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CJFIELDS / BioPerl-1.6.922 / t / data / aaml_pairwise.mlc 
AAML (in paml 3.13, August 2002)    abglobin.aa   Model: Empirical_F (wag.dat) 
ns = 5  	ls = 285
# site patterns = 126
   16   21   10    1    1   10   17    1    1    2    1    1    3    1   13
    1    2    1    1    5    2    1    5   15    1    1    5    1   10    1
    1    7   10    1   14    1    1    1    1    1    3    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    4    1    4    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1

human                 VLSPADKTNV AAWGGAHAEY GAEALERMFL SPTPHFLSHA QVKGKADTNV AVDMNALANL CLALPAEFAV LSSTPESAVT ALGNVDEVQF ETPDVMGKLG ASDLANFTCR VLCVAHFEPV AAYVNK
goat-cow              ...A...S.. .....GN.A. .......... .......... ....E.A.K. GL.LGT.D.. S.C..ND... .N..A.A... .F.K...... ..A...N..D S.NMKD.A.K ..V..R..VL .DF..R
rabbit                .........I T..E.S.G.. ....V..... G.....FT.E .I.A.SE.K. GL.LG..T.. ..NH.S.... .N.SS..... .....E.... .SAN..N..A ..E.S..K.. ..I.S...Q. ......
rat                   ...AD....I NC...G.G.. .E...Q...A A..S.IV.P. ...A...AKA D.ELG..T.F ..CH.GD..M ....DAA..N ....P.D..Y DSASI...IN .N..K..H.. MII.G.L.CA ..F.S.
marsupial             ...D....H. .I...G..A. A....A.T.. ........P. .IQ....SQ. .L.LGTMK.. .I..SKDLE. F.A.S.NCI. TISQ..QTT. GS.G..SA.T SGEVK.YK.K IIIC.E.DEC V.WLH.




Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
human                          0.1263 0.0211 0.0351 0.0526 0.0105 0.0140 0.0421 0.0702 0.0632 0.0000 0.1263 0.0772 0.0105 0.0526 0.0491 0.0561 0.0561 0.0105 0.0211 0.1053
goat-cow                       0.1193 0.0246 0.0421 0.0632 0.0070 0.0140 0.0386 0.0737 0.0526 0.0000 0.1298 0.0842 0.0105 0.0596 0.0351 0.0596 0.0526 0.0105 0.0175 0.1053
rabbit                         0.0982 0.0211 0.0421 0.0386 0.0070 0.0175 0.0596 0.0702 0.0667 0.0140 0.1228 0.0842 0.0070 0.0561 0.0386 0.0737 0.0561 0.0105 0.0211 0.0947
rat                            0.1193 0.0211 0.0386 0.0667 0.0175 0.0175 0.0316 0.0807 0.0667 0.0246 0.1123 0.0842 0.0140 0.0491 0.0386 0.0596 0.0456 0.0105 0.0211 0.0807
marsupial                      0.1088 0.0175 0.0211 0.0561 0.0175 0.0281 0.0351 0.0702 0.0632 0.0281 0.1088 0.0842 0.0175 0.0491 0.0351 0.0737 0.0667 0.0140 0.0211 0.0842

Average                        0.1144 0.0211 0.0358 0.0554 0.0119 0.0182 0.0414 0.0730 0.0625 0.0133 0.1200 0.0828 0.0119 0.0533 0.0393 0.0646 0.0554 0.0112 0.0204 0.0940

# constant sites:    170 (59.65%)
ln Lmax (unconstrained) = -1189.106658

AA distances (raw proportions of different sites)

human          
goat-cow         0.1439
rabbit           0.1368  0.1825
rat              0.2000  0.2351  0.2035
marsupial        0.2456  0.2561  0.2877  0.3123

ML distances of aa seqs.
human          
goat-cow         0.1551
rabbit           0.1474  0.2020
rat              0.2267  0.2694  0.2306
marsupial        0.2870  0.3024  0.3392  0.3861