# HG changeset patch
# User tduigou
# Date 1747388343 0
# Node ID dc450979fcd4948d8a22063bc4d3606c1db98dac
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
diff -r 000000000000 -r dc450979fcd4 cloning_similation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cloning_similation.xml Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,251 @@
+
+ A cloning simulator for synthetic biology
+
+ 0
+ 0.1.0
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+ flametree
+ biopython
+ proglog
+ pandas
+ dnacauldron
+ pdf-reports
+ sequenticon
+ dna_features_viewer
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+ `_).
+
+**Parameters**:
+---------------
+* **assemnby csv**: csv file containes the construct names with their parts.
+* **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
+* **topology**: Can be "circular", "linear".
+* **enzyme**: It will be selected automatically, or you can set one from this dictionnary : `dict `_
+* **assembly_class**:
+ - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset `_
+ - "gibson_assembly": GibsonAssembly `ex. dataset `_
+ - "BASIC_assembly": BASICAssembly `ex. dataset `_
+ - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset `_
+ - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset `_
+ ]]>
+
+
+ @unpublished{cloning_simulation
+ author = {Ramiz Khaled},
+ title = {{cloning_simulation}},
+ url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
+ }
+
+
+
diff -r 000000000000 -r dc450979fcd4 cloning_simulation.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cloning_simulation.py Fri May 16 09:39:03 2025 +0000
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+import os
+import dnacauldron
+from Bio import SeqIO
+import pandas
+import argparse
+import zipfile
+
+def cloning_simulation(files_to_assembly, domesticated_list,
+ csv_file, assembly_type, topology,
+ file_name_mapping, file_name_mapping_dom,
+ use_file_names_as_id,
+ outdir_simulation, output_simulation,enzyme):
+
+ files_to_assembly = files_to_assembly.split(',')
+
+ repository = dnacauldron.SequenceRepository()
+ repository.import_records(files=files_to_assembly,
+ use_file_names_as_ids=use_file_names_as_id,
+ topology=topology)
+ if domesticated_list:
+ domesticated_files = domesticated_list.split(',')
+ repository.import_records(files=domesticated_files,
+ use_file_names_as_ids=use_file_names_as_id,
+ topology=topology)
+
+ #refine the real record name dict
+ if isinstance(file_name_mapping, str):
+ file_name_mapping = dict(
+ item.split(":") for item in file_name_mapping.split(",")
+ )
+ real_names = {
+ os.path.splitext(os.path.basename(k))[0]: v.replace(".gb", "")
+ for k, v in file_name_mapping.items()
+ }
+
+ #refine the real record name dict_dom
+ if file_name_mapping_dom == "":
+ file_name_mapping_dom={}
+ else:
+ if isinstance(file_name_mapping_dom, str):
+ file_name_mapping_dom = dict(
+ item.split(":") for item in file_name_mapping_dom.split(",")
+ )
+ dom_real_names = {
+ os.path.splitext(os.path.basename(k))[0]: v.replace(".gb", "")
+ for k, v in file_name_mapping_dom.items()
+ }
+ real_names.update(dom_real_names)
+
+ #update the records
+
+ for key, record in list(repository.collections["parts"].items()):
+ current_id = record.id
+ if current_id in real_names:
+ new_id = real_names[current_id]
+ record.id = new_id
+ record.name = new_id
+ record.description = new_id
+ repository.collections["parts"][new_id] = repository.collections["parts"].pop(key)
+ ########################################################
+ #print (f"repo: {vars(repository)}")
+ any(pandas.read_csv(csv_file, index_col=0, header=None).duplicated())
+
+ if assembly_type == "Type2sRestrictionAssembly":
+ assembly_class = dnacauldron.Type2sRestrictionAssembly
+ elif assembly_type == "GibsonAssembly":
+ assembly_class = dnacauldron.GibsonAssembly
+ elif assembly_type == "BASICAssembly":
+ assembly_class = dnacauldron.BASICAssembly
+ elif assembly_type == "BioBrickStandardAssembly":
+ assembly_class = dnacauldron.BioBrickStandardAssembly
+ elif assembly_type == "OligoPairAnnealin":
+ assembly_class = dnacauldron.OligoPairAnnealin
+ elif assembly_type == "LigaseCyclingReactionAssembly":
+ assembly_class = dnacauldron.LigaseCyclingReactionAssembly
+ else:
+ raise ValueError(f"Unsupported assembly type: {assembly_type}")
+
+ new_csvname = "assambly.csv"
+ os.rename(csv_file, new_csvname)
+
+ assembly_plan = dnacauldron.AssemblyPlan.from_spreadsheet(
+ name="auto_from_filename",
+ path=new_csvname,
+ assembly_class=assembly_class
+ )
+ if enzyme != 'auto':
+ for assembly in assembly_plan.assemblies:
+ assembly.enzyme = enzyme
+
+ simulation = assembly_plan.simulate(sequence_repository=repository)
+ stats = simulation.compute_stats()
+ print(stats)
+
+ report_writer = dnacauldron.AssemblyReportWriter(
+ include_mix_graphs=True,
+ include_assembly_plots=True,
+ show_overhangs_in_graph=True,
+ annotate_parts_homologies=True,
+ include_pdf_report=True,
+ )
+ simulation.write_report(outdir_simulation, assembly_report_writer=report_writer)
+
+ # Append report files to .dat (ZIP)
+ with zipfile.ZipFile(output_simulation, mode='a', compression=zipfile.ZIP_DEFLATED) as zipf:
+ for root, dirs, files in os.walk(outdir_simulation):
+ for file in files:
+ full_path = os.path.join(root, file)
+ arcname = os.path.relpath(full_path, outdir_simulation)
+ zipf.write(full_path, arcname)
+ print("Files in the zip archive:")
+ for info in zipf.infolist():
+ print(info.filename)
+
+ return output_simulation
+
+
+def parse_command_line_args():
+ parser = argparse.ArgumentParser(description="Domestication")
+
+ parser.add_argument("--parts_files", required=True,
+ help="List of GenBank files (Comma-separated)")
+ parser.add_argument("--domesticated_seq", required=True,
+ help="output of domestication (ganbank list)")
+ parser.add_argument("--assembly_csv", required=True,
+ help="csv assembly")
+ parser.add_argument('--assembly_plan_name', type=str,
+ help='type of assembly')
+ parser.add_argument('--topology', type=str,
+ help='"circular" or "linear"')
+ parser.add_argument('--file_name_mapping', type=str,
+ help='Mapping of Galaxy filenames to original filenames')
+ parser.add_argument('--file_name_mapping_dom', type=str,
+ help='Mapping of Galaxy filenames to original domestication filenames')
+ parser.add_argument("--use_file_names_as_id", type=lambda x: x.lower() == 'true', default=True,
+ help="Use file names as IDs (True/False)")
+ parser.add_argument("--outdir_simulation", required=True,
+ help="dir output for cloning simulation results")
+ parser.add_argument("--output_simulation", required=True,
+ help="zip output for cloning simulation results")
+ parser.add_argument('--enzyme', type=str,
+ help='enzyme to use')
+
+ return parser.parse_args()
+
+if __name__ == "__main__":
+ args = parse_command_line_args()
+
+ cloning_simulation(
+ args.parts_files, args.domesticated_seq,
+ args.assembly_csv, args.assembly_plan_name, args.topology,
+ args.file_name_mapping, args.file_name_mapping_dom,
+ args.use_file_names_as_id,
+ args.outdir_simulation,args.output_simulation, args.enzyme
+ )
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 output.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output.html Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,291 @@
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+ Test Results (powered by Planemo)
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+
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 output.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output.json Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,1370 @@
+{
+ "summary": {
+ "num_errors": 0,
+ "num_failures": 0,
+ "num_skips": 0,
+ "num_tests": 6
+ },
+ "tests": [
+ {
+ "data": {
+ "inputs": {
+ "adv|use_file_names_as_ids": true,
+ "assembly_csv": {
+ "id": "a2e8f3fd1611e7f5",
+ "src": "hda"
+ },
+ "assembly_plan_name": "Type2sRestrictionAssembly",
+ "genbank_files": {
+ "id": "1d1943aa60deb628",
+ "src": "hdca"
+ },
+ "topology": "circular"
+ },
+ "job": {
+ "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/6/a/4/dataset_6a407f29-14a2-4358-8781-97a5a60006bf.dat,/tmp/tmps36anksu/files/9/c/0/dataset_9c05120b-2a93-4298-a718-2db482dec9e0.dat,/tmp/tmps36anksu/files/e/9/d/dataset_e9dd6c4a-5d1c-48d6-b072-bb67929590f5.dat,/tmp/tmps36anksu/files/c/2/a/dataset_c2a67b9c-bd0d-483b-b229-1f396bc8c275.dat,/tmp/tmps36anksu/files/5/3/d/dataset_53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00.dat,/tmp/tmps36anksu/files/4/0/f/dataset_40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0.dat,/tmp/tmps36anksu/files/1/4/b/dataset_14b815cb-038e-4836-bb4e-3f049395271c.dat,/tmp/tmps36anksu/files/3/2/7/dataset_32719970-8009-4818-a623-ba980af84d70.dat,/tmp/tmps36anksu/files/6/8/e/dataset_68e30a2d-a44d-40e6-a619-efa1e8cd6e4b.dat,/tmp/tmps36anksu/files/2/3/c/dataset_23c06fae-96cc-4ff8-9e23-111139ce1a92.dat,/tmp/tmps36anksu/files/d/2/9/dataset_d29c16a7-2470-418e-a8f1-1da7c5372dde.dat,/tmp/tmps36anksu/files/2/9/0/dataset_290bfdf4-f595-42f1-a2f0-0f9a9d8e71df.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/4/2/0/dataset_420c4b07-ea17-4e63-9f48-4cc364e28432.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/6/a/4/dataset_6a407f29-14a2-4358-8781-97a5a60006bf.dat:part_A.gb,/tmp/tmps36anksu/files/9/c/0/dataset_9c05120b-2a93-4298-a718-2db482dec9e0.dat:part_B.gb,/tmp/tmps36anksu/files/e/9/d/dataset_e9dd6c4a-5d1c-48d6-b072-bb67929590f5.dat:part_C.gb,/tmp/tmps36anksu/files/c/2/a/dataset_c2a67b9c-bd0d-483b-b229-1f396bc8c275.dat:part_D.gb,/tmp/tmps36anksu/files/5/3/d/dataset_53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00.dat:part_E.gb,/tmp/tmps36anksu/files/4/0/f/dataset_40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0.dat:part_F.gb,/tmp/tmps36anksu/files/1/4/b/dataset_14b815cb-038e-4836-bb4e-3f049395271c.dat:part_G.gb,/tmp/tmps36anksu/files/3/2/7/dataset_32719970-8009-4818-a623-ba980af84d70.dat:part_H.gb,/tmp/tmps36anksu/files/6/8/e/dataset_68e30a2d-a44d-40e6-a619-efa1e8cd6e4b.dat:part_I.gb,/tmp/tmps36anksu/files/2/3/c/dataset_23c06fae-96cc-4ff8-9e23-111139ce1a92.dat:part_J.gb,/tmp/tmps36anksu/files/d/2/9/dataset_d29c16a7-2470-418e-a8f1-1da7c5372dde.dat:part_K.gb,/tmp/tmps36anksu/files/2/9/0/dataset_290bfdf4-f595-42f1-a2f0-0f9a9d8e71df.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/14/outputs/dataset_19827d46-96d8-48c8-b434-17f9e4732aec.dat'",
+ "command_version": "",
+ "copied_from_job_id": null,
+ "create_time": "2025-05-16T08:54:45.629427",
+ "dependencies": [],
+ "exit_code": 0,
+ "external_id": "69472",
+ "galaxy_version": "24.2",
+ "handler": null,
+ "history_id": "1d1943aa60deb628",
+ "id": "306d449b91ecb0a3",
+ "inputs": {
+ "assembly_csv": {
+ "id": "a2e8f3fd1611e7f5",
+ "src": "hda",
+ "uuid": "420c4b07-ea17-4e63-9f48-4cc364e28432"
+ },
+ "genbank_files1": {
+ "id": "1d1943aa60deb628",
+ "src": "hda",
+ "uuid": "6a407f29-14a2-4358-8781-97a5a60006bf"
+ },
+ "genbank_files10": {
+ "id": "b55875807068e59e",
+ "src": "hda",
+ "uuid": "23c06fae-96cc-4ff8-9e23-111139ce1a92"
+ },
+ "genbank_files11": {
+ "id": "4b64a67f616af776",
+ "src": "hda",
+ "uuid": "d29c16a7-2470-418e-a8f1-1da7c5372dde"
+ },
+ "genbank_files12": {
+ "id": "1fda217ac9617c88",
+ "src": "hda",
+ "uuid": "290bfdf4-f595-42f1-a2f0-0f9a9d8e71df"
+ },
+ "genbank_files2": {
+ "id": "13a3899f03fff34a",
+ "src": "hda",
+ "uuid": "9c05120b-2a93-4298-a718-2db482dec9e0"
+ },
+ "genbank_files3": {
+ "id": "6872e1ad22eb2e5d",
+ "src": "hda",
+ "uuid": "e9dd6c4a-5d1c-48d6-b072-bb67929590f5"
+ },
+ "genbank_files4": {
+ "id": "248d7f69d2402068",
+ "src": "hda",
+ "uuid": "c2a67b9c-bd0d-483b-b229-1f396bc8c275"
+ },
+ "genbank_files5": {
+ "id": "a363c57bce5ddac4",
+ "src": "hda",
+ "uuid": "53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00"
+ },
+ "genbank_files6": {
+ "id": "8ab843ac4a5890da",
+ "src": "hda",
+ "uuid": "40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0"
+ },
+ "genbank_files7": {
+ "id": "6206f91299006d13",
+ "src": "hda",
+ "uuid": "14b815cb-038e-4836-bb4e-3f049395271c"
+ },
+ "genbank_files8": {
+ "id": "278f145ab0478700",
+ "src": "hda",
+ "uuid": "32719970-8009-4818-a623-ba980af84d70"
+ },
+ "genbank_files9": {
+ "id": "84aedadb70ef205b",
+ "src": "hda",
+ "uuid": "68e30a2d-a44d-40e6-a619-efa1e8cd6e4b"
+ }
+ },
+ "job_messages": [],
+ "job_metrics": [],
+ "job_runner_name": null,
+ "job_stderr": "",
+ "job_stdout": "",
+ "model_class": "Job",
+ "output_collections": {},
+ "outputs": {
+ "output_zip": {
+ "id": "306d449b91ecb0a3",
+ "src": "hda",
+ "uuid": "19827d46-96d8-48c8-b434-17f9e4732aec"
+ }
+ },
+ "params": {
+ "__input_ext": "\"input\"",
+ "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+ "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
+ "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+ "dbkey": "\"?\"",
+ "domesticated_input": null,
+ "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
+ "topology": "\"circular\""
+ },
+ "state": "ok",
+ "stderr": "\rassembly: 0%| | 0/4 [00:00L2RBS-1P_fwd
+GGACTAGTCCTGTGTGATTTTCTGCTACCCTTATCTCAG
+>L2RBS-1P_adapter
+ATCACACAGGACTA
+>LMA-S_fwd
+CTCGGGTAAGAACTCGCACTTCGTGGAAACACTATTA
+>LMA-S_adapter
+CGAGTTCTTACC
+>L1RBS-xS_fwd
+CTCGTTGAACACCGTCTCAGGTAAGTATCAGTTGTAA
+>L1RBS-xS_adapter
+GACGGTGTTCAA
+>L1RBS-1P_fwd
+GGACTAGTCCTGTGTGATTTACAACTGATACTTACCTGA
+>L1RBS-1P_adapter
+ATCACACAGGACTA
+>L2RBS-xS_fwd
+CTCGTGTTACTATTGGCTGAGATAAGGGTAGCAGAAA
+>L2RBS-xS_adapter
+CCAATAGTAACA
+>LMA-P_fwd
+GGACAGAGACCCACCAGATAATAGTGTTTCCACGAAGTG
+>LMA-P_adapter
+TCTGGTGGGTCTCT
+>LMB-S_fwd
+CTCGGGAGACCTATCGGTAATAACAGTCCAATCTGGTGT
+>LMB-S_adapter
+CGATAGGTCTCC
+>LMB-P_fwd
+GGACGATTCCGAAGTTACACCAGATTGGACTGTTATTAC
+>LMB-P_adapter
+AACTTCGGAATC
diff -r 000000000000 -r dc450979fcd4 test-data/BASIC_assembly_dataset/p15A_kan.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BASIC_assembly_dataset/p15A_kan.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,75 @@
+LOCUS F0001_p15A-Kan.xdna 2235 bp DNA linear 22/05/2017
+DEFINITION
+ACCESSION
+VERSION
+SOURCE
+ ORGANISM
+COMMENT Serial Cloner Genbank Format
+COMMENT SerialCloner_Type=DNA
+COMMENT SerialCloner_Comments=
+COMMENT SerialCloner_Ends=0,0,,0,
+FEATURES Location/Qualifiers
+ misc_feature complement(72..887)
+ /label=p15A
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=True
+ /SerialCloner_Arrow=True
+ misc_feature complement(1223..2043)
+ /label=kanR
+ /SerialCloner_Color=&hFF0000
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=True
+ /SerialCloner_Arrow=True
+ misc_feature 1..18
+ /label=iPrefix
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=True
+ /SerialCloner_Arrow=True
+ misc_feature 2218..2235
+ /label=iSuffix
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=True
+ /SerialCloner_Arrow=True
+ORIGIN
+ 1 TCTGGTGGGT CTCTGTCCCG TCAAGTCAGC GTAATGCTCT GCCAGTGTTA CAACCAATTA
+ 61 ACCAATTCTG ATTAGAAAAA CTCATCGAGC ATCAAATGAA ACTGCAATTT ATTCATATCA
+ 121 GGATTATCAA TACCATATTT TTGAAAAAGC CGTTTCTGTA ATGAAGGAGA AAACTCACCG
+ 181 AGGCAGTTCC ATAGGATGGC AAGATCCTGG TATCGGTCTG CGATTCCGAC TCGTCCAACA
+ 241 TCAATACAAC CTATTAATTT CCCCTCGTCA AAAATAAGGT TATCAAGTGA GAAATCACCA
+ 301 TGAGTGACGA CTGAATCCGG TGAGAATGGC AAAAGCTTAT GCATTTCTTT CCAGACTTGT
+ 361 TCAACAGGCC AGCCATTACG CTCGTCATCA AAATCACTCG CATCAACCAA ACCGTTATTC
+ 421 ATTCGTGATT GCGCCTGAGC GAGACGAAAT ACGCGATCGC TGTTAAAAGG ACAATTACAA
+ 481 ACAGGAATCG AATGCAACCG GCGCAGGAAC ACTGCCAGCG CATCAACAAT ATTTTCACCT
+ 541 GAATCAGGAT ATTCTTCTAA TACCTGGAAT GCTGTTTTCC CGGGGATCGC AGTGGTGAGT
+ 601 AACCATGCAT CATCAGGAGT ACGGATAAAA TGCTTGATGG TCGGAAGAGG CATAAATTCC
+ 661 GTCAGCCAGT TTAGTCTGAC CATCTCATCT GTAACATCAT TGGCAACGCT ACCTTTGCCA
+ 721 TGTTTCAGAA ACAACTCTGG CGCATCGGGC TTCCCATACA ATCGATAGAT TGTCGCACCT
+ 781 GATTGCCCGA CATTATCGCG AGCCCATTTA TACCCATATA AATCAGCATC CATGTTGGAA
+ 841 TTTAATCGCG GCCTCGAGCA AGACGTTTCC CGTTGAATAT GGCTCATAAC ACCCCTTGTA
+ 901 TTACTGTTTA TGTAAGCAGA CAGTTTTATT GTTCATGATG ATATATTTTT ATCTTGTGCA
+ 961 ATGTAACATC AGAGATTTTG AGACACAACG TGGCTTTGTT GAATAAATCG AACTTTTGCT
+ 1021 GAGTTGAAGG ATCAGATCAC GCATCTTCCC GACAACGCAG ACCGTTCCGT GGCAAAGCAA
+ 1081 AAGTTCAAAA TCACCAACTG GTCCACCTAC AACAAAGCTC TCATCAACCG TGGCTCCCTC
+ 1141 ACTTTCTGGC TGGATGATGG GGCGATTCAG GCCTGGTATG AGTCAGCAAC ACCTTCTTCA
+ 1201 CGAGGCAGAC CTCAGCGCTA GCGGAGTGTA TACTGGCTTA CTATGTTGGC ACTGATGAGG
+ 1261 GTGTCAGTGA AGTGCTTCAT GTGGCAGGAG AAAAAAGGCT GCACCGGTGC GTCAGCAGAA
+ 1321 TATGTGATAC AGGATATATT CCGCTTCCTC GCTCACTGAC TCGCTACGCT CGGTCGTTCG
+ 1381 ACTGCGGCGA GCGGAAATGG CTTACGAACG GGGCGGAGAT TTCCTGGAAG ATGCCAGGAA
+ 1441 GATACTTAAC AGGGAAGTGA GAGGGCCGCG GCAAAGCCGT TTTTCCATAG GCTCCGCCCC
+ 1501 CCTGACAAGC ATCACGAAAT CTGACGCTCA AATCAGTGGT GGCGAAACCC GACAGGACTA
+ 1561 TAAAGATACC AGGCGTTTCC CCTGGCGGCT CCCTCGTGCG CTCTCCTGTT CCTGCCTTTC
+ 1621 GGTTTACCGG TGTCATTCCG CTGTTATGGC CGCGTTTGTC TCATTCCACG CCTGACACTC
+ 1681 AGTTCCGGGT AGGCAGTTCG CTCCAAGCTG GACTGTATGC ACGAACCCCC CGTTCAGTCC
+ 1741 GACCGCTGCG CCTTATCCGG TAACTATCGT CTTGAGTCCA ACCCGGAAAG ACATGCAAAA
+ 1801 GCACCACTGG CAGCAGCCAC TGGTAATTGA TTTAGAGGAG TTAGTCTTGA AGTCATGCGC
+ 1861 CGGTTAAGGC TAAACTGAAA GGACAAGTTT TGGTGACTGC GCTCCTCCAA GCCAGTTACC
+ 1921 TCGGTTCAAA GAGTTGGTAG CTCAGAGAAC CTTCGAAAAA CCGCCCTGCA AGGCGGTTTT
+ 1981 TTCGTTTTCA GAGCAAGAGA TTACGCGCAG ACCAAAACGA TCTCAAGAAG ATCATCTTAT
+ 2041 TAAGGGGTCT GACGCTCAGT GGAACGAAAA CTCACGTTAA GGGATTTTGG TCATGAGATT
+ 2101 ATCAAAAAGG ATCTTCACCT AGATCCTTTT AAATTAAAAA TGAAGTTTTA AATCAATCTA
+ 2161 AAGTATATAT GAGTAAACTT GGTCTGACAG TTACCAATGC TTAATCAGTG AGGCACCGGC
+ 2221 TCGGGAGACC TATCG
+//
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 test-data/BASIC_assembly_dataset/promoter.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BASIC_assembly_dataset/promoter.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,170 @@
+LOCUS promoter 4361 bp DNA circular UNK 01-JAN-1980
+DEFINITION
+ACCESSION
+VERSION
+SOURCE
+ ORGANISM
+COMMENT Serial Cloner Genbank Format
+COMMENT SerialCloner_Type=DNA
+COMMENT SerialCloner_Comments=
+COMMENT SerialCloner_Ends=0,0,,0,
+FEATURES Location/Qualifiers
+ misc_feature 984..1028
+ /label=Linker01
+ /SerialCloner_Color=&h8000FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 1168..1212
+ /label=Linker02
+ /SerialCloner_Color=&h8000FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 1327..1361
+ /label=PJ23105
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ primer_bind 4295..4314
+ /label=T7
+ /SerialCloner_Color=&h008B8B
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ rep_origin complement(2161..2789)
+ /label=ColE1 origin
+ /SerialCloner_Color=&h4682B4
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ CDS complement(2941..3600)
+ /label=AmpR
+ /SerialCloner_Color=&h8FBC8F
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ CDS 168..824
+ /label=CmR
+ /SerialCloner_Color=&h8FBC8F
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ Promoter complement(3840..3868)
+ /label=Amp prom
+ /SerialCloner_Color=&h4682B4
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 1033..1161
+ /label=terminator_B0015
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 4295..4311
+ /label=T7-promoter
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 1..18
+ /label=Prefix
+ /SerialCloner_Color=&hFF0080
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 1370..1387
+ /label=Suffix
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 3601..3797
+ /label=pB1a promoter
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 1327..1361
+ /label=ANDERSON 024
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ORIGIN
+ 1 tctggtgggt ctctGTCCTT GATACCGGGA AGCCCTGGGC CAACTTTTGG CGAAAATGAG
+ 61 ACGTTGATCG GCACGTAAGA GGTTCCAACT TTCACCATAA TGAAATAAGA TCACTACCGG
+ 121 GCGTATTTTT TGAGTTATCG AGATTTTCAG GAGCTAAGGA AGCTAAAATG GAGAAAAAAA
+ 181 TCACTGGATA TACCACCGTT GATATATCCC AATGGCATCG TAAAGAACAT TTTGAGGCAT
+ 241 TTCAGTCAGT TGCTCAATGT ACCTATAACC AGACCGTTCA GCTGGATATT ACGGCCTTTT
+ 301 TAAAGACCGT AAAGAAAAAT AAGCACAAGT TTTATCCGGC CTTTATTCAC ATTCTTGCCC
+ 361 GCCTGATGAA TGCTCATCCG GAATTCCGTA TGGCAATGAA AGACGGTGAG CTGGTGATAT
+ 421 GGGATAGTGT TCACCCTTGT TACACCGTTT TCCATGAGCA AACTGAAACG TTTTCATCGC
+ 481 TCTGGAGTGA ATACCACGAC GATTTCCGGC AGTTTCTACA CATATATTCG CAAGATGTGG
+ 541 CGTGTTACGG TGAAAACCTG GCCTATTTCC CTAAAGGGTT TATTGAGAAT ATGTTTTTCG
+ 601 TCTCAGCCAA TCCCTGGGTG AGTTTCACCA GTTTTGATTT AAACGTGGCC AATATGGACA
+ 661 ACTTCTTCGC CCCCGTTTTC ACCATGGGCA AATATTATAC GCAAGGCGAC AAGGTGCTGA
+ 721 TGCCGCTGGC GATTCAGGTT CATCATGCCG TCTGTGATGG CTTCCATGTC GGCAGAATGC
+ 781 TTAATGAATT ACAACAGTAC TGCGATGAGT GGCAGGGCGG GGCGTAATTT TTTTAAGGCA
+ 841 GTTATTGGTG CCCTTAAACG CCTGGTGCTA CGCCTGAATA AGTGATAATA AGCGGATGAA
+ 901 TGGCAGAAAT TCGAAAGCAA ATTCGACCCG GTCGTCGGTT CAGGGCAGGG TCGTTAAATA
+ 961 GCCGCTTATG TCTATTGGGC TCGttactta cgacactccg agacagtcag agggtattta
+ 1021 ttgaactaGT CCCCAGGCAT CAAATAAAAC GAAAGGCTCA GTCGAAAGAC TGGGCCTTTC
+ 1081 GTTTTATCTG TTGTTTGTCG GTGAACGCTC TCTACTAGAG TCACACTGGC TCACCTTCGG
+ 1141 GTGGGCCTTT CTGCGTTTAT AGGCTCGATC GGTGTGAAAA GTCAGTATCC AGTCGTGTAG
+ 1201 TTCTTATTAC CTGTCCAGAC CTTTACGCCG CTGGAGACTA GTCACAGCTA ACACCACGTC
+ 1261 GTCCCTATCT GCTGCCCTAG GTCTATGAGT GGTTGCTGGA TAACGAATTC GCGGCCGCTT
+ 1321 CTAGAGTTTA CGGCTAGCTC AGTCCTAGGT ACTATGCTAG CTACTAGAGG GCTCGggaga
+ 1381 cctatcgATC TTTCTAGAAG ATCTCCTACA ATATTCTCAG CTGCCATGGA AAATCGATGT
+ 1441 TCTTCTTTTA TTCTCTCAAG ATTTTCAGGC TGTATATTAA AACTTATATT AAGAACTATG
+ 1501 CTAACCACCT CATCAGGAAC CGTTGTAGGT GGCGTGGGTT TTCTTGGCAA TCGACTCTCA
+ 1561 TGAAAACTAC GAGCTAAATA TTCAATATGT TCCTCTTGAC CAACTTTATT CTGCATTTTT
+ 1621 TTTGAACGAG GTTTAGAGCA AGCTTCAGGA AACTGAGACA GGAATTTTAT TAAAAATTTA
+ 1681 AATTTTGAAG AAAGTTCAGG GTTAATAGCA TCCATTTTTT GCTTTGCAAG TTCCTCAGCA
+ 1741 TTCTTAACAA AAGACGTCTC TTTTGACATG TTTAAAGTTT AAACCTCCTG TGTGAAATTA
+ 1801 TTATCCGCTC ATAATTCCAC ACATTATACG AGCCGGAAGC ATAAAGTGTA AAGCCTGGGG
+ 1861 TGCCTAATGA GTGAGCTAAC TCACATTAAT TGCGTTGCGC TCACTGCCAA TTGCTTTCCA
+ 1921 GTCGGGAAAC CTGTCGTGCC AGCTGCATTA ATGAATCGGC CAACGCGCGG GGAGAGGCGG
+ 1981 TTTGCGTATT GGGCGCTCTT CCGCTTCCTC GCTCACTGAC TCGCTGCGCT CGGTCGTTCG
+ 2041 GCTGCGGCGA GCGGTATCAG CTCACTCAAA GGCGGTAATA CGGTTATCCA CAGAATCAGG
+ 2101 GGATAACGCA GGAAAGAACA TGTGAGCAAA AGGCCAGCAA AAGGCCAGGA ACCGTAAAAA
+ 2161 GGCCGCGTTG CTGGCGTTTT TCCATAGGCT CCGCCCCCCT GACGAGCATC ACAAAAATCG
+ 2221 ACGCTCAAGT CAGAGGTGGC GAAACCCGAC AGGACTATAA AGATACCAGG CGTTTCCCCC
+ 2281 TGGAAGCTCC CTCGTGCGCT CTCCTGTTCC GACCCTGCCG CTTACCGGAT ACCTGTCCGC
+ 2341 CTTTCTCCCT TCGGGAAGCG TGGCGCTTTC TCATAGCTCA CGCTGTAGGT ATCTCAGTTC
+ 2401 GGTGTAGGTC GTTCGCTCCA AGCTGGGCTG TGTGCACGAA CCCCCCGTTC AGCCCGACCG
+ 2461 CTGCGCCTTA TCCGGTAACT ATCGTCTTGA GTCCAACCCG GTAAGACACG ACTTATCGCC
+ 2521 ACTGGCAGCA GCCACTGGTA ACAGGATTAG CAGAGCGAGG TATGTAGGCG GTGCTACAGA
+ 2581 GTTCTTGAAG TGGTGGCCTA ACTACGGCTA CACTAGAAGG ACAGTATTTG GTATCTGCGC
+ 2641 TCTGCTGAAG CCAGTTACCT TCGGAAAAAG AGTTGGTAGC TCTTGATCCG GCAAACAAAC
+ 2701 CACCGCTGGT AGCGGTGGTT TTTTTGTTTG CAAGCAGCAG ATTACGCGCA GAAAAAAAGG
+ 2761 ATCTCAAGAA GATCCTTTGA TCTTTTCTAC GGGGTCTGAC GCTCAGTGGA ACGAAAACTC
+ 2821 ACGTTAAGGG ATTTTGGTCA TGAGATTATC AAAAAGGATC TTCACCTAGA TCCTTTTAAA
+ 2881 TTAAAAATGA AGTTTTAAAT CAATCTAAAG TATATATGAG TAAACTTGGT CTGACAGTTA
+ 2941 CCAATGCTTA ATCAGTGAGG CACCTATCTC AGCGATCTGT CTATTTCGTT CATCCATAGT
+ 3001 TGCCTGACTC CCCGTCGTGT AGATAACTAC GATACGGGAG GGCTTACCAT CTGGCCCCAG
+ 3061 TGCTGCAATG ATACCGCGAG ACCCACGCTC ACCGGCTCCA GATTTATCAG CAATAAACCA
+ 3121 GCCAGCCGGA AGGGCCGAGC GCAGAAGTGG TCCTGCAACT TTATCCGCCT CCATCCAGTC
+ 3181 TATTAATTGT TGCCGGGAAG CTAGAGTAAG TAGTTCGCCA GTTAATAGTT TGCGCAACGT
+ 3241 TGTTGCCATT GCTACAGGCA TCGTGGTGTC ACGCTCGTCG TTTGGTATGG CTTCATTCAG
+ 3301 CTCCGGTTCC CAACGATCAA GGCGAGTTAC ATGATCCCCC ATGTTGTGCA AAAAAGCGGT
+ 3361 TAGCTCCTTC GGTCCTCCGA TCGTTGTCAG AAGTAAGTTG GCCGCAGTGT TATCACTCAT
+ 3421 GGTTATGGCA GCACTGCATA ATTCTCTTAC TGTCATGCCA TCCGTAAGAT GCTTTTCTGT
+ 3481 GACTGGTGAG TACTCAACCA AGTCATTCTG AGAATAGTGT ATGCGGCGAC CGAGTTGCTC
+ 3541 TTGCCCGGCG TCAATACGGG ATAATACCGC GCCACATAGC AGAACTTTAA AAGTGCTCAT
+ 3601 CATTGGAAAA CGTTCTTCGG GGCGAAAACT CTCAAGGATC TTACCGCTGT TGAGATCCAG
+ 3661 TTCGATGTAA CCCACTCGTG CACCCAACTG ATCTTCAGCA TCTTTTACTT TCACCAGCGT
+ 3721 TTCTGGGTGA GCAAAAACAG GAAGGCAAAA TGCCGCAAAA AAGGGAATAA GGGCGACACG
+ 3781 GAAATGTTGA ATACTCATAC TCTTCCTTTT TCAATATTAT TGAAGCATTT ATCAGGGTTA
+ 3841 TTGTCTCATG AGCGGATACA TATTTGAATG TATTTAGAAA AATAAACAAA TAGGGGTTCC
+ 3901 GCGCACATTT CCCCGAAAAG TGCCACCTGA CGTCTAAGAA ACCATTATTA TCATGACATT
+ 3961 AACCTATAAA AATAGGCGTA TCACGAGGCC GCCCCTGCAG CCGAATTATA TTATTTTTGC
+ 4021 CAAATAATTT TTAACAAAAG CTCTGAAGTC TTCTTCATTT AAATTCTTAG ATGATACTTC
+ 4081 ATCTGGAAAA TTGTCCCAAT TAGTAGCATC ACGCTGTGAG TAAGTTCTAA ACCATTTTTT
+ 4141 TATTGTTGTA TTATCTCTAA TCTTACTACT CGATGAGTTT TCGGTATTAT CTCTATTTTT
+ 4201 AACTTGGAGC AGGTTCCATT CATTGTTTTT TTCATCATAG TGAATAAAAT CAACTGCTTT
+ 4261 AACACTTGTG CCTGAACACC ATATCCATCC GGCGTAATAC GACTCACTAT AGGGAGAGCG
+ 4321 GCCGCCAGAT CTTCCGGATG GCTCGAGTTT TTCAGCAAGA T
+//
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 test-data/BioBrick_assembly_dataset/BBa_E0040_GFP.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BioBrick_assembly_dataset/BBa_E0040_GFP.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,85 @@
+LOCUS BBa_E0040_GFP 2875 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION BBa_E0040_GFP
+VERSION BBa_E0040_GFP
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature 1..21
+ /label="suffix"
+ misc_feature 22..93
+ /label="E. coli his operon terminator"
+ stem_loop 30..64
+ /label="terminator stem loop"
+ primer_bind 157..176
+ /label="VR"
+ CDS 261..875
+ /label="rep(pMB1) (rev)"
+ misc_feature 276
+ /label="ORI"
+ CDS 1035..1895
+ /label="ampR (rev)"
+ primer_bind 2018..2037
+ /label="VF2"
+ misc_feature 2094..2097
+ /label="end of terminator"
+ stem_loop 2107..2126
+ /label="terminator stem loop"
+ misc_feature 2136..2157
+ /label="prefix"
+ CDS 2156..2875
+ /label="GFP protein"
+ misc_feature 2156..2875
+ /label="BBa_E0040_GFP"
+ORIGIN
+ 1 tactagtagc ggccgctgca gtccggcaaa aaagggcaag gtgtcaccac cctgcccttt
+ 61 ttctttaaaa ccgaaaagat tacttcgcgt tatgcaggct tcctcgctca ctgactcgct
+ 121 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
+ 181 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
+ 241 caggaaccgt aaaaaggccg cgttgctggc gtttttccac aggctccgcc cccctgacga
+ 301 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
+ 361 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
+ 421 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg
+ 481 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
+ 541 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
+ 601 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
+ 661 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt
+ 721 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
+ 781 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
+ 841 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
+ 901 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
+ 961 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
+ 1021 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
+ 1081 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
+ 1141 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
+ 1201 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
+ 1261 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
+ 1321 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
+ 1381 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
+ 1441 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
+ 1501 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
+ 1561 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
+ 1621 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
+ 1681 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
+ 1741 gctgttgaga tccagttcga tataacccac tcgtgcaccc aactgatctt cagcatcttt
+ 1801 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
+ 1861 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
+ 1921 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
+ 1981 acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat
+ 2041 tattatcatg acattaacct ataaaaatag gcgtatcacg aggcagaatt tcagataaaa
+ 2101 aaaatcctta gctttcgcta aggatgattt ctggaattcg cggccgcttc tagagatgcg
+ 2161 taaaggagaa gaacttttca ctggagttgt cccaattctt gttgaattag atggtgatgt
+ 2221 taatgggcac aaattttctg tcagtggaga gggtgaaggt gatgcaacat acggaaaact
+ 2281 tacccttaaa tttatttgca ctactggaaa actacctgtt ccatggccaa cacttgtcac
+ 2341 tactttcggt tatggtgttc aatgctttgc gagataccca gatcatatga aacagcatga
+ 2401 ctttttcaag agtgccatgc ccgaaggtta tgtacaggaa agaactatat ttttcaaaga
+ 2461 tgacgggaac tacaagacac gtgctgaagt caagtttgaa ggtgataccc ttgttaatag
+ 2521 aatcgagtta aaaggtattg attttaaaga agatggaaac attcttggac acaaattgga
+ 2581 atacaactat aactcacaca atgtatacat catggcagac aaacaaaaga atggaatcaa
+ 2641 agttaacttc aaaattagac acaacattga agatggaagc gttcaactag cagaccatta
+ 2701 tcaacaaaat actccaattg gcgatggccc tgtcctttta ccagacaacc attacctgtc
+ 2761 cacacaatct gccctttcga aagatcccaa cgaaaagaga gaccacatgg tccttcttga
+ 2821 gtttgtaaca gctgctggga ttacacatgg catggatgaa ctatacaaat aataa
+//
diff -r 000000000000 -r dc450979fcd4 test-data/BioBrick_assembly_dataset/BBa_J23119_prom.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BioBrick_assembly_dataset/BBa_J23119_prom.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,72 @@
+LOCUS BBa_J23119_prom 2190 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION BBa_J23119_prom
+VERSION BBa_J23119_prom
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature 1..21
+ /label="suffix"
+ misc_feature 22..93
+ /label="E. coli his operon terminator"
+ stem_loop 30..64
+ /label="terminator stem loop"
+ primer_bind 157..176
+ /label="VR"
+ CDS 261..875
+ /label="rep(pMB1) (rev)"
+ misc_feature 276
+ /label="ORI"
+ CDS 1035..1895
+ /label="ampR (rev)"
+ primer_bind 2018..2037
+ /label="VF2"
+ misc_feature 2094..2097
+ /label="end of terminator"
+ stem_loop 2107..2126
+ /label="terminator stem loop"
+ misc_feature 2136..2157
+ /label="prefix"
+ misc_feature 2156..2190
+ /label="BBa_J23119_prom"
+ORIGIN
+ 1 tactagtagc ggccgctgca gtccggcaaa aaagggcaag gtgtcaccac cctgcccttt
+ 61 ttctttaaaa ccgaaaagat tacttcgcgt tatgcaggct tcctcgctca ctgactcgct
+ 121 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
+ 181 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
+ 241 caggaaccgt aaaaaggccg cgttgctggc gtttttccac aggctccgcc cccctgacga
+ 301 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
+ 361 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
+ 421 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg
+ 481 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
+ 541 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
+ 601 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
+ 661 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt
+ 721 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
+ 781 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
+ 841 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
+ 901 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
+ 961 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
+ 1021 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
+ 1081 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
+ 1141 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
+ 1201 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
+ 1261 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
+ 1321 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
+ 1381 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
+ 1441 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
+ 1501 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
+ 1561 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
+ 1621 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
+ 1681 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
+ 1741 gctgttgaga tccagttcga tataacccac tcgtgcaccc aactgatctt cagcatcttt
+ 1801 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
+ 1861 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
+ 1921 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
+ 1981 acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat
+ 2041 tattatcatg acattaacct ataaaaatag gcgtatcacg aggcagaatt tcagataaaa
+ 2101 aaaatcctta gctttcgcta aggatgattt ctggaattcg cggccgcttc tagagttgac
+ 2161 agctagctca gtcctaggta taatgctagc
+//
diff -r 000000000000 -r dc450979fcd4 test-data/BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,72 @@
+LOCUS BBa_J23119_prom 2190 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION BBa_J23119_prom
+VERSION BBa_J23119_prom
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature 1..21
+ /label="suffix"
+ misc_feature 22..93
+ /label="E. coli his operon terminator"
+ stem_loop 30..64
+ /label="terminator stem loop"
+ primer_bind 157..176
+ /label="VR"
+ CDS 261..875
+ /label="rep(pMB1) (rev)"
+ misc_feature 276
+ /label="ORI"
+ CDS 1035..1895
+ /label="ampR (rev)"
+ primer_bind 2018..2037
+ /label="VF2"
+ misc_feature 2094..2097
+ /label="end of terminator"
+ stem_loop 2107..2126
+ /label="terminator stem loop"
+ misc_feature 2136..2157
+ /label="prefix"
+ misc_feature 2156..2190
+ /label="BBa_J23119_prom"
+ORIGIN
+ 1 tactagtagc ggccgctgca gtccggcaaa aaagggcaag gtgtcaccac cctgcccttt
+ 61 ttctttaaaa ccgaaaagat tacttcgcgt tatgcaggct tcctcgctca ctgactcgct
+ 121 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
+ 181 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
+ 241 caggaaccgt aaaaaggccg cgttgctggc gtttttccac aggctccgcc cccctgacga
+ 301 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
+ 361 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
+ 421 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg
+ 481 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
+ 541 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
+ 601 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
+ 661 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt
+ 721 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
+ 781 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
+ 841 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
+ 901 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
+ 961 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
+ 1021 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
+ 1081 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
+ 1141 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
+ 1201 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
+ 1261 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
+ 1321 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
+ 1381 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
+ 1441 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
+ 1501 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
+ 1561 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
+ 1621 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
+ 1681 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
+ 1741 gctgttgaga tccagttcga tataacccac tcgtgcaccc aactgatctt cagcatcttt
+ 1801 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
+ 1861 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
+ 1921 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
+ 1981 acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat
+ 2041 tattatcatg acattaacct ataaaaatag gcgtatcacg aggcagaatt tcagataaaa
+ 2101 aaaatcctta gctttcgcta aggatgattt ctggatttcg cggccgcttc tagagttgac
+ 2161 agctagctca gtcctaggta taatgctagc
+//
diff -r 000000000000 -r dc450979fcd4 test-data/BioBrick_assembly_dataset/BBa_J61048_term.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BioBrick_assembly_dataset/BBa_J61048_term.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,73 @@
+LOCUS BBa_J61048_term 2268 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION BBa_J61048_term
+VERSION BBa_J61048_term
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature 1..21
+ /label="suffix"
+ misc_feature 22..93
+ /label="E. coli his operon terminator"
+ stem_loop 30..64
+ /label="terminator stem loop"
+ primer_bind 157..176
+ /label="VR"
+ CDS 261..875
+ /label="rep(pMB1) (rev)"
+ misc_feature 276
+ /label="ORI"
+ CDS 1035..1895
+ /label="ampR (rev)"
+ primer_bind 2018..2037
+ /label="VF2"
+ misc_feature 2094..2097
+ /label="end of terminator"
+ stem_loop 2107..2126
+ /label="terminator stem loop"
+ misc_feature 2136..2157
+ /label="prefix"
+ misc_feature 2156..2268
+ /label="BBa_J61048_term"
+ORIGIN
+ 1 tactagtagc ggccgctgca gtccggcaaa aaagggcaag gtgtcaccac cctgcccttt
+ 61 ttctttaaaa ccgaaaagat tacttcgcgt tatgcaggct tcctcgctca ctgactcgct
+ 121 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
+ 181 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
+ 241 caggaaccgt aaaaaggccg cgttgctggc gtttttccac aggctccgcc cccctgacga
+ 301 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
+ 361 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
+ 421 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg
+ 481 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
+ 541 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
+ 601 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
+ 661 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt
+ 721 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
+ 781 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
+ 841 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
+ 901 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
+ 961 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
+ 1021 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
+ 1081 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
+ 1141 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
+ 1201 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
+ 1261 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
+ 1321 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
+ 1381 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
+ 1441 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
+ 1501 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
+ 1561 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
+ 1621 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
+ 1681 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
+ 1741 gctgttgaga tccagttcga tataacccac tcgtgcaccc aactgatctt cagcatcttt
+ 1801 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
+ 1861 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
+ 1921 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
+ 1981 acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat
+ 2041 tattatcatg acattaacct ataaaaatag gcgtatcacg aggcagaatt tcagataaaa
+ 2101 aaaatcctta gctttcgcta aggatgattt ctggaattcg cggccgcttc tagagccggc
+ 2161 ttatcggtca gtttcacctg atttacgtaa aaacccgctt cggcgggttt ttgcttttgg
+ 2221 aggggcagaa agatgaatga ctgtccacga cgctataccc aaaagaaa
+//
diff -r 000000000000 -r dc450979fcd4 test-data/BioBrick_assembly_dataset/BBa_K611094_bar.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BioBrick_assembly_dataset/BBa_K611094_bar.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,74 @@
+LOCUS BBa_K611094_br 2180 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION BBa_K611094_br
+VERSION BBa_K611094_br
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature 1..21
+ /label="suffix"
+ misc_feature 22..93
+ /label="E. coli his operon terminator"
+ stem_loop 30..64
+ /label="terminator stem loop"
+ primer_bind 157..176
+ /label="VR"
+ CDS 261..875
+ /label="rep(pMB1) (rev)"
+ misc_feature 276
+ /label="ORI"
+ CDS 1035..1895
+ /label="ampR (rev)"
+ primer_bind 2018..2037
+ /label="VF2"
+ misc_feature 2094..2097
+ /label="end of terminator"
+ stem_loop 2107..2126
+ /label="terminator stem loop"
+ misc_feature 2136..2157
+ /label="prefix"
+ misc_feature 2156..2180
+ /label="Barcode"
+ misc_feature 2156..2180
+ /label="BBa_K611094_br"
+ORIGIN
+ 1 tactagtagc ggccgctgca gtccggcaaa aaagggcaag gtgtcaccac cctgcccttt
+ 61 ttctttaaaa ccgaaaagat tacttcgcgt tatgcaggct tcctcgctca ctgactcgct
+ 121 gcgctcggtc gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt
+ 181 atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc
+ 241 caggaaccgt aaaaaggccg cgttgctggc gtttttccac aggctccgcc cccctgacga
+ 301 gcatcacaaa aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata
+ 361 ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac
+ 421 cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg
+ 481 taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc
+ 541 cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag
+ 601 acacgactta tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt
+ 661 aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt
+ 721 atttggtatc tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg
+ 781 atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac
+ 841 gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca
+ 901 gtggaacgaa aactcacgtt aagggatttt ggtcatgaga ttatcaaaaa ggatcttcac
+ 961 ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac
+ 1021 ttggtctgac agttaccaat gcttaatcag tgaggcacct atctcagcga tctgtctatt
+ 1081 tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt
+ 1141 accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt
+ 1201 atcagcaata aaccagccag ccggaagggc cgagcgcaga agtggtcctg caactttatc
+ 1261 cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa
+ 1321 tagtttgcgc aacgttgttg ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg
+ 1381 tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt
+ 1441 gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc
+ 1501 agtgttatca ctcatggtta tggcagcact gcataattct cttactgtca tgccatccgt
+ 1561 aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg
+ 1621 gcgaccgagt tgctcttgcc cggcgtcaat acgggataat accgcgccac atagcagaac
+ 1681 tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc
+ 1741 gctgttgaga tccagttcga tataacccac tcgtgcaccc aactgatctt cagcatcttt
+ 1801 tactttcacc agcgtttctg ggtgagcaaa aacaggaagg caaaatgccg caaaaaaggg
+ 1861 aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag
+ 1921 catttatcag ggttattgtc tcatgagcgg atacatattt gaatgtattt agaaaaataa
+ 1981 acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat
+ 2041 tattatcatg acattaacct ataaaaatag gcgtatcacg aggcagaatt tcagataaaa
+ 2101 aaaatcctta gctttcgcta aggatgattt ctggaattcg cggccgcttc tagagcgctg
+ 2161 atagtgctag tgtagatcgc
+//
diff -r 000000000000 -r dc450979fcd4 test-data/BioBrick_assembly_dataset/hierarchical_biobrick.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BioBrick_assembly_dataset/hierarchical_biobrick.csv Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,4 @@
+construct,parts,
+C1_prom_barcode,BBa_K611094_bar,BBa_J23119_prom
+C2_gfp_term,BBa_E0040_GFP,BBa_J61048_term
+C3_final,C1_prom_barcode,C2_gfp_term
diff -r 000000000000 -r dc450979fcd4 test-data/Gibson_assembly_dataset/gibson_assembly.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gibson_assembly_dataset/gibson_assembly.csv Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,6 @@
+construct, parts,,,,
+construct_1,Frag_1,Frag_2,Frag_3,Frag_4,Frag_5
+construct_2,Frag_1,Frag_2,Frag_3,Frag_4b,Frag_5
+construct_3,Frag_1,Frag_2,Frag_3,Frag_4c,Frag_5b
+construct_4,Frag_1,Frag_2,Frag_3,Frag_4,
+construct_5,Frag_1,Frag_2,Frag_3,Frag_4,Frag_4b
diff -r 000000000000 -r dc450979fcd4 test-data/Gibson_assembly_dataset/gibson_sequences.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gibson_assembly_dataset/gibson_sequences.fa Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,347 @@
+>expected_sequence
+CTCCACCTGCGTCTATCGTACAGTGCTAAAATGGCAGCAGATAGTGAAACTTCCGCTAAG
+CTAGCCCCTCAGGGTACACTGCACCGAGGCGTGCTGTCAATACTTGATTAAGTCGGGTTG
+TCGGGGACCTGCCGTCACGCTTCCGAGTGTATATCCGGATTTAGTTGACGTCATACAGAG
+GCACTAAGAAGAATAAACGCTTACCTCCAGCAATCGTGTAGTGTCAGGTGTACGTTCTCC
+CTTGCGCCGTTCGGCAAGCGTCCGGTGTCGGGCTGCAAGGAATAAATCTTTATGGACCAG
+AGGGGCTTGTTTCCTCATATGGGTGCGTGCACTTATACGATTCAAAGGTGGATATGGCCG
+CATAACACGTAGCCAGGCTATAGTCCCGCGGCCTAATTCCTTCGAGTGCGGGTGCCTGTT
+TTTGTTTTTCCTTTACGACACGAACCGCTCTAACCTGCTCTATTTCGCCACGTTCCAGTG
+AACCTCTTAGCCTACCGCCCACGTACGGTGGGACGCGTCGAGCAGTTAAGGTACTGTGGA
+GAAATCGTTCAATATTAGAAAACAGGCGGTGTACGAATTACTGTGTCCCGGTGTTGCCCG
+TTTAACGGCTGCCGTGGTCATACCGTGAGGCACCACGAGGGGATGCTACGCAACATGCGA
+GGTGTAATCAGCAGGGAAGATCCCGGGGATCGAAAGCGGTCCGCGATTTGCGACCGATAT
+GCATAAGGTGTCATTTATATTACACCTACGACACTGGTACCGGCTCACAGCCAAATGCAC
+AGTCTCAAGATAGAATTCGCAAAAATTAGGCTTATCGGGCGCTTACTCTTTGTTACACTT
+CTGGTCTGTGAGTGACGCCCTGTGTCCCATCACTGCATGTGAGGATGCGTGTACTGCACC
+TGTGAATTACAGACGTTTCCCTACCAGGGCGCTACGTTATAATGTTCGGTTGCAACCCTC
+TATAGGGTGATCTCGACATACCACTATGGTTTGCGCGTCTCGGGTGCTTTTGGCGAGGGC
+CAGGTACGGCGGTGAGACAGCGTATTTTGCGAATAGGGTATTCGGACGCACGGTGTATAG
+CTCTTGGAAAACGACTCTTCGACGGGCGTGTAGAAGTAGCCAAGCAGTTCGGTTGTTATC
+ACTAAATGCGGACCATGTGCAGCCGTTTAGGAGAGGAGTCTGCAATGGATCAGCTGGTCA
+GATTGTACCACTCGGTTGAGCCTAAGGCACTTCAGGTGCTCGGATTGTAATGAACCCTCA
+GGTTACGCCGTTGCGCTGAGATCCCACAAGCCATAAGCAATGAGAATCGAGCAGCTATCG
+AATTACGCAGCACTTGCTGATGAACTGGGTGCACCTAAAGCGCCCGATAAAACGGAGGGA
+GTGAGGTAACTACTACATTGCGAGTAGTGCGAGGGGCCTCCGAGACTACATTAGAGCAGC
+CATGCCGAATACGACAAAATCTATAGCCTTGCGAACGTAGGGGACTGATTTATGGACAAC
+AGGACCGAAACAAGTTGGAGCCACAACGGAGCTATGGACGTTTTCACTATTGATGGGTGG
+CTTGCGTCCGCATCCCAGGTTTCTCTGGTTAATTTTCATGACGATTCTTTGTGGTACGAT
+CCAGGCATAAGATAGGGCACCTAACCCGATACTGTGAACTTATATGACGGCTGAACATGC
+CCTAATAGTCTGCCAAAAGGGAAACCTATAACGGCTCTAAACGGGCCCCGGGTACGTAAC
+AGCAATGTTCCTGTCCACCAAGGCGTTTTTAGTAACCGCCGATCGATCTCGATCGAATTC
+CGTTTTACGCCCCAGATCGCAGCTCCCTTGACAGTGTCAGTTGAATCCCCATTCTAGGTT
+TCCTGATAAAACTAAGTACGGGGACGCATCAGTCGAAAGCAATCACAGATAATAGATATC
+TTGAGCAGAAAGACGTCTTCACGAATCAGGAGCGAGTGTCCCCTTTGAAAGTGCGGGCAA
+CAATAGGTGTGAGGTTTCACGGTTGCTTGATCAGTAGCTGTTCACTCTCTCGCAGGCCTA
+CATAGTGAGGTGGTGAGATTGTTCAGGTCTGTCTCCTGCGCGGTTGTCGAGCCCCGTCGG
+GCACGCTAACAAGGACAGGAATTCGGGTCGTCAAATAACAATTTACGTCATCGCATCCCT
+CAAGGGTAAGGCGTGATCTCCATCTCGGTTCCCAATTGGTCATTGTGATAGCCACACTGC
+AGTTACCGAAGGCGATTTTATACTACCCTGATAAGTGCTCGCAGCCCCTCCTCCCTAATA
+ATGTAACGACGAGCATTAACCCAGGAGTATTTCTCACGTTGCTCGTGCCCAGCCAAGGCG
+ATCAACGCAGACCGGATAGCGTTAGCTAGCCCACGGGTAAAAGCGATTGTTGTACTCTTT
+CATATGAATACAGCACTCGCGAATGCAAGCCTACGTCGGCTCGATTCTCTTCCTCACCAC
+ACTGGAGGCGATGATCTAGCCCGTCTTTCACCCCGTACCTTTATACTCGGCCGCGTATTT
+CTCCACCGGGAGCTCTGCCTACCAAAGCGTCGTACGCCCAGGAAGCCGTTTCCTTTATCC
+TCCCTCATGTCTCAACGCGCGAGCATCGGAGAGTACGCGAAATCGACTGTCTGGCCAACA
+CTGGACAGACGCGCGAGACGCTGATAAACCCCCATTTTCGTGGGGTTAGTAAATCGGTGG
+CTTCAAACGGTTCGATCGCTCGCACGAGCATTAGTCAGGAGTATGATTGCGCATCATCTC
+TACTCCGTACTAGGTTCTGTAGCTCAGGATCTCCGGGGGGATCAAGCTTTTATGTCCCGC
+GGGATTAGAAGATATCCATCCATATGTTTACTTTGATGCGGGTCCGAGCTCTCTATGATG
+CTGCTTTGACAAAATGTGGAAAGCCTCAGCGACCGCTCTGGGGTCAAAGCTCTACGACAC
+GTTGATGCTAAACAAGTTGGACTACTAAGCAAATGAAGCGGAAGAGATACTGAGCGCTCT
+CTCTATGACTTTCGCTATATGGCGACGTGCGAAAAACGCGATTTGGCCGAAATCTCAAAT
+AATAATGCAATGTGTTGGCTAAGCTCGGGCAAACTCAGGATGTGACCTAGTACCCTCTGC
+CCCGTGAGTACCCATACCCAATCAAGCCAGCCCAATTCGCGATAGGTACAGATAAGCCTT
+ACTCGTCCCGATCCTTGACTAAAACACTCATCCTCGATAGTACGTGCCTTGTAGAGTCCG
+ACGGCCATAGGTAAACGACCAGTTAGTGTCGTAGGGTCCTCCACTTTAGCTACGATTGCA
+ACTCCCTTACCTTCGTGCCGGCGCGCTCCTCTTGCTACCATCACGCTTCAAATCGGGTGG
+AAGACCAACTGATGAATGAGGGTGCAGACCCCAGTGGAGCATAATACGATGCGCCCACGA
+TACTCTAGAGCCACGCGTCGACGTTCGTAAGATGTCCCGGGCCCGTGGGTGGCCACATCG
+GCCGCCCATCCTTGTGTCTTCCGATAAGTACTCCCTTTCAAGGACTCTCCGATACCGGCT
+TAGAACACGAACGGACAACGCTTTCAGCGCTGAGAAATGACGGCTGCTTCAACCAGAACG
+ATACAGCCTTCTTTGCTAGATAGCCTCTAGTGTCAGCCACCAAGTCCGCCACCTAATCCT
+TCGCCGAGGGTCAAAGCTTCTGACCATCCAATTGTTAGGCACTCTTGGAACCTTGCAAGT
+ACCTGATCATGCAGAAAATGGACTTGCCCGGAGCATATTCATTATAAGTACCATTCACGG
+CAGGTTATAGTATGCGTTGACGCGGGGTGATACGGTAATGCAAGTAACCATCGGGCCGCG
+GTATGCACATAGAAGGGTGTTTGACTTGGTTTCTTACAGTGCAACTGCATATGTGGACCG
+CCATTCCAAGTGAAAGGATACGAAGGGAGGTTTCGGACTGCTATCCAGAGCATGGAAAGC
+CTTCAAGGTGGTGCGCACTGGAATAGTGACTCGGGGATTGTATGTCGAGCCGCGTCCAGT
+CTTTCCTATACTTATGCGAGCAAATAGACCGAGTGGAACTTGATTGCATCAGCCGAATCA
+CGATGAAAACTCAGCTTACAATTCGTAAGCACTTCAAATATATGCCCGGAAAATCGCCGT
+CCAGTGACTTGTAATAGCTCCAGGGTCAGTAGCGCTGCCCTGGCCGAACCAGGTGACGGT
+TACGTGGACCTCACAGTATCAATGTTGCAGTGCGCCACCAGATTAAGCTGGCCGTGTCAT
+GGTGAACAACCGTGATAAAAGAACGGGAGTATGAGAGTGCCACCCAAGAGTGGTACTCCA
+GGATTCGGAAAGGGGAGGGGGCTTTTCCTGCTTAACAACCTTCCTCGGCACGGTCTAAGC
+GTCTCACTCGTCCTAAACTCTACCATCATGCAGCTAGGCGAAAGTATAACTTTAGGGTCT
+ATCAGGATGAGCTATCTGTACCACGGTGATGAGATAAGTAGGGGGTGCGCTAGGGTCGTT
+CGTGTTTTCATCGTCTATAGTACCTATTTCTCGTCTTCCATTAGCGCATACGGCCATCTC
+GCGGCGGCTACGTCAGCCAGCGTCAACCCCAAGTCACTAATTTCCGTTATTATAGGTGTA
+GCTCATAACTTCTTCTGCCGACCAAGCCAAAAGCTTTGCGGCAGCTGCAAGGCCACGTTA
+GGCTCTCGGACGGCAGATATTTATTAATAACACCACTGGGTTCCAGCTCTTAACGCACTT
+CCCTTCACTGGATCACCTGTACGCCCATAAGCTAAGCCTGAAGCCACGGCCTCAATCGTG
+GACATTACTCTTAGCAAATCCACATTACCATGTCACCAATCCCCGAACCCCGCGCCGACC
+TAAGGCGGGGTACCTCGTGCACGGCAGCATCGAGGGAAATATATTACAAAAGACGCGGCG
+ATCCAACGGTTGATAAAAACAGTTCCGTGGAAGGCGGACGTGTGCTTAGCGCATGCTTCT
+CACCGAGTGACAGCACCGATTCCATCTCGCTAGCACGCCGATGAGCCTCGCTGTGGGACT
+ATGGTCCAGCCTATGCTTAACTAGGCAGAACAGAGAGTATGGTGGTCCTCGGTAAGGTCG
+ATTTGGTGGCACTCGCAAGATACGCGGGTTATTAGTAGAGCGCAGTCAGGGCCCATCGCC
+AGCATTTGCATGCTCGCCGTACGCTATCCTTGTACTACGGTTCCTCAGTGGCTATAAAGG
+AATGTCACAACTCCATTAGCCCCTTTTGTTCAGCGCTTAGTCATGGTGGGACTGACTCAC
+CGAGACTACATACGGATTGTGCCCGCAGAGACATGCCTTTCATGCTGGGGTTTTGTAAGC
+AGCTCCACGGGGTAGTGTCACCATGCCTTCGACCTATGCTTATGAAACCCGAGGTAATGC
+GGCAGGATCCCGTGGATCCTACGCTTAGCCTGTTTAAGCCATCGTTCTCCTCGGCCCCCA
+GCCAGCGCGTATTCCGCGCATTCCTCCGAGTGCGTATCGCGCAAACCACAAGATACCTCT
+CAACGACTAGCGGTGAACCACCAAGCTTGACATACGTGCCCCTTCGGAAACGTTATTAGT
+GGTCCTGAGTGGTACGTCCCGAGTATACGGGGCAGCGATAGTAACGCTACAAATAGCTAG
+GCGAGGTTGCGATACCTGAATGAATATCCAACAGTGGCAACGAGACGCTTAGAAAGGGAA
+ACTACATACCAGTTCAATCCGGGATGACTTCAAAAGGGTATGTTTGTTTTGAAGCGAAGC
+TTTGGTTGTCATTCAGTTCCTAGAGTTTACGGCGCTGATATGGCTCTAGGAGTCCAGTGA
+ATTCGTCAGCATAAGCCCCACATCGTAGGAAATTGCCCGGTCGTCGGTCTAGCAAATGCT
+CGGTAAACTGGGAGTGTACTAACACCATGTCGTGGTAACCCGGTGGACCGGCTACTAGAG
+ACATATTTATTCATGCTCAGTTGAACCTGTTTCGAGGGGGCCGAGTTAACATAAAGTGAT
+TAGTCACAGCGCATTAAGATAGAACAGGGATATAGCTCGTTGCATCCATAAATTGCCCAC
+CGTAGGGAGAACGCCGTTGGAAAATGAGAGTTAGGCGATGAGCGGTTGTCGCCCGCACAG
+ACAAAGGATGCCTTTATAAATAGTAGCGGCCTTGTCTGCACCAGACGTTTGTGGGTCGAC
+GTGCTATTCTAGCCAAAAGCAAAATGTATCATACTACAGGCAATAGGCCCTATGCTGACC
+AAACTTGGGGACCCTTGCGCCTTCTCTCTTACGCATAACATGCATAGGTACCTCTACTCA
+TCAGGCAGGGCGGCGTGAGGTCACTATGGCTCAAGATGTGTACGACTAAAGAAAGGTTTA
+TGCTCCTTCCCCAAGGACGCATTTGGGACTGCTACTTGCCCCTAGCGAATTCACTAGGAT
+TTTTGTAGAACCATGAGCGCCCTATCCGATAGCACAGAGACAATGCTACAAGCAACTGTG
+CATGCGCTCGATCGCCGTGCATTAATACGTATTATAGCGTATCGTGTACGCTAATATCTT
+AGTGCACCGCACGCTGGTTGGATACAATTCCGTGAAATAATTCCTGCTTACACAGGGGCT
+TTCTGGCGCATGGCTGTGTCTGGATGTTTGTGATAAGAGGCTCCATGAACCCGGCGGGAA
+ATGAGGGGAAACCCCGGGGAGCAACGACACTAAGCCTGGCAGTTGTTCAGATAGGACGCT
+TTTGTCAGTGGGCGGTTTTGCATCCACTAACTATCATAAACGACACAACGTCGAATGATC
+ATCGGCGGTTTGCATGTAGAGACAGCTCCTGCAACACCATACCGGCTCGTGGAATTACGC
+TGTGCGCCGGCCCTCATTCGATTGTGTCCAGCGTCGGCGCGAATGATGATTGAGATGTGC
+TTCGGCTCAGAGCGTGCACAGGTAGTTCTCCCCCCTTACCTAGCTGATCCAGCAATTCCA
+CGCTGGCCCGCGCGTCCTTGGGTAACACTGGATCTGTACCCAAATACACCGTCGTGATTG
+TTAACTACCGTATGGCGGTTACGATCGAGTGACACTATTATTAGACCGCTACTCCAAGTC
+CCAACTTTTCATCGCCATACAGAAGAGAACGAGAAAGTCGAAGAGTTATAGCGTGTACAC
+TTCTGATTAGCTAACGAATCGATGCGTACAGCATACTCGAGCAACTTTATGGGTCGTCTG
+TCTCCTTGTACCCCGCTTGACGAGGATGTGTTTGTAGGCGGCTTGGATATCGGCAGTGTA
+TCCGCATGGTCAAACACTTTAGCCCGACCGGTGCTCAAGGTCGAAATCCTAATATAGATT
+GGGATAGGACCCGTCCATTACTAGGCGACATTCGCAGTCACGAGCCCGCACGGGGTGCCT
+CAACACGGTGACACTCAATTCGCCGGCACTGAGTACGACGATCGTGATTGCCATACCGTC
+ATGTTTTGTGTTACCCCTGATAAGAAGCGCAGATATGGCACGGGGGCAGAGGGCGGAGTA
+GACCCATGCAAAACTCTAGCCTCTGGGCAGCATGATCGACGTAGAACGCCGTTGTGACTC
+ACTAGTTTCAGTTATGATGTTCAGCCAAGAATCCTCCATTTTGACGTGAACCTTCTCCCT
+TTACACCTTGAAGCTGCAATATTAAGTCGACCCTTTAAGTTGCCTTGTCTTGGTCTAGAG
+CCCGCAGCTCACCGATAAAATGAGCAGTCAATTTTAGCGGCGGTTGTCCAGGTTACATGC
+ACTTTGGGCTGGAACCGCGTTACGTTTGGAGTACTTAGAAGTGTCGTAGGCATAGGAGAG
+CCGAAACTTGATATTGGGTCTAGTTAGTGCTCTACCCCGCTTCGGATCCGTAATAGTGAT
+GTTGCATGAGACGCTTGCCTCAAGGCGACATACGGTGGCGGTTGCTGGAAATGACGCCCC
+ACCCCGTGATAATTTGGGGACGAGCCGCACGATAACTTCTGCCAGCGACCGCCCCTCCCA
+CGTCCGATGGTGATTCCGAA
+>Frag_1
+CTCCACCTGCGTCTATCGTACAGTGCTAAAATGGCAGCAGATAGTGAAACTTCCGCTAAG
+CTAGCCCCTCAGGGTACACTGCACCGAGGCGTGCTGTCAATACTTGATTAAGTCGGGTTG
+TCGGGGACCTGCCGTCACGCTTCCGAGTGTATATCCGGATTTAGTTGACGTCATACAGAG
+GCACTAAGAAGAATAAACGCTTACCTCCAGCAATCGTGTAGTGTCAGGTGTACGTTCTCC
+CTTGCGCCGTTCGGCAAGCGTCCGGTGTCGGGCTGCAAGGAATAAATCTTTATGGACCAG
+AGGGGCTTGTTTCCTCATATGGGTGCGTGCACTTATACGATTCAAAGGTGGATATGGCCG
+CATAACACGTAGCCAGGCTATAGTCCCGCGGCCTAATTCCTTCGAGTGCGGGTGCCTGTT
+TTTGTTTTTCCTTTACGACACGAACCGCTCTAACCTGCTCTATTTCGCCACGTTCCAGTG
+AACCTCTTAGCCTACCGCCCACGTACGGTGGGACGCGTCGAGCAGTTAAGGTACTGTGGA
+GAAATCGTTCAATATTAGAAAACAGGCGGTGTACGAATTACTGTGTCCCGGTGTTGCCCG
+TTTAACGGCTGCCGTGGTCATACCGTGAGGCACCACGAGGGGATGCTACGCAACATGCGA
+GGTGTAATCAGCAGGGAAGATCCCGGGGATCGAAAGCGGTCCGCGATTTGCGACCGATAT
+GCATAAGGTGTCATTTATATTACACCTACGACACTGGTACCGGCTCACAGCCAAATGCAC
+AGTCTCAAGATAGAATTCGCAAAAATTAGGCTTATCGGGCGCTTACTCTTTGTTACACTT
+CTGGTCTGTGAGTGACGCCCTGTGTCCCATCACTGCATGTGAGGATGCGTGTACTGCACC
+TGTGAATTACAGACGTTTCCCTACCAGGGCGCTACGTTATAATGTTCGGTTGCAACCCTC
+TATAGGGTGATCTCGACATACCACTATGGTTTGCGCGTCTCGGGTGCTTTTGGCGAGGGC
+CAGGTACGGCGGTGAGACAGCGTATTTTGCGAATAGGGTATTCGGACGCACGGTGTATAG
+CTCTTGGAAAACGACTCTTCGACGGGCGTGTAGAAGTAGCCAAGCAGTTCGGTTGTTATC
+ACTAAATGCGGACCATGTGCAGCCGTTTAGGAGAGGAGTCTGCAATGGATCAGCTGGTCA
+GATTGTACCACTCGGTTGAGCCTAAGGCACTTCAGGTGCTCGGATTGTAATGAACCCTCA
+GGTTACGCCGTTGCGCTGAGATCCCACAAGCCATAAGCAATGAGAATCGAGCAGCTATCG
+AATTACGCAGCACTTGCTGATGAACTGGGTGCACCTAAAGCGCCCGATAAAACGGAGGGA
+GTGAGGTAACTACTACATTGCGAGTAGTGCGAGGGGCCTCCGAGACTACATTAGAGCAGC
+CATGCCGAATACGACAAAATCTATAGCCTTGCGAACGTAGGGGACTGATTTATGGACAAC
+AGGACCGAAACAAGTTGGAGCCACAACGGAGCTATGGACGTTTTCACTATTGATGGGTGG
+CTTGCGTCCGCATCCCAGGTTTCTCTGGTTAATTTTCATGACGATTCTTTGTGGTACGAT
+CCAGGCATAAGATAGGGCACCTAACCCGATACTGTGAACTTATATGACGGCTGAACATGC
+CCTAATAGTCTGCCAAAAGGGAAACCTATAACGGCTCTAAACGGGCCCCGGGTACGTAAC
+AGCAATGTTCCTGTCCACCAAGGCGTTTTTAGTAACCGCCGATCGATCTCGATCGAATTC
+CGTTTTACGC
+>Frag_2
+GATCGAATTCCGTTTTACGCCCCAGATCGCAGCTCCCTTGACAGTGTCAGTTGAATCCCC
+ATTCTAGGTTTCCTGATAAAACTAAGTACGGGGACGCATCAGTCGAAAGCAATCACAGAT
+AATAGATATCTTGAGCAGAAAGACGTCTTCACGAATCAGGAGCGAGTGTCCCCTTTGAAA
+GTGCGGGCAACAATAGGTGTGAGGTTTCACGGTTGCTTGATCAGTAGCTGTTCACTCTCT
+CGCAGGCCTACATAGTGAGGTGGTGAGATTGTTCAGGTCTGTCTCCTGCGCGGTTGTCGA
+GCCCCGTCGGGCACGCTAACAAGGACAGGAATTCGGGTCGTCAAATAACAATTTACGTCA
+TCGCATCCCTCAAGGGTAAGGCGTGATCTCCATCTCGGTTCCCAATTGGTCATTGTGATA
+GCCACACTGCAGTTACCGAAGGCGATTTTATACTACCCTGATAAGTGCTCGCAGCCCCTC
+CTCCCTAATAATGTAACGACGAGCATTAACCCAGGAGTATTTCTCACGTTGCTCGTGCCC
+AGCCAAGGCGATCAACGCAGACCGGATAGCGTTAGCTAGCCCACGGGTAAAAGCGATTGT
+TGTACTCTTTCATATGAATACAGCACTCGCGAATGCAAGCCTACGTCGGCTCGATTCTCT
+TCCTCACCACACTGGAGGCGATGATCTAGCCCGTCTTTCACCCCGTACCTTTATACTCGG
+CCGCGTATTTCTCCACCGGGAGCTCTGCCTACCAAAGCGTCGTACGCCCAGGAAGCCGTT
+TCCTTTATCCTCCCTCATGTCTCAACGCGCGAGCATCGGAGAGTACGCGAAATCGACTGT
+CTGGCCAACACTGGACAGACGCGCGAGACGCTGATAAACCCCCATTTTCGTGGGGTTAGT
+AAATCGGTGGCTTCAAACGGTTCGATCGCTCGCACGAGCATTAGTCAGGAGTATGATTGC
+GCATCATCTCTACTCCGTACTAGGTTCTGTAGCTCAGGATCTCCGGGGGGATCAAGCTTT
+TATGTCCCGCGGGATTAGAAGATATCCATCCATATGTTTACTTTGATGCGGGTCCGAGCT
+CTCTATGATGCTGCTTTGACAAAATGTGGAAAGCCTCAGCGACCGCTCTGGGGTCAAAGC
+TCTACGACACGTTGATGCTAAACAAGTTGGACTACTAAGCAAATGAAGCGGAAGAGATAC
+TGAGCGCTCTCTCTATGACTTTCGCTATATGGCGACGTGCGAAAAACGCGATTTGGCCGA
+AATCTCAAATAATAATGCAATGTGTTGGCTAAGCTCGGGCAAACTCAGGATGTGACCTAG
+TACCCTCTGCCCCGTGAGTACCCATACCCAATCAAGCCAGCCCAATTCGCGATAGGTACA
+GATAAGCCTTACTCGTCCCGATCCTTGACTAAAACACTCATCCTCGATAGTACGTGCCTT
+GTAGAGTCCGACGGCCATAGGTAAACGACCAGTTAGTGTCGTAGGGTCCTCCACTTTAGC
+TACGATTGCAACTCCCTTACCTTCGTGCCGGCGCGCTCCTCTTGCTACCATCACGCTTCA
+AATCGGGTGGAAGACCAACTGATGAATGAGGGTGCAGACCCCAGTGGAGCATAATACGAT
+GCGCCCACGATACTCTAGAGCCACGCGTCGACGTTCGTAAGATGTCCCGGGCCCGTGGGT
+GGCCACATCGGCCGCCCATCCTTGTGTCTTCCGATAAGTACTCCCTTTCAAGGACTCTCC
+GATACCGGCTTAGAACACGAACGGACAACGCTTTCAGCGCTGAGAAATGACGGCTGCTTC
+AACCAGAACGATACAGCCTT
+>Frag_3
+AACCAGAACGATACAGCCTTCTTTGCTAGATAGCCTCTAGTGTCAGCCACCAAGTCCGCC
+ACCTAATCCTTCGCCGAGGGTCAAAGCTTCTGACCATCCAATTGTTAGGCACTCTTGGAA
+CCTTGCAAGTACCTGATCATGCAGAAAATGGACTTGCCCGGAGCATATTCATTATAAGTA
+CCATTCACGGCAGGTTATAGTATGCGTTGACGCGGGGTGATACGGTAATGCAAGTAACCA
+TCGGGCCGCGGTATGCACATAGAAGGGTGTTTGACTTGGTTTCTTACAGTGCAACTGCAT
+ATGTGGACCGCCATTCCAAGTGAAAGGATACGAAGGGAGGTTTCGGACTGCTATCCAGAG
+CATGGAAAGCCTTCAAGGTGGTGCGCACTGGAATAGTGACTCGGGGATTGTATGTCGAGC
+CGCGTCCAGTCTTTCCTATACTTATGCGAGCAAATAGACCGAGTGGAACTTGATTGCATC
+AGCCGAATCACGATGAAAACTCAGCTTACAATTCGTAAGCACTTCAAATATATGCCCGGA
+AAATCGCCGTCCAGTGACTTGTAATAGCTCCAGGGTCAGTAGCGCTGCCCTGGCCGAACC
+AGGTGACGGTTACGTGGACCTCACAGTATCAATGTTGCAGTGCGCCACCAGATTAAGCTG
+GCCGTGTCATGGTGAACAACCGTGATAAAAGAACGGGAGTATGAGAGTGCCACCCAAGAG
+TGGTACTCCAGGATTCGGAAAGGGGAGGGGGCTTTTCCTGCTTAACAACCTTCCTCGGCA
+CGGTCTAAGCGTCTCACTCGTCCTAAACTCTACCATCATGCAGCTAGGCGAAAGTATAAC
+TTTAGGGTCTATCAGGATGAGCTATCTGTACCACGGTGATGAGATAAGTAGGGGGTGCGC
+TAGGGTCGTTCGTGTTTTCATCGTCTATAGTACCTATTTCTCGTCTTCCATTAGCGCATA
+CGGCCATCTCGCGGCGGCTACGTCAGCCAGCGTCAACCCCAAGTCACTAATTTCCGTTAT
+TATAGGTGTAGCTCATAACTTCTTCTGCCGACCAAGCCAAAAGCTTTGCGGCAGCTGCAA
+GGCCACGTTAGGCTCTCGGACGGCAGATATTTATTAATAACACCACTGGGTTCCAGCTCT
+TAACGCACTTCCCTTCACTGGATCACCTGTACGCCCATAAGCTAAGCCTGAAGCCACGGC
+CTCAATCGTGGACATTACTCTTAGCAAATCCACATTACCATGTCACCAATCCCCGAACCC
+CGCGCCGACCTAAGGCGGGGTACCTCGTGCACGGCAGCATCGAGGGAAATATATTACAAA
+AGACGCGGCGATCCAACGGTTGATAAAAACAGTTCCGTGGAAGGCGGACGTGTGCTTAGC
+GCATGCTTCTCACCGAGTGACAGCACCGATTCCATCTCGCTAGCACGCCGATGAGCCTCG
+CTGTGGGACTATGGTCCAGCCTATGCTTAACTAGGCAGAACAGAGAGTATGGTGGTCCTC
+GGTAAGGTCGATTTGGTGGCACTCGCAAGATACGCGGGTTATTAGTAGAGCGCAGTCAGG
+GCCCATCGCCAGCATTTGCATGCTCGCCGTACGCTATCCTTGTACTACGGTTCCTCAGTG
+GCTATAAAGGAATGTCACAACTCCATTAGCCCCTTTTGTTCAGCGCTTAGTCATGGTGGG
+ACTGACTCACCGAGACTACATACGGATTGTGCCCGCAGAGACATGCCTTTCATGCTGGGG
+TTTTGTAAGCAGCTCCACGGGGTAGTGTCACCATGCCTTCGACCTATGCTTATGAAACCC
+GAGGTAATGCGGCAGGATC
+>Frag_4
+AGGTAATGCGGCAGGATCCCGTGGATCCTACGCTTAGCCTGTTTAAGCCATCGTTCTCCT
+CGGCCCCCAGCCAGCGCGTATTCCGCGCATTCCTCCGAGTGCGTATCGCGCAAACCACAA
+GATACCTCTCAACGACTAGCGGTGAACCACCAAGCTTGACATACGTGCCCCTTCGGAAAC
+GTTATTAGTGGTCCTGAGTGGTACGTCCCGAGTATACGGGGCAGCGATAGTAACGCTACA
+AATAGCTAGGCGAGGTTGCGATACCTGAATGAATATCCAACAGTGGCAACGAGACGCTTA
+GAAAGGGAAACTACATACCAGTTCAATCCGGGATGACTTCAAAAGGGTATGTTTGTTTTG
+AAGCGAAGCTTTGGTTGTCATTCAGTTCCTAGAGTTTACGGCGCTGATATGGCTCTAGGA
+GTCCAGTGAATTCGTCAGCATAAGCCCCACATCGTAGGAAATTGCCCGGTCGTCGGTCTA
+GCAAATGCTCGGTAAACTGGGAGTGTACTAACACCATGTCGTGGTAACCCGGTGGACCGG
+CTACTAGAGACATATTTATTCATGCTCAGTTGAACCTGTTTCGAGGGGGCCGAGTTAACA
+TAAAGTGATTAGTCACAGCGCATTAAGATAGAACAGGGATATAGCTCGTTGCATCCATAA
+ATTGCCCACCGTAGGGAGAACGCCGTTGGAAAATGAGAGTTAGGCGATGAGCGGTTGTCG
+CCCGCACAGACAAAGGATGCCTTTATAAATAGTAGCGGCCTTGTCTGCACCAGACGTTTG
+TGGGTCGACGTGCTATTCTAGCCAAAAGCAAAATGTATCATACTACAGGCAATAGGCCCT
+ATGCTGACCAAACTTGGGGACCCTTGCGCCTTCTCTCTTACGCATAACATGCATAGGTAC
+CTCTACTCATCAGGCAGGGCGGCGTGAGGTCACTATGGCTCAAGATGTGTACGACTAAAG
+AAAGGTTTATGCTCCTTCCCCAAGGACGCATTTGGGACTGCTACTTGCCCCTAGCGAATT
+CACTAGGATTTTTGTAGAACCATGAGCGCCCTATCCGATAGCACAGAGACAATGCTACAA
+GCAACTGTGCATGCGCTCGATCGCCGTGCATTAATACGTATTATAGCGTATCGTGTACGC
+TAATATCTTAGTGCACCGCACGCTGGTTGGATACAATTCCGTGAAATAATTCCTGCTTAC
+ACAGGGGCTTTCTGGCGC
+>Frag_4b
+AGGTAATGCGGCAGGATCCCGTGGATCCTACGCTTAGCCTGTTACCCCCCCCGTTCTCCT
+CGGCCCCCAGCCAGCGCGTATTCCGCGCATTCCTCCGAGTGCGTATCGCGCAAACCACAA
+GATACCTCTCAACGACTAGCGGTGAACCACCAAGCTTGACATACGTGCCCCTTCGGAAAC
+GTTATTAGTGGTCCTGAGTGGTACGTCCCGAGTATACGGGGCAGCGATAGTAACGCTACA
+AATAGCTAGACCGACGACAAACACAGCACTGAATATCCAACAGTGGCAACGAGACGCTTA
+GAAAGGGAAACTACATACCAGTTCAATCCGGGATGACTTCAAAAGGGTATGTTTGTTTTG
+AAGCGAAGCTTTGGTTGTCATTCAGTTCCTAGAGTTTACGGCGCTGATATGGCTCTAGGA
+GTCCAGTGAATTCGTCAGCATAAGCCCCACATCGTAGGAAATTGCCCGGTCGTCGGTCTA
+GCAAATGCTCGGTAAACTGGGAGTGTACTAACACCATGTCGTGGTAACCCGGTGGACCGG
+CTACTAGAGACATATTTATTCATGCTCAGTTGAACCTGTTTCGAGGGGGCCGAGTTAACA
+TAAAGTGATTAGTCACAGCGCATTAAGATAGAACAGGGATATAGCTCGTTGCATCCATAA
+ATTGCCCACCGTAGGGAGAACGCCGTTGGAAAATGAGAGTTAGGCGATGAGCGGTTGTCG
+CCCGCACAGACAAAGGATGCCTTTATAAATAGTAGCGGCCTTGTCTGCACCAGACGTTTG
+TGGGTCGACGTGCTATTCTAGCCAAAAGCAAAATGTATCATACTACAGGCAATAGGCCCT
+ATGCTGACCAAACTTGGGGACCCTTGCGCCTTCTCTCTTACGCATAACATGCATAGGTAC
+CTCTACTCATCAGGCAGGGCGGCGTGAGGTCACTATGGCTCAAGATGTGTACGACTAAAG
+AAAGGTTTATGCTCCTTCCCCAAGGACGCATTTGGGACTGCTACTTGCCCCTAGCGAATT
+CACTAGGATTTTTGTAGAACCATGAGCGCCCTATCCGATAGCACAGAGACAATGCTACAA
+GCAACTGTGCATGCGCTCGATCGCCGTGCATTAATACGTATTATAGCGTATCGTGTACGC
+TAATATCTTAGTGCACCGCACGCTGGTTGGATACAATTCCGTGAAATAATTCCTGCTTAC
+ACAGGGGCTTTCTGGCGC
+>Frag_4c
+AGGTAATGCGGCAGGATCCCGTGGATCCTACGCTTAGCCTGTTAGGGGGGGGGTTCTCCT
+CGGCCCCCAGCCAGCGCGTATTCCGCGCATTCCTCCGAGTGCGTATCGCGCAAACCACAA
+GATACCTCTCAACGACTAGCGGTGAACCACCAAGCTTGACATACGTGCCCCTTCGGAAAC
+GTTATTAGTGGTCCTGAGTGGTACGTCCCGAGTATACGGGGCAGCGATAGTAACGCTACA
+AATAGCTAGACCGACGACAAACACAGCACTGAATATCCAACAGTGGCAACGAGACGCTTA
+GAAAGGGAAACTACATACCAGTTCAATCCGGGATGACTTCAAAAGGGTATGTTTGTTTTG
+AAGCGAAGCTTTGGTTGTCATTCAGTTCCTAGAGTTTACGGCGCTGATATGGCTCTAGGA
+GTCCAGTGAATTCGTCAGCATAAGCCCCACATCGTAGGAAATTGCCCGGTCGTCGGTCTA
+GCAAATGCTCGGTAAACTGGGAGTGTACTAACACCATGTCGTGGTAACCCGGTGGACCGG
+CTACTAGAGACATATTTATTCATGCTCAGTTGAACCTGTTTCGAGGGGGCCGAGTTAACA
+TAAAGTGATTAGTCACAGCGCATTAAGATAGAACAGGGATATAGCTCGTTGCATCCATAA
+ATTGCCCACCGTAGGGAGAACGCCGTTGGAAAATGAGAGTTAGGCGATGAGCGGTTGTCG
+CCCGCACAGACAAAGGATGCCTTTATAAATAGTAGCGGCCTTGTCTGCACCAGACGTTTG
+TGGGTCGACGTGCTATTCTAGCCAAAAGCAAAATGTATCATACTACAGGCAATAGGCCCT
+ATGCTGACCAAACTTGGGGACCCTTGCGCCTTCTCTCTTACGCATAACATGCATAGGTAC
+CTCTACTCATCAGGCAGGGCGGCGTGAGGTCACTATGGCTCAAGATGTGTACGACTAAAG
+AAAGGTTTATGCTCCTTCCCCAAGGACGCATTTGGGACTGCTACTTGCCCCTAGCGAATT
+CACTAGGATTTTTGTAGAACCATGAGCGCCCTATCCGATAGCACAGAGACAATGCTACAA
+GCAACTGTGCATGCGCTCGATCGCCGTGCATTAATACGTATTATAGCGTATCGTGTACGC
+TAATATCTTAGTGCACCGCACGCTGGTTGGATACAATTCCGTGAAATAATTCCTGCTTAC
+ACAGGGGCTTTCTGGCGC
+>Frag_5
+ACAGGGGCTTTCTGGCGCATGGCTGTGTCTGGATGTTTGTGATAAGAGGCTCCATGAACC
+CGGCGGGAAATGAGGGGAAACCCCGGGGAGCAACGACACTAAGCCTGGCAGTTGTTCAGA
+TAGGACGCTTTTGTCAGTGGGCGGTTTTGCATCCACTAACTATCATAAACGACACAACGT
+CGAATGATCATCGGCGGTTTGCATGTAGAGACAGCTCCTGCAACACCATACCGGCTCGTG
+GAATTACGCTGTGCGCCGGCCCTCATTCGATTGTGTCCAGCGTCGGCGCGAATGATGATT
+GAGATGTGCTTCGGCTCAGAGCGTGCACAGGTAGTTCTCCCCCCTTACCTAGCTGATCCA
+GCAATTCCACGCTGGCCCGCGCGTCCTTGGGTAACACTGGATCTGTACCCAAATACACCG
+TCGTGATTGTTAACTACCGTATGGCGGTTACGATCGAGTGACACTATTATTAGACCGCTA
+CTCCAAGTCCCAACTTTTCATCGCCATACAGAAGAGAACGAGAAAGTCGAAGAGTTATAG
+CGTGTACACTTCTGATTAGCTAACGAATCGATGCGTACAGCATACTCGAGCAACTTTATG
+GGTCGTCTGTCTCCTTGTACCCCGCTTGACGAGGATGTGTTTGTAGGCGGCTTGGATATC
+GGCAGTGTATCCGCATGGTCAAACACTTTAGCCCGACCGGTGCTCAAGGTCGAAATCCTA
+ATATAGATTGGGATAGGACCCGTCCATTACTAGGCGACATTCGCAGTCACGAGCCCGCAC
+GGGGTGCCTCAACACGGTGACACTCAATTCGCCGGCACTGAGTACGACGATCGTGATTGC
+CATACCGTCATGTTTTGTGTTACCCCTGATAAGAAGCGCAGATATGGCACGGGGGCAGAG
+GGCGGAGTAGACCCATGCAAAACTCTAGCCTCTGGGCAGCATGATCGACGTAGAACGCCG
+TTGTGACTCACTAGTTTCAGTTATGATGTTCAGCCAAGAATCCTCCATTTTGACGTGAAC
+CTTCTCCCTTTACACCTTGAAGCTGCAATATTAAGTCGACCCTTTAAGTTGCCTTGTCTT
+GGTCTAGAGCCCGCAGCTCACCGATAAAATGAGCAGTCAATTTTAGCGGCGGTTGTCCAG
+GTTACATGCACTTTGGGCTGGAACCGCGTTACGTTTGGAGTACTTAGAAGTGTCGTAGGC
+ATAGGAGAGCCGAAACTTGATATTGGGTCTAGTTAGTGCTCTACCCCGCTTCGGATCCGT
+AATAGTGATGTTGCATGAGACGCTTGCCTCAAGGCGACATACGGTGGCGGTTGCTGGAAA
+TGACGCCCCACCCCGTGATAATTTGGGGACGAGCCGCACGATAACTTCTGCCAGCGACCG
+CCCCTCCCACGTCCGATGGTGATTCCGAACTCCACCTGCGTCTATCGT
+>Frag_5b
+ACAGGGGCTTTCTGGCGCATGGCTGTGTCTGGAAAAAAAAAAAAAAAAAAAACATGAACC
+CGGCGGGAAATGAGGGGAAACCCCGGGGAGCAACGACACTAAGCCTGGCAGTTGTTCAGA
+TAGGACGCTTTTGTCAGTGGGCGGTTTTGCATCCACTAACTATCATAAACGACACAACGT
+CGAATGATCATCGGCGGTTTGCATGTAGAGACAGCTCCTGCAACACCATACCGGCTCGTG
+GAATTACGCTGTGCGCCGGCCCTCATTCGATTGTGTCCAGCGTCGGCGCGAATGATGATT
+GAGATGTGCTTCGGCTCAGAGCGTGCACAGGTAGTTCTCCCCCCTTACCTAGCTGATCCA
+GCAATTCCACGCTGGCCCGCGCGTCCTTGGGTAACACTGGATCTGTACCCAAATACACCG
+TCGTGATTGTTAACTACCGTATGGCGGTTACGATCGAGTGACACTATTATTAGACCGCTA
+CTCCAAGTCCCAACTTTTCATCGCCATACAGAAGAGAACGAGAAAGTCGAAGAGTTATAG
+CGTGTACACTTCTGATTAGCTAACGAATCGATGCGTACAGCATACTCGAGCAACTTTATG
+GGTCGTCTGTCTCCTTGTACCCCGCTTGACGAGGATGTGTTTGTAGGCGGCTTGGATATC
+GGCAGTGTATCCGCATGGTCAAACACTTTAGCCCGACCGGTGCTCAAGGTCGAAATCCTA
+ATATAGATTGGGATAGGACCCGTCCATTACTAGGCGACATTCGCAGTCACGAGCCCGCAC
+GGGGTGCCTCAACACGGTGACACTCAATTCGCCGGCACTGAGTACGACGATCGTGATTGC
+CATACCGTCATGTTTTGTGTTACCCCTGATAAGAAGCGCAGATATGGCACGGGGGCAGAG
+GGCGGAGTAGACCCATGCAAAACTCTAGCCTCTGGGCAGCATGATCGACGTAGAACGCCG
+TTGTGACTCACTAGTTTCAGTTATGATGTTCAGCCAAGAATCCTCCATTTTGACGTGAAC
+CTTCTCCCTTTACACCTTGAAGCTGCAATATTAAGTCGACCCTTTAAGTTGCCTTGTCTT
+GGTCTAGAGCCCGCAGCTCACCGATAAAATGAGCAGTCAATTTTAGCGGCGGTTGTCCAG
+GTTACATGCACTTTGGGCTGGAACCGCGTTACGTTTGGAGTACTTAGAAGTGTCGTAGGC
+ATAGGAGAGCCGAAACTTGATATTGGGTCTAGTTAGTGCTCTACCCCGCTTCGGATCCGT
+AATAGTGATGTTGCATGAGACGCTTGCCTCAAGGCGACATACGGTGGCGGTTGCTGGAAA
+TGACGCCCCACCCCGTGATAATTTGGGGACGAGCCGCACGATAACTTCTGCCAGCGACCG
+CCCCTCCCACGTCCGATGGTGATTCCGAACTCCACCTGCGTCTATCGT
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 test-data/example_genetic_parts_and_backbone/parts/partA.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example_genetic_parts_and_backbone/parts/partA.gb Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,94 @@
+LOCUS Exported 4022 bp ds-DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA
+ACCESSION RFP_GFP_BO_10232
+TGGCTCGAGTTTTTCAGCAAGATTCCCTATCAGTGATAGAGATTGACATCC
+
+> RFP_GFP_BO_10233
+CGGATCTGAAAGAGGAGAAAGGATCTATGGCGAGTAGCGAAGACGT
+
+> RFP_GFP_BO_10234
+GTGTTGTTACCGTTACCCAGGACTCCTCCCTGCAAGACGGTG
+
+> RFP_GFP_BO_10235
+GGCCGCGTGTTACAACCAATGAAAGTGAAACGTGATTTCATGCGT
+
+> RFP_GFP_BO_10236
+AATGGTAAACTGACGCTGAAGTTCATCTGTACTACTGGTAAACTGCCGG
+
+> RFP_GFP_BO_10237
+CATAAGCTGGAATACAATTTTAACAGCCACAATGTTTACATCACCGCCGATAAACAAAAAAA
+
+> RFP_GFP_BO_10238
+CGGGTGGGCCTTTCTGCGTTTATAATCTTTCTAGAAGATCTCCTACAATATTCTCAGC
+
+> RFP_GFP_BO_10244
+GGGTGGGCCTTTCTGCGTTTATAATCTTTCTAGAAGATCTCCTACAATATTCTCAGC
+
+> RFP_GFP_BO_10268
+GGCCGCGTGTTACAACCAATGAAAGTGAAACGTGATTTCATGCGTC
+
+> RFP_GFP_BO_10281
+AGCTGGAATACAATTTTAACAGCCACAATGTTTACATCACCGCCGATAAACAA
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 test-data/lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,93 @@
+> p1_mRFP1-part1
+TCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATACTGAGCACGGATCTGAAAGAGGAGAAAGGATCT
+
+> p2_mRFP1-part2
+ATGGCGAGTAGCGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGAAGGTTCC
+GTTAACGGTCACGAGTTCGAAATCGAAGGTGAAGGTGAAGGTCGTCCGTACGAAGGTACTCA
+GACCGCTAAACTGAAAGTTACCAAAGGTGGTCCGCTGCCGTTCGCTTGGGACATCCTGTCCCC
+GCAGTTCCAGTACGGTTCCAAAGCTTACGTTAAACACCCGGCTGACATCCCGGACTACCTGAA
+ACTGTCCTTCCCGGAAGGTTTCAAATGGGAACGTGTTATGAACTTCGAAGACGGTGGTGTTGTT
+ACCGTTACCCAGGAC
+
+> p3_mRFP1-part3
+TCCTCCCTGCAAGACGGTGAGTTCATCTACAAAGTTAAACTGCGTGGTACTAACTTCCCGTCCG
+ACGGTCCGGTTATGCAGAAAAAAACCATGGGTTGGGAAGCTTCCACCGAACGTATGTACCCGG
+AAGACGGTGCTCTGAAAGGTGAAATCAAAATGCGTCTGAAACTGAAAGACGGTGGTCACTAC
+GACGCTGAAGTTAAAACCACCTACATGGCTAAAAAACCGGTTCAGCTGCCGGGTGCTTACAAA
+ACCGACATCAAACTGGACATCACCTCCCACAACGAAGACTACACCATCGTTGAACAGTACGAA
+CGTGCTGAAGGTCGTCACTCCACCGGTGCTTAATAAGGATCTCCAGGCATCAAATAAAACGAA
+AGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCTACTA
+GAGTCACACTGGCTCACCTTCGGGTGGGCCTTTCTGCGTTTATAAGTCGGTCTCACCGAGCGGC
+CGCGTGTTACAACCAAT
+
+> p4_sfGFP-part1
+GAAAGTGAAACGTGATTTCATGCGTCATTTTGAACATTTTGTAAATCTTATTTAATAATGTGTG
+CGGCAATTCACATTTAATTTATGAATGTTTTCTTAACATCGCGGCAACTCAAGAAACGGCAGGT
+TCGGATCTTAGCTACTAGAGAAAGAGGAGAAATACTAGATGCGTAAAGGCGAAGAGCTGTTC
+ACTGGTGTCGTCCCTATTCTGGTGGAACTGGATGGTGATGTCAACGGTCATAAGTTTTCCGTGC
+GTGGCGAGGGTGAAGGTGACGCAACTAATGGTAAACTGACGCTGAAGTTCA
+
+> p5_sfGFP-part2
+TCTGTACTACTGGTAAACTGCCGGTTCCTTGGCCGACTCTGGTAACGACGCTGACTTATGGTGT
+TCAGTGCTTTGCTCGTTATCCGGACCATATGAAGCAGCATGACTTCTTCAAGTCCGCCATGCCG
+GAAGGCTATGTGCAGGAACGCACGATTTCCTTTAAGGATGACGGCACGTACAAAACGCGTGCG
+GAAGTGAAATTTGAAGGCGATACCCTGGTAAACCGCATTGAGCTGAAAGGCATTGACTTTAAA
+GAGGACGGCAATATCCTGGGCCATAAGCTGGAATACAATTTTAACAGCCACA
+
+> p6_sfGFP-part3
+ATGTTTACATCACCGCCGATAAACAAAAAAATGGCATTAAAGCGAATTTTAAAATTCGCCACA
+ACGTGGAGGATGGCAGCGTGCAGCTGGCTGATCACTACCAGCAAAACACTCCAATCGGTGATG
+GTCCTGTTCTGCTGCCAGACAATCACTATCTGAGCACGCAAAGCGTTCTGTCTAAAGATCCGA
+ACGAGAAACGCGATCATATGGTTCTGCTGGAGTTCGTAACCGCAGCGGGCATCACGCATGGTA
+TGGATGAACTGTACAAATGACCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGG
+CCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCTACTAGAGTCACACTGGCTCACCTTCG
+GGTGGGCCTTTCTGCGTTTATA
+
+> p7_backbone
+ATCTTTCTAGAAGATCTCCTACAATATTCTCAGCTGCCATGGAAAATCGATGTTCTTCTTTTATT
+CTCTCAAGATTTTCAGGCTGTATATTAAAACTTATATTAAGAACTATGCTAACCACCTCATCAG
+GAACCGTTGTAGGTGGCGTGGGTTTTCTTGGCAATCGACTCTCATGAAAACTACGAGCTAAAT
+ATTCAATATGTTCCTCTTGACCAACTTTATTCTGCATTTTTTTTGAACGAGGTTTAGAGCAAGCT
+TCAGGAAACTGAGACAGGAATTTTATTAAAAATTTAAATTTTGAAGAAAGTTCAGGGTTAATA
+GCATCCATTTTTTGCTTTGCAAGTTCCTCAGCATTCTTAACAAAAGACGTCTCTTTTGACATGTT
+TAAAGTTTAAACCTCCTGTGTGAAATTATTATCCGCTCATAATTCCACACATTATACGAGCCGG
+AAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCG
+CTCACTGCCAATTGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAA
+CGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGC
+GCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCA
+CAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAA
+CCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAA
+AAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTC
+CCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGC
+CTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTG
+TAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCT
+TATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAG
+CCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGT
+GGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTA
+CCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTT
+TTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCT
+TTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGAT
+TATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAG
+TATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCG
+ATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGG
+AGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAG
+ATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTAT
+CCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAG
+TTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCT
+TCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAA
+GCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCA
+TGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGAC
+TGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCC
+GGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAA
+ACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCC
+ACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAA
+CAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATA
+CTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATT
+TGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACC
+TGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCC
+GCCCCTGCAGCCGAATTATATTATTTTTGCCAAATAATTTTTAACAAAAGCTCTGAAGTCTTCT
+TCATTTAAATTCTTAGATGATACTTCATCTGGAAAATTGTCCCAATTAGTAGCATCACGCTGTG
+AGTAAGTTCTAAACCATTTTTTTATTGTTGTATTATCTCTAATCTTACTACTCGATGAGTTTTCG
+GTATTATCTCTATTTTTAACTTGGAGCAGGTTCCATTCATTGTTTTTTTCATCATAGTGAATAAA
+ATCAACTGCTTTAACACTTGTGCCTGAACACCATATCCATCCGGCGTAATACGACTCACTATAG
+GGAGAGCGGCCGCCAGATCTTCCGGATGGCTCGAGTTTTTCAGCAAGAT
\ No newline at end of file
diff -r 000000000000 -r dc450979fcd4 test-data/lcr_assembly_dataset/assembly_plan.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lcr_assembly_dataset/assembly_plan.csv Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,2 @@
+Construct1,RFP_GFP_BO_10232,oligo_indicator: _BO_,RFP_GFP_BO_10234,RFP_GFP_BO_10236,RFP_GFP_BO_10244,RFP_GFP_BO_10268,RFP_GFP_BO_10281,p1_mRFP1-part1,p2_mRFP1-part2,p3_mRFP1-part3,p4_sfGFP-part1,p5_sfGFP-part2,p6_sfGFP-part3,p7_backbone
+Construct2_flawed,RFP_GFP_BO_10232,RFP_GFP_BO_10233,RFP_GFP_BO_10244,RFP_GFP_BO_10268,RFP_GFP_BO_10281,p1_mRFP1-part1,p2_mRFP1-part2,p3_mRFP1-part3,p4_sfGFP-part1,p5_sfGFP-part2,p6_sfGFP-part3,p7_backbone,,