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@@ -58,3 +58,60 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_length.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_length_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_length_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_length_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_partition.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_partition_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_partition_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_partition_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_priority.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_priority_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_priority_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_ablation/eval_Ablation_no_priority_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_2048.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_2048_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_2048_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_2048_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_3072.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_3072_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_3072_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_3072_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_4096.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_4096_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_4096_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_4096_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_5120.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_5120_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_5120_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_5120_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_len2_base.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom/eval_Merged_uni_tf_idf.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_2048.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_2048_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_2048_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_2048_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_3072.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_3072_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_3072_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_3072_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_4096.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_4096_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_4096_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_4096_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_5120.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_5120_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_5120_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_all_chrom_baseline_bpe/eval_Baseline_bpe_5120_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_dnabert2_grover/eval_DNAbert2.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_dnabert2_grover/eval_Grover.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_cCRE_region_BPE.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_cCRE_region_BPE_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_cCRE_region_BPE_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_cCRE_region_BPE_neutral.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_motif_region_BPE.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_motif_region_BPE_accelerated.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_motif_region_BPE_conserved.csv filter=lfs diff=lfs merge=lfs -text
+eval_outputs_new_tokenizers/eval_motif_region_BPE_neutral.csv filter=lfs diff=lfs merge=lfs -text

analyze_ablation.py

@@ -0,0 +1,310 @@
+"""
+Ablation analysis — mirrors all_chrom_evaluation.ipynb but for:
+  - Ablation_no_partition, Ablation_no_priority, Ablation_no_length
+  - Plus Baseline_bpe_5120 and Merged_uni_len2_5120 as references
+Saves all plots to eval_outputs_ablation/plots/
+"""
+
+import os
+import pandas as pd
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+# ── Directories ──────────────────────────────────────────────────────────────
+ABLATION_DIR = "/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation"
+MERGED_DIR   = "/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_all_chrom"
+BASELINE_DIR = "/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_all_chrom_baseline_bpe"
+PLOT_DIR     = os.path.join(ABLATION_DIR, "plots")
+os.makedirs(PLOT_DIR, exist_ok=True)
+
+pd.set_option("display.max_columns", 20)
+pd.set_option("display.width", 200)
+pd.set_option("display.float_format", "{:.6f}".format)
+
+# ── Helper: compute summary row from an agg CSV ─────────────────────────────
+def summarize_agg(agg: pd.DataFrame, name: str, scope: str, region: str = None):
+    row = {
+        "tokenizer": name,
+        "scope": scope,
+        "mean_of_mean_phyloP": agg["mean_mean"].mean(),
+        "median_of_mean_phyloP": agg["mean_mean"].median(),
+        "pct_mean_phyloP_above_0": (agg["mean_mean"] > 0).mean() * 100,
+        "mean_of_variance": agg["mean_var"].mean(),
+        "median_of_variance": agg["mean_var"].median(),
+        "pct_variance_below_0.1": (agg["mean_var"] < 0.1).mean() * 100,
+        "num_tokens": len(agg),
+        "mean_token_count": agg["count"].mean(),
+        "median_token_count": agg["count"].median(),
+    }
+    if region:
+        row["region"] = region
+    return row
+
+
+# ── 1. Window-Based Summary ──────────────────────────────────────────────────
+print("=" * 80)
+print("1. WINDOW-BASED SUMMARY")
+print("=" * 80)
+
+ablation_names = ["Ablation_no_partition", "Ablation_no_priority", "Ablation_no_length"]
+ref_names = {
+    "Baseline_bpe_5120":    os.path.join(BASELINE_DIR, "agg_Baseline_bpe_5120.csv"),
+    "Merged_uni_len2_5120": os.path.join(MERGED_DIR,   "agg_Merged_uni_len2_5120.csv"),
+}
+
+# Load all agg data (window)
+agg_data = {}
+window_summaries = []
+
+for name in ablation_names:
+    path = os.path.join(ABLATION_DIR, f"agg_{name}.csv")
+    agg = pd.read_csv(path)
+    agg_data[name] = agg
+    window_summaries.append(summarize_agg(agg, name, "all_chrom_window"))
+
+for name, path in ref_names.items():
+    agg = pd.read_csv(path)
+    agg_data[name] = agg
+    window_summaries.append(summarize_agg(agg, name, "all_chrom_window"))
+
+df_window = pd.DataFrame(window_summaries)
+cols = ["tokenizer", "mean_of_mean_phyloP", "median_of_mean_phyloP",
+        "pct_mean_phyloP_above_0", "mean_of_variance", "median_of_variance",
+        "pct_variance_below_0.1", "num_tokens", "mean_token_count", "median_token_count"]
+df_window = df_window[cols]
+print(df_window.to_string(index=False))
+df_window.to_csv(os.path.join(ABLATION_DIR, "summary_ablation_window.csv"), index=False)
+
+
+# ── 2. Region-Based Summary ─────────────────────────────────────────────────
+print("\n" + "=" * 80)
+print("2. REGION-BASED SUMMARY")
+print("=" * 80)
+
+agg_region = {}
+region_summaries = []
+
+for name in ablation_names:
+    for region in ["conserved", "neutral", "accelerated"]:
+        path = os.path.join(ABLATION_DIR, f"agg_{name}_{region}.csv")
+        if os.path.exists(path):
+            agg = pd.read_csv(path)
+            agg_region[(name, region)] = agg
+            region_summaries.append(summarize_agg(agg, name, "all_chrom_region", region))
+
+for name, base_path in ref_names.items():
+    base_dir = os.path.dirname(base_path)
+    for region in ["conserved", "neutral", "accelerated"]:
+        path = os.path.join(base_dir, f"agg_{name}_{region}.csv")
+        if os.path.exists(path):
+            agg = pd.read_csv(path)
+            agg_region[(name, region)] = agg
+            region_summaries.append(summarize_agg(agg, name, "all_chrom_region", region))
+
+df_region = pd.DataFrame(region_summaries)
+cols_region = ["tokenizer", "region", "mean_of_mean_phyloP", "median_of_mean_phyloP",
+               "pct_mean_phyloP_above_0", "mean_of_variance", "median_of_variance",
+               "pct_variance_below_0.1", "num_tokens", "mean_token_count", "median_token_count"]
+df_region = df_region[cols_region]
+
+for region in ["conserved", "neutral", "accelerated"]:
+    print(f"\n=== {region.upper()} ===")
+    print(df_region[df_region["region"] == region].to_string(index=False))
+
+df_region.to_csv(os.path.join(ABLATION_DIR, "summary_ablation_all_regions.csv"), index=False)
+
+
+# ── Color scheme ─────────────────────────────────────────────────────────────
+COLORS = {
+    "Baseline_bpe_5120":      "steelblue",
+    "Merged_uni_len2_5120":   "tomato",
+    "Ablation_no_partition":  "#2ca02c",   # green
+    "Ablation_no_priority":   "#9467bd",   # purple
+    "Ablation_no_length":     "#ff7f0e",   # orange
+}
+
+
+# ── 3. Scatter: Mean phyloP vs Variance (Window) ────────────────────────────
+print("\n" + "=" * 80)
+print("3. SCATTER PLOTS: Mean phyloP vs Variance")
+print("=" * 80)
+
+fig, axes = plt.subplots(1, 2, figsize=(18, 8))
+
+for ax_idx, (xcol, xlabel) in enumerate([("mean_mean", "Mean phyloP"), ("median_mean", "Median Mean phyloP")]):
+    ax = axes[ax_idx]
+    for name, color in COLORS.items():
+        if name in agg_data:
+            d = agg_data[name]
+            ax.scatter(d[xcol], d["mean_var"], alpha=0.4, s=20, label=name, color=color)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel("Mean Variance")
+    ax.set_title(f"Token Conservation: {xlabel} vs Variance")
+    ax.legend(fontsize=8)
+
+plt.tight_layout()
+plt.savefig(os.path.join(PLOT_DIR, "scatter_mean_vs_var.png"), dpi=150, bbox_inches="tight")
+plt.close()
+print(f"  Saved scatter_mean_vs_var.png")
+
+
+# ── 4. Histograms: Mean phyloP and Variance distributions ───────────────────
+print("\n" + "=" * 80)
+print("4. HISTOGRAMS")
+print("=" * 80)
+
+fig, axes = plt.subplots(1, 2, figsize=(18, 6))
+
+ax = axes[0]
+for name, color in COLORS.items():
+    if name in agg_data:
+        ax.hist(agg_data[name]["mean_mean"], bins=50, alpha=0.5, label=name, color=color)
+ax.set_xlabel("Mean phyloP")
+ax.set_ylabel("Token Count")
+ax.set_title("Mean Conservation Distribution")
+ax.legend(fontsize=8)
+
+ax = axes[1]
+for name, color in COLORS.items():
+    if name in agg_data:
+        ax.hist(agg_data[name]["mean_var"], bins=50, alpha=0.5, label=name, color=color)
+ax.set_xlabel("Mean Variance")
+ax.set_ylabel("Token Count")
+ax.set_title("Variance Distribution")
+ax.legend(fontsize=8)
+
+plt.tight_layout()
+plt.savefig(os.path.join(PLOT_DIR, "histograms_mean_var.png"), dpi=150, bbox_inches="tight")
+plt.close()
+print(f"  Saved histograms_mean_var.png")
+
+
+# ── 5. Region scatter: by region ─────────────────────────────────────────────
+print("\n" + "=" * 80)
+print("5. REGION SCATTER PLOTS")
+print("=" * 80)
+
+fig, axes = plt.subplots(1, 3, figsize=(21, 7))
+
+for i, region in enumerate(["conserved", "neutral", "accelerated"]):
+    ax = axes[i]
+    for name, color in COLORS.items():
+        key = (name, region)
+        if key in agg_region:
+            d = agg_region[key]
+            ax.scatter(d["mean_mean"], d["mean_var"], alpha=0.4, s=20, label=name, color=color)
+    ax.set_xlabel("Mean phyloP")
+    ax.set_ylabel("Mean Variance")
+    ax.set_title(f"{region.capitalize()} Regions")
+    ax.legend(fontsize=7, loc="upper left")
+
+plt.suptitle("Region-Based: Ablation vs References", fontsize=14)
+plt.tight_layout()
+plt.savefig(os.path.join(PLOT_DIR, "scatter_by_region.png"), dpi=150, bbox_inches="tight")
+plt.close()
+print(f"  Saved scatter_by_region.png")
+
+
+# ── 6. Bar charts: Summary metrics by tokenizer and region ──────────────────
+print("\n" + "=" * 80)
+print("6. BAR CHARTS: Summary metrics")
+print("=" * 80)
+
+metrics = ["mean_of_mean_phyloP", "pct_mean_phyloP_above_0", "mean_of_variance", "pct_variance_below_0.1"]
+metric_labels = ["Mean of Mean phyloP", "% Mean phyloP > 0", "Mean of Variance", "% Variance < 0.1"]
+
+fig, axes = plt.subplots(2, 2, figsize=(18, 12))
+
+for idx, (metric, label) in enumerate(zip(metrics, metric_labels)):
+    ax = axes[idx // 2, idx % 2]
+    for region in ["conserved", "neutral", "accelerated"]:
+        subset = df_region[df_region["region"] == region].copy()
+        subset = subset.sort_values("tokenizer")
+        x = range(len(subset))
+        offset = {"conserved": -0.25, "neutral": 0, "accelerated": 0.25}[region]
+        color = {"conserved": "forestgreen", "neutral": "gray", "accelerated": "firebrick"}[region]
+        ax.bar([xi + offset for xi in x], subset[metric], width=0.25,
+               label=region, color=color, alpha=0.8)
+    ax.set_xticks(range(len(subset)))
+    ax.set_xticklabels(subset["tokenizer"], rotation=45, ha="right", fontsize=8)
+    ax.set_ylabel(label)
+    ax.set_title(label)
+    ax.legend(fontsize=8)
+
+plt.suptitle("Ablation: Region-Based Metrics", fontsize=14)
+plt.tight_layout()
+plt.savefig(os.path.join(PLOT_DIR, "bar_region_metrics.png"), dpi=150, bbox_inches="tight")
+plt.close()
+print(f"  Saved bar_region_metrics.png")
+
+
+# ── 7. Grouped bar: Ablation comparison (window metrics) ────────���───────────
+print("\n" + "=" * 80)
+print("7. GROUPED BAR: Window metrics comparison")
+print("=" * 80)
+
+order = ["Baseline_bpe_5120", "Ablation_no_partition", "Ablation_no_priority",
+         "Ablation_no_length", "Merged_uni_len2_5120"]
+df_w_ordered = df_window.set_index("tokenizer").loc[order].reset_index()
+
+fig, axes = plt.subplots(1, 3, figsize=(20, 6))
+
+# Mean phyloP
+ax = axes[0]
+bars = ax.barh(df_w_ordered["tokenizer"], df_w_ordered["mean_of_mean_phyloP"],
+               color=[COLORS[n] for n in df_w_ordered["tokenizer"]])
+ax.set_xlabel("Mean of Mean phyloP")
+ax.set_title("Conservation Signal (Higher is Better)")
+ax.invert_yaxis()
+for bar, val in zip(bars, df_w_ordered["mean_of_mean_phyloP"]):
+    ax.text(bar.get_width() + 0.001, bar.get_y() + bar.get_height()/2,
+            f"{val:.4f}", va="center", fontsize=9)
+
+# % above 0
+ax = axes[1]
+bars = ax.barh(df_w_ordered["tokenizer"], df_w_ordered["pct_mean_phyloP_above_0"],
+               color=[COLORS[n] for n in df_w_ordered["tokenizer"]])
+ax.set_xlabel("% Mean phyloP > 0")
+ax.set_title("Positive Conservation Rate (Higher is Better)")
+ax.invert_yaxis()
+for bar, val in zip(bars, df_w_ordered["pct_mean_phyloP_above_0"]):
+    ax.text(bar.get_width() + 0.1, bar.get_y() + bar.get_height()/2,
+            f"{val:.1f}%", va="center", fontsize=9)
+
+# Mean variance
+ax = axes[2]
+bars = ax.barh(df_w_ordered["tokenizer"], df_w_ordered["mean_of_variance"],
+               color=[COLORS[n] for n in df_w_ordered["tokenizer"]])
+ax.set_xlabel("Mean of Variance")
+ax.set_title("Internal Variance (Lower is Better)")
+ax.invert_yaxis()
+for bar, val in zip(bars, df_w_ordered["mean_of_variance"]):
+    ax.text(bar.get_width() + 0.001, bar.get_y() + bar.get_height()/2,
+            f"{val:.4f}", va="center", fontsize=9)
+
+plt.suptitle("Ablation: Window-Based Summary Metrics", fontsize=14)
+plt.tight_layout()
+plt.savefig(os.path.join(PLOT_DIR, "bar_window_comparison.png"), dpi=150, bbox_inches="tight")
+plt.close()
+print(f"  Saved bar_window_comparison.png")
+
+
+# ── 8. Print final comparison table ─────────────────────────────────────────
+print("\n" + "=" * 80)
+print("8. FINAL COMPARISON TABLE")
+print("=" * 80)
+print("\nWindow-based:")
+print(df_w_ordered[["tokenizer", "mean_of_mean_phyloP", "pct_mean_phyloP_above_0",
+                     "mean_of_variance", "pct_variance_below_0.1", "num_tokens"]].to_string(index=False))
+
+print("\nRegion-based (conserved only):")
+cons = df_region[df_region["region"] == "conserved"].copy()
+cons = cons[cons["tokenizer"].isin(order)]
+print(cons[["tokenizer", "mean_of_mean_phyloP", "pct_mean_phyloP_above_0",
+            "mean_of_variance", "num_tokens"]].to_string(index=False))
+
+print(f"\nAll plots saved to: {PLOT_DIR}/")
+print("All summary CSVs saved to:", ABLATION_DIR)

baseline_bpe/tokenizer.json

@@ -0,0 +1,2107 @@
+{
+  "version": "1.0",
+  "truncation": null,
+  "padding": null,
+  "added_tokens": [
+    {
+      "id": 0,
+      "content": "[PAD]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 1,
+      "content": "[UNK]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 2,
+      "content": "[CLS]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 3,
+      "content": "[SEP]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 4,
+      "content": "[MASK]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    }
+  ],
+  "normalizer": null,
+  "pre_tokenizer": null,
+  "post_processor": null,
+  "decoder": null,
+  "model": {
+    "type": "BPE",
+    "dropout": null,
+    "unk_token": "[UNK]",
+    "continuing_subword_prefix": null,
+    "end_of_word_suffix": null,
+    "fuse_unk": false,
+    "byte_fallback": false,
+    "vocab": {
+      "[PAD]": 0,
+      "[UNK]": 1,
+      "[CLS]": 2,
+      "[SEP]": 3,
+      "[MASK]": 4,
+      "A": 5,
+      "C": 6,
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+    },
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+      "AGG AG",
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+      "TTGG C",
+      "AG AAG",
+      "ATC AC",
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+      "AGGG G",
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+      "AA ATC",
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+      "AC ATT",
+      "AG ATG",
+      "AG AAC",
+      "TC TCC",
+      "AA AGG",
+      "TAT CC",
+      "AT ATC",
+      "AT AAG",
+      "TG CCC",
+      "TC G",
+      "AG AAAA",
+      "AA AGC",
+      "TATT G",
+      "TC ATT",
+      "TC TTC",
+      "TT AAAA",
+      "TG TGG",
+      "TG AAG",
+      "AG AGG",
+      "GG GG",
+      "TG TAG",
+      "TT AAG",
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+      "AAGG G",
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+      "T ATGC",
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+      "TG TTC",
+      "TT TAT",
+      "TTG AA",
+      "TT ATC",
+      "TCCC AGC",
+      "AT AGC",
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+      "TC TGC",
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+      "AG ACC",
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+      "AA TAG",
+      "TG AGGC",
+      "AA TGG",
+      "AAG AC",
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+      "AA TCC",
+      "TG TCC",
+      "TAA GG",
+      "TC ACC",
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+      "TC AAG",
+      "TTGG CC",
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+      "AG TGG",
+      "TG TTTT",
+      "AC AGG",
+      "AA TTG",
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+      "AC AAC",
+      "TG ACC",
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+      "AG TGC",
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+      "AG TAG",
+      "TAA TTTT",
+      "TAA CC",
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+      "AG TT",
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+      "TC TAC",
+      "AA TATT",
+      "TAA TAA",
+      "ATT TTG",
+      "TGGG ATTAC",
+      "AGG AGG",
+      "AG TAC",
+      "TTC G",
+      "TCAC TGC",
+      "TG TCTC",
+      "ACAC ACAC",
+      "TTC AC",
+      "AGC G",
+      "AGGC TGG",
+      "ATT TT",
+      "AG TTTT",
+      "AAAA GC",
+      "AGG TC",
+      "TTCC CC",
+      "AAC G",
+      "AC GG",
+      "AAAA CC",
+      "TC TAG",
+      "AAAA GG",
+      "TCC TGCC",
+      "AGG AAG",
+      "AAAG TGC",
+      "TTG CCC",
+      "AGCC CC",
+      "TT TGTG",
+      "AA ACAC",
+      "TG TAT",
+      "AAAA ATT",
+      "TTC AAG",
+      "TC TGCC",
+      "TGC G",
+      "AG AGAA",
+      "TGGG GC",
+      "AC GC",
+      "AC TAG",
+      "TGTG TGTG",
+      "TG AGAC",
+      "AGG AGAA",
+      "ATT TCC",
+      "TGTAA TCCCAGC",
+      "TGGG CC",
+      "AAC AC",
+      "TC GC",
+      "TCC G",
+      "AGGG GC",
+      "TTTG CC",
+      "TT TCCC",
+      "ACTT TGGG",
+      "ATT TTTT",
+      "AGGG CC",
+      "AT ATAC",
+      "AAG AA",
+      "AGC AC",
+      "TGGG GG",
+      "ATT TG",
+      "ATC G",
+      "TC TTTC",
+      "TTTT GC",
+      "AC AGAA",
+      "AT AGAA",
+      "TAT ATT",
+      "TGTG GC",
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+      "AGC AGC",
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+      "AGG AC",
+      "TTC TG",
+      "AT ATTG",
+      "AAG AAG",
+      "TAA ATG",
+      "ATGG CC",
+      "G TGG",
+      "TT TATG",
+      "TTTG GC",
+      "AA TTTC",
+      "TAA AAC",
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+      "AGG TGG",
+      "TT TGGG",
+      "TAA AC",
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+      "AT ACAC",
+      "TTC TCC",
+      "TG TTTC",
+      "TT TAAG",
+      "AGGC TGGAG",
+      "AG TCTC",
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+      "ATG TC",
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+      "TCC AC",
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+      "TCCC AAAGTGC",
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+      "TAA ATT",
+      "ATC ACC",
+      "AAC AAC",
+      "ATG AC",
+      "AA AGAC",
+      "TTGC AGTG",
+      "ATTG CC",
+      "TC AGAA",
+      "TAA AAG",
+      "AG AGGC",
+      "TT ATAA",
+      "AA ATGG",
+      "ATT TGC",
+      "TGGGATTAC AGGC",
+      "TTC TGC",
+      "AG AGGG",
+      "TTC AAC",
+      "TTGG GC",
+      "ATT TATT",
+      "AAG AAAA",
+      "AT ATCC",
+      "TT TAAC",
+      "TAT ATG",
+      "ACC TCC",
+      "AAGG GC",
+      "TTGG GG",
+      "ATT CCC",
+      "AGG CCC",
+      "AG TATT",
+      "ATAT ATAT",
+      "AAGG GG",
+      "TAC TAAAA",
+      "AA AGAG",
+      "TTTAG TAG",
+      "TT AGCC",
+      "TAC G",
+      "AC TTTT",
+      "ATG ATG",
+      "AAC TCC",
+      "AGG AGC",
+      "TC TTCC",
+      "AA AGGC",
+      "TGG AAG",
+      "AT ATGG",
+      "AG ACAC",
+      "TG AAAC",
+      "TGG CCC",
+      "AG TGGC",
+      "TTG TTG",
+      "AA TGAA",
+      "TGC AAG",
+      "TC TCCC",
+      "TC ACCC",
+      "ATC TCC",
+      "AG ATAA",
+      "AA AGCC",
+      "ATT TAG",
+      "TGG AC",
+      "AGC TCC",
+      "ATG GGG",
+      "AG ATTC",
+      "TC AAAA",
+      "TG AGCC",
+      "TT AGAA",
+      "ACC AGCC",
+      "ATG TAA",
+      "AGG AAC",
+      "GC G",
+      "TT AAAC",
+      "TCTC G",
+      "AT AAGG",
+      "AGC AAG",
+      "TTTT TAA",
+      "ACC ACC",
+      "ATC TTC",
+      "AGGG GG",
+      "AA TTAA",
+      "AGAA CC",
+      "AGC TGC",
+      "AG TAT",
+      "ATG TG",
+      "TGCAG TGGC",
+      "AA ATCC",
+      "TTG AAC",
+      "ATG AAG",
+      "CCC AGC",
+      "AG AGCC",
+      "AA TCTC",
+      "AAAA AC",
+      "TTG AC",
+      "TC GG",
+      "AT AGAG",
+      "AA TGGC",
+      "TGC TG",
+      "TAAG CC",
+      "TAGC TGGG",
+      "AT AGGC",
+      "AAG AAC",
+      "AA ATTG",
+      "ATC ATC",
+      "TGC TTC",
+      "TTG TC",
+      "ATT TGG",
+      "AGG ATG",
+      "AA TATG",
+      "AGG TG",
+      "AGC TG",
+      "AAC ATGG",
+      "AA ATATT",
+      "TTTT TC",
+      "TT ATTG",
+      "AA AGGG",
+      "ATC ATG",
+      "TAC AC",
+      "AA AGTG",
+      "AA TTCC",
+      "AT ACCC",
+      "TCCTGCC TCAGCC",
+      "TCC CCC",
+      "TGAA CC",
+      "AA TTTG",
+      "ATC TG",
+      "TTC ATT",
+      "ATAA GC",
+      "TGG TGC",
+      "AC TCTG",
+      "TC ATTC",
+      "AACC CC",
+      "TAT AAAA",
+      "TTC TAG",
+      "TTTT TTG",
+      "ACC CCC",
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+      "G TCTC",
+      "AA TTAC",
+      "AT AGTG",
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+      "TTAA CC",
+      "TC TGTG",
+      "TCC TTC",
+      "TG TTCC",
+      "TGGC TCAC",
+      "TCCTG ACCTC",
+      "TGG AGG",
+      "AAG ATG",
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+      "ATC TGC",
+      "TC TATT",
+      "TCACTGC AACC",
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+      "TTAA GC",
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+      "AA TGTG",
+      "TG TGGG",
+      "TCC ACC",
+      "AG TGGG",
+      "TGGGC AAC",
+      "ATC TTG",
+      "AGG AAAA",
+      "AGC ATT",
+      "AG TAAC",
+      "TT TAGC",
+      "TTC TTTT",
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+      "TC TTTG",
+      "TATG CC",
+      "TAG AAG",
+      "TAG AC",
+      "ACC TTG",
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+      "ATG CCC",
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+      "TAGG CC",
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+      "AAC AAAA",
+      "AG TGTG",
+      "AT AGCC",
+      "TG AGAG",
+      "AG TGAA",
+      "ATG TGC",
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+      "ATT TTTC",
+      "AA TAAG",
+      "AT AGGG",
+      "AG ACCC",
+      "AT AAAAC",
+      "AC TGTG",
+      "ATAA ATAA",
+      "TAC AAAA",
+      "ATG AGCC",
+      "TC TGGG",
+      "AGC AAC",
+      "TG TATG",
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+      "AAG CCC",
+      "ATG AAC",
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+      "AGC ACC",
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+      "TTC TGG",
+      "AGG TTG",
+      "AGG TAG",
+      "AG TTAA",
+      "TC AAGC",
+      "TTTC TTTC",
+      "TGTAATCCCAGC ACTTTGGG",
+      "TT ATAC",
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+      "TAT ATC",
+      "TGC TCC",
+      "AC AGCC",
+      "TG ATGG",
+      "ATT AAC",
+      "AA TCAC",
+      "TT ATCC",
+      "TAT AAC",
+      "TTGCAGTG AGCC",
+      "TATG GC",
+      "TC AGGG",
+      "TTTG TAA",
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+      "AAAA AAG",
+      "TACC CC",
+      "AG TAAG",
+      "TTG AAG",
+      "TTGAA CCC",
+      "TCAC AGAG",
+      "TTG TAG",
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+      "ATG ATT",
+      "TCC TGAG",
+      "AG TCAC",
+      "ATAT ATT",
+      "TC AGGC",
+      "TGAA ACCCC",
+      "AG AAAAG",
+      "TG ATAA",
+      "TT AGAG",
+      "AGC AGG",
+      "AC AAAC",
+      "TCC TTG",
+      "AT AAAAG",
+      "TCCC AGG",
+      "TGG TAG",
+      "GTG AGCC",
+      "ATC AAC",
+      "TC ACAC",
+      "TAC TAA",
+      "G TGC",
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+      "TTC TAC",
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+      "AA ATAG",
+      "TCC ATG",
+      "AA TGGG",
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+      "TTC TTTC",
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+      "TCC GCC",
+      "CCC G",
+      "AG AAAAC",
+      "TG TTGG",
+      "AGG ATT",
+      "TCTC TCTC",
+      "AGAC AGGG",
+      "TGC AGC",
+      "TT ACCC",
+      "TG TCCC",
+      "TAC ATG",
+      "AG ATCC",
+      "TC AGGAG",
+      "TCC AGC",
+      "ACC TAA",
+      "AG ATTG",
+      "AAG AGC",
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+      "AC AGGG",
+      "TGC TGG",
+      "AGG AGGC",
+      "AAAAAAAA AAAA",
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+      "TCC ATC",
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+      "AAC TTC",
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+      "AGAG AGAG",
+      "AC ATTC",
+      "TTTC ACCATG",
+      "TG TTAA",
+      "TCC TGGG",
+      "TC ATCC",
+      "TT ATGC",
+      "TTTTTTTT TTTT",
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+      "TTG AACC",
+      "TAG AAAA",
+      "AGG ATGG",
+      "AC AGGC",
+      "AA TACC",
+      "GG GGC",
+      "TTG TATT",
+      "TC TGAA",
+      "TC ATTG",
+      "TAATTTT TGTATT",
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+      "ACC TTC",
+      "TT AGGG",
+      "TG TATC",
+      "AG TTGG",
+      "AG TAGC",
+      "ATAA TAA",
+      "TCC AAG",
+      "ATT AAG",
+      "AG TATC",
+      "AC TTTG",
+      "TG TAAG",
+      "TC TTGG",
+      "TAG TAA",
+      "TCCCAGC TAC",
+      "AGAA AGAA",
+      "TG AGTG",
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+      "TTTT ATT",
+      "ACC ATC",
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+      "TG TCAC",
+      "TGG TAA",
+      "ACC AGC",
+      "ATG ATC",
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+      "TG TTGC",
+      "TCC TAA",
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+      "ACTGC ACTCCAGCC",
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+      "AGG TAC",
+      "TGGG TGAC",
+      "AGG AAAC",
+      "TTG TTC",
+      "TC AAGG",
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+      "AGGC G",
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+      "TGC ATT",
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+      "TTC AGC",
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+      "TCC AGCC",
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+      "AG TACC",
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+      "AC ATAC",
+      "TAA AAAA",
+      "ATT TGAA",
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+      "TT AGTG",
+      "AAG AGG",
+      "TCTC AAAC",
+      "TG TTTTC",
+      "AAG TGG",
+      "AAC AGC",
+      "TAA GGC",
+      "ACC ACG",
+      "TAA TTC",
+      "ATT TCTC",
+      "TTTAA CC",
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+      "TGC GG",
+      "TTTT TTC",
+      "TG ATTG",
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+      "AAAC AAAC",
+      "TC TTAA",
+      "AGG ATC",
+      "TC AACC",
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+      "AAG TAG",
+      "AC AAGG",
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+      "TC TATC",
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+      "AGC TAG",
+      "TTTT GCC",
+      "TG ATAC",
+      "AAAA ATG",
+      "TCC AAC",
+      "TTGGCC AGGCTGG",
+      "AGAC GGGG",
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+      "AC ACCC",
+      "TC AGAC",
+      "ATAA ATG",
+      "TAC TTC",
+      "TCCCAAAGTGC TGGGATTACAGGC",
+      "TC ATGC",
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+      "AGAA GGC",
+      "TTTT CCC",
+      "AA TTTTC",
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+      "ATAT ATG",
+      "TC AGTC",
+      "ATGG TGGC",
+      "ATT TTCC",
+      "AC ATTG",
+      "AG TTTTC",
+      "TATT TTC",
+      "ACC ATCC",
+      "AC TTGG",
+      "GC GC",
+      "TGGCC CC",
+      "TGG ATC",
+      "AGAC AGAG",
+      "AAC TAC",
+      "AGAC GG",
+      "TC TATG",
+      "TTGG AAAC",
+      "AGAG AAG",
+      "AC AAAG",
+      "TAA ATC",
+      "TC TACC",
+      "TTC TTCC",
+      "ATT GGG",
+      "T A",
+      "AGC TTG",
+      "TGC TAC",
+      "AC TGGC",
+      "TC TTTTC",
+      "TG TAGG",
+      "AGC GG",
+      "AATT CCC",
+      "ATT TTTG",
+      "TG TAGC",
+      "TGG AAAA",
+      "TGG TAC",
+      "ATG TGCC",
+      "ATC TAG",
+      "TTCC TTCC",
+      "AC TTGC",
+      "ACC TAG",
+      "TTTT TATT",
+      "TAA TAG"
+    ]
+  }
+}

baseline_bpe/vocab_2048/2048_tokenizer.json

@@ -0,0 +1,4155 @@
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+  "padding": null,
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+      "AG TAG",
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+      "AGG AGG",
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+      "AGC AGC",
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+      "AA ATGG",
+      "TG AGAC",
+      "AC AGAA",
+      "AGG AGAA",
+      "AT ATTG",
+      "AG TCTC",
+      "ATC G",
+      "AG AGGG",
+      "TGTAA TCCCAGC",
+      "TTTT GC",
+      "TTC TG",
+      "AAG AAG",
+      "TAA ATG",
+      "AA AGAC",
+      "ATT TAC",
+      "TGGG CC",
+      "TTC TCC",
+      "TGGG GG",
+      "AG ATAA",
+      "AT ACAC",
+      "ATT TGC",
+      "TGTG CC",
+      "AG AGGC",
+      "TCC TC",
+      "ACTT TGGG",
+      "TT TCCC",
+      "AG TATT",
+      "TTTT GG",
+      "AGG TGG",
+      "AAC AC",
+      "ATT TATT",
+      "TT TATG",
+      "AG TAT",
+      "G TGG",
+      "AGGG GC",
+      "AATG GC",
+      "ATG TG",
+      "AGGG CC",
+      "TC AAAA",
+      "AA ATTG",
+      "TCC TCC",
+      "AA AGAG",
+      "AGG TG",
+      "AG ACAC",
+      "TAA AAG",
+      "TTC TGC",
+      "TTTG GC",
+      "AGC AC",
+      "ATT CCC",
+      "AT ATGC",
+      "TTG AAC",
+      "TAA AC",
+      "AGGC TGAGGC",
+      "TATT CC",
+      "TG TTTC",
+      "AG ATTC",
+      "AA AGTG",
+      "TGC TGC",
+      "AT ATCC",
+      "AAC AAC",
+      "AAG AAAA",
+      "TG AGAA",
+      "ATAT ATAT",
+      "AGG AC",
+      "TC TTCC",
+      "AA TATG",
+      "TT TAAG",
+      "TT TGGG",
+      "TAT ATT",
+      "AA ATCC",
+      "TAT AC",
+      "TT ATAA",
+      "TAT ATG",
+      "AT ATGG",
+      "AA AGCC",
+      "AA TATC",
+      "ATC TTC",
+      "TC TCCC",
+      "TCTG GC",
+      "TT TATC",
+      "AG TAGC",
+      "AA TCTC",
+      "AA TTTG",
+      "AA ATATT",
+      "ACTCC AGCC",
+      "AAC TC",
+      "TAC TC",
+      "ATC ACC",
+      "AA AGGG",
+      "AGG AGC",
+      "AA AGGC",
+      "TAC G",
+      "TT ATTC",
+      "ATC TCC",
+      "AGTG CC",
+      "TAA ATT",
+      "AAC TCC",
+      "ATGG CC",
+      "ATG ATG",
+      "AA TTCC",
+      "AAGG CC",
+      "TTG TTG",
+      "ATTG CC",
+      "TGC AC",
+      "TGG AAG",
+      "TTGC AGTG",
+      "ACC TCC",
+      "GC G",
+      "AGC TC",
+      "AG AGCC",
+      "AA TAAC",
+      "ATT TAG",
+      "TTTT TAA",
+      "AATT GC",
+      "TTGG GG",
+      "AATG CC",
+      "AAG AAC",
+      "AAG ACC",
+      "TCCC AAAGTGC",
+      "TGC TG",
+      "TC ATTC",
+      "TC ACCC",
+      "TC GG",
+      "AGCC G",
+      "ATG TAA",
+      "ATCC CC",
+      "ATG AC",
+      "CCC AGC",
+      "AT AGAG",
+      "TT TAAC",
+      "TCC AC",
+      "TGGGATTAC AGGC",
+      "TTGG GC",
+      "TG AAAC",
+      "ATT TGG",
+      "ATG TGG",
+      "AGC AGG",
+      "AAGG GG",
+      "AA ACCC",
+      "TC TGTG",
+      "ATG AAG",
+      "TT AAAC",
+      "TTC AAC",
+      "TCCC G",
+      "AGGCTGG AGTGC",
+      "AG TTCC",
+      "AA TAAG",
+      "TGC AGC",
+      "AA TGTG",
+      "TAAAA ATAC",
+      "AGG AAC",
+      "AGAA CC",
+      "AAAA AC",
+      "ATC ATC",
+      "TC TATT",
+      "TGC TTC",
+      "TCTC G",
+      "AGC TCC",
+      "AG ATGC",
+      "AAGG GC",
+      "ACC ACC",
+      "TC TTTG",
+      "AT AGTG",
+      "ATC TG",
+      "TAT AAAA",
+      "TTC TTTT",
+      "AC AGAG",
+      "ATG GGG",
+      "AG TGGG",
+      "TAG AGAC",
+      "TT AGAA",
+      "AC TCTG",
+      "AACC CC",
+      "AG TGTG",
+      "TTC TTG",
+      "TGG AGC",
+      "TC TTGC",
+      "TT AATT",
+      "AGG CCC",
+      "AT AGGC",
+      "TGCC CC",
+      "AGC AAG",
+      "TTC TAA",
+      "AT ACCC",
+      "ATG TTG",
+      "AT AGAC",
+      "ATG TGC",
+      "AGG TGC",
+      "ATAA GC",
+      "ATC TTG",
+      "ATT TTTC",
+      "TTTT TTG",
+      "TTC TAG",
+      "TGG CCC",
+      "AGC TG",
+      "AAG TAA",
+      "AC TTTC",
+      "AGC TGC",
+      "AGG TTC",
+      "AGG TC",
+      "ATT AAAA",
+      "ATC ATG",
+      "TT ATTG",
+      "AAGC G",
+      "AAG ATG",
+      "TAAG CC",
+      "AG TATG",
+      "ATC TGC",
+      "AG ACCC",
+      "AG ATAC",
+      "TCC TTC",
+      "AAC ATGG",
+      "TGG TGG",
+      "TAG AC",
+      "AG TCTG",
+      "ATT TAT",
+      "AA TCAC",
+      "TT AGCC",
+      "AGGG GG",
+      "TCC CCC",
+      "ATAA GG",
+      "AAG TC",
+      "ACC GC",
+      "TTC TGG",
+      "TTG TG",
+      "TTC ATG",
+      "ATT ATG",
+      "AGC TGG",
+      "TAC AC",
+      "TATT TATT",
+      "AAAAAAAA AAAAAAAA",
+      "TCCTGCC TCAGCC",
+      "GGG CC",
+      "AAG AGG",
+      "ATT AAC",
+      "TT TACC",
+      "AGC TAC",
+      "TG TTTG",
+      "AG ATTG",
+      "TGC TC",
+      "ATC TAA",
+      "TTTTTTTT TTTTTTTT",
+      "AG TAAC",
+      "TCC ACC",
+      "AA TCTG",
+      "AAC AAAA",
+      "TTG AC",
+      "AG TCAC",
+      "TTC TT",
+      "AAAT ATC",
+      "TAA AAAA",
+      "TTG AACC",
+      "AGG ATG",
+      "TTC ATC",
+      "TAG AAC",
+      "TGG TG",
+      "TAC AAAA",
+      "AA TAGC",
+      "AA ATAT",
+      "AT AGTT",
+      "CCC G",
+      "TAG AAG",
+      "TCC TGC",
+      "TAC TAAAAATAC",
+      "TT AAAG",
+      "TTG TAA",
+      "AGG AAAA",
+      "ATAA CC",
+      "AA TGGG",
+      "TGG AC",
+      "AT AAAAC",
+      "ATG GGC",
+      "TC TAT",
+      "AG TAAG",
+      "ATG AAC",
+      "TTC AGC",
+      "AAG AGC",
+      "TT AATG",
+      "TG TATG",
+      "TGG AGG",
+      "TATT GC",
+      "AA TCCC",
+      "AC TGTG",
+      "TG ATTC",
+      "TCC AGC",
+      "TG AAGG",
+      "TGG AAC",
+      "AGG TAA",
+      "AG AAAAG",
+      "TCCTG ACCTC",
+      "AGGCC G",
+      "TC TGGG",
+      "AA TACC",
+      "TTC ATT",
+      "TG TGGG",
+      "AG AAAAC",
+      "AG TCCC",
+      "AAG ATC",
+      "TCC ATG",
+      "AG TTGG",
+      "AG TTAC",
+      "AT AGCC",
+      "TT TAGC",
+      "TAGG CC",
+      "TCACTGC AACC",
+      "ACC CCC",
+      "AGGC GG",
+      "ATAA ATAA",
+      "AC TTCC",
+      "TCC TGG",
+      "AG ATCC",
+      "AA ATAG",
+      "ACC TGC",
+      "G TCTC",
+      "TG TTCC",
+      "AG TATC",
+      "ACTGC ACTCCAGCC",
+      "AG TTTTG",
+      "TAT ATC",
+      "TC AGGG",
+      "TTC AAG",
+      "TTG TAG",
+      "TTC TTTC",
+      "TATG CC",
+      "GCC CC",
+      "ATT ATC",
+      "TAT AAC",
+      "TG AGCC",
+      "TTC TAC",
+      "AT AGGG",
+      "AAG CCC",
+      "TGGGC AAC",
+      "ATG CCC",
+      "TG AAGC",
+      "AGC AAC",
+      "TC ACAC",
+      "TTG TTTT",
+      "AC ATGG",
+      "AC ATTC",
+      "AAAT AAAA",
+      "TGG TGC",
+      "TAA TAC",
+      "ATC AAC",
+      "TG AGAG",
+      "AG TTGC",
+      "TC AGGC",
+      "TTG AGG",
+      "TT ATAC",
+      "TG ATCC",
+      "AAAA AAG",
+      "TCAC AGAG",
+      "TC AGAG",
+      "TG AATG",
+      "AGC ATC",
+      "AC AGCC",
+      "AC AGGC",
+      "ATT AAG",
+      "TG TCTG",
+      "AGACC AGCC",
+      "TATG GC",
+      "ATG AGCC",
+      "AT AAAAG",
+      "AAAA AAC",
+      "TCC TTG",
+      "TC ATTG",
+      "TC AAAC",
+      "TG ATAA",
+      "TT ATTTT",
+      "TCCC AAG",
+      "AC AAAC",
+      "G TGC",
+      "TC ATGCC",
+      "TTTC TTTC",
+      "ACC AAC",
+      "TC AAGC",
+      "TTG AAG",
+      "ATG TTC",
+      "TAT CCC",
+      "ATT TCTC",
+      "AGGCTGAGGC AGGAGAA",
+      "TGTAATCCCAGC ACTTTGGG",
+      "TG AGGG",
+      "TAG AAAA",
+      "TG ATGG",
+      "AA TAGG",
+      "AC AGGG",
+      "AGC ACC",
+      "AGC TTC",
+      "AA TTGG",
+      "TGGC TCAC",
+      "TT TAGG",
+      "AC AGTG",
+      "AGC TAA",
+      "TACC CC",
+      "TAC ATG",
+      "AAC ATC",
+      "TAC TAA",
+      "TT AAGG",
+      "TCC ATC",
+      "TCC AGG",
+      "AGC ATT",
+      "TTC AGG",
+      "AC TTTG",
+      "TT ATCC",
+      "TC AAGG",
+      "TC ATCC",
+      "TC TTGG",
+      "ACC TTG",
+      "TCC TGAG",
+      "AGC ATG",
+      "TCTC TCTC",
+      "AAG TGC",
+      "ACC TGG",
+      "ATT TTTG",
+      "TC AGTG",
+      "TGGG ACTAC",
+      "TT ACAC",
+      "TG AATT",
+      "ACC TAA",
+      "AAAC GGG",
+      "AATC TGC",
+      "AC TAT",
+      "AG TAGG",
+      "ATT TTCC",
+      "AC ATAA",
+      "AC AGAC",
+      "ATG AAAA",
+      "AAAC G",
+      "AGG TAG",
+      "TATT GG",
+      "AT AGTC",
+      "TCC TAA",
+      "AGG TTG",
+      "TG AAAG",
+      "TGC TGG",
+      "TTG AACCC",
+      "ATT GGC",
+      "GTG AGCC",
+      "TC ATAA",
+      "TAG TAA",
+      "AAC TTC",
+      "AAC ATG",
+      "AGG TGTG",
+      "TT AAATT",
+      "AC ATGC",
+      "TG ACAC",
+      "ATC TAC",
+      "TCC GCC",
+      "TG TTGG",
+      "TG AGTG",
+      "TT AGAG",
+      "AC AATG",
+      "TT AAGC",
+      "ATC ATT",
+      "TG TATC",
+      "TGG TAA",
+      "TTG TATT",
+      "TTTTTTTT TTTT",
+      "AGAG AGAG",
+      "AC TATT",
+      "TGC ATG",
+      "AAAG AAAA",
+      "AAG TTG",
+      "TGC TCC",
+      "TATG GG",
+      "AAAAAAAA AAAA",
+      "ACAC G",
+      "TC ATGG",
+      "TGC AGG",
+      "TGG ATG",
+      "AAG TTC",
+      "TTTT AAAA",
+      "AC TGGG",
+      "TT AACC",
+      "GG GGC",
+      "ATAA TAA",
+      "ACC ATC",
+      "AG TACC",
+      "ATAT ATG",
+      "TG TAAG",
+      "TCC TGGG",
+      "ACC AGC",
+      "AC TGCC",
+      "TG ATGC",
+      "TT ATGC",
+      "AGAA AGAA",
+      "AG ATATT",
+      "ATT TTAC",
+      "TC AAAG",
+      "TTTC ACCATG",
+      "AAC TAA",
+      "TT AATC",
+      "AAAA ATG",
+      "AC ATCC",
+      "TGAA ACCCC",
+      "TG TCCC",
+      "AGG ATGG",
+      "ATAA ATG",
+      "AC TCTC",
+      "AAG TAG",
+      "AGGC G",
+      "AC ATAC",
+      "AGG ATC",
+      "TG TCAC",
+      "AATT TAA",
+      "ACC TTC",
+      "TT ACCC",
+      "AGGC TGC",
+      "AGG TAC",
+      "TC AATG",
+      "TC TTAC",
+      "TCCCAGC TAC",
+      "TC TATC",
+      "AGAA ATG",
+      "TG TTGC",
+      "TC TATG",
+      "TC ATGC",
+      "AA TTTTG",
+      "TG TCTT",
+      "AC AAGG",
+      "TC GGCC",
+      "ATC TGG",
+      "TT ATATT",
+      "AGAC G",
+      "TAATTTT TGTATT",
+      "TCC AAC",
+      "TTTGTG ATG",
+      "ACC TAC",
+      "ATT GGG",
+      "AC TATG",
+      "TGGC G",
+      "TGGG TGAC",
+      "ATTC TCCTGCCTCAGCC",
+      "ATTC TCAGAA",
+      "TTG TTC",
+      "ATT AGG",
+      "ATG ATC",
+      "TAA ATC",
+      "ATG TCC",
+      "AC TCCC",
+      "AAAT AAC",
+      "AAG TAC",
+      "GC GG",
+      "TATT TTG",
+      "TT AAATG",
+      "AC ATTG",
+      "TATT TTTT",
+      "TAA TTC",
+      "AGATG GGG",
+      "TG TAAC",
+      "TGGGC G",
+      "TT ATGG",
+      "TT AGTG",
+      "AAAA TAC",
+      "AAG TCC",
+      "TAG ATG",
+      "AGG AGGC",
+      "AAC AGC",
+      "ATTTC G",
+      "TTTG TAA",
+      "TTTC TTTT",
+      "TT AATAA",
+      "AAATT CC",
+      "AC AAAG",
+      "ACC TGCC",
+      "TTTAG TAGAGAC",
+      "TC AGAC",
+      "ATTTT TAA",
+      "ATG TAC",
+      "TTG TGC",
+      "TGG ATC",
+      "ATTC G",
+      "TAT AAG",
+      "TC AACC",
+      "TTG AGC",
+      "AAC TAC",
+      "TT AGGG",
+      "TATT TTC",
+      "AAAC AAAC",
+      "AAC TGC",
+      "TG TTAC",
+      "TGGG AGG",
+      "AC ACCC",
+      "TTTG TTTT",
+      "TT TATTC",
+      "AAC ATT",
+      "ACC AAG",
+      "AC TTGG",
+      "TGG AAAA",
+      "TGG TTC",
+      "ATG AGG",
+      "TT AGAC",
+      "TC AGTC",
+      "TC TACC",
+      "AGTTC G",
+      "TCTG TCTC",
+      "AG ATAG",
+      "AG ATTTC",
+      "TATT TAA",
+      "AGGCC CC",
+      "ATAT ATT",
+      "TGC TAA",
+      "AC TCAC",
+      "ATTC AAC",
+      "AC TGGC",
+      "ATAT AAAA",
+      "ATC AGC",
+      "TG TTTTC",
+      "ACC AGG",
+      "TAG TTTT",
+      "TTG TAC",
+      "AAAC TCC",
+      "ATGG TGGC",
+      "TAT AGC",
+      "AC TTGC",
+      "AAAG AAG",
+      "TT AGTT",
+      "ATT TCTG",
+      "TG ACCC",
+      "TTGG AAACGGG",
+      "TCC AAG",
+      "TAA GGC",
+      "TG AACC",
+      "T A",
+      "ATAC G",
+      "TAG TAG",
+      "TTC TTCC",
+      "AC GCC",
+      "ACC ACG",
+      "ATG AGC",
+      "TCAC G",
+      "TCC AGCC",
+      "TTG AAAA",
+      "TG AATC",
+      "TAT ATAA",
+      "TTG TGG",
+      "AGAA TAA",
+      "AGC TGAG",
+      "AC TTAC",
+      "TT AAAAC",
+      "TGC ATC",
+      "TC TAAG",
+      "ATT AGC",
+      "TC AGTT",
+      "AGG AAGG",
+      "TCTT CCC",
+      "TTTC G",
+      "TG AGTC",
+      "TAC TTC",
+      "TAG GGC",
+      "TTTCC CC",
+      "TTG ATG",
+      "TT AGGC",
+      "AGG AAAC",
+      "TG ATTG",
+      "TAA TGC",
+      "AAC AAG",
+      "ATAG AGC",
+      "TTC ACC",
+      "TTG TCC",
+      "ATC GC",
+      "AATT TGC",
+      "ATC AAG",
+      "AAATG CC",
+      "TGG TAG",
+      "ATT TTGG",
+      "AAAT ATG",
+      "TAC TGC",
+      "TTTAG TAG",
+      "GC GC",
+      "AC TGAC",
+      "AAAA AATT",
+      "ATATT TGG",
+      "TTTT GCC",
+      "ACAG AGC",
+      "AGGCTGGAGTGC AGTGGC",
+      "AGCC AAG",
+      "ACACACAC ACACACAC",
+      "TT TATTG",
+      "TCTT TTC",
+      "TG TAGG",
+      "TTGGCC AGGCTGG",
+      "TAC AAC",
+      "ATT ACC",
+      "TTTT TCC",
+      "TAC AGC",
+      "TTTT TTC",
+      "AATT TTC",
+      "ATG TAG",
+      "TG TAGC",
+      "TG ATAC",
+      "AC AAGC",
+      "TTCC TTCC",
+      "GG CCC",
+      "ATC TAG",
+      "TAA AGC",
+      "TTTT CCC",
+      "AA ACCCC",
+      "TAA TAG",
+      "AAAA TGC",
+      "AGAA GGC",
+      "AAAG AAC",
+      "TGGCC CC",
+      "ATG TGCC",
+      "TGTGTGTG TGTGTGTG",
+      "AGAG AAG",
+      "ATT TTGC",
+      "TTC TGCC",
+      "AGG TCAGG",
+      "TCCCAAAGTGC TGGGATTACAGGC",
+      "AAACAC TCTTTT",
+      "AAATG GG",
+      "AA TATTC",
+      "TC TAAC",
+      "AAC ACC",
+      "TC AATT",
+      "TTTC TTC",
+      "TG TACC",
+      "TGG TAC",
+      "AGC GC",
+      "TG AGTT",
+      "TG AAATT",
+      "TGC GG",
+      "TAT ACC",
+      "TAA TTG",
+      "ACAG AAG",
+      "AC AATT",
+      "ATT TCTT",
+      "TAT ATTC",
+      "TC TAGC",
+      "TT ATTTC",
+      "ATT TATC",
+      "AAC TTG",
+      "TCC TAC",
+      "TAA AGG",
+      "TT AAAAG",
+      "ATC AAAA",
+      "AGAC AGAG",
+      "TCC TAG",
+      "ATG TTTT",
+      "TACTC GGG",
+      "AG AGGCC",
+      "AGC TGGG",
+      "TTC TTTG",
+      "TC GCC",
+      "AGTT TGG",
+      "TGC TTG",
+      "AGAC GG",
+      "AGGC TGAGG",
+      "CCC AGG",
+      "TGC TAC",
+      "TCCTGAG TAGC",
+      "TCC TTCC",
+      "TGC TAG",
+      "TC TAGG",
+      "ATC TTTT",
+      "AC AACC",
+      "TGGG ATT",
+      "TGG TTG",
+      "AG ATAT",
+      "TC ATAC",
+      "ACC TCCC",
+      "TTC TCTC",
+      "TC GGC",
+      "ATT ATAA",
+      "AGAAG CC",
+      "AAG AAAC",
+      "TAA AATG",
+      "ATCTC GGC",
+      "AGG TTGCAGTG",
+      "AC AATC",
+      "TTC AAAA",
+      "AGCC AGGC",
+      "TTTC TCC",
+      "TT ATAT",
+      "TAC TAC",
+      "ACC TAG",
+      "TCG CCC",
+      "TGG ATT",
+      "ATC AGG",
+      "AGC TTG",
+      "TGGG GCC",
+      "TT ATAG",
+      "TCCCAAG TAGC",
+      "AAG AGAA",
+      "AC AGTC",
+      "AAATG GC",
+      "AAATT GC",
+      "AGC TAG",
+      "TAC TTTT",
+      "TTC AAGC",
+      "TT AGTC",
+      "TGGCC AACATGG",
+      "AAAT AAG",
+      "TGG TTTT",
+      "AGG AAGC",
+      "ATT TATG",
+      "AAAC AAAA",
+      "TG TTTTG",
+      "TCTT TAA",
+      "TCCC GGG",
+      "ATGG TGG",
+      "AAC TAG",
+      "ATATT CC",
+      "TG AATAA",
+      "GG GGG",
+      "TGC TTTT",
+      "ATT TGTG",
+      "TCC TCCC",
+      "TCC TTTT",
+      "G AGG",
+      "ATT TCCC",
+      "TG AAAAC",
+      "TGGG GGC",
+      "TAG GGG",
+      "TAC TTG",
+      "TC GGG",
+      "GC TCTG",
+      "ATT ATTC",
+      "ACCTC AGCC",
+      "TAA ATAA",
+      "AGTT TTC",
+      "ATCC ACCC",
+      "TCAC ACC",
+      "AAC TGG",
+      "TTTG TTTG",
+      "TGC AAG",
+      "TCTG CCC",
+      "AAAA ATC",
+      "AGG ACC",
+      "TAAC G",
+      "TGC AGTG",
+      "TCTC AGC",
+      "TGTG TCC",
+      "AAAG TAA",
+      "AC GGC",
+      "ATT TCAC",
+      "AAAA TAG",
+      "AC TATC",
+      "TCC GC",
+      "AGATC G",
+      "TCCCG AGTAGC",
+      "AAC AGAA",
+      "ACC TGGC",
+      "TTTC TAA",
+      "TTCC G",
+      "ACCC G",
+      "TTG AGCCC",
+      "AAGG AAGG",
+      "ACCC AGC",
+      "AAC TCCTGACCTC",
+      "TAG CCC",
+      "TAC AAG",
+      "AGTT TCC",
+      "TCTT TGC",
+      "TAT ATAT",
+      "AGCC AGG",
+      "TCTT TCC",
+      "AA ATCTC",
+      "AC TAAG",
+      "TGC ACC",
+      "AATT CCC",
+      "TAA TATT",
+      "AGAA GGG",
+      "AGC GG",
+      "TAC ATT",
+      "AGATG GG",
+      "AAC AGG",
+      "TTTT TTTC",
+      "TTTT TATT",
+      "TAA GGG",
+      "TGGG TGG",
+      "TGAGG TCAGG",
+      "TACTAAAAATAC AAAAATT",
+      "ATGC G",
+      "TGGGACTAC AGGC",
+      "ATC ATTC",
+      "AATC G",
+      "TAT ATAC",
+      "TGTAATCCCAGC TAC",
+      "TGC TTTC",
+      "TAT AAAC",
+      "TTG ACC",
+      "AG ATTTT",
+      "TGAC G",
+      "TGC AAC",
+      "ATG ATT",
+      "AGAAGC ATTCTCAGAA",
+      "TTG ATC",
+      "TAA AAAC",
+      "AGAA ATC",
+      "ATTAC AGGC",
+      "TG AAAAG",
+      "TAT AATT",
+      "TC AATAA",
+      "TC ATTTT",
+      "TG AAATG",
+      "TAT ATATT",
+      "AGGG AGG",
+      "AGC AAAA",
+      "TAC ATC",
+      "TAG TTC",
+      "AGAA AGG",
+      "TGCC G",
+      "TC TTTTG",
+      "AGTTC AAGACC",
+      "TC AATC",
+      "TTAC G",
+      "AG ATTGC",
+      "TATT TCC",
+      "ATTCC CC",
+      "ATTC AAG",
+      "TAG AGG",
+      "AGC TGGGC",
+      "AAAT CCC",
+      "AAAT ACC",
+      "AAATT GG",
+      "TAA AATT",
+      "AGGCCG AGGC",
+      "AA TATTG",
+      "TTTAA CC",
+      "GGC G",
+      "AGAG CCC",
+      "TGGCTCAC GCC",
+      "ATT TAAG",
+      "ATT TAAC",
+      "AAGCC CC",
+      "AGAA AGC",
+      "TTTG AGGCC",
+      "TAC TCC",
+      "TAG AGC",
+      "TAT AGG",
+      "TAC TGG",
+      "AC TAAC",
+      "TTCC TTC",
+      "TTTG TATT",
+      "TGTT TCC",
+      "TGTAA TCCC",
+      "AGAC AGGG",
+      "ATCTC AGC",
+      "TTTC ACC",
+      "TG AGGCC",
+      "GC TGC",
+      "ACTT CCC",
+      "ACCC TGTCTC",
+      "AAAA TATT",
+      "AGCC TGG",
+      "TTC ATTC",
+      "AA AGGGC",
+      "ATG TATT",
+      "ATG TGTG",
+      "TAA TGG",
+      "CCC GGC",
+      "TGC TGGG",
+      "TAA AATAA",
+      "AGG TCC",
+      "AGGG GCC",
+      "TGGC TAAC",
+      "TAA CCC",
+      "ACC AAAA",
+      "AGAA ATAA",
+      "TTTG AAG",
+      "TTTT TAG",
+      "TTTG TAG",
+      "AC TACC",
+      "TAA TCC",
+      "AAAA ATAA",
+      "AC ATGCC",
+      "GGCC CC",
+      "TTTC TTTTC",
+      "AAGC TGG",
+      "AAC TTTT",
+      "AGCC TCC",
+      "TTTC TGC",
+      "TGG TGTG",
+      "AGGG AAG",
+      "TTTC TTG",
+      "TTC TCCC",
+      "AG ATGCC",
+      "GTGG TGGC",
+      "AGATG GC",
+      "TTC TCTG",
+      "TTTG AGG",
+      "AAAAG AAAA",
+      "ATCC G",
+      "AAGG AAG",
+      "TC TCCCC",
+      "TATTC AAC",
+      "ATTC TGG",
+      "TTTG TTG",
+      "ATG ACC",
+      "TAC AGG",
+      "AG ATATG",
+      "AT AAGCC",
+      "AC TAGG",
+      "TT TGGGG",
+      "TTTG CCC",
+      "TGC GC",
+      "AAC GC",
+      "AC AGTT",
+      "AAG AATG",
+      "TATT TAC",
+      "TT TATCC",
+      "AGC TGTG",
+      "ATC TTTC",
+      "ATTC TCC",
+      "ATT TGGG",
+      "TAG TTG",
+      "TAA ACC",
+      "AG ATTCC",
+      "AG TGGGG",
+      "AGGC AGAGG",
+      "TGG TCC",
+      "TGTAG TCCCAGCTAC",
+      "TCTC AAAC",
+      "TTC TATT",
+      "AAAG ATG",
+      "AG ACCCC",
+      "ATT TGTC",
+      "TAT ATTG",
+      "TTCC TCC",
+      "AC AAAAC",
+      "AC ATTTT",
+      "AGAGC G",
+      "ATGGG GG",
+      "AGAG AAC",
+      "AGG TGCC",
+      "AAAA GGC",
+      "ATATT GG",
+      "TTCC TTG",
+      "AG AGGGC",
+      "TCCCC CC",
+      "AAAA TTC",
+      "AA TTCTC",
+      "TGC TGCC",
+      "AGAG AGC",
+      "AC AATAA",
+      "TGGCC AAC",
+      "TTC TGTG",
+      "ATT TGTT",
+      "AATT TAC",
+      "ATTTC TTC",
+      "TCCC TCCC",
+      "TGGG AAG",
+      "TTCC CCC",
+      "ATATG GC",
+      "TGAA TAG",
+      "TGC AGCC",
+      "AGAA TGG",
+      "AGAC TCC",
+      "AG TGGGC",
+      "TAG TGG",
+      "TGAA CCC",
+      "ACC ACAC",
+      "TC ATAG",
+      "AAG TTTT",
+      "AGTC TGC",
+      "ATAT ATAA",
+      "AC ATATT",
+      "AGAG AAAA",
+      "AT ATCTC",
+      "AAG ATT",
+      "TCTG TAA",
+      "AGAG ATG",
+      "AGG AGGG",
+      "AC ATAG",
+      "TAT AAAG",
+      "TC TTGCC",
+      "AA AGGCC",
+      "AAAAC G",
+      "TC AAATT",
+      "ACTC G",
+      "ATG TTTC",
+      "ATATG CC",
+      "TG ATATT",
+      "AAAA AGC",
+      "ACC ATGCC",
+      "TCCC AGGTTC",
+      "AG AGGGG",
+      "ATT ATTG",
+      "TTGC G",
+      "AAAA GCC",
+      "TGG AGGC",
+      "TTG TTTC",
+      "AGCC CCC",
+      "TTC TCAC",
+      "TGC TGTG",
+      "AGGTGTG AGCC",
+      "AAAA TGG",
+      "AGAG AGG",
+      "TTTT TAC",
+      "TAT AATAA",
+      "AC TCTT",
+      "AATT TCC",
+      "TAT AGAA",
+      "AACC G",
+      "AC GGG",
+      "AC TTTTC",
+      "TGC ATT",
+      "AATG TAA",
+      "TGG TGGC",
+      "ATG AGAA",
+      "AAAA CCC",
+      "TAG ATC",
+      "AGGC AGG",
+      "AGTC G",
+      "AGTT CCC",
+      "TGG ACC",
+      "TC ATATT",
+      "TCAC GCC",
+      "TCC TAGC",
+      "TAA TTTC",
+      "ATAA TTTT",
+      "AAC ATTC",
+      "TGTGG TGGC",
+      "ATCC ATG",
+      "TGTG ATG",
+      "TCTC TGC",
+      "ATT TGCC",
+      "TCC TTTC",
+      "AAAG CCC",
+      "AAAA AGG",
+      "TTCC AAG",
+      "TGG AAGG",
+      "TTG AGCC",
+      "ATC ACG",
+      "AGACC ATCC",
+      "ACC AGCC",
+      "AA TATCC",
+      "TAT ATGC",
+      "TTGAACC TGGG",
+      "TCC GG",
+      "TTCC AGC",
+      "TTTT TGC",
+      "AA TATGG",
+      "AGGG CCC",
+      "ACAC AGC",
+      "AAAA TTG",
+      "TAT AAATT",
+      "TAG TAC",
+      "ATC TTGGC",
+      "TT ATATG",
+      "TTTT GGC",
+      "TC AAAAC",
+      "AGAA ATT",
+      "ATC TCTC",
+      "AAAG AGG",
+      "TCC TCTC",
+      "AGGCC AAGGC",
+      "AAAG AGC",
+      "TAT AATG",
+      "TC AAATG",
+      "AAAC TGC",
+      "TGTC G",
+      "ATTC TGC",
+      "TAG ATT",
+      "TGAG AAC",
+      "GCCC GCC",
+      "TTAA TTTT",
+      "ATC TTTG",
+      "TCCC TGC",
+      "AA TGGGG",
+      "TGTG CCC",
+      "TT ATTCC",
+      "AAAA GGG",
+      "TAC GG",
+      "AA AGGGG",
+      "AGG ATT",
+      "AG ATAAC",
+      "AAAC AAC",
+      "TT ATAAAA",
+      "AGCCG AGATC",
+      "TGG AAGC",
+      "TC TTCTC",
+      "AG TATTC",
+      "AGAAAA GG",
+      "TAT ATTTT",
+      "AGGG GGC",
+      "TTTAA GG",
+      "GC GCC",
+      "TGTT CCC",
+      "AGTC TTGC",
+      "AAG ATGG",
+      "ATTC ATC",
+      "ATAA ATT",
+      "TGGG CCC",
+      "AC AAATT",
+      "TTTC TAC",
+      "TGGG GGG",
+      "AAAT AGC",
+      "ACAC ACC",
+      "TG ATTTT",
+      "TGG AGTGC",
+      "TTGCCC AGGCTGG",
+      "AG ATATC",
+      "AC ATAT",
+      "TTG ATT",
+      "ATATT GC",
+      "TGGG TTC",
+      "TGTGC G",
+      "ATTC TTC",
+      "AG TGGCC",
+      "AATG AAC",
+      "TC ATTTC",
+      "AC TAGC",
+      "AAAG TAC",
+      "ATC TGCC",
+      "AGAA ACC",
+      "GGGG TTTC",
+      "TATC G",
+      "AGTTCG AGACCAGCC",
+      "AG ATAAG",
+      "TATT TGC",
+      "TGAG CCC",
+      "TGG AAAC",
+      "TGAC TTC",
+      "ATC TTCC",
+      "AGAA TTC",
+      "TCAG CCC",
+      "AC AAAAG",
+      "TGTG AAG",
+      "TCCC ACC",
+      "AGGC AGC",
+      "AA TATGC",
+      "AGTT TAA",
+      "TTGG GGG",
+      "TGTT TGC",
+      "GC ACC",
+      "GC AGC",
+      "TCCCAAAGTGC TGGGATTAC",
+      "TAG TTTC",
+      "AGTG AGC",
+      "AAC GG",
+      "ATGG AGC",
+      "AAAA ATAC",
+      "AAC AATG",
+      "TTTT GGG",
+      "TTG TCTC",
+      "AGGG AGGG",
+      "AG ATACC",
+      "TCCC TCC",
+      "AC AAATG",
+      "TCCC AGG",
+      "TTGCC CC",
+      "AGCC GGGC",
+      "ATTC TAA",
+      "ACC ATT",
+      "TTTG TTC",
+      "AATCTGC AAGTGG",
+      "TACC G",
+      "ATATATAT ATATATAT",
+      "AG ATAAAA",
+      "TG ATAG",
+      "AGTT TGC",
+      "AGTTTG AGACCAGCC",
+      "TGAAACCCC GTCTC",
+      "TT TGGCC",
+      "ATTC TTTT",
+      "ATC TATT",
+      "AGGC TAG",
+      "AGTTCAAGACC AGCC",
+      "AAAAC AAAAC",
+      "TAC AGAA",
+      "AGG TTTG",
+      "ACAG AAC",
+      "AAG AAGG",
+      "GCC G",
+      "TAG TGC",
+      "TGG AATT",
+      "TTTTG TTTT",
+      "ACTG CCC",
+      "ATTTCG TTGGAAACGGG",
+      "ATTG TAA",
+      "ATGC TGC",
+      "ATC TCTG",
+      "TT TATGC",
+      "AGC TTCC",
+      "TGG TCTC",
+      "TATG TTG",
+      "TAT ACAC",
+      "TATC TATC",
+      "TG ATTTC",
+      "TGG TTTC",
+      "ATG AATG",
+      "TTTTG TATT",
+      "AAAA ACC",
+      "AGC AGCC",
+      "TAG AAAC",
+      "TGCC CCC",
+      "GG AAG",
+      "AGTG AAC",
+      "AAAAG AAG",
+      "TTTT ATT",
+      "ATTC ATTC",
+      "ATAT ATC",
+      "AG TCCCC",
+      "TG AAGCC",
+      "AAAA AATAA",
+      "AGG TTGC",
+      "TT ATAAG",
+      "TCTC TCC",
+      "AG TTCTC",
+      "TGG TATT",
+      "AGG AATG",
+      "AAG TATT",
+      "TTTT ATG",
+      "AAAT ATAA",
+      "AAC AAAC",
+      "TCTC TTC",
+      "AGG TGGG",
+      "ACAG CCC",
+      "ATC TGTG",
+      "AA ACCTC",
+      "TT AGAAG",
+      "TGC TTCC",
+      "ATC TCAC",
+      "AGC AGAG",
+      "TAC TAG",
+      "AGC ATGG",
+      "TTTTC TTTT",
+      "TAA AACC",
+      "AGAGC AAG",
+      "ATGCC CC",
+      "TCC TGGC",
+      "AC AGTGGC",
+      "AGG AGAG",
+      "TGTAG TCCCAGC",
+      "ACC ATGG",
+      "AGGCTGGAGTGC AGTGG",
+      "ATTG TTC",
+      "AAGG AAC",
+      "TCC ATT",
+      "TGG AGAA",
+      "TCC TCAC",
+      "AATT AAAA",
+      "TTTT AAG",
+      "TC TATTC",
+      "AATT TATT",
+      "TGTAG CC",
+      "AGG AGAC",
+      "TC AAAAG",
+      "ACTT TAA",
+      "TGCC TCAGCC",
+      "ATC ACAC",
+      "TGGG AGC",
+      "AG ATCTC",
+      "TAATTTT TTGTATT",
+      "TCACTGCAACC TCTGCC",
+      "ATAT ATAC",
+      "TCACTGC AAGC",
+      "ATT AAAC",
+      "TCTT TAG",
+      "TCCG TCTC",
+      "ATG AAAC",
+      "AGG ACAC",
+      "GC TTTC",
+      "ATTC AGC",
+      "ACC TCTC",
+      "AGG TTTT",
+      "TGTT TAA",
+      "TGTC TCC",
+      "TG TTCTC",
+      "AAG ATAA",
+      "AC ATTTC",
+      "ACCCC CC",
+      "TTG AAAC",
+      "TG TATTC",
+      "ATC AGAG",
+      "ATAT AAC",
+      "AGAA CCC",
+      "TGTG TGC",
+      "AAG AAGC",
+      "ATTC TAC",
+      "TT AGTAA",
+      "AATAA CC",
+      "TATG TAA",
+      "AG TAAAA",
+      "TC ATTCC",
+      "ATTC ATG",
+      "TTCC TGG",
+      "ATTC TTG",
+      "TTTG TGG",
+      "TC GTG",
+      "ACTT TGG",
+      "AATAA GC",
+      "ATG TTGG",
+      "AGC TGCC",
+      "AAAG TTC",
+      "TTTTC TTC",
+      "TC TGGGG",
+      "ATT TGGC",
+      "ATTG CCC",
+      "ATG TAT",
+      "AG ATCCC",
+      "ATTTT AAAA",
+      "TG TGGCC",
+      "ATGC ACC",
+      "TGC AAAA",
+      "AGG TTGG",
+      "AGTG TAA",
+      "TATT TTTC",
+      "TAGC G",
+      "AGC TTTT",
+      "AGAA TAC",
+      "ATAA TAC",
+      "TC TGGGC",
+      "AGTG CCC",
+      "TC ATTGC",
+      "AGAA TAG",
+      "TC TTGGC",
+      "ATT ATAC",
+      "TCTT TAC",
+      "ACAC TGC",
+      "ATC TTGG",
+      "TCC AAAA",
+      "AATT TAG",
+      "AGG TTTC",
+      "CCC AGCC",
+      "TGGG TAA",
+      "TCTC ACTCTG",
+      "TTC GG",
+      "TG ACCTC",
+      "TC AGGCTGG",
+      "AAAG TAG",
+      "TCAC AGC",
+      "TAGG AAG",
+      "ATAA TTG",
+      "AAC AGAG",
+      "GGG TGG",
+      "TAT AA",
+      "TTC AAGG",
+      "TGAA ACAC",
+      "TGGG TGC",
+      "AATG AAG",
+      "TCAG AAG",
+      "TGATT GG",
+      "TTC GC",
+      "TG TCCCC",
+      "TAT ATCC",
+      "ATAT ATATT",
+      "TTTT TGG",
+      "ACCC AGCC",
+      "TGTT TGG",
+      "TC TGGCC",
+      "TATC TGG",
+      "TAA AATC",
+      "TT TATGG",
+      "TAT ATGG",
+      "ACCAC GCC",
+      "ATAC AAAA",
+      "TTC TGGG",
+      "ATT TTTTC",
+      "AAAG AGAA",
+      "AAAG ATC",
+      "TT ATATC",
+      "AGGC GC",
+      "ATT AATT",
+      "AAGG GGC",
+      "TTTC TTTTG",
+      "TTC TTGG",
+      "TTG TGTG",
+      "TATCC CC",
+      "ATT TACC",
+      "AGG TATT",
+      "TTTAA GC",
+      "TCC ACCC",
+      "TGAA ATC",
+      "ATCTC TAC",
+      "TAT ATATG",
+      "ACAA AGC",
+      "TCACTGC AGCC",
+      "ATG AAGC",
+      "ATT TGAC",
+      "TAC TTTC",
+      "TGG ATTC",
+      "ATAT CCC",
+      "AAAAC AAAA",
+      "TT TGGGC",
+      "TTTTG TAG",
+      "GGGC GG",
+      "TTG TTTG",
+      "AAG TTTC",
+      "AT AGGCC",
+      "AAAC AGC",
+      "TGG ATAA",
+      "TT AGAAC",
+      "TAG ACC",
+      "TG AAGGC",
+      "ACTG TAA",
+      "TGG AGAC",
+      "ATTGC ACTCCAGCC",
+      "TAC ACC",
+      "TGG TGGG",
+      "AGG TGGC",
+      "ATG TATG",
+      "TCCCAGC ACTTTGGG",
+      "TGTTTT CC",
+      "ATAA ATC",
+      "TC AGGCC",
+      "ACTGC ACTCC",
+      "TT AGAAAA",
+      "TGC ACCC",
+      "AATG ATG",
+      "TAA ATAC",
+      "AAAG TTG",
+      "TAT AATC",
+      "AGTAA CC",
+      "AG ACCTC",
+      "TGC TCTG",
+      "AAAA AAATT",
+      "TGAG AAG",
+      "ATC TCCC",
+      "ATGGC G",
+      "TTTC TCTC",
+      "AGG AGCC",
+      "AGAA TTG",
+      "AGGC AAG",
+      "TT ATAAC",
+      "TT AGATT",
+      "AAAC TAA",
+      "ATC GG",
+      "TTC AGCC",
+      "AGTT TAC",
+      "ACC TTCC",
+      "TTATT GC",
+      "TCCCAAAGTGCTGGGATTACAGGC GTGAGCC",
+      "TGG AGGG",
+      "AAAT ATTC",
+      "ACC GG",
+      "AGC TTTC",
+      "TAAG AAG",
+      "TAA ATTC",
+      "TAAG AAC",
+      "AA TTGCC",
+      "ATTTT TATT",
+      "TGTC TTC",
+      "G TCC",
+      "AC ATATG",
+      "TGC TGGC",
+      "ATT AATG",
+      "AATAG CC",
+      "TAA AAGC",
+      "ATG ATCC",
+      "AAAC TAC",
+      "ATGC TGG",
+      "ATAA AGC",
+      "ATG ATTC",
+      "AGTG AAG",
+      "ATT TAGC",
+      "AATAA GG",
+      "AAC TTCC",
+      "TTTAGTAG AGATGGGG",
+      "AAGG AAAA",
+      "TTTT TTTG",
+      "AAAG TGG",
+      "AGCC GC",
+      "TG ATGGG",
+      "TATT TGG",
+      "ATAA TTC",
+      "TGTAA CC",
+      "ATGG AAG",
+      "TAA AGAA",
+      "TTGG GGC",
+      "ACAG AAAA",
+      "AGAAAA CC",
+      "TGTT TAC",
+      "TC ACCCC",
+      "ACAG TGC",
+      "AA TGGCC",
+      "AGGC ACC",
+      "AAGG CCC",
+      "TC AAAGC",
+      "AGATT GG",
+      "TTGAACCC GGG",
+      "ATG TGGC",
+      "TAA ATGC",
+      "ATAG AAAA",
+      "TTTT AAC",
+      "TATT CCC",
+      "ATT TAGG",
+      "AAAC ATC",
+      "TT ATGCC",
+      "AAG ACAC",
+      "AATG AATG",
+      "ATCC AGC",
+      "AC TTTTG",
+      "TTATT GG",
+      "ATG ATGG",
+      "AGGCC AGG",
+      "AGGG AGC",
+      "ATAG ATAG",
+      "AAG TAGC",
+      "ACTG TGG",
+      "TGAA TTC",
+      "TTCC TGC",
+      "ACAA TGG",
+      "AGGG AAC",
+      "AAAG ACC",
+      "ATG ATTG",
+      "AAACACTCTTTT TGTAG",
+      "TCTG TGC",
+      "TGAA AGC",
+      "ATAA TAG",
+      "ATCC ATCC",
+      "AGTT TAG",
+      "TGGCTCAC ACC",
+      "TATT TAG",
+      "ATG TATC",
+      "TTCG TTGGAAACGGG",
+      "TGCC TGCC",
+      "TTC TTGC",
+      "AAAG TCC",
+      "TG AGGGC",
+      "AAC TTTC",
+      "TT AAAT",
+      "TT AGTAG",
+      "TCAAG TGATCC",
+      "TTC AGAA",
+      "ACCC ACC",
+      "ATTG TGG",
+      "ACAG ATG",
+      "ATCC CCC",
+      "AAGG AGC",
+      "ACTT TCC",
+      "TT ATGGC",
+      "TGGC TAA",
+      "AC ATGGC",
+      "TGCC TCC",
+      "ATTC TAG",
+      "TTGG GCC",
+      "ATTG TAG",
+      "ACTG TAC",
+      "AAGG GCC",
+      "AGCC TGC",
+      "TCTG TTG",
+      "ATG AACC",
+      "TG ACCCC",
+      "AG ATAGC",
+      "AATG TTG",
+      "TGTC TGC",
+      "TGTAA GG",
+      "ATT TTTTG",
+      "AATT TGG",
+      "TG TGGGG",
+      "ACC ATGC",
+      "TTTG TAC",
+      "ACAC AGG",
+      "AGAG AGAA",
+      "AGGG TGG",
+      "AAAC TTC",
+      "ATGG ATGG",
+      "ATTG TTTT",
+      "AG TTGGG",
+      "AAG AGAC",
+      "TTTC TTCC",
+      "ATT AGAA",
+      "AAG AGTG",
+      "TCTG TCACCC",
+      "TCC AGGC",
+      "AATT AAC",
+      "TGGG AAC",
+      "TG ATTCC",
+      "ATC AGAA",
+      "TAA TAT",
+      "TTTC TGG",
+      "TTTG AAC",
+      "TGC AACC",
+      "ATTG TTG",
+      "AG TTGGC",
+      "ATT ATCC",
+      "TC AGGGC",
+      "TTTC AGC",
+      "TTC TGGC",
+      "TC TTGGG",
+      "AATT ATG",
+      "TTTAG CC",
+      "TTTC TAG",
+      "GG AGC",
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+      "AGG TATG",
+      "TACTCGGG AGGCTGAGGCAGGAGAA",
+      "TTCAC GCC",
+      "AAG TCAC",
+      "AGAC AGC",
+      "TTC AAGCG",
+      "AGGCC AAGG",
+      "AG AAAAAAAA"
+    ]
+  }
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eval.py

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+import pickle
+import numpy as np
+import pandas as pd
+from tokenizers import Tokenizer
+import os
+
+DATA_PATH = "/home/n5huang/dna_token/tokenizer_evaluation/eval_data.pkl"
+RESULTS_PATH = "/home/n5huang/dna_token/tokenizer_evaluation/evaluation_results.pkl"
+
+# Ensure these match the filenames you upload to the server
+VOCAB_PATHS = {
+    "Merged_uni": "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram.json",
+    "Merged_word": "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_wordPiece.json",
+    "Weighted": "/home/n5huang/dna_token/tokenizer_evaluation/weighted_bpe/tokenizer.json", # Adjust filename if needed
+    "SeqOnly": "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",   # Adjust filename if needed
+    "DNAbert2": "/home/n5huang/dna_token/pretrain/models/DNAbert2_Pretrained/tokenizer.json",
+    "Grover": "/home/n5huang/dna_token/pretrain/models/Grover_Pretrained/tokenizer.json",
+}
+
+def evaluate_tokenizer_on_phyloP(tokenizer, sequences, phyloPs):
+    """
+    For each tokenizer, compute:
+      - token_mean_scores: list of mean phyloP per token occurrence
+      - token_variances:   list of variance per token occurrence
+      - token_names:       list of token strings
+    """
+
+    token_means = []
+    token_vars = []
+    token_names = []
+
+    total_tokens = 0
+
+    
+
+    for seq, scores in zip(sequences, phyloPs):
+        # Skip if chunk is too small (end of chrom) or has N padding
+        if len(seq) < 100: 
+            continue
+
+        enc = tokenizer.encode(seq.upper())
+        total_tokens += len(enc.ids)
+
+        for tok, (start, end) in zip(enc.tokens, enc.offsets):
+            region = scores[start:end]
+
+            if len(region) == 0:
+                continue
+
+            m = region.mean()
+            v = region.var()
+
+            token_means.append(m)
+            token_vars.append(v)
+            token_names.append(tok)
+
+    print(f"  -> Processed {total_tokens:,} tokens.")
+    return {
+        "mean": np.array(token_means),
+        "var": np.array(token_vars),
+        "token": token_names
+    }
+
+
+# --- 3. MAIN EXECUTION ---
+if __name__ == "__main__":
+    print("Loading data from pickle...")
+    with open(DATA_PATH, "rb") as f:
+        data = pickle.load(f)
+        
+    sequences = data["test_sequences"]
+    phyloPs = data["test_phyloP"]
+    print(f"Loaded {len(sequences)} genomic windows.")
+
+    # Load Tokenizers
+    tokenizers = {}
+    print("Loading tokenizers...")
+    for name, path in VOCAB_PATHS.items():
+        if os.path.exists(path):
+            tokenizers[name] = Tokenizer.from_file(path)
+            print(f"✅ Loaded {name}")
+        else:
+            print(f"❌ Warning: File {path} not found. Skipping.")
+
+    # Run Eval
+    results = {}
+    print("\nStarting Benchmark (with Token Names)...")
+    
+    for name, tok in tokenizers.items():
+        print(f"Evaluating {name}...")
+        results[name] = evaluate_tokenizer_on_phyloP(tok, sequences, phyloPs)
+
+    # Save Results
+    print(f"\nSaving results to {RESULTS_PATH}...")
+    with open(RESULTS_PATH, "wb") as f:
+        pickle.dump(results, f)
+        
+    print("Success! Download 'evaluation_results.pkl' (Note: File size will be larger).")

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eval_outputs_ablation/file_index.csv

@@ -0,0 +1,30 @@
+file,path
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+eval_Ablation_no_length.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/eval_Ablation_no_length.csv
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+eval_Ablation_no_length_conserved.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/eval_Ablation_no_length_conserved.csv
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+eval_Ablation_no_partition_conserved.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/eval_Ablation_no_partition_conserved.csv
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+eval_data_all_chrom.pkl,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/eval_data_all_chrom.pkl
+eval_data_all_chrom_windows.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/eval_data_all_chrom_windows.csv
+summary_ablation_region.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/summary_ablation_region.csv
+summary_all_chrom_window.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/summary_all_chrom_window.csv
+summary_region_partition_priority.csv,/home/n5huang/dna_token/tokenizer_evaluation/eval_outputs_ablation/summary_region_partition_priority.csv

eval_outputs_ablation/summary_ablation_all_regions.csv

@@ -0,0 +1,16 @@
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