--- 
"[bifooxir]": 
  MOTIF_LENGTH: 
    :description: motif length identified by bifooxi tool
    :value: 15
  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_cu]": 
  MOTIF_LENGTH: 
    :description: motif length identified by chi-square criterion
    :value: 15
  SIGNIFICANCE_LEVEL: 
    :description: chi-square criterion significance level
    :value: 0.05
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterations for background sampling
    :value: 1
"[bifooxi]": 
  MOTIF_LENGTH: 
    :description: motif length identified by chi-square criterion
    :value: 13
  SIGNIFICANCE_LEVEL: 
    :description: chi-square criterion significance level
    :value: 0.05
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterations for background sampling
    :value: 1024
"[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: 11
  POSITION_INFOCOD: 
    :description: best discrete information content for motif Trl (bismark=TRL_motif_15.xml)
    :value: 
    - -1.24532579985087
    - -1.04690943630293
    - -0.415964258970408
    - -0.942414204851416
    - -1.20614276867485
    - -0.793157908210369
    - -1.12908618534627
    - -0.995968511615683
    - -0.648686914138238
    - -0.921873763336995
    - -0.707857072651383
    - -0.452759237463138
    - -0.893276622907942
    - -1.1329038984056
    - -0.903233237563806
  EXTENDED_MODE: 
    :description: extended search mode
    :value: false
  BEST_PAIR: 
    :description: words pair used for initial PCM construction
    :value: 
    - CGCAGTCGCGGCGCA
    - GGAACGCAGCAGCCG
  MOTIF_LOGO: 
    :path: TRL_motif_15.xml.png
    :description: resulting motif logo
  FLANK_LENGTH: 
    :description: flank length used
    :value: 11
  TOTAL_INFOCOD: 
    :description: best discrete information content for motif Trl (bismark=TRL_motif_15.xml)
    :value: -13.4355598202899
  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: 77
"[bifoosig]": 
  MIN_SEQUENCE_LENGTH: 
    :description: length of the shortest sequence in the set
    :value: 5
  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: 
    - 0
    - 3
    - 3
    - 2
    - 5
    - 9
    - 9
    - 9
    - 12
    - 11
  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: 
    - -2.98990529581255
    - -4.09614544266072
    - -5.26099928097211
    - -6.42779058030232
    - -7.57963465544647
    - -8.76588862922998
    - -9.94857104133574
    - -11.0897145376803
    - -12.2300066571311
    - -13.4355598202899
  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: 77
  START_FLANK_LENGTH: 
    :description: starting flank length used for the shortest motif
    :value: 2
  MAX_MOTIF_LENGTH: 
    :description: maximum motif length allowed
    :value: 15
"[bifooxi_cons]": 
  MOTIF_LENGTH: 
    :description: motif length identified by chi-square criterion
    :value: 15
  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: TRL_footprints.xml
    :description: segments extracted from bismark db using source_id=BE_DMEL, factor_name=Trl
"[flkscn3]": 
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterated words for PWMs longer than 10
    :value: 1048576
"[flancalc]": 
  FLANK_LENGTH: 
    :description: calculated flank length
    :value: 9
"[pmfin]": 
  MONTECARLO_COUNT: 
    :description: number of montecarlo iterated words for PWMs longer than 10
    :value: 1048576
  SEQUENCE_COUNT: 
    :description: initial sequence count
    :value: 77
