# HG changeset patch
# User tduigou
# Date 1749634379 0
# Node ID 3a3b0f7cb5c2d3368800a5d7840979769b084e6f
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
diff -r 000000000000 -r 3a3b0f7cb5c2 cloning_similation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cloning_similation.xml Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,393 @@
+
+ A cloning simulator for synthetic biology
+
+ 0
+ 0.1.0
+
+
+ flametree
+ biopython
+ proglog
+ pandas
+ dnacauldron
+ pdf-reports
+ sequenticon
+ dna_features_viewer
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+ `_).
+
+**Parameters**:
+---------------
+* **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
+* **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
+* **Domesticated GenBank**: Dimesticated GenBank list (Optional)
+* **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+ @unpublished{cloning_simulation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 3a3b0f7cb5c2 cloning_simulation.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cloning_simulation.py Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,177 @@
+import argparse
+import os
+import zipfile
+import pandas
+import dnacauldron
+
+
+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, outdir_gb):
+
+ 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())
+ df = pandas.read_csv(csv_file, index_col=0, header=None)
+ if df.duplicated().any():
+ raise ValueError("Duplicate rows found in the data!")
+
+ 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,
+ dataframe=None,
+ header=None,
+ 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)
+ for member in zipf.namelist():
+ # Only extract actual files inside 'all_construct_records/' (not subfolders)
+ if member.startswith("assambly_simulation/all_construct_records/") and not member.endswith("/"):
+ # Get the file name only (strip folder path)
+ filename = os.path.basename(member)
+ if not filename:
+ continue # skip any edge cases
+
+ # Destination path directly in outdir_dir
+ target_path = os.path.join(outdir_gb, filename)
+
+ # Write the file content
+ with zipf.open(member) as source, open(target_path, "wb") as target:
+ target.write(source.read())
+
+ return output_simulation, outdir_gb
+
+
+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')
+ parser.add_argument("--outdir_gb", required=True,
+ help="dir output constructs gb files")
+
+ 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, args.outdir_gb
+ )
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/2-step-golden_gate_plan.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/2-step-golden_gate_plan.csv Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,4 @@
+construct_3,construct_1,part_L,part_J,part_K,,
+construct_4,construct_2,part_L,part_J,part_K,,
+construct_1,part_A,part_B,part_C,part_D,part_E,part_F
+construct_2,part_A,part_G,part_H,part_I,part_F,
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,197 @@
+LOCUS part_A 4292 bp ds-DNA circular UNK 28-OCT-2019
+DEFINITION .
+ACCESSION part_A
+VERSION part_A
+KEYWORDS "creator:SynthSys Center".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ RBS 2332..2343
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2208..2238
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ promoter 2289..2323
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 3162..3178
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 228..233
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 1009..2028
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 51..56
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2350..3027
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ff00ff"
+ CDS complement(3376..4191)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_RNA 87..639
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 2257
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 3119..3146
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 2053..2100
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 2278..2281
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_RNA complement(90..197)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 726..734
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 2274..2277
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 51..639
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2161..2185
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 206..211
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature complement(3292..3332)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ rep_origin 760..1008
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ terminator 3032..3103
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 3158..3161
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 3173..3178
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(3376..4191)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 2258..2262
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3342..3365
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3204..3227
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 2256..2273
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 72..77
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 2029..2052
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 1009..2028
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3237..3265
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3154..3157
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 3180..3290
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 2212..2236
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1..24
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ORIGIN
+ 1 tcacaggatg gtccaacgaa actaggcttt agacgaggga tgaatgaccg acccccactc
+ 61 gtggcactaa cggacagact tccctgacgg ttattcgacc attaaagtca gacatgcggg
+ 121 ggtgaataaa ttagccaaat tgtgtcgaag aaaagacgtg cggctggcac ataaggcagt
+ 181 cttgatccta gtcttgcagg gatgcacgta agtcgcctca attaactgca gccgagctcc
+ 241 aggttaccaa agaccctagt atgccagggc ctaacggttg gagtatatta tgggtacgca
+ 301 atagtgcgga agttaacctg ggcaacatcc aggtgagagg ttggacggaa gcgacagtaa
+ 361 gtggccatag actgccgagt cgtgttaatg aatcgctata cgcccatgga gttgtggggt
+ 421 cgttttatcc gagtaggggc ccgctgacta cttcgtccag acaatatgcc gtcttcaata
+ 481 gtctacctga gagtcatgcc ggcatttccg acgctgagtg aaacccgcgt agccaggcga
+ 541 aatttgcatc ttgaaatacc actgcagatc agccagtaag gcccatataa gggcgctggt
+ 601 gttctggcga cagataaagt gttatctaat gtaacccgcg gacttttaga ggatacttga
+ 661 atgcgggcat atcgtcccac cagcgtcacg tggtcgggct agcggcagac aaactctgcc
+ 721 gatgtttttc tttgccgcga tagcgggcta gtcaattcac tatccggcga tgaagcatag
+ 781 attgttatcg cgcttatgcg gaggataatc aagtcttggc agaacctgct cgctcatgca
+ 841 ctggtgaggc gtggttatcc taacaaccgc ctaggacgaa gaatgggctc ggtagggaca
+ 901 gttcgtgcgt ttagcttcgt cccatcttaa tgctgtctgg agggaggcta catgcgaaca
+ 961 gaagccgtgg gcgaaagttg ttgatccggg tctaacacgg ataagggcca tggtgaacgc
+ 1021 atcatgcgat acttcttggt agttcttcta acatgaccgt gccatagccc ttaccctttg
+ 1081 aagaagttaa cctatctgcc gtctcctgca cgaatagcga ctggactcgg gtattttgga
+ 1141 tacctcacga aagcacttcg atcggccgaa gcatggatat ttcgccggac gggcccgaat
+ 1201 agagagcctt gtatgtcggt tagtacaacg cagtcctgga gacatctacg cggatgggcc
+ 1261 taggggctgg acttaacatt gggtaacgta cctggtccaa agtgaatgca aagcactttt
+ 1321 acaaagcgcg ggtccccgtg ggtgtttagg gtagaagatt ggcggatgct acgaacgatc
+ 1381 ccgctttgaa actatcatta catcgtgtaa aagagacact taacaaaggc caataaactg
+ 1441 ccagtaagaa tcgctcagtg cggtgctggg gacgctaagt aggggcaaca gccagtgaag
+ 1501 gacgtgaccg acctttctca gataagatat gctggcgtct atctaataag catagtgaaa
+ 1561 aaccaaccat ttcacttaca cgaagtacat ttgcattgct agtaaagacg cctaaacaga
+ 1621 agtgcccttg catgctgtat gtctatagtc cttagggaag catcagccct tctacttatt
+ 1681 cgaggtctga gaaaccctgg acaagctccg aattattcaa tgtgcctgtc tccgaggtta
+ 1741 gatagcgcta tgctcttaag agttgcacag aatgaccatc ctggaatgtc cctggagggg
+ 1801 tctaggtatg ctgatcgaag ggtgctctaa ggacttgacg tgcgtccgag gagggtgctg
+ 1861 cctccttcgc ctttagatcc aacgcggatc acatgcgcgt gagctaatag gatcaccttc
+ 1921 tgctccgatt tttaccctcc tgggtcactt ccgaatgagg tagcgggcga aatataatgt
+ 1981 ctccactcgt aggtgttccc tgtatgtgaa gctctatagt ggacaaaggt ttgatgaact
+ 2041 agcccccgta tacgctctca ccgacggacg cgggggtctg ttatttgaag catcatacat
+ 2101 gcgaaggtgc cttctcagca acgaaaggta gtgggagtgt acaagttcaa tgcgccgcca
+ 2161 taggtctgag tatacaaggg gatgccccca tccacaacgg gattggctac ccggagagct
+ 2221 ggctccgctc caacaaataa ttatattaac ctattggaat tccacctgca tatcagagga
+ 2281 gagagacctt tacggctatt ctgtttaccg gatccatcgg taccaaggat cagaaagtga
+ 2341 cacggtttga acgggttgtt gtaatacttt gagtatacct ctgacgctga gcgtgtcgtc
+ 2401 ctgagcgcag actcaataac atagcagtcc gacatcgccg tgatatgtaa atgcaacgaa
+ 2461 tttaggtctt gactcggtct accatgtcaa aagggtagcc agatttcagc gcgaaattga
+ 2521 actttgtgtt tagtgtgggg tcctcggtta caaaatagga tcagacatgt gtgattttgg
+ 2581 taacctagtc tggcagtccg acagacttcg ctatgatttg atggggccgg cctataattg
+ 2641 gcttgcgcaa cccgctcatc tcgggcgtgt tttacttcct gcggtcccca cgccctattt
+ 2701 tcgggccagc tgtaggtgct agagtgaatg ctggcgaata agattccccg ctatttggcg
+ 2761 cctcgccaca gctctggcac tatgggggga gtttctctgt tccttaaaca gcacccgttt
+ 2821 ttgaggtgta ttggtttcgg ttctgcatta ggcaattcgt accgtacaat caattacgac
+ 2881 acattggcgg cagttatcag ctacccatcg caaagcacac acccacatgt atctattttt
+ 2941 cgcaaattcc aaaagcttcg attgagattg catcggtagt ccctcagaca tgtcgtaatc
+ 3001 gaatgcctct tgttccatga gagagagaag tatggcgcga accgctctgc ctttaatttg
+ 3061 gttctaccat ccacgagttt aaggggcata accctgccca gcactttccg aggctcacgt
+ 3121 tcatgctacg gtagcacctt tctgcgggtc tcacgctgtc aatatgcagg tgctgcagga
+ 3181 atttgtctcc aatcgacttg agatatcgca agcatgaaat tatattagac acgccagaga
+ 3241 acttgggaag cagcactggt agtgatagca acccgagtac agtaacgagt gagcttctga
+ 3301 tcatgagctc tcctacggcg tcaatgcgac gaatgcccag catgcactct cgctatccat
+ 3361 gcctgctagg gtggcattat gctcaggaac agttgtagct tggatatcgt ctagatgaaa
+ 3421 tacctggaca ctggttagcg tcgtcaagca ccaaggacat tcacacgctc gcggtctttc
+ 3481 gtctccctaa gcgttcggca gtcgggcgtg aagaggttgt aatcagacgg aacaaagcct
+ 3541 gaaaaaattc cagcgacgta gtattcatga tcctgtacca tctgtagccg ccgcggcgca
+ 3601 cgattgaatg taggctacta accccatccg tgttagcgat gtgagtttct accgcaacga
+ 3661 atgctcaagc gaaccttctt ctttcgtccg caacccacaa gccgtggtta tgacagctaa
+ 3721 attgtcccag acatcccttt attacacaag agctccagcg gaatacctag tcacagcggt
+ 3781 aatgacacaa agctcttagt tagtccaggg actacttctg tctacagcac atcacactca
+ 3841 ttatcagcat cagtgtagag acggagaaca tgggctatcc tataccaaga tccgccatct
+ 3901 aaacatttga agtttcccgt cttctataac ttagcactcg acgctattct gctgagtgcg
+ 3961 cttagtctgt agcgacttgc gaaatccata aactgagaat tgaaagagag tgcataaccg
+ 4021 aaacctttgt ggcatatttc cgttgaaacg taccagaaca gccgtttagt gcggaacata
+ 4081 cagtatcctg ataaagcact caacccaaca gacaccctat gccgatagcg ggatgctaac
+ 4141 aagtatagtc atgatgattt ctcggacagc ggggtttggt acagctgcaa tccgtgattt
+ 4201 aaattcggac ctctgcacac accgacggtt acccatatcc tctacggctg taggaagttt
+ 4261 taccttggat gtcattctga tttcggcgta tc
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,124 @@
+LOCUS part_B 4259 bp ds-DNA circular UNK 29-OCT-2019
+DEFINITION .
+ACCESSION part_B
+VERSION part_B
+KEYWORDS "Source" "Sequence" "Freezer" "Shelf" "Box" "Concentration" "Use".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ primer_bind 531..550
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ terminator 3078..3135
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS complement(join(4216..4259,1..616))
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ exon 2863..3060
+ /label="feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ gene 2863..3060
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ terminator 4101..4195
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#9eafd2"
+ primer_bind complement(3410..3429)
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind 778..796
+ /label="another feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ misc_feature 859..862
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ primer_bind complement(3159..3176)
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 863..3060
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ rep_origin complement(3330..3918)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3061..3064
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ terminator 800..843
+ /label="another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ORIGIN
+ 1 cgggtctagc cacgcggctg aaaatgcgcc tcaccaagtt cagagagttg taatttaaag
+ 61 gaccaaagaa cgtccattat gaagacacca atgagaaaag ttcattgcga tcgcagctta
+ 121 gactgacgtg aagttccaac atttggcata cgtacttgtt aagttcctcc ggctatatgc
+ 181 gctaggcgca ggtatattag ccggacatct gcaaggttga cgctgaagcc ttatcggtaa
+ 241 tgcaagcaca acggtattgc agacacacaa taggaagtta tgttaacagg agagggtgat
+ 301 gccgatgatt acgccccgcg tcgacagtac aataaaacag ctagatcatg tcgaaagtgt
+ 361 aggcaaaaca ggtaggtgca ggacaggagg gttccctcaa gtcggcttgc tttatgtggc
+ 421 gaatctgata cccataccgg ctatacatcg gccagggaat atcacagatt ttaaatgagc
+ 481 ggagatagac ctatgggacc gcatcgatgc aagacatcgc ctacagatac ataatctgga
+ 541 agacgcagat atcagtacgc tccttcctgg gaggcgtggt ccttggcacc agtcggccac
+ 601 cccttagcgt ttcacctaag caacgaatcc aggactcctc ttttagcgtt tgggtgtcag
+ 661 gcgcatcagg agtggttaaa tgaacgctgt acttcgcaag ataattgtga agatctctgc
+ 721 tattccttaa cattaccacc aactttgcct acatatggcg taatcaaaaa tgcagcgggg
+ 781 tgctcgatcg tgaaccctca atcacgatgt gctatggcgt agccacacaa catagttccg
+ 841 gtctggaatt cggtctctgg agagcatacg gtgctctggg ctcacacgta cttcctcttg
+ 901 tcacgcgcct ttgtagagca ttagggcgga ggtcactggg acggggatca gagagcttaa
+ 961 aatcccaagt agcagtgcct aaggtgtaga atcttgtgca gatcttcgtc tggcccgaaa
+ 1021 cctgggcctc cacaacaatg tcgggtcttt tataatttga aaacatcgcg ccttacccgc
+ 1081 accgcgcagg acgattagac acagggggtc atgtccatgg ttcggggtaa gccaaattta
+ 1141 catcgagtgt gggcttcatt gaggagaggg cgttacgata cccgttaaat gaaaacccgg
+ 1201 acagtctcta actgataggc ctgataatcg ccaaatgaag tcgcaattag cagtacatga
+ 1261 ctggcagata tgtcgccgga gacggtatgg gggacctatc ctaggttggc acgcgagcgc
+ 1321 gaatgacgcc tatcttatcc ccctgcacgt gatggtatcg tcccaactat cttttacctc
+ 1381 atcaacgttt tcctgcataa tctgcaagat ggagagtccg cgagtgcggg gagtacgaga
+ 1441 tcacaaatct gccctgaaga caaagctcgc aggccgtact caggaaatag catcgactca
+ 1501 cacatatcgg gaacggcaaa gagtgcatcg gccaatgcaa actattgaac gtccatgaaa
+ 1561 ttgtgtcaaa ctactagtgt gtggacttgc gtcaaggcca tggcgcaata ctcaaagccc
+ 1621 cggtatttat cccccgcaga gtatccgtgc ggatggagtt ccacagctct ttggacatgc
+ 1681 aatgcgtggc gctacatgct ccgctgatac agaatatcta atgtctcgcc tcttgccgtc
+ 1741 gaccctacaa ctactgcacg ggcagagtgg acgcgacccc tgagcggtgc agaaccttag
+ 1801 tataaggcaa gggtggcacg gccgagccgc acttgctcct actaggccgt gctcgaagct
+ 1861 attgatgcaa gcacagtatt cccgatttgt aaagcaaggt gcccgtagcc atacacccag
+ 1921 ctactcaccg gccaatttcg accctctcta tctcagacct ccgcatattc ccaaactcct
+ 1981 gctcaagtat gaaatgaccg gctcctccta aggcctgcgg acatggagtc atgcgtggaa
+ 2041 tgccgtgtag gtagggtaca cacagcctta ccatgtaggg caataaatta tagactactg
+ 2101 acattgattc cttgagggcc cgttcacttg tgggggaacc aggaaggcgc cgatagtcat
+ 2161 cacttaaaca catgcgacgc atccatttca agaaagacac gctacgggtc tacaccgcct
+ 2221 atagttctaa tttgggcccc ggtacgcaca tcgatgtact ctccattaca gcatagcaca
+ 2281 tcagcggccc tagttagcgc ttctttttgt tccaacattc aatagcgggg actgcattat
+ 2341 cctcacccta tttgttgcat aggtatttgg ccgtatactt gggaaagagc aaccacggga
+ 2401 gtgcactaga aactgattca cccatgttat aacgcgttgc tcgcaagtcg tactgtggcc
+ 2461 acgcacaggt caggcaatcg caaccatgtc ttagcagttt gtaagaagac ctttaaacat
+ 2521 gtacctcaca gcaatctcgg aacttttaat tttcctgagt caatgacatg ctagctccgt
+ 2581 ccacttgtaa tcaccgtcat aacacagtta gcctgcaaaa gggcgtgtac accttgccac
+ 2641 tttaaagctg accgaataac ctacctacag gagatgctta gtgccacgga atgatctcgc
+ 2701 aatgcttagt cttacaccca gtgaatcaac ccaagacctc gccgactgaa cggtattgag
+ 2761 tccaatcccg agaggcaatt tatggccgtt agtgacagtc ggtcgctgat agaataaggc
+ 2821 agactcgtct taagcgggct gctttaagag aaaatggagc cctgacgaag aagtggatga
+ 2881 accaggtttt gacaacgtcc catattggta atgtaggctc gttatcaaga gataggttta
+ 2941 gaaggctcaa tgctcgacgt aaaagaagtc ttaagctcta tgagccagtg atgagagcta
+ 3001 attatagggc gcattcgttg gggtaaggtt gcgaattgtc atttaactaa aaccgacggc
+ 3061 aatgtgagac cctgcagtcc gcctacacct ggctcactga ggcggcaacc gttatcgaag
+ 3121 cagcatgtat tggtagtacc tgtcgccgat ttccttggga gtgcgctgtt gcgataacgc
+ 3181 ttatttatgg tttgcgcggg atgtatctaa tgcggccgcc gcccgatcag cctgaacact
+ 3241 gcggtcatga gccggtccat catgcagttc gcctgtaatt ataacctatt tgttaatggg
+ 3301 gcttacagag gagcttccaa cgcatctacg agtaacggct gggatcacaa cttagccacc
+ 3361 ttgtagcagg gacataccgc tttgcgacta ctgcgattct ctaacgagtc ttctgattgg
+ 3421 tcctatgctc tttcaaaatc tcgataccgt agccaaccct gctgcccacc ttaaactatg
+ 3481 acaggacaca ccattgtgcc aacctacacc ttaccagtag ttctgctctc caccactaat
+ 3541 acgatgtcag aggccagaag gagcaccgtc aacaaacgcg ataatcaggg cggcgaagat
+ 3601 ggaagtagct tgggttgtcg gtgggcaggt caggcgttag tgttatttga ataccaactg
+ 3661 ttagaccaca gcgactcgaa cagtccgcaa gtcaagtgcg gtcggctttt acaggtggcg
+ 3721 gattttcatt ccaccattcg ggtctaggtg tggtactaac cgcggtcata cgtggagttg
+ 3781 aaccgcctga cgcactaagc tatgcgggca acaatatcgc caaagtcatt gtgttgggtt
+ 3841 ttcacaacag tcacttcgct cacggccgaa ttaaatatct ctaactatta agccattttc
+ 3901 caaccatcgg ctatcccagc ggttcaatcc gaatcgttac cagtgggtag ctgcagagga
+ 3961 tcctaagggc gggtcccgct tactgtaact cgtcatgtct cgtggtctac caattcggtt
+ 4021 agtattcgtg ccatgtatct cataagggtt gcagtttcgt cattgtcgta gttccttaat
+ 4081 ggactggtac gacccggttg ttatacaacc atcaatcgtt aacggacatt agtgagccga
+ 4141 ggagaagacc catcagcgga taacccgcca ttatcaccga tactgacata tgagtgccat
+ 4201 actgggactg gcttcacgtg agggacctca aagtgagtcg tacaaggcag ctcctcaaa
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,99 @@
+LOCUS part_C 3423 bp ds-DNA linear UNK 20-NOV-2019
+DEFINITION .
+ACCESSION part_C
+VERSION part_C
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ CDS 18..3275
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 3276..3404
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2486
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 3411..3423
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 3407..3410
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 14..17
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1..13
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 3131
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 2078
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 14
+ /label="feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ORIGIN
+ 1 tggctaggtc tccaatggtt tcaccggagc tgagatcgca ttaaagtcac actacgaatt
+ 61 atttgtcccc gcggctccag agacaaattt ctaggagtgg gttcatggag aaccgtgaca
+ 121 agcatggtag cttcaaatag cgtcatcgga tcttaaagtg attgtgacat atatgggatt
+ 181 gcgcgtctct cttacacaag ctagtgtgcg cgaggtgctg aacacctatt acgtcaactc
+ 241 ccgggatccc ggcgggttac agagacataa gcagggtgtc catcattaac ttcgatgttg
+ 301 agcccgtgcc ctgatcaaac acctctcgta gtagtgggtg ccggccgtgt attattttgg
+ 361 gggagaggat gcgccctaag caatttcttt ccatcggcca gccattcgac gccggcacgc
+ 421 aagttgttgc gggcactgtt gcagttcccg tactagagtc tcaagtctag aggtaccagc
+ 481 atcaggaaga tgggtacttc gtgtggatct tctcctgaac ctgaaacctg aagagctaaa
+ 541 gcgcgtcgcg ctgccatacg ataagtcgct ctcatttccg gaagacgtcg ttgggtgatg
+ 601 gcgaacaatc gcgaaacgaa aatcgcggtc ggtatgttga ttcaagacgg gctacgggcg
+ 661 ggttactaac aggtgcgcag aaatgtgatg ggtcacttga ccatgaactt tcgcgccgtc
+ 721 gcttctgtgg actggccggc tccctgatag tgcactagcc cgttgatatg cccattacca
+ 781 tttggcggcg cagtgtgcca gcgggattaa gatgcgtggc gtacaactat ccgcactttg
+ 841 ctgacgcaca aaggcaactg atggacagcc ttcgggcatt cgactggttg gctgagttcg
+ 901 cctgcctatt aatatgcttg tggaaattga tttacagcgc ctacttctac ttaggtgtac
+ 961 ctatttacgg cacagggata aaggctgaca gaaaagtcct ggacaggtca taggtagttg
+ 1021 tcagacctac aatggtataa cttgagagtc ctgtaccgca catgcggttg tagctagatg
+ 1081 tccagaagac cgtagctagc gacgagtggg ttgcacgcgc attttgggaa ggggctgcgc
+ 1141 gagggtgggg tcacgggtta ttccatttct aaatgctaaa ccagcagttg ctttagttct
+ 1201 gacctagcag gcatgtcata tgtatggcta gattattagt acaatgcagg actaagaaag
+ 1261 cctgagactt aaatgcgttg gtttttcagc cgacgggccg ggagggcaga tggccgaatg
+ 1321 cgcactgagg agtgcattgc gagggaatag gcggaccacc aggtcccctc acatactgtg
+ 1381 gataaaccta cccagggaca actcacgcca tcattttcaa gagtagcact actttccact
+ 1441 aagtacggtt tgtcgagagc cggtggcacc gtgcgacgag cttgtgggca ctaggcgaac
+ 1501 cgggttatat aggactgcct tgcggtgcgg gaatacttta ccccgtggag aggccataaa
+ 1561 agcttacatt tattgtagcc gctagcggtt tcgacgcgct caagtggggc tttatcttag
+ 1621 agtatcaaat aatgccctct cagcttcatc ttgatttttg tgtttggggt agtgtatccg
+ 1681 atgggtcacc ttcttgacct tggggagctc catccatcgt accaatactc cgtttctttg
+ 1741 tgttgcctac cgagtaatcg aataccgcac gagggctaga atctaattta aggtgggtct
+ 1801 tatccctgtt gtttggacct aacgctgtaa caaatcactt ccgcgacggg tgtcattacg
+ 1861 tcttctatcc gccaccggtt caacagtgcg tcgaatgcca agtccctatt acccgcattg
+ 1921 taaagccatt acaatacctc cggtgatata attgattgcc ggttggcaag ggatcatctg
+ 1981 tacgggccgc gattgattgc tgataaggaa cggcggtaag gaacgtatcg cgtacgaggt
+ 2041 tgtacactgg aaccgctaaa caagcggtat cgctaaatta ccggcgatta tatcaaggga
+ 2101 atcttaggta gcacgaagcc ctacgccctg gaaacaggat cggcgcgagg ccgtggacat
+ 2161 attagcctac gtttttttac acccagattt ccgacgatgt ccacagctaa ggctatccta
+ 2221 aaccgcaaac acatataacc gcagtataaa gcacgggatg attccttggc catcttgcaa
+ 2281 gcagtgcaag gcaattctgg tgataggggc aaggcagtga accgagtggt cagcgtattg
+ 2341 tgaccctgca attgtcatgg cagataattg tttatgaacc tgtttcacac acccatccct
+ 2401 tggatctcca gcgtagttac taatagtacg atttcctggt gttctgtcac ccgccttgct
+ 2461 gccttcacgc ctgccccacg ttttgctgtc cactgaatat cgctctaatt aataggtgtc
+ 2521 acactgtatc aggtaagtcc attccgggtg ctattggatc attcctgaga tgtaccaccg
+ 2581 atcccatagg cgttaggtct tacatctgga gtgaaaaaga tcagcatcga actataggta
+ 2641 gataaaggtc atgactgtta acagagaatc gttcctatcg caaccttcac taactggaag
+ 2701 gcacccccac actttgatta gtaagcccct agcgaatgta gtgatccaag aacatcgagt
+ 2761 atactttagc tctcggttca ggcatgtatg caatcgacca cccttccgtt cagagtactc
+ 2821 tcaaccagca gatttctaaa ctttatagcc tccgcccact aaaattgcct tatctcaggt
+ 2881 tgactcttgg atgtagctgt aatctaacat acacatggag ctgcggcaaa ttatcgtacg
+ 2941 tccaaaccac caccggatca gtggcgatac tattctcgca aaaaagccat ccagcattgg
+ 3001 aacaagtgtt aaccagcatt tttctgagtc ccccggaaag aaagttgact acactacatc
+ 3061 cataaatgct agagtgtgga ttcgccatgt gttacaacgg tcaaccgaaa ggttagcatg
+ 3121 atacttcgtt gttcaatcgg acgttcgagc gccctccctg tttatcactt gatccccctt
+ 3181 ttgaaacatg tgcgctgcga cgcagggctg ggagagtcac cggaaaccaa aagcccgacc
+ 3241 tcggacgtgt agggccctcc gtttgccatc aatggcgatg taggattctc ttttaataca
+ 3301 acgttcactc aattaacgtc ttggtataag cgtcgaacgt gaccgaggtt gacaccagtg
+ 3361 tcacggctgc gccggggttt gttgctccgc gtgtacaggg tattggttcg tgagacctag
+ 3421 cca
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,96 @@
+LOCUS part_D 2682 bp ds-DNA circular UNK 30-OCT-2019
+DEFINITION .
+ACCESSION part_D
+VERSION part_D
+KEYWORDS "Source:Subcloned from vector Andrew" "Sequence" "Freezer" "Shelf"
+ "Box:Mobius box" "Concentration" "Use:Mobius".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ rep_origin complement(262..850)
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2642..2671
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ terminator 1991..2034
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS 2054..2566
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 1919..1938
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ misc_feature 2050..2053
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 2576..2641
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ terminator 10..67
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 143..162
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ misc_feature 2675..2678
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ CDS 2618..2641
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ CDS complement(1148..1807)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ terminator 1033..1127
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+ 1 accctgcagt ccgtgaatta agaccaatcc actggagctc tatacaggac atcagcgatc
+ 61 ggtcgagtaa aaccgagttt ctggactccc ttagtctgag aattgtacct tattacgaat
+ 121 ccggaaatga agtgcgctca taaaatcttg atcgctaact gttttccgct ttttgaacct
+ 181 acagtcagct atttcgccgc aagcgaggtt tatccccttt tgtgtgtgtc agcgggcgaa
+ 241 cgtggaggac aattatgacg aatgcctaat aaccaacgta ggcttggctg gtgaggacat
+ 301 tgcccttccc cttctactaa ccagtgttgt tcagatcatg taccaagtgc agtaatgcta
+ 361 atcccctgaa ttctgacgtt ggatttggag cgtgattggc aattatccgc tgcaaggcgt
+ 421 agtatcgcta tctgggaaaa cttagggttg caagcaaggt catcgcccgt ctctagatcc
+ 481 gacgggagcc tcaccctgca tgaggaagtc ctaatccgct ctaaacaaga gctgaacact
+ 541 ggatgtctcg cagtagattt gctagaatgc aatgctggct cgtgtgcagc ctcaaggtca
+ 601 ccatgcttcc gttaaattcc acgctctccg agtctgctgg ttcgggataa atctacgtga
+ 661 cattcgcgag gtcccggcct gtagatcgtc tcggcaggag agaacacggt tgatccccca
+ 721 cgcggaaccg atagatgcca ggctagatga tgactgaagg tagtttgtac gagtgacctc
+ 781 tctagccaag tattttcccg tctcttaagt tatagccgct ctcattccgg gttgtgatat
+ 841 ccttcatatc cactctctgt aaaatgctgg gttgttcttc tctccacggt cagggaatcg
+ 901 cctcttttcg gataaacgac attatttcgc gccacagaac ggtttggggg tcgaaggacc
+ 961 ctagactttg ggtatcccac tcttaccgga tggtaccgct atctccccag ggtccatcgg
+ 1021 aatggctagc cacgttaccc ttatctgtca gtatcagtct cagacttaag tataccacgg
+ 1081 tagcgacagc tgtcttttaa tggcccgggc agggagccgg gcccaccgtc catggtccac
+ 1141 tgtaagggta tctgcaacct tcgccgagct tcttccccaa ggaggtagta ccttaccaaa
+ 1201 cttccgagtc agtatcgtca aaggggcccc tagggctcac accatcgagt ttccgcggct
+ 1261 taccagtcta gcctgatatg tttcaggtca ggaaataaga ggtatagccc cgtggacacg
+ 1321 tactgttcga gcggctagat gtaggttgag ttaagtacag tagacgcgtt ggataccgtc
+ 1381 gaacattact ccgtctgcca agggtagccg agtacttctt ccggctcggc cattccgact
+ 1441 aagttagttt cgaattgacg tgccaaagcg tggctcccag tcatttgtcc ttaaattaaa
+ 1501 cataagtttt ttacctgctc gcgtgccggc cgcttgaggg ggcagcaaga agtcggttca
+ 1561 aatggggtgt taagaccggt gttgcaagcg gaccatccag agttagcgtc ctcgacgaaa
+ 1621 cgttaacaat cgtgagatta gaggtcgaat atccccttcg tagggggttt tattgtgcaa
+ 1681 gatgcgcaaa tgaaccccaa ccttgcgggc ctgtagcgaa caggcgaaaa ggtccaatac
+ 1741 ggcgcccgat gcaccgtaaa acaggtcctc taactgtgtg ttctacgctc tccggatcct
+ 1801 gtatataaga acgaatcccc ttttcctagg gcccggccgc gtagacccag tacacttgac
+ 1861 tttcacgaag atccatccta ctcccatacg cttgagagtg ccaacgtagt ttgtaaccga
+ 1921 ccttgcctcg gctagaaagg cattttgtcg catgtggcca gcctgtcagg gcgtgctcta
+ 1981 ggcttgacga ttagtgctac gggatgattc gtaaccgagc tgacgggacg cctctggaat
+ 2041 tcggtctctt tcgatggtgc ctcctctacg tagatctact ggataaccgt ccccaatatc
+ 2101 cgcttcccaa cgtagattgc cgacaggcat aagcttcggg ggcgcaaagg ccgacgtccg
+ 2161 cattgcagtg tagctttgtg agcaggaagt gtgatagtct ttcgattatt aaagtctgag
+ 2221 ctgaatgaaa aaaggtccaa cgaatggagg acgcgaagac atgggtgtct cttatggccc
+ 2281 gagcgggagt aatggcggtt cgtacataaa ggctgaaagg attctggcgt tagctgtctt
+ 2341 acgttggatt ggcccttcaa attatcgatg ttagctgatt cggtgtaccg ggcgaggaaa
+ 2401 gcgctctcag aacaacttca tatacgaggt tcgactataa tggtctaagc tcctgggcta
+ 2461 gtctcaagaa gcgggtacct ttagtagcac gtatcgacgg caaagcaaag aataaaaact
+ 2521 tggctttgca tcgtgcaaag atttctaact aggttgttta agggctggta tctatgtccc
+ 2581 gctataacag cgcgcctaca gtagaagttt aaccatgaca tacctttgaa gtgttcgtat
+ 2641 cacacacaag gaaggagcat gtggacacca ctgagctttg ag
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,38 @@
+LOCUS part_E 347 bp ds-DNA linear UNK 20-OCT-2019
+DEFINITION .
+ACCESSION part_E
+VERSION part_E
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ 3'UTR 21..330
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 1..13
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 18..20
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 14..17
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 331..334
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 14..17
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 335..347
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ORIGIN
+ 1 tggctaggtc tccgctttga tcagcacgcg tctcagagtt tcagggggac ccaaattact
+ 61 ggtcctcaat tgggacgcga ccgcatctcc ccacgaaagc ttatggggat tgcccactgc
+ 121 ccagcttcaa atctgaaggt tcggcttatt gacagggtct aacacgcagc tcaactgctc
+ 181 gaggttagag gcgtaatgac gggccccgat agccttctac gattacgtcc agcaggaacc
+ 241 ccacagcttt tccctacgtc taacaccgtg aaagcaaaac tgtctgccct tttacatggt
+ 301 ctttaaggaa tctctgcact tatgttatta ggtatgagac ctagcca
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,74 @@
+LOCUS part_F 2470 bp ds-DNA circular UNK 20-OCT-2019
+DEFINITION .
+ACCESSION part_F
+VERSION part_F
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ terminator 1991..2034
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ terminator 10..67
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ rep_origin complement(262..850)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS complement(1148..1807)
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 2054..2462
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(2351..2371)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ terminator 1033..1127
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+ 1 accctgcagt ccgctcacgg accgcaagga cgggctaatt aggaggcaac gccgatgggg
+ 61 ccgcagttca gcgctgcaat gtttgctgaa cagggatgtc acgcatactc gtctacaccg
+ 121 cccgtgaccc gttatcacgg ttgaagtgtc gaggactagt gctgccgctg cgtgagggac
+ 181 acaagctgct atttgtccat acgccatgtg ctccgagctc atgctgccat gagacaatga
+ 241 gacatgtcgc caataatcga gtgacgagtc agaatgacct ggctccgcat aaccgttcaa
+ 301 agttattgac aacgcatctt tcgtagttcg tgcagcagcg gtctttcttc tatagccgac
+ 361 tagatgttaa gggactcctg gataccgcta gttttaccct ctccaggaag ccagcgaggg
+ 421 cgtgccgcaa gtcccaatag ataccgggca tgatcaaggg gccctgtgct ctgagtctgg
+ 481 aggcgacagt gcgctgcagc tcagaggtgg ttattgcgaa ccggcaccgc tggacagcac
+ 541 ccacggggac acgtaagtaa tttagggtct gggccaacgg ctcagcgcca gtaggattaa
+ 601 caaactcgac taatcaatgt gccagctact tccgccgggt ctgacggggc ggcacccatt
+ 661 accatgtgta ctgaataggg attccgagcg accgtaaagg cgttcctaag tgtcatatac
+ 721 tggcaactag aggcactcac atcggggtta agggcccacc gtaatggcca cgcaggatac
+ 781 caattggccg ggtgaggatc tattcacgcc gatggggagt tctaagcccg agttattggt
+ 841 gctagtggct tggacctgtg tgtcgatgat gcgcgatata gaggcgcggg actagctggg
+ 901 gtccacaggt gctatgttgg gtgcgctcta tggacgtccg gaaagagact aatgcaacgg
+ 961 tatggcatca agcgcgaccg atggggagac tggaaattgt gaaatagtgt actggcgcga
+ 1021 tcattaaata ttgcatacgc tgtccgttat gacctagagg ggattatttg aacgagaggt
+ 1081 cttgggaact gcattggaga tggtcagatg gaatgcgaaa tgtatcacca cgggcggccg
+ 1141 aaggggagac agactatccc tagttggctt cggtaaccgt aatcagatgg aacggcgggt
+ 1201 aatgctgata ccgagcgctc gtacggcgcg tggtgatgac acggtctgat gtcgtagcaa
+ 1261 acgagccggt cctcgtacaa caggctcaca tctcaatcac gcataccaac cgattacata
+ 1321 acgcgatcta tatttgggga actctactta ctaccctgtc tgcagagtgc gttctatgat
+ 1381 cctcccctac gtgacggcca acgattagtc ggcctaggtc taacggataa aaggactccc
+ 1441 cagtacatgt gaccatatga gccaggccgt cgagcgcgac cactccccag cctatagtga
+ 1501 ggaggagcgg tattcggtta aagtttagct agcgactttt ttgtcaccga agtagggacg
+ 1561 ggcatattgt ttacccttaa agcggggatc aatccattgg ggtcggcagt cataaaagga
+ 1621 tctaagcccc caaagcgcat ggtaaggtac tcccgggttt cccgaaatct aggcaagtct
+ 1681 cggtgggtgt cagcctgacg agtagggcac gttaccgagg ccacggtgct tgatgactac
+ 1741 gggtgaatcg aaccgatcaa acgcacagca tctaaaccct ggtgtactgg tccacagggg
+ 1801 gacaagtctt tgaagtgtcg cttcagatga cggccgcggg ccaatctgaa ttgttagaca
+ 1861 ccgacagtag ggtgtgcaac tcgctcgggc aagagtgtaa aggcacatcc tccccgaggt
+ 1921 aagttatacc gctctaacgg cgcgggcagc ttttcaactc aacacttccg cggttcagtc
+ 1981 ctgagcatta ggctgcatgt ctatcacaag aggtgcgggg aacgacaagg gctctggaat
+ 2041 tcggtctctg gtaagctccc ataagagcac cacttcgtgt accttgctaa ctcccttcat
+ 2101 ccccacccgc gaaaacttaa gacgtcaccc ctgttattat cccgtgcact cctaaagtgc
+ 2161 gatgggcaag aacgcaaaca attgtctgag atttatatgg gcggcggaca tagtcagaga
+ 2221 gccttatata atctcccacg tcttgccagt ccgagttatg agaaacccgg gaccgatgac
+ 2281 gctattacgg tcgcccagcg aggttcaaca gagcgaggca taggagtcat tacgcgtgtt
+ 2341 agcttcaaca tgcgtggaag tgaaacggat ctataaaacg gcgtggagtc atcagcttga
+ 2401 gcagatctaa cttactcgcc acgcgcgcaa atcgtctttc gctgtccacg ttatacgtaa
+ 2461 ctcgcttgag
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,36 @@
+LOCUS part_G 1119 bp ds-DNA linear UNK 25-OCT-2019
+DEFINITION .
+ACCESSION part_G
+VERSION part_G
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ GoldenGate 1..13
+ /label="feature"
+ /ApEinfo_fwdcolor="#faac61"
+ GoldenGate 1107..1119
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ORIGIN
+ 1 tggctaggtc tccggaggaa cttctatggg acgaaagatg cgcagctcga caaatctcaa
+ 61 attggaaacc gtctaaggtc tttgagccca cgctaggcca ccgaatagtt gcgagctcgt
+ 121 gggcaattgc tggctagcgg tttgtatcgt atacgtaaca agagattgcg ccggattcat
+ 181 tcgtgtgggg tgctttcaca tcggaatact caagagtggg ggtttgcgct ttaatatgac
+ 241 ggcctcatgc accccaaaaa taagagcgcc aatttcatcg accacattcc ggacaattct
+ 301 gacttccctg tcggatcgac cctcgctcac aactcctaga actccaagac ggtaggacgt
+ 361 cagccgaaaa ggaggagtga cgacgggccc tcctagctga agcaatgggg ggcgtcgacc
+ 421 ctagcctggt gtgggacttc ggagggtcgg gcgtgtggcc attcctgcac gaggggccct
+ 481 tgcagtatcg aactttgacg agaaagtggg gggcgaccta taaacatagc ggagttcaat
+ 541 actcctgcaa gtgcatgatg acgttcagcg ttggcacatc gaacgcgtcg ctacacttgc
+ 601 tcaccggaag gcaaaataga ccggcagctg gcccgcacgg acgtctagac tcctacgctg
+ 661 tcaaatgcac gatgactatt agcatgcgga attcgaggcg gccggtacat cgagacacgc
+ 721 tggtcttaat acctgtgtta tgtcaaaaca agtgtctcgg cggctttgta ctacgctgtg
+ 781 aatgcgcatg atgttgcgag aagctgaacg ttggtagcag tctacaacag aaccgacgag
+ 841 ctacggacgg gttacagcag gatcccctct taaggcatta ttcgacgact ccaggttcta
+ 901 accgatcagt aattgcctcg gatggtcgta cgtgttaacc gagacagcaa ggcaccacat
+ 961 agacaactgc atagggcgcc tacaggtcca caatcagggt ggcccaagat cctcaaagac
+ 1021 ttgttgcagt ctctgcttat tccgtttaac acgttgtgtg agctctagct tactacctca
+ 1081 tcggtgtcgg gagtgattta ggaatgtgag acctagcca
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,109 @@
+LOCUS part_H 4246 bp ds-DNA circular UNK 07-NOV-2019
+DEFINITION .
+ACCESSION part_H
+VERSION part_H
+KEYWORDS "creator:militzis" "marker:SmR".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ primer_bind 1966..1982
+ /label="feature"
+ /ApEinfo_fwdcolor="#a020f0"
+ terminator 3774..3860
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ rep_origin complement(63..651)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 2015..3667
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ promoter 1987..2005
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS complement(744..1535)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 3667..3670
+ /label="feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ terminator 3952..3979
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ primer_bind complement(3694..3710)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#a020f0"
+ORIGIN
+ 1 aacatggatc cgttacacaa ggtctactcc gcgatgtggg ctcaccccct agatcccttt
+ 61 tcctaccgcc cgatcgcaaa ctacgcgtag cttcacggct ctctgtctgt cggctgacct
+ 121 gcggctcatt tttcatccat ttagtatagg ttgcaagggg tgtgactgat ttctctacat
+ 181 aaagaagcct atagtaccac atgcaatgcc gatccggtga gtgctgtagt ccttattccg
+ 241 gcttggtggc ctcctgccac ttaggatcgc aacggaattc tagttcctaa cgtcccttct
+ 301 acctgattaa gtgagagaaa acggaaccaa cctaagacat ctatgcatcg atgttttaca
+ 361 atgacgagag tgctccatgg ttcatactgg ggacatagtt tcgggcattt aggcccgcaa
+ 421 gagttcgggt atctagtttt tccgtacgaa aaacaccacc ttagaacagg tcacacgagt
+ 481 acagagagta aacccgtaat gttttcaccc attccccgat ttgactgcaa acaaacaagt
+ 541 ctccccgtat cgcttcattg ttttatcaac gggggcggaa tcgtagacca ataattaacg
+ 601 acaactctag gcttttcaac cgacgggggc aaagtctgaa atgcctgaga aaggcacaac
+ 661 gacggtggga ggggcccctg caaatattgt tctagcactc caggattcac accaacctcg
+ 721 gggccagcca ttccggtact tttggttata cggcaggata ccacgtccct aagcggagta
+ 781 tacacggagt tgccttagcc aggtacccgc ttaaccgtcc aactcccctg agtggtacgt
+ 841 ccatcacgcc gcgtaaacgg tttccaaaag agtaagctta ggcattcctc acctgtcacg
+ 901 tccctcttaa gatccctgcc tcgaactggg atcttgtaaa aatgtggcca tgggagcagg
+ 961 agttcatgtg gggcgacggc gatcggacgc ccctttaaac cagagccctt gacgctagga
+ 1021 gatcagtaga gttacccgga atgagatctc taatctaagt ttgatacgac gaaagcggcc
+ 1081 tgacgggcgc tactcatgct cttagaatcc gtcacttatt ctgccacaga tccgaggtac
+ 1141 tgtggatgtt atttgcggag actggcctcg gattaggggt actaagtccg agatgtcatg
+ 1201 agttaagccc aattcactag ttgcattgtc aacgagtgga cctccaaaac gatgttaggg
+ 1261 tcactacccc aagcgagcac ctccgctagg accacacacc cccactttca aggtattttg
+ 1321 ttcgcatcac ataccgtctt ccctttgcgg tctaatagtg aagcttggga caaggaacgg
+ 1381 ccagtcgcag caatactacg agtgagagtc ctaggcgcaa ctacgtaggt tccgcaaacg
+ 1441 tgttgtggat tactgttgag gtttgagttt atccggaggg ctgtgtaaga attaccagct
+ 1501 agtcaaaagc cctgcatggc ctgatctcat tagatacctc ggccgggccg aggcaaatcc
+ 1561 gtgaacaaaa accatgcatt tattctatca tagaaacatt tgttacacat ctactggccg
+ 1621 tgtgccgtga acaagaactc aatttagtta tcaagggact gctgtaaacg gagccgcgtc
+ 1681 acccgcgtgc acacgtgtag tgcttacgcc ggcccccgtc cagcgacacc gtagtcaagt
+ 1741 aaaaaatgcg tattcacgac ctcacgtacc cgtttcggag ggtgccttga cgcatagagt
+ 1801 tgtctgtgtg attggaattt gtaaggggtc cgcccatgta aaatagagcc catgtcttac
+ 1861 gaggacatga ggaaacatag gttctggtgg ccttccaaga agctgcctct acactccttc
+ 1921 tctttaatca ccgaaaacct taccttgaga ggacgtcatt cgtcaaaaca aaatattggt
+ 1981 ggcaaattaa gattaccact ataggcggtc tcaaatggaa gacgcgttta gtcttcggcc
+ 2041 cccagacggc accggcagag ccactgccaa tgccttttac gctgaactct tcgactttgg
+ 2101 catgtgcgac tgactatacg ccgatggccc taccctgcag cggaaaggca cagggccaaa
+ 2161 aacagtggaa gcgcaccgct agagctttac taaatccttt agggtgaacc ggtgttcagt
+ 2221 caacagaaac atatgactag tccttaatgg cactactaaa ggcggcccat ctcttttgta
+ 2281 ggtcacgtct catcgtttag caagcgtccg ccatccgagg agtatcctag tacgtgagag
+ 2341 ggtgttttac ctcatcacat ggtttttggc tagatgtggc agatgccagc tgatacctta
+ 2401 caacccgcta taacggtttc tggatcgacg atacaacctg cttcggcata tcataatggc
+ 2461 ggcctcatag gacttccaat catggttatg cgagtttgat gtgttgaaga ttgtgagggg
+ 2521 aaaccttttt ccgagtacgt tgaatctgcg actgatggtg aacaactcat cgagagggat
+ 2581 gtgcgggcag tctccttgat gcgcgaaaag gagtcgcgac cgcgtgttcg tgacgcactt
+ 2641 gatgctagac cgtaggggct cattatctcc tgaaacagta gctagctttt ggtgtccgag
+ 2701 tcagcttagg cacagtaatt gaaaagaagg aaatgcgtga aaactaaacg tagacactcc
+ 2761 ttgctaagaa ttccctggtc tttttcgagc atagactacc gtaggtaaaa ggcttgtcgt
+ 2821 gtcacaaata gacttgatct gttcggcata tacacatcct actgcttcag taaccaagga
+ 2881 cgattctccg gccattggac tgtgggacca cccgcgttca aacggaatcc tctacgaacg
+ 2941 gttaagaaag gagcccactg cttgcggaga catatcgttg ctgagtggta caccggtgag
+ 3001 tcaaaaagta ctgacactac tggtggactc tcgggtacga tgtgtggggt attggcatac
+ 3061 tatggcgcta agcgtggaat agtgtttcca atagcccttt acctaagaag cattctgaca
+ 3121 catgggttgg acttttacac agacctataa ctcgtatccg gcctggtgat gtatgtccgc
+ 3181 ttatcactga atgcaggatt ccgccaattc cgctcgcggg ttctcggaca acgggccatg
+ 3241 gagatggatc aatgagccat gttgattacc atttcactac acacggttag tcaattccgg
+ 3301 agatcataat tcgacaattg aatatgcgtg atacgctttc tgttaccagg atcgttgcta
+ 3361 attagtttcc aatgtcacag tgttgggcgg cgaggtatca cggcgctctg ggtagaatgg
+ 3421 cggtgcctga ctggacctca taactggtaa catacctatg accaaaggag gtcagacacc
+ 3481 gatgagtcgg tgacatgggc ggtcacagcg tgccctgcat agtaatacag ctcgtttcta
+ 3541 gacatttgtc ctaattcgcc acacaagtac gagagcgggg gtaacccatc accatcgtgc
+ 3601 ccgtaggtac ctaatcttca tcgagcgcta ttgttaaagt ggactcaggg atcggcatct
+ 3661 cgtgtagctt tgagaccggg gcccgaggat gtatgccttg catggaactt gactaatctc
+ 3721 agtaatactg gccgtgtatt ggtgtgtctt ccttggcctc acatgggaac attaccacat
+ 3781 ataacatcat ggggttcagt ctattactaa cgaagtcact aaaacgtact cgacggcgca
+ 3841 tgcgagtatc gacgtagcgg ttggttacct taagctgact tggtctatgc atacactgat
+ 3901 tagcttgtag cggtggcctt cgacgtctgt atcgtaggcg ttgtttgttg caaacacaaa
+ 3961 cgacctagcg tcaagacccc ttctagagaa agagagtgac gactcttgtc agttcaactc
+ 4021 tgtggtacgc cgctgcgaga tgcgcgttgc cacggcagac cccatgaact cgttcaagct
+ 4081 aaactctagt tcacgctaca tgtgtttgtt tctgcgtacg caaaagtact aggtacagct
+ 4141 atcttttggg ccccaagtgg gaccacactt tcggtcttcc tagcaaggct ataaaaccgt
+ 4201 atggcatgag tccttgatct gcatttcgtt tagacagagc gagatg
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,69 @@
+LOCUS part_I 2396 bp ds-DNA circular UNK 29-OCT-2019
+DEFINITION .
+ACCESSION part_I
+VERSION part_I
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ terminator 1991..2034
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ terminator 10..67
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ rep_origin complement(262..850)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2054..2388
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ CDS complement(1148..1807)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ terminator 1033..1127
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+ 1 accctgcagt ccgcatccaa gcttgctggg gcctctatcc gggacctgct tccgtacccc
+ 61 gtccgcctat caggctaacg actctgcctg ccattcaggc tcaccggcaa gttggagtga
+ 121 cctcttcatc gatacaaata gcgcatacgc cagacatacc gcccacgcac tcgaccataa
+ 181 aattccccgt cacggcgcgc acctccacac tccgtggcct aaggaacgtg gcagccggct
+ 241 gggccacttt ttagactacc atcggctcat ttttagaagg ccaccggctg tccgtcaatc
+ 301 gtacccgttt aggcctcctt aacacagttc cgaatagtta cctcaagatg cggatacagg
+ 361 atggctcccc caggggtcta gttcagtctt ttgtcgcctg cgcttgaacc tttatgcagc
+ 421 gatccacaaa cggaacaccg agatttgtat ttgggagggc aggctttgga ggaacggtgt
+ 481 atgtactttt gcttggtacc ctaggtaccc cacgatctaa tcggtcttcc tgacaggtga
+ 541 cagaggaggc cgtaactgcg accacaggct aactgcggcc ttaacttatg gtcgcgaact
+ 601 gcataagggc gtcgccgccc gttgtcagtg cgaattctgt tagtcgtcgt gtacaccttc
+ 661 cggtctaaca tctcgtagtt actagaagag cggatgggtc ctgtaaagag agcaggttcc
+ 721 cgtcttctct cactttaccg gtactggtgt gaccgggtgt gagtgatact gtgattccgc
+ 781 tactattgct atgcctgccg tcgtagctag atacgatccc agaacatttt gggctgattt
+ 841 caagtctctc cgggattccg taacgacggt tctcgaactg aatagctttg agatatcgca
+ 901 atattccttg gttgactctt gtccccggga cacaagtcgt gtgcaatatg tatacgtcag
+ 961 tatgctcgag actcctaagg ccgcatatct atgctatcac tattgcctat gcagtaactg
+ 1021 gctaagcttg tggggtactt gcacatgact catgtcaagg tcggaggatt cccagacagt
+ 1081 tggcatcatc agtgcgttca aggcggggag cgaccagcca gatattgatc gacgaggtgc
+ 1141 cacgaagtgt tccaaggtta tttttagtat gttacatcca tcagcgggtc taggccatac
+ 1201 cggtctatat tatggtgagt cgtataggct gtaatgccgg ctgcacaatc tacggccgat
+ 1261 tgcacataaa atggtcaact aacgacaagc tctgattctc aacttggata aaccttatca
+ 1321 caaaaggtcc gacacggttc agccgaggta aatcaaagtg attatgactc caggagcgac
+ 1381 acaaagttgc actgtctact gttggtcatc accgtactgc aaacgggtaa agatacttag
+ 1441 ctttgttagc tattgcagaa cctaattgct ttcctgccct aaggcgatcc ggatcctcta
+ 1501 tttatcaagt taattatcag agcttagctc aagtcaaagg tcttagtcag gtatggttta
+ 1561 gtcggcttat ctcgctccga taaacccctc gcgcctcgga ttcattcacg cgtttatatg
+ 1621 gtgaggggcg acccgtaggc tagtcgcact cctcggcaat taatcctaca gaaacctaga
+ 1681 catgggagtt gcgatcctcg agatacggcc tgagagggtc ggcaaagtgg gtgcttcatt
+ 1741 ctcttcggcg gagttcgcag gctctagaat gcctggtttt catctcgaca taaattacga
+ 1801 tgttatctcg tgcattatta ccccttttct gcaggtttta agtcgagtct agtcttacta
+ 1861 acgctgttct tcccgagaag gtgtccaggt tagatctcgg catattttca ctggcgcgct
+ 1921 atccgacagg aagacagcac ccgttaagcg ccccagtcac atcaagatca gtcctatgtt
+ 1981 gactcttgct ggaggtcttc tcgaatccag ctaatgttgg attacccgcc cctctggaat
+ 2041 tcggtctctg cttttattat ccggcatgca tgcggcgttg catcgcttca tcgtcatcga
+ 2101 catatcgtta gcgggactta tcagggtccc atcacggctg tgacagctgt tcataagtgt
+ 2161 aatagcagtc accccaccaa atgcaagact gttcccaaac taagtgctag ggaggttggc
+ 2221 tacctatcgg cgtggcagtt gaccgggttt ttcttagtac ctgccttcca atctccgata
+ 2281 aaagcaagat gacttcctgc ttgcgctaaa gtctgaattc gctaaggggg cagattcatt
+ 2341 accagagact gccaaagtca accgccgaac gatactggaa tatatggagg tatgag
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,196 @@
+LOCUS part_J 4380 bp ds-DNA circular UNK 31-OCT-2019
+DEFINITION .
+ACCESSION part_J
+VERSION part_J
+KEYWORDS "Source" "Sequence" "Freezer" "Shelf" "Box" "Concentration" "Use"
+ "creator:SynthSys Center" "marker:SmR".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ rep_origin join(4298..4380,1..166)
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ promoter 1442..1476
+ /label="another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 2345..2362
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(2550..3341)
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 1187..1210
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1366..1396
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(2550..3455)
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 2421..2449
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 3766..3771
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 167..1186
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 2526..2549
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 167..1186
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 3744..3749
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 1503..2222
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 1409..1426
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 3589..3594
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ terminator 2227..2298
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 1319..1343
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1370..1394
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_RNA 3625..4177
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ terminator 2314..2341
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 2364..2474
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA complement(3628..3735)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 4264..4272
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ RBS 1485..1496
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2353..2356
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature complement(2476..2516)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 3539..3562
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1427..1430
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ -10_signal 3610..3615
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1211..1258
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ gene complement(2550..3455)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 3589..4177
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 1414..1419
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 2388..2411
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ terminator 1409..1411
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 2357..2362
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ORIGIN
+ 1 ctcatgggag tgtagcgcta gccatagttg acctgtcagc cggtcaaggt tggtccgaac
+ 61 ctagccagtt agacgaccag ctcccccact attgcacagt gcctgtataa gcacgtcagt
+ 121 gtctggcacc actgtgcgcg gtgtggtcct cgggacgatc ttcctacggc tacccatgcg
+ 181 ctagtgatta cagacgatcg ttttttcttt ttctgtggtg caaatacaca agatacgtca
+ 241 agagtcctag cagcctcatc ttgccaattg caggggtacc gattcaccca tggtatcagt
+ 301 cacgcaaaaa aagacgacat cggagttgct ggcgactggc aaaagaaaac atctatctgc
+ 361 cgtggcgttc gtctagcgca gcgagccgac tgactactcc gttatctcaa atttagtttc
+ 421 gtaagatctt cacgggagcc ggccagctga agaatctata ggtctaccgc tagaggaagc
+ 481 ccgtttacaa ccgacgtact agtccgacag caatcgtcag catgccaatt tattgtatca
+ 541 ggttgagaat gcaccactac ggaatcgacg tgccactggc cgcacgatac tagtgcgctg
+ 601 gtaaacaggc caggagctct aaatctggag tggtgtgaat ttaaccgcgg aacgattgtt
+ 661 gcacgcggtc cctgtgactc tgttgggagc actgtccccg gctccggata agtgatgtga
+ 721 acgaaaaggt gggctgacca gagatagggt taaggacggg cgatcgtagt ggacgattac
+ 781 tgctgatctt ccgagcactc tgagtcgcgc ggcgtatcgg gagttacccc gctcgctaca
+ 841 catctgaatt ccgccggata ctatgggtgc agagtggatc accttttcgt gacccgtata
+ 901 ttcgtcgttc tcatcactgt cctccgcgat ttatttcaat cgtcggtttc gccagatgca
+ 961 ttcctgggga agtcatcgcg acagtgcgct gcgcgcacag ctcttcttgg tttattcgag
+ 1021 attgtggttt atcaacatgg tctatctacg gactgattag aatattccca cgttaagccg
+ 1081 acgtgcattg gtactggctc cttaattaag cgcagagggt aggcgccttt tcttgtgcaa
+ 1141 accattatat gaggaactag caaacactat ggcgcaatat gtccacgtga ctcgagcatt
+ 1201 ctgtgttgcg gtagcgattt cactagtcac aaacggatag attctacggc gcacccggtg
+ 1261 catcgttgta tgttcagcaa tttggtcata tcccgctcct ctattcaatc tcttttttcg
+ 1321 tcaggggggg cacatacttg gagcagctgc gcctaacatt acaataagca gtcggagctc
+ 1381 agtacaaaac ccttatctta gcggtccgtt ctggaattcg gtctcaggag atatgcaggt
+ 1441 gtttacggct aggcacttac gcgaaatttc agctcgcggc aaactgtgct tatgcgactt
+ 1501 cagctagtcg tcatcgagtg ctgacgcgct tgttctacct taaggtgccc gctatcgcat
+ 1561 tgtccagggt tcggctatga gggtcggaac cagatcgcac ctacatgatg tcacgatact
+ 1621 attattcacg tcgttagaga acggacggtc cttcgtcctc acaggaaaat tattagaaat
+ 1681 ggtcaaccgg gtccacaaac gggcaattgc cactttggta gtacggttgc acataagatg
+ 1741 atatttacgc cttctgcgtt caggttacga tagtcgttga tggggctcgc tccgggtgaa
+ 1801 gttgatccag taaaatgggc gtcgatactt ctcctgtgag ctaagcgtct aaattcattc
+ 1861 ctagtctcgt gacgagaaca gaaaagacta aaccacgcgt gatggacctt ggtaagcgct
+ 1921 tgtcggtcta acttgtctca tctcacacgg tatgttcttg tgagcgctga ccagcccgtg
+ 1981 tccctgacgg ggaattcatt ctaacttacg gcttgggcgt cgtgatgttt cggaatccag
+ 2041 gatattacac agtagatgta gcttgtggcc gaacgagtgt atttcctgcg tcggattacc
+ 2101 tcatttcttg ttaatctgcc tacaattaag ccctttcagc agccttccct ctcgtttata
+ 2161 tttcgacagt caccgtgaca gtgtgatcga gctgtgggaa aatcacaata tagacgttag
+ 2221 ttgcttcgac agaaacggcg aatgtacgcg gttgtgatgg atgagacagg ccattcaatt
+ 2281 ctattcagcg aagttcagat tggttgctac tgctaaagga tgcgcatttg tcctttctgc
+ 2341 gcacctgcat atacccctaa gatgccagcg caatacggca tcgcagggca agcaacaccg
+ 2401 cacagcatgt ccctaaaggg aagatttaat acggactcag tcaagttgtg agaaacgaca
+ 2461 atacattgag tggaatgccc tttggtacgt tggcgataga tctaacgaga aacttcaacg
+ 2521 agatctagag tatcggactg agatgcatca tggctaggga ttgctgaatg gatatctttg
+ 2581 ccaaaatgag ctcgactagg aatctcagac tgccagctac gaaaagctgg gggatattca
+ 2641 tttccgctct tgtaaggcgc acgatgaccc tgtggagcaa aattcgacgc ggcaacgtag
+ 2701 tcaaagtacg gcctatctgg gacggagatg ggattgtttc tgtattcatg ccggcctctt
+ 2761 gagattgtaa ggatacccgg ccacagtctc gtaagaaacc cgatatcgct caaacgaatt
+ 2821 gacatcagtt agggcttgcg ctctagcaac cacgcgtcgg gtgttcgact gaatttaaga
+ 2881 tccagcgcaa accattcctt aaaggcggtc caggtgaaac cggctctgat aatgtacagt
+ 2941 ggattgtcca gttcgcttca aagtgcaatc aggcaaggta ctggcaagtc accgcttggg
+ 3001 gccggtttca gtggagcttt atcgacaaaa ggccgggccc tttggcctag agctcacttt
+ 3061 tggtgtcgtt cacgagtgag aactttggct cgcagcttga atgcttgtca cgtttagggt
+ 3121 tatacaacgt ttctataaac tacctatgac aaatcccgat cttctgaaac tccataagga
+ 3181 ctaagagagt ccgcgacagt ttcacttggt cggtgctatt gactatgtca cgcatgcccg
+ 3241 gtaaagcttt taagcaaagc ctgatatatc acgggaggtt actcaaagca ttttctaaag
+ 3301 ggacagcgga ctcacattag cctaatataa acccgatcag gccatgcacc tcgattcacc
+ 3361 ggaaggtagt accatgcacc ggatatttgg gacaacagtg aatagtacat cgtaaaatgt
+ 3421 caaggcctag ctatttttca ctggtgtctt atctctatta caacacacac ggatgtcccg
+ 3481 agcctacact ttcaaatata ctcaaggttc gctgttaagg gtaatacaag agtgctcggt
+ 3541 ttagtatcca tatgttggta caagtgactg tgctagccgt aaattaattc ggcttccatt
+ 3601 ccagcttggg tgtttagggt ctagacggtt gaaaccagaa agagtacaga caaaaccgta
+ 3661 gctctcccaa ggttgatcct ccagacacct acccacacta gtagcgcagg cctagaggag
+ 3721 acgttaggag cggaattgta cattcagtat cgcattaagc acaaagacag acaaacctag
+ 3781 aagccactta tcccctcgta ggagtacaac ggcagcgctt tcgggaggag ttgcctaact
+ 3841 acgctctgga cagcaagtcc cagaatgaag aaaatgactt ggcgagaacc caccactaca
+ 3901 tgcagggtct tgggaccggt cagcacagct tatccatgcg gcaattccgg acgaccgcga
+ 3961 atgaggatca cgacactgcc gatgttgcac cattgacctt ctcctatgca acaagggctt
+ 4021 aagatggtag atggtaatag agtagcctgc gaccttatgc ggtaatacac aaaaaccggt
+ 4081 aaacagtgcg ttgatgctgt gtgctggcgc atttgtgtac cttgctgggc tcgtataaaa
+ 4141 ttctgtcagc aggacgttca cctcccttct gctagtcgct aggcacaaac ggaaaaggtc
+ 4201 taatcgcgcg cgtgctcgtt agagtactgg ggcctcccac cacggatgat cacctcgccg
+ 4261 atacatttgg ccttatgtct caataagacc tcatggtcta tcctacacca tagatttgga
+ 4321 aagtctagtt gctgcctagc aggctgatag caagcgtcgt acgaggatcg aggaagggca
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,108 @@
+LOCUS part_K 3634 bp ds-DNA circular UNK 28-OCT-2019
+DEFINITION .
+ACCESSION part_K
+VERSION part_K
+KEYWORDS "creator:SynthSys Center" "marker:KanR, BlpR".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature 1268..1284
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(join(3199..3634,1..380))
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 2374..2377
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 2395..2419
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ promoter 1382..1560
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 2370..2373
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 2389..2393
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 1239..1261
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ rep_origin complement(2510..3098)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ terminator 2117..2369
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS 1562..2112
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ rep_origin 671..1106
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ORIGIN
+ 1 accagacagc ttccctgctg cttagagtgc catggggaat tgatctgtgt tcaatgactt
+ 61 taccataagc gcgcatcgtc attgcatcac gtgctttatc tctcgtagct agtagggaac
+ 121 aagagtttgc gaccactggt ggaatttcta gccgctatgt gaaaagtcac tagtagtatt
+ 181 aatagtcggc acatcgcgta cgcagtgctg agattcccct cactgttact tgagctagtc
+ 241 gcgccttgac agaccgcctt tcgaaggtgg cagagtgcct aatatattgc cacgttgagc
+ 301 gtactccttc ccggagtttc atcttaccgc cgggcgcgcg aagctacgtt tttcgaattt
+ 361 actaacgcac gctgacggtg gaagggcgat tggactggtt agattcaggt atgccttaag
+ 421 cgtactttac aaccagaggc tttatttgat tgtctaatct tcgtcaaaga acgaatacca
+ 481 gcgcttgagg ggtgactaga ctaataggag acaccgtctg tatcactcgt cggctatggc
+ 541 cgtactgtga acgcgacggg ccctaccagg ccacagattc ctatgtacgt tgcaagggtg
+ 601 ggctttgacc gttgcaacgg cgcactaggt ggcattcttc tctgctgcca atgatccgcc
+ 661 tcgccgagct aggggcgaag caggttatga cgcagcggaa cggtagtact atctaatatc
+ 721 aactaaaatt gtttctcaaa ggttcaaact agtattcttt attagaaacg atgatggcat
+ 781 ccggaacagg gttatggccc aggtgctgga tgaagccttg cctcgaggga cttagtcgcg
+ 841 tcgcccctct accaaggcgc taacggctag cgagatggtt gaggcgggag ccccgccact
+ 901 ttctagttga attcagagct acgtatcctg atgctaatcc ctcgaagaac tttccgatgc
+ 961 agctactatc tctttcgtaa agttagaata ggaacccggt aacggtggaa cgtcccgtca
+ 1021 taggaggttg tctcctacac tatctaagta cgtcagaaga tcgatttcct cagccgctga
+ 1081 ccccgtccgg catgaccagc gccgaacgta taggccgtat tgctgccgga acgactgctt
+ 1141 caaaggtaac catagccgtg gtacagtgac aacccactta gctattaaat catgcgcact
+ 1201 ctagacctct tgcacatacg gagcaactat gtatctaatt ggcacgagac atagaggagg
+ 1261 gccaatcaca gtagtttact ggtcgaattc cacctgcata tggagagaca ctccttcatc
+ 1321 aacagcagag gttacatacg tttaacctga ccgatggttg cccatcgaaa gcaaggaccc
+ 1381 acgggtaggc agctgttgtt tgatatgctt ttgtccccgg aaggcgccga taaaattata
+ 1441 cgccgtcccc cgcgtccgtt acgagcttcg tgatgttgcg ggctgaagtt ccctacgagt
+ 1501 caataggcca actcgaatgg ctaaatggtt gcaacccaca ggctcaactt tgaaggtaat
+ 1561 acgccaaaat ccaatatgct ctttcgggta gcgcataaaa ccttctgggg gccactgcag
+ 1621 acagtcatgg aggactacgt gcaacactac gctctagagt gatgatgtgg cagtcaaccg
+ 1681 agggctgtta agagaagtct gtgcacgaaa atcaatgagt cggtgtaatc ttcaccttcc
+ 1741 tacaaaccaa ggcttgaggg cctcaatttc gagcaccact tcttgaccaa gccgttcgcc
+ 1801 ggtataggag ttacgaattc gggtcgtctg ccgtctttga accatagata agtacctccc
+ 1861 gagtcgggag aacacgaatc gcatcagaac tcatcgaagg gtgttacttt gcccatcggc
+ 1921 atccccgaag attaattgca ttcgaaattt taacttcgag aatcatccgt gctaaccaac
+ 1981 gtggacgagc tatgaacgtt tacgtgttca gtatctagga attgacacgt ctccgatagc
+ 2041 gggagtcacg gcatgagtta cggcttttgt gaccagcgtc tgtgtaattt tattgacagt
+ 2101 ttcatatata gtgtctcgtc ttgcctttga gattcacagg ctgtaagagg gatgccgtcg
+ 2161 tgtatatgcc tgcagttaga gcttccttgt caggacgagc aactcactcc ttctggtgat
+ 2221 gctttgctag catgtagctt cgggtacttg cggaaaagga cagcctacag tgtctgcggc
+ 2281 ggtacgtcac taatatgaca tacgctgtgg acatcgtgaa gcggcgaatc gctccagatt
+ 2341 gaggtttaca gagtactcca tagtcacaca actcagaata tgcaggtgct gcagtgaccg
+ 2401 aatcctctca ggtcgcgctg gcggcccgtt tgagagtgct gaaagcgaag tttatccgca
+ 2461 ccgtcatcca gtgcacctcc cccagagaat gattacttgt gaatgcggtt aacctgaggg
+ 2521 ccgacgccgc gattaaattt ttaacgtgat gcacaagctg ggggcactct cccctggggt
+ 2581 caggttataa ttttaaaccc actacggacc tggactgcaa gatgcttagt ccacgcgtct
+ 2641 catagaccgt cggtctatag ccatgttcaa cgccgccagg ctgggcgcat aactgtatgt
+ 2701 gactttgtcc acatccaagg cgacgatggc ggcagttggc cggagggctg gctgtcaagg
+ 2761 ggccacgcgg atgaagggag ctcatacgca actatggagc gcggtatata gtataggatc
+ 2821 cgccgggaca cgcgggaatc aagggacaaa ggagcagtca gcgtgaaatc tttacgggtg
+ 2881 aagcgcgctc gtaccaccta gtcccgccta aggcccttgt gtcgtgcaac atcgctgggg
+ 2941 cgacggatga caatatgatc aaggcccgag agctttgaat gtaagaggcg tattataaag
+ 3001 cctaggtccg catgttgata cggggagcag cccatgcgca gtaggaaggt ccgaccaccc
+ 3061 ttttctgagg tctactccaa cctccttgcc gagtgctctc cgctatctcc acgcatagca
+ 3121 tactccgctt ctaacatctt cttcaaagca tacacgctac ttagcagagc aaatcgacac
+ 3181 gcccatggag tggtccgctc aaaccgcgca attaagtata agctaatgtg acggaccgga
+ 3241 cctacgattt cccccaactc gtggggatca gttgactcgt ctcagcttat gagacataat
+ 3301 tacggtcata gggtacgcct atgcccctca gagatctcta ggtcatatgc cctatcgggt
+ 3361 gctcggtgac cattgtctca tacaaagtca tatttggcag ggcttctatg gacgagtatt
+ 3421 atgtgcccaa aagggaacgt ctgagttggg attcgcttct aaccaatact ctaatggtac
+ 3481 ctaatttaat gtggtcgctg cgcaccccgc cgggtacaac tgctgagttc ctgagatcgg
+ 3541 tacggcaaac atcttttatc cagacgaggg ttctggccag aattgatgtt cagatacgag
+ 3601 aaggcatgtc atgtcacaag gattttggag aatt
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,79 @@
+LOCUS part_L 2267 bp ds-DNA circular UNK 28-OCT-2019
+DEFINITION .
+ACCESSION part_L
+VERSION part_L
+KEYWORDS "creator:SynthSys Center" "marker:KanR".
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ misc_feature join(2263..2267,1)
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 2..59
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS complement(1140..1955)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 2206..2209
+ /label="feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 2202..2205
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ terminator 2139..2182
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ rep_origin complement(254..842)
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 2248..2251
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 2185..2190
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 1025..1119
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ORIGIN
+ 1 gtccgatgcg agcaccacct atagataccc taatcagcat ggtcccggtg accattacca
+ 61 ccgacggcct tgttttaaac gaaggcgctc actatacaag aaactaatgt ctcccacaag
+ 121 gctcagaccc agccggtgct ttcagcgctc cccgttggcg ccccccgaag accatagaga
+ 181 ggtgctctgt taacaactat aatgaaaggg attattgagg gagtcggagg tgaattctga
+ 241 agccttaccc ctacggtcgt ggtcatcatc acggatcgcg ataagcggcc ggtctgttac
+ 301 ggacgccact acgaggaggg tttcttggca atcaaggcta cgcattacaa ccatcggggt
+ 361 cggtctggct gaacaatctt gatgttcaac ctttgttacc ggctccttgt gttattatcc
+ 421 ggtttttttg atctatatgt ttataaggaa gcggtgcaga ccgtagagaa ataccggcta
+ 481 aggcagtcgc tcaatgcaca ccagcatcgc cgagacatat aaagccataa acattaattg
+ 541 gaatgctagt cacagcgtgt tgactggacg cttaaaagtt tctacaaaag gtatagtttt
+ 601 aacatttctc tgagttagcg ctatcgggtc gactgacatc tagaattgac acgttactca
+ 661 cctggatcct agtcacactc cgggaaccgc tcgcttagtg gcagtagcgg ggggcgtccc
+ 721 taggatagct gcgcaaagcg tggtttatct aatcgtggct tgtgtggaca tgatgctgtt
+ 781 caggcgcatc tgtggccgcc acagcattac caagctaatc agaaaccgcg gcatgtcccc
+ 841 gcgatgcgag aggcatctgt tagagccaaa gagtggaggt ctgtaatatc gctagcggag
+ 901 attttctaag gggcgtggga ctttatcccg atatggctga acgatccaac ggcaaatggt
+ 961 tctgccattg aactttaacc atgaatagac tccaggcgag ggataatgga aataatagca
+ 1021 ggaaatgaca atctactagg tgcgcactat caagattgta tgtttgcgta tcgtagttct
+ 1081 aatggtcttg tgtcccgtat tgggtcggac ggtgctgttc ctgatcgtag caatgcccgg
+ 1141 ttagaatcac gcatcggagc gatcatttcg ggcgatacgc gttcgttctg tccactcttg
+ 1201 tgggagtccg acgtatgcct gctcggtatt gttttattca ggcgacagta cctcccattc
+ 1261 aaatatacag ggttatacta cacaccacga gtaataaaga cttgtgttgt gccaattcct
+ 1321 cgtgggactg ccacgctcgt gagcttcgcg gttacatacc cctatgtccc caactgttgg
+ 1381 tggcaaatcc ctaatctaat ctattgtatc acagtcggtc aacgactgaa attggggcaa
+ 1441 caccaacagt gctcttacga tattcgtctg tgtctaacaa tccaacaaaa agctgttatt
+ 1501 atgatggagg atcttggatt gcgtcagtac tacggtgttg tacgagaatt gcatgatgat
+ 1561 tcctcgatgt cgagtccttg caagatcgtg atctatagcc aagctgctgc tgtagatcaa
+ 1621 cctcaccggg gcgggggtcc cattactatg ggcggcatta gagtaccata gatgaacgcg
+ 1681 agcagagaca tgtcaatgta tcccagtcct gcagtactac gtcagtctct gctcctgggg
+ 1741 ccaatgcacg cctgtagaat agggccgtgt tcccatgaga aatttgaggg acttacgatt
+ 1801 agatggcctt ggcaggggac tccgcgtacg tgtggggatg aaccggcacc ggccttggcc
+ 1861 ctgagtaaat gtaagcgata tcaacttcgc tattcatgat cagtggtatt cgtgtaggca
+ 1921 ccgaaagtcc cttggcgaaa gtagagacat acgatacgga ccgcaagcga gcagaatttc
+ 1981 agcacatgac agttattagc ttttttctaa tggtgctccc attatgattg tcaagtcccg
+ 2041 actgctagct gtaggatgaa acacatccac acacgtgtta ccatactgat tttgacacta
+ 2101 cttcctaacc gggccgaatg gtatctgctg cgatgcttag ttacgtaaca gccgaatgtc
+ 2161 acgccactgc atattgtggt tctggaattc cacctgcata tgtcacgcta gagaccgtat
+ 2221 gaggtgggcg gatagtggtg acttcaaacc catatgcagg tgctgca
+//
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/BASIC_assembly_dataset/GFP.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BASIC_assembly_dataset/GFP.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,130 @@
+LOCUS GFP 3735 bp DNA circular UNK 01-JAN-1980
+DEFINITION
+ACCESSION
+VERSION
+SOURCE
+ ORGANISM
+COMMENT Serial Cloner Genbank Format
+COMMENT SerialCloner_Type=DNA
+COMMENT SerialCloner_Comments=seq 20140514
+COMMENT SerialCloner_Ends=0,0,,0,
+FEATURES Location/Qualifiers
+ primer_bind 3668..3687
+ /label=T7
+ /SerialCloner_Color=&h008B8B
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ rep_origin complement(1534..2162)
+ /label=ColE1 origin
+ /SerialCloner_Color=&h4682B4
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ CDS complement(2314..2973)
+ /label=AmpR
+ /SerialCloner_Color=&h8FBC8F
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ Promoter complement(3213..3241)
+ /label=Amp prom
+ /SerialCloner_Color=&h4682B4
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 3668..3684
+ /label=T7-promoter
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 19..732
+ /label=GFP-SF-pep
+ /SerialCloner_Color=&h80FF80
+ /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 742..759
+ /label=Suffix
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 2974..3170
+ /label=pB1a promoter
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ORIGIN
+ 1 TCTGGTGGGT CTCTGTCCat gcgtaaaggc gaagaactgt tcacgggcgt agttccgatt
+ 61 ctggtcgagc tggacggcga tgtgaacggt cataagttta gcgttcgcgg tgaaggtgag
+ 121 ggcgacgcga ccaacggcaa actgaccctg aagttcatct gcaccaccgg taaactgccg
+ 181 gtgccttggc cgaccttggt gacgacgttg acgtatggcg tgcagtgttt tgcgcgttat
+ 241 ccggaccaca tgaaacaaca cgatttcttc aaatctgcga tgccggaggg ttacgtccag
+ 301 gagcgtacca tttccttcaa ggatgatggc acttacaaaa ctcgcgcaga ggttaagttt
+ 361 gaaggtgaca cgctggtcaa tcgtatcgaa ttgaagggta tcgactttaa agaggatggt
+ 421 aacattctgg gccataaact ggagtataac ttcaacagcc ataatgttta cattacggca
+ 481 gacaagcaaa agaacggcat caaggccaat ttcaagattc gccacaatgt tgaggacggt
+ 541 agcgtccaac tggccgacca ttaccagcag aacaccccaa ttggtgacgg tccggttttg
+ 601 ctgccggata atcactatct gagcacccaa agcgtgctga gcaaagatcc gaacgaaaaa
+ 661 cgtgatcaca tggtcctgct ggaatttgtg accgctgcgg gcatcaccca cggtatggac
+ 721 gagctgtata agcgtccgta aGGCTCGGGA GACCTATCGT ATCTTTCTAG AAGATCTCCT
+ 781 ACAATATTCT CAGCTGCCAT GGAAAATCGA TGTTCTTCTT TTATTCTCTC AAGATTTTCA
+ 841 GGCTGTATAT TAAAACTTAT ATTAAGAACT ATGCTAACCA CCTCATCAGG AACCGTTGTA
+ 901 GGTGGCGTGG GTTTTCTTGG CAATCGACTC TCATGAAAAC TACGAGCTAA ATATTCAATA
+ 961 TGTTCCTCTT GACCAACTTT ATTCTGCATT TTTTTTGAAC GAGGTTTAGA GCAAGCTTCA
+ 1021 GGAAACTGAG ACAGGAATTT TATTAAAAAT TTAAATTTTG AAGAAAGTTC AGGGTTAATA
+ 1081 GCATCCATTT TTTGCTTTGC AAGTTCCTCA GCATTCTTAA CAAAAGACGT CTCTTTTGAC
+ 1141 ATGTTTAAAG TTTAAACCTC CTGTGTGAAA TTaTTATCCG CTCAtAATTC CACACATTAT
+ 1201 ACGAGCCGGA AGCATAAAGT GTAAAGCCTG GGGTGCCTAA TGAGTGAGCT AACTCACATT
+ 1261 AATTGCGTTG CGCTCACTGC CAATTGCTTT CCAGTCGGGA AACCTGTCGT GCCAGCTGCA
+ 1321 TTAATGAATC GGCCAACGCG CGGGGAGAGG CGGTTTGCGT ATTGGGCGCT CTTCCGCTTC
+ 1381 CTCGCTCACT GACTCGCTGC GCTCGGTCGT TCGGCTGCGG CGAGCGGTAT CAGCTCACTC
+ 1441 AAAGGCGGTA ATACGGTTAT CCACAGAATC AGGGGATAAC GCAGGAAAGA ACATGTGAGC
+ 1501 AAAAGGCCAG CAAAAGGCCA GGAACCGTAA AAAGGCCGCG TTGCTGGCGT TTTTCCATAG
+ 1561 GCTCCGCCCC CCTGACGAGC ATCACAAAAA TCGACGCTCA AGTCAGAGGT GGCGAAACCC
+ 1621 GACAGGACTA TAAAGATACC AGGCGTTTCC CCCTGGAAGC TCCCTCGTGC GCTCTCCTGT
+ 1681 TCCGACCCTG CCGCTTACCG GATACCTGTC CGCCTTTCTC CCTTCGGGAA GCGTGGCGCT
+ 1741 TTCTCATAGC TCACGCTGTA GGTATCTCAG TTCGGTGTAG GTCGTTCGCT CCAAGCTGGG
+ 1801 CTGTGTGCAC GAACCCCCCG TTCAGCCCGA CCGCTGCGCC TTATCCGGTA ACTATCGTCT
+ 1861 TGAGTCCAAC CCGGTAAGAC ACGACTTATC GCCACTGGCA GCAGCCACTG GTAACAGGAT
+ 1921 TAGCAGAGCG AGGTATGTAG GCGGTGCTAC AGAGTTCTTG AAGTGGTGGC CTAACTACGG
+ 1981 CTACACTAGA AGGACAGTAT TTGGTATCTG CGCTCTGCTG AAGCCAGTTA CCTTCGGAAA
+ 2041 AAGAGTTGGT AGCTCTTGAT CCGGCAAACA AACCACCGCT GGTAGCGGTG GTTTTTTTGT
+ 2101 TTGCAAGCAG CAGATTACGC GCAGAAAAAA AGGATCTCAA GAAGATCCTT TGATCTTTTC
+ 2161 TACGGGGTCT GACGCTCAGT GGAACGAAAA CTCACGTTAA GGGATTTTGG TCATGAGATT
+ 2221 ATCAAAAAGG ATCTTCACCT AGATCCTTTT AAATTAAAAA TGAAGTTTTA AATCAATCTA
+ 2281 AAGTATATAT GAGTAAACTT GGTCTGACAG TTACCAATGC TTAATCAGTG AGGCACCTAT
+ 2341 CTCAGCGATC TGTCTATTTC GTTCATCCAT AGTTGCCTGA CTCCCCGTCG TGTAGATAAC
+ 2401 TACGATACGG GAGGGCTTAC CATCTGGCCC CAGTGCTGCA ATGATACCGC GAGACCCACG
+ 2461 CTCACCGGCT CCAGATTTAT CAGCAATAAA CCAGCCAGCC GGAAGGGCCG AGCGCAGAAG
+ 2521 TGGTCCTGCA ACTTTATCCG CCTCCATCCA GTCTATTAAT TGTTGCCGGG AAGCTAGAGT
+ 2581 AAGTAGTTCG CCAGTTAATA GTTTGCGCAA CGTTGTTGCC ATTGCTACAG GCATCGTGGT
+ 2641 GTCACGCTCG TCGTTTGGTA TGGCTTCATT CAGCTCCGGT TCCCAACGAT CAAGGCGAGT
+ 2701 TACATGATCC CCCATGTTGT GCAAAAAAGC GGTTAGCTCC TTCGGTCCTC CGATCGTTGT
+ 2761 CAGAAGTAAG TTGGCCGCAG TGTTATCACT CATGGTTATG GCAGCACTGC ATAATTCTCT
+ 2821 TACTGTCATG CCATCCGTAA GATGCTTTTC TGTGACTGGT GAGTACTCAA CCAAGTCATT
+ 2881 CTGAGAATAG TGTATGCGGC GACCGAGTTG CTCTTGCCCG GCGTCAATAC GGGATAATAC
+ 2941 CGCGCCACAT AGCAGAACTT TAAAAGTGCT CATCATTGGA AAACGTTCTT CGGGGCGAAA
+ 3001 ACTCTCAAGG ATCTTACCGC TGTTGAGATC CAGTTCGATG TAACCCACTC GTGCACCCAA
+ 3061 CTGATCTTCA GCATCTTTTA CTTTCACCAG CGTTTCTGGG TGAGCAAAAA CAGGAAGGCA
+ 3121 AAATGCCGCA AAAAAGGGAA TAAGGGCGAC ACGGAAATGT TGAATACTCA TACTCTTCCT
+ 3181 TTTTCAATAT TATTGAAGCA TTTATCAGGG TTATTGTCTC ATGAGCGGAT ACATATTTGA
+ 3241 ATGTATTTAG AAAAATAAAC AAATAGGGGT TCCGCGCACA TTTCCCCGAA AAGTGCCACC
+ 3301 TGACGTCTAA GAAACCATTA TTATCATGAC ATTAACCTAT AAAAATAGGC GTATCACGAG
+ 3361 GCCGCCCCTG CAGCCGAATT ATATTATTTT TGCCAAATAA TTTTTAACAA AAGCTCTGAA
+ 3421 GTCTTCTTCA TTTAAATTCT TAGATGATAC TTCATCTGGA AAATTGTCCC AATTAGTAGC
+ 3481 ATCACGCTGT GAGTAAGTTC TAAACCATTT TTTTATTGTT GTATTATCTC TAATCTTACT
+ 3541 ACTCGATGAG TTTTCGGTAT TATCTCTATT TTTAACTTGG AGCAGGTTCC ATTCATTGTT
+ 3601 TTTTTCATCA TAGTGAATAA AATCAACTGC TTTAACACTT GTGCCTGAAC ACCATATCCA
+ 3661 TCCGGCGTAA TACGACTCAC TATAGGGAGA GCGGCCGCCA GATCTTCCGG ATGGCTCGAG
+ 3721 TTTTTCAGCA AGATA
+//
\ No newline at end of file
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/BASIC_assembly_dataset/RFP.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BASIC_assembly_dataset/RFP.gb Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,136 @@
+LOCUS RFP 3723 bp DNA circular UNK 01-JAN-1980
+DEFINITION
+ACCESSION
+VERSION
+SOURCE
+ ORGANISM
+COMMENT Serial Cloner Genbank Format
+COMMENT SerialCloner_Type=DNA
+COMMENT SerialCloner_Comments=seq verified 20140514
+COMMENT SerialCloner_Ends=0,0,,0,
+FEATURES Location/Qualifiers
+ primer_bind complement(796..815)
+ /label=T7
+ /SerialCloner_Color=&h008B8B
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ rep_origin 2321..2949
+ /label=ColE1 origin
+ /SerialCloner_Color=&h4682B4
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_binding 3292..3314
+ /label=LacO
+ /SerialCloner_Color=&h6495ED
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ CDS 1510..2169
+ /label=AmpR
+ /SerialCloner_Color=&h8FBC8F
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ Promoter 1242..1270
+ /label=Amp prom
+ /SerialCloner_Color=&h4682B4
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature complement(799..815)
+ /label=T7-promoter
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature 19..726
+ /label=mcherry
+ /SerialCloner_Color=&hFF0080
+ /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 730..747
+ /label=Suffix
+ /SerialCloner_Color=&hFF00FF
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ misc_feature complement(1313..1509)
+ /label=pB1a promoter
+ /SerialCloner_Color=&h84A4C0
+ /SerialCloner_Show=True
+ /SerialCloner_Protect=False
+ /SerialCloner_Arrow=True
+ORIGIN
+ 1 TCTGGTGGGT CTCTGTCCAT GGTGAGCAAG GGCGAGGAGG ATAACATGGC CATCATCAAG
+ 61 GAGTTCATGC GCTTCAAGGT GCACATGGAG GGCTCCGTGA ACGGCCACGA GTTCGAGATC
+ 121 GAGGGCGAGG GCGAGGGCCG CCCCTACGAG GGCACCCAGA CCGCCAAGCT GAAGGTGACC
+ 181 AAGGGTGGCC CCCTGCCCTT CGCCTGGGAC ATCCTGTCCC CTCAGTTCAT GTACGGCTCC
+ 241 AAGGCCTACG TGAAGCACCC CGCCGACATC CCCGACTACT TGAAGCTGTC CTTCCCCGAG
+ 301 GGCTTCAAGT GGGAGCGCGT GATGAACTTC GAGGACGGCG GCGTGGTGAC CGTGACCCAG
+ 361 GACTCCTCCT TGCAGGACGG CGAGTTCATC TACAAGGTGA AGCTGCGCGG CACCAACTTC
+ 421 CCCTCCGACG GCCCCGTAAT GCAGAAGAAG ACCATGGGCT GGGAGGCCTC CTCCGAGCGG
+ 481 ATGTACCCCG AGGACGGCGC CCTGAAGGGC GAGATCAAGC AGAGGCTGAA GCTGAAGGAC
+ 541 GGCGGCCACT ACGACGCTGA GGTCAAGACC ACCTACAAGG CCAAGAAGCC CGTGCAGCTG
+ 601 CCCGGCGCCT ACAACGTCAA CATCAAGTTG GACATCACCT CCCACAACGA GGACTACACC
+ 661 ATCGTGGAAC AGTACGAACG CGCCGAGGGC CGCCACTCCA CCGGCGGCAT GGACGAGCTG
+ 721 TACAAGTAAG GCTCGGGAGA CCTATCGTAT CTTGCTGAAA AACTCGAGCC ATCCGGAAGA
+ 781 TCTGGCGGCC GCTCTCCCTA TAGTGAGTCG TATTACGCCG GATGGATATG GTGTTCAGGC
+ 841 ACAAGTGTTA AAGCAGTTGA TTTTATTCAC TATGATGAAA AAAACAATGA ATGGAACCTG
+ 901 CTCCAAGTTA AAAATAGAGA TAATACCGAA AACTCATCGA GTAGTAAGAT TAGAGATAAT
+ 961 ACAACAATAA AAAAATGGTT TAGAACTTAC TCACAGCGTG ATGCTACTAA TTGGGACAAT
+ 1021 TTTCCAGATG AAGTATCATC TAAGAATTTA AATGAAGAAG ACTTCAGAGC TTTTGTTAAA
+ 1081 AATTATTTGG CAAAAATAAT ATAATTCGGC TGCAGGGGCG GCCTCGTGAT ACGCCTATTT
+ 1141 TTATAGGTTA ATGTCATGAT AATAATGGTT TCTTAGACGT CAGGTGGCAC TTTTCGGGGA
+ 1201 AATGTGCGCG GAACCCCTAT TTGTTTATTT TTCTAAATAC ATTCAAATAT GTATCCGCTC
+ 1261 ATGAGACAAT AACCCTGATA AATGCTTCAA TAATATTGAA AAAGGAAGAG TATGAGTATT
+ 1321 CAACATTTCC GTGTCGCCCT TATTCCCTTT TTTGCGGCAT TTTGCCTTCC TGTTTTTGCT
+ 1381 CACCCAGAAA CGCTGGTGAA AGTAAAAGAT GCTGAAGATC AGTTGGGTGC ACGAGTGGGT
+ 1441 TACATCGAAC TGGATCTCAA CAGCGGTAAG ATCCTTGAGA GTTTTCGCCC CGAAGAACGT
+ 1501 TTTCCAATGA TGAGCACTTT TAAAGTTCTG CTATGTGGCG CGGTATTATC CCGTATTGAC
+ 1561 GCCGGGCAAG AGCAACTCGG TCGCCGCATA CACTATTCTC AGAATGACTT GGTTGAGTAC
+ 1621 TCACCAGTCA CAGAAAAGCA TCTTACGGAT GGCATGACAG TAAGAGAATT ATGCAGTGCT
+ 1681 GCCATAACCA TGAGTGATAA CACTGCGGCC AACTTACTTC TGACAACGAT CGGAGGACCG
+ 1741 AAGGAGCTAA CCGCTTTTTT GCACAACATG GGGGATCATG TAACTCGCCT TGATCGTTGG
+ 1801 GAACCGGAGC TGAATGAAGC CATACCAAAC GACGAGCGTG ACACCACGAT GCCTGTAGCA
+ 1861 ATGGCAACAA CGTTGCGCAA ACTATTAACT GGCGAACTAC TTACTCTAGC TTCCCGGCAA
+ 1921 CAATTAATAG ACTGGATGGA GGCGGATAAA GTTGCAGGAC CACTTCTGCG CTCGGCCCTT
+ 1981 CCGGCTGGCT GGTTTATTGC TGATAAATCT GGAGCCGGTG AGCGTGGGTC TCGCGGTATC
+ 2041 ATTGCAGCAC TGGGGCCAGA TGGTAAGCCC TCCCGTATCG TAGTTATCTA CACGACGGGG
+ 2101 AGTCAGGCAA CTATGGATGA ACGAAATAGA CAGATCGCTG AGATAGGTGC CTCACTGATT
+ 2161 AAGCATTGGT AACTGTCAGA CCAAGTTTAC TCATATATAC TTTAGATTGA TTTAAAACTT
+ 2221 CATTTTTAAT TTAAAAGGAT CTAGGTGAAG ATCCTTTTTG ATAATCTCAT GACCAAAATC
+ 2281 CCTTAACGTG AGTTTTCGTT CCACTGAGCG TCAGACCCCG TAGAAAAGAT CAAAGGATCT
+ 2341 TCTTGAGATC CTTTTTTTCT GCGCGTAATC TGCTGCTTGC AAACAAAAAA ACCACCGCTA
+ 2401 CCAGCGGTGG TTTGTTTGCC GGATCAAGAG CTACCAACTC TTTTTCCGAA GGTAACTGGC
+ 2461 TTCAGCAGAG CGCAGATACC AAATACTGTC CTTCTAGTGT AGCCGTAGTT AGGCCACCAC
+ 2521 TTCAAGAACT CTGTAGCACC GCCTACATAC CTCGCTCTGC TAATCCTGTT ACCAGTGGCT
+ 2581 GCTGCCAGTG GCGATAAGTC GTGTCTTACC GGGTTGGACT CAAGACGATA GTTACCGGAT
+ 2641 AAGGCGCAGC GGTCGGGCTG AACGGGGGGT TCGTGCACAC AGCCCAGCTT GGAGCGAACG
+ 2701 ACCTACACCG AACTGAGATA CCTACAGCGT GAGCTATGAG AAAGCGCCAC GCTTCCCGAA
+ 2761 GGGAGAAAGG CGGACAGGTA TCCGGTAAGC GGCAGGGTCG GAACAGGAGA GCGCACGAGG
+ 2821 GAGCTTCCAG GGGGAAACGC CTGGTATCTT TATAGTCCTG TCGGGTTTCG CCACCTCTGA
+ 2881 CTTGAGCGTC GATTTTTGTG ATGCTCGTCA GGGGGGCGGA GCCTATGGAA AAACGCCAGC
+ 2941 AACGCGGCCT TTTTACGGTT CCTGGCCTTT TGCTGGCCTT TTGCTCACAT GTTCTTTCCT
+ 3001 GCGTTATCCC CTGATTCTGT GGATAACCGT ATTACCGCCT TTGAGTGAGC TGATACCGCT
+ 3061 CGCCGCAGCC GAACGACCGA GCGCAGCGAG TCAGTGAGCG AGGAAGCGGA AGAGCGCCCA
+ 3121 ATACGCAAAC CGCCTCTCCC CGCGCGTTGG CCGATTCATT AATGCAGCTG GCACGACAGG
+ 3181 TTTCCCGACT GGAAAGCAAT TGGCAGTGAG CGCAACGCAA TTAATGTGAG TTAGCTCACT
+ 3241 CATTAGGCAC CCCAGGCTTT ACACTTTATG CTTCCGGCTC GTATAATGTG TGGAATTGTG
+ 3301 AGCGGATAAC AATTTCACAC AGGAGGTTTA AACTTTAAAC ATGTCAAAAG AGACGTCTTT
+ 3361 TGTTAAGAAT GCTGAGGAAC TTGCAAAGCA AAAAATGGAT GCTATTAACC CTGAACTTTC
+ 3421 TTCAAAATTT AAATTTTTAA TAAAATTCCT GTCTCAGTTT CCTGAAGCTT GCTCTAAACC
+ 3481 TCGTTCAAAA AAAATGCAGA ATAAAGTTGG TCAAGAGGAA CATATTGAAT ATTTAGCTCG
+ 3541 TAGTTTTCAT GAGAGTCGAT TGCCAAGAAA ACCCACGCCA CCTACAACGG TTCCTGATGA
+ 3601 GGTGGTTAGC ATAGTTCTTA ATATAAGTTT TAATATACAG CCTGAAAATC TTGAGAGAAT
+ 3661 AAAAGAAGAA CATCGATTTT CCATGGCAGC TGAGAATATT GTAGGAGATC TTCTAGAAAG
+ 3721 ATA
+//
\ No newline at end of file
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/BASIC_assembly_dataset/basic_assembly.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BASIC_assembly_dataset/basic_assembly.csv Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,10 @@
+L2RBS-1P,L2RBS-1P_fwd,L2RBS-1P_adapter,,,,,,,,,,
+LMA-S,LMA-S_fwd,LMA-S_adapter,,,,,,,,,,
+L1RBS-xS,L1RBS-xS_fwd,L1RBS-xS_adapter,,,,,,,,,,
+L1RBS-1P,L1RBS-1P_fwd,L1RBS-1P_adapter,,,,,,,,,,
+L2RBS-xS,L2RBS-xS_fwd,L2RBS-xS_adapter,,,,,,,,,,
+LMA-P,LMA-P_fwd,LMA-P_adapter,,,,,,,,,,
+LMB-S,LMB-S_fwd,LMB-S_adapter,,,,,,,,,,
+LMB-P,LMB-P_fwd,LMB-P_adapter,,,,,,,,,,
+asm_GFP_RFP,LMA-P,promoter,L1RBS-xS,L1RBS-1P,GFP,L2RBS-xS,L2RBS-1P,RFP,LMB-S,LMB-P,p15A_kan,LMA-S
+asm_RFP_GFP,LMA-P,promoter,L1RBS-xS,L1RBS-1P,RFP,L2RBS-xS,L2RBS-1P,GFP,LMB-S,LMB-P,p15A_kan,LMA-S
diff -r 000000000000 -r 3a3b0f7cb5c2 test-data/BASIC_assembly_dataset/oligos.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BASIC_assembly_dataset/oligos.fa Wed Jun 11 09:32:59 2025 +0000
@@ -0,0 +1,32 @@
+>L2RBS-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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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 3a3b0f7cb5c2 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 Wed Jun 11 09:32:59 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,,