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diff --git a/GCF_002288925.2_ASM228892v3/genome.fa.gz.gzi b/GCF_002288925.2_ASM228892v3/genome.fa.gz.gzi
deleted file mode 100644
index e2ae364173795ab2240e765f020b93e8a724660d..0000000000000000000000000000000000000000
--- a/GCF_002288925.2_ASM228892v3/genome.fa.gz.gzi
+++ /dev/null
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diff --git a/GCF_002288925.2_ASM228892v3/pseudogenes.bed b/GCF_002288925.2_ASM228892v3/pseudogenes.bed
deleted file mode 100644
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diff --git a/GCF_002288925.2_ASM228892v3/reference.gff3.gz b/GCF_002288925.2_ASM228892v3/reference.gff3.gz
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diff --git a/GCF_003473485.1_MtrunA17r5.0-ANR/demo_log_probs/log_probs.npz b/GCF_003473485.1_MtrunA17r5.0-ANR/demo_log_probs/log_probs.npz
deleted file mode 100644
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--- a/GCF_003473485.1_MtrunA17r5.0-ANR/demo_log_probs/log_probs.npz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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diff --git a/GCF_003473485.1_MtrunA17r5.0-ANR/demo_log_probs/meta.json b/GCF_003473485.1_MtrunA17r5.0-ANR/demo_log_probs/meta.json
deleted file mode 100644
index 428102f7946713067a694cdb364e06dae3b6a592..0000000000000000000000000000000000000000
--- a/GCF_003473485.1_MtrunA17r5.0-ANR/demo_log_probs/meta.json
+++ /dev/null
@@ -1,70 +0,0 @@
-{
-  "model": "InstaDeepAI/NTv3_annot_plants",
-  "code_revision": "ea80a2df95bb605f33e1077b652da3c36c1dad56",
-  "assembly": "GCF_003473485.1_MtrunA17r5.0-ANR",
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-  "keep_target_center_fraction": 0.75,
-  "compute_dtype": "torch.bfloat16",
-  "device": "NVIDIA H100 80GB HBM3",
-  "windows": [
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-      11010048,
-      11796480
-    ],
-    [
-      11665408,
-      11796480,
-      12582912
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-  ],
-  "timing": [
-    {
-      "what": "window_0",
-      "batch": 2,
-      "seconds": 2.124892234802246,
-      "peak_gb": 57.432303104
-    },
-    {
-      "what": "window_1",
-      "batch": 2,
-      "seconds": 1.7003798484802246,
-      "peak_gb": 57.431744
-    },
-    {
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-      "seconds": 1.6897294521331787,
-      "peak_gb": 57.431744
-    },
-    {
-      "what": "upper_window_1",
-      "batch": 2,
-      "seconds": 1.6884651184082031,
-      "peak_gb": 57.431744
-    },
-    {
-      "what": "window_0_one_strand",
-      "batch": 1,
-      "seconds": 0.856881856918335,
-      "peak_gb": 30.554138112
-    },
-    {
-      "what": "full_window",
-      "batch": 2,
-      "seconds": 1.7242932319641113,
-      "peak_gb": 57.431781888
-    }
-  ],
-  "agreement_with_released": {
-    "ours": 147,
-    "released": 147,
-    "identical": 146
-  },
-  "full_window_start": 10878976
-}
\ No newline at end of file
diff --git a/GCF_003473485.1_MtrunA17r5.0-ANR/genome.fa.gz b/GCF_003473485.1_MtrunA17r5.0-ANR/genome.fa.gz
deleted file mode 100644
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--- a/GCF_003473485.1_MtrunA17r5.0-ANR/genome.fa.gz
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/GCF_003473485.1_MtrunA17r5.0-ANR/genome.fa.gz.fai b/GCF_003473485.1_MtrunA17r5.0-ANR/genome.fa.gz.fai
deleted file mode 100644
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diff --git a/class_counts.json b/class_counts.json
deleted file mode 100644
index 49f9c7a4492e20975c674a2ad189e2f25c1e64f1..0000000000000000000000000000000000000000
--- a/class_counts.json
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-{
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-  35557067,
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-  6600866,
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- ],
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- ],
- "MguttatusvarIM62v3.1": [
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- "GCF_018687715.1_C.illinoinensisPawnee_v1": [
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- ],
- "GCF_036884655.1_Cavendish_Baxijiao_AAA": [
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- ],
- "GCF_958298935.1_lpPhrAust1.1": [
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-  19076249,
-  18576351,
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-  6888485,
-  35405890,
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-  35907,
-  35903,
-  35901,
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- "IRGSP-1.0": [
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-  12188196,
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-  5702334,
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-  25619,
-  25405,
-  64660,
-  28497,
-  28497
- ]
-}
\ No newline at end of file
diff --git a/class_weights.json b/class_weights.json
deleted file mode 100644
index 9756b8c36be0a6f3f2700f1353119651da2145c1..0000000000000000000000000000000000000000
--- a/class_weights.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
- "intergenic": 9.559469873630118e-05,
- "intron_p0": 0.00477916312651311,
- "intron_p1": 0.004970995979928906,
- "intron_p2": 0.0020630310906505087,
- "CDS_p0": 0.011884328250057662,
- "CDS_p1": 0.0022346622315229363,
- "CDS_p2": 0.010161727773601286,
- "splice_acceptor_p0": 0.8695092533937269,
- "splice_acceptor_p1": 2.2315761404095316,
- "splice_acceptor_p2": 2.254272468575282,
- "splice_donor_p0": 2.232413838286931,
- "splice_donor_p1": 2.2527808861642047,
- "splice_donor_p2": 0.8695190774639706,
- "start_codon": 2.1268694162776716,
- "stop_codon": 2.1268694162776716
-}
\ No newline at end of file
diff --git a/metadata.tsv b/metadata.tsv
deleted file mode 100644
index 211c9082157ff49897c0dc0c2c8372be5938d76d..0000000000000000000000000000000000000000
--- a/metadata.tsv
+++ /dev/null
@@ -1,31 +0,0 @@
-assembly	species	role	tier	source	accession	eval_chromosomes
-GCF_000002775.5_P.trichocarpa_v4.1	Populus trichocarpa	validation		NCBI RefSeq	GCF_000002775.5	NC_037293.2
-Tlatifoliav1.1	Typha latifolia	validation		JGI (GenBank copy)	GCA_059706395.1	Chr15
-MguttatusvarIM62v3.1	Mimulus guttatus	test		JGI (GenBank copy)	GCA_051942635.1	Chr_11
-GCF_003473485.1_MtrunA17r5.0-ANR	Medicago truncatula	test		NCBI RefSeq	GCF_003473485.1	NC_053047.1
-TAIR10	Arabidopsis thaliana	train	1	Ensembl Plants (Araport11 genes)	GCA_000001735.1	
-GCF_000004075.3_Cucumber_9930_V3	Cucumis sativus	train	1	NCBI RefSeq	GCF_000004075.3	
-GCF_022201045.2_DVS_A1.0	Citrus sinensis	train	1	NCBI RefSeq	GCF_022201045.2	
-GCF_019578655.1_ASM1957865v1	Ricinus communis	train	1	NCBI RefSeq	GCF_019578655.1	
-GCF_020921035.1_ASM2092103v1	Rhodamnia argentea	train	1	NCBI RefSeq	GCF_020921035.1	
-GCF_005286985.2_Setaria_viridis_v4.0	Setaria viridis	train	1	NCBI RefSeq	GCF_005286985.2	
-GCF_016808095.1_ASM1680809v1	Vigna angularis	train	1	NCBI RefSeq	GCF_016808095.1	
-GCF_030704535.1_ASM3070453v1	Vitis vinifera	train	1	NCBI RefSeq	GCF_030704535.1	
-GCF_031755915.1_ASM3175591v1	Ziziphus jujuba	train	2	NCBI RefSeq	GCF_031755915.1	
-GCF_018687715.1_C.illinoinensisPawnee_v1	Carya illinoinensis	train	2	NCBI RefSeq	GCF_018687715.1	
-GCF_036884655.1_Cavendish_Baxijiao_AAA	Musa acuminata	train	2	NCBI RefSeq	GCF_036884655.1	
-GCF_958298935.1_lpPhrAust1.1	Phragmites australis	train	2	NCBI RefSeq	GCF_958298935.1	
-IRGSP-1.0	Oryza sativa	train	2	Ensembl Plants genome, NCBI RefSeq genes	GCF_001433935.1	
-GCF_000309985.2_CAAS_Brap_v3.01	Brassica rapa	train	3	NCBI RefSeq	GCF_000309985.2	
-GCF_025177605.1_USDA_Cmelo_AY_1.0	Cucumis melo	train	3	NCBI RefSeq	GCF_025177605.1	
-GCF_002994745.2_RchiOBHm-V2	Rosa chinensis	train	3	NCBI RefSeq	GCF_002994745.2	
-GCF_019419815.1_Pyrus_bretschneideri_v1	Pyrus bretschneideri	train	3	NCBI RefSeq	GCF_019419815.1	
-GCF_042453785.1_GDT2T_hap1	Malus domestica	train	3	NCBI RefSeq	GCF_042453785.1	
-GCF_937616625.2_ddMerAnnu1.2	Mercurialis annua	train	3	NCBI RefSeq	GCF_937616625.2	
-GCF_963576675.1_ddEupLath1.1	Euphorbia lathyris	train	3	NCBI RefSeq	GCF_963576675.1	
-GCF_020379485.1_Da-Ae	Brassica napus	train	3	NCBI RefSeq	GCF_020379485.1	
-GCF_030052815.1_ASM3005281v1	Hevea brasiliensis	train	3	NCBI RefSeq	GCF_030052815.1	
-GCF_904849725.1_MorexV3_pseudomolecules_assembly	Hordeum vulgare	train	3	NCBI RefSeq	GCF_904849725.1	
-Zm-B73-REFERENCE-NAM-5.0	Zea mays	train	3	Ensembl Plants genome, NCBI RefSeq genes	GCF_902167145.1	
-Gossypium_hirsutum_v2.1	Gossypium hirsutum	train	3	NCBI RefSeq	GCF_007990345.1	
-Glycine_max_v2.1	Glycine max	train	4	Ensembl Plants (INSDC genes)	GCA_000004515.4	
diff --git a/reference_curves.csv b/reference_curves.csv
deleted file mode 100644
index 802e9a45cfa4f8263a3a47e77a167628c59ddd75..0000000000000000000000000000000000000000
--- a/reference_curves.csv
+++ /dev/null
@@ -1,25 +0,0 @@
-source,tokens,val_gene_f1,val_cds_f1
-"full preset, 8 genomes, 1B tokens (bf16)",100139008,0.0,0.0
-"full preset, 8 genomes, 1B tokens (bf16)",200015872,6.164690621351667,12.636238385623354
-"full preset, 8 genomes, 1B tokens (bf16)",300154880,21.48521181158158,18.046800860487963
-"full preset, 8 genomes, 1B tokens (bf16)",400031744,24.349722078521506,25.60567917030285
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