SequenceLen = 141 SequenceNum = 6 OutputFilename = "outfile" InputType = 20 /* 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 ChooseFromLeaves = False #TheTree = ((a:3,b:5):7,(c:4,d:3,e:5):6,(f:2,g:3):5,h:3); TheSequence = "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR" TheMutationProbability = [1.0, 1.0, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 1.0, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.0, 0.2, 0.1, 0.2, 0.1, 0.1, 0.0, 1.0, 1.0, 0.5, 1.0, 1.0, 1.0, 0.7, 0.7, 0.7, 0.7, 0.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.7, 0.7, 0.7, 0.0, 0.2, 0.2, 0.1, 0.0, 0.7, 1.0, 1.0, 1.0, 1.0, 1.0, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.1, 0.1, 0.2, 0.2, 0.0, 0.7, 0.7, 0.7, 1.0, 1.0, 1.0, 1.0, 1.0, 0.7, 0.7, 0.7, 0.7, 0.7, 0.0, 0.1, 0.2, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 1.0, 1.0, 1.0] TheInsertThreshold = 0.03 TheDeleteThreshold = 0.03 TheInsFunc = [.2,.3,.4,.4,.3,.2,.1] TheDelFunc = [.2,.3,.4,.4,.3,.2,.1] 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]]