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"  58                                                                         "
"  54  45                                                                     "
"  81  16 528                                                                 "
"  56 113  34  10                                                             "
"  57 310  86  49   9                                                         "
" 105  29  58 767   5 323                                                     "
" 179 137  81 130  59  26 119                                                 "
"  27 328 391 112  69 597  26  23                                             "
"  36  22  47  11  17   9  12   6  16                                         "
"  30  38  12   7  23  72   9   6  56 229                                     "
"  35 646 263  26   7 292 181  27  45  21  14                                 "
"  54  44  30  15  31  43  18  14  33 479 388  65                             "
"  15   5  10   4  78   4   5   5  40  89 248   4  43                         "
" 194  74  15  15  14 164  18  24 115  10 102  21  16  17                     "
" 378 101 503  59 223  53  30 201  73  40  59  47  29  92 285                 "
" 475  64 232  38  42  51  32  33  46 245  25 103 226  12 118 477             "
"   9 126   8   4 115  18  10  55   8   9  52  10  24  53   6  35  12         "
"  11  20  70  46 209  24   7   8 573  32  24   8  18 536  10  63  21  71     "
" 298  17  16  31  62  20  45  47  11 961 180  14 323  62  23  38 112  25  16 "
" 0.076748 0.051691 0.042645 0.051544 0.019803 0.040752 0.061830 "
" 0.073152 0.022944 0.053761 0.091904 0.058676 0.023826 0.040126 "
" 0.050901 0.068765 0.058565 0.014261 0.032102 0.066005 "
" Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val "
" S_ij = S_ji and PI_i for the Jones model based on the SWISSPROT "
" Version 22 data. "
" Rate Q_ij=S_ij*PI_j. "
" The rest of the file is not used.   "
" Prepared by Z. Yang, March 1995. "
" See the following reference for notation: "
" Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and "
" applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. "
" ----------------------------------------------------------------------- "
"   426  "
"   333  185                                                                   "
"   596   80 2134                                                                   "
"   159  214   54   20                                                             "
"   332 1203  277  192   14                                                       "
"   920  176  286 4497   11 1497                                                       "
"  1853  954  470  907  158  144  999                                                 "
"    88  716  704  244   58 1027   69   71                                           "
"   286  114  198   59   34   37   72   44   37                                   "
"   394  332   88   62   79  497  101   80  217 2086                              "
"   294 3606 1209  148   15 1289 1210  215  115  121  140                            "
"   185  100   56   34   27   78   50   47   33 1129 1567  167                      "
"    84   21   33   16  115   14   23   28   69  354 1690   17   76               "
"  1395  360   64   74   27  629  106  171  249   54  882  117   36   66              "
"  3664  661 2706  390  559  278  236 1861  214  274  691  351   89  468 1839       "
"  3920  360 1069  216   91  227  217  266  116 1420  256  653  579   54  653 3527     "
"    19  171    9    5   60   20   17  106    5   13  127   16   15   56    8   64  18 "
"    49   62  178  142  246   59   26   34  777  102  131   30   25 1276   32  259   73  60      "
"  2771  111   86  195  150  100  336  420   32 6260 2020   99  937  307  142  320  805  44  63  "
"     A    R    N    D    C    Q    E    G    H    I    L    K    M    F    P    S    T   W   Y  V "
"   Ala  Arg  Asn  Asp  Cys  Gln  Glu  Gly  His  Ile  Leu  Lys  Met  Phe  Pro  Ser  Thr Trp Tyr Val "
" Accepted point mutations (x10), similar to Figure 80 of Dayhoff et "
" al. (1978).  SwissProt version 22 data. "
" ------------------------------------------------------------------------------ "
"  256458     426     333     596     159     332     920    1853      88     286     394     294     185      84    1395    3664    3920      19      49    2771  "
"     426  182302     185      80     214    1203     176     954     716     114     332    3606     100      21     360     661     360     171      62     111  "
"     333     185  150772    2134      54     277     286     470     704     198      88    1209      56      33      64    2706    1069       9     178      86  "
"     596      80    2134  178390      20     192    4497     907     244      59      62     148      34      16      74     390     216       5     142     195  "
"     159     214      54      20   68120      14      11     158      58      34      79      15      27     115      27     559      91      60     246     150  "
"     332    1203     277     192      14  139546    1497     144    1027      37     497    1289      78      14     629     278     227      20      59     100  "
"     920     176     286    4497      11    1497  218432     999      69      72     101    1210      50      23     106     236     217      17      26     336  "
"    1853     954     470     907     158     144     999  255274      71      44      80     215      47      28     171    1861     266     106      34     420  "
"      88     716     704     244      58    1027      69      71   77124      37     217     115      33      69     249     214     116       5     777      32  "
"     286     114     198      59      34      37      72      44      37  191018    2086     121    1129     354      54     274    1420      13     102    6260  "
"     394     332      88      62      79     497     101      80     217    2086  319504     140    1567    1690     882     691     256     127     131    2020  "
"     294    3606    1209     148      15    1289    1210     215     115     121     140  206568     167      17     117     351     653      16      30      99  "
"     185     100      56      34      27      78      50      47      33    1129    1567     167   84670      76      36      89     579      15      25     937  "
"      84      21      33      16     115      14      23      28      69     354    1690      17      76  143088      66     468      54      56    1276     307  "
"    1395     360      64      74      27     629     106     171     249      54     882     117      36      66  175488    1839     653       8      32     142  "
"    3664     661    2706     390     559     278     236    1861     214     274     691     351      89     468    1839  234536    3527      64     259     320  "
"    3920     360    1069     216      91     227     217     266     116    1420     256     653     579      54     653    3527  203636      18      73     805  "
"      19     171       9       5      60      20      17     106       5      13     127      16      15      56       8      64      18   50486      60      44  "
"      49      62     178     142     246      59      26      34     777     102     131      30      25    1276      32     259      73      60  114728      63  "
"    2771     111      86     195     150     100     336     420      32    6260    2020      99     937     307     142     320     805      44      63  223724  "
" Observed difference counts from pairwise comparisons, with ancestral sequences  "
" constructed by parsimony.  F(t) = PI*P(t). "
" Based on the SwissProt 22 data, kindly provided by D. Jones (Jones et al. 1992) "
" ------------------------------------------------------------------------------- "
" Ala 0.98754 0.00030 0.00023 0.00042 0.00011 0.00023 0.00065 0.00130 0.00006 0.00020 0.00028 0.00021 0.00013 0.00006 0.00098 0.00257 0.00275 0.00001 0.00003 0.00194 "
" Arg 0.00044 0.98974 0.00019 0.00008 0.00022 0.00125 0.00018 0.00099 0.00075 0.00012 0.00035 0.00376 0.00010 0.00002 0.00037 0.00069 0.00037 0.00018 0.00006 0.00012 "
" Asn 0.00042 0.00023 0.98720 0.00269 0.00007 0.00035 0.00036 0.00059 0.00089 0.00025 0.00011 0.00153 0.00007 0.00004 0.00008 0.00342 0.00135 0.00001 0.00022 0.00011 "
" Asp 0.00062 0.00008 0.00223 0.98954 0.00002 0.00020 0.00470 0.00095 0.00025 0.00006 0.00006 0.00015 0.00004 0.00002 0.00008 0.00041 0.00023 0.00001 0.00015 0.00020 "
" Cys 0.00043 0.00058 0.00015 0.00005 0.99432 0.00004 0.00003 0.00043 0.00016 0.00009 0.00021 0.00004 0.00007 0.00031 0.00007 0.00152 0.00025 0.00016 0.00067 0.00041 "
" Gln 0.00044 0.00159 0.00037 0.00025 0.00002 0.98955 0.00198 0.00019 0.00136 0.00005 0.00066 0.00170 0.00010 0.00002 0.00083 0.00037 0.00030 0.00003 0.00008 0.00013 "
" Glu 0.00080 0.00015 0.00025 0.00392 0.00001 0.00130 0.99055 0.00087 0.00006 0.00006 0.00009 0.00105 0.00004 0.00002 0.00009 0.00021 0.00019 0.00001 0.00002 0.00029 "
" Gly 0.00136 0.00070 0.00035 0.00067 0.00012 0.00011 0.00074 0.99350 0.00005 0.00003 0.00006 0.00016 0.00003 0.00002 0.00013 0.00137 0.00020 0.00008 0.00003 0.00031 "
" His 0.00021 0.00168 0.00165 0.00057 0.00014 0.00241 0.00016 0.00017 0.98864 0.00009 0.00051 0.00027 0.00008 0.00016 0.00058 0.00050 0.00027 0.00001 0.00182 0.00008 "
" Ile 0.00029 0.00011 0.00020 0.00006 0.00003 0.00004 0.00007 0.00004 0.00004 0.98729 0.00209 0.00012 0.00113 0.00035 0.00005 0.00027 0.00142 0.00001 0.00010 0.00627 "
" Leu 0.00023 0.00019 0.00005 0.00004 0.00005 0.00029 0.00006 0.00005 0.00013 0.00122 0.99330 0.00008 0.00092 0.00099 0.00052 0.00040 0.00015 0.00007 0.00008 0.00118 "
" Lys 0.00027 0.00331 0.00111 0.00014 0.00001 0.00118 0.00111 0.00020 0.00011 0.00011 0.00013 0.99100 0.00015 0.00002 0.00011 0.00032 0.00060 0.00001 0.00003 0.00009 "
" Met 0.00042 0.00023 0.00013 0.00008 0.00006 0.00018 0.00011 0.00011 0.00007 0.00255 0.00354 0.00038 0.98818 0.00017 0.00008 0.00020 0.00131 0.00003 0.00006 0.00212 "
" Phe 0.00011 0.00003 0.00004 0.00002 0.00015 0.00002 0.00003 0.00004 0.00009 0.00047 0.00227 0.00002 0.00010 0.99360 0.00009 0.00063 0.00007 0.00008 0.00171 0.00041 "
" Pro 0.00148 0.00038 0.00007 0.00008 0.00003 0.00067 0.00011 0.00018 0.00026 0.00006 0.00093 0.00012 0.00004 0.00007 0.99270 0.00194 0.00069 0.00001 0.00003 0.00015 "
" Ser 0.00287 0.00052 0.00212 0.00031 0.00044 0.00022 0.00018 0.00146 0.00017 0.00021 0.00054 0.00027 0.00007 0.00037 0.00144 0.98556 0.00276 0.00005 0.00020 0.00025 "
" Thr 0.00360 0.00033 0.00098 0.00020 0.00008 0.00021 0.00020 0.00024 0.00011 0.00131 0.00024 0.00060 0.00053 0.00005 0.00060 0.00324 0.98665 0.00002 0.00007 0.00074 "
" Trp 0.00007 0.00065 0.00003 0.00002 0.00023 0.00008 0.00006 0.00040 0.00002 0.00005 0.00048 0.00006 0.00006 0.00021 0.00003 0.00024 0.00007 0.99686 0.00023 0.00017 "
" Tyr 0.00008 0.00010 0.00030 0.00024 0.00041 0.00010 0.00004 0.00006 0.00130 0.00017 0.00022 0.00005 0.00004 0.00214 0.00005 0.00043 0.00012 0.00010 0.99392 0.00011 "
" Val 0.00226 0.00009 0.00007 0.00016 0.00012 0.00008 0.00027 0.00034 0.00003 0.00511 0.00165 0.00008 0.00076 0.00025 0.00012 0.00026 0.00066 0.00004 0.00005 0.98761 "
" P(0.01), amino acid exchange data generated from SWISSPROT Release 22.0 "
" Ref. Jones D.T., Taylor W.R. and Thornton J.M. (1992) CABIOS 8:275-282 "
" Usable sequences: 23824 "
" Final alignments: 5437 "
" Accepted point mutations: 92883 "
" A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V "
"  0.0767477          100      "
"  0.0516907          82.3263  "
"  0.0426448          102.697  "
"  0.0515445          83.8924  "
"  0.0198027          45.6097  "
"  0.0407523          83.8825  "
"  0.0618296          75.7914  "
"  0.0731516          52.1273  "
"  0.0229438          91.1374  "
"  0.0537609          101.99   "
"  0.0919042          53.7672  "
"  0.0586762          72.2308  "
"  0.0238262          94.8144  "
"  0.0401265          51.3146  "
"  0.0509007          58.5874  "
"  0.0687652          115.899  "
"  0.0585647          107.092  "
"  0.0142613          25.2297  "
"  0.0321015          48.7629  "
"  0.0660051          99.4571  "
"               "
" Normalized          Relative  "
" frequency           mutabilities "
" (SUM m*f) = 80.240436 "
" ------------------------------------------- "