letter A val is 0.250000
letter T val is 0.250000
letter G val is 0.250000
letter C val is 0.250000
Running in ENH mode
node 0 name dmel qval 0.367879 parent dmel_
node 1 name dmel_ qval 0 parent (null)
//
NA bcd *
PW 0.000000
PO         A          C          G          T       cons         inf
00      9.00      18.00       3.00      18.00          H        0.07
01      8.00       3.00       1.00      36.00          T        0.73
02     45.00       1.00       1.00       1.00          A        1.40
03     47.00       0.00       1.00       0.00          A        1.67
04      1.00       0.00      16.00      31.00          T        0.78
05      1.00      44.00       0.00       3.00          C        1.35
06      2.00      26.00       3.00      17.00          C        0.39
07      5.00      12.00      18.00      13.00          B       -0.04
//
//
NA cad *
PW 0.000000
PO         A          C          G          T       cons         inf
00      0.00       5.00       3.00       5.00          Y        0.03
01      2.00       0.00       3.00       8.00          T        0.24
02      0.00       0.00       0.00      13.00          T        1.50
03      1.00       0.00       0.00      12.00          T        1.14
04      6.00       2.00       1.00       4.00          W       -0.13
05      0.00       4.00       3.00       6.00          Y        0.05
06      3.00       1.00       9.00       0.00          G        0.43
07      7.00       3.00       2.00       1.00          A       -0.06
08      0.00       4.00       0.00       9.00          T        0.65
//
//
NA dl *
PW 0.000000
PO         A          C          G          T       cons         inf
00      2.00       8.00      22.00       6.00          G        0.23
01      8.00       4.00      26.00       0.00          G        0.61
02      3.00       0.00      34.00       1.00          G        1.22
03     33.00       1.00       4.00       0.00          A        1.14
04     34.00       2.00       0.00       2.00          A        1.20
05     36.00       0.00       1.00       1.00          A        1.44
06     24.00       1.00       2.00      11.00          A        0.51
07      4.00      12.00       3.00      19.00          Y        0.15
08      8.00      23.00       2.00       5.00          C        0.29
09      8.00      24.00       4.00       2.00          C        0.35
//
//
NA hb *
PW 0.000000
PO         A          C          G          T       cons         inf
00     17.00      13.00       7.00      66.00          T        0.43
01      0.00       0.00       3.00     100.00          T        1.71
02      1.00       5.00       1.00      96.00          T        1.47
03      0.00       1.00       0.00     102.00          T        1.82
04      0.00       0.00       0.00     103.00          T        1.89
05      1.00       4.00       0.00      98.00          T        1.59
06     59.00       7.00      29.00       8.00          A        0.38
07     20.00      17.00      14.00      52.00          N        0.13
//
//
NA kni *
PW 0.000000
PO         A          C          G          T       cons         inf
00      1.00       1.00      18.00       0.00          G        1.11
01     11.00       1.00       2.00       6.00          A        0.16
02      3.00       3.00       5.00       9.00          N       -0.14
03      0.00      19.00       0.00       1.00          C        1.37
04      0.00       5.00       6.00       9.00          B        0.14
05      7.00      11.00       1.00       1.00          C        0.26
06      8.00       4.00       4.00       4.00          N       -0.22
07      6.00       2.00       2.00      10.00          W        0.02
08      0.00       1.00       1.00      18.00          T        1.11
09      1.00       5.00       1.00      13.00          T        0.36
//
//
NA Kr *
PW 0.000000
PO         A          C          G          T       cons         inf
00     37.00       0.00       4.00       3.00          A        1.03
01     33.00       6.00       1.00       4.00          A        0.68
02     20.00      11.00       9.00       4.00          V        0.03
03      2.00       0.00      40.00       2.00          G        1.29
04      4.00       1.00      37.00       2.00          G        0.97
05      6.00       3.00      35.00       0.00          G        0.90
06      1.00       3.00       4.00      36.00          T        0.89
07      8.00       4.00       4.00      28.00          T        0.34
08     28.00       6.00       5.00       5.00          A        0.31
09     16.00       8.00       5.00      15.00          H       -0.04
//
//
NA tll *
PW 0.000000
PO         A          C          G          T       cons         inf
00     25.00       2.00       6.00       4.00          A        0.42
01     26.00       3.00       7.00       1.00          A        0.56
02     27.00       0.00       8.00       2.00          A        0.75
03      8.00       1.00      27.00       1.00          G        0.71
04      0.00       1.00       0.00      36.00          T        1.60
05      1.00      20.00       1.00      15.00          C        0.51
06     28.00       2.00       7.00       0.00          A        0.81
//
final prior bcd * is 0.001429 0.001429
final prior cad * is 0.001429 0.001429
final prior dl * is 0.001429 0.001429
final prior hb * is 0.001429 0.001429
final prior kni * is 0.001429 0.001429
final prior Kr * is 0.001429 0.001429
final prior tll * is 0.001429 0.001429
UFE wm prior 0.000000 0.000000
bg prior 0.990000 0.990000
ref species is dmel
treestring is (dmel:1)
em_prior is 1
em_wm is 0
do_segment is 0
seglen is 0
bg[0] = 0.250000
bg[1] = 0.250000
bg[2] = 0.250000
bg[3] = 0.250000
allocated memory
read sequences
parsed sequences
mybgfile is set to 
Calculating background frequencies from input sequence
Calculating background model (markov order = 2) ... 
AAA: 0 = 0.395674
CAA: 1 = 0.323653
GAA: 2 = 0.325897
TAA: 3 = 0.328715
ACA: 4 = 0.353652
CCA: 5 = 0.342473
GCA: 6 = 0.310616
TCA: 7 = 0.277533
AGA: 8 = 0.265438
CGA: 9 = 0.321839
GGA: 10 = 0.241507
TGA: 11 = 0.210670
ATA: 12 = 0.240734
CTA: 13 = 0.174402
GTA: 14 = 0.184574
TTA: 15 = 0.183949
AAC: 16 = 0.171687
CAC: 17 = 0.230417
GAC: 18 = 0.189622
TAC: 19 = 0.173913
ACC: 20 = 0.201511
CCC: 21 = 0.234946
GCC: 22 = 0.224115
TCC: 23 = 0.249633
AGC: 24 = 0.280378
CGC: 25 = 0.259528
GGC: 26 = 0.303079
TGC: 27 = 0.282321
ATC: 28 = 0.185678
CTC: 29 = 0.229116
GTC: 30 = 0.194149
TTC: 31 = 0.177070
AAG: 32 = 0.170318
CAG: 33 = 0.214368
GAG: 34 = 0.233269
TAG: 35 = 0.164357
ACG: 36 = 0.176322
CCG: 37 = 0.196237
GCG: 38 = 0.216252
TCG: 39 = 0.216838
AGG: 40 = 0.210159
CGG: 41 = 0.211131
GGG: 42 = 0.260616
TGG: 43 = 0.242212
ATG: 44 = 0.226700
CTG: 45 = 0.252076
GTG: 46 = 0.293085
TTG: 47 = 0.221401
AAT: 48 = 0.262322
CAT: 49 = 0.231563
GAT: 50 = 0.251212
TAT: 51 = 0.333015
ACT: 52 = 0.268514
CCT: 53 = 0.226344
GCT: 54 = 0.249017
TCT: 55 = 0.255996
AGT: 56 = 0.244024
CGT: 57 = 0.207502
GGT: 58 = 0.194798
TGT: 59 = 0.264798
ATT: 60 = 0.346887
CTT: 61 = 0.344406
GTT: 62 = 0.328191
TTT: 63 = 0.417580
done
Enhancer predictions:
  window length is 450
  step length is 150
  em prior difference is 0.050000
Enhancer predictions done ...
