1     M         1.485   1.487   1.508   1.816   1.821   1.852   1.568   1.570   1.595
2     V        -1.292  -1.290  -1.257  -1.569  -1.566  -1.504  -1.130  -1.126  -1.070
3     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     H        -0.124  -0.121  -0.161  -0.194  -0.193  -0.316  -0.231  -0.226  -0.286
6     S         1.485   1.487   1.508   1.469   1.474   1.508   1.568   1.570   1.595
7     K        -1.292  -1.290  -1.257  -1.129  -1.115  -1.068  -1.130  -1.126  -1.070
8     N         1.485   1.487   1.508   1.713   1.722   1.749   1.568   1.570   1.595
9     V        -0.124  -0.121  -0.161   0.020   0.027  -0.052  -0.231  -0.226  -0.286
10    K        -0.124  -0.147  -0.178  -0.007  -0.037  -0.076  -0.231  -0.265  -0.312
11    G        -1.292  -1.290  -1.257  -1.211  -1.208  -1.149  -1.130  -1.126  -1.070
12    F        -0.124  -0.098  -0.161  -0.565  -0.535  -0.583  -0.231  -0.190  -0.286
13    L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
14    E        -1.292  -1.290  -1.257  -1.129  -1.125  -1.068  -1.130  -1.126  -1.070
15    N        -1.292  -1.290  -1.257  -1.202  -1.196  -1.140  -1.130  -1.126  -1.070
16    T        -0.124  -0.147  -0.178   0.047   0.016  -0.037  -0.231  -0.265  -0.312
17    L        -0.124  -0.121  -0.161  -0.682  -0.680  -0.718  -0.231  -0.226  -0.286
18    K        -0.124  -0.147  -0.178  -0.124  -0.162  -0.217  -0.231  -0.265  -0.312
19    P        -0.124  -0.147  -0.178   0.067   0.026  -0.038  -0.231  -0.265  -0.312
20    Y        -1.292  -1.290  -1.257  -0.895  -0.887  -0.836  -1.130  -1.126  -1.070
21    D        -0.124  -0.121  -0.161  -0.007  -0.004  -0.053  -0.231  -0.226  -0.286
22    L        -0.124  -0.147  -0.178  -0.627  -0.660  -0.672  -0.231  -0.265  -0.312
23    H        -0.124  -0.098  -0.161  -0.588  -0.559  -0.610  -0.231  -0.190  -0.286
24    S        -0.124  -0.098  -0.161  -0.180  -0.127  -0.259  -0.231  -0.190  -0.286
25    V        -0.124  -0.098  -0.161  -0.014   0.027  -0.075  -0.231  -0.190  -0.286
26    D        -1.292  -1.290  -1.257  -1.351  -1.342  -1.289  -1.130  -1.126  -1.070
27    F        -0.267  -0.266  -0.236  -0.178  -0.175  -0.125  -0.456  -0.453  -0.404
28    K        -0.267  -0.266  -0.236  -0.238  -0.235  -0.185  -0.456  -0.453  -0.404
29    T        -0.124  -0.147  -0.178   0.014  -0.021  -0.077  -0.231  -0.265  -0.312
30    S        -0.124  -0.098  -0.161  -0.014   0.038  -0.100  -0.231  -0.190  -0.286
31    S        -1.292  -1.290  -1.257  -1.211  -1.203  -1.149  -1.130  -1.126  -1.070
32    L        -0.124  -0.121  -0.161  -0.541  -0.541  -0.556  -0.231  -0.226  -0.286
33    Q        -1.292  -1.290  -1.257  -0.886  -0.886  -0.828  -1.130  -1.126  -1.070
34    S        -0.124  -0.121  -0.161  -0.209  -0.201  -0.265  -0.231  -0.226  -0.286
35    S        -0.124  -0.147  -0.178  -0.180  -0.214  -0.258  -0.231  -0.265  -0.312
36    M        -0.124  -0.147  -0.178   0.114   0.073   0.011  -0.231  -0.265  -0.312
37    I        -0.124  -0.147  -0.178  -0.368  -0.421  -0.530  -0.231  -0.265  -0.312
38    I        -0.124  -0.147  -0.178  -0.368  -0.421  -0.530  -0.231  -0.265  -0.312
39    T        -0.124  -0.147  -0.178  -0.110  -0.150  -0.227  -0.231  -0.265  -0.312
40    A         1.485   1.487   1.508   1.695   1.700   1.732   1.568   1.570   1.595
41    T        -1.292  -1.290  -1.257  -1.351  -1.348  -1.289  -1.130  -1.126  -1.070
42    N        -1.292  -1.290  -1.257  -1.202  -1.191  -1.140  -1.130  -1.126  -1.070
43    G         1.485   1.487   1.508   1.653   1.654   1.690   1.568   1.570   1.595
44    G        -0.124  -0.098  -0.161  -0.223  -0.180  -0.282  -0.231  -0.190  -0.286
45    I         1.485   1.487   1.508   1.638   1.646   1.675   1.568   1.570   1.595
46    L        -0.124  -0.147  -0.178  -0.682  -0.716  -0.739  -0.231  -0.265  -0.312
47    S        -0.124  -0.121  -0.161  -0.062  -0.056  -0.096  -0.231  -0.226  -0.286
48    Y        -0.124  -0.147  -0.178   0.160   0.125   0.074  -0.231  -0.265  -0.312
49    A        -1.292  -1.290  -1.257  -1.238  -1.242  -1.177  -1.130  -1.126  -1.070
50    T        -1.292  -1.290  -1.257  -1.202  -1.194  -1.140  -1.130  -1.126  -1.070
51    S        -1.292  -1.290  -1.257  -1.351  -1.343  -1.289  -1.130  -1.126  -1.070
52    N        -1.292  -1.290  -1.257  -1.058  -1.048  -0.998  -1.130  -1.126  -1.070
53    N        -1.292  -1.290  -1.257  -1.202  -1.197  -1.140  -1.130  -1.126  -1.070
54    D        -1.292  -1.290  -1.257  -1.579  -1.596  -1.514  -1.130  -1.126  -1.070
55    V        -0.124  -0.098  -0.161  -0.055  -0.009  -0.114  -0.231  -0.190  -0.286
56    P        -0.267  -0.266  -0.236  -0.384  -0.381  -0.329  -0.456  -0.453  -0.404
57    K        -0.267  -0.266  -0.236  -0.287  -0.284  -0.233  -0.456  -0.453  -0.404
58    N        -0.124  -0.147  -0.178   0.074   0.041  -0.012  -0.231  -0.265  -0.312
59    S        -0.124  -0.147  -0.178  -0.223  -0.261  -0.309  -0.231  -0.265  -0.312
60    I        -0.267  -0.266  -0.236  -0.178  -0.175  -0.125  -0.456  -0.453  -0.404
61    N        -0.267  -0.266  -0.236  -0.268  -0.266  -0.215  -0.456  -0.453  -0.404
62    E         1.485   1.487   1.508   1.632   1.636   1.669   1.568   1.570   1.595
63    I        -0.267  -0.266  -0.236  -0.208  -0.205  -0.155  -0.456  -0.453  -0.404
64    N        -0.267  -0.266  -0.236  -0.392  -0.390  -0.337  -0.456  -0.453  -0.404
65    S         1.485   1.487   1.508   1.469   1.474   1.508   1.568   1.570   1.595
66    V        -0.124  -0.098  -0.161  -0.627  -0.595  -0.655  -0.231  -0.190  -0.286
67    N        -0.124  -0.121  -0.161   0.014   0.025  -0.054  -0.231  -0.226  -0.286
68    N         1.485   1.487   1.508   1.713   1.722   1.749   1.568   1.570   1.595
69    L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
70    K        -0.124  -0.147  -0.178  -0.007  -0.038  -0.076  -0.231  -0.265  -0.312
71    M        -0.124  -0.147  -0.178   0.088   0.049  -0.021  -0.231  -0.265  -0.312
72    M         1.485   1.487   1.508   1.816   1.821   1.852   1.568   1.570   1.595
73    S        -0.124  -0.098  -0.161  -0.096  -0.049  -0.179  -0.231  -0.190  -0.286
74    L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
75    L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
76    I        -0.124  -0.147  -0.178  -0.027  -0.060  -0.115  -0.231  -0.265  -0.312
77    K         1.485   1.487   1.508   1.577   1.583   1.615   1.568   1.570   1.595
78    D         1.485   1.487   1.508   1.577   1.578   1.615   1.568   1.570   1.595
79    K         1.485   1.487   1.508   1.577   1.583   1.615   1.568   1.570   1.595
80    W        -0.124  -0.147  -0.178   0.341   0.304   0.242  -0.231  -0.265  -0.312
81    S        -0.124  -0.121  -0.161  -0.075  -0.070  -0.112  -0.231  -0.226  -0.286
82    E        -0.124  -0.147  -0.178  -0.180  -0.220  -0.293  -0.231  -0.265  -0.312
83    D         1.485   1.487   1.508   1.577   1.578   1.615   1.568   1.570   1.595
84    E        -0.124  -0.121  -0.161   0.020   0.028  -0.027  -0.231  -0.226  -0.286
85    N        -1.292  -1.290  -1.257  -1.266  -1.263  -1.204  -1.130  -1.126  -1.070
86    D        -1.292  -1.290  -1.257  -1.726  -1.724  -1.660  -1.130  -1.126  -1.070
87    T        -0.124  -0.147  -0.178  -0.110  -0.150  -0.227  -0.231  -0.265  -0.312
88    E        -1.292  -1.290  -1.257  -1.023  -1.011  -0.963  -1.130  -1.126  -1.070
89    E        -0.124  -0.121  -0.161  -0.082  -0.073  -0.145  -0.231  -0.226  -0.286
90    Q        -1.292  -1.290  -1.257  -1.147  -1.151  -1.086  -1.130  -1.126  -1.070
91    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    P        -0.267  -0.266  -0.236  -0.208  -0.205  -0.155  -0.456  -0.453  -0.404
98    V        -0.267  -0.266  -0.236  -0.223  -0.220  -0.170  -0.456  -0.453  -0.404
99    E        -0.267  -0.266  -0.236  -0.423  -0.421  -0.369  -0.456  -0.453  -0.404
100   I        -0.267  -0.266  -0.236  -0.701  -0.699  -0.644  -0.456  -0.453  -0.404
101   D         1.485   1.487   1.508   1.524   1.528   1.563   1.568   1.570   1.595
102   S        -0.267  -0.266  -0.236  -0.519  -0.517  -0.464  -0.456  -0.453  -0.404
103   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   K        -0.267  -0.266  -0.236  -0.376  -0.374  -0.322  -0.456  -0.453  -0.404
105   T        -0.267  -0.266  -0.236  -0.163  -0.160  -0.110  -0.456  -0.453  -0.404
106   K        -1.292  -1.290  -1.257  -1.085  -1.070  -1.024  -1.130  -1.126  -1.070
107   I        -0.124  -0.147  -0.178  -0.048  -0.083  -0.140  -0.231  -0.265  -0.312
108   Y        -0.124  -0.121  -0.161   0.141   0.144   0.079  -0.231  -0.226  -0.286
109   T        -0.124  -0.121  -0.161   0.047   0.054  -0.010  -0.231  -0.226  -0.286
110   Y        -0.124  -0.121  -0.161   0.160   0.166   0.101  -0.231  -0.226  -0.286
111   E        -0.124  -0.147  -0.178  -0.131  -0.170  -0.233  -0.231  -0.265  -0.312
112   M        -1.292  -1.290  -1.257  -1.448  -1.448  -1.385  -1.130  -1.126  -1.070
113   E         1.485   1.487   1.508   1.607   1.615   1.645   1.568   1.570   1.595
114   D         1.485   1.487   1.508   1.577   1.578   1.615   1.568   1.570   1.595
115   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
116   H         1.485   1.487   1.508   1.816   1.818   1.852   1.568   1.570   1.595
117   T        -1.292  -1.290  -1.257  -1.174  -1.167  -1.113  -1.130  -1.126  -1.070
118   C        -1.292  -1.290  -1.257  -1.102  -1.113  -1.042  -1.130  -1.126  -1.070
119   V        -0.124  -0.121  -0.161  -0.266  -0.263  -0.385  -0.231  -0.226  -0.286
120   A        -0.124  -0.147  -0.178  -0.000  -0.040  -0.097  -0.231  -0.265  -0.312
121   Q        -0.124  -0.098  -0.161   0.284   0.325   0.222  -0.231  -0.190  -0.286
122   I         1.485   1.487   1.508   1.638   1.646   1.675   1.568   1.570   1.595
123   P         1.485   1.487   1.508   1.787   1.791   1.823   1.568   1.570   1.595
124   N        -0.124  -0.098  -0.161  -0.096  -0.053  -0.156  -0.231  -0.190  -0.286
125   S         1.485   1.487   1.508   1.469   1.474   1.508   1.568   1.570   1.595
126   D        -0.124  -0.121  -0.161  -0.145  -0.141  -0.212  -0.231  -0.226  -0.286
127   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
128   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
129   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
130   L        -1.292  -1.290  -1.257  -1.448  -1.425  -1.385  -1.130  -1.126  -1.070
131   F        -0.124  -0.098  -0.161  -0.565  -0.535  -0.583  -0.231  -0.190  -0.286
132   I        -0.124  -0.147  -0.178  -0.368  -0.421  -0.530  -0.231  -0.265  -0.312
133   A         1.485   1.487   1.508   1.698   1.698   1.735   1.568   1.570   1.595
134   E        -1.292  -1.290  -1.257  -1.138  -1.131  -1.077  -1.130  -1.126  -1.070
135   G        -1.292  -1.290  -1.257  -1.023  -1.013  -0.963  -1.130  -1.126  -1.070
136   S        -1.292  -1.290  -1.257  -1.400  -1.392  -1.336  -1.130  -1.126  -1.070
137   F         1.485   1.487   1.508   1.860   1.865   1.896   1.568   1.570   1.595
138   P         1.485   1.487   1.508   1.787   1.791   1.823   1.568   1.570   1.595
139   Y        -0.124  -0.121  -0.161   0.094   0.102   0.025  -0.231  -0.226  -0.286
140   G         1.485   1.487   1.508   1.653   1.654   1.690   1.568   1.570   1.595
141   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
142   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
143   V        -1.292  -1.290  -1.257  -1.120  -1.116  -1.059  -1.130  -1.126  -1.070
144   I        -1.292  -1.290  -1.257  -1.518  -1.507  -1.454  -1.130  -1.126  -1.070
145   K         1.485   1.487   1.508   1.577   1.583   1.615   1.568   1.570   1.595
146   I        -0.124  -0.098  -0.161  -0.682  -0.645  -0.718  -0.231  -0.190  -0.286
147   E        -0.124  -0.098  -0.161  -0.145  -0.096  -0.212  -0.231  -0.190  -0.286
148   R        -1.292  -1.290  -1.257  -0.954  -0.959  -0.895  -1.130  -1.126  -1.070
149   A        -0.124  -0.147  -0.178   0.127   0.091   0.056  -0.231  -0.265  -0.312
150   M        -1.292  -1.290  -1.257  -1.448  -1.448  -1.385  -1.130  -1.126  -1.070
151   R        -1.292  -1.290  -1.257  -1.023  -1.027  -0.963  -1.130  -1.126  -1.070
152   E        -1.292  -1.290  -1.257  -1.323  -1.322  -1.260  -1.130  -1.126  -1.070
153   L        -0.124  -0.098  -0.161  -0.152  -0.091  -0.276  -0.231  -0.190  -0.286
154   T        -1.292  -1.290  -1.257  -1.067  -1.064  -1.007  -1.130  -1.126  -1.070
155   D        -0.124  -0.147  -0.178  -0.007  -0.041  -0.076  -0.231  -0.265  -0.312
156   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
157   F        -1.292  -1.290  -1.257  -1.049  -1.045  -0.989  -1.130  -1.126  -1.070
158   G         1.485   1.487   1.508   1.653   1.654   1.690   1.568   1.570   1.595
159   Y         1.485   1.487   1.508   1.787   1.791   1.823   1.568   1.570   1.595
160   K        -0.124  -0.147  -0.178  -0.007  -0.038  -0.076  -0.231  -0.265  -0.312
161   L         1.485   1.487   1.508   0.984   0.984   1.027   1.568   1.570   1.595
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   G        -0.124  -0.121  -0.161  -0.138  -0.135  -0.218  -0.231  -0.226  -0.286
* 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/P38247
Output conservation file - output/P38247
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
