[
{
    "function": "addTable",
    "countTableFile": "$countTableFile$",
    "variableRegionLength": $variableLength$,
    "nColumns": $ncols$,
    "modeledColumns": $colList$,
    "rightFlank": "$rF$",
    "leftFlank": "$lF$"
},
{
    "function": "addSELEX",
    "rounds": $colList$,
    "bindingModes": [ -1 ],
    "bindingModeInteractions": [ -1 ]
},
{
    "function": "addNS"
},
{
    "function": "addBindingMode",
    "size": 12,
    "dinucleotideDistance": 0

},
{
    "function": "addBindingMode",
    "size": 16,
    "dinucleotideDistance": 0

},
{
    "function": "bindingModeSeed",
    "index": 1,
    "mononucleotideIUPAC": "NNNCANNTGNNN"
},
{
    "function": "bindingModeConstraints",
    "index": 1,
    "maxFlankLength": -1,
    "fittingStages": [
        { "optimizeFlankLength": true },
        { "optimizeMotifShift": false },
        { "optimizeMotifShiftHeuristic": false }
    ]
},
{
    "function": "symmetry",
    "index": 1,
    "symmetryString":
    "abcdefFEDCBA"
},
{
    "function": "bindingModeSeed",
    "index": 2,
    "mononucleotideIUPAC": "NNNNNNNNNNNNNNNN"
},
{
    "function": "bindingModeConstraints",
    "index": 2,
    "maxFlankLength": -1,
    "fittingStages": [
        { "optimizeFlankLength": true },
        { "optimizeMotifShift": false },
        { "optimizeMotifShiftHeuristic": false }
    ]
},
{
    "function": "symmetry",
    "index": 2,
    "symmetryString":
    "abcdefghHGFEDCBA"
},
{
    "function": "output",
    "outputPath": "$outPath$",
    "baseName": "fit"
},
{
    "function": "lbfgsSettings",
    "maxIters": 2000
},
{
    "function": "optimizerSetting",
    "lambdaL2": 1e-6,
    "pseudocount": 20,
    "likelihoodThreshold": 0.0002,
    "nThreads": 12
}
]