--- 
"[bifooxir]": 
  MOTIF_LENGTH: 
    :description: motif length identified by bifooxi tool
    :value: 10
  SIGNIFICANCE_HIGH: 
    :description: chi-square criterion significance upper border
    :value: 0.01
  SIGNIFICANCE_LOW: 
    :description: chi-square criterion significance lower border
    :value: 0.05
  SIGNIFICANCE_DELTA: 
    :description: chi-square criterion significance delta
    :value: 0.005
"[bifooxi]": 
  MOTIF_LENGTH: 
    :description: motif length identified by chi-square criterion
    :value: 8
  SIGNIFICANCE_LEVEL: 
    :description: chi-square criterion significance level
    :value: 0.05
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterations for background sampling
    :value: 1024
"[bifooxi_cu]": 
  MOTIF_LENGTH: 
    :description: motif length identified by chi-square criterion
    :value: 11
  SIGNIFICANCE_LEVEL: 
    :description: chi-square criterion significance level
    :value: 0.05
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterations for background sampling
    :value: 1
"[bigfoot]": 
  MOTIF_LENGTH: 
    :description: motif length used
    :value: 15
  LEADER_DELTA: 
    :description: delta for word-pair corresponding to matrix with the best final discrete information content
    :value: 7
  POSITION_INFOCOD: 
    :description: best discrete information content for motif tll (bismark=TLL_motif_15.xml)
    :value: 
    - -1.09803646358367
    - -0.348374353404558
    - -0.562193921486233
    - -0.704086545201882
    - -0.517809388097736
    - -0.624425951028161
    - -0.87799980868282
    - -0.844994008393581
    - -0.833182833641029
    - -0.966351852158791
    - -0.772054101249882
    - -1.16080369926719
    - -1.08375199869541
    - -1.09538834443721
    - -1.19383049142472
  EXTENDED_MODE: 
    :description: extended search mode
    :value: false
  BEST_PAIR: 
    :description: words pair used for initial PCM construction
    :value: 
    - AATGACGCCGACATT
    - CTTGACTTATGCATT
  MOTIF_LOGO: 
    :path: TLL_motif_15.xml.png
    :description: resulting motif logo
  FLANK_LENGTH: 
    :description: flank length used
    :value: 10
  TOTAL_INFOCOD: 
    :description: best discrete information content for motif tll (bismark=TLL_motif_15.xml)
    :value: -12.6832837607529
  LEADER_PHASE: 
    :description: <Footstep> search phase corresponding to matrix with the best final discrete information content
    :value: 0
  SEQUENCE_COUNT: 
    :description: sequence set size
    :value: 37
"[bifoosig]": 
  MIN_SEQUENCE_LENGTH: 
    :description: length of the shortest sequence in the set
    :value: 6
  EXTENDED_MODE: 
    :description: extended search mode
    :value: "false"
  LEADER_DELTA: 
    :description: delta for word-pair corresponding to matrix with the best final discrete information content for different motif lengths
    :value: 
    - 1
    - 0
    - 1
    - 3
    - 6
    - 5
    - 7
    - 8
    - 3
    - 7
  ADD_FLANK_LENGTH: 
    :description: additional flank length
    :value: 1
  MIN_MOTIF_LENGTH: 
    :description: minimum motif length allowed
    :value: 6
  MOTIF_FOUND: 
    :description: no motif found till length 15
    :value: false
  TOTAL_INFOCOD: 
    :description: best total discrete information content for different motif lengths
    :value: 
    - -3.38653726704236
    - -4.2747405428549
    - -5.22418109597231
    - -6.31262779265623
    - -7.3400390470041
    - -8.33119050189208
    - -9.44456987457309
    - -10.5096820848421
    - -11.4990575473853
    - -12.6832837607529
  LEADER_PHASE: 
    :description: <Footstep> search phase corresponding to matricx with the best final discrete information content for different motif lengths
    :value: 
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
  LENGTH_MODE: 
    :description: motif length identification mode
    :value: disabled
  SEQUENCE_COUNT: 
    :description: total number of sequences in the set
    :value: 37
  START_FLANK_LENGTH: 
    :description: starting flank length used for the shortest motif
    :value: 1
  MAX_MOTIF_LENGTH: 
    :description: maximum motif length allowed
    :value: 15
"[bifooxi_cons]": 
  MOTIF_LENGTH: 
    :description: motif length identified by chi-square criterion
    :value: 10
  SIGNIFICANCE_LEVEL: 
    :description: chi-square criterion significance level
    :value: 0.05
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterations for background sampling
    :value: 2048
"[segexbsm]": 
  BISMARK_OUT: 
    :path: TLL_footprints.xml
    :description: segments extracted from bismark db using source_id=BE_DMEL, factor_name=tll
"[flancalc]": 
  FLANK_LENGTH: 
    :description: calculated flank length
    :value: 3
"[flkscn3]": 
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterated words for PWMs longer than 10
    :value: 1048576
"[pmfin]": 
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterated words for PWMs longer than 10
    :value: 1048576
  SEQUENCE_COUNT: 
    :description: initial sequence count
    :value: 37
