{
  "model": "dnabert2",
  "experiment": "phase6_natural",
  "timestamp": "20260715_131122",
  "results": {
    "per_rna": {
      "5S_rRNA_ecoli": {
        "skipped": true,
        "reason": "< 15 WC pairs (4 found)",
        "n_wc_pairs_total": 4
      },
      "6S_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "7SK_RNA": {
        "best_ps": -0.04979753494262695,
        "best_layer": 0,
        "per_layer_ps": [
          -0.04979753494262695
        ],
        "n_eligible_pairs": 30,
        "n_stems": 17,
        "n_wc_pairs_total": 80,
        "positive_control": {
          "pass": false,
          "p_value": 0.9133309170703651,
          "mean_stem_delta": 0.09252237824105128,
          "mean_loop_delta": 0.09123804804719524
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -0.07476919889450073,
        "ps_au_pairs": -0.037311702966690063,
        "quarantined": false,
        "null_95th_primary": 0.0,
        "null_95th_conservative": NaN,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "Bacterial_SRP": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "CRISPR_leader": {
        "skipped": true,
        "reason": "< 15 WC pairs (6 found)",
        "n_wc_pairs_total": 6
      },
      "Corona_5UTR": {
        "best_ps": -0.0009984241591559516,
        "best_layer": 0,
        "per_layer_ps": [
          -0.0009984241591559516
        ],
        "n_eligible_pairs": 40,
        "n_stems": 16,
        "n_wc_pairs_total": 83,
        "positive_control": {
          "pass": false,
          "p_value": 0.013900449483233565,
          "mean_stem_delta": 0.10135825526490005,
          "mean_loop_delta": 0.12074507897098859
        },
        "h3_precision": {
          "fraction": 0.3333333333333333,
          "n": 3,
          "partner_max_count": 1,
          "p_value": 0.7037037037037037
        },
        "ps_gc_pairs": -0.0001274198293685913,
        "ps_au_pairs": -0.0016952276229858399,
        "quarantined": false,
        "null_95th_primary": 0.0004598697026570638,
        "null_95th_conservative": 0.0004598697026570638,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "Corona_s2m": {
        "skipped": true,
        "reason": "< 15 WC pairs (12 found)",
        "n_wc_pairs_total": 12
      },
      "CrPV_IRES": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "FMN_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "HDV_ribozyme": {
        "skipped": true,
        "reason": "< 15 WC pairs (6 found)",
        "n_wc_pairs_total": 6
      },
      "Hepatitis_C_IRES_III": {
        "best_ps": 0.013651534914970398,
        "best_layer": 0,
        "per_layer_ps": [
          0.013651534914970398
        ],
        "n_eligible_pairs": 42,
        "n_stems": 19,
        "n_wc_pairs_total": 93,
        "positive_control": {
          "pass": false,
          "p_value": 0.04154301405551803,
          "mean_stem_delta": 0.19783053812349127,
          "mean_loop_delta": 0.2152109473184626
        },
        "h3_precision": {
          "fraction": 0.5,
          "n": 2,
          "partner_max_count": 1,
          "p_value": 0.5555555555555556
        },
        "ps_gc_pairs": 0.013651534914970398,
        "ps_au_pairs": null,
        "quarantined": false,
        "null_95th_primary": -0.002903565764427185,
        "null_95th_conservative": -0.002903565764427185,
        "null_available": true,
        "exceeds_null_primary": true,
        "exceeds_null_conservative": true
      },
      "Histone_3prime": {
        "skipped": true,
        "reason": "< 15 WC pairs (6 found)",
        "n_wc_pairs_total": 6
      },
      "IRES_HCV_domainII": {
        "skipped": true,
        "reason": "< 15 WC pairs (12 found)",
        "n_wc_pairs_total": 12
      },
      "IRE_stem_loop": {
        "skipped": true,
        "reason": "< 15 WC pairs (14 found)",
        "n_wc_pairs_total": 14
      },
      "RNaseP_specificity": {
        "skipped": true,
        "reason": "sequence/dot_bracket length mismatch (94 vs 91)"
      },
      "SAH_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (13 found)",
        "n_wc_pairs_total": 13
      },
      "SAM_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (13 found)",
        "n_wc_pairs_total": 13
      },
      "SECIS_element": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "SRP_RNA_helix8": {
        "skipped": true,
        "reason": "< 15 WC pairs (4 found)",
        "n_wc_pairs_total": 4
      },
      "THF_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "TPP_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (8 found)",
        "n_wc_pairs_total": 8
      },
      "T_box_leader": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U1_snRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U2_snRNA_stem": {
        "skipped": true,
        "reason": "< 15 WC pairs (0 found)",
        "n_wc_pairs_total": 0
      },
      "U4_snRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U5_snRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U6_snRNA": {
        "skipped": true,
        "reason": "< 15 WC pairs (5 found)",
        "n_wc_pairs_total": 5
      },
      "Vault_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "Y_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "ZMP_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "c_di_GMP_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "cobalamin_riboswitch": {
        "best_ps": -0.010582596063613892,
        "best_layer": 0,
        "per_layer_ps": [
          -0.010582596063613892
        ],
        "n_eligible_pairs": 14,
        "n_stems": 7,
        "n_wc_pairs_total": 40,
        "positive_control": {
          "pass": false,
          "p_value": 0.021889241164015576,
          "mean_stem_delta": 0.18362211703571668,
          "mean_loop_delta": 0.25423911519880804
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 1,
          "partner_max_count": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -0.010582596063613892,
        "ps_au_pairs": null,
        "quarantined": false,
        "null_95th_primary": 0.00039005279541015625,
        "null_95th_conservative": 0.00039005279541015625,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "fluoride_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (8 found)",
        "n_wc_pairs_total": 8
      },
      "glmS_ribozyme": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "glycine_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "group_II_intron_D5": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "group_I_intron_P4P6": {
        "best_ps": -0.025336623191833496,
        "best_layer": 0,
        "per_layer_ps": [
          -0.025336623191833496
        ],
        "n_eligible_pairs": 19,
        "n_stems": 9,
        "n_wc_pairs_total": 43,
        "positive_control": {
          "pass": false,
          "p_value": 0.007122512343583305,
          "mean_stem_delta": 0.1551523156632158,
          "mean_loop_delta": 0.19598543969945167
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": 0.028147518634796143,
        "ps_au_pairs": -0.07882076501846313,
        "quarantined": false,
        "null_95th_primary": 0.0,
        "null_95th_conservative": NaN,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "hammerhead_ribozyme": {
        "skipped": true,
        "reason": "< 15 WC pairs (0 found)",
        "n_wc_pairs_total": 0
      },
      "hatchet_ribozyme": {
        "best_ps": -0.001371234655380249,
        "best_layer": 0,
        "per_layer_ps": [
          -0.001371234655380249
        ],
        "n_eligible_pairs": 14,
        "n_stems": 3,
        "n_wc_pairs_total": 24,
        "positive_control": {
          "pass": false,
          "p_value": 0.05411133597178187,
          "mean_stem_delta": 0.1060472489373774,
          "mean_loop_delta": 0.13996556246860808
        },
        "h3_precision": {
          "fraction": 0.5,
          "n": 2,
          "partner_max_count": 1,
          "p_value": 0.5555555555555556
        },
        "ps_gc_pairs": 0.0012225508689880371,
        "ps_au_pairs": -0.0022358298301696777,
        "quarantined": false,
        "null_95th_primary": 0.00044392049312591553,
        "null_95th_conservative": 0.00044392049312591553,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "lysine_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "manganese_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "mir_122_precursor": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "mir_155_precursor": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "mir_21_precursor": {
        "skipped": true,
        "reason": "< 15 WC pairs (0 found)",
        "n_wc_pairs_total": 0
      },
      "mir_let7_precursor": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "pistol_ribozyme": {
        "best_ps": -0.003688812255859375,
        "best_layer": 0,
        "per_layer_ps": [
          -0.003688812255859375
        ],
        "n_eligible_pairs": 9,
        "n_stems": 3,
        "n_wc_pairs_total": 16,
        "positive_control": {
          "pass": false,
          "p_value": 0.1528271839577643,
          "mean_stem_delta": 0.034320374211621665,
          "mean_loop_delta": 0.08771444691552056
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -0.000508427619934082,
        "ps_au_pairs": -0.006869196891784668,
        "quarantined": false,
        "null_95th_primary": 0.0,
        "null_95th_conservative": NaN,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "preQ1_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (5 found)",
        "n_wc_pairs_total": 5
      },
      "purine_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "tRNA_Ala_human": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "tRNA_Phe_yeast": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "tmRNA": {
        "best_ps": -0.050496041774749756,
        "best_layer": 0,
        "per_layer_ps": [
          -0.050496041774749756
        ],
        "n_eligible_pairs": 26,
        "n_stems": 10,
        "n_wc_pairs_total": 65,
        "positive_control": {
          "pass": false,
          "p_value": 0.06184027346415773,
          "mean_stem_delta": 0.13194596622170524,
          "mean_loop_delta": 0.12325794962412086
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -0.050496041774749756,
        "ps_au_pairs": null,
        "quarantined": false,
        "null_95th_primary": 0.0,
        "null_95th_conservative": NaN,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "twister_ribozyme": {
        "skipped": true,
        "reason": "no valid PS values"
      }
    },
    "families_total": 0,
    "families_quarantined": [],
    "families_skipped": [
      "5S_rRNA_ecoli",
      "6S_RNA",
      "Bacterial_SRP",
      "CRISPR_leader",
      "Corona_s2m",
      "CrPV_IRES",
      "FMN_riboswitch",
      "HDV_ribozyme",
      "Histone_3prime",
      "IRES_HCV_domainII",
      "IRE_stem_loop",
      "RNaseP_specificity",
      "SAH_riboswitch",
      "SAM_riboswitch",
      "SECIS_element",
      "SRP_RNA_helix8",
      "THF_riboswitch",
      "TPP_riboswitch",
      "T_box_leader",
      "U1_snRNA",
      "U2_snRNA_stem",
      "U4_snRNA",
      "U5_snRNA",
      "U6_snRNA",
      "Vault_RNA",
      "Y_RNA",
      "ZMP_riboswitch",
      "c_di_GMP_riboswitch",
      "fluoride_riboswitch",
      "glmS_ribozyme",
      "glycine_riboswitch",
      "group_II_intron_D5",
      "hammerhead_ribozyme",
      "lysine_riboswitch",
      "manganese_riboswitch",
      "mir_122_precursor",
      "mir_155_precursor",
      "mir_21_precursor",
      "mir_let7_precursor",
      "preQ1_riboswitch",
      "purine_riboswitch",
      "tRNA_Ala_human",
      "tRNA_Phe_yeast",
      "twister_ribozyme"
    ],
    "families_failed_gate": [
      "7SK_RNA",
      "Corona_5UTR",
      "Hepatitis_C_IRES_III",
      "cobalamin_riboswitch",
      "group_I_intron_P4P6",
      "hatchet_ribozyme",
      "pistol_ribozyme",
      "tmRNA"
    ]
  }
}