#
# Default rose include file for proteins
#

InputType = 1 // PROTEIN
TheAlphabet = "ARNDCQEGHILKMFPSTWYV"
TheFreq = [.087, .041, .040, .047, .033, .038, .050, .089, .034, .037,
           .085, .081, .015, .040, .051, .070, .058, .010, .030, .065]
Relatedness = 250

TheInsertThreshold = 0.00005
TheDeleteThreshold = 0.00005

TheInsFunc = [.1,.1,.1,.1,.1,.1,.05,.05,.05,.05,.05,.05,.05,.05]
TheDelFunc = [.1,.1,.1,.1,.1,.1,.05,.05,.05,.05,.05,.05,.05,.05]

ThePAMMatrix = [[9867.0,   2.0,   9.0,  10.0,   3.0,   8.0,  17.0,  21.0,   2.0,
   6.0,   4.0,   2.0,   6.0,   2.0,  22.0,  35.0,  32.0,   0.0,   2.0,  18.0],
                [   1.0,9913.0,   1.0,   0.0,   1.0,  10.0,   0.0,   0.0,  10.0,
   3.0,   1.0,  19.0,   4.0,   1.0,   4.0,   6.0,   1.0,   8.0,   0.0,   1.0],
                [   4.0,   1.0,9822.0,  36.0,   0.0,   4.0,   6.0,   6.0,  21.0,
   3.0,   1.0,  13.0,   0.0,   1.0,   2.0,  20.0,   9.0,   1.0,   4.0,   1.0],
                [   6.0,   0.0,  42.0,9859.0,   0.0,   6.0,  53.0,   6.0,   4.0,
   1.0,   0.0,   3.0,   0.0,   0.0,   1.0,   5.0,   3.0,   0.0,   0.0,   1.0],
                [   1.0,   1.0,   0.0,   0.0,9973.0,   0.0,   0.0,   0.0,   1.0,
   1.0,   0.0,   0.0,   0.0,   0.0,   1.0,   5.0,   1.0,   0.0,   3.0,   2.0],
                [   3.0,   9.0,   4.0,   5.0,   0.0,9876.0,  27.0,   1.0,  23.0,
   1.0,   3.0,   6.0,   4.0,   0.0,   6.0,   2.0,   2.0,   0.0,   0.0,   1.0],
                [  10.0,   0.0,   7.0,  56.0,   0.0,  35.0,9865.0,   4.0,   2.0,
   3.0,   1.0,   4.0,   1.0,   0.0,   3.0,   4.0,   2.0,   0.0,   1.0,   2.0],
                [  21.0,   1.0,  12.0,  11.0,   1.0,   3.0,   7.0,9935.0,   1.0,
   0.0,   1.0,   2.0,   1.0,   1.0,   3.0,  21.0,   3.0,   0.0,   0.0,   5.0],
                [   1.0,   8.0,  18.0,   3.0,   1.0,  20.0,   1.0,   0.0,9912.0,
   0.0,   1.0,   1.0,   0.0,   2.0,   3.0,   1.0,   1.0,   1.0,   4.0,   1.0],
                [   2.0,   2.0,   3.0,   1.0,   2.0,   1.0,   2.0,   0.0,   0.0,
9872.0,   9.0,   2.0,  12.0,   7.0,   0.0,   1.0,   7.0,   0.0,   1.0,  33.0],
                [   3.0,   1.0,   3.0,   0.0,   0.0,   6.0,   1.0,   1.0,   4.0,
  22.0,9947.0,   2.0,  45.0,  13.0,   3.0,   1.0,   3.0,   4.0,   2.0,  15.0],
                [   2.0,  37.0,  25.0,   6.0,   0.0,  12.0,   7.0,   2.0,   2.0,
   4.0,   1.0,9926.0,  20.0,   0.0,   3.0,   8.0,  11.0,   0.0,   1.0,   1.0],
                [   1.0,   1.0,   0.0,   0.0,   0.0,   2.0,   0.0,   0.0,   0.0,
   5.0,   8.0,   4.0,9874.0,   1.0,   0.0,   1.0,   2.0,   0.0,   0.0,   4.0],
                [   1.0,   1.0,   1.0,   0.0,   0.0,   0.0,   0.0,   1.0,   2.0,
   8.0,   6.0,   0.0,   4.0,9946.0,   0.0,   2.0,   1.0,   3.0,  28.0,   0.0],
                [  13.0,   5.0,   2.0,   1.0,   1.0,   8.0,   3.0,   2.0,   5.0,
   1.0,   2.0,   2.0,   1.0,   1.0,9926.0,  12.0,   4.0,   0.0,   0.0,   2.0],
                [  28.0,  11.0,  34.0,   7.0,  11.0,   4.0,   6.0,  16.0,   2.0,
   2.0,   1.0,   7.0,   4.0,   3.0,  17.0,9840.0,  38.0,   5.0,   2.0,   2.0],
                [  22.0,   2.0,  13.0,   4.0,   1.0,   3.0,   2.0,   2.0,   1.0,
  11.0,   2.0,   8.0,   6.0,   1.0,   5.0,  32.0,9871.0,   0.0,   2.0,   9.0],
                [   0.0,   2.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,
   0.0,   0.0,   0.0,   0.0,   1.0,   0.0,   1.0,   0.0,9976.0,   1.0,   0.0],
                [   1.0,   0.0,   3.0,   0.0,   3.0,   0.0,   1.0,   0.0,   4.0,
   1.0,   1.0,   0.0,   0.0,  21.0,   0.0,   1.0,   1.0,   2.0,9945.0,   1.0],
                [  13.0,   2.0,   1.0,   1.0,   3.0,   2.0,   2.0,   3.0,   3.0,
  57.0,  11.0,   1.0,  17.0,   1.0,   3.0,   2.0,  10.0,   0.0,   2.0,9901.0]]

