   1.193   1.201   1.217   1.245   1.247   1.262
160   V        -0.279  -0.244  -0.322  -0.330  -0.266  -0.406  -0.391  -0.336  -0.453
161   D        -0.279  -0.310  -0.342  -0.346  -0.402  -0.465  -0.391  -0.437  -0.483
162   R         1.195   1.198   1.211   1.297   1.298   1.320   1.245   1.247   1.262
163   Y        -0.279  -0.244  -0.322  -0.282  -0.230  -0.344  -0.391  -0.336  -0.453
164   L        -1.350  -1.345  -1.316  -1.520  -1.498  -1.456  -1.208  -1.200  -1.152
165   D        -1.350  -1.345  -1.316  -1.306  -1.300  -1.246  -1.208  -1.200  -1.152
166   F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
167   V        -0.279  -0.244  -0.322  -0.039   0.027  -0.133  -0.391  -0.336  -0.453
168   K        -1.350  -1.345  -1.316  -1.459  -1.441  -1.397  -1.208  -1.200  -1.152
169   D        -1.350  -1.345  -1.316  -1.271  -1.267  -1.211  -1.208  -1.200  -1.152
170   V         1.195   1.198   1.211   1.193   1.201   1.217   1.245   1.247   1.262
171   R        -0.279  -0.273  -0.330  -0.309  -0.297  -0.415  -0.391  -0.380  -0.465
172   L        -0.279  -0.310  -0.342  -0.456  -0.500  -0.533  -0.391  -0.437  -0.483
173   T         1.195   1.198   1.211   1.331   1.331   1.354   1.245   1.247   1.262
174   L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
175   L        -1.350  -1.345  -1.316  -1.222  -1.206  -1.163  -1.208  -1.200  -1.152
176   L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
177   N         1.195   1.198   1.211   1.343   1.347   1.365   1.245   1.247   1.262
178   G         1.195   1.198   1.211   1.411   1.415   1.432   1.245   1.247   1.262
179   G         1.195   1.198   1.211   1.411   1.415   1.432   1.245   1.247   1.262
180   H         1.195   1.198   1.211   1.399   1.404   1.421   1.245   1.247   1.262
181   S        -0.279  -0.273  -0.330  -0.213  -0.207  -0.269  -0.391  -0.380  -0.465
182   F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
183   I         1.195   1.198   1.211   1.216   1.221   1.240   1.245   1.247   1.262
184   F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
185   D         1.195   1.198   1.211   1.228   1.231   1.252   1.245   1.247   1.262
186   V        -0.279  -0.310  -0.342  -0.341  -0.388  -0.448  -0.391  -0.437  -0.483
187   M        -0.279  -0.273  -0.330  -0.161  -0.148  -0.286  -0.391  -0.380  -0.465
188   L         1.195   1.198   1.211   1.002   1.005   1.030   1.245   1.247   1.262
189   Q         1.195   1.198   1.211   1.343   1.343   1.365   1.245   1.247   1.262
190   A        -1.350  -1.345  -1.316  -1.222  -1.224  -1.163  -1.208  -1.200  -1.152
191   K        -0.279  -0.310  -0.342  -0.390  -0.432  -0.473  -0.391  -0.437  -0.483
192   E        -1.350  -1.345  -1.316  -1.328  -1.320  -1.267  -1.208  -1.200  -1.152
193   V        -0.279  -0.273  -0.330  -0.379  -0.362  -0.473  -0.391  -0.380  -0.465
194   F         1.195   1.198   1.211   1.193   1.193   1.217   1.245   1.247   1.262
195   D        -0.279  -0.310  -0.342  -0.250  -0.300  -0.346  -0.391  -0.437  -0.483
196   K        -0.279  -0.310  -0.342  -0.445  -0.493  -0.541  -0.391  -0.437  -0.483
197   M        -1.350  -1.345  -1.316  -1.342  -1.345  -1.281  -1.208  -1.200  -1.152
198   Q        -0.279  -0.244  -0.322  -0.335  -0.282  -0.394  -0.391  -0.336  -0.453
199   K        -0.279  -0.273  -0.330  -0.395  -0.384  -0.463  -0.391  -0.380  -0.465
200   -        -0.411  -0.408  -0.383  -0.502  -0.498  -0.453  -0.595  -0.591  -0.548
201   -         1.195   1.198   1.211   1.121   1.124   1.146   1.245   1.247   1.262
202   -        -0.411  -0.408  -0.383  -0.574  -0.569  -0.523  -0.595  -0.591  -0.548
203   -        -0.411  -0.408  -0.383  -0.562  -0.557  -0.512  -0.595  -0.591  -0.548
204   -         1.195   1.198   1.211   1.300   1.304   1.324   1.245   1.247   1.262
205   -        -0.411  -0.408  -0.383  -0.538  -0.534  -0.488  -0.595  -0.591  -0.548
206   -        -0.411  -0.408  -0.383  -0.610  -0.606  -0.559  -0.595  -0.591  -0.548
207   -        -0.411  -0.408  -0.383  -0.455  -0.451  -0.407  -0.595  -0.591  -0.548
208   E        -1.350  -1.345  -1.316  -1.236  -1.220  -1.176  -1.208  -1.200  -1.152
* 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/P38231
Output conservation file - output/P38231
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
