{
  "modelSeeding": {"bindingModes": [
    {"seedScale": 1},
    {
      "seedScale": 10,
      "mononucleotideString": ".....Y....."
    }
  ]},
  "optimizerSetting": {
    "output": {
      "storeHessian": false,
      "outputPath": "./",
      "printTrajectory": false,
      "baseName": "fit.21930",
      "printPSAM": false,
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    "lbfgsSettings": {
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      "convergence": 1.0E-7,
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      "maxIters": 2000
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    "likelihoodThreshold": 0,
    "lambdaL2": 1.0E-6,
    "sgdSettings": {},
    "fixedLibrarySize": false,
    "pseudocount": 5,
    "patternSearchSettings": {},
    "expBound": 40,
    "minimizerType": "lbfgs",
    "nRetries": 3
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  "modelSettings": {
    "enrichmentModel": [
      {
        "r0KUsed": 1,
        "round": 1,
        "bindingSaturation": false,
        "roundSpecificBindingModeInteractions": [[]],
        "concentration": 1,
        "modelType": "SELEX",
        "bindingModeInteractions": [-1],
        "roundSpecificBindingModes": [[]],
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        "modifications": ["None"]
      }
    ],
    "letterOrder": "ACDEFGHIKLMNPQRSTVWY",
    "countTable": [
      {
        "leftFlank": "GQSGQ",
        "transliterate": {
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          "out": []
        },
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        "modeledColumns": [
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        ],
        "inputFileType": "tsv.gz",
        "errorModel": "Poisson",
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        "rightFlank": "GGQSGQSGDY",
        "countTableFile": "../countTables/6673.20230724_nX11_cMyc_Fyn_R1.tsv.gz",
        "probeBias": true
      },
      {
        "leftFlank": "GQSGQ",
        "transliterate": {
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          "out": []
        },
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        "rightFlank": "GGQSGQSGDY",
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      }
    ],
    "bindingModeInteractions": [],
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        "fitLogActivity": true,
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        "dinucleotideDistance": 0,
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        "singleStrand": true,
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        "flankLength": 5,
        "dinucleotideDistance": 0,
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    ],
    "letterComplement": "A-A,C-C,D-D,E-E,F-F,G-G,H-H,I-I,K-K,L-L,M-M,N-N,P-P,Q-Q,R-R,S-S,T-T,V-V,W-W,Y-Y"
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        "trySaturation": false,
        "roundSpecificRho": true
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        "fitDelta": [false],
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        "roundSpecificRho": true
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    "nShifts": 0,
    "countTable": [
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      {}
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    "addBindingModesSequentially": true,
    "flankLengths": [0],
    "bindingModeInteractions": [],
    "singleModeLengthSweep": false,
    "bindingModes": [
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        "maxSize": -1,
        "optimizeFlankLength": false,
        "symmetryString": "null",
        "roundSpecificActivity": true,
        "informationThreshold": 0.1,
        "optimizeMotifShift": false,
        "fittingStages": [],
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        "experimentSpecificPositionBias": true,
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        "symmetryString": "bcdef.ghijk",
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        "optimizeSize": false
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    ]
  }
}