# HG changeset patch
# User tduigou
# Date 1747395126 0
# Node ID 3171db614963703600f561d2be64797e3537c34f
# Parent 32e44a646b68a8af25da165ac200a8d64412aa31
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
diff -r 32e44a646b68 -r 3171db614963 cloning_similation.xml
--- a/cloning_similation.xml Fri May 16 09:41:19 2025 +0000
+++ b/cloning_similation.xml Fri May 16 11:32:06 2025 +0000
@@ -24,7 +24,7 @@
#set domesticated_input_paths = ""
#set file_name_mapping_dom = ""
#end if
- mkdir 'outdir_zip' &&
+ mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
python '$__tool_directory__/cloning_simulation.py'
--parts_files '$genbank_file_paths'
--domesticated_seq '$domesticated_input_paths'
@@ -34,6 +34,7 @@
--file_name_mapping_dom '$file_name_mapping_dom'
--use_file_names_as_id '$adv.use_file_names_as_ids'
--outdir_simulation 'outdir_zip'
+ --outdir_gb 'outdir_gb'
--output_simulation 'output_zip.zip'
--enzyme '$adv.enzyme'
--topology '$topology'&&
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diff -r 32e44a646b68 -r 3171db614963 cloning_simulation.py
--- a/cloning_simulation.py Fri May 16 09:41:19 2025 +0000
+++ b/cloning_simulation.py Fri May 16 11:32:06 2025 +0000
@@ -9,7 +9,7 @@
csv_file, assembly_type, topology,
file_name_mapping, file_name_mapping_dom,
use_file_names_as_id,
- outdir_simulation, output_simulation,enzyme):
+ outdir_simulation, output_simulation,enzyme,outdir_gb):
files_to_assembly = files_to_assembly.split(',')
@@ -108,11 +108,26 @@
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)
+ #print("Files in the zip archive:")
+ #for info in zipf.infolist():
+ #print(info.filename)
+ with zipfile.ZipFile(output_simulation, 'r') as zipf:
+ for member in zipf.namelist():
+ # Only extract actual files inside 'all_construct_records/' (not subfolders)
+ if member.startswith("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
- return output_simulation
+ # 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():
@@ -140,6 +155,8 @@
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()
@@ -150,6 +167,6 @@
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.use_file_names_as_id, args.outdir_simulation,
+ args.output_simulation, args.enzyme, args.outdir_gb
)
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_all_required_parts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_all_required_parts.txt Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,12 @@
+part_A
+part_B
+part_C
+part_D
+part_E
+part_F
+part_G
+part_H
+part_I
+part_J
+part_K
+part_L
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_constructs_level_1.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_constructs_level_1.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+construct,parts
+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
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_constructs_level_2.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_constructs_level_2.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+construct,parts
+construct_3,construct_1,part_L,part_J,part_K
+construct_4,construct_2,part_L,part_J,part_K
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_simulation_stats.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_simulation_stats.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+cancelled_assemblies: 0
+errored_assemblies: 0
+valid_assemblies: 4
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/2-step-golden_gate_plan_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,5 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,enzymes,used_in,parts
+construct_1,construct_1,1,10366,6,,BsaI,construct_3,part_A & part_B & part_C & part_D & part_E & part_F
+construct_2,construct_2,1,6910,5,,BsaI,construct_4,part_A & part_G & part_H & part_I & part_F
+construct_3,construct_3,2,11530,4,construct_1,AarI,,construct_1 & part_L & part_J & part_K
+construct_4,construct_4,2,8074,4,construct_2,AarI,,construct_2 & part_L & part_J & part_K
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/Report.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/Report.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,385 @@
+LOCUS construct_1 10366 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_1
+VERSION construct_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(223..1038)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature complement(139..179)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 5..8
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 20..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(223..1038)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 189..212
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 51..74
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 84..112
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 27..137
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3347..3377
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1367..1372
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1190..1195
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 1226..1778
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3396
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3192..3239
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_RNA complement(1229..1336)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1865..1873
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3413..3416
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 1190..1778
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3300..3324
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1345..1350
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 1899..2147
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3397..3401
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3395..3412
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1211..1216
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3168..3191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3351..3375
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1140..1163
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5..3416
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3417..3420
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ exon 5421..5618
+ /label="feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ gene 5421..5618
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 3421..5618
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ misc_feature 3421..5618
+ /source="part_B"
+ /indicates_part=True
+ /note="From part_B"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 5619..5622
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS 5623..8880
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 8881..9009
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 8091
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 8736
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 7683
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 5623..9011
+ /source="part_C"
+ /indicates_part=True
+ /note="From part_C"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9012..9015
+ /label="TTCG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9604..9633
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ CDS 9016..9528
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 9538..9603
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS 9580..9603
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 9016..9636
+ /source="part_D"
+ /indicates_part=True
+ /note="From part_D"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9637..9640
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ 3'UTR 9644..9953
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 9641..9643
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 9641..9953
+ /source="part_E"
+ /indicates_part=True
+ /note="From part_E"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9954..9957
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9958..10366
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(10255..10275)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 9958..10366
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cgctgtcaat atgcaggtgc tgcaggaatt tgtctccaat cgacttgaga tatcgcaagc
+ 61 atgaaattat attagacacg ccagagaact tgggaagcag cactggtagt gatagcaacc
+ 121 cgagtacagt aacgagtgag cttctgatca tgagctctcc tacggcgtca atgcgacgaa
+ 181 tgcccagcat gcactctcgc tatccatgcc tgctagggtg gcattatgct caggaacagt
+ 241 tgtagcttgg atatcgtcta gatgaaatac ctggacactg gttagcgtcg tcaagcacca
+ 301 aggacattca cacgctcgcg gtctttcgtc tccctaagcg ttcggcagtc gggcgtgaag
+ 361 aggttgtaat cagacggaac aaagcctgaa aaaattccag cgacgtagta ttcatgatcc
+ 421 tgtaccatct gtagccgccg cggcgcacga ttgaatgtag gctactaacc ccatccgtgt
+ 481 tagcgatgtg agtttctacc gcaacgaatg ctcaagcgaa ccttcttctt tcgtccgcaa
+ 541 cccacaagcc gtggttatga cagctaaatt gtcccagaca tccctttatt acacaagagc
+ 601 tccagcggaa tacctagtca cagcggtaat gacacaaagc tcttagttag tccagggact
+ 661 acttctgtct acagcacatc acactcatta tcagcatcag tgtagagacg gagaacatgg
+ 721 gctatcctat accaagatcc gccatctaaa catttgaagt ttcccgtctt ctataactta
+ 781 gcactcgacg ctattctgct gagtgcgctt agtctgtagc gacttgcgaa atccataaac
+ 841 tgagaattga aagagagtgc ataaccgaaa cctttgtggc atatttccgt tgaaacgtac
+ 901 cagaacagcc gtttagtgcg gaacatacag tatcctgata aagcactcaa cccaacagac
+ 961 accctatgcc gatagcggga tgctaacaag tatagtcatg atgatttctc ggacagcggg
+ 1021 gtttggtaca gctgcaatcc gtgatttaaa ttcggacctc tgcacacacc gacggttacc
+ 1081 catatcctct acggctgtag gaagttttac cttggatgtc attctgattt cggcgtatct
+ 1141 cacaggatgg tccaacgaaa ctaggcttta gacgagggat gaatgaccga cccccactcg
+ 1201 tggcactaac ggacagactt ccctgacggt tattcgacca ttaaagtcag acatgcgggg
+ 1261 gtgaataaat tagccaaatt gtgtcgaaga aaagacgtgc ggctggcaca taaggcagtc
+ 1321 ttgatcctag tcttgcaggg atgcacgtaa gtcgcctcaa ttaactgcag ccgagctcca
+ 1381 ggttaccaaa gaccctagta tgccagggcc taacggttgg agtatattat gggtacgcaa
+ 1441 tagtgcggaa gttaacctgg gcaacatcca ggtgagaggt tggacggaag cgacagtaag
+ 1501 tggccataga ctgccgagtc gtgttaatga atcgctatac gcccatggag ttgtggggtc
+ 1561 gttttatccg agtaggggcc cgctgactac ttcgtccaga caatatgccg tcttcaatag
+ 1621 tctacctgag agtcatgccg gcatttccga cgctgagtga aacccgcgta gccaggcgaa
+ 1681 atttgcatct tgaaatacca ctgcagatca gccagtaagg cccatataag ggcgctggtg
+ 1741 ttctggcgac agataaagtg ttatctaatg taacccgcgg acttttagag gatacttgaa
+ 1801 tgcgggcata tcgtcccacc agcgtcacgt ggtcgggcta gcggcagaca aactctgccg
+ 1861 atgtttttct ttgccgcgat agcgggctag tcaattcact atccggcgat gaagcataga
+ 1921 ttgttatcgc gcttatgcgg aggataatca agtcttggca gaacctgctc gctcatgcac
+ 1981 tggtgaggcg tggttatcct aacaaccgcc taggacgaag aatgggctcg gtagggacag
+ 2041 ttcgtgcgtt tagcttcgtc ccatcttaat gctgtctgga gggaggctac atgcgaacag
+ 2101 aagccgtggg cgaaagttgt tgatccgggt ctaacacgga taagggccat ggtgaacgca
+ 2161 tcatgcgata cttcttggta gttcttctaa catgaccgtg ccatagccct taccctttga
+ 2221 agaagttaac ctatctgccg tctcctgcac gaatagcgac tggactcggg tattttggat
+ 2281 acctcacgaa agcacttcga tcggccgaag catggatatt tcgccggacg ggcccgaata
+ 2341 gagagccttg tatgtcggtt agtacaacgc agtcctggag acatctacgc ggatgggcct
+ 2401 aggggctgga cttaacattg ggtaacgtac ctggtccaaa gtgaatgcaa agcactttta
+ 2461 caaagcgcgg gtccccgtgg gtgtttaggg tagaagattg gcggatgcta cgaacgatcc
+ 2521 cgctttgaaa ctatcattac atcgtgtaaa agagacactt aacaaaggcc aataaactgc
+ 2581 cagtaagaat cgctcagtgc ggtgctgggg acgctaagta ggggcaacag ccagtgaagg
+ 2641 acgtgaccga cctttctcag ataagatatg ctggcgtcta tctaataagc atagtgaaaa
+ 2701 accaaccatt tcacttacac gaagtacatt tgcattgcta gtaaagacgc ctaaacagaa
+ 2761 gtgcccttgc atgctgtatg tctatagtcc ttagggaagc atcagccctt ctacttattc
+ 2821 gaggtctgag aaaccctgga caagctccga attattcaat gtgcctgtct ccgaggttag
+ 2881 atagcgctat gctcttaaga gttgcacaga atgaccatcc tggaatgtcc ctggaggggt
+ 2941 ctaggtatgc tgatcgaagg gtgctctaag gacttgacgt gcgtccgagg agggtgctgc
+ 3001 ctccttcgcc tttagatcca acgcggatca catgcgcgtg agctaatagg atcaccttct
+ 3061 gctccgattt ttaccctcct gggtcacttc cgaatgaggt agcgggcgaa atataatgtc
+ 3121 tccactcgta ggtgttccct gtatgtgaag ctctatagtg gacaaaggtt tgatgaacta
+ 3181 gcccccgtat acgctctcac cgacggacgc gggggtctgt tatttgaagc atcatacatg
+ 3241 cgaaggtgcc ttctcagcaa cgaaaggtag tgggagtgta caagttcaat gcgccgccat
+ 3301 aggtctgagt atacaagggg atgcccccat ccacaacggg attggctacc cggagagctg
+ 3361 gctccgctcc aacaaataat tatattaacc tattggaatt ccacctgcat atcagaggag
+ 3421 agcatacggt gctctgggct cacacgtact tcctcttgtc acgcgccttt gtagagcatt
+ 3481 agggcggagg tcactgggac ggggatcaga gagcttaaaa tcccaagtag cagtgcctaa
+ 3541 ggtgtagaat cttgtgcaga tcttcgtctg gcccgaaacc tgggcctcca caacaatgtc
+ 3601 gggtctttta taatttgaaa acatcgcgcc ttacccgcac cgcgcaggac gattagacac
+ 3661 agggggtcat gtccatggtt cggggtaagc caaatttaca tcgagtgtgg gcttcattga
+ 3721 ggagagggcg ttacgatacc cgttaaatga aaacccggac agtctctaac tgataggcct
+ 3781 gataatcgcc aaatgaagtc gcaattagca gtacatgact ggcagatatg tcgccggaga
+ 3841 cggtatgggg gacctatcct aggttggcac gcgagcgcga atgacgccta tcttatcccc
+ 3901 ctgcacgtga tggtatcgtc ccaactatct tttacctcat caacgttttc ctgcataatc
+ 3961 tgcaagatgg agagtccgcg agtgcgggga gtacgagatc acaaatctgc cctgaagaca
+ 4021 aagctcgcag gccgtactca ggaaatagca tcgactcaca catatcggga acggcaaaga
+ 4081 gtgcatcggc caatgcaaac tattgaacgt ccatgaaatt gtgtcaaact actagtgtgt
+ 4141 ggacttgcgt caaggccatg gcgcaatact caaagccccg gtatttatcc cccgcagagt
+ 4201 atccgtgcgg atggagttcc acagctcttt ggacatgcaa tgcgtggcgc tacatgctcc
+ 4261 gctgatacag aatatctaat gtctcgcctc ttgccgtcga ccctacaact actgcacggg
+ 4321 cagagtggac gcgacccctg agcggtgcag aaccttagta taaggcaagg gtggcacggc
+ 4381 cgagccgcac ttgctcctac taggccgtgc tcgaagctat tgatgcaagc acagtattcc
+ 4441 cgatttgtaa agcaaggtgc ccgtagccat acacccagct actcaccggc caatttcgac
+ 4501 cctctctatc tcagacctcc gcatattccc aaactcctgc tcaagtatga aatgaccggc
+ 4561 tcctcctaag gcctgcggac atggagtcat gcgtggaatg ccgtgtaggt agggtacaca
+ 4621 cagccttacc atgtagggca ataaattata gactactgac attgattcct tgagggcccg
+ 4681 ttcacttgtg ggggaaccag gaaggcgccg atagtcatca cttaaacaca tgcgacgcat
+ 4741 ccatttcaag aaagacacgc tacgggtcta caccgcctat agttctaatt tgggccccgg
+ 4801 tacgcacatc gatgtactct ccattacagc atagcacatc agcggcccta gttagcgctt
+ 4861 ctttttgttc caacattcaa tagcggggac tgcattatcc tcaccctatt tgttgcatag
+ 4921 gtatttggcc gtatacttgg gaaagagcaa ccacgggagt gcactagaaa ctgattcacc
+ 4981 catgttataa cgcgttgctc gcaagtcgta ctgtggccac gcacaggtca ggcaatcgca
+ 5041 accatgtctt agcagtttgt aagaagacct ttaaacatgt acctcacagc aatctcggaa
+ 5101 cttttaattt tcctgagtca atgacatgct agctccgtcc acttgtaatc accgtcataa
+ 5161 cacagttagc ctgcaaaagg gcgtgtacac cttgccactt taaagctgac cgaataacct
+ 5221 acctacagga gatgcttagt gccacggaat gatctcgcaa tgcttagtct tacacccagt
+ 5281 gaatcaaccc aagacctcgc cgactgaacg gtattgagtc caatcccgag aggcaattta
+ 5341 tggccgttag tgacagtcgg tcgctgatag aataaggcag actcgtctta agcgggctgc
+ 5401 tttaagagaa aatggagccc tgacgaagaa gtggatgaac caggttttga caacgtccca
+ 5461 tattggtaat gtaggctcgt tatcaagaga taggtttaga aggctcaatg ctcgacgtaa
+ 5521 aagaagtctt aagctctatg agccagtgat gagagctaat tatagggcgc attcgttggg
+ 5581 gtaaggttgc gaattgtcat ttaactaaaa ccgacggcaa tggtttcacc ggagctgaga
+ 5641 tcgcattaaa gtcacactac gaattatttg tccccgcggc tccagagaca aatttctagg
+ 5701 agtgggttca tggagaaccg tgacaagcat ggtagcttca aatagcgtca tcggatctta
+ 5761 aagtgattgt gacatatatg ggattgcgcg tctctcttac acaagctagt gtgcgcgagg
+ 5821 tgctgaacac ctattacgtc aactcccggg atcccggcgg gttacagaga cataagcagg
+ 5881 gtgtccatca ttaacttcga tgttgagccc gtgccctgat caaacacctc tcgtagtagt
+ 5941 gggtgccggc cgtgtattat tttgggggag aggatgcgcc ctaagcaatt tctttccatc
+ 6001 ggccagccat tcgacgccgg cacgcaagtt gttgcgggca ctgttgcagt tcccgtacta
+ 6061 gagtctcaag tctagaggta ccagcatcag gaagatgggt acttcgtgtg gatcttctcc
+ 6121 tgaacctgaa acctgaagag ctaaagcgcg tcgcgctgcc atacgataag tcgctctcat
+ 6181 ttccggaaga cgtcgttggg tgatggcgaa caatcgcgaa acgaaaatcg cggtcggtat
+ 6241 gttgattcaa gacgggctac gggcgggtta ctaacaggtg cgcagaaatg tgatgggtca
+ 6301 cttgaccatg aactttcgcg ccgtcgcttc tgtggactgg ccggctccct gatagtgcac
+ 6361 tagcccgttg atatgcccat taccatttgg cggcgcagtg tgccagcggg attaagatgc
+ 6421 gtggcgtaca actatccgca ctttgctgac gcacaaaggc aactgatgga cagccttcgg
+ 6481 gcattcgact ggttggctga gttcgcctgc ctattaatat gcttgtggaa attgatttac
+ 6541 agcgcctact tctacttagg tgtacctatt tacggcacag ggataaaggc tgacagaaaa
+ 6601 gtcctggaca ggtcataggt agttgtcaga cctacaatgg tataacttga gagtcctgta
+ 6661 ccgcacatgc ggttgtagct agatgtccag aagaccgtag ctagcgacga gtgggttgca
+ 6721 cgcgcatttt gggaaggggc tgcgcgaggg tggggtcacg ggttattcca tttctaaatg
+ 6781 ctaaaccagc agttgcttta gttctgacct agcaggcatg tcatatgtat ggctagatta
+ 6841 ttagtacaat gcaggactaa gaaagcctga gacttaaatg cgttggtttt tcagccgacg
+ 6901 ggccgggagg gcagatggcc gaatgcgcac tgaggagtgc attgcgaggg aataggcgga
+ 6961 ccaccaggtc ccctcacata ctgtggataa acctacccag ggacaactca cgccatcatt
+ 7021 ttcaagagta gcactacttt ccactaagta cggtttgtcg agagccggtg gcaccgtgcg
+ 7081 acgagcttgt gggcactagg cgaaccgggt tatataggac tgccttgcgg tgcgggaata
+ 7141 ctttaccccg tggagaggcc ataaaagctt acatttattg tagccgctag cggtttcgac
+ 7201 gcgctcaagt ggggctttat cttagagtat caaataatgc cctctcagct tcatcttgat
+ 7261 ttttgtgttt ggggtagtgt atccgatggg tcaccttctt gaccttgggg agctccatcc
+ 7321 atcgtaccaa tactccgttt ctttgtgttg cctaccgagt aatcgaatac cgcacgaggg
+ 7381 ctagaatcta atttaaggtg ggtcttatcc ctgttgtttg gacctaacgc tgtaacaaat
+ 7441 cacttccgcg acgggtgtca ttacgtcttc tatccgccac cggttcaaca gtgcgtcgaa
+ 7501 tgccaagtcc ctattacccg cattgtaaag ccattacaat acctccggtg atataattga
+ 7561 ttgccggttg gcaagggatc atctgtacgg gccgcgattg attgctgata aggaacggcg
+ 7621 gtaaggaacg tatcgcgtac gaggttgtac actggaaccg ctaaacaagc ggtatcgcta
+ 7681 aattaccggc gattatatca agggaatctt aggtagcacg aagccctacg ccctggaaac
+ 7741 aggatcggcg cgaggccgtg gacatattag cctacgtttt tttacaccca gatttccgac
+ 7801 gatgtccaca gctaaggcta tcctaaaccg caaacacata taaccgcagt ataaagcacg
+ 7861 ggatgattcc ttggccatct tgcaagcagt gcaaggcaat tctggtgata ggggcaaggc
+ 7921 agtgaaccga gtggtcagcg tattgtgacc ctgcaattgt catggcagat aattgtttat
+ 7981 gaacctgttt cacacaccca tcccttggat ctccagcgta gttactaata gtacgatttc
+ 8041 ctggtgttct gtcacccgcc ttgctgcctt cacgcctgcc ccacgttttg ctgtccactg
+ 8101 aatatcgctc taattaatag gtgtcacact gtatcaggta agtccattcc gggtgctatt
+ 8161 ggatcattcc tgagatgtac caccgatccc ataggcgtta ggtcttacat ctggagtgaa
+ 8221 aaagatcagc atcgaactat aggtagataa aggtcatgac tgttaacaga gaatcgttcc
+ 8281 tatcgcaacc ttcactaact ggaaggcacc cccacacttt gattagtaag cccctagcga
+ 8341 atgtagtgat ccaagaacat cgagtatact ttagctctcg gttcaggcat gtatgcaatc
+ 8401 gaccaccctt ccgttcagag tactctcaac cagcagattt ctaaacttta tagcctccgc
+ 8461 ccactaaaat tgccttatct caggttgact cttggatgta gctgtaatct aacatacaca
+ 8521 tggagctgcg gcaaattatc gtacgtccaa accaccaccg gatcagtggc gatactattc
+ 8581 tcgcaaaaaa gccatccagc attggaacaa gtgttaacca gcatttttct gagtcccccg
+ 8641 gaaagaaagt tgactacact acatccataa atgctagagt gtggattcgc catgtgttac
+ 8701 aacggtcaac cgaaaggtta gcatgatact tcgttgttca atcggacgtt cgagcgccct
+ 8761 ccctgtttat cacttgatcc cccttttgaa acatgtgcgc tgcgacgcag ggctgggaga
+ 8821 gtcaccggaa accaaaagcc cgacctcgga cgtgtagggc cctccgtttg ccatcaatgg
+ 8881 cgatgtagga ttctctttta atacaacgtt cactcaatta acgtcttggt ataagcgtcg
+ 8941 aacgtgaccg aggttgacac cagtgtcacg gctgcgccgg ggtttgttgc tccgcgtgta
+ 9001 cagggtattg gttcgatggt gcctcctcta cgtagatcta ctggataacc gtccccaata
+ 9061 tccgcttccc aacgtagatt gccgacaggc ataagcttcg ggggcgcaaa ggccgacgtc
+ 9121 cgcattgcag tgtagctttg tgagcaggaa gtgtgatagt ctttcgatta ttaaagtctg
+ 9181 agctgaatga aaaaaggtcc aacgaatgga ggacgcgaag acatgggtgt ctcttatggc
+ 9241 ccgagcggga gtaatggcgg ttcgtacata aaggctgaaa ggattctggc gttagctgtc
+ 9301 ttacgttgga ttggcccttc aaattatcga tgttagctga ttcggtgtac cgggcgagga
+ 9361 aagcgctctc agaacaactt catatacgag gttcgactat aatggtctaa gctcctgggc
+ 9421 tagtctcaag aagcgggtac ctttagtagc acgtatcgac ggcaaagcaa agaataaaaa
+ 9481 cttggctttg catcgtgcaa agatttctaa ctaggttgtt taagggctgg tatctatgtc
+ 9541 ccgctataac agcgcgccta cagtagaagt ttaaccatga catacctttg aagtgttcgt
+ 9601 atcacacaca aggaaggagc atgtggacac cactgagctt tgatcagcac gcgtctcaga
+ 9661 gtttcagggg gacccaaatt actggtcctc aattgggacg cgaccgcatc tccccacgaa
+ 9721 agcttatggg gattgcccac tgcccagctt caaatctgaa ggttcggctt attgacaggg
+ 9781 tctaacacgc agctcaactg ctcgaggtta gaggcgtaat gacgggcccc gatagccttc
+ 9841 tacgattacg tccagcagga accccacagc ttttccctac gtctaacacc gtgaaagcaa
+ 9901 aactgtctgc ccttttacat ggtctttaag gaatctctgc acttatgtta ttaggtaagc
+ 9961 tcccataaga gcaccacttc gtgtaccttg ctaactccct tcatccccac ccgcgaaaac
+ 10021 ttaagacgtc acccctgtta ttatcccgtg cactcctaaa gtgcgatggg caagaacgca
+ 10081 aacaattgtc tgagatttat atgggcggcg gacatagtca gagagcctta tataatctcc
+ 10141 cacgtcttgc cagtccgagt tatgagaaac ccgggaccga tgacgctatt acggtcgccc
+ 10201 agcgaggttc aacagagcga ggcataggag tcattacgcg tgttagcttc aacatgcgtg
+ 10261 gaagtgaaac ggatctataa aacggcgtgg agtcatcagc ttgagcagat ctaacttact
+ 10321 cgccacgcgc gcaaatcgtc tttcgctgtc cacgttatac gtaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,279 @@
+LOCUS construct_2 6910 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_2
+VERSION construct_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(223..1038)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature complement(139..179)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 5..8
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 20..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(223..1038)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 189..212
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 51..74
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 84..112
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 27..137
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3347..3377
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1367..1372
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1190..1195
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 1226..1778
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3396
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3192..3239
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_RNA complement(1229..1336)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1865..1873
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3413..3416
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 1190..1778
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3300..3324
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1345..1350
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 1899..2147
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3397..3401
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3395..3412
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1211..1216
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3168..3191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3351..3375
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1140..1163
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5..3416
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3417..3420
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3421..4505
+ /source="part_G"
+ /indicates_part=True
+ /note="From part_G"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4506..4509
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4510..6158
+ /source="part_H"
+ /indicates_part=True
+ /note="From part_H"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6159..6162
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6163..6497
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 6163..6497
+ /source="part_I"
+ /indicates_part=True
+ /note="From part_I"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6498..6501
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6502..6910
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(6799..6819)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 6502..6910
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cgctgtcaat atgcaggtgc tgcaggaatt tgtctccaat cgacttgaga tatcgcaagc
+ 61 atgaaattat attagacacg ccagagaact tgggaagcag cactggtagt gatagcaacc
+ 121 cgagtacagt aacgagtgag cttctgatca tgagctctcc tacggcgtca atgcgacgaa
+ 181 tgcccagcat gcactctcgc tatccatgcc tgctagggtg gcattatgct caggaacagt
+ 241 tgtagcttgg atatcgtcta gatgaaatac ctggacactg gttagcgtcg tcaagcacca
+ 301 aggacattca cacgctcgcg gtctttcgtc tccctaagcg ttcggcagtc gggcgtgaag
+ 361 aggttgtaat cagacggaac aaagcctgaa aaaattccag cgacgtagta ttcatgatcc
+ 421 tgtaccatct gtagccgccg cggcgcacga ttgaatgtag gctactaacc ccatccgtgt
+ 481 tagcgatgtg agtttctacc gcaacgaatg ctcaagcgaa ccttcttctt tcgtccgcaa
+ 541 cccacaagcc gtggttatga cagctaaatt gtcccagaca tccctttatt acacaagagc
+ 601 tccagcggaa tacctagtca cagcggtaat gacacaaagc tcttagttag tccagggact
+ 661 acttctgtct acagcacatc acactcatta tcagcatcag tgtagagacg gagaacatgg
+ 721 gctatcctat accaagatcc gccatctaaa catttgaagt ttcccgtctt ctataactta
+ 781 gcactcgacg ctattctgct gagtgcgctt agtctgtagc gacttgcgaa atccataaac
+ 841 tgagaattga aagagagtgc ataaccgaaa cctttgtggc atatttccgt tgaaacgtac
+ 901 cagaacagcc gtttagtgcg gaacatacag tatcctgata aagcactcaa cccaacagac
+ 961 accctatgcc gatagcggga tgctaacaag tatagtcatg atgatttctc ggacagcggg
+ 1021 gtttggtaca gctgcaatcc gtgatttaaa ttcggacctc tgcacacacc gacggttacc
+ 1081 catatcctct acggctgtag gaagttttac cttggatgtc attctgattt cggcgtatct
+ 1141 cacaggatgg tccaacgaaa ctaggcttta gacgagggat gaatgaccga cccccactcg
+ 1201 tggcactaac ggacagactt ccctgacggt tattcgacca ttaaagtcag acatgcgggg
+ 1261 gtgaataaat tagccaaatt gtgtcgaaga aaagacgtgc ggctggcaca taaggcagtc
+ 1321 ttgatcctag tcttgcaggg atgcacgtaa gtcgcctcaa ttaactgcag ccgagctcca
+ 1381 ggttaccaaa gaccctagta tgccagggcc taacggttgg agtatattat gggtacgcaa
+ 1441 tagtgcggaa gttaacctgg gcaacatcca ggtgagaggt tggacggaag cgacagtaag
+ 1501 tggccataga ctgccgagtc gtgttaatga atcgctatac gcccatggag ttgtggggtc
+ 1561 gttttatccg agtaggggcc cgctgactac ttcgtccaga caatatgccg tcttcaatag
+ 1621 tctacctgag agtcatgccg gcatttccga cgctgagtga aacccgcgta gccaggcgaa
+ 1681 atttgcatct tgaaatacca ctgcagatca gccagtaagg cccatataag ggcgctggtg
+ 1741 ttctggcgac agataaagtg ttatctaatg taacccgcgg acttttagag gatacttgaa
+ 1801 tgcgggcata tcgtcccacc agcgtcacgt ggtcgggcta gcggcagaca aactctgccg
+ 1861 atgtttttct ttgccgcgat agcgggctag tcaattcact atccggcgat gaagcataga
+ 1921 ttgttatcgc gcttatgcgg aggataatca agtcttggca gaacctgctc gctcatgcac
+ 1981 tggtgaggcg tggttatcct aacaaccgcc taggacgaag aatgggctcg gtagggacag
+ 2041 ttcgtgcgtt tagcttcgtc ccatcttaat gctgtctgga gggaggctac atgcgaacag
+ 2101 aagccgtggg cgaaagttgt tgatccgggt ctaacacgga taagggccat ggtgaacgca
+ 2161 tcatgcgata cttcttggta gttcttctaa catgaccgtg ccatagccct taccctttga
+ 2221 agaagttaac ctatctgccg tctcctgcac gaatagcgac tggactcggg tattttggat
+ 2281 acctcacgaa agcacttcga tcggccgaag catggatatt tcgccggacg ggcccgaata
+ 2341 gagagccttg tatgtcggtt agtacaacgc agtcctggag acatctacgc ggatgggcct
+ 2401 aggggctgga cttaacattg ggtaacgtac ctggtccaaa gtgaatgcaa agcactttta
+ 2461 caaagcgcgg gtccccgtgg gtgtttaggg tagaagattg gcggatgcta cgaacgatcc
+ 2521 cgctttgaaa ctatcattac atcgtgtaaa agagacactt aacaaaggcc aataaactgc
+ 2581 cagtaagaat cgctcagtgc ggtgctgggg acgctaagta ggggcaacag ccagtgaagg
+ 2641 acgtgaccga cctttctcag ataagatatg ctggcgtcta tctaataagc atagtgaaaa
+ 2701 accaaccatt tcacttacac gaagtacatt tgcattgcta gtaaagacgc ctaaacagaa
+ 2761 gtgcccttgc atgctgtatg tctatagtcc ttagggaagc atcagccctt ctacttattc
+ 2821 gaggtctgag aaaccctgga caagctccga attattcaat gtgcctgtct ccgaggttag
+ 2881 atagcgctat gctcttaaga gttgcacaga atgaccatcc tggaatgtcc ctggaggggt
+ 2941 ctaggtatgc tgatcgaagg gtgctctaag gacttgacgt gcgtccgagg agggtgctgc
+ 3001 ctccttcgcc tttagatcca acgcggatca catgcgcgtg agctaatagg atcaccttct
+ 3061 gctccgattt ttaccctcct gggtcacttc cgaatgaggt agcgggcgaa atataatgtc
+ 3121 tccactcgta ggtgttccct gtatgtgaag ctctatagtg gacaaaggtt tgatgaacta
+ 3181 gcccccgtat acgctctcac cgacggacgc gggggtctgt tatttgaagc atcatacatg
+ 3241 cgaaggtgcc ttctcagcaa cgaaaggtag tgggagtgta caagttcaat gcgccgccat
+ 3301 aggtctgagt atacaagggg atgcccccat ccacaacggg attggctacc cggagagctg
+ 3361 gctccgctcc aacaaataat tatattaacc tattggaatt ccacctgcat atcagaggag
+ 3421 gaacttctat gggacgaaag atgcgcagct cgacaaatct caaattggaa accgtctaag
+ 3481 gtctttgagc ccacgctagg ccaccgaata gttgcgagct cgtgggcaat tgctggctag
+ 3541 cggtttgtat cgtatacgta acaagagatt gcgccggatt cattcgtgtg gggtgctttc
+ 3601 acatcggaat actcaagagt gggggtttgc gctttaatat gacggcctca tgcaccccaa
+ 3661 aaataagagc gccaatttca tcgaccacat tccggacaat tctgacttcc ctgtcggatc
+ 3721 gaccctcgct cacaactcct agaactccaa gacggtagga cgtcagccga aaaggaggag
+ 3781 tgacgacggg ccctcctagc tgaagcaatg gggggcgtcg accctagcct ggtgtgggac
+ 3841 ttcggagggt cgggcgtgtg gccattcctg cacgaggggc ccttgcagta tcgaactttg
+ 3901 acgagaaagt ggggggcgac ctataaacat agcggagttc aatactcctg caagtgcatg
+ 3961 atgacgttca gcgttggcac atcgaacgcg tcgctacact tgctcaccgg aaggcaaaat
+ 4021 agaccggcag ctggcccgca cggacgtcta gactcctacg ctgtcaaatg cacgatgact
+ 4081 attagcatgc ggaattcgag gcggccggta catcgagaca cgctggtctt aatacctgtg
+ 4141 ttatgtcaaa acaagtgtct cggcggcttt gtactacgct gtgaatgcgc atgatgttgc
+ 4201 gagaagctga acgttggtag cagtctacaa cagaaccgac gagctacgga cgggttacag
+ 4261 caggatcccc tcttaaggca ttattcgacg actccaggtt ctaaccgatc agtaattgcc
+ 4321 tcggatggtc gtacgtgtta accgagacag caaggcacca catagacaac tgcatagggc
+ 4381 gcctacaggt ccacaatcag ggtggcccaa gatcctcaaa gacttgttgc agtctctgct
+ 4441 tattccgttt aacacgttgt gtgagctcta gcttactacc tcatcggtgt cgggagtgat
+ 4501 ttaggaatgg aagacgcgtt tagtcttcgg cccccagacg gcaccggcag agccactgcc
+ 4561 aatgcctttt acgctgaact cttcgacttt ggcatgtgcg actgactata cgccgatggc
+ 4621 cctaccctgc agcggaaagg cacagggcca aaaacagtgg aagcgcaccg ctagagcttt
+ 4681 actaaatcct ttagggtgaa ccggtgttca gtcaacagaa acatatgact agtccttaat
+ 4741 ggcactacta aaggcggccc atctcttttg taggtcacgt ctcatcgttt agcaagcgtc
+ 4801 cgccatccga ggagtatcct agtacgtgag agggtgtttt acctcatcac atggtttttg
+ 4861 gctagatgtg gcagatgcca gctgatacct tacaacccgc tataacggtt tctggatcga
+ 4921 cgatacaacc tgcttcggca tatcataatg gcggcctcat aggacttcca atcatggtta
+ 4981 tgcgagtttg atgtgttgaa gattgtgagg ggaaaccttt ttccgagtac gttgaatctg
+ 5041 cgactgatgg tgaacaactc atcgagaggg atgtgcgggc agtctccttg atgcgcgaaa
+ 5101 aggagtcgcg accgcgtgtt cgtgacgcac ttgatgctag accgtagggg ctcattatct
+ 5161 cctgaaacag tagctagctt ttggtgtccg agtcagctta ggcacagtaa ttgaaaagaa
+ 5221 ggaaatgcgt gaaaactaaa cgtagacact ccttgctaag aattccctgg tctttttcga
+ 5281 gcatagacta ccgtaggtaa aaggcttgtc gtgtcacaaa tagacttgat ctgttcggca
+ 5341 tatacacatc ctactgcttc agtaaccaag gacgattctc cggccattgg actgtgggac
+ 5401 cacccgcgtt caaacggaat cctctacgaa cggttaagaa aggagcccac tgcttgcgga
+ 5461 gacatatcgt tgctgagtgg tacaccggtg agtcaaaaag tactgacact actggtggac
+ 5521 tctcgggtac gatgtgtggg gtattggcat actatggcgc taagcgtgga atagtgtttc
+ 5581 caatagccct ttacctaaga agcattctga cacatgggtt ggacttttac acagacctat
+ 5641 aactcgtatc cggcctggtg atgtatgtcc gcttatcact gaatgcagga ttccgccaat
+ 5701 tccgctcgcg ggttctcgga caacgggcca tggagatgga tcaatgagcc atgttgatta
+ 5761 ccatttcact acacacggtt agtcaattcc ggagatcata attcgacaat tgaatatgcg
+ 5821 tgatacgctt tctgttacca ggatcgttgc taattagttt ccaatgtcac agtgttgggc
+ 5881 ggcgaggtat cacggcgctc tgggtagaat ggcggtgcct gactggacct cataactggt
+ 5941 aacataccta tgaccaaagg aggtcagaca ccgatgagtc ggtgacatgg gcggtcacag
+ 6001 cgtgccctgc atagtaatac agctcgtttc tagacatttg tcctaattcg ccacacaagt
+ 6061 acgagagcgg gggtaaccca tcaccatcgt gcccgtaggt acctaatctt catcgagcgc
+ 6121 tattgttaaa gtggactcag ggatcggcat ctcgtgtagc ttttattatc cggcatgcat
+ 6181 gcggcgttgc atcgcttcat cgtcatcgac atatcgttag cgggacttat cagggtccca
+ 6241 tcacggctgt gacagctgtt cataagtgta atagcagtca ccccaccaaa tgcaagactg
+ 6301 ttcccaaact aagtgctagg gaggttggct acctatcggc gtggcagttg accgggtttt
+ 6361 tcttagtacc tgccttccaa tctccgataa aagcaagatg acttcctgct tgcgctaaag
+ 6421 tctgaattcg ctaagggggc agattcatta ccagagactg ccaaagtcaa ccgccgaacg
+ 6481 atactggaat atatggaggt aagctcccat aagagcacca cttcgtgtac cttgctaact
+ 6541 cccttcatcc ccacccgcga aaacttaaga cgtcacccct gttattatcc cgtgcactcc
+ 6601 taaagtgcga tgggcaagaa cgcaaacaat tgtctgagat ttatatgggc ggcggacata
+ 6661 gtcagagagc cttatataat ctcccacgtc ttgccagtcc gagttatgag aaacccggga
+ 6721 ccgatgacgc tattacggtc gcccagcgag gttcaacaga gcgaggcata ggagtcatta
+ 6781 cgcgtgttag cttcaacatg cgtggaagtg aaacggatct ataaaacggc gtggagtcat
+ 6841 cagcttgagc agatctaact tactcgccac gcgcgcaaat cgtctttcgc tgtccacgtt
+ 6901 atacgtaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,457 @@
+LOCUS construct_3 11530 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_3
+VERSION construct_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CAGA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ homology 5..8
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ exon 2009..2206
+ /label="feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ gene 2009..2206
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 9..2206
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ misc_feature 9..2206
+ /source="part_B"
+ /indicates_part=True
+ /note="From part_B"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 2207..2210
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS 2211..5468
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 5469..5597
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 4679
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 5324
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 4271
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 2211..5599
+ /source="part_C"
+ /indicates_part=True
+ /note="From part_C"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 5600..5603
+ /label="TTCG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6192..6221
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ CDS 5604..6116
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 6126..6191
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS 6168..6191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 5604..6224
+ /source="part_D"
+ /indicates_part=True
+ /note="From part_D"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6225..6228
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ 3'UTR 6232..6541
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 6229..6231
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 6229..6541
+ /source="part_E"
+ /indicates_part=True
+ /note="From part_E"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6542..6545
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6546..6954
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(6843..6863)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 6546..6954
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6955..6958
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3420^3421
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 10374^10375
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 5..6958
+ /source="construct_1"
+ /indicates_part=True
+ /note="From construct_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6959..6962
+ /label="GTCA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6963..6966
+ /label="feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 6963..7004
+ /source="part_L"
+ /indicates_part=True
+ /note="From part_L"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 7005..7008
+ /label="ACCC"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS complement(7202..7993)
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS complement(7202..8107)
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 7073..7101
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 8418..8423
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 7178..7201
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 8396..8401
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 8241..8246
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 8277..8829
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 7016..7126
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA complement(8280..8387)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 8916..8924
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature complement(7128..7168)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 8191..8214
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 8262..8267
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene complement(7202..8107)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 8241..8829
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 7040..7063
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 7009..7014
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 10219..10242
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10398..10428
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 9199..10218
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ gene 9199..10218
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10441..10458
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10351..10375
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10402..10426
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 10243..10290
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 10446..10451
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 10441..10443
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 7009..10458
+ /source="part_J"
+ /indicates_part=True
+ /note="From part_J"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 10459..10462
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ promoter 10539..10717
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 11527..11530
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ terminator 11274..11526
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS 10719..11269
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 10463..11530
+ /source="part_K"
+ /indicates_part=True
+ /note="From part_K"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cagaggagag catacggtgc tctgggctca cacgtacttc ctcttgtcac gcgcctttgt
+ 61 agagcattag ggcggaggtc actgggacgg ggatcagaga gcttaaaatc ccaagtagca
+ 121 gtgcctaagg tgtagaatct tgtgcagatc ttcgtctggc ccgaaacctg ggcctccaca
+ 181 acaatgtcgg gtcttttata atttgaaaac atcgcgcctt acccgcaccg cgcaggacga
+ 241 ttagacacag ggggtcatgt ccatggttcg gggtaagcca aatttacatc gagtgtgggc
+ 301 ttcattgagg agagggcgtt acgatacccg ttaaatgaaa acccggacag tctctaactg
+ 361 ataggcctga taatcgccaa atgaagtcgc aattagcagt acatgactgg cagatatgtc
+ 421 gccggagacg gtatggggga cctatcctag gttggcacgc gagcgcgaat gacgcctatc
+ 481 ttatccccct gcacgtgatg gtatcgtccc aactatcttt tacctcatca acgttttcct
+ 541 gcataatctg caagatggag agtccgcgag tgcggggagt acgagatcac aaatctgccc
+ 601 tgaagacaaa gctcgcaggc cgtactcagg aaatagcatc gactcacaca tatcgggaac
+ 661 ggcaaagagt gcatcggcca atgcaaacta ttgaacgtcc atgaaattgt gtcaaactac
+ 721 tagtgtgtgg acttgcgtca aggccatggc gcaatactca aagccccggt atttatcccc
+ 781 cgcagagtat ccgtgcggat ggagttccac agctctttgg acatgcaatg cgtggcgcta
+ 841 catgctccgc tgatacagaa tatctaatgt ctcgcctctt gccgtcgacc ctacaactac
+ 901 tgcacgggca gagtggacgc gacccctgag cggtgcagaa ccttagtata aggcaagggt
+ 961 ggcacggccg agccgcactt gctcctacta ggccgtgctc gaagctattg atgcaagcac
+ 1021 agtattcccg atttgtaaag caaggtgccc gtagccatac acccagctac tcaccggcca
+ 1081 atttcgaccc tctctatctc agacctccgc atattcccaa actcctgctc aagtatgaaa
+ 1141 tgaccggctc ctcctaaggc ctgcggacat ggagtcatgc gtggaatgcc gtgtaggtag
+ 1201 ggtacacaca gccttaccat gtagggcaat aaattataga ctactgacat tgattccttg
+ 1261 agggcccgtt cacttgtggg ggaaccagga aggcgccgat agtcatcact taaacacatg
+ 1321 cgacgcatcc atttcaagaa agacacgcta cgggtctaca ccgcctatag ttctaatttg
+ 1381 ggccccggta cgcacatcga tgtactctcc attacagcat agcacatcag cggccctagt
+ 1441 tagcgcttct ttttgttcca acattcaata gcggggactg cattatcctc accctatttg
+ 1501 ttgcataggt atttggccgt atacttggga aagagcaacc acgggagtgc actagaaact
+ 1561 gattcaccca tgttataacg cgttgctcgc aagtcgtact gtggccacgc acaggtcagg
+ 1621 caatcgcaac catgtcttag cagtttgtaa gaagaccttt aaacatgtac ctcacagcaa
+ 1681 tctcggaact tttaattttc ctgagtcaat gacatgctag ctccgtccac ttgtaatcac
+ 1741 cgtcataaca cagttagcct gcaaaagggc gtgtacacct tgccacttta aagctgaccg
+ 1801 aataacctac ctacaggaga tgcttagtgc cacggaatga tctcgcaatg cttagtctta
+ 1861 cacccagtga atcaacccaa gacctcgccg actgaacggt attgagtcca atcccgagag
+ 1921 gcaatttatg gccgttagtg acagtcggtc gctgatagaa taaggcagac tcgtcttaag
+ 1981 cgggctgctt taagagaaaa tggagccctg acgaagaagt ggatgaacca ggttttgaca
+ 2041 acgtcccata ttggtaatgt aggctcgtta tcaagagata ggtttagaag gctcaatgct
+ 2101 cgacgtaaaa gaagtcttaa gctctatgag ccagtgatga gagctaatta tagggcgcat
+ 2161 tcgttggggt aaggttgcga attgtcattt aactaaaacc gacggcaatg gtttcaccgg
+ 2221 agctgagatc gcattaaagt cacactacga attatttgtc cccgcggctc cagagacaaa
+ 2281 tttctaggag tgggttcatg gagaaccgtg acaagcatgg tagcttcaaa tagcgtcatc
+ 2341 ggatcttaaa gtgattgtga catatatggg attgcgcgtc tctcttacac aagctagtgt
+ 2401 gcgcgaggtg ctgaacacct attacgtcaa ctcccgggat cccggcgggt tacagagaca
+ 2461 taagcagggt gtccatcatt aacttcgatg ttgagcccgt gccctgatca aacacctctc
+ 2521 gtagtagtgg gtgccggccg tgtattattt tgggggagag gatgcgccct aagcaatttc
+ 2581 tttccatcgg ccagccattc gacgccggca cgcaagttgt tgcgggcact gttgcagttc
+ 2641 ccgtactaga gtctcaagtc tagaggtacc agcatcagga agatgggtac ttcgtgtgga
+ 2701 tcttctcctg aacctgaaac ctgaagagct aaagcgcgtc gcgctgccat acgataagtc
+ 2761 gctctcattt ccggaagacg tcgttgggtg atggcgaaca atcgcgaaac gaaaatcgcg
+ 2821 gtcggtatgt tgattcaaga cgggctacgg gcgggttact aacaggtgcg cagaaatgtg
+ 2881 atgggtcact tgaccatgaa ctttcgcgcc gtcgcttctg tggactggcc ggctccctga
+ 2941 tagtgcacta gcccgttgat atgcccatta ccatttggcg gcgcagtgtg ccagcgggat
+ 3001 taagatgcgt ggcgtacaac tatccgcact ttgctgacgc acaaaggcaa ctgatggaca
+ 3061 gccttcgggc attcgactgg ttggctgagt tcgcctgcct attaatatgc ttgtggaaat
+ 3121 tgatttacag cgcctacttc tacttaggtg tacctattta cggcacaggg ataaaggctg
+ 3181 acagaaaagt cctggacagg tcataggtag ttgtcagacc tacaatggta taacttgaga
+ 3241 gtcctgtacc gcacatgcgg ttgtagctag atgtccagaa gaccgtagct agcgacgagt
+ 3301 gggttgcacg cgcattttgg gaaggggctg cgcgagggtg gggtcacggg ttattccatt
+ 3361 tctaaatgct aaaccagcag ttgctttagt tctgacctag caggcatgtc atatgtatgg
+ 3421 ctagattatt agtacaatgc aggactaaga aagcctgaga cttaaatgcg ttggtttttc
+ 3481 agccgacggg ccgggagggc agatggccga atgcgcactg aggagtgcat tgcgagggaa
+ 3541 taggcggacc accaggtccc ctcacatact gtggataaac ctacccaggg acaactcacg
+ 3601 ccatcatttt caagagtagc actactttcc actaagtacg gtttgtcgag agccggtggc
+ 3661 accgtgcgac gagcttgtgg gcactaggcg aaccgggtta tataggactg ccttgcggtg
+ 3721 cgggaatact ttaccccgtg gagaggccat aaaagcttac atttattgta gccgctagcg
+ 3781 gtttcgacgc gctcaagtgg ggctttatct tagagtatca aataatgccc tctcagcttc
+ 3841 atcttgattt ttgtgtttgg ggtagtgtat ccgatgggtc accttcttga ccttggggag
+ 3901 ctccatccat cgtaccaata ctccgtttct ttgtgttgcc taccgagtaa tcgaataccg
+ 3961 cacgagggct agaatctaat ttaaggtggg tcttatccct gttgtttgga cctaacgctg
+ 4021 taacaaatca cttccgcgac gggtgtcatt acgtcttcta tccgccaccg gttcaacagt
+ 4081 gcgtcgaatg ccaagtccct attacccgca ttgtaaagcc attacaatac ctccggtgat
+ 4141 ataattgatt gccggttggc aagggatcat ctgtacgggc cgcgattgat tgctgataag
+ 4201 gaacggcggt aaggaacgta tcgcgtacga ggttgtacac tggaaccgct aaacaagcgg
+ 4261 tatcgctaaa ttaccggcga ttatatcaag ggaatcttag gtagcacgaa gccctacgcc
+ 4321 ctggaaacag gatcggcgcg aggccgtgga catattagcc tacgtttttt tacacccaga
+ 4381 tttccgacga tgtccacagc taaggctatc ctaaaccgca aacacatata accgcagtat
+ 4441 aaagcacggg atgattcctt ggccatcttg caagcagtgc aaggcaattc tggtgatagg
+ 4501 ggcaaggcag tgaaccgagt ggtcagcgta ttgtgaccct gcaattgtca tggcagataa
+ 4561 ttgtttatga acctgtttca cacacccatc ccttggatct ccagcgtagt tactaatagt
+ 4621 acgatttcct ggtgttctgt cacccgcctt gctgccttca cgcctgcccc acgttttgct
+ 4681 gtccactgaa tatcgctcta attaataggt gtcacactgt atcaggtaag tccattccgg
+ 4741 gtgctattgg atcattcctg agatgtacca ccgatcccat aggcgttagg tcttacatct
+ 4801 ggagtgaaaa agatcagcat cgaactatag gtagataaag gtcatgactg ttaacagaga
+ 4861 atcgttccta tcgcaacctt cactaactgg aaggcacccc cacactttga ttagtaagcc
+ 4921 cctagcgaat gtagtgatcc aagaacatcg agtatacttt agctctcggt tcaggcatgt
+ 4981 atgcaatcga ccacccttcc gttcagagta ctctcaacca gcagatttct aaactttata
+ 5041 gcctccgccc actaaaattg ccttatctca ggttgactct tggatgtagc tgtaatctaa
+ 5101 catacacatg gagctgcggc aaattatcgt acgtccaaac caccaccgga tcagtggcga
+ 5161 tactattctc gcaaaaaagc catccagcat tggaacaagt gttaaccagc atttttctga
+ 5221 gtcccccgga aagaaagttg actacactac atccataaat gctagagtgt ggattcgcca
+ 5281 tgtgttacaa cggtcaaccg aaaggttagc atgatacttc gttgttcaat cggacgttcg
+ 5341 agcgccctcc ctgtttatca cttgatcccc cttttgaaac atgtgcgctg cgacgcaggg
+ 5401 ctgggagagt caccggaaac caaaagcccg acctcggacg tgtagggccc tccgtttgcc
+ 5461 atcaatggcg atgtaggatt ctcttttaat acaacgttca ctcaattaac gtcttggtat
+ 5521 aagcgtcgaa cgtgaccgag gttgacacca gtgtcacggc tgcgccgggg tttgttgctc
+ 5581 cgcgtgtaca gggtattggt tcgatggtgc ctcctctacg tagatctact ggataaccgt
+ 5641 ccccaatatc cgcttcccaa cgtagattgc cgacaggcat aagcttcggg ggcgcaaagg
+ 5701 ccgacgtccg cattgcagtg tagctttgtg agcaggaagt gtgatagtct ttcgattatt
+ 5761 aaagtctgag ctgaatgaaa aaaggtccaa cgaatggagg acgcgaagac atgggtgtct
+ 5821 cttatggccc gagcgggagt aatggcggtt cgtacataaa ggctgaaagg attctggcgt
+ 5881 tagctgtctt acgttggatt ggcccttcaa attatcgatg ttagctgatt cggtgtaccg
+ 5941 ggcgaggaaa gcgctctcag aacaacttca tatacgaggt tcgactataa tggtctaagc
+ 6001 tcctgggcta gtctcaagaa gcgggtacct ttagtagcac gtatcgacgg caaagcaaag
+ 6061 aataaaaact tggctttgca tcgtgcaaag atttctaact aggttgttta agggctggta
+ 6121 tctatgtccc gctataacag cgcgcctaca gtagaagttt aaccatgaca tacctttgaa
+ 6181 gtgttcgtat cacacacaag gaaggagcat gtggacacca ctgagctttg atcagcacgc
+ 6241 gtctcagagt ttcaggggga cccaaattac tggtcctcaa ttgggacgcg accgcatctc
+ 6301 cccacgaaag cttatgggga ttgcccactg cccagcttca aatctgaagg ttcggcttat
+ 6361 tgacagggtc taacacgcag ctcaactgct cgaggttaga ggcgtaatga cgggccccga
+ 6421 tagccttcta cgattacgtc cagcaggaac cccacagctt ttccctacgt ctaacaccgt
+ 6481 gaaagcaaaa ctgtctgccc ttttacatgg tctttaagga atctctgcac ttatgttatt
+ 6541 aggtaagctc ccataagagc accacttcgt gtaccttgct aactcccttc atccccaccc
+ 6601 gcgaaaactt aagacgtcac ccctgttatt atcccgtgca ctcctaaagt gcgatgggca
+ 6661 agaacgcaaa caattgtctg agatttatat gggcggcgga catagtcaga gagccttata
+ 6721 taatctccca cgtcttgcca gtccgagtta tgagaaaccc gggaccgatg acgctattac
+ 6781 ggtcgcccag cgaggttcaa cagagcgagg cataggagtc attacgcgtg ttagcttcaa
+ 6841 catgcgtgga agtgaaacgg atctataaaa cggcgtggag tcatcagctt gagcagatct
+ 6901 aacttactcg ccacgcgcgc aaatcgtctt tcgctgtcca cgttatacgt aactcgctgt
+ 6961 cacgctagag accgtatgag gtgggcggat agtggtgact tcaaacccct aagatgccag
+ 7021 cgcaatacgg catcgcaggg caagcaacac cgcacagcat gtccctaaag ggaagattta
+ 7081 atacggactc agtcaagttg tgagaaacga caatacattg agtggaatgc cctttggtac
+ 7141 gttggcgata gatctaacga gaaacttcaa cgagatctag agtatcggac tgagatgcat
+ 7201 catggctagg gattgctgaa tggatatctt tgccaaaatg agctcgacta ggaatctcag
+ 7261 actgccagct acgaaaagct gggggatatt catttccgct cttgtaaggc gcacgatgac
+ 7321 cctgtggagc aaaattcgac gcggcaacgt agtcaaagta cggcctatct gggacggaga
+ 7381 tgggattgtt tctgtattca tgccggcctc ttgagattgt aaggataccc ggccacagtc
+ 7441 tcgtaagaaa cccgatatcg ctcaaacgaa ttgacatcag ttagggcttg cgctctagca
+ 7501 accacgcgtc gggtgttcga ctgaatttaa gatccagcgc aaaccattcc ttaaaggcgg
+ 7561 tccaggtgaa accggctctg ataatgtaca gtggattgtc cagttcgctt caaagtgcaa
+ 7621 tcaggcaagg tactggcaag tcaccgcttg gggccggttt cagtggagct ttatcgacaa
+ 7681 aaggccgggc cctttggcct agagctcact tttggtgtcg ttcacgagtg agaactttgg
+ 7741 ctcgcagctt gaatgcttgt cacgtttagg gttatacaac gtttctataa actacctatg
+ 7801 acaaatcccg atcttctgaa actccataag gactaagaga gtccgcgaca gtttcacttg
+ 7861 gtcggtgcta ttgactatgt cacgcatgcc cggtaaagct tttaagcaaa gcctgatata
+ 7921 tcacgggagg ttactcaaag cattttctaa agggacagcg gactcacatt agcctaatat
+ 7981 aaacccgatc aggccatgca cctcgattca ccggaaggta gtaccatgca ccggatattt
+ 8041 gggacaacag tgaatagtac atcgtaaaat gtcaaggcct agctattttt cactggtgtc
+ 8101 ttatctctat tacaacacac acggatgtcc cgagcctaca ctttcaaata tactcaaggt
+ 8161 tcgctgttaa gggtaataca agagtgctcg gtttagtatc catatgttgg tacaagtgac
+ 8221 tgtgctagcc gtaaattaat tcggcttcca ttccagcttg ggtgtttagg gtctagacgg
+ 8281 ttgaaaccag aaagagtaca gacaaaaccg tagctctccc aaggttgatc ctccagacac
+ 8341 ctacccacac tagtagcgca ggcctagagg agacgttagg agcggaattg tacattcagt
+ 8401 atcgcattaa gcacaaagac agacaaacct agaagccact tatcccctcg taggagtaca
+ 8461 acggcagcgc tttcgggagg agttgcctaa ctacgctctg gacagcaagt cccagaatga
+ 8521 agaaaatgac ttggcgagaa cccaccacta catgcagggt cttgggaccg gtcagcacag
+ 8581 cttatccatg cggcaattcc ggacgaccgc gaatgaggat cacgacactg ccgatgttgc
+ 8641 accattgacc ttctcctatg caacaagggc ttaagatggt agatggtaat agagtagcct
+ 8701 gcgaccttat gcggtaatac acaaaaaccg gtaaacagtg cgttgatgct gtgtgctggc
+ 8761 gcatttgtgt accttgctgg gctcgtataa aattctgtca gcaggacgtt cacctccctt
+ 8821 ctgctagtcg ctaggcacaa acggaaaagg tctaatcgcg cgcgtgctcg ttagagtact
+ 8881 ggggcctccc accacggatg atcacctcgc cgatacattt ggccttatgt ctcaataaga
+ 8941 cctcatggtc tatcctacac catagatttg gaaagtctag ttgctgccta gcaggctgat
+ 9001 agcaagcgtc gtacgaggat cgaggaaggg cactcatggg agtgtagcgc tagccatagt
+ 9061 tgacctgtca gccggtcaag gttggtccga acctagccag ttagacgacc agctccccca
+ 9121 ctattgcaca gtgcctgtat aagcacgtca gtgtctggca ccactgtgcg cggtgtggtc
+ 9181 ctcgggacga tcttcctacg gctacccatg cgctagtgat tacagacgat cgttttttct
+ 9241 ttttctgtgg tgcaaataca caagatacgt caagagtcct agcagcctca tcttgccaat
+ 9301 tgcaggggta ccgattcacc catggtatca gtcacgcaaa aaaagacgac atcggagttg
+ 9361 ctggcgactg gcaaaagaaa acatctatct gccgtggcgt tcgtctagcg cagcgagccg
+ 9421 actgactact ccgttatctc aaatttagtt tcgtaagatc ttcacgggag ccggccagct
+ 9481 gaagaatcta taggtctacc gctagaggaa gcccgtttac aaccgacgta ctagtccgac
+ 9541 agcaatcgtc agcatgccaa tttattgtat caggttgaga atgcaccact acggaatcga
+ 9601 cgtgccactg gccgcacgat actagtgcgc tggtaaacag gccaggagct ctaaatctgg
+ 9661 agtggtgtga atttaaccgc ggaacgattg ttgcacgcgg tccctgtgac tctgttggga
+ 9721 gcactgtccc cggctccgga taagtgatgt gaacgaaaag gtgggctgac cagagatagg
+ 9781 gttaaggacg ggcgatcgta gtggacgatt actgctgatc ttccgagcac tctgagtcgc
+ 9841 gcggcgtatc gggagttacc ccgctcgcta cacatctgaa ttccgccgga tactatgggt
+ 9901 gcagagtgga tcaccttttc gtgacccgta tattcgtcgt tctcatcact gtcctccgcg
+ 9961 atttatttca atcgtcggtt tcgccagatg cattcctggg gaagtcatcg cgacagtgcg
+ 10021 ctgcgcgcac agctcttctt ggtttattcg agattgtggt ttatcaacat ggtctatcta
+ 10081 cggactgatt agaatattcc cacgttaagc cgacgtgcat tggtactggc tccttaatta
+ 10141 agcgcagagg gtaggcgcct tttcttgtgc aaaccattat atgaggaact agcaaacact
+ 10201 atggcgcaat atgtccacgt gactcgagca ttctgtgttg cggtagcgat ttcactagtc
+ 10261 acaaacggat agattctacg gcgcacccgg tgcatcgttg tatgttcagc aatttggtca
+ 10321 tatcccgctc ctctattcaa tctctttttt cgtcaggggg ggcacatact tggagcagct
+ 10381 gcgcctaaca ttacaataag cagtcggagc tcagtacaaa acccttatct tagcggtccg
+ 10441 ttctggaatt cggtctcagg agagacactc cttcatcaac agcagaggtt acatacgttt
+ 10501 aacctgaccg atggttgccc atcgaaagca aggacccacg ggtaggcagc tgttgtttga
+ 10561 tatgcttttg tccccggaag gcgccgataa aattatacgc cgtcccccgc gtccgttacg
+ 10621 agcttcgtga tgttgcgggc tgaagttccc tacgagtcaa taggccaact cgaatggcta
+ 10681 aatggttgca acccacaggc tcaactttga aggtaatacg ccaaaatcca atatgctctt
+ 10741 tcgggtagcg cataaaacct tctgggggcc actgcagaca gtcatggagg actacgtgca
+ 10801 acactacgct ctagagtgat gatgtggcag tcaaccgagg gctgttaaga gaagtctgtg
+ 10861 cacgaaaatc aatgagtcgg tgtaatcttc accttcctac aaaccaaggc ttgagggcct
+ 10921 caatttcgag caccacttct tgaccaagcc gttcgccggt ataggagtta cgaattcggg
+ 10981 tcgtctgccg tctttgaacc atagataagt acctcccgag tcgggagaac acgaatcgca
+ 11041 tcagaactca tcgaagggtg ttactttgcc catcggcatc cccgaagatt aattgcattc
+ 11101 gaaattttaa cttcgagaat catccgtgct aaccaacgtg gacgagctat gaacgtttac
+ 11161 gtgttcagta tctaggaatt gacacgtctc cgatagcggg agtcacggca tgagttacgg
+ 11221 cttttgtgac cagcgtctgt gtaattttat tgacagtttc atatatagtg tctcgtcttg
+ 11281 cctttgagat tcacaggctg taagagggat gccgtcgtgt atatgcctgc agttagagct
+ 11341 tccttgtcag gacgagcaac tcactccttc tggtgatgct ttgctagcat gtagcttcgg
+ 11401 gtacttgcgg aaaaggacag cctacagtgt ctgcggcggt acgtcactaa tatgacatac
+ 11461 gctgtggaca tcgtgaagcg gcgaatcgct ccagattgag gtttacagag tactccatag
+ 11521 tcacacaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_4.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/all_construct_records/construct_4.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,350 @@
+LOCUS construct_4 8074 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_4
+VERSION construct_4
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CAGA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ homology 5..8
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..1093
+ /source="part_G"
+ /indicates_part=True
+ /note="From part_G"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 1094..1097
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1098..2746
+ /source="part_H"
+ /indicates_part=True
+ /note="From part_H"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 2747..2750
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 2751..3085
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 2751..3085
+ /source="part_I"
+ /indicates_part=True
+ /note="From part_I"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3086..3089
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3090..3498
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(3387..3407)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 3090..3498
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3499..3502
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3420^3421
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6918^6919
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 5..3502
+ /source="construct_2"
+ /indicates_part=True
+ /note="From construct_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3503..3506
+ /label="GTCA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3507..3510
+ /label="feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 3507..3548
+ /source="part_L"
+ /indicates_part=True
+ /note="From part_L"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3549..3552
+ /label="ACCC"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS complement(3746..4537)
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS complement(3746..4651)
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3617..3645
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 4962..4967
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3722..3745
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 4940..4945
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 4785..4790
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 4821..5373
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3560..3670
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA complement(4824..4931)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5460..5468
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature complement(3672..3712)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 4735..4758
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 4806..4811
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene complement(3746..4651)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 4785..5373
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3584..3607
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3553..3558
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 6763..6786
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6942..6972
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 5743..6762
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ gene 5743..6762
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6985..7002
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6895..6919
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6946..6970
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 6787..6834
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 6990..6995
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 6985..6987
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 3553..7002
+ /source="part_J"
+ /indicates_part=True
+ /note="From part_J"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 7003..7006
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ promoter 7083..7261
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 8071..8074
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ terminator 7818..8070
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS 7263..7813
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 7007..8074
+ /source="part_K"
+ /indicates_part=True
+ /note="From part_K"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cagaggagga acttctatgg gacgaaagat gcgcagctcg acaaatctca aattggaaac
+ 61 cgtctaaggt ctttgagccc acgctaggcc accgaatagt tgcgagctcg tgggcaattg
+ 121 ctggctagcg gtttgtatcg tatacgtaac aagagattgc gccggattca ttcgtgtggg
+ 181 gtgctttcac atcggaatac tcaagagtgg gggtttgcgc tttaatatga cggcctcatg
+ 241 caccccaaaa ataagagcgc caatttcatc gaccacattc cggacaattc tgacttccct
+ 301 gtcggatcga ccctcgctca caactcctag aactccaaga cggtaggacg tcagccgaaa
+ 361 aggaggagtg acgacgggcc ctcctagctg aagcaatggg gggcgtcgac cctagcctgg
+ 421 tgtgggactt cggagggtcg ggcgtgtggc cattcctgca cgaggggccc ttgcagtatc
+ 481 gaactttgac gagaaagtgg ggggcgacct ataaacatag cggagttcaa tactcctgca
+ 541 agtgcatgat gacgttcagc gttggcacat cgaacgcgtc gctacacttg ctcaccggaa
+ 601 ggcaaaatag accggcagct ggcccgcacg gacgtctaga ctcctacgct gtcaaatgca
+ 661 cgatgactat tagcatgcgg aattcgaggc ggccggtaca tcgagacacg ctggtcttaa
+ 721 tacctgtgtt atgtcaaaac aagtgtctcg gcggctttgt actacgctgt gaatgcgcat
+ 781 gatgttgcga gaagctgaac gttggtagca gtctacaaca gaaccgacga gctacggacg
+ 841 ggttacagca ggatcccctc ttaaggcatt attcgacgac tccaggttct aaccgatcag
+ 901 taattgcctc ggatggtcgt acgtgttaac cgagacagca aggcaccaca tagacaactg
+ 961 catagggcgc ctacaggtcc acaatcaggg tggcccaaga tcctcaaaga cttgttgcag
+ 1021 tctctgctta ttccgtttaa cacgttgtgt gagctctagc ttactacctc atcggtgtcg
+ 1081 ggagtgattt aggaatggaa gacgcgttta gtcttcggcc cccagacggc accggcagag
+ 1141 ccactgccaa tgccttttac gctgaactct tcgactttgg catgtgcgac tgactatacg
+ 1201 ccgatggccc taccctgcag cggaaaggca cagggccaaa aacagtggaa gcgcaccgct
+ 1261 agagctttac taaatccttt agggtgaacc ggtgttcagt caacagaaac atatgactag
+ 1321 tccttaatgg cactactaaa ggcggcccat ctcttttgta ggtcacgtct catcgtttag
+ 1381 caagcgtccg ccatccgagg agtatcctag tacgtgagag ggtgttttac ctcatcacat
+ 1441 ggtttttggc tagatgtggc agatgccagc tgatacctta caacccgcta taacggtttc
+ 1501 tggatcgacg atacaacctg cttcggcata tcataatggc ggcctcatag gacttccaat
+ 1561 catggttatg cgagtttgat gtgttgaaga ttgtgagggg aaaccttttt ccgagtacgt
+ 1621 tgaatctgcg actgatggtg aacaactcat cgagagggat gtgcgggcag tctccttgat
+ 1681 gcgcgaaaag gagtcgcgac cgcgtgttcg tgacgcactt gatgctagac cgtaggggct
+ 1741 cattatctcc tgaaacagta gctagctttt ggtgtccgag tcagcttagg cacagtaatt
+ 1801 gaaaagaagg aaatgcgtga aaactaaacg tagacactcc ttgctaagaa ttccctggtc
+ 1861 tttttcgagc atagactacc gtaggtaaaa ggcttgtcgt gtcacaaata gacttgatct
+ 1921 gttcggcata tacacatcct actgcttcag taaccaagga cgattctccg gccattggac
+ 1981 tgtgggacca cccgcgttca aacggaatcc tctacgaacg gttaagaaag gagcccactg
+ 2041 cttgcggaga catatcgttg ctgagtggta caccggtgag tcaaaaagta ctgacactac
+ 2101 tggtggactc tcgggtacga tgtgtggggt attggcatac tatggcgcta agcgtggaat
+ 2161 agtgtttcca atagcccttt acctaagaag cattctgaca catgggttgg acttttacac
+ 2221 agacctataa ctcgtatccg gcctggtgat gtatgtccgc ttatcactga atgcaggatt
+ 2281 ccgccaattc cgctcgcggg ttctcggaca acgggccatg gagatggatc aatgagccat
+ 2341 gttgattacc atttcactac acacggttag tcaattccgg agatcataat tcgacaattg
+ 2401 aatatgcgtg atacgctttc tgttaccagg atcgttgcta attagtttcc aatgtcacag
+ 2461 tgttgggcgg cgaggtatca cggcgctctg ggtagaatgg cggtgcctga ctggacctca
+ 2521 taactggtaa catacctatg accaaaggag gtcagacacc gatgagtcgg tgacatgggc
+ 2581 ggtcacagcg tgccctgcat agtaatacag ctcgtttcta gacatttgtc ctaattcgcc
+ 2641 acacaagtac gagagcgggg gtaacccatc accatcgtgc ccgtaggtac ctaatcttca
+ 2701 tcgagcgcta ttgttaaagt ggactcaggg atcggcatct cgtgtagctt ttattatccg
+ 2761 gcatgcatgc ggcgttgcat cgcttcatcg tcatcgacat atcgttagcg ggacttatca
+ 2821 gggtcccatc acggctgtga cagctgttca taagtgtaat agcagtcacc ccaccaaatg
+ 2881 caagactgtt cccaaactaa gtgctaggga ggttggctac ctatcggcgt ggcagttgac
+ 2941 cgggtttttc ttagtacctg ccttccaatc tccgataaaa gcaagatgac ttcctgcttg
+ 3001 cgctaaagtc tgaattcgct aagggggcag attcattacc agagactgcc aaagtcaacc
+ 3061 gccgaacgat actggaatat atggaggtaa gctcccataa gagcaccact tcgtgtacct
+ 3121 tgctaactcc cttcatcccc acccgcgaaa acttaagacg tcacccctgt tattatcccg
+ 3181 tgcactccta aagtgcgatg ggcaagaacg caaacaattg tctgagattt atatgggcgg
+ 3241 cggacatagt cagagagcct tatataatct cccacgtctt gccagtccga gttatgagaa
+ 3301 acccgggacc gatgacgcta ttacggtcgc ccagcgaggt tcaacagagc gaggcatagg
+ 3361 agtcattacg cgtgttagct tcaacatgcg tggaagtgaa acggatctat aaaacggcgt
+ 3421 ggagtcatca gcttgagcag atctaactta ctcgccacgc gcgcaaatcg tctttcgctg
+ 3481 tccacgttat acgtaactcg ctgtcacgct agagaccgta tgaggtgggc ggatagtggt
+ 3541 gacttcaaac ccctaagatg ccagcgcaat acggcatcgc agggcaagca acaccgcaca
+ 3601 gcatgtccct aaagggaaga tttaatacgg actcagtcaa gttgtgagaa acgacaatac
+ 3661 attgagtgga atgccctttg gtacgttggc gatagatcta acgagaaact tcaacgagat
+ 3721 ctagagtatc ggactgagat gcatcatggc tagggattgc tgaatggata tctttgccaa
+ 3781 aatgagctcg actaggaatc tcagactgcc agctacgaaa agctggggga tattcatttc
+ 3841 cgctcttgta aggcgcacga tgaccctgtg gagcaaaatt cgacgcggca acgtagtcaa
+ 3901 agtacggcct atctgggacg gagatgggat tgtttctgta ttcatgccgg cctcttgaga
+ 3961 ttgtaaggat acccggccac agtctcgtaa gaaacccgat atcgctcaaa cgaattgaca
+ 4021 tcagttaggg cttgcgctct agcaaccacg cgtcgggtgt tcgactgaat ttaagatcca
+ 4081 gcgcaaacca ttccttaaag gcggtccagg tgaaaccggc tctgataatg tacagtggat
+ 4141 tgtccagttc gcttcaaagt gcaatcaggc aaggtactgg caagtcaccg cttggggccg
+ 4201 gtttcagtgg agctttatcg acaaaaggcc gggccctttg gcctagagct cacttttggt
+ 4261 gtcgttcacg agtgagaact ttggctcgca gcttgaatgc ttgtcacgtt tagggttata
+ 4321 caacgtttct ataaactacc tatgacaaat cccgatcttc tgaaactcca taaggactaa
+ 4381 gagagtccgc gacagtttca cttggtcggt gctattgact atgtcacgca tgcccggtaa
+ 4441 agcttttaag caaagcctga tatatcacgg gaggttactc aaagcatttt ctaaagggac
+ 4501 agcggactca cattagccta atataaaccc gatcaggcca tgcacctcga ttcaccggaa
+ 4561 ggtagtacca tgcaccggat atttgggaca acagtgaata gtacatcgta aaatgtcaag
+ 4621 gcctagctat ttttcactgg tgtcttatct ctattacaac acacacggat gtcccgagcc
+ 4681 tacactttca aatatactca aggttcgctg ttaagggtaa tacaagagtg ctcggtttag
+ 4741 tatccatatg ttggtacaag tgactgtgct agccgtaaat taattcggct tccattccag
+ 4801 cttgggtgtt tagggtctag acggttgaaa ccagaaagag tacagacaaa accgtagctc
+ 4861 tcccaaggtt gatcctccag acacctaccc acactagtag cgcaggccta gaggagacgt
+ 4921 taggagcgga attgtacatt cagtatcgca ttaagcacaa agacagacaa acctagaagc
+ 4981 cacttatccc ctcgtaggag tacaacggca gcgctttcgg gaggagttgc ctaactacgc
+ 5041 tctggacagc aagtcccaga atgaagaaaa tgacttggcg agaacccacc actacatgca
+ 5101 gggtcttggg accggtcagc acagcttatc catgcggcaa ttccggacga ccgcgaatga
+ 5161 ggatcacgac actgccgatg ttgcaccatt gaccttctcc tatgcaacaa gggcttaaga
+ 5221 tggtagatgg taatagagta gcctgcgacc ttatgcggta atacacaaaa accggtaaac
+ 5281 agtgcgttga tgctgtgtgc tggcgcattt gtgtaccttg ctgggctcgt ataaaattct
+ 5341 gtcagcagga cgttcacctc ccttctgcta gtcgctaggc acaaacggaa aaggtctaat
+ 5401 cgcgcgcgtg ctcgttagag tactggggcc tcccaccacg gatgatcacc tcgccgatac
+ 5461 atttggcctt atgtctcaat aagacctcat ggtctatcct acaccataga tttggaaagt
+ 5521 ctagttgctg cctagcaggc tgatagcaag cgtcgtacga ggatcgagga agggcactca
+ 5581 tgggagtgta gcgctagcca tagttgacct gtcagccggt caaggttggt ccgaacctag
+ 5641 ccagttagac gaccagctcc cccactattg cacagtgcct gtataagcac gtcagtgtct
+ 5701 ggcaccactg tgcgcggtgt ggtcctcggg acgatcttcc tacggctacc catgcgctag
+ 5761 tgattacaga cgatcgtttt ttctttttct gtggtgcaaa tacacaagat acgtcaagag
+ 5821 tcctagcagc ctcatcttgc caattgcagg ggtaccgatt cacccatggt atcagtcacg
+ 5881 caaaaaaaga cgacatcgga gttgctggcg actggcaaaa gaaaacatct atctgccgtg
+ 5941 gcgttcgtct agcgcagcga gccgactgac tactccgtta tctcaaattt agtttcgtaa
+ 6001 gatcttcacg ggagccggcc agctgaagaa tctataggtc taccgctaga ggaagcccgt
+ 6061 ttacaaccga cgtactagtc cgacagcaat cgtcagcatg ccaatttatt gtatcaggtt
+ 6121 gagaatgcac cactacggaa tcgacgtgcc actggccgca cgatactagt gcgctggtaa
+ 6181 acaggccagg agctctaaat ctggagtggt gtgaatttaa ccgcggaacg attgttgcac
+ 6241 gcggtccctg tgactctgtt gggagcactg tccccggctc cggataagtg atgtgaacga
+ 6301 aaaggtgggc tgaccagaga tagggttaag gacgggcgat cgtagtggac gattactgct
+ 6361 gatcttccga gcactctgag tcgcgcggcg tatcgggagt taccccgctc gctacacatc
+ 6421 tgaattccgc cggatactat gggtgcagag tggatcacct tttcgtgacc cgtatattcg
+ 6481 tcgttctcat cactgtcctc cgcgatttat ttcaatcgtc ggtttcgcca gatgcattcc
+ 6541 tggggaagtc atcgcgacag tgcgctgcgc gcacagctct tcttggttta ttcgagattg
+ 6601 tggtttatca acatggtcta tctacggact gattagaata ttcccacgtt aagccgacgt
+ 6661 gcattggtac tggctcctta attaagcgca gagggtaggc gccttttctt gtgcaaacca
+ 6721 ttatatgagg aactagcaaa cactatggcg caatatgtcc acgtgactcg agcattctgt
+ 6781 gttgcggtag cgatttcact agtcacaaac ggatagattc tacggcgcac ccggtgcatc
+ 6841 gttgtatgtt cagcaatttg gtcatatccc gctcctctat tcaatctctt ttttcgtcag
+ 6901 ggggggcaca tacttggagc agctgcgcct aacattacaa taagcagtcg gagctcagta
+ 6961 caaaaccctt atcttagcgg tccgttctgg aattcggtct caggagagac actccttcat
+ 7021 caacagcaga ggttacatac gtttaacctg accgatggtt gcccatcgaa agcaaggacc
+ 7081 cacgggtagg cagctgttgt ttgatatgct tttgtccccg gaaggcgccg ataaaattat
+ 7141 acgccgtccc ccgcgtccgt tacgagcttc gtgatgttgc gggctgaagt tccctacgag
+ 7201 tcaataggcc aactcgaatg gctaaatggt tgcaacccac aggctcaact ttgaaggtaa
+ 7261 tacgccaaaa tccaatatgc tctttcgggt agcgcataaa accttctggg ggccactgca
+ 7321 gacagtcatg gaggactacg tgcaacacta cgctctagag tgatgatgtg gcagtcaacc
+ 7381 gagggctgtt aagagaagtc tgtgcacgaa aatcaatgag tcggtgtaat cttcaccttc
+ 7441 ctacaaacca aggcttgagg gcctcaattt cgagcaccac ttcttgacca agccgttcgc
+ 7501 cggtatagga gttacgaatt cgggtcgtct gccgtctttg aaccatagat aagtacctcc
+ 7561 cgagtcggga gaacacgaat cgcatcagaa ctcatcgaag ggtgttactt tgcccatcgg
+ 7621 catccccgaa gattaattgc attcgaaatt ttaacttcga gaatcatccg tgctaaccaa
+ 7681 cgtggacgag ctatgaacgt ttacgtgttc agtatctagg aattgacacg tctccgatag
+ 7741 cgggagtcac ggcatgagtt acggcttttg tgaccagcgt ctgtgtaatt ttattgacag
+ 7801 tttcatatat agtgtctcgt cttgcctttg agattcacag gctgtaagag ggatgccgtc
+ 7861 gtgtatatgc ctgcagttag agcttccttg tcaggacgag caactcactc cttctggtga
+ 7921 tgctttgcta gcatgtagct tcgggtactt gcggaaaagg acagcctaca gtgtctgcgg
+ 7981 cggtacgtca ctaatatgac atacgctgtg gacatcgtga agcggcgaat cgctccagat
+ 8041 tgaggtttac agagtactcc atagtcacac aact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/assembly_plan_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/assembly_plan_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,385 @@
+LOCUS construct_1 10366 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_1
+VERSION construct_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(223..1038)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature complement(139..179)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 5..8
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 20..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(223..1038)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 189..212
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 51..74
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 84..112
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 27..137
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3347..3377
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1367..1372
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1190..1195
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 1226..1778
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3396
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3192..3239
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_RNA complement(1229..1336)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1865..1873
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3413..3416
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 1190..1778
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3300..3324
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1345..1350
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 1899..2147
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3397..3401
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3395..3412
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1211..1216
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3168..3191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3351..3375
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1140..1163
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5..3416
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3417..3420
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ exon 5421..5618
+ /label="feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ gene 5421..5618
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 3421..5618
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ misc_feature 3421..5618
+ /source="part_B"
+ /indicates_part=True
+ /note="From part_B"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 5619..5622
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS 5623..8880
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 8881..9009
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 8091
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 8736
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 7683
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 5623..9011
+ /source="part_C"
+ /indicates_part=True
+ /note="From part_C"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9012..9015
+ /label="TTCG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9604..9633
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ CDS 9016..9528
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 9538..9603
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS 9580..9603
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 9016..9636
+ /source="part_D"
+ /indicates_part=True
+ /note="From part_D"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9637..9640
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ 3'UTR 9644..9953
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 9641..9643
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 9641..9953
+ /source="part_E"
+ /indicates_part=True
+ /note="From part_E"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9954..9957
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9958..10366
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(10255..10275)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 9958..10366
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cgctgtcaat atgcaggtgc tgcaggaatt tgtctccaat cgacttgaga tatcgcaagc
+ 61 atgaaattat attagacacg ccagagaact tgggaagcag cactggtagt gatagcaacc
+ 121 cgagtacagt aacgagtgag cttctgatca tgagctctcc tacggcgtca atgcgacgaa
+ 181 tgcccagcat gcactctcgc tatccatgcc tgctagggtg gcattatgct caggaacagt
+ 241 tgtagcttgg atatcgtcta gatgaaatac ctggacactg gttagcgtcg tcaagcacca
+ 301 aggacattca cacgctcgcg gtctttcgtc tccctaagcg ttcggcagtc gggcgtgaag
+ 361 aggttgtaat cagacggaac aaagcctgaa aaaattccag cgacgtagta ttcatgatcc
+ 421 tgtaccatct gtagccgccg cggcgcacga ttgaatgtag gctactaacc ccatccgtgt
+ 481 tagcgatgtg agtttctacc gcaacgaatg ctcaagcgaa ccttcttctt tcgtccgcaa
+ 541 cccacaagcc gtggttatga cagctaaatt gtcccagaca tccctttatt acacaagagc
+ 601 tccagcggaa tacctagtca cagcggtaat gacacaaagc tcttagttag tccagggact
+ 661 acttctgtct acagcacatc acactcatta tcagcatcag tgtagagacg gagaacatgg
+ 721 gctatcctat accaagatcc gccatctaaa catttgaagt ttcccgtctt ctataactta
+ 781 gcactcgacg ctattctgct gagtgcgctt agtctgtagc gacttgcgaa atccataaac
+ 841 tgagaattga aagagagtgc ataaccgaaa cctttgtggc atatttccgt tgaaacgtac
+ 901 cagaacagcc gtttagtgcg gaacatacag tatcctgata aagcactcaa cccaacagac
+ 961 accctatgcc gatagcggga tgctaacaag tatagtcatg atgatttctc ggacagcggg
+ 1021 gtttggtaca gctgcaatcc gtgatttaaa ttcggacctc tgcacacacc gacggttacc
+ 1081 catatcctct acggctgtag gaagttttac cttggatgtc attctgattt cggcgtatct
+ 1141 cacaggatgg tccaacgaaa ctaggcttta gacgagggat gaatgaccga cccccactcg
+ 1201 tggcactaac ggacagactt ccctgacggt tattcgacca ttaaagtcag acatgcgggg
+ 1261 gtgaataaat tagccaaatt gtgtcgaaga aaagacgtgc ggctggcaca taaggcagtc
+ 1321 ttgatcctag tcttgcaggg atgcacgtaa gtcgcctcaa ttaactgcag ccgagctcca
+ 1381 ggttaccaaa gaccctagta tgccagggcc taacggttgg agtatattat gggtacgcaa
+ 1441 tagtgcggaa gttaacctgg gcaacatcca ggtgagaggt tggacggaag cgacagtaag
+ 1501 tggccataga ctgccgagtc gtgttaatga atcgctatac gcccatggag ttgtggggtc
+ 1561 gttttatccg agtaggggcc cgctgactac ttcgtccaga caatatgccg tcttcaatag
+ 1621 tctacctgag agtcatgccg gcatttccga cgctgagtga aacccgcgta gccaggcgaa
+ 1681 atttgcatct tgaaatacca ctgcagatca gccagtaagg cccatataag ggcgctggtg
+ 1741 ttctggcgac agataaagtg ttatctaatg taacccgcgg acttttagag gatacttgaa
+ 1801 tgcgggcata tcgtcccacc agcgtcacgt ggtcgggcta gcggcagaca aactctgccg
+ 1861 atgtttttct ttgccgcgat agcgggctag tcaattcact atccggcgat gaagcataga
+ 1921 ttgttatcgc gcttatgcgg aggataatca agtcttggca gaacctgctc gctcatgcac
+ 1981 tggtgaggcg tggttatcct aacaaccgcc taggacgaag aatgggctcg gtagggacag
+ 2041 ttcgtgcgtt tagcttcgtc ccatcttaat gctgtctgga gggaggctac atgcgaacag
+ 2101 aagccgtggg cgaaagttgt tgatccgggt ctaacacgga taagggccat ggtgaacgca
+ 2161 tcatgcgata cttcttggta gttcttctaa catgaccgtg ccatagccct taccctttga
+ 2221 agaagttaac ctatctgccg tctcctgcac gaatagcgac tggactcggg tattttggat
+ 2281 acctcacgaa agcacttcga tcggccgaag catggatatt tcgccggacg ggcccgaata
+ 2341 gagagccttg tatgtcggtt agtacaacgc agtcctggag acatctacgc ggatgggcct
+ 2401 aggggctgga cttaacattg ggtaacgtac ctggtccaaa gtgaatgcaa agcactttta
+ 2461 caaagcgcgg gtccccgtgg gtgtttaggg tagaagattg gcggatgcta cgaacgatcc
+ 2521 cgctttgaaa ctatcattac atcgtgtaaa agagacactt aacaaaggcc aataaactgc
+ 2581 cagtaagaat cgctcagtgc ggtgctgggg acgctaagta ggggcaacag ccagtgaagg
+ 2641 acgtgaccga cctttctcag ataagatatg ctggcgtcta tctaataagc atagtgaaaa
+ 2701 accaaccatt tcacttacac gaagtacatt tgcattgcta gtaaagacgc ctaaacagaa
+ 2761 gtgcccttgc atgctgtatg tctatagtcc ttagggaagc atcagccctt ctacttattc
+ 2821 gaggtctgag aaaccctgga caagctccga attattcaat gtgcctgtct ccgaggttag
+ 2881 atagcgctat gctcttaaga gttgcacaga atgaccatcc tggaatgtcc ctggaggggt
+ 2941 ctaggtatgc tgatcgaagg gtgctctaag gacttgacgt gcgtccgagg agggtgctgc
+ 3001 ctccttcgcc tttagatcca acgcggatca catgcgcgtg agctaatagg atcaccttct
+ 3061 gctccgattt ttaccctcct gggtcacttc cgaatgaggt agcgggcgaa atataatgtc
+ 3121 tccactcgta ggtgttccct gtatgtgaag ctctatagtg gacaaaggtt tgatgaacta
+ 3181 gcccccgtat acgctctcac cgacggacgc gggggtctgt tatttgaagc atcatacatg
+ 3241 cgaaggtgcc ttctcagcaa cgaaaggtag tgggagtgta caagttcaat gcgccgccat
+ 3301 aggtctgagt atacaagggg atgcccccat ccacaacggg attggctacc cggagagctg
+ 3361 gctccgctcc aacaaataat tatattaacc tattggaatt ccacctgcat atcagaggag
+ 3421 agcatacggt gctctgggct cacacgtact tcctcttgtc acgcgccttt gtagagcatt
+ 3481 agggcggagg tcactgggac ggggatcaga gagcttaaaa tcccaagtag cagtgcctaa
+ 3541 ggtgtagaat cttgtgcaga tcttcgtctg gcccgaaacc tgggcctcca caacaatgtc
+ 3601 gggtctttta taatttgaaa acatcgcgcc ttacccgcac cgcgcaggac gattagacac
+ 3661 agggggtcat gtccatggtt cggggtaagc caaatttaca tcgagtgtgg gcttcattga
+ 3721 ggagagggcg ttacgatacc cgttaaatga aaacccggac agtctctaac tgataggcct
+ 3781 gataatcgcc aaatgaagtc gcaattagca gtacatgact ggcagatatg tcgccggaga
+ 3841 cggtatgggg gacctatcct aggttggcac gcgagcgcga atgacgccta tcttatcccc
+ 3901 ctgcacgtga tggtatcgtc ccaactatct tttacctcat caacgttttc ctgcataatc
+ 3961 tgcaagatgg agagtccgcg agtgcgggga gtacgagatc acaaatctgc cctgaagaca
+ 4021 aagctcgcag gccgtactca ggaaatagca tcgactcaca catatcggga acggcaaaga
+ 4081 gtgcatcggc caatgcaaac tattgaacgt ccatgaaatt gtgtcaaact actagtgtgt
+ 4141 ggacttgcgt caaggccatg gcgcaatact caaagccccg gtatttatcc cccgcagagt
+ 4201 atccgtgcgg atggagttcc acagctcttt ggacatgcaa tgcgtggcgc tacatgctcc
+ 4261 gctgatacag aatatctaat gtctcgcctc ttgccgtcga ccctacaact actgcacggg
+ 4321 cagagtggac gcgacccctg agcggtgcag aaccttagta taaggcaagg gtggcacggc
+ 4381 cgagccgcac ttgctcctac taggccgtgc tcgaagctat tgatgcaagc acagtattcc
+ 4441 cgatttgtaa agcaaggtgc ccgtagccat acacccagct actcaccggc caatttcgac
+ 4501 cctctctatc tcagacctcc gcatattccc aaactcctgc tcaagtatga aatgaccggc
+ 4561 tcctcctaag gcctgcggac atggagtcat gcgtggaatg ccgtgtaggt agggtacaca
+ 4621 cagccttacc atgtagggca ataaattata gactactgac attgattcct tgagggcccg
+ 4681 ttcacttgtg ggggaaccag gaaggcgccg atagtcatca cttaaacaca tgcgacgcat
+ 4741 ccatttcaag aaagacacgc tacgggtcta caccgcctat agttctaatt tgggccccgg
+ 4801 tacgcacatc gatgtactct ccattacagc atagcacatc agcggcccta gttagcgctt
+ 4861 ctttttgttc caacattcaa tagcggggac tgcattatcc tcaccctatt tgttgcatag
+ 4921 gtatttggcc gtatacttgg gaaagagcaa ccacgggagt gcactagaaa ctgattcacc
+ 4981 catgttataa cgcgttgctc gcaagtcgta ctgtggccac gcacaggtca ggcaatcgca
+ 5041 accatgtctt agcagtttgt aagaagacct ttaaacatgt acctcacagc aatctcggaa
+ 5101 cttttaattt tcctgagtca atgacatgct agctccgtcc acttgtaatc accgtcataa
+ 5161 cacagttagc ctgcaaaagg gcgtgtacac cttgccactt taaagctgac cgaataacct
+ 5221 acctacagga gatgcttagt gccacggaat gatctcgcaa tgcttagtct tacacccagt
+ 5281 gaatcaaccc aagacctcgc cgactgaacg gtattgagtc caatcccgag aggcaattta
+ 5341 tggccgttag tgacagtcgg tcgctgatag aataaggcag actcgtctta agcgggctgc
+ 5401 tttaagagaa aatggagccc tgacgaagaa gtggatgaac caggttttga caacgtccca
+ 5461 tattggtaat gtaggctcgt tatcaagaga taggtttaga aggctcaatg ctcgacgtaa
+ 5521 aagaagtctt aagctctatg agccagtgat gagagctaat tatagggcgc attcgttggg
+ 5581 gtaaggttgc gaattgtcat ttaactaaaa ccgacggcaa tggtttcacc ggagctgaga
+ 5641 tcgcattaaa gtcacactac gaattatttg tccccgcggc tccagagaca aatttctagg
+ 5701 agtgggttca tggagaaccg tgacaagcat ggtagcttca aatagcgtca tcggatctta
+ 5761 aagtgattgt gacatatatg ggattgcgcg tctctcttac acaagctagt gtgcgcgagg
+ 5821 tgctgaacac ctattacgtc aactcccggg atcccggcgg gttacagaga cataagcagg
+ 5881 gtgtccatca ttaacttcga tgttgagccc gtgccctgat caaacacctc tcgtagtagt
+ 5941 gggtgccggc cgtgtattat tttgggggag aggatgcgcc ctaagcaatt tctttccatc
+ 6001 ggccagccat tcgacgccgg cacgcaagtt gttgcgggca ctgttgcagt tcccgtacta
+ 6061 gagtctcaag tctagaggta ccagcatcag gaagatgggt acttcgtgtg gatcttctcc
+ 6121 tgaacctgaa acctgaagag ctaaagcgcg tcgcgctgcc atacgataag tcgctctcat
+ 6181 ttccggaaga cgtcgttggg tgatggcgaa caatcgcgaa acgaaaatcg cggtcggtat
+ 6241 gttgattcaa gacgggctac gggcgggtta ctaacaggtg cgcagaaatg tgatgggtca
+ 6301 cttgaccatg aactttcgcg ccgtcgcttc tgtggactgg ccggctccct gatagtgcac
+ 6361 tagcccgttg atatgcccat taccatttgg cggcgcagtg tgccagcggg attaagatgc
+ 6421 gtggcgtaca actatccgca ctttgctgac gcacaaaggc aactgatgga cagccttcgg
+ 6481 gcattcgact ggttggctga gttcgcctgc ctattaatat gcttgtggaa attgatttac
+ 6541 agcgcctact tctacttagg tgtacctatt tacggcacag ggataaaggc tgacagaaaa
+ 6601 gtcctggaca ggtcataggt agttgtcaga cctacaatgg tataacttga gagtcctgta
+ 6661 ccgcacatgc ggttgtagct agatgtccag aagaccgtag ctagcgacga gtgggttgca
+ 6721 cgcgcatttt gggaaggggc tgcgcgaggg tggggtcacg ggttattcca tttctaaatg
+ 6781 ctaaaccagc agttgcttta gttctgacct agcaggcatg tcatatgtat ggctagatta
+ 6841 ttagtacaat gcaggactaa gaaagcctga gacttaaatg cgttggtttt tcagccgacg
+ 6901 ggccgggagg gcagatggcc gaatgcgcac tgaggagtgc attgcgaggg aataggcgga
+ 6961 ccaccaggtc ccctcacata ctgtggataa acctacccag ggacaactca cgccatcatt
+ 7021 ttcaagagta gcactacttt ccactaagta cggtttgtcg agagccggtg gcaccgtgcg
+ 7081 acgagcttgt gggcactagg cgaaccgggt tatataggac tgccttgcgg tgcgggaata
+ 7141 ctttaccccg tggagaggcc ataaaagctt acatttattg tagccgctag cggtttcgac
+ 7201 gcgctcaagt ggggctttat cttagagtat caaataatgc cctctcagct tcatcttgat
+ 7261 ttttgtgttt ggggtagtgt atccgatggg tcaccttctt gaccttgggg agctccatcc
+ 7321 atcgtaccaa tactccgttt ctttgtgttg cctaccgagt aatcgaatac cgcacgaggg
+ 7381 ctagaatcta atttaaggtg ggtcttatcc ctgttgtttg gacctaacgc tgtaacaaat
+ 7441 cacttccgcg acgggtgtca ttacgtcttc tatccgccac cggttcaaca gtgcgtcgaa
+ 7501 tgccaagtcc ctattacccg cattgtaaag ccattacaat acctccggtg atataattga
+ 7561 ttgccggttg gcaagggatc atctgtacgg gccgcgattg attgctgata aggaacggcg
+ 7621 gtaaggaacg tatcgcgtac gaggttgtac actggaaccg ctaaacaagc ggtatcgcta
+ 7681 aattaccggc gattatatca agggaatctt aggtagcacg aagccctacg ccctggaaac
+ 7741 aggatcggcg cgaggccgtg gacatattag cctacgtttt tttacaccca gatttccgac
+ 7801 gatgtccaca gctaaggcta tcctaaaccg caaacacata taaccgcagt ataaagcacg
+ 7861 ggatgattcc ttggccatct tgcaagcagt gcaaggcaat tctggtgata ggggcaaggc
+ 7921 agtgaaccga gtggtcagcg tattgtgacc ctgcaattgt catggcagat aattgtttat
+ 7981 gaacctgttt cacacaccca tcccttggat ctccagcgta gttactaata gtacgatttc
+ 8041 ctggtgttct gtcacccgcc ttgctgcctt cacgcctgcc ccacgttttg ctgtccactg
+ 8101 aatatcgctc taattaatag gtgtcacact gtatcaggta agtccattcc gggtgctatt
+ 8161 ggatcattcc tgagatgtac caccgatccc ataggcgtta ggtcttacat ctggagtgaa
+ 8221 aaagatcagc atcgaactat aggtagataa aggtcatgac tgttaacaga gaatcgttcc
+ 8281 tatcgcaacc ttcactaact ggaaggcacc cccacacttt gattagtaag cccctagcga
+ 8341 atgtagtgat ccaagaacat cgagtatact ttagctctcg gttcaggcat gtatgcaatc
+ 8401 gaccaccctt ccgttcagag tactctcaac cagcagattt ctaaacttta tagcctccgc
+ 8461 ccactaaaat tgccttatct caggttgact cttggatgta gctgtaatct aacatacaca
+ 8521 tggagctgcg gcaaattatc gtacgtccaa accaccaccg gatcagtggc gatactattc
+ 8581 tcgcaaaaaa gccatccagc attggaacaa gtgttaacca gcatttttct gagtcccccg
+ 8641 gaaagaaagt tgactacact acatccataa atgctagagt gtggattcgc catgtgttac
+ 8701 aacggtcaac cgaaaggtta gcatgatact tcgttgttca atcggacgtt cgagcgccct
+ 8761 ccctgtttat cacttgatcc cccttttgaa acatgtgcgc tgcgacgcag ggctgggaga
+ 8821 gtcaccggaa accaaaagcc cgacctcgga cgtgtagggc cctccgtttg ccatcaatgg
+ 8881 cgatgtagga ttctctttta atacaacgtt cactcaatta acgtcttggt ataagcgtcg
+ 8941 aacgtgaccg aggttgacac cagtgtcacg gctgcgccgg ggtttgttgc tccgcgtgta
+ 9001 cagggtattg gttcgatggt gcctcctcta cgtagatcta ctggataacc gtccccaata
+ 9061 tccgcttccc aacgtagatt gccgacaggc ataagcttcg ggggcgcaaa ggccgacgtc
+ 9121 cgcattgcag tgtagctttg tgagcaggaa gtgtgatagt ctttcgatta ttaaagtctg
+ 9181 agctgaatga aaaaaggtcc aacgaatgga ggacgcgaag acatgggtgt ctcttatggc
+ 9241 ccgagcggga gtaatggcgg ttcgtacata aaggctgaaa ggattctggc gttagctgtc
+ 9301 ttacgttgga ttggcccttc aaattatcga tgttagctga ttcggtgtac cgggcgagga
+ 9361 aagcgctctc agaacaactt catatacgag gttcgactat aatggtctaa gctcctgggc
+ 9421 tagtctcaag aagcgggtac ctttagtagc acgtatcgac ggcaaagcaa agaataaaaa
+ 9481 cttggctttg catcgtgcaa agatttctaa ctaggttgtt taagggctgg tatctatgtc
+ 9541 ccgctataac agcgcgccta cagtagaagt ttaaccatga catacctttg aagtgttcgt
+ 9601 atcacacaca aggaaggagc atgtggacac cactgagctt tgatcagcac gcgtctcaga
+ 9661 gtttcagggg gacccaaatt actggtcctc aattgggacg cgaccgcatc tccccacgaa
+ 9721 agcttatggg gattgcccac tgcccagctt caaatctgaa ggttcggctt attgacaggg
+ 9781 tctaacacgc agctcaactg ctcgaggtta gaggcgtaat gacgggcccc gatagccttc
+ 9841 tacgattacg tccagcagga accccacagc ttttccctac gtctaacacc gtgaaagcaa
+ 9901 aactgtctgc ccttttacat ggtctttaag gaatctctgc acttatgtta ttaggtaagc
+ 9961 tcccataaga gcaccacttc gtgtaccttg ctaactccct tcatccccac ccgcgaaaac
+ 10021 ttaagacgtc acccctgtta ttatcccgtg cactcctaaa gtgcgatggg caagaacgca
+ 10081 aacaattgtc tgagatttat atgggcggcg gacatagtca gagagcctta tataatctcc
+ 10141 cacgtcttgc cagtccgagt tatgagaaac ccgggaccga tgacgctatt acggtcgccc
+ 10201 agcgaggttc aacagagcga ggcataggag tcattacgcg tgttagcttc aacatgcgtg
+ 10261 gaagtgaaac ggatctataa aacggcgtgg agtcatcagc ttgagcagat ctaacttact
+ 10321 cgccacgcgc gcaaatcgtc tttcgctgtc cacgttatac gtaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,enzymes,used_in,parts
+construct_1,construct_1,1,10366,6,,BsaI,construct_3,part_A & part_B & part_C & part_D & part_E & part_F
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_A.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_A.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,197 @@
+LOCUS part_A 4292 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_B.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_B.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,124 @@
+LOCUS part_B 4259 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_C.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_C.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,99 @@
+LOCUS part_C 3423 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_D.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_D.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,96 @@
+LOCUS part_D 2682 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_E.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_E.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,38 @@
+LOCUS part_E 347 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_F.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_1/provided_parts_records/part_F.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,74 @@
+LOCUS part_F 2470 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,279 @@
+LOCUS construct_2 6910 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_2
+VERSION construct_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(223..1038)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature complement(139..179)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 5..8
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 20..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(223..1038)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 189..212
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 51..74
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 84..112
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 27..137
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3347..3377
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1367..1372
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1190..1195
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 1226..1778
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3396
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3192..3239
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_RNA complement(1229..1336)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1865..1873
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3413..3416
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 1190..1778
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3300..3324
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1345..1350
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 1899..2147
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3397..3401
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3395..3412
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1211..1216
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3168..3191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3351..3375
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1140..1163
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5..3416
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3417..3420
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3421..4505
+ /source="part_G"
+ /indicates_part=True
+ /note="From part_G"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4506..4509
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4510..6158
+ /source="part_H"
+ /indicates_part=True
+ /note="From part_H"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6159..6162
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6163..6497
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 6163..6497
+ /source="part_I"
+ /indicates_part=True
+ /note="From part_I"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6498..6501
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6502..6910
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(6799..6819)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 6502..6910
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cgctgtcaat atgcaggtgc tgcaggaatt tgtctccaat cgacttgaga tatcgcaagc
+ 61 atgaaattat attagacacg ccagagaact tgggaagcag cactggtagt gatagcaacc
+ 121 cgagtacagt aacgagtgag cttctgatca tgagctctcc tacggcgtca atgcgacgaa
+ 181 tgcccagcat gcactctcgc tatccatgcc tgctagggtg gcattatgct caggaacagt
+ 241 tgtagcttgg atatcgtcta gatgaaatac ctggacactg gttagcgtcg tcaagcacca
+ 301 aggacattca cacgctcgcg gtctttcgtc tccctaagcg ttcggcagtc gggcgtgaag
+ 361 aggttgtaat cagacggaac aaagcctgaa aaaattccag cgacgtagta ttcatgatcc
+ 421 tgtaccatct gtagccgccg cggcgcacga ttgaatgtag gctactaacc ccatccgtgt
+ 481 tagcgatgtg agtttctacc gcaacgaatg ctcaagcgaa ccttcttctt tcgtccgcaa
+ 541 cccacaagcc gtggttatga cagctaaatt gtcccagaca tccctttatt acacaagagc
+ 601 tccagcggaa tacctagtca cagcggtaat gacacaaagc tcttagttag tccagggact
+ 661 acttctgtct acagcacatc acactcatta tcagcatcag tgtagagacg gagaacatgg
+ 721 gctatcctat accaagatcc gccatctaaa catttgaagt ttcccgtctt ctataactta
+ 781 gcactcgacg ctattctgct gagtgcgctt agtctgtagc gacttgcgaa atccataaac
+ 841 tgagaattga aagagagtgc ataaccgaaa cctttgtggc atatttccgt tgaaacgtac
+ 901 cagaacagcc gtttagtgcg gaacatacag tatcctgata aagcactcaa cccaacagac
+ 961 accctatgcc gatagcggga tgctaacaag tatagtcatg atgatttctc ggacagcggg
+ 1021 gtttggtaca gctgcaatcc gtgatttaaa ttcggacctc tgcacacacc gacggttacc
+ 1081 catatcctct acggctgtag gaagttttac cttggatgtc attctgattt cggcgtatct
+ 1141 cacaggatgg tccaacgaaa ctaggcttta gacgagggat gaatgaccga cccccactcg
+ 1201 tggcactaac ggacagactt ccctgacggt tattcgacca ttaaagtcag acatgcgggg
+ 1261 gtgaataaat tagccaaatt gtgtcgaaga aaagacgtgc ggctggcaca taaggcagtc
+ 1321 ttgatcctag tcttgcaggg atgcacgtaa gtcgcctcaa ttaactgcag ccgagctcca
+ 1381 ggttaccaaa gaccctagta tgccagggcc taacggttgg agtatattat gggtacgcaa
+ 1441 tagtgcggaa gttaacctgg gcaacatcca ggtgagaggt tggacggaag cgacagtaag
+ 1501 tggccataga ctgccgagtc gtgttaatga atcgctatac gcccatggag ttgtggggtc
+ 1561 gttttatccg agtaggggcc cgctgactac ttcgtccaga caatatgccg tcttcaatag
+ 1621 tctacctgag agtcatgccg gcatttccga cgctgagtga aacccgcgta gccaggcgaa
+ 1681 atttgcatct tgaaatacca ctgcagatca gccagtaagg cccatataag ggcgctggtg
+ 1741 ttctggcgac agataaagtg ttatctaatg taacccgcgg acttttagag gatacttgaa
+ 1801 tgcgggcata tcgtcccacc agcgtcacgt ggtcgggcta gcggcagaca aactctgccg
+ 1861 atgtttttct ttgccgcgat agcgggctag tcaattcact atccggcgat gaagcataga
+ 1921 ttgttatcgc gcttatgcgg aggataatca agtcttggca gaacctgctc gctcatgcac
+ 1981 tggtgaggcg tggttatcct aacaaccgcc taggacgaag aatgggctcg gtagggacag
+ 2041 ttcgtgcgtt tagcttcgtc ccatcttaat gctgtctgga gggaggctac atgcgaacag
+ 2101 aagccgtggg cgaaagttgt tgatccgggt ctaacacgga taagggccat ggtgaacgca
+ 2161 tcatgcgata cttcttggta gttcttctaa catgaccgtg ccatagccct taccctttga
+ 2221 agaagttaac ctatctgccg tctcctgcac gaatagcgac tggactcggg tattttggat
+ 2281 acctcacgaa agcacttcga tcggccgaag catggatatt tcgccggacg ggcccgaata
+ 2341 gagagccttg tatgtcggtt agtacaacgc agtcctggag acatctacgc ggatgggcct
+ 2401 aggggctgga cttaacattg ggtaacgtac ctggtccaaa gtgaatgcaa agcactttta
+ 2461 caaagcgcgg gtccccgtgg gtgtttaggg tagaagattg gcggatgcta cgaacgatcc
+ 2521 cgctttgaaa ctatcattac atcgtgtaaa agagacactt aacaaaggcc aataaactgc
+ 2581 cagtaagaat cgctcagtgc ggtgctgggg acgctaagta ggggcaacag ccagtgaagg
+ 2641 acgtgaccga cctttctcag ataagatatg ctggcgtcta tctaataagc atagtgaaaa
+ 2701 accaaccatt tcacttacac gaagtacatt tgcattgcta gtaaagacgc ctaaacagaa
+ 2761 gtgcccttgc atgctgtatg tctatagtcc ttagggaagc atcagccctt ctacttattc
+ 2821 gaggtctgag aaaccctgga caagctccga attattcaat gtgcctgtct ccgaggttag
+ 2881 atagcgctat gctcttaaga gttgcacaga atgaccatcc tggaatgtcc ctggaggggt
+ 2941 ctaggtatgc tgatcgaagg gtgctctaag gacttgacgt gcgtccgagg agggtgctgc
+ 3001 ctccttcgcc tttagatcca acgcggatca catgcgcgtg agctaatagg atcaccttct
+ 3061 gctccgattt ttaccctcct gggtcacttc cgaatgaggt agcgggcgaa atataatgtc
+ 3121 tccactcgta ggtgttccct gtatgtgaag ctctatagtg gacaaaggtt tgatgaacta
+ 3181 gcccccgtat acgctctcac cgacggacgc gggggtctgt tatttgaagc atcatacatg
+ 3241 cgaaggtgcc ttctcagcaa cgaaaggtag tgggagtgta caagttcaat gcgccgccat
+ 3301 aggtctgagt atacaagggg atgcccccat ccacaacggg attggctacc cggagagctg
+ 3361 gctccgctcc aacaaataat tatattaacc tattggaatt ccacctgcat atcagaggag
+ 3421 gaacttctat gggacgaaag atgcgcagct cgacaaatct caaattggaa accgtctaag
+ 3481 gtctttgagc ccacgctagg ccaccgaata gttgcgagct cgtgggcaat tgctggctag
+ 3541 cggtttgtat cgtatacgta acaagagatt gcgccggatt cattcgtgtg gggtgctttc
+ 3601 acatcggaat actcaagagt gggggtttgc gctttaatat gacggcctca tgcaccccaa
+ 3661 aaataagagc gccaatttca tcgaccacat tccggacaat tctgacttcc ctgtcggatc
+ 3721 gaccctcgct cacaactcct agaactccaa gacggtagga cgtcagccga aaaggaggag
+ 3781 tgacgacggg ccctcctagc tgaagcaatg gggggcgtcg accctagcct ggtgtgggac
+ 3841 ttcggagggt cgggcgtgtg gccattcctg cacgaggggc ccttgcagta tcgaactttg
+ 3901 acgagaaagt ggggggcgac ctataaacat agcggagttc aatactcctg caagtgcatg
+ 3961 atgacgttca gcgttggcac atcgaacgcg tcgctacact tgctcaccgg aaggcaaaat
+ 4021 agaccggcag ctggcccgca cggacgtcta gactcctacg ctgtcaaatg cacgatgact
+ 4081 attagcatgc ggaattcgag gcggccggta catcgagaca cgctggtctt aatacctgtg
+ 4141 ttatgtcaaa acaagtgtct cggcggcttt gtactacgct gtgaatgcgc atgatgttgc
+ 4201 gagaagctga acgttggtag cagtctacaa cagaaccgac gagctacgga cgggttacag
+ 4261 caggatcccc tcttaaggca ttattcgacg actccaggtt ctaaccgatc agtaattgcc
+ 4321 tcggatggtc gtacgtgtta accgagacag caaggcacca catagacaac tgcatagggc
+ 4381 gcctacaggt ccacaatcag ggtggcccaa gatcctcaaa gacttgttgc agtctctgct
+ 4441 tattccgttt aacacgttgt gtgagctcta gcttactacc tcatcggtgt cgggagtgat
+ 4501 ttaggaatgg aagacgcgtt tagtcttcgg cccccagacg gcaccggcag agccactgcc
+ 4561 aatgcctttt acgctgaact cttcgacttt ggcatgtgcg actgactata cgccgatggc
+ 4621 cctaccctgc agcggaaagg cacagggcca aaaacagtgg aagcgcaccg ctagagcttt
+ 4681 actaaatcct ttagggtgaa ccggtgttca gtcaacagaa acatatgact agtccttaat
+ 4741 ggcactacta aaggcggccc atctcttttg taggtcacgt ctcatcgttt agcaagcgtc
+ 4801 cgccatccga ggagtatcct agtacgtgag agggtgtttt acctcatcac atggtttttg
+ 4861 gctagatgtg gcagatgcca gctgatacct tacaacccgc tataacggtt tctggatcga
+ 4921 cgatacaacc tgcttcggca tatcataatg gcggcctcat aggacttcca atcatggtta
+ 4981 tgcgagtttg atgtgttgaa gattgtgagg ggaaaccttt ttccgagtac gttgaatctg
+ 5041 cgactgatgg tgaacaactc atcgagaggg atgtgcgggc agtctccttg atgcgcgaaa
+ 5101 aggagtcgcg accgcgtgtt cgtgacgcac ttgatgctag accgtagggg ctcattatct
+ 5161 cctgaaacag tagctagctt ttggtgtccg agtcagctta ggcacagtaa ttgaaaagaa
+ 5221 ggaaatgcgt gaaaactaaa cgtagacact ccttgctaag aattccctgg tctttttcga
+ 5281 gcatagacta ccgtaggtaa aaggcttgtc gtgtcacaaa tagacttgat ctgttcggca
+ 5341 tatacacatc ctactgcttc agtaaccaag gacgattctc cggccattgg actgtgggac
+ 5401 cacccgcgtt caaacggaat cctctacgaa cggttaagaa aggagcccac tgcttgcgga
+ 5461 gacatatcgt tgctgagtgg tacaccggtg agtcaaaaag tactgacact actggtggac
+ 5521 tctcgggtac gatgtgtggg gtattggcat actatggcgc taagcgtgga atagtgtttc
+ 5581 caatagccct ttacctaaga agcattctga cacatgggtt ggacttttac acagacctat
+ 5641 aactcgtatc cggcctggtg atgtatgtcc gcttatcact gaatgcagga ttccgccaat
+ 5701 tccgctcgcg ggttctcgga caacgggcca tggagatgga tcaatgagcc atgttgatta
+ 5761 ccatttcact acacacggtt agtcaattcc ggagatcata attcgacaat tgaatatgcg
+ 5821 tgatacgctt tctgttacca ggatcgttgc taattagttt ccaatgtcac agtgttgggc
+ 5881 ggcgaggtat cacggcgctc tgggtagaat ggcggtgcct gactggacct cataactggt
+ 5941 aacataccta tgaccaaagg aggtcagaca ccgatgagtc ggtgacatgg gcggtcacag
+ 6001 cgtgccctgc atagtaatac agctcgtttc tagacatttg tcctaattcg ccacacaagt
+ 6061 acgagagcgg gggtaaccca tcaccatcgt gcccgtaggt acctaatctt catcgagcgc
+ 6121 tattgttaaa gtggactcag ggatcggcat ctcgtgtagc ttttattatc cggcatgcat
+ 6181 gcggcgttgc atcgcttcat cgtcatcgac atatcgttag cgggacttat cagggtccca
+ 6241 tcacggctgt gacagctgtt cataagtgta atagcagtca ccccaccaaa tgcaagactg
+ 6301 ttcccaaact aagtgctagg gaggttggct acctatcggc gtggcagttg accgggtttt
+ 6361 tcttagtacc tgccttccaa tctccgataa aagcaagatg acttcctgct tgcgctaaag
+ 6421 tctgaattcg ctaagggggc agattcatta ccagagactg ccaaagtcaa ccgccgaacg
+ 6481 atactggaat atatggaggt aagctcccat aagagcacca cttcgtgtac cttgctaact
+ 6541 cccttcatcc ccacccgcga aaacttaaga cgtcacccct gttattatcc cgtgcactcc
+ 6601 taaagtgcga tgggcaagaa cgcaaacaat tgtctgagat ttatatgggc ggcggacata
+ 6661 gtcagagagc cttatataat ctcccacgtc ttgccagtcc gagttatgag aaacccggga
+ 6721 ccgatgacgc tattacggtc gcccagcgag gttcaacaga gcgaggcata ggagtcatta
+ 6781 cgcgtgttag cttcaacatg cgtggaagtg aaacggatct ataaaacggc gtggagtcat
+ 6841 cagcttgagc agatctaact tactcgccac gcgcgcaaat cgtctttcgc tgtccacgtt
+ 6901 atacgtaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,enzymes,used_in,parts
+construct_2,construct_2,1,6910,5,,BsaI,construct_4,part_A & part_G & part_H & part_I & part_F
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_A.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_A.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,197 @@
+LOCUS part_A 4292 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_F.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_F.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,74 @@
+LOCUS part_F 2470 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_G.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_G.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,36 @@
+LOCUS part_G 1119 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_H.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_H.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,109 @@
+LOCUS part_H 4246 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_I.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_2/provided_parts_records/part_I.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,69 @@
+LOCUS part_I 2396 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,457 @@
+LOCUS construct_3 11530 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_3
+VERSION construct_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CAGA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ homology 5..8
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ exon 2009..2206
+ /label="feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ gene 2009..2206
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 9..2206
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ misc_feature 9..2206
+ /source="part_B"
+ /indicates_part=True
+ /note="From part_B"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 2207..2210
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS 2211..5468
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 5469..5597
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 4679
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 5324
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 4271
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 2211..5599
+ /source="part_C"
+ /indicates_part=True
+ /note="From part_C"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 5600..5603
+ /label="TTCG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6192..6221
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ CDS 5604..6116
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 6126..6191
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS 6168..6191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 5604..6224
+ /source="part_D"
+ /indicates_part=True
+ /note="From part_D"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6225..6228
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ 3'UTR 6232..6541
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 6229..6231
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 6229..6541
+ /source="part_E"
+ /indicates_part=True
+ /note="From part_E"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6542..6545
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6546..6954
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(6843..6863)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 6546..6954
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6955..6958
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3420^3421
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 10374^10375
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 5..6958
+ /source="construct_1"
+ /indicates_part=True
+ /note="From construct_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6959..6962
+ /label="GTCA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6963..6966
+ /label="feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 6963..7004
+ /source="part_L"
+ /indicates_part=True
+ /note="From part_L"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 7005..7008
+ /label="ACCC"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS complement(7202..7993)
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS complement(7202..8107)
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 7073..7101
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 8418..8423
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 7178..7201
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 8396..8401
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 8241..8246
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 8277..8829
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 7016..7126
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA complement(8280..8387)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 8916..8924
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature complement(7128..7168)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 8191..8214
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 8262..8267
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene complement(7202..8107)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 8241..8829
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 7040..7063
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 7009..7014
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 10219..10242
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10398..10428
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 9199..10218
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ gene 9199..10218
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10441..10458
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10351..10375
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 10402..10426
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 10243..10290
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 10446..10451
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 10441..10443
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 7009..10458
+ /source="part_J"
+ /indicates_part=True
+ /note="From part_J"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 10459..10462
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ promoter 10539..10717
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 11527..11530
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ terminator 11274..11526
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS 10719..11269
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 10463..11530
+ /source="part_K"
+ /indicates_part=True
+ /note="From part_K"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cagaggagag catacggtgc tctgggctca cacgtacttc ctcttgtcac gcgcctttgt
+ 61 agagcattag ggcggaggtc actgggacgg ggatcagaga gcttaaaatc ccaagtagca
+ 121 gtgcctaagg tgtagaatct tgtgcagatc ttcgtctggc ccgaaacctg ggcctccaca
+ 181 acaatgtcgg gtcttttata atttgaaaac atcgcgcctt acccgcaccg cgcaggacga
+ 241 ttagacacag ggggtcatgt ccatggttcg gggtaagcca aatttacatc gagtgtgggc
+ 301 ttcattgagg agagggcgtt acgatacccg ttaaatgaaa acccggacag tctctaactg
+ 361 ataggcctga taatcgccaa atgaagtcgc aattagcagt acatgactgg cagatatgtc
+ 421 gccggagacg gtatggggga cctatcctag gttggcacgc gagcgcgaat gacgcctatc
+ 481 ttatccccct gcacgtgatg gtatcgtccc aactatcttt tacctcatca acgttttcct
+ 541 gcataatctg caagatggag agtccgcgag tgcggggagt acgagatcac aaatctgccc
+ 601 tgaagacaaa gctcgcaggc cgtactcagg aaatagcatc gactcacaca tatcgggaac
+ 661 ggcaaagagt gcatcggcca atgcaaacta ttgaacgtcc atgaaattgt gtcaaactac
+ 721 tagtgtgtgg acttgcgtca aggccatggc gcaatactca aagccccggt atttatcccc
+ 781 cgcagagtat ccgtgcggat ggagttccac agctctttgg acatgcaatg cgtggcgcta
+ 841 catgctccgc tgatacagaa tatctaatgt ctcgcctctt gccgtcgacc ctacaactac
+ 901 tgcacgggca gagtggacgc gacccctgag cggtgcagaa ccttagtata aggcaagggt
+ 961 ggcacggccg agccgcactt gctcctacta ggccgtgctc gaagctattg atgcaagcac
+ 1021 agtattcccg atttgtaaag caaggtgccc gtagccatac acccagctac tcaccggcca
+ 1081 atttcgaccc tctctatctc agacctccgc atattcccaa actcctgctc aagtatgaaa
+ 1141 tgaccggctc ctcctaaggc ctgcggacat ggagtcatgc gtggaatgcc gtgtaggtag
+ 1201 ggtacacaca gccttaccat gtagggcaat aaattataga ctactgacat tgattccttg
+ 1261 agggcccgtt cacttgtggg ggaaccagga aggcgccgat agtcatcact taaacacatg
+ 1321 cgacgcatcc atttcaagaa agacacgcta cgggtctaca ccgcctatag ttctaatttg
+ 1381 ggccccggta cgcacatcga tgtactctcc attacagcat agcacatcag cggccctagt
+ 1441 tagcgcttct ttttgttcca acattcaata gcggggactg cattatcctc accctatttg
+ 1501 ttgcataggt atttggccgt atacttggga aagagcaacc acgggagtgc actagaaact
+ 1561 gattcaccca tgttataacg cgttgctcgc aagtcgtact gtggccacgc acaggtcagg
+ 1621 caatcgcaac catgtcttag cagtttgtaa gaagaccttt aaacatgtac ctcacagcaa
+ 1681 tctcggaact tttaattttc ctgagtcaat gacatgctag ctccgtccac ttgtaatcac
+ 1741 cgtcataaca cagttagcct gcaaaagggc gtgtacacct tgccacttta aagctgaccg
+ 1801 aataacctac ctacaggaga tgcttagtgc cacggaatga tctcgcaatg cttagtctta
+ 1861 cacccagtga atcaacccaa gacctcgccg actgaacggt attgagtcca atcccgagag
+ 1921 gcaatttatg gccgttagtg acagtcggtc gctgatagaa taaggcagac tcgtcttaag
+ 1981 cgggctgctt taagagaaaa tggagccctg acgaagaagt ggatgaacca ggttttgaca
+ 2041 acgtcccata ttggtaatgt aggctcgtta tcaagagata ggtttagaag gctcaatgct
+ 2101 cgacgtaaaa gaagtcttaa gctctatgag ccagtgatga gagctaatta tagggcgcat
+ 2161 tcgttggggt aaggttgcga attgtcattt aactaaaacc gacggcaatg gtttcaccgg
+ 2221 agctgagatc gcattaaagt cacactacga attatttgtc cccgcggctc cagagacaaa
+ 2281 tttctaggag tgggttcatg gagaaccgtg acaagcatgg tagcttcaaa tagcgtcatc
+ 2341 ggatcttaaa gtgattgtga catatatggg attgcgcgtc tctcttacac aagctagtgt
+ 2401 gcgcgaggtg ctgaacacct attacgtcaa ctcccgggat cccggcgggt tacagagaca
+ 2461 taagcagggt gtccatcatt aacttcgatg ttgagcccgt gccctgatca aacacctctc
+ 2521 gtagtagtgg gtgccggccg tgtattattt tgggggagag gatgcgccct aagcaatttc
+ 2581 tttccatcgg ccagccattc gacgccggca cgcaagttgt tgcgggcact gttgcagttc
+ 2641 ccgtactaga gtctcaagtc tagaggtacc agcatcagga agatgggtac ttcgtgtgga
+ 2701 tcttctcctg aacctgaaac ctgaagagct aaagcgcgtc gcgctgccat acgataagtc
+ 2761 gctctcattt ccggaagacg tcgttgggtg atggcgaaca atcgcgaaac gaaaatcgcg
+ 2821 gtcggtatgt tgattcaaga cgggctacgg gcgggttact aacaggtgcg cagaaatgtg
+ 2881 atgggtcact tgaccatgaa ctttcgcgcc gtcgcttctg tggactggcc ggctccctga
+ 2941 tagtgcacta gcccgttgat atgcccatta ccatttggcg gcgcagtgtg ccagcgggat
+ 3001 taagatgcgt ggcgtacaac tatccgcact ttgctgacgc acaaaggcaa ctgatggaca
+ 3061 gccttcgggc attcgactgg ttggctgagt tcgcctgcct attaatatgc ttgtggaaat
+ 3121 tgatttacag cgcctacttc tacttaggtg tacctattta cggcacaggg ataaaggctg
+ 3181 acagaaaagt cctggacagg tcataggtag ttgtcagacc tacaatggta taacttgaga
+ 3241 gtcctgtacc gcacatgcgg ttgtagctag atgtccagaa gaccgtagct agcgacgagt
+ 3301 gggttgcacg cgcattttgg gaaggggctg cgcgagggtg gggtcacggg ttattccatt
+ 3361 tctaaatgct aaaccagcag ttgctttagt tctgacctag caggcatgtc atatgtatgg
+ 3421 ctagattatt agtacaatgc aggactaaga aagcctgaga cttaaatgcg ttggtttttc
+ 3481 agccgacggg ccgggagggc agatggccga atgcgcactg aggagtgcat tgcgagggaa
+ 3541 taggcggacc accaggtccc ctcacatact gtggataaac ctacccaggg acaactcacg
+ 3601 ccatcatttt caagagtagc actactttcc actaagtacg gtttgtcgag agccggtggc
+ 3661 accgtgcgac gagcttgtgg gcactaggcg aaccgggtta tataggactg ccttgcggtg
+ 3721 cgggaatact ttaccccgtg gagaggccat aaaagcttac atttattgta gccgctagcg
+ 3781 gtttcgacgc gctcaagtgg ggctttatct tagagtatca aataatgccc tctcagcttc
+ 3841 atcttgattt ttgtgtttgg ggtagtgtat ccgatgggtc accttcttga ccttggggag
+ 3901 ctccatccat cgtaccaata ctccgtttct ttgtgttgcc taccgagtaa tcgaataccg
+ 3961 cacgagggct agaatctaat ttaaggtggg tcttatccct gttgtttgga cctaacgctg
+ 4021 taacaaatca cttccgcgac gggtgtcatt acgtcttcta tccgccaccg gttcaacagt
+ 4081 gcgtcgaatg ccaagtccct attacccgca ttgtaaagcc attacaatac ctccggtgat
+ 4141 ataattgatt gccggttggc aagggatcat ctgtacgggc cgcgattgat tgctgataag
+ 4201 gaacggcggt aaggaacgta tcgcgtacga ggttgtacac tggaaccgct aaacaagcgg
+ 4261 tatcgctaaa ttaccggcga ttatatcaag ggaatcttag gtagcacgaa gccctacgcc
+ 4321 ctggaaacag gatcggcgcg aggccgtgga catattagcc tacgtttttt tacacccaga
+ 4381 tttccgacga tgtccacagc taaggctatc ctaaaccgca aacacatata accgcagtat
+ 4441 aaagcacggg atgattcctt ggccatcttg caagcagtgc aaggcaattc tggtgatagg
+ 4501 ggcaaggcag tgaaccgagt ggtcagcgta ttgtgaccct gcaattgtca tggcagataa
+ 4561 ttgtttatga acctgtttca cacacccatc ccttggatct ccagcgtagt tactaatagt
+ 4621 acgatttcct ggtgttctgt cacccgcctt gctgccttca cgcctgcccc acgttttgct
+ 4681 gtccactgaa tatcgctcta attaataggt gtcacactgt atcaggtaag tccattccgg
+ 4741 gtgctattgg atcattcctg agatgtacca ccgatcccat aggcgttagg tcttacatct
+ 4801 ggagtgaaaa agatcagcat cgaactatag gtagataaag gtcatgactg ttaacagaga
+ 4861 atcgttccta tcgcaacctt cactaactgg aaggcacccc cacactttga ttagtaagcc
+ 4921 cctagcgaat gtagtgatcc aagaacatcg agtatacttt agctctcggt tcaggcatgt
+ 4981 atgcaatcga ccacccttcc gttcagagta ctctcaacca gcagatttct aaactttata
+ 5041 gcctccgccc actaaaattg ccttatctca ggttgactct tggatgtagc tgtaatctaa
+ 5101 catacacatg gagctgcggc aaattatcgt acgtccaaac caccaccgga tcagtggcga
+ 5161 tactattctc gcaaaaaagc catccagcat tggaacaagt gttaaccagc atttttctga
+ 5221 gtcccccgga aagaaagttg actacactac atccataaat gctagagtgt ggattcgcca
+ 5281 tgtgttacaa cggtcaaccg aaaggttagc atgatacttc gttgttcaat cggacgttcg
+ 5341 agcgccctcc ctgtttatca cttgatcccc cttttgaaac atgtgcgctg cgacgcaggg
+ 5401 ctgggagagt caccggaaac caaaagcccg acctcggacg tgtagggccc tccgtttgcc
+ 5461 atcaatggcg atgtaggatt ctcttttaat acaacgttca ctcaattaac gtcttggtat
+ 5521 aagcgtcgaa cgtgaccgag gttgacacca gtgtcacggc tgcgccgggg tttgttgctc
+ 5581 cgcgtgtaca gggtattggt tcgatggtgc ctcctctacg tagatctact ggataaccgt
+ 5641 ccccaatatc cgcttcccaa cgtagattgc cgacaggcat aagcttcggg ggcgcaaagg
+ 5701 ccgacgtccg cattgcagtg tagctttgtg agcaggaagt gtgatagtct ttcgattatt
+ 5761 aaagtctgag ctgaatgaaa aaaggtccaa cgaatggagg acgcgaagac atgggtgtct
+ 5821 cttatggccc gagcgggagt aatggcggtt cgtacataaa ggctgaaagg attctggcgt
+ 5881 tagctgtctt acgttggatt ggcccttcaa attatcgatg ttagctgatt cggtgtaccg
+ 5941 ggcgaggaaa gcgctctcag aacaacttca tatacgaggt tcgactataa tggtctaagc
+ 6001 tcctgggcta gtctcaagaa gcgggtacct ttagtagcac gtatcgacgg caaagcaaag
+ 6061 aataaaaact tggctttgca tcgtgcaaag atttctaact aggttgttta agggctggta
+ 6121 tctatgtccc gctataacag cgcgcctaca gtagaagttt aaccatgaca tacctttgaa
+ 6181 gtgttcgtat cacacacaag gaaggagcat gtggacacca ctgagctttg atcagcacgc
+ 6241 gtctcagagt ttcaggggga cccaaattac tggtcctcaa ttgggacgcg accgcatctc
+ 6301 cccacgaaag cttatgggga ttgcccactg cccagcttca aatctgaagg ttcggcttat
+ 6361 tgacagggtc taacacgcag ctcaactgct cgaggttaga ggcgtaatga cgggccccga
+ 6421 tagccttcta cgattacgtc cagcaggaac cccacagctt ttccctacgt ctaacaccgt
+ 6481 gaaagcaaaa ctgtctgccc ttttacatgg tctttaagga atctctgcac ttatgttatt
+ 6541 aggtaagctc ccataagagc accacttcgt gtaccttgct aactcccttc atccccaccc
+ 6601 gcgaaaactt aagacgtcac ccctgttatt atcccgtgca ctcctaaagt gcgatgggca
+ 6661 agaacgcaaa caattgtctg agatttatat gggcggcgga catagtcaga gagccttata
+ 6721 taatctccca cgtcttgcca gtccgagtta tgagaaaccc gggaccgatg acgctattac
+ 6781 ggtcgcccag cgaggttcaa cagagcgagg cataggagtc attacgcgtg ttagcttcaa
+ 6841 catgcgtgga agtgaaacgg atctataaaa cggcgtggag tcatcagctt gagcagatct
+ 6901 aacttactcg ccacgcgcgc aaatcgtctt tcgctgtcca cgttatacgt aactcgctgt
+ 6961 cacgctagag accgtatgag gtgggcggat agtggtgact tcaaacccct aagatgccag
+ 7021 cgcaatacgg catcgcaggg caagcaacac cgcacagcat gtccctaaag ggaagattta
+ 7081 atacggactc agtcaagttg tgagaaacga caatacattg agtggaatgc cctttggtac
+ 7141 gttggcgata gatctaacga gaaacttcaa cgagatctag agtatcggac tgagatgcat
+ 7201 catggctagg gattgctgaa tggatatctt tgccaaaatg agctcgacta ggaatctcag
+ 7261 actgccagct acgaaaagct gggggatatt catttccgct cttgtaaggc gcacgatgac
+ 7321 cctgtggagc aaaattcgac gcggcaacgt agtcaaagta cggcctatct gggacggaga
+ 7381 tgggattgtt tctgtattca tgccggcctc ttgagattgt aaggataccc ggccacagtc
+ 7441 tcgtaagaaa cccgatatcg ctcaaacgaa ttgacatcag ttagggcttg cgctctagca
+ 7501 accacgcgtc gggtgttcga ctgaatttaa gatccagcgc aaaccattcc ttaaaggcgg
+ 7561 tccaggtgaa accggctctg ataatgtaca gtggattgtc cagttcgctt caaagtgcaa
+ 7621 tcaggcaagg tactggcaag tcaccgcttg gggccggttt cagtggagct ttatcgacaa
+ 7681 aaggccgggc cctttggcct agagctcact tttggtgtcg ttcacgagtg agaactttgg
+ 7741 ctcgcagctt gaatgcttgt cacgtttagg gttatacaac gtttctataa actacctatg
+ 7801 acaaatcccg atcttctgaa actccataag gactaagaga gtccgcgaca gtttcacttg
+ 7861 gtcggtgcta ttgactatgt cacgcatgcc cggtaaagct tttaagcaaa gcctgatata
+ 7921 tcacgggagg ttactcaaag cattttctaa agggacagcg gactcacatt agcctaatat
+ 7981 aaacccgatc aggccatgca cctcgattca ccggaaggta gtaccatgca ccggatattt
+ 8041 gggacaacag tgaatagtac atcgtaaaat gtcaaggcct agctattttt cactggtgtc
+ 8101 ttatctctat tacaacacac acggatgtcc cgagcctaca ctttcaaata tactcaaggt
+ 8161 tcgctgttaa gggtaataca agagtgctcg gtttagtatc catatgttgg tacaagtgac
+ 8221 tgtgctagcc gtaaattaat tcggcttcca ttccagcttg ggtgtttagg gtctagacgg
+ 8281 ttgaaaccag aaagagtaca gacaaaaccg tagctctccc aaggttgatc ctccagacac
+ 8341 ctacccacac tagtagcgca ggcctagagg agacgttagg agcggaattg tacattcagt
+ 8401 atcgcattaa gcacaaagac agacaaacct agaagccact tatcccctcg taggagtaca
+ 8461 acggcagcgc tttcgggagg agttgcctaa ctacgctctg gacagcaagt cccagaatga
+ 8521 agaaaatgac ttggcgagaa cccaccacta catgcagggt cttgggaccg gtcagcacag
+ 8581 cttatccatg cggcaattcc ggacgaccgc gaatgaggat cacgacactg ccgatgttgc
+ 8641 accattgacc ttctcctatg caacaagggc ttaagatggt agatggtaat agagtagcct
+ 8701 gcgaccttat gcggtaatac acaaaaaccg gtaaacagtg cgttgatgct gtgtgctggc
+ 8761 gcatttgtgt accttgctgg gctcgtataa aattctgtca gcaggacgtt cacctccctt
+ 8821 ctgctagtcg ctaggcacaa acggaaaagg tctaatcgcg cgcgtgctcg ttagagtact
+ 8881 ggggcctccc accacggatg atcacctcgc cgatacattt ggccttatgt ctcaataaga
+ 8941 cctcatggtc tatcctacac catagatttg gaaagtctag ttgctgccta gcaggctgat
+ 9001 agcaagcgtc gtacgaggat cgaggaaggg cactcatggg agtgtagcgc tagccatagt
+ 9061 tgacctgtca gccggtcaag gttggtccga acctagccag ttagacgacc agctccccca
+ 9121 ctattgcaca gtgcctgtat aagcacgtca gtgtctggca ccactgtgcg cggtgtggtc
+ 9181 ctcgggacga tcttcctacg gctacccatg cgctagtgat tacagacgat cgttttttct
+ 9241 ttttctgtgg tgcaaataca caagatacgt caagagtcct agcagcctca tcttgccaat
+ 9301 tgcaggggta ccgattcacc catggtatca gtcacgcaaa aaaagacgac atcggagttg
+ 9361 ctggcgactg gcaaaagaaa acatctatct gccgtggcgt tcgtctagcg cagcgagccg
+ 9421 actgactact ccgttatctc aaatttagtt tcgtaagatc ttcacgggag ccggccagct
+ 9481 gaagaatcta taggtctacc gctagaggaa gcccgtttac aaccgacgta ctagtccgac
+ 9541 agcaatcgtc agcatgccaa tttattgtat caggttgaga atgcaccact acggaatcga
+ 9601 cgtgccactg gccgcacgat actagtgcgc tggtaaacag gccaggagct ctaaatctgg
+ 9661 agtggtgtga atttaaccgc ggaacgattg ttgcacgcgg tccctgtgac tctgttggga
+ 9721 gcactgtccc cggctccgga taagtgatgt gaacgaaaag gtgggctgac cagagatagg
+ 9781 gttaaggacg ggcgatcgta gtggacgatt actgctgatc ttccgagcac tctgagtcgc
+ 9841 gcggcgtatc gggagttacc ccgctcgcta cacatctgaa ttccgccgga tactatgggt
+ 9901 gcagagtgga tcaccttttc gtgacccgta tattcgtcgt tctcatcact gtcctccgcg
+ 9961 atttatttca atcgtcggtt tcgccagatg cattcctggg gaagtcatcg cgacagtgcg
+ 10021 ctgcgcgcac agctcttctt ggtttattcg agattgtggt ttatcaacat ggtctatcta
+ 10081 cggactgatt agaatattcc cacgttaagc cgacgtgcat tggtactggc tccttaatta
+ 10141 agcgcagagg gtaggcgcct tttcttgtgc aaaccattat atgaggaact agcaaacact
+ 10201 atggcgcaat atgtccacgt gactcgagca ttctgtgttg cggtagcgat ttcactagtc
+ 10261 acaaacggat agattctacg gcgcacccgg tgcatcgttg tatgttcagc aatttggtca
+ 10321 tatcccgctc ctctattcaa tctctttttt cgtcaggggg ggcacatact tggagcagct
+ 10381 gcgcctaaca ttacaataag cagtcggagc tcagtacaaa acccttatct tagcggtccg
+ 10441 ttctggaatt cggtctcagg agagacactc cttcatcaac agcagaggtt acatacgttt
+ 10501 aacctgaccg atggttgccc atcgaaagca aggacccacg ggtaggcagc tgttgtttga
+ 10561 tatgcttttg tccccggaag gcgccgataa aattatacgc cgtcccccgc gtccgttacg
+ 10621 agcttcgtga tgttgcgggc tgaagttccc tacgagtcaa taggccaact cgaatggcta
+ 10681 aatggttgca acccacaggc tcaactttga aggtaatacg ccaaaatcca atatgctctt
+ 10741 tcgggtagcg cataaaacct tctgggggcc actgcagaca gtcatggagg actacgtgca
+ 10801 acactacgct ctagagtgat gatgtggcag tcaaccgagg gctgttaaga gaagtctgtg
+ 10861 cacgaaaatc aatgagtcgg tgtaatcttc accttcctac aaaccaaggc ttgagggcct
+ 10921 caatttcgag caccacttct tgaccaagcc gttcgccggt ataggagtta cgaattcggg
+ 10981 tcgtctgccg tctttgaacc atagataagt acctcccgag tcgggagaac acgaatcgca
+ 11041 tcagaactca tcgaagggtg ttactttgcc catcggcatc cccgaagatt aattgcattc
+ 11101 gaaattttaa cttcgagaat catccgtgct aaccaacgtg gacgagctat gaacgtttac
+ 11161 gtgttcagta tctaggaatt gacacgtctc cgatagcggg agtcacggca tgagttacgg
+ 11221 cttttgtgac cagcgtctgt gtaattttat tgacagtttc atatatagtg tctcgtcttg
+ 11281 cctttgagat tcacaggctg taagagggat gccgtcgtgt atatgcctgc agttagagct
+ 11341 tccttgtcag gacgagcaac tcactccttc tggtgatgct ttgctagcat gtagcttcgg
+ 11401 gtacttgcgg aaaaggacag cctacagtgt ctgcggcggt acgtcactaa tatgacatac
+ 11461 gctgtggaca tcgtgaagcg gcgaatcgct ccagattgag gtttacagag tactccatag
+ 11521 tcacacaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,enzymes,used_in,parts
+construct_3,construct_3,2,11530,4,construct_1,AarI,,construct_1 & part_L & part_J & part_K
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/construct_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/construct_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,385 @@
+LOCUS construct_1 10366 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_1
+VERSION construct_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(223..1038)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature complement(139..179)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 5..8
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 20..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(223..1038)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 189..212
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 51..74
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 84..112
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 27..137
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3347..3377
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1367..1372
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1190..1195
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 1226..1778
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3396
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3192..3239
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_RNA complement(1229..1336)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1865..1873
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3413..3416
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 1190..1778
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3300..3324
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1345..1350
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 1899..2147
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3397..3401
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3395..3412
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1211..1216
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3168..3191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3351..3375
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1140..1163
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5..3416
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3417..3420
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ exon 5421..5618
+ /label="feature"
+ /ApEinfo_fwdcolor="#75c6a9"
+ gene 5421..5618
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 3421..5618
+ /label="another feature"
+ /ApEinfo_fwdcolor="#f58a5e"
+ misc_feature 3421..5618
+ /source="part_B"
+ /indicates_part=True
+ /note="From part_B"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 5619..5622
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS 5623..8880
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ CDS 8881..9009
+ /label="another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 8091
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 8736
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 7683
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 5623..9011
+ /source="part_C"
+ /indicates_part=True
+ /note="From part_C"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9012..9015
+ /label="TTCG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9604..9633
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ CDS 9016..9528
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 9538..9603
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS 9580..9603
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 9016..9636
+ /source="part_D"
+ /indicates_part=True
+ /note="From part_D"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9637..9640
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ 3'UTR 9644..9953
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 9641..9643
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b1ff67"
+ misc_feature 9641..9953
+ /source="part_E"
+ /indicates_part=True
+ /note="From part_E"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 9954..9957
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9958..10366
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(10255..10275)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 9958..10366
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cgctgtcaat atgcaggtgc tgcaggaatt tgtctccaat cgacttgaga tatcgcaagc
+ 61 atgaaattat attagacacg ccagagaact tgggaagcag cactggtagt gatagcaacc
+ 121 cgagtacagt aacgagtgag cttctgatca tgagctctcc tacggcgtca atgcgacgaa
+ 181 tgcccagcat gcactctcgc tatccatgcc tgctagggtg gcattatgct caggaacagt
+ 241 tgtagcttgg atatcgtcta gatgaaatac ctggacactg gttagcgtcg tcaagcacca
+ 301 aggacattca cacgctcgcg gtctttcgtc tccctaagcg ttcggcagtc gggcgtgaag
+ 361 aggttgtaat cagacggaac aaagcctgaa aaaattccag cgacgtagta ttcatgatcc
+ 421 tgtaccatct gtagccgccg cggcgcacga ttgaatgtag gctactaacc ccatccgtgt
+ 481 tagcgatgtg agtttctacc gcaacgaatg ctcaagcgaa ccttcttctt tcgtccgcaa
+ 541 cccacaagcc gtggttatga cagctaaatt gtcccagaca tccctttatt acacaagagc
+ 601 tccagcggaa tacctagtca cagcggtaat gacacaaagc tcttagttag tccagggact
+ 661 acttctgtct acagcacatc acactcatta tcagcatcag tgtagagacg gagaacatgg
+ 721 gctatcctat accaagatcc gccatctaaa catttgaagt ttcccgtctt ctataactta
+ 781 gcactcgacg ctattctgct gagtgcgctt agtctgtagc gacttgcgaa atccataaac
+ 841 tgagaattga aagagagtgc ataaccgaaa cctttgtggc atatttccgt tgaaacgtac
+ 901 cagaacagcc gtttagtgcg gaacatacag tatcctgata aagcactcaa cccaacagac
+ 961 accctatgcc gatagcggga tgctaacaag tatagtcatg atgatttctc ggacagcggg
+ 1021 gtttggtaca gctgcaatcc gtgatttaaa ttcggacctc tgcacacacc gacggttacc
+ 1081 catatcctct acggctgtag gaagttttac cttggatgtc attctgattt cggcgtatct
+ 1141 cacaggatgg tccaacgaaa ctaggcttta gacgagggat gaatgaccga cccccactcg
+ 1201 tggcactaac ggacagactt ccctgacggt tattcgacca ttaaagtcag acatgcgggg
+ 1261 gtgaataaat tagccaaatt gtgtcgaaga aaagacgtgc ggctggcaca taaggcagtc
+ 1321 ttgatcctag tcttgcaggg atgcacgtaa gtcgcctcaa ttaactgcag ccgagctcca
+ 1381 ggttaccaaa gaccctagta tgccagggcc taacggttgg agtatattat gggtacgcaa
+ 1441 tagtgcggaa gttaacctgg gcaacatcca ggtgagaggt tggacggaag cgacagtaag
+ 1501 tggccataga ctgccgagtc gtgttaatga atcgctatac gcccatggag ttgtggggtc
+ 1561 gttttatccg agtaggggcc cgctgactac ttcgtccaga caatatgccg tcttcaatag
+ 1621 tctacctgag agtcatgccg gcatttccga cgctgagtga aacccgcgta gccaggcgaa
+ 1681 atttgcatct tgaaatacca ctgcagatca gccagtaagg cccatataag ggcgctggtg
+ 1741 ttctggcgac agataaagtg ttatctaatg taacccgcgg acttttagag gatacttgaa
+ 1801 tgcgggcata tcgtcccacc agcgtcacgt ggtcgggcta gcggcagaca aactctgccg
+ 1861 atgtttttct ttgccgcgat agcgggctag tcaattcact atccggcgat gaagcataga
+ 1921 ttgttatcgc gcttatgcgg aggataatca agtcttggca gaacctgctc gctcatgcac
+ 1981 tggtgaggcg tggttatcct aacaaccgcc taggacgaag aatgggctcg gtagggacag
+ 2041 ttcgtgcgtt tagcttcgtc ccatcttaat gctgtctgga gggaggctac atgcgaacag
+ 2101 aagccgtggg cgaaagttgt tgatccgggt ctaacacgga taagggccat ggtgaacgca
+ 2161 tcatgcgata cttcttggta gttcttctaa catgaccgtg ccatagccct taccctttga
+ 2221 agaagttaac ctatctgccg tctcctgcac gaatagcgac tggactcggg tattttggat
+ 2281 acctcacgaa agcacttcga tcggccgaag catggatatt tcgccggacg ggcccgaata
+ 2341 gagagccttg tatgtcggtt agtacaacgc agtcctggag acatctacgc ggatgggcct
+ 2401 aggggctgga cttaacattg ggtaacgtac ctggtccaaa gtgaatgcaa agcactttta
+ 2461 caaagcgcgg gtccccgtgg gtgtttaggg tagaagattg gcggatgcta cgaacgatcc
+ 2521 cgctttgaaa ctatcattac atcgtgtaaa agagacactt aacaaaggcc aataaactgc
+ 2581 cagtaagaat cgctcagtgc ggtgctgggg acgctaagta ggggcaacag ccagtgaagg
+ 2641 acgtgaccga cctttctcag ataagatatg ctggcgtcta tctaataagc atagtgaaaa
+ 2701 accaaccatt tcacttacac gaagtacatt tgcattgcta gtaaagacgc ctaaacagaa
+ 2761 gtgcccttgc atgctgtatg tctatagtcc ttagggaagc atcagccctt ctacttattc
+ 2821 gaggtctgag aaaccctgga caagctccga attattcaat gtgcctgtct ccgaggttag
+ 2881 atagcgctat gctcttaaga gttgcacaga atgaccatcc tggaatgtcc ctggaggggt
+ 2941 ctaggtatgc tgatcgaagg gtgctctaag gacttgacgt gcgtccgagg agggtgctgc
+ 3001 ctccttcgcc tttagatcca acgcggatca catgcgcgtg agctaatagg atcaccttct
+ 3061 gctccgattt ttaccctcct gggtcacttc cgaatgaggt agcgggcgaa atataatgtc
+ 3121 tccactcgta ggtgttccct gtatgtgaag ctctatagtg gacaaaggtt tgatgaacta
+ 3181 gcccccgtat acgctctcac cgacggacgc gggggtctgt tatttgaagc atcatacatg
+ 3241 cgaaggtgcc ttctcagcaa cgaaaggtag tgggagtgta caagttcaat gcgccgccat
+ 3301 aggtctgagt atacaagggg atgcccccat ccacaacggg attggctacc cggagagctg
+ 3361 gctccgctcc aacaaataat tatattaacc tattggaatt ccacctgcat atcagaggag
+ 3421 agcatacggt gctctgggct cacacgtact tcctcttgtc acgcgccttt gtagagcatt
+ 3481 agggcggagg tcactgggac ggggatcaga gagcttaaaa tcccaagtag cagtgcctaa
+ 3541 ggtgtagaat cttgtgcaga tcttcgtctg gcccgaaacc tgggcctcca caacaatgtc
+ 3601 gggtctttta taatttgaaa acatcgcgcc ttacccgcac cgcgcaggac gattagacac
+ 3661 agggggtcat gtccatggtt cggggtaagc caaatttaca tcgagtgtgg gcttcattga
+ 3721 ggagagggcg ttacgatacc cgttaaatga aaacccggac agtctctaac tgataggcct
+ 3781 gataatcgcc aaatgaagtc gcaattagca gtacatgact ggcagatatg tcgccggaga
+ 3841 cggtatgggg gacctatcct aggttggcac gcgagcgcga atgacgccta tcttatcccc
+ 3901 ctgcacgtga tggtatcgtc ccaactatct tttacctcat caacgttttc ctgcataatc
+ 3961 tgcaagatgg agagtccgcg agtgcgggga gtacgagatc acaaatctgc cctgaagaca
+ 4021 aagctcgcag gccgtactca ggaaatagca tcgactcaca catatcggga acggcaaaga
+ 4081 gtgcatcggc caatgcaaac tattgaacgt ccatgaaatt gtgtcaaact actagtgtgt
+ 4141 ggacttgcgt caaggccatg gcgcaatact caaagccccg gtatttatcc cccgcagagt
+ 4201 atccgtgcgg atggagttcc acagctcttt ggacatgcaa tgcgtggcgc tacatgctcc
+ 4261 gctgatacag aatatctaat gtctcgcctc ttgccgtcga ccctacaact actgcacggg
+ 4321 cagagtggac gcgacccctg agcggtgcag aaccttagta taaggcaagg gtggcacggc
+ 4381 cgagccgcac ttgctcctac taggccgtgc tcgaagctat tgatgcaagc acagtattcc
+ 4441 cgatttgtaa agcaaggtgc ccgtagccat acacccagct actcaccggc caatttcgac
+ 4501 cctctctatc tcagacctcc gcatattccc aaactcctgc tcaagtatga aatgaccggc
+ 4561 tcctcctaag gcctgcggac atggagtcat gcgtggaatg ccgtgtaggt agggtacaca
+ 4621 cagccttacc atgtagggca ataaattata gactactgac attgattcct tgagggcccg
+ 4681 ttcacttgtg ggggaaccag gaaggcgccg atagtcatca cttaaacaca tgcgacgcat
+ 4741 ccatttcaag aaagacacgc tacgggtcta caccgcctat agttctaatt tgggccccgg
+ 4801 tacgcacatc gatgtactct ccattacagc atagcacatc agcggcccta gttagcgctt
+ 4861 ctttttgttc caacattcaa tagcggggac tgcattatcc tcaccctatt tgttgcatag
+ 4921 gtatttggcc gtatacttgg gaaagagcaa ccacgggagt gcactagaaa ctgattcacc
+ 4981 catgttataa cgcgttgctc gcaagtcgta ctgtggccac gcacaggtca ggcaatcgca
+ 5041 accatgtctt agcagtttgt aagaagacct ttaaacatgt acctcacagc aatctcggaa
+ 5101 cttttaattt tcctgagtca atgacatgct agctccgtcc acttgtaatc accgtcataa
+ 5161 cacagttagc ctgcaaaagg gcgtgtacac cttgccactt taaagctgac cgaataacct
+ 5221 acctacagga gatgcttagt gccacggaat gatctcgcaa tgcttagtct tacacccagt
+ 5281 gaatcaaccc aagacctcgc cgactgaacg gtattgagtc caatcccgag aggcaattta
+ 5341 tggccgttag tgacagtcgg tcgctgatag aataaggcag actcgtctta agcgggctgc
+ 5401 tttaagagaa aatggagccc tgacgaagaa gtggatgaac caggttttga caacgtccca
+ 5461 tattggtaat gtaggctcgt tatcaagaga taggtttaga aggctcaatg ctcgacgtaa
+ 5521 aagaagtctt aagctctatg agccagtgat gagagctaat tatagggcgc attcgttggg
+ 5581 gtaaggttgc gaattgtcat ttaactaaaa ccgacggcaa tggtttcacc ggagctgaga
+ 5641 tcgcattaaa gtcacactac gaattatttg tccccgcggc tccagagaca aatttctagg
+ 5701 agtgggttca tggagaaccg tgacaagcat ggtagcttca aatagcgtca tcggatctta
+ 5761 aagtgattgt gacatatatg ggattgcgcg tctctcttac acaagctagt gtgcgcgagg
+ 5821 tgctgaacac ctattacgtc aactcccggg atcccggcgg gttacagaga cataagcagg
+ 5881 gtgtccatca ttaacttcga tgttgagccc gtgccctgat caaacacctc tcgtagtagt
+ 5941 gggtgccggc cgtgtattat tttgggggag aggatgcgcc ctaagcaatt tctttccatc
+ 6001 ggccagccat tcgacgccgg cacgcaagtt gttgcgggca ctgttgcagt tcccgtacta
+ 6061 gagtctcaag tctagaggta ccagcatcag gaagatgggt acttcgtgtg gatcttctcc
+ 6121 tgaacctgaa acctgaagag ctaaagcgcg tcgcgctgcc atacgataag tcgctctcat
+ 6181 ttccggaaga cgtcgttggg tgatggcgaa caatcgcgaa acgaaaatcg cggtcggtat
+ 6241 gttgattcaa gacgggctac gggcgggtta ctaacaggtg cgcagaaatg tgatgggtca
+ 6301 cttgaccatg aactttcgcg ccgtcgcttc tgtggactgg ccggctccct gatagtgcac
+ 6361 tagcccgttg atatgcccat taccatttgg cggcgcagtg tgccagcggg attaagatgc
+ 6421 gtggcgtaca actatccgca ctttgctgac gcacaaaggc aactgatgga cagccttcgg
+ 6481 gcattcgact ggttggctga gttcgcctgc ctattaatat gcttgtggaa attgatttac
+ 6541 agcgcctact tctacttagg tgtacctatt tacggcacag ggataaaggc tgacagaaaa
+ 6601 gtcctggaca ggtcataggt agttgtcaga cctacaatgg tataacttga gagtcctgta
+ 6661 ccgcacatgc ggttgtagct agatgtccag aagaccgtag ctagcgacga gtgggttgca
+ 6721 cgcgcatttt gggaaggggc tgcgcgaggg tggggtcacg ggttattcca tttctaaatg
+ 6781 ctaaaccagc agttgcttta gttctgacct agcaggcatg tcatatgtat ggctagatta
+ 6841 ttagtacaat gcaggactaa gaaagcctga gacttaaatg cgttggtttt tcagccgacg
+ 6901 ggccgggagg gcagatggcc gaatgcgcac tgaggagtgc attgcgaggg aataggcgga
+ 6961 ccaccaggtc ccctcacata ctgtggataa acctacccag ggacaactca cgccatcatt
+ 7021 ttcaagagta gcactacttt ccactaagta cggtttgtcg agagccggtg gcaccgtgcg
+ 7081 acgagcttgt gggcactagg cgaaccgggt tatataggac tgccttgcgg tgcgggaata
+ 7141 ctttaccccg tggagaggcc ataaaagctt acatttattg tagccgctag cggtttcgac
+ 7201 gcgctcaagt ggggctttat cttagagtat caaataatgc cctctcagct tcatcttgat
+ 7261 ttttgtgttt ggggtagtgt atccgatggg tcaccttctt gaccttgggg agctccatcc
+ 7321 atcgtaccaa tactccgttt ctttgtgttg cctaccgagt aatcgaatac cgcacgaggg
+ 7381 ctagaatcta atttaaggtg ggtcttatcc ctgttgtttg gacctaacgc tgtaacaaat
+ 7441 cacttccgcg acgggtgtca ttacgtcttc tatccgccac cggttcaaca gtgcgtcgaa
+ 7501 tgccaagtcc ctattacccg cattgtaaag ccattacaat acctccggtg atataattga
+ 7561 ttgccggttg gcaagggatc atctgtacgg gccgcgattg attgctgata aggaacggcg
+ 7621 gtaaggaacg tatcgcgtac gaggttgtac actggaaccg ctaaacaagc ggtatcgcta
+ 7681 aattaccggc gattatatca agggaatctt aggtagcacg aagccctacg ccctggaaac
+ 7741 aggatcggcg cgaggccgtg gacatattag cctacgtttt tttacaccca gatttccgac
+ 7801 gatgtccaca gctaaggcta tcctaaaccg caaacacata taaccgcagt ataaagcacg
+ 7861 ggatgattcc ttggccatct tgcaagcagt gcaaggcaat tctggtgata ggggcaaggc
+ 7921 agtgaaccga gtggtcagcg tattgtgacc ctgcaattgt catggcagat aattgtttat
+ 7981 gaacctgttt cacacaccca tcccttggat ctccagcgta gttactaata gtacgatttc
+ 8041 ctggtgttct gtcacccgcc ttgctgcctt cacgcctgcc ccacgttttg ctgtccactg
+ 8101 aatatcgctc taattaatag gtgtcacact gtatcaggta agtccattcc gggtgctatt
+ 8161 ggatcattcc tgagatgtac caccgatccc ataggcgtta ggtcttacat ctggagtgaa
+ 8221 aaagatcagc atcgaactat aggtagataa aggtcatgac tgttaacaga gaatcgttcc
+ 8281 tatcgcaacc ttcactaact ggaaggcacc cccacacttt gattagtaag cccctagcga
+ 8341 atgtagtgat ccaagaacat cgagtatact ttagctctcg gttcaggcat gtatgcaatc
+ 8401 gaccaccctt ccgttcagag tactctcaac cagcagattt ctaaacttta tagcctccgc
+ 8461 ccactaaaat tgccttatct caggttgact cttggatgta gctgtaatct aacatacaca
+ 8521 tggagctgcg gcaaattatc gtacgtccaa accaccaccg gatcagtggc gatactattc
+ 8581 tcgcaaaaaa gccatccagc attggaacaa gtgttaacca gcatttttct gagtcccccg
+ 8641 gaaagaaagt tgactacact acatccataa atgctagagt gtggattcgc catgtgttac
+ 8701 aacggtcaac cgaaaggtta gcatgatact tcgttgttca atcggacgtt cgagcgccct
+ 8761 ccctgtttat cacttgatcc cccttttgaa acatgtgcgc tgcgacgcag ggctgggaga
+ 8821 gtcaccggaa accaaaagcc cgacctcgga cgtgtagggc cctccgtttg ccatcaatgg
+ 8881 cgatgtagga ttctctttta atacaacgtt cactcaatta acgtcttggt ataagcgtcg
+ 8941 aacgtgaccg aggttgacac cagtgtcacg gctgcgccgg ggtttgttgc tccgcgtgta
+ 9001 cagggtattg gttcgatggt gcctcctcta cgtagatcta ctggataacc gtccccaata
+ 9061 tccgcttccc aacgtagatt gccgacaggc ataagcttcg ggggcgcaaa ggccgacgtc
+ 9121 cgcattgcag tgtagctttg tgagcaggaa gtgtgatagt ctttcgatta ttaaagtctg
+ 9181 agctgaatga aaaaaggtcc aacgaatgga ggacgcgaag acatgggtgt ctcttatggc
+ 9241 ccgagcggga gtaatggcgg ttcgtacata aaggctgaaa ggattctggc gttagctgtc
+ 9301 ttacgttgga ttggcccttc aaattatcga tgttagctga ttcggtgtac cgggcgagga
+ 9361 aagcgctctc agaacaactt catatacgag gttcgactat aatggtctaa gctcctgggc
+ 9421 tagtctcaag aagcgggtac ctttagtagc acgtatcgac ggcaaagcaa agaataaaaa
+ 9481 cttggctttg catcgtgcaa agatttctaa ctaggttgtt taagggctgg tatctatgtc
+ 9541 ccgctataac agcgcgccta cagtagaagt ttaaccatga catacctttg aagtgttcgt
+ 9601 atcacacaca aggaaggagc atgtggacac cactgagctt tgatcagcac gcgtctcaga
+ 9661 gtttcagggg gacccaaatt actggtcctc aattgggacg cgaccgcatc tccccacgaa
+ 9721 agcttatggg gattgcccac tgcccagctt caaatctgaa ggttcggctt attgacaggg
+ 9781 tctaacacgc agctcaactg ctcgaggtta gaggcgtaat gacgggcccc gatagccttc
+ 9841 tacgattacg tccagcagga accccacagc ttttccctac gtctaacacc gtgaaagcaa
+ 9901 aactgtctgc ccttttacat ggtctttaag gaatctctgc acttatgtta ttaggtaagc
+ 9961 tcccataaga gcaccacttc gtgtaccttg ctaactccct tcatccccac ccgcgaaaac
+ 10021 ttaagacgtc acccctgtta ttatcccgtg cactcctaaa gtgcgatggg caagaacgca
+ 10081 aacaattgtc tgagatttat atgggcggcg gacatagtca gagagcctta tataatctcc
+ 10141 cacgtcttgc cagtccgagt tatgagaaac ccgggaccga tgacgctatt acggtcgccc
+ 10201 agcgaggttc aacagagcga ggcataggag tcattacgcg tgttagcttc aacatgcgtg
+ 10261 gaagtgaaac ggatctataa aacggcgtgg agtcatcagc ttgagcagat ctaacttact
+ 10321 cgccacgcgc gcaaatcgtc tttcgctgtc cacgttatac gtaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/part_J.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/part_J.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,196 @@
+LOCUS part_J 4380 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/part_K.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/part_K.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,108 @@
+LOCUS part_K 3634 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/part_L.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_3/provided_parts_records/part_L.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,79 @@
+LOCUS part_L 2267 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,350 @@
+LOCUS construct_4 8074 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_4
+VERSION construct_4
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CAGA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ homology 5..8
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..1093
+ /source="part_G"
+ /indicates_part=True
+ /note="From part_G"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 1094..1097
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1098..2746
+ /source="part_H"
+ /indicates_part=True
+ /note="From part_H"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 2747..2750
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 2751..3085
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 2751..3085
+ /source="part_I"
+ /indicates_part=True
+ /note="From part_I"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3086..3089
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3090..3498
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(3387..3407)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 3090..3498
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3499..3502
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3420^3421
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6918^6919
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 5..3502
+ /source="construct_2"
+ /indicates_part=True
+ /note="From construct_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3503..3506
+ /label="GTCA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3507..3510
+ /label="feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ misc_feature 3507..3548
+ /source="part_L"
+ /indicates_part=True
+ /note="From part_L"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3549..3552
+ /label="ACCC"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ CDS complement(3746..4537)
+ /label="feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ CDS complement(3746..4651)
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3617..3645
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 4962..4967
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3722..3745
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 4940..4945
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 4785..4790
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 4821..5373
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3560..3670
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA complement(4824..4931)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5460..5468
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature complement(3672..3712)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 4735..4758
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 4806..4811
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene complement(3746..4651)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 4785..5373
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3584..3607
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3553..3558
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 6763..6786
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6942..6972
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 5743..6762
+ /label="feature"
+ /ApEinfo_fwdcolor="#993366"
+ gene 5743..6762
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6985..7002
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6895..6919
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 6946..6970
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 6787..6834
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 6990..6995
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ terminator 6985..6987
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 3553..7002
+ /source="part_J"
+ /indicates_part=True
+ /note="From part_J"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 7003..7006
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ promoter 7083..7261
+ /label="another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 8071..8074
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ff0000"
+ terminator 7818..8070
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ CDS 7263..7813
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b7e6d7"
+ misc_feature 7007..8074
+ /source="part_K"
+ /indicates_part=True
+ /note="From part_K"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cagaggagga acttctatgg gacgaaagat gcgcagctcg acaaatctca aattggaaac
+ 61 cgtctaaggt ctttgagccc acgctaggcc accgaatagt tgcgagctcg tgggcaattg
+ 121 ctggctagcg gtttgtatcg tatacgtaac aagagattgc gccggattca ttcgtgtggg
+ 181 gtgctttcac atcggaatac tcaagagtgg gggtttgcgc tttaatatga cggcctcatg
+ 241 caccccaaaa ataagagcgc caatttcatc gaccacattc cggacaattc tgacttccct
+ 301 gtcggatcga ccctcgctca caactcctag aactccaaga cggtaggacg tcagccgaaa
+ 361 aggaggagtg acgacgggcc ctcctagctg aagcaatggg gggcgtcgac cctagcctgg
+ 421 tgtgggactt cggagggtcg ggcgtgtggc cattcctgca cgaggggccc ttgcagtatc
+ 481 gaactttgac gagaaagtgg ggggcgacct ataaacatag cggagttcaa tactcctgca
+ 541 agtgcatgat gacgttcagc gttggcacat cgaacgcgtc gctacacttg ctcaccggaa
+ 601 ggcaaaatag accggcagct ggcccgcacg gacgtctaga ctcctacgct gtcaaatgca
+ 661 cgatgactat tagcatgcgg aattcgaggc ggccggtaca tcgagacacg ctggtcttaa
+ 721 tacctgtgtt atgtcaaaac aagtgtctcg gcggctttgt actacgctgt gaatgcgcat
+ 781 gatgttgcga gaagctgaac gttggtagca gtctacaaca gaaccgacga gctacggacg
+ 841 ggttacagca ggatcccctc ttaaggcatt attcgacgac tccaggttct aaccgatcag
+ 901 taattgcctc ggatggtcgt acgtgttaac cgagacagca aggcaccaca tagacaactg
+ 961 catagggcgc ctacaggtcc acaatcaggg tggcccaaga tcctcaaaga cttgttgcag
+ 1021 tctctgctta ttccgtttaa cacgttgtgt gagctctagc ttactacctc atcggtgtcg
+ 1081 ggagtgattt aggaatggaa gacgcgttta gtcttcggcc cccagacggc accggcagag
+ 1141 ccactgccaa tgccttttac gctgaactct tcgactttgg catgtgcgac tgactatacg
+ 1201 ccgatggccc taccctgcag cggaaaggca cagggccaaa aacagtggaa gcgcaccgct
+ 1261 agagctttac taaatccttt agggtgaacc ggtgttcagt caacagaaac atatgactag
+ 1321 tccttaatgg cactactaaa ggcggcccat ctcttttgta ggtcacgtct catcgtttag
+ 1381 caagcgtccg ccatccgagg agtatcctag tacgtgagag ggtgttttac ctcatcacat
+ 1441 ggtttttggc tagatgtggc agatgccagc tgatacctta caacccgcta taacggtttc
+ 1501 tggatcgacg atacaacctg cttcggcata tcataatggc ggcctcatag gacttccaat
+ 1561 catggttatg cgagtttgat gtgttgaaga ttgtgagggg aaaccttttt ccgagtacgt
+ 1621 tgaatctgcg actgatggtg aacaactcat cgagagggat gtgcgggcag tctccttgat
+ 1681 gcgcgaaaag gagtcgcgac cgcgtgttcg tgacgcactt gatgctagac cgtaggggct
+ 1741 cattatctcc tgaaacagta gctagctttt ggtgtccgag tcagcttagg cacagtaatt
+ 1801 gaaaagaagg aaatgcgtga aaactaaacg tagacactcc ttgctaagaa ttccctggtc
+ 1861 tttttcgagc atagactacc gtaggtaaaa ggcttgtcgt gtcacaaata gacttgatct
+ 1921 gttcggcata tacacatcct actgcttcag taaccaagga cgattctccg gccattggac
+ 1981 tgtgggacca cccgcgttca aacggaatcc tctacgaacg gttaagaaag gagcccactg
+ 2041 cttgcggaga catatcgttg ctgagtggta caccggtgag tcaaaaagta ctgacactac
+ 2101 tggtggactc tcgggtacga tgtgtggggt attggcatac tatggcgcta agcgtggaat
+ 2161 agtgtttcca atagcccttt acctaagaag cattctgaca catgggttgg acttttacac
+ 2221 agacctataa ctcgtatccg gcctggtgat gtatgtccgc ttatcactga atgcaggatt
+ 2281 ccgccaattc cgctcgcggg ttctcggaca acgggccatg gagatggatc aatgagccat
+ 2341 gttgattacc atttcactac acacggttag tcaattccgg agatcataat tcgacaattg
+ 2401 aatatgcgtg atacgctttc tgttaccagg atcgttgcta attagtttcc aatgtcacag
+ 2461 tgttgggcgg cgaggtatca cggcgctctg ggtagaatgg cggtgcctga ctggacctca
+ 2521 taactggtaa catacctatg accaaaggag gtcagacacc gatgagtcgg tgacatgggc
+ 2581 ggtcacagcg tgccctgcat agtaatacag ctcgtttcta gacatttgtc ctaattcgcc
+ 2641 acacaagtac gagagcgggg gtaacccatc accatcgtgc ccgtaggtac ctaatcttca
+ 2701 tcgagcgcta ttgttaaagt ggactcaggg atcggcatct cgtgtagctt ttattatccg
+ 2761 gcatgcatgc ggcgttgcat cgcttcatcg tcatcgacat atcgttagcg ggacttatca
+ 2821 gggtcccatc acggctgtga cagctgttca taagtgtaat agcagtcacc ccaccaaatg
+ 2881 caagactgtt cccaaactaa gtgctaggga ggttggctac ctatcggcgt ggcagttgac
+ 2941 cgggtttttc ttagtacctg ccttccaatc tccgataaaa gcaagatgac ttcctgcttg
+ 3001 cgctaaagtc tgaattcgct aagggggcag attcattacc agagactgcc aaagtcaacc
+ 3061 gccgaacgat actggaatat atggaggtaa gctcccataa gagcaccact tcgtgtacct
+ 3121 tgctaactcc cttcatcccc acccgcgaaa acttaagacg tcacccctgt tattatcccg
+ 3181 tgcactccta aagtgcgatg ggcaagaacg caaacaattg tctgagattt atatgggcgg
+ 3241 cggacatagt cagagagcct tatataatct cccacgtctt gccagtccga gttatgagaa
+ 3301 acccgggacc gatgacgcta ttacggtcgc ccagcgaggt tcaacagagc gaggcatagg
+ 3361 agtcattacg cgtgttagct tcaacatgcg tggaagtgaa acggatctat aaaacggcgt
+ 3421 ggagtcatca gcttgagcag atctaactta ctcgccacgc gcgcaaatcg tctttcgctg
+ 3481 tccacgttat acgtaactcg ctgtcacgct agagaccgta tgaggtgggc ggatagtggt
+ 3541 gacttcaaac ccctaagatg ccagcgcaat acggcatcgc agggcaagca acaccgcaca
+ 3601 gcatgtccct aaagggaaga tttaatacgg actcagtcaa gttgtgagaa acgacaatac
+ 3661 attgagtgga atgccctttg gtacgttggc gatagatcta acgagaaact tcaacgagat
+ 3721 ctagagtatc ggactgagat gcatcatggc tagggattgc tgaatggata tctttgccaa
+ 3781 aatgagctcg actaggaatc tcagactgcc agctacgaaa agctggggga tattcatttc
+ 3841 cgctcttgta aggcgcacga tgaccctgtg gagcaaaatt cgacgcggca acgtagtcaa
+ 3901 agtacggcct atctgggacg gagatgggat tgtttctgta ttcatgccgg cctcttgaga
+ 3961 ttgtaaggat acccggccac agtctcgtaa gaaacccgat atcgctcaaa cgaattgaca
+ 4021 tcagttaggg cttgcgctct agcaaccacg cgtcgggtgt tcgactgaat ttaagatcca
+ 4081 gcgcaaacca ttccttaaag gcggtccagg tgaaaccggc tctgataatg tacagtggat
+ 4141 tgtccagttc gcttcaaagt gcaatcaggc aaggtactgg caagtcaccg cttggggccg
+ 4201 gtttcagtgg agctttatcg acaaaaggcc gggccctttg gcctagagct cacttttggt
+ 4261 gtcgttcacg agtgagaact ttggctcgca gcttgaatgc ttgtcacgtt tagggttata
+ 4321 caacgtttct ataaactacc tatgacaaat cccgatcttc tgaaactcca taaggactaa
+ 4381 gagagtccgc gacagtttca cttggtcggt gctattgact atgtcacgca tgcccggtaa
+ 4441 agcttttaag caaagcctga tatatcacgg gaggttactc aaagcatttt ctaaagggac
+ 4501 agcggactca cattagccta atataaaccc gatcaggcca tgcacctcga ttcaccggaa
+ 4561 ggtagtacca tgcaccggat atttgggaca acagtgaata gtacatcgta aaatgtcaag
+ 4621 gcctagctat ttttcactgg tgtcttatct ctattacaac acacacggat gtcccgagcc
+ 4681 tacactttca aatatactca aggttcgctg ttaagggtaa tacaagagtg ctcggtttag
+ 4741 tatccatatg ttggtacaag tgactgtgct agccgtaaat taattcggct tccattccag
+ 4801 cttgggtgtt tagggtctag acggttgaaa ccagaaagag tacagacaaa accgtagctc
+ 4861 tcccaaggtt gatcctccag acacctaccc acactagtag cgcaggccta gaggagacgt
+ 4921 taggagcgga attgtacatt cagtatcgca ttaagcacaa agacagacaa acctagaagc
+ 4981 cacttatccc ctcgtaggag tacaacggca gcgctttcgg gaggagttgc ctaactacgc
+ 5041 tctggacagc aagtcccaga atgaagaaaa tgacttggcg agaacccacc actacatgca
+ 5101 gggtcttggg accggtcagc acagcttatc catgcggcaa ttccggacga ccgcgaatga
+ 5161 ggatcacgac actgccgatg ttgcaccatt gaccttctcc tatgcaacaa gggcttaaga
+ 5221 tggtagatgg taatagagta gcctgcgacc ttatgcggta atacacaaaa accggtaaac
+ 5281 agtgcgttga tgctgtgtgc tggcgcattt gtgtaccttg ctgggctcgt ataaaattct
+ 5341 gtcagcagga cgttcacctc ccttctgcta gtcgctaggc acaaacggaa aaggtctaat
+ 5401 cgcgcgcgtg ctcgttagag tactggggcc tcccaccacg gatgatcacc tcgccgatac
+ 5461 atttggcctt atgtctcaat aagacctcat ggtctatcct acaccataga tttggaaagt
+ 5521 ctagttgctg cctagcaggc tgatagcaag cgtcgtacga ggatcgagga agggcactca
+ 5581 tgggagtgta gcgctagcca tagttgacct gtcagccggt caaggttggt ccgaacctag
+ 5641 ccagttagac gaccagctcc cccactattg cacagtgcct gtataagcac gtcagtgtct
+ 5701 ggcaccactg tgcgcggtgt ggtcctcggg acgatcttcc tacggctacc catgcgctag
+ 5761 tgattacaga cgatcgtttt ttctttttct gtggtgcaaa tacacaagat acgtcaagag
+ 5821 tcctagcagc ctcatcttgc caattgcagg ggtaccgatt cacccatggt atcagtcacg
+ 5881 caaaaaaaga cgacatcgga gttgctggcg actggcaaaa gaaaacatct atctgccgtg
+ 5941 gcgttcgtct agcgcagcga gccgactgac tactccgtta tctcaaattt agtttcgtaa
+ 6001 gatcttcacg ggagccggcc agctgaagaa tctataggtc taccgctaga ggaagcccgt
+ 6061 ttacaaccga cgtactagtc cgacagcaat cgtcagcatg ccaatttatt gtatcaggtt
+ 6121 gagaatgcac cactacggaa tcgacgtgcc actggccgca cgatactagt gcgctggtaa
+ 6181 acaggccagg agctctaaat ctggagtggt gtgaatttaa ccgcggaacg attgttgcac
+ 6241 gcggtccctg tgactctgtt gggagcactg tccccggctc cggataagtg atgtgaacga
+ 6301 aaaggtgggc tgaccagaga tagggttaag gacgggcgat cgtagtggac gattactgct
+ 6361 gatcttccga gcactctgag tcgcgcggcg tatcgggagt taccccgctc gctacacatc
+ 6421 tgaattccgc cggatactat gggtgcagag tggatcacct tttcgtgacc cgtatattcg
+ 6481 tcgttctcat cactgtcctc cgcgatttat ttcaatcgtc ggtttcgcca gatgcattcc
+ 6541 tggggaagtc atcgcgacag tgcgctgcgc gcacagctct tcttggttta ttcgagattg
+ 6601 tggtttatca acatggtcta tctacggact gattagaata ttcccacgtt aagccgacgt
+ 6661 gcattggtac tggctcctta attaagcgca gagggtaggc gccttttctt gtgcaaacca
+ 6721 ttatatgagg aactagcaaa cactatggcg caatatgtcc acgtgactcg agcattctgt
+ 6781 gttgcggtag cgatttcact agtcacaaac ggatagattc tacggcgcac ccggtgcatc
+ 6841 gttgtatgtt cagcaatttg gtcatatccc gctcctctat tcaatctctt ttttcgtcag
+ 6901 ggggggcaca tacttggagc agctgcgcct aacattacaa taagcagtcg gagctcagta
+ 6961 caaaaccctt atcttagcgg tccgttctgg aattcggtct caggagagac actccttcat
+ 7021 caacagcaga ggttacatac gtttaacctg accgatggtt gcccatcgaa agcaaggacc
+ 7081 cacgggtagg cagctgttgt ttgatatgct tttgtccccg gaaggcgccg ataaaattat
+ 7141 acgccgtccc ccgcgtccgt tacgagcttc gtgatgttgc gggctgaagt tccctacgag
+ 7201 tcaataggcc aactcgaatg gctaaatggt tgcaacccac aggctcaact ttgaaggtaa
+ 7261 tacgccaaaa tccaatatgc tctttcgggt agcgcataaa accttctggg ggccactgca
+ 7321 gacagtcatg gaggactacg tgcaacacta cgctctagag tgatgatgtg gcagtcaacc
+ 7381 gagggctgtt aagagaagtc tgtgcacgaa aatcaatgag tcggtgtaat cttcaccttc
+ 7441 ctacaaacca aggcttgagg gcctcaattt cgagcaccac ttcttgacca agccgttcgc
+ 7501 cggtatagga gttacgaatt cgggtcgtct gccgtctttg aaccatagat aagtacctcc
+ 7561 cgagtcggga gaacacgaat cgcatcagaa ctcatcgaag ggtgttactt tgcccatcgg
+ 7621 catccccgaa gattaattgc attcgaaatt ttaacttcga gaatcatccg tgctaaccaa
+ 7681 cgtggacgag ctatgaacgt ttacgtgttc agtatctagg aattgacacg tctccgatag
+ 7741 cgggagtcac ggcatgagtt acggcttttg tgaccagcgt ctgtgtaatt ttattgacag
+ 7801 tttcatatat agtgtctcgt cttgcctttg agattcacag gctgtaagag ggatgccgtc
+ 7861 gtgtatatgc ctgcagttag agcttccttg tcaggacgag caactcactc cttctggtga
+ 7921 tgctttgcta gcatgtagct tcgggtactt gcggaaaagg acagcctaca gtgtctgcgg
+ 7981 cggtacgtca ctaatatgac atacgctgtg gacatcgtga agcggcgaat cgctccagat
+ 8041 tgaggtttac agagtactcc atagtcacac aact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,enzymes,used_in,parts
+construct_4,construct_4,2,8074,4,construct_2,AarI,,construct_2 & part_L & part_J & part_K
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf
Binary file test-data/init/2-step-golden_gate_plan_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/construct_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/construct_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,279 @@
+LOCUS construct_2 6910 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_2
+VERSION construct_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1..4
+ /label="CGCT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 9..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS complement(223..1038)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature complement(139..179)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_feature 5..8
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ misc_feature 20..25
+ /label="feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ gene complement(223..1038)
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 189..212
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 51..74
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 84..112
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 27..137
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3347..3377
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1367..1372
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ gene 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -35_signal 1190..1195
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_RNA 1226..1778
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3396
+ /label="another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3192..3239
+ /label="feature"
+ /ApEinfo_fwdcolor="#c6c9d1"
+ misc_RNA complement(1229..1336)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 1865..1873
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3413..3416
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ rep_origin 1190..1778
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3300..3324
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1345..1350
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ rep_origin 1899..2147
+ /label="feature"
+ /ApEinfo_fwdcolor="#ffef86"
+ misc_feature 3397..3401
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#84b0dc"
+ misc_feature 3395..3412
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ -10_signal 1211..1216
+ /label="feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 3168..3191
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ CDS 2148..3167
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#993366"
+ misc_feature 3351..3375
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 1140..1163
+ /label="another feature"
+ /ApEinfo_fwdcolor="#b4abac"
+ misc_feature 5..3416
+ /source="part_A"
+ /indicates_part=True
+ /note="From part_A"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3417..3420
+ /label="GGAG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3421..4505
+ /source="part_G"
+ /indicates_part=True
+ /note="From part_G"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4506..4509
+ /label="AATG"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4510..6158
+ /source="part_H"
+ /indicates_part=True
+ /note="From part_H"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6159..6162
+ /label="GCTT"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6163..6497
+ /label="feature"
+ /ApEinfo_fwdcolor="#f8d3a9"
+ misc_feature 6163..6497
+ /source="part_I"
+ /indicates_part=True
+ /note="From part_I"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6498..6501
+ /label="GGTA"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 6502..6910
+ /label="another feature"
+ /ApEinfo_fwdcolor="#faac61"
+ primer_bind complement(6799..6819)
+ /label="yet another feature"
+ /ApEinfo_fwdcolor="#85dae9"
+ misc_feature 6502..6910
+ /source="part_F"
+ /indicates_part=True
+ /note="From part_F"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cgctgtcaat atgcaggtgc tgcaggaatt tgtctccaat cgacttgaga tatcgcaagc
+ 61 atgaaattat attagacacg ccagagaact tgggaagcag cactggtagt gatagcaacc
+ 121 cgagtacagt aacgagtgag cttctgatca tgagctctcc tacggcgtca atgcgacgaa
+ 181 tgcccagcat gcactctcgc tatccatgcc tgctagggtg gcattatgct caggaacagt
+ 241 tgtagcttgg atatcgtcta gatgaaatac ctggacactg gttagcgtcg tcaagcacca
+ 301 aggacattca cacgctcgcg gtctttcgtc tccctaagcg ttcggcagtc gggcgtgaag
+ 361 aggttgtaat cagacggaac aaagcctgaa aaaattccag cgacgtagta ttcatgatcc
+ 421 tgtaccatct gtagccgccg cggcgcacga ttgaatgtag gctactaacc ccatccgtgt
+ 481 tagcgatgtg agtttctacc gcaacgaatg ctcaagcgaa ccttcttctt tcgtccgcaa
+ 541 cccacaagcc gtggttatga cagctaaatt gtcccagaca tccctttatt acacaagagc
+ 601 tccagcggaa tacctagtca cagcggtaat gacacaaagc tcttagttag tccagggact
+ 661 acttctgtct acagcacatc acactcatta tcagcatcag tgtagagacg gagaacatgg
+ 721 gctatcctat accaagatcc gccatctaaa catttgaagt ttcccgtctt ctataactta
+ 781 gcactcgacg ctattctgct gagtgcgctt agtctgtagc gacttgcgaa atccataaac
+ 841 tgagaattga aagagagtgc ataaccgaaa cctttgtggc atatttccgt tgaaacgtac
+ 901 cagaacagcc gtttagtgcg gaacatacag tatcctgata aagcactcaa cccaacagac
+ 961 accctatgcc gatagcggga tgctaacaag tatagtcatg atgatttctc ggacagcggg
+ 1021 gtttggtaca gctgcaatcc gtgatttaaa ttcggacctc tgcacacacc gacggttacc
+ 1081 catatcctct acggctgtag gaagttttac cttggatgtc attctgattt cggcgtatct
+ 1141 cacaggatgg tccaacgaaa ctaggcttta gacgagggat gaatgaccga cccccactcg
+ 1201 tggcactaac ggacagactt ccctgacggt tattcgacca ttaaagtcag acatgcgggg
+ 1261 gtgaataaat tagccaaatt gtgtcgaaga aaagacgtgc ggctggcaca taaggcagtc
+ 1321 ttgatcctag tcttgcaggg atgcacgtaa gtcgcctcaa ttaactgcag ccgagctcca
+ 1381 ggttaccaaa gaccctagta tgccagggcc taacggttgg agtatattat gggtacgcaa
+ 1441 tagtgcggaa gttaacctgg gcaacatcca ggtgagaggt tggacggaag cgacagtaag
+ 1501 tggccataga ctgccgagtc gtgttaatga atcgctatac gcccatggag ttgtggggtc
+ 1561 gttttatccg agtaggggcc cgctgactac ttcgtccaga caatatgccg tcttcaatag
+ 1621 tctacctgag agtcatgccg gcatttccga cgctgagtga aacccgcgta gccaggcgaa
+ 1681 atttgcatct tgaaatacca ctgcagatca gccagtaagg cccatataag ggcgctggtg
+ 1741 ttctggcgac agataaagtg ttatctaatg taacccgcgg acttttagag gatacttgaa
+ 1801 tgcgggcata tcgtcccacc agcgtcacgt ggtcgggcta gcggcagaca aactctgccg
+ 1861 atgtttttct ttgccgcgat agcgggctag tcaattcact atccggcgat gaagcataga
+ 1921 ttgttatcgc gcttatgcgg aggataatca agtcttggca gaacctgctc gctcatgcac
+ 1981 tggtgaggcg tggttatcct aacaaccgcc taggacgaag aatgggctcg gtagggacag
+ 2041 ttcgtgcgtt tagcttcgtc ccatcttaat gctgtctgga gggaggctac atgcgaacag
+ 2101 aagccgtggg cgaaagttgt tgatccgggt ctaacacgga taagggccat ggtgaacgca
+ 2161 tcatgcgata cttcttggta gttcttctaa catgaccgtg ccatagccct taccctttga
+ 2221 agaagttaac ctatctgccg tctcctgcac gaatagcgac tggactcggg tattttggat
+ 2281 acctcacgaa agcacttcga tcggccgaag catggatatt tcgccggacg ggcccgaata
+ 2341 gagagccttg tatgtcggtt agtacaacgc agtcctggag acatctacgc ggatgggcct
+ 2401 aggggctgga cttaacattg ggtaacgtac ctggtccaaa gtgaatgcaa agcactttta
+ 2461 caaagcgcgg gtccccgtgg gtgtttaggg tagaagattg gcggatgcta cgaacgatcc
+ 2521 cgctttgaaa ctatcattac atcgtgtaaa agagacactt aacaaaggcc aataaactgc
+ 2581 cagtaagaat cgctcagtgc ggtgctgggg acgctaagta ggggcaacag ccagtgaagg
+ 2641 acgtgaccga cctttctcag ataagatatg ctggcgtcta tctaataagc atagtgaaaa
+ 2701 accaaccatt tcacttacac gaagtacatt tgcattgcta gtaaagacgc ctaaacagaa
+ 2761 gtgcccttgc atgctgtatg tctatagtcc ttagggaagc atcagccctt ctacttattc
+ 2821 gaggtctgag aaaccctgga caagctccga attattcaat gtgcctgtct ccgaggttag
+ 2881 atagcgctat gctcttaaga gttgcacaga atgaccatcc tggaatgtcc ctggaggggt
+ 2941 ctaggtatgc tgatcgaagg gtgctctaag gacttgacgt gcgtccgagg agggtgctgc
+ 3001 ctccttcgcc tttagatcca acgcggatca catgcgcgtg agctaatagg atcaccttct
+ 3061 gctccgattt ttaccctcct gggtcacttc cgaatgaggt agcgggcgaa atataatgtc
+ 3121 tccactcgta ggtgttccct gtatgtgaag ctctatagtg gacaaaggtt tgatgaacta
+ 3181 gcccccgtat acgctctcac cgacggacgc gggggtctgt tatttgaagc atcatacatg
+ 3241 cgaaggtgcc ttctcagcaa cgaaaggtag tgggagtgta caagttcaat gcgccgccat
+ 3301 aggtctgagt atacaagggg atgcccccat ccacaacggg attggctacc cggagagctg
+ 3361 gctccgctcc aacaaataat tatattaacc tattggaatt ccacctgcat atcagaggag
+ 3421 gaacttctat gggacgaaag atgcgcagct cgacaaatct caaattggaa accgtctaag
+ 3481 gtctttgagc ccacgctagg ccaccgaata gttgcgagct cgtgggcaat tgctggctag
+ 3541 cggtttgtat cgtatacgta acaagagatt gcgccggatt cattcgtgtg gggtgctttc
+ 3601 acatcggaat actcaagagt gggggtttgc gctttaatat gacggcctca tgcaccccaa
+ 3661 aaataagagc gccaatttca tcgaccacat tccggacaat tctgacttcc ctgtcggatc
+ 3721 gaccctcgct cacaactcct agaactccaa gacggtagga cgtcagccga aaaggaggag
+ 3781 tgacgacggg ccctcctagc tgaagcaatg gggggcgtcg accctagcct ggtgtgggac
+ 3841 ttcggagggt cgggcgtgtg gccattcctg cacgaggggc ccttgcagta tcgaactttg
+ 3901 acgagaaagt ggggggcgac ctataaacat agcggagttc aatactcctg caagtgcatg
+ 3961 atgacgttca gcgttggcac atcgaacgcg tcgctacact tgctcaccgg aaggcaaaat
+ 4021 agaccggcag ctggcccgca cggacgtcta gactcctacg ctgtcaaatg cacgatgact
+ 4081 attagcatgc ggaattcgag gcggccggta catcgagaca cgctggtctt aatacctgtg
+ 4141 ttatgtcaaa acaagtgtct cggcggcttt gtactacgct gtgaatgcgc atgatgttgc
+ 4201 gagaagctga acgttggtag cagtctacaa cagaaccgac gagctacgga cgggttacag
+ 4261 caggatcccc tcttaaggca ttattcgacg actccaggtt ctaaccgatc agtaattgcc
+ 4321 tcggatggtc gtacgtgtta accgagacag caaggcacca catagacaac tgcatagggc
+ 4381 gcctacaggt ccacaatcag ggtggcccaa gatcctcaaa gacttgttgc agtctctgct
+ 4441 tattccgttt aacacgttgt gtgagctcta gcttactacc tcatcggtgt cgggagtgat
+ 4501 ttaggaatgg aagacgcgtt tagtcttcgg cccccagacg gcaccggcag agccactgcc
+ 4561 aatgcctttt acgctgaact cttcgacttt ggcatgtgcg actgactata cgccgatggc
+ 4621 cctaccctgc agcggaaagg cacagggcca aaaacagtgg aagcgcaccg ctagagcttt
+ 4681 actaaatcct ttagggtgaa ccggtgttca gtcaacagaa acatatgact agtccttaat
+ 4741 ggcactacta aaggcggccc atctcttttg taggtcacgt ctcatcgttt agcaagcgtc
+ 4801 cgccatccga ggagtatcct agtacgtgag agggtgtttt acctcatcac atggtttttg
+ 4861 gctagatgtg gcagatgcca gctgatacct tacaacccgc tataacggtt tctggatcga
+ 4921 cgatacaacc tgcttcggca tatcataatg gcggcctcat aggacttcca atcatggtta
+ 4981 tgcgagtttg atgtgttgaa gattgtgagg ggaaaccttt ttccgagtac gttgaatctg
+ 5041 cgactgatgg tgaacaactc atcgagaggg atgtgcgggc agtctccttg atgcgcgaaa
+ 5101 aggagtcgcg accgcgtgtt cgtgacgcac ttgatgctag accgtagggg ctcattatct
+ 5161 cctgaaacag tagctagctt ttggtgtccg agtcagctta ggcacagtaa ttgaaaagaa
+ 5221 ggaaatgcgt gaaaactaaa cgtagacact ccttgctaag aattccctgg tctttttcga
+ 5281 gcatagacta ccgtaggtaa aaggcttgtc gtgtcacaaa tagacttgat ctgttcggca
+ 5341 tatacacatc ctactgcttc agtaaccaag gacgattctc cggccattgg actgtgggac
+ 5401 cacccgcgtt caaacggaat cctctacgaa cggttaagaa aggagcccac tgcttgcgga
+ 5461 gacatatcgt tgctgagtgg tacaccggtg agtcaaaaag tactgacact actggtggac
+ 5521 tctcgggtac gatgtgtggg gtattggcat actatggcgc taagcgtgga atagtgtttc
+ 5581 caatagccct ttacctaaga agcattctga cacatgggtt ggacttttac acagacctat
+ 5641 aactcgtatc cggcctggtg atgtatgtcc gcttatcact gaatgcagga ttccgccaat
+ 5701 tccgctcgcg ggttctcgga caacgggcca tggagatgga tcaatgagcc atgttgatta
+ 5761 ccatttcact acacacggtt agtcaattcc ggagatcata attcgacaat tgaatatgcg
+ 5821 tgatacgctt tctgttacca ggatcgttgc taattagttt ccaatgtcac agtgttgggc
+ 5881 ggcgaggtat cacggcgctc tgggtagaat ggcggtgcct gactggacct cataactggt
+ 5941 aacataccta tgaccaaagg aggtcagaca ccgatgagtc ggtgacatgg gcggtcacag
+ 6001 cgtgccctgc atagtaatac agctcgtttc tagacatttg tcctaattcg ccacacaagt
+ 6061 acgagagcgg gggtaaccca tcaccatcgt gcccgtaggt acctaatctt catcgagcgc
+ 6121 tattgttaaa gtggactcag ggatcggcat ctcgtgtagc ttttattatc cggcatgcat
+ 6181 gcggcgttgc atcgcttcat cgtcatcgac atatcgttag cgggacttat cagggtccca
+ 6241 tcacggctgt gacagctgtt cataagtgta atagcagtca ccccaccaaa tgcaagactg
+ 6301 ttcccaaact aagtgctagg gaggttggct acctatcggc gtggcagttg accgggtttt
+ 6361 tcttagtacc tgccttccaa tctccgataa aagcaagatg acttcctgct tgcgctaaag
+ 6421 tctgaattcg ctaagggggc agattcatta ccagagactg ccaaagtcaa ccgccgaacg
+ 6481 atactggaat atatggaggt aagctcccat aagagcacca cttcgtgtac cttgctaact
+ 6541 cccttcatcc ccacccgcga aaacttaaga cgtcacccct gttattatcc cgtgcactcc
+ 6601 taaagtgcga tgggcaagaa cgcaaacaat tgtctgagat ttatatgggc ggcggacata
+ 6661 gtcagagagc cttatataat ctcccacgtc ttgccagtcc gagttatgag aaacccggga
+ 6721 ccgatgacgc tattacggtc gcccagcgag gttcaacaga gcgaggcata ggagtcatta
+ 6781 cgcgtgttag cttcaacatg cgtggaagtg aaacggatct ataaaacggc gtggagtcat
+ 6841 cagcttgagc agatctaact tactcgccac gcgcgcaaat cgtctttcgc tgtccacgtt
+ 6901 atacgtaact
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/part_J.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/part_J.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,196 @@
+LOCUS part_J 4380 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/part_K.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/part_K.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,108 @@
+LOCUS part_K 3634 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/part_L.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/construct_4/provided_parts_records/part_L.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,79 @@
+LOCUS part_L 2267 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_A.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_A.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,197 @@
+LOCUS part_A 4292 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_B.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_B.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,124 @@
+LOCUS part_B 4259 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_C.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_C.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,99 @@
+LOCUS part_C 3423 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_D.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_D.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,96 @@
+LOCUS part_D 2682 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_E.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_E.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,38 @@
+LOCUS part_E 347 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_F.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_F.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,74 @@
+LOCUS part_F 2470 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_G.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_G.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,36 @@
+LOCUS part_G 1119 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_H.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_H.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,109 @@
+LOCUS part_H 4246 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_I.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_I.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,69 @@
+LOCUS part_I 2396 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_J.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_J.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,196 @@
+LOCUS part_J 4380 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_K.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_K.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,108 @@
+LOCUS part_K 3634 bp 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 32e44a646b68 -r 3171db614963 test-data/init/2-step-golden_gate_plan_simulation/part_records/part_L.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/2-step-golden_gate_plan_simulation/part_records/part_L.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,79 @@
+LOCUS part_L 2267 bp 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 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/Report.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/construct_1_connections_graph.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/error.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_1/error.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+assembly_name;message;suggestion;data
+construct_1;Wrong number of constructs;expected_: 1,found: 0
+construct_1;Some parts are unused;unused_parts: partA & partB & partC & receptor
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/fragments_in_construct_1_homology_mix/partA_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/fragments_in_construct_1_homology_mix/partB_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/fragments_in_construct_1_homology_mix/partC_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/fragments_in_construct_1_homology_mix/receptor_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_plots/partA.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_plots/partB.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_plots/partC.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_plots/receptor.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/partA.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/partA.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,95 @@
+LOCUS Exported 4022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partA
+VERSION partA
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 4022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..4022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..1001
+ /label="pA"
+ /label="nonstandard type: annotation"
+ CDS 1123..2022
+ /label="AmpR"
+ misc_feature 3023..3522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaatt gtaagataga acagggatat agctcgttgc atccataaat tgcccaccgt
+ 61 agggagaacg ccgttggaaa atgagagtta ggcgatgagc ggttgtcgcc cgcacagaca
+ 121 aaggatgcct ttataaatag tagcggcctt gtctgcacca gacgtttgtg ggtcgacgtg
+ 181 ctattctagc caaaagcaaa atgtatcata ctacaggcaa taggccctat gctgaccaaa
+ 241 cttggggacc cttgcgcctt ctctcttacg cataacatgc ataggtacct ctactcatca
+ 301 ggcagggcgg cgtgaggtca ctatggctca agatgtgtac gactaaagaa aggtttatgc
+ 361 tccttcccca aggacgcatt tgggactgct acttgcccct agcgaattca ctaggatttt
+ 421 tgtagaacca tgagcgccct atccgatagc acagagacaa tgctacaagc aactgtgcat
+ 481 gcgctcgatc gccgtgcatt aatacgtatt atagcgtatc gtgtacgcta atatcttagt
+ 541 gcaccgcacg ctggttggat acaattccgt gaaataattc ctgcttacac aggggctttc
+ 601 tggcgcatgg ctgtgtctgg atgtttgtga taagaggctc catgaacccg gcgggaaatg
+ 661 aggggaaacc ccggggagca acgacactaa gcctggcagt tgttcagata ggacgctttt
+ 721 gtcagtgggc ggttttgcat ccactaacta tcataaacga cacaacgtcg aatgatcatc
+ 781 ggcggtttgc atgtagagac agctcctgca acaccatacc ggctcgtgga attacgctgt
+ 841 gcgccggccc tcattcgatt gtgtccagcg tcggcgcgaa tgatgattga gatgtgcttc
+ 901 ggctcagagc gtgcacaggt agttctcccc ccttacctag ctgatccagc aattccacgc
+ 961 tggcccgcgc gtccttgggt aacactggat ctgtacccaa atacaccgtc gggctagaga
+ 1021 cgctccacct gcgtctatcg tacagtgcta aaatggcagc agatagtgaa acttccgcta
+ 1081 agctagcccc tcagggtaca ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt
+ 1141 tgtcggggac ctgccgtcac gcttccgagt gtatatccgg atttagttga cgtcatacag
+ 1201 aggcactaag aagaataaac gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct
+ 1261 cccttgcgcc gttcggcaag cgtccggtgt cgggctgcaa ggaataaatc tttatggacc
+ 1321 agaggggctt gtttcctcat atgggtgcgt gcacttatac gattcaaagg tggatatggc
+ 1381 cgcataacac gtagccaggc tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg
+ 1441 tttttgtttt tcctttacga cacgaaccgc tctaacctgc tctatttcgc cacgttccag
+ 1501 tgaacctctt agcctaccgc ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg
+ 1561 gagaaatcgt tcaatattag aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc
+ 1621 cgtttaacgg ctgccgtggt cataccgtga ggcaccacga ggggatgcta cgcaacatgc
+ 1681 gaggtgtaat cagcagggaa gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat
+ 1741 atgcataagg tgtcatttat attacaccta cgacactggt accggctcac agccaaatgc
+ 1801 acagtctcaa gatagaattc gcaaaaatta ggcttatcgg gcgcttactc tttgttacac
+ 1861 ttctggtctg tgagtgacgc cctgtgtccc atcactgcat gtgaggatgc gtgtactgca
+ 1921 cctgtgaatt acagacgttt ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc
+ 1981 tctatagggt gatctcgaca taccactatg gtttgcgcgt ttcgggtgct tttggcgagg
+ 2041 gccaggtacg gcggtgagac agcgtatttt gcgaataggg tattcggacg cacggtgtat
+ 2101 agctcttgga aaacgactct tcgacgggcg tgtagaagta gccaagcagt tcggttgtta
+ 2161 tcactaaatg cggaccatgt gcagccgttt aggagaggag tctgcaatgg atcagctggt
+ 2221 cagattgtac cactcggttg agcctaaggc acttcaggtg ctcggattgt aatgaaccct
+ 2281 caggttacgc cgttgcgctg agatcccaca agccataagc aatgagaatc gagcagctat
+ 2341 cgaattacgc agcacttgct gatgaactgg gtgcacctaa agcgcccgat aaaacggagg
+ 2401 gagtgaggta actactacat tgcgagtagt gcgaggggcc tccgagacta cattagagca
+ 2461 gccatgccga atacgacaaa atctatagcc ttgcgaacgt aggggactga tttatggaca
+ 2521 acaggaccga aacaagttgg agccacaacg gagctatgga cgttttcact attgatgggt
+ 2581 ggcttgcgtc cgcatcccag gtttctctgg ttaattttca tgacgattct ttgtggtacg
+ 2641 atccaggcat aagatagggc acctaacccg atactgtgaa cttatatgac ggctgaacat
+ 2701 gccctaatag tctgccaaaa gggaaaccta taacggctct aaacgggccc cgggtacgta
+ 2761 acagcaatgt tcctgtccac caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat
+ 2821 tccgttttac gccccagatc gcagctccct tgacagtgtc agttgaatcc ccattctagg
+ 2881 tttcctgata aaactaagta cggggacgca tcagtcgaaa gcaatcacag ataatagata
+ 2941 tcttgagcag aaagacgtct tcacgaatca ggagcgagtg tcccctttga aagtgcgggc
+ 3001 aacaataggt gtgaggtttc acggttgctt gatcagtagc tgttcactct ctcgcaggcc
+ 3061 tacatagtga ggtggtgaga ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc
+ 3121 gggcacgcta acaaggacag gaattcgggt cgtcaaataa caatttacgt catcgcatcc
+ 3181 ctcaagggta aggcgtgatc tccatctcgg ttcccaattg gtcattgtga tagccacact
+ 3241 gcagttaccg aaggcgattt tatactaccc tgataagtgc tcgcagcccc tcctccctaa
+ 3301 taatgtaacg acgagcatta acccaggagt atttctcacg ttgctcgtgc ccagccaagg
+ 3361 cgatcaacgc agaccggata gcgttagcta gcccacgggt aaaagcgatt gttgtactct
+ 3421 ttcatatgaa tacagcactc gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc
+ 3481 acactggagg cgatgatcta gcccgtcttt caccccgtac ctttatactc ggccgcgtat
+ 3541 ttctccaccg ggagctctgc ctaccaaagc gtcgtacgcc caggaagccg tttcctttat
+ 3601 cctccctcat gtctcaacgc gcgagcatcg gagagtacgc gaaatcgact gtctggccaa
+ 3661 cactggacag acgcgcgaga cactgataaa cccccatttt cgtggggtta gtaaatcggt
+ 3721 ggcttcaaac ggttcgatcg ctcgcacgag cattagtcag gagtatgatt gcgcatcatc
+ 3781 tctactccgt actaggttct gtagctcagg atctccgggg ggatcaagct tttatgtccc
+ 3841 gcgggattag aagatatcca tccatatgtt tactttgatg cgggtccgag ctctctatga
+ 3901 tgctgctttg acaaaatgtg gaaagcctca gcgaccgctc tggggtcaaa gctctacgac
+ 3961 acgttgatgc taaacaagtt ggactactaa gcaaatgaag cggaagagat actgagcgct
+ 4021 ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/partB.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/partB.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,111 @@
+LOCUS Exported 5022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partB
+VERSION partB
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 5022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..5022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..2001
+ /label="pB"
+ /label="nonstandard type: annotation"
+ CDS 2123..3022
+ /label="AmpR"
+ misc_feature 4023..4522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaggc ttgattgtta actaccgtat ggcggttacg atcgagtgac actattatta
+ 61 gaccgctact ccaagtccca acttttcatc gccatacaga agagaacgag aaagtcgaag
+ 121 agttatagcg tgtacacttc tgattagcta acgaatcgat gcgtacagca tactcgagca
+ 181 actttatggg tcgtctgtct ccttgtaccc cgcttgacga ggatgtgttt gtaggcggct
+ 241 tggatatcgg cagtgtatcc gcatggtcaa acactttagc ccgaccggtg ctcaaggtcg
+ 301 aaatcctaat atagattggg ataggacccg tccattacta ggcgacattc gcagtcacga
+ 361 gcccgcacgg ggtgcctcaa cacggtgaca ctcaattcgc cggcactgag tacgacgatc
+ 421 gtgattgcca taccgtcatg ttttgtgtta cccctgataa gaagcgcaga tatggcacgg
+ 481 gggcagaggg cggagtagac ccatgcaaaa ctctagcctc tgggcagcat gatcgacgta
+ 541 gaacgccgtt gtgactcact agtttcagtt atgatgttca gccaagaatc ctccattttg
+ 601 acgtgaacct tctcccttta caccttgaag ctgcaatatt aagtcgaccc tttaagttgc
+ 661 cttgtcttgg tctagagccc gcagctcacc gataaaatga gcagtcaatt ttagcggcgg
+ 721 ttgtccaggt tacatgcact ttgggctgga accgcgttac gtttggagta cttagaagtg
+ 781 tcgtaggcat aggagagccg aaacttgata ttgggtctag ttagtgctct accccgcttc
+ 841 ggatccgtaa tagtgatgtt gcataagacg cttgcctcaa ggcgacatac ggtggcggtt
+ 901 gctggaaatg acgccccacc ccgtgataat ttggggacga gccgcacgat aacttctgcc
+ 961 agcgaccgcc cctcccacgt ccgatggtga ttccgaattt tgattacatg ccagacacgc
+ 1021 tttaatctcg ccaccacatt ggcaccccca ccaagtaatg tatgtaagaa gcagctgcgc
+ 1081 cccaagttac gtgccgtttc cgatgggagc agcaataatg tcgatagcaa ccacccccct
+ 1141 ctctactgac gaagcaacac cggggacacc gtcaccttgg cttcatttcg tattcattca
+ 1201 cctacgcaca accgcctgac cgttcgttat cacgagccta tccccttcaa gcaatttccc
+ 1261 ccccttgttc agcagcctac actatacgtt ggtacactgt gtgcgacaga tatttggtgc
+ 1321 ccgtcttatt ctattctgag agagtttaat agccaaaaga tatgagtagg aacgggaggt
+ 1381 acccgactcg cgttgaagca ctcttaagac ctctcttagc acttcgaagg gtaggtgcgt
+ 1441 tcaaagaacc tctgctttta actaagatca aaaggattgc gtacaacttc cccgttaact
+ 1501 ctccagagga tccgtagaag tctacaccaa aatacgtttg gtttcgccaa ggtgactatc
+ 1561 ggtacttgtg cacgtaacag ggtaaagaat tgaaagcctc aaattgtacg acgttacgcc
+ 1621 cggacggtcg ccggtgatag ggtgacgcat ttgcgtttgt catatcattt gggattagac
+ 1681 ggagctggtg tacctctatg gacgttacaa aaccttgtgg taacagcctg ggtgccatcc
+ 1741 acctagtccg aagtttcctt ctaaccgcgg catcagatgg atatgtacct tatggcgctt
+ 1801 cccgggaagt ccaattcttc gtgttgaagg gacagctcta caggcctggc cacttgtggc
+ 1861 gcatctaagt agtctaggtg catgattctc tcccttgggg gcgctgtcgt gggtcctgcc
+ 1921 gagccacacc ctaacctcac gtcgcaagac ttggtaaata gctttttttt ttatgcccaa
+ 1981 tctatttacg taacaatcga catcagagga ggggcagaga cgctccacct gcgtctatcg
+ 2041 tacagtgcta aaatggcagc agatagtgaa acttccgcta agctagcccc tcagggtaca
+ 2101 ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt tgtcggggac ctgccgtcac
+ 2161 gcttccgagt gtatatccgg atttagttga cgtcatacag aggcactaag aagaataaac
+ 2221 gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct cccttgcgcc gttcggcaag
+ 2281 cgtccggtgt cgggctgcaa ggaataaatc tttatggacc agaggggctt gtttcctcat
+ 2341 atgggtgcgt gcacttatac gattcaaagg tggatatggc cgcataacac gtagccaggc
+ 2401 tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg tttttgtttt tcctttacga
+ 2461 cacgaaccgc tctaacctgc tctatttcgc cacgttccag tgaacctctt agcctaccgc
+ 2521 ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg gagaaatcgt tcaatattag
+ 2581 aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc cgtttaacgg ctgccgtggt
+ 2641 cataccgtga ggcaccacga ggggatgcta cgcaacatgc gaggtgtaat cagcagggaa
+ 2701 gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat atgcataagg tgtcatttat
+ 2761 attacaccta cgacactggt accggctcac agccaaatgc acagtctcaa gatagaattc
+ 2821 gcaaaaatta ggcttatcgg gcgcttactc tttgttacac ttctggtctg tgagtgacgc
+ 2881 cctgtgtccc atcactgcat gtgaggatgc gtgtactgca cctgtgaatt acagacgttt
+ 2941 ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc tctatagggt gatctcgaca
+ 3001 taccactatg gtttgcgcgt ttcgggtgct tttggcgagg gccaggtacg gcggtgagac
+ 3061 agcgtatttt gcgaataggg tattcggacg cacggtgtat agctcttgga aaacgactct
+ 3121 tcgacgggcg tgtagaagta gccaagcagt tcggttgtta tcactaaatg cggaccatgt
+ 3181 gcagccgttt aggagaggag tctgcaatgg atcagctggt cagattgtac cactcggttg
+ 3241 agcctaaggc acttcaggtg ctcggattgt aatgaaccct caggttacgc cgttgcgctg
+ 3301 agatcccaca agccataagc aatgagaatc gagcagctat cgaattacgc agcacttgct
+ 3361 gatgaactgg gtgcacctaa agcgcccgat aaaacggagg gagtgaggta actactacat
+ 3421 tgcgagtagt gcgaggggcc tccgagacta cattagagca gccatgccga atacgacaaa
+ 3481 atctatagcc ttgcgaacgt aggggactga tttatggaca acaggaccga aacaagttgg
+ 3541 agccacaacg gagctatgga cgttttcact attgatgggt ggcttgcgtc cgcatcccag
+ 3601 gtttctctgg ttaattttca tgacgattct ttgtggtacg atccaggcat aagatagggc
+ 3661 acctaacccg atactgtgaa cttatatgac ggctgaacat gccctaatag tctgccaaaa
+ 3721 gggaaaccta taacggctct aaacgggccc cgggtacgta acagcaatgt tcctgtccac
+ 3781 caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat tccgttttac gccccagatc
+ 3841 gcagctccct tgacagtgtc agttgaatcc ccattctagg tttcctgata aaactaagta
+ 3901 cggggacgca tcagtcgaaa gcaatcacag ataatagata tcttgagcag aaagacgtct
+ 3961 tcacgaatca ggagcgagtg tcccctttga aagtgcgggc aacaataggt gtgaggtttc
+ 4021 acggttgctt gatcagtagc tgttcactct ctcgcaggcc tacatagtga ggtggtgaga
+ 4081 ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc gggcacgcta acaaggacag
+ 4141 gaattcgggt cgtcaaataa caatttacgt catcgcatcc ctcaagggta aggcgtgatc
+ 4201 tccatctcgg ttcccaattg gtcattgtga tagccacact gcagttaccg aaggcgattt
+ 4261 tatactaccc tgataagtgc tcgcagcccc tcctccctaa taatgtaacg acgagcatta
+ 4321 acccaggagt atttctcacg ttgctcgtgc ccagccaagg cgatcaacgc agaccggata
+ 4381 gcgttagcta gcccacgggt aaaagcgatt gttgtactct ttcatatgaa tacagcactc
+ 4441 gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc acactggagg cgatgatcta
+ 4501 gcccgtcttt caccccgtac ctttatactc ggccgcgtat ttctccaccg ggagctctgc
+ 4561 ctaccaaagc gtcgtacgcc caggaagccg tttcctttat cctccctcat gtctcaacgc
+ 4621 gcgagcatcg gagagtacgc gaaatcgact gtctggccaa cactggacag acgcgcgaga
+ 4681 cactgataaa cccccatttt cgtggggtta gtaaatcggt ggcttcaaac ggttcgatcg
+ 4741 ctcgcacgag cattagtcag gagtatgatt gcgcatcatc tctactccgt actaggttct
+ 4801 gtagctcagg atctccgggg ggatcaagct tttatgtccc gcgggattag aagatatcca
+ 4861 tccatatgtt tactttgatg cgggtccgag ctctctatga tgctgctttg acaaaatgtg
+ 4921 gaaagcctca gcgaccgctc tggggtcaaa gctctacgac acgttgatgc taaacaagtt
+ 4981 ggactactaa gcaaatgaag cggaagagat actgagcgct ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/partC.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/partC.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,111 @@
+LOCUS Exported 5022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partC
+VERSION partC
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 5022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..5022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..2001
+ /label="pC"
+ /label="nonstandard type: annotation"
+ CDS 2123..3022
+ /label="AmpR"
+ misc_feature 4023..4522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaggg caaagattac gatagaaaaa cactcgacac agagtagtat gataaaagtt
+ 61 gggacggcat gctggactcg agaagtgtcg atccggcaat ccagatacgg caatggtacc
+ 121 ggtcacacct cattctaaga gcagtcaggg gctgtcaggt ctacagggca ccggccctga
+ 181 ggcccttggg ctagggtctg tcacccctat ctgcactgac tttaaagtaa ccgagcaata
+ 241 agacaatcaa tcgcagggct ctggatcggg gtccgaaggc ggggtgcagt gtctccctaa
+ 301 ttgttaagct caaaagagca gccactcgtt ctcgatcctt agtccatcgc cgtgaggtac
+ 361 aagcagtaca cccacggaag gcccggcatt gaagatgcaa gaaatagagc actggggtga
+ 421 cgacggcatg ctaaggtaag aaggcaaatt ctggaggact gacttcccca caagcggcgt
+ 481 aagctcggat aagattggga taaacggacc acggcggctg gatcttcacc cctttgcacg
+ 541 gtatgaaaac ggatcaggat tctcttccac ctattgcacc tgctgagaag agagcgctgg
+ 601 ggggacgtta cttatcccaa tcgcgacgtc acggacaaca tcgtgttaca ggtcaggctc
+ 661 gaaatcctag gcagctggta tccgacgcgc aagttatcta ccaaataagt taggcgatcg
+ 721 aaatcatagg ctgtttagtg cttttcttgg tatcatcctg aacttctgtc acctccgagg
+ 781 ccgaagcaac tattatgagg acgactcgat gattgtccgg agatgttgca ccccggcaag
+ 841 cctagaaaac cccggtcctt tgagttttaa tctaatagta gaagttctcg gaaatcagag
+ 901 ctggagactc ggtgacgtta tagaaatgtt cgcacgaaga gcgcgacatg tcctacttca
+ 961 caagatgctt tctaggaggg gatctggatt ctcaagccct acacatggtc cgtggtgtat
+ 1021 gttggatcgt agtgctttta ccgactatgt cgcgttaaat tgtctttcat ttctacaatt
+ 1081 cggggagcat ggggccatgt gacttaggtt cagaaggtgc gagcgggcgt actacgtttg
+ 1141 gtggtcgtgt ataatcagaa gaatcggcga tatccgctag caagcaaagt gtccttgacg
+ 1201 cttgtggaaa tccaactatt tcctgcctct caagtgttta gaaaaatatc ccctggagga
+ 1261 gatatcgctc ctctcttctg cgaccaacac cagttcaatt ccgcagtgca gcagtcctat
+ 1321 tccgcatgga tcacgctgac gagatgcggg gttgagacta ccccaaaaga tatgttgaga
+ 1381 taaattacca ggatggataa tctggtaccg gtgcgaaagg gtggttacac cagagtcgcc
+ 1441 tgatgagctt atgcgcaatt tcaagtccct atgttttact atgaaagtac gaccgagccg
+ 1501 ctagcctgag tcaaatagcg cagaatttgg gtcgtggaga tcgcgcttgt taacctggtc
+ 1561 taggcgcatc tgagtcataa cggggttata acgactgtca acgtgtgacc gcatatcctg
+ 1621 caaggcgaac aaataacgcc ccgcccaaaa tattacattt aagtagttat ctaactcccg
+ 1681 gcatgcgggg catttggggg cagcgtgccc attccgcccc tatgcctgtt tcaacacgca
+ 1741 accgtagaga ttggctagga tgggttttca cgagccaact gccacattag acatagaatt
+ 1801 ccgataagta taagagatat cagcgaggtt cagggtagtt tggaacgaca gccggttcag
+ 1861 aagttcagta tggtcattca tcatccgttg tgttgagtcc tttagatcgt ggctttatca
+ 1921 tgcatgtctc ccgccagccc tcaaactatg tcgtcacgcg catgtttaca ttatatggaa
+ 1981 caaaacgaga ggtagaagcc aatcactatc cggcaagaga cgctccacct gcgtctatcg
+ 2041 tacagtgcta aaatggcagc agatagtgaa acttccgcta agctagcccc tcagggtaca
+ 2101 ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt tgtcggggac ctgccgtcac
+ 2161 gcttccgagt gtatatccgg atttagttga cgtcatacag aggcactaag aagaataaac
+ 2221 gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct cccttgcgcc gttcggcaag
+ 2281 cgtccggtgt cgggctgcaa ggaataaatc tttatggacc agaggggctt gtttcctcat
+ 2341 atgggtgcgt gcacttatac gattcaaagg tggatatggc cgcataacac gtagccaggc
+ 2401 tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg tttttgtttt tcctttacga
+ 2461 cacgaaccgc tctaacctgc tctatttcgc cacgttccag tgaacctctt agcctaccgc
+ 2521 ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg gagaaatcgt tcaatattag
+ 2581 aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc cgtttaacgg ctgccgtggt
+ 2641 cataccgtga ggcaccacga ggggatgcta cgcaacatgc gaggtgtaat cagcagggaa
+ 2701 gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat atgcataagg tgtcatttat
+ 2761 attacaccta cgacactggt accggctcac agccaaatgc acagtctcaa gatagaattc
+ 2821 gcaaaaatta ggcttatcgg gcgcttactc tttgttacac ttctggtctg tgagtgacgc
+ 2881 cctgtgtccc atcactgcat gtgaggatgc gtgtactgca cctgtgaatt acagacgttt
+ 2941 ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc tctatagggt gatctcgaca
+ 3001 taccactatg gtttgcgcgt ttcgggtgct tttggcgagg gccaggtacg gcggtgagac
+ 3061 agcgtatttt gcgaataggg tattcggacg cacggtgtat agctcttgga aaacgactct
+ 3121 tcgacgggcg tgtagaagta gccaagcagt tcggttgtta tcactaaatg cggaccatgt
+ 3181 gcagccgttt aggagaggag tctgcaatgg atcagctggt cagattgtac cactcggttg
+ 3241 agcctaaggc acttcaggtg ctcggattgt aatgaaccct caggttacgc cgttgcgctg
+ 3301 agatcccaca agccataagc aatgagaatc gagcagctat cgaattacgc agcacttgct
+ 3361 gatgaactgg gtgcacctaa agcgcccgat aaaacggagg gagtgaggta actactacat
+ 3421 tgcgagtagt gcgaggggcc tccgagacta cattagagca gccatgccga atacgacaaa
+ 3481 atctatagcc ttgcgaacgt aggggactga tttatggaca acaggaccga aacaagttgg
+ 3541 agccacaacg gagctatgga cgttttcact attgatgggt ggcttgcgtc cgcatcccag
+ 3601 gtttctctgg ttaattttca tgacgattct ttgtggtacg atccaggcat aagatagggc
+ 3661 acctaacccg atactgtgaa cttatatgac ggctgaacat gccctaatag tctgccaaaa
+ 3721 gggaaaccta taacggctct aaacgggccc cgggtacgta acagcaatgt tcctgtccac
+ 3781 caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat tccgttttac gccccagatc
+ 3841 gcagctccct tgacagtgtc agttgaatcc ccattctagg tttcctgata aaactaagta
+ 3901 cggggacgca tcagtcgaaa gcaatcacag ataatagata tcttgagcag aaagacgtct
+ 3961 tcacgaatca ggagcgagtg tcccctttga aagtgcgggc aacaataggt gtgaggtttc
+ 4021 acggttgctt gatcagtagc tgttcactct ctcgcaggcc tacatagtga ggtggtgaga
+ 4081 ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc gggcacgcta acaaggacag
+ 4141 gaattcgggt cgtcaaataa caatttacgt catcgcatcc ctcaagggta aggcgtgatc
+ 4201 tccatctcgg ttcccaattg gtcattgtga tagccacact gcagttaccg aaggcgattt
+ 4261 tatactaccc tgataagtgc tcgcagcccc tcctccctaa taatgtaacg acgagcatta
+ 4321 acccaggagt atttctcacg ttgctcgtgc ccagccaagg cgatcaacgc agaccggata
+ 4381 gcgttagcta gcccacgggt aaaagcgatt gttgtactct ttcatatgaa tacagcactc
+ 4441 gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc acactggagg cgatgatcta
+ 4501 gcccgtcttt caccccgtac ctttatactc ggccgcgtat ttctccaccg ggagctctgc
+ 4561 ctaccaaagc gtcgtacgcc caggaagccg tttcctttat cctccctcat gtctcaacgc
+ 4621 gcgagcatcg gagagtacgc gaaatcgact gtctggccaa cactggacag acgcgcgaga
+ 4681 cactgataaa cccccatttt cgtggggtta gtaaatcggt ggcttcaaac ggttcgatcg
+ 4741 ctcgcacgag cattagtcag gagtatgatt gcgcatcatc tctactccgt actaggttct
+ 4801 gtagctcagg atctccgggg ggatcaagct tttatgtccc gcgggattag aagatatcca
+ 4861 tccatatgtt tactttgatg cgggtccgag ctctctatga tgctgctttg acaaaatgtg
+ 4921 gaaagcctca gcgaccgctc tggggtcaaa gctctacgac acgttgatgc taaacaagtt
+ 4981 ggactactaa gcaaatgaag cggaagagat actgagcgct ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/receptor.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_1/provided_parts_records/receptor.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,75 @@
+LOCUS Exported 3022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION receptor
+VERSION receptor
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 3022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..3022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ CDS 523..1222
+ /label="KanR"
+ misc_feature 2023..2522
+ /label="RepO_2"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 attgagagac gcgtctcagg cactttcgct atatggcgac gtgcgaaaaa cgcgatttgg
+ 61 ccgaaatctc aaataataat gcaatgtgtt ggctaagctc gggcaaactc aggatgtgac
+ 121 ctagtaccct ctgccccgtg agtacccata cccaatcaag ccagcccaat tcgcgatagg
+ 181 tacagataag ccttactcgt cccgatcctt gactaaaaca ctcatcctcg atagtacgtg
+ 241 ccttgtagag tccgacggcc ataggtaaac gaccagttag tgtcgtaggg tcctccactt
+ 301 tagctacgat tgcaactccc ttaccttcgt gccggcgcgc tcctcttgct accatcacgc
+ 361 ttcaaatcgg gtggaagacc aactgatgaa tgagggtgca gaccccagtg gagcataata
+ 421 cgatgcgccc acgatactct agagccacgc gtcgacgttc gtaagatgtc ccgggcccgt
+ 481 gggtggccac atcggccgcc catccttgtg tcttccgata agtactccct ttcaaggact
+ 541 ctccgatacc ggcttagaac acgaacggac aacgctttca gcgctgagaa atgacggctg
+ 601 cttcaaccag aacgatacag ccttctttgc tagatagcct ctagtgtcag ccaccaagtc
+ 661 cgccacctaa tccttcgccg agggtcaaag cttctgacca tccaattgtt aggcactctt
+ 721 ggaaccttgc aagtacctga tcatgcagaa aatggacttg cccggagcat attcattata
+ 781 agtaccattc acggcaggtt atagtatgcg ttgacgcggg gtgatacggt aatgcaagta
+ 841 accatcgggc cgcggtatgc acatagaagg gtgtttgact tggtttctta cagtgcaact
+ 901 gcatatgtgg accgccattc caagtgaaag gatacgaagg gaggtttcgg actgctatcc
+ 961 agagcatgga aagccttcaa ggtggtgcgc actggaatag tgactcgggg attgtatgtc
+ 1021 gagccgcgtc cagtctttcc tatacttatg cgagcaaata gaccgagtgg aacttgattg
+ 1081 catcagccga atcacgatga aaactcagct tacaattcgt aagcacttca aatatatgcc
+ 1141 cggaaaatcg ccgtccagtg acttgtaata gctccagggt cagtagcgct gccctggccg
+ 1201 aaccaggtga cggttacgtg gacctcacag tatcaatgtt gcagtgcgcc accagattaa
+ 1261 gctggccgtg tcatggtgaa caaccgtgat aaaagaacgg gagtatgaga gtgccaccca
+ 1321 agagtggtac tccaggattc ggaaagggga gggggctttt cctgcttaac aaccttcctc
+ 1381 ggcacggtct aagggtctca ctcgtcctaa actctaccat catgcagcta ggcgaaagta
+ 1441 taactttagg gtctctcagg atgagctatc tgtaccacgg tgatgagata agtagggggt
+ 1501 gcgctagggt cgttcgtgtt ttcatcgtct atagtaccta tttctcgtct tccattagcg
+ 1561 catacggcca tctcgcggcg gctacgtcag ccagcgtcaa ccccaagtca ctaatttccg
+ 1621 ttattatagg tgtagctcat aacttcttct gccgaccaag ccaaaagctt tgcggcagct
+ 1681 gcaaggccac gttaggctct cggacggcag atatttatta ataacaccac tgggttccag
+ 1741 ctcttaacgc acttcccttc actggatcac ctgtacgccc ataagctaag cctgaagcca
+ 1801 cggcctcaat cgtggacatt actcttagca aatccacatt accatgtcac caatccccga
+ 1861 accccgcgcc gacctaaggc ggggtacctc gtgcacggca gcatcgaggg aaatatatta
+ 1921 caaaagacgc ggcgatccaa cggttgataa aaacagttcc gtggaaggcg gacgtgtgct
+ 1981 tagcgcatgc ttctcaccga gtgacagcac cgattccatc tcgctagcac gccgatgagc
+ 2041 ctcgctgtgg gactatggtc cagcctatgc ttaactaggc agaacagaga gtatggtggt
+ 2101 cctcggtaag gtcgatttgg tggcactcgc aagatacgcg ggttattagt agagcgcagt
+ 2161 cagggcccat cgccagcatt tgcatgctcg ccgtacgcta tccttgtact acggttcctc
+ 2221 agtggctata aaggaatgtc acaactccat tagccccttt tgttcagcgc ttagtcatgg
+ 2281 tgggactgac tcaccgagac tacatacgga ttgtgcccgc agagacctgc ctttcatgct
+ 2341 ggggttttgt aagcagctcc acggggtagt gtcaccatgc cttcgaccta tgcttatgaa
+ 2401 acccgaggta atgcggcagg atcccgtgga tcctacgctt agcctgttta agccatcgtt
+ 2461 ctcctcggcc cccagccagc gcgtattccg cgcattcctc cgagtgcgta tcgcgcaaac
+ 2521 cacaagatac ctctcaacga ctagcggtga accaccaagc ttgacatacg tgccccttcg
+ 2581 gaaacgttat tagtggtcct gagtggtacg tcccgagtat acggggcagc gatagtaacg
+ 2641 ctacaaatag ctaggcgagg ttgcgatacc tgaatgaata tccaacagtg gcaacgaggc
+ 2701 gcttagaaag ggaaactaca taccagttca atccgggatg acttcaaaag ggtatgtttg
+ 2761 ttttgaagcg aagctttggt tgtcattcag ttcctagagt ttacggcgct gatatggctc
+ 2821 taggagtcca gtgaattcgt cagcataagc cccacatcgt aggaaattgc ccggtcgtcg
+ 2881 gtctagcaaa tgctcggtaa actgggagtg tactaacacc atgtcgtggt aacccggtgg
+ 2941 accggctact agagacatat ttattcatgc tcagttgaac ctgtttcgag ggggccgagt
+ 3001 taacataaag tgattagtca ca
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/construct_2_connections_graph.pdf
Binary file test-data/init/example_assembly_plan_simulation/construct_2/construct_2_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/error.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_2/error.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+assembly_name;message;suggestion;data
+construct_2;Wrong number of constructs;expected_: 1,found: 0
+construct_2;Some parts are unused;unused_parts: partA2 & partB2 & partC & receptor
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/fragments_in_construct_2_homology_mix/partA2_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/fragments_in_construct_2_homology_mix/partB2_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/fragments_in_construct_2_homology_mix/partC_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/fragments_in_construct_2_homology_mix/receptor_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_plots/partA2.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_plots/partB2.pdf
Binary file test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_plots/partB2.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_plots/partC.pdf
Binary file test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_plots/partC.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_plots/receptor.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/partA2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/partA2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,95 @@
+LOCUS Exported 4022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partA2
+VERSION partA2
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 4022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..4022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..1001
+ /label="pA2"
+ /label="nonstandard type: annotation"
+ CDS 1123..2022
+ /label="AmpR"
+ misc_feature 3023..3522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaatt gtaagataga acagggatat agctcgttgc atccataaat tgcccaccgt
+ 61 agggagaacg ccgttggaaa atgagagtta ggcgatgagc ggttgtcgcc cgcacagaca
+ 121 aaggatgcct ttataaatag tagcggcctt gtctgcacca gacgtttgtg ggtcgacgtg
+ 181 ctattctagc caaaagcaaa atgtatcata ctacaggcaa taggccctat gctgaccaaa
+ 241 cttggggacc cttgcgcctt ctctcttacg cataacatgc ataggtacct ctactcatca
+ 301 ggcagggcgg cgtgaggtca ctatggctca agatgtgtac gactaaagaa aggtttatgc
+ 361 tccttcccca aggacgcatt tgggactgct acttgcccct agcgaattca ctaggatttt
+ 421 tgtagaacca tgagcgccct atccgatagc acagagacaa tgctacaagc aactgtgcat
+ 481 gcgctcgatc gccgtgcatt aatacgtatt atagagtatc gtgtacgcta atatcttagt
+ 541 gcaccgcacg ctggttggat acaattccgt gaaataattc ctgcttacac aggggctttc
+ 601 tggcgcatgg ctgtgtctgg atgtttgtga taagaggctc caagaacccg gcgggaaatg
+ 661 aggggaaacc ccggggagca acgacactaa gcctggcagt tgttcagata ggacgctttt
+ 721 gtcagtgggc ggttttgcat ccactaacta tcataaacga cacaacgtcg aatgatcatc
+ 781 ggcggtttgc atgtagagac agctcctgca acaccatacc ggctcgtgga attacgctgt
+ 841 gcgccggccc tcattcgatt gtgtccagcg tcggcgcgaa tgatgattga gatgtgcttc
+ 901 ggctcagagc gtgcacaggt agttctcccc ccttacctag ctaatccagc aattccacgc
+ 961 tggcccgcgc gtccttgggt aacactggat ctgtacccaa atacaccgtc gggctagaga
+ 1021 cgctccacct gcgtctatcg tacagtgcta aaatggcagc agatagtgaa acttccgcta
+ 1081 agctagcccc tcagggtaca ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt
+ 1141 tgtcggggac ctgccgtcac gcttccgagt gtatatccgg atttagttga cgtcatacag
+ 1201 aggcactaag aagaataaac gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct
+ 1261 cccttgcgcc gttcggcaag cgtccggtgt cgggctgcaa ggaataaatc tttatggacc
+ 1321 agaggggctt gtttcctcat atgggtgcgt gcacttatac gattcaaagg tggatatggc
+ 1381 cgcataacac gtagccaggc tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg
+ 1441 tttttgtttt tcctttacga cacgaaccgc tctaacctgc tctatttcgc cacgttccag
+ 1501 tgaacctctt agcctaccgc ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg
+ 1561 gagaaatcgt tcaatattag aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc
+ 1621 cgtttaacgg ctgccgtggt cataccgtga ggcaccacga ggggatgcta cgcaacatgc
+ 1681 gaggtgtaat cagcagggaa gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat
+ 1741 atgcataagg tgtcatttat attacaccta cgacactggt accggctcac agccaaatgc
+ 1801 acagtctcaa gatagaattc gcaaaaatta ggcttatcgg gcgcttactc tttgttacac
+ 1861 ttctggtctg tgagtgacgc cctgtgtccc atcactgcat gtgaggatgc gtgtactgca
+ 1921 cctgtgaatt acagacgttt ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc
+ 1981 tctatagggt gatctcgaca taccactatg gtttgcgcgt ttcgggtgct tttggcgagg
+ 2041 gccaggtacg gcggtgagac agcgtatttt gcgaataggg tattcggacg cacggtgtat
+ 2101 agctcttgga aaacgactct tcgacgggcg tgtagaagta gccaagcagt tcggttgtta
+ 2161 tcactaaatg cggaccatgt gcagccgttt aggagaggag tctgcaatgg atcagctggt
+ 2221 cagattgtac cactcggttg agcctaaggc acttcaggtg ctcggattgt aatgaaccct
+ 2281 caggttacgc cgttgcgctg agatcccaca agccataagc aatgagaatc gagcagctat
+ 2341 cgaattacgc agcacttgct gatgaactgg gtgcacctaa agcgcccgat aaaacggagg
+ 2401 gagtgaggta actactacat tgcgagtagt gcgaggggcc tccgagacta cattagagca
+ 2461 gccatgccga atacgacaaa atctatagcc ttgcgaacgt aggggactga tttatggaca
+ 2521 acaggaccga aacaagttgg agccacaacg gagctatgga cgttttcact attgatgggt
+ 2581 ggcttgcgtc cgcatcccag gtttctctgg ttaattttca tgacgattct ttgtggtacg
+ 2641 atccaggcat aagatagggc acctaacccg atactgtgaa cttatatgac ggctgaacat
+ 2701 gccctaatag tctgccaaaa gggaaaccta taacggctct aaacgggccc cgggtacgta
+ 2761 acagcaatgt tcctgtccac caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat
+ 2821 tccgttttac gccccagatc gcagctccct tgacagtgtc agttgaatcc ccattctagg
+ 2881 tttcctgata aaactaagta cggggacgca tcagtcgaaa gcaatcacag ataatagata
+ 2941 tcttgagcag aaagacgtct tcacgaatca ggagcgagtg tcccctttga aagtgcgggc
+ 3001 aacaataggt gtgaggtttc acggttgctt gatcagtagc tgttcactct ctcgcaggcc
+ 3061 tacatagtga ggtggtgaga ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc
+ 3121 gggcacgcta acaaggacag gaattcgggt cgtcaaataa caatttacgt catcgcatcc
+ 3181 ctcaagggta aggcgtgatc tccatctcgg ttcccaattg gtcattgtga tagccacact
+ 3241 gcagttaccg aaggcgattt tatactaccc tgataagtgc tcgcagcccc tcctccctaa
+ 3301 taatgtaacg acgagcatta acccaggagt atttctcacg ttgctcgtgc ccagccaagg
+ 3361 cgatcaacgc agaccggata gcgttagcta gcccacgggt aaaagcgatt gttgtactct
+ 3421 ttcatatgaa tacagcactc gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc
+ 3481 acactggagg cgatgatcta gcccgtcttt caccccgtac ctttatactc ggccgcgtat
+ 3541 ttctccaccg ggagctctgc ctaccaaagc gtcgtacgcc caggaagccg tttcctttat
+ 3601 cctccctcat gtctcaacgc gcgagcatcg gagagtacgc gaaatcgact gtctggccaa
+ 3661 cactggacag acgcgcgaga cactgataaa cccccatttt cgtggggtta gtaaatcggt
+ 3721 ggcttcaaac ggttcgatcg ctcgcacgag cattagtcag gagtatgatt gcgcatcatc
+ 3781 tctactccgt actaggttct gtagctcagg atctccgggg ggatcaagct tttatgtccc
+ 3841 gcgggattag aagatatcca tccatatgtt tactttgatg cgggtccgag ctctctatga
+ 3901 tgctgctttg acaaaatgtg gaaagcctca gcgaccgctc tggggtcaaa gctctacgac
+ 3961 acgttgatgc taaacaagtt ggactactaa gcaaatgaag cggaagagat actgagcgct
+ 4021 ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/partB2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/partB2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,111 @@
+LOCUS Exported 5022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partB2
+VERSION partB2
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 5022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..5022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..2001
+ /label="pB2"
+ /label="nonstandard type: annotation"
+ CDS 2123..3022
+ /label="AmpR"
+ misc_feature 4023..4522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaggc ttgattgtta actaccgtat ggcggttacg atcgagtgac actattatta
+ 61 gaccgctact ccaagtccca acttttcatc gccatacaga agagaacgag aaagtcgaag
+ 121 agttatagcg tgtacacttc tgattagcta acgaatcgat gcgtacagca tactcgagca
+ 181 actttatggg tcgtctgtct ccttgtaccc cgcttgacga ggatgtgttt gtaggcggct
+ 241 tggatatcgg cagtgtatcc gcatggtcaa acactttagc ccgaccggtg ctcaaggtcg
+ 301 aaatcctaat atagattggg ataggacccg tccattacta ggcgacattc gcagtcacga
+ 361 gcccgcacgg ggtgcctcaa cacggtgaca ctcaattcgc cgacactgag tacgacgatc
+ 421 gtgattgcca taccgtcatg ttttgtgtta cccctgataa gaagcgcaga tatggcacgg
+ 481 gggcagaggg cggagtagac ccaagcaaaa ctctagcctc tgggcagcat gatcgacgta
+ 541 gaacgccgtt gtgactcact agtttcagtt atgatgttca gccaagaatc ctccattttg
+ 601 acgtgaacct tctcccttta caccttgaag ctgcaatatt aagtcgaccc tttaagttgc
+ 661 cttgtcttgg tctagagccc gcagctcacc gataaaatga gcagtcaatt ttagcggcgg
+ 721 ttgtccaggt tacatgcact ttgggctgga accgcgttac gtttggagta cttagaagtg
+ 781 tcgtaggcat aggagagccg aaacttgata ttgggtctag ttagtgctct accccgcttc
+ 841 ggatccgtaa tagtgatgtt gcataagacg cttgcctcaa ggcgacatac ggtggcggtt
+ 901 gctggaaatg acgccccacc ccgtgataat ttggggacga gccacacgat aacttctgcc
+ 961 agcgaccgcc cctcccacgt ccgatggtga ttccgaattt tgattacatg ccagacacgc
+ 1021 tttaatctcg ccaccacatt ggcaccccca ccaagtaatg tatgtaagaa gcagctgcgc
+ 1081 cccaagttac gtgccgtttc cgatgggagc agcaataatg tcgatagcaa ccacccccct
+ 1141 ctctactgac gaagcaacac cggggacacc gtcaccttgg cttcatttcg tattcattca
+ 1201 cctacgcaca accgcctgac cgttcgttat cacgagccta tccccttcaa gcaatttccc
+ 1261 ccccttgttc agcagcctac actatacgtt ggtacactgt gtgcgacaga tatttggtgc
+ 1321 ccgtcttatt ctattctgag agagtttaat agccaaaaga tatgagtagg aacgggaggt
+ 1381 acccgactcg cgttgaagca ctcttaagac ctctcttagc acttcgaagg gtaggtgcgt
+ 1441 tcaaagaacc tctgctttta actaagatca aaaggattgc gtacaacttc cccgttaact
+ 1501 ctccagagga tccgtagaag tctacaccaa aatacgtttg gtttcgccaa ggtgactatc
+ 1561 ggtacttgtg cacgtaacag ggtaaagaat tgaaagcctc aaattgtacg acgttacgcc
+ 1621 cggacggtcg ccggtgatag ggtgacgcat ttgcgtttgt catatcattt gggattagac
+ 1681 ggagctggtg tacctctatg gacgttacaa aaccttgtgg taacagcctg ggtgccatcc
+ 1741 acctagtccg aagtttcctt ctaaccgcgg catcagatgg atatgtacct tatggcgctt
+ 1801 cccgggaagt ccaattcttc gtgttgaagg gacagctcta caggcctggc cacttgtggc
+ 1861 gcatctaagt agtctaggtg catgattctc tcccttgggg gcgctgtcgt gggtcctgcc
+ 1921 gagccacacc ctaacctcac gtcgcaagac ttggtaaata gctttttttt ttatgcccaa
+ 1981 tctatttacg taacaatcga catcagagga ggggcagaga cgctccacct gcgtctatcg
+ 2041 tacagtgcta aaatggcagc agatagtgaa acttccgcta agctagcccc tcagggtaca
+ 2101 ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt tgtcggggac ctgccgtcac
+ 2161 gcttccgagt gtatatccgg atttagttga cgtcatacag aggcactaag aagaataaac
+ 2221 gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct cccttgcgcc gttcggcaag
+ 2281 cgtccggtgt cgggctgcaa ggaataaatc tttatggacc agaggggctt gtttcctcat
+ 2341 atgggtgcgt gcacttatac gattcaaagg tggatatggc cgcataacac gtagccaggc
+ 2401 tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg tttttgtttt tcctttacga
+ 2461 cacgaaccgc tctaacctgc tctatttcgc cacgttccag tgaacctctt agcctaccgc
+ 2521 ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg gagaaatcgt tcaatattag
+ 2581 aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc cgtttaacgg ctgccgtggt
+ 2641 cataccgtga ggcaccacga ggggatgcta cgcaacatgc gaggtgtaat cagcagggaa
+ 2701 gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat atgcataagg tgtcatttat
+ 2761 attacaccta cgacactggt accggctcac agccaaatgc acagtctcaa gatagaattc
+ 2821 gcaaaaatta ggcttatcgg gcgcttactc tttgttacac ttctggtctg tgagtgacgc
+ 2881 cctgtgtccc atcactgcat gtgaggatgc gtgtactgca cctgtgaatt acagacgttt
+ 2941 ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc tctatagggt gatctcgaca
+ 3001 taccactatg gtttgcgcgt ttcgggtgct tttggcgagg gccaggtacg gcggtgagac
+ 3061 agcgtatttt gcgaataggg tattcggacg cacggtgtat agctcttgga aaacgactct
+ 3121 tcgacgggcg tgtagaagta gccaagcagt tcggttgtta tcactaaatg cggaccatgt
+ 3181 gcagccgttt aggagaggag tctgcaatgg atcagctggt cagattgtac cactcggttg
+ 3241 agcctaaggc acttcaggtg ctcggattgt aatgaaccct caggttacgc cgttgcgctg
+ 3301 agatcccaca agccataagc aatgagaatc gagcagctat cgaattacgc agcacttgct
+ 3361 gatgaactgg gtgcacctaa agcgcccgat aaaacggagg gagtgaggta actactacat
+ 3421 tgcgagtagt gcgaggggcc tccgagacta cattagagca gccatgccga atacgacaaa
+ 3481 atctatagcc ttgcgaacgt aggggactga tttatggaca acaggaccga aacaagttgg
+ 3541 agccacaacg gagctatgga cgttttcact attgatgggt ggcttgcgtc cgcatcccag
+ 3601 gtttctctgg ttaattttca tgacgattct ttgtggtacg atccaggcat aagatagggc
+ 3661 acctaacccg atactgtgaa cttatatgac ggctgaacat gccctaatag tctgccaaaa
+ 3721 gggaaaccta taacggctct aaacgggccc cgggtacgta acagcaatgt tcctgtccac
+ 3781 caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat tccgttttac gccccagatc
+ 3841 gcagctccct tgacagtgtc agttgaatcc ccattctagg tttcctgata aaactaagta
+ 3901 cggggacgca tcagtcgaaa gcaatcacag ataatagata tcttgagcag aaagacgtct
+ 3961 tcacgaatca ggagcgagtg tcccctttga aagtgcgggc aacaataggt gtgaggtttc
+ 4021 acggttgctt gatcagtagc tgttcactct ctcgcaggcc tacatagtga ggtggtgaga
+ 4081 ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc gggcacgcta acaaggacag
+ 4141 gaattcgggt cgtcaaataa caatttacgt catcgcatcc ctcaagggta aggcgtgatc
+ 4201 tccatctcgg ttcccaattg gtcattgtga tagccacact gcagttaccg aaggcgattt
+ 4261 tatactaccc tgataagtgc tcgcagcccc tcctccctaa taatgtaacg acgagcatta
+ 4321 acccaggagt atttctcacg ttgctcgtgc ccagccaagg cgatcaacgc agaccggata
+ 4381 gcgttagcta gcccacgggt aaaagcgatt gttgtactct ttcatatgaa tacagcactc
+ 4441 gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc acactggagg cgatgatcta
+ 4501 gcccgtcttt caccccgtac ctttatactc ggccgcgtat ttctccaccg ggagctctgc
+ 4561 ctaccaaagc gtcgtacgcc caggaagccg tttcctttat cctccctcat gtctcaacgc
+ 4621 gcgagcatcg gagagtacgc gaaatcgact gtctggccaa cactggacag acgcgcgaga
+ 4681 cactgataaa cccccatttt cgtggggtta gtaaatcggt ggcttcaaac ggttcgatcg
+ 4741 ctcgcacgag cattagtcag gagtatgatt gcgcatcatc tctactccgt actaggttct
+ 4801 gtagctcagg atctccgggg ggatcaagct tttatgtccc gcgggattag aagatatcca
+ 4861 tccatatgtt tactttgatg cgggtccgag ctctctatga tgctgctttg acaaaatgtg
+ 4921 gaaagcctca gcgaccgctc tggggtcaaa gctctacgac acgttgatgc taaacaagtt
+ 4981 ggactactaa gcaaatgaag cggaagagat actgagcgct ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/partC.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/partC.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,111 @@
+LOCUS Exported 5022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partC
+VERSION partC
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 5022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..5022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..2001
+ /label="pC"
+ /label="nonstandard type: annotation"
+ CDS 2123..3022
+ /label="AmpR"
+ misc_feature 4023..4522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaggg caaagattac gatagaaaaa cactcgacac agagtagtat gataaaagtt
+ 61 gggacggcat gctggactcg agaagtgtcg atccggcaat ccagatacgg caatggtacc
+ 121 ggtcacacct cattctaaga gcagtcaggg gctgtcaggt ctacagggca ccggccctga
+ 181 ggcccttggg ctagggtctg tcacccctat ctgcactgac tttaaagtaa ccgagcaata
+ 241 agacaatcaa tcgcagggct ctggatcggg gtccgaaggc ggggtgcagt gtctccctaa
+ 301 ttgttaagct caaaagagca gccactcgtt ctcgatcctt agtccatcgc cgtgaggtac
+ 361 aagcagtaca cccacggaag gcccggcatt gaagatgcaa gaaatagagc actggggtga
+ 421 cgacggcatg ctaaggtaag aaggcaaatt ctggaggact gacttcccca caagcggcgt
+ 481 aagctcggat aagattggga taaacggacc acggcggctg gatcttcacc cctttgcacg
+ 541 gtatgaaaac ggatcaggat tctcttccac ctattgcacc tgctgagaag agagcgctgg
+ 601 ggggacgtta cttatcccaa tcgcgacgtc acggacaaca tcgtgttaca ggtcaggctc
+ 661 gaaatcctag gcagctggta tccgacgcgc aagttatcta ccaaataagt taggcgatcg
+ 721 aaatcatagg ctgtttagtg cttttcttgg tatcatcctg aacttctgtc acctccgagg
+ 781 ccgaagcaac tattatgagg acgactcgat gattgtccgg agatgttgca ccccggcaag
+ 841 cctagaaaac cccggtcctt tgagttttaa tctaatagta gaagttctcg gaaatcagag
+ 901 ctggagactc ggtgacgtta tagaaatgtt cgcacgaaga gcgcgacatg tcctacttca
+ 961 caagatgctt tctaggaggg gatctggatt ctcaagccct acacatggtc cgtggtgtat
+ 1021 gttggatcgt agtgctttta ccgactatgt cgcgttaaat tgtctttcat ttctacaatt
+ 1081 cggggagcat ggggccatgt gacttaggtt cagaaggtgc gagcgggcgt actacgtttg
+ 1141 gtggtcgtgt ataatcagaa gaatcggcga tatccgctag caagcaaagt gtccttgacg
+ 1201 cttgtggaaa tccaactatt tcctgcctct caagtgttta gaaaaatatc ccctggagga
+ 1261 gatatcgctc ctctcttctg cgaccaacac cagttcaatt ccgcagtgca gcagtcctat
+ 1321 tccgcatgga tcacgctgac gagatgcggg gttgagacta ccccaaaaga tatgttgaga
+ 1381 taaattacca ggatggataa tctggtaccg gtgcgaaagg gtggttacac cagagtcgcc
+ 1441 tgatgagctt atgcgcaatt tcaagtccct atgttttact atgaaagtac gaccgagccg
+ 1501 ctagcctgag tcaaatagcg cagaatttgg gtcgtggaga tcgcgcttgt taacctggtc
+ 1561 taggcgcatc tgagtcataa cggggttata acgactgtca acgtgtgacc gcatatcctg
+ 1621 caaggcgaac aaataacgcc ccgcccaaaa tattacattt aagtagttat ctaactcccg
+ 1681 gcatgcgggg catttggggg cagcgtgccc attccgcccc tatgcctgtt tcaacacgca
+ 1741 accgtagaga ttggctagga tgggttttca cgagccaact gccacattag acatagaatt
+ 1801 ccgataagta taagagatat cagcgaggtt cagggtagtt tggaacgaca gccggttcag
+ 1861 aagttcagta tggtcattca tcatccgttg tgttgagtcc tttagatcgt ggctttatca
+ 1921 tgcatgtctc ccgccagccc tcaaactatg tcgtcacgcg catgtttaca ttatatggaa
+ 1981 caaaacgaga ggtagaagcc aatcactatc cggcaagaga cgctccacct gcgtctatcg
+ 2041 tacagtgcta aaatggcagc agatagtgaa acttccgcta agctagcccc tcagggtaca
+ 2101 ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt tgtcggggac ctgccgtcac
+ 2161 gcttccgagt gtatatccgg atttagttga cgtcatacag aggcactaag aagaataaac
+ 2221 gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct cccttgcgcc gttcggcaag
+ 2281 cgtccggtgt cgggctgcaa ggaataaatc tttatggacc agaggggctt gtttcctcat
+ 2341 atgggtgcgt gcacttatac gattcaaagg tggatatggc cgcataacac gtagccaggc
+ 2401 tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg tttttgtttt tcctttacga
+ 2461 cacgaaccgc tctaacctgc tctatttcgc cacgttccag tgaacctctt agcctaccgc
+ 2521 ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg gagaaatcgt tcaatattag
+ 2581 aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc cgtttaacgg ctgccgtggt
+ 2641 cataccgtga ggcaccacga ggggatgcta cgcaacatgc gaggtgtaat cagcagggaa
+ 2701 gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat atgcataagg tgtcatttat
+ 2761 attacaccta cgacactggt accggctcac agccaaatgc acagtctcaa gatagaattc
+ 2821 gcaaaaatta ggcttatcgg gcgcttactc tttgttacac ttctggtctg tgagtgacgc
+ 2881 cctgtgtccc atcactgcat gtgaggatgc gtgtactgca cctgtgaatt acagacgttt
+ 2941 ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc tctatagggt gatctcgaca
+ 3001 taccactatg gtttgcgcgt ttcgggtgct tttggcgagg gccaggtacg gcggtgagac
+ 3061 agcgtatttt gcgaataggg tattcggacg cacggtgtat agctcttgga aaacgactct
+ 3121 tcgacgggcg tgtagaagta gccaagcagt tcggttgtta tcactaaatg cggaccatgt
+ 3181 gcagccgttt aggagaggag tctgcaatgg atcagctggt cagattgtac cactcggttg
+ 3241 agcctaaggc acttcaggtg ctcggattgt aatgaaccct caggttacgc cgttgcgctg
+ 3301 agatcccaca agccataagc aatgagaatc gagcagctat cgaattacgc agcacttgct
+ 3361 gatgaactgg gtgcacctaa agcgcccgat aaaacggagg gagtgaggta actactacat
+ 3421 tgcgagtagt gcgaggggcc tccgagacta cattagagca gccatgccga atacgacaaa
+ 3481 atctatagcc ttgcgaacgt aggggactga tttatggaca acaggaccga aacaagttgg
+ 3541 agccacaacg gagctatgga cgttttcact attgatgggt ggcttgcgtc cgcatcccag
+ 3601 gtttctctgg ttaattttca tgacgattct ttgtggtacg atccaggcat aagatagggc
+ 3661 acctaacccg atactgtgaa cttatatgac ggctgaacat gccctaatag tctgccaaaa
+ 3721 gggaaaccta taacggctct aaacgggccc cgggtacgta acagcaatgt tcctgtccac
+ 3781 caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat tccgttttac gccccagatc
+ 3841 gcagctccct tgacagtgtc agttgaatcc ccattctagg tttcctgata aaactaagta
+ 3901 cggggacgca tcagtcgaaa gcaatcacag ataatagata tcttgagcag aaagacgtct
+ 3961 tcacgaatca ggagcgagtg tcccctttga aagtgcgggc aacaataggt gtgaggtttc
+ 4021 acggttgctt gatcagtagc tgttcactct ctcgcaggcc tacatagtga ggtggtgaga
+ 4081 ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc gggcacgcta acaaggacag
+ 4141 gaattcgggt cgtcaaataa caatttacgt catcgcatcc ctcaagggta aggcgtgatc
+ 4201 tccatctcgg ttcccaattg gtcattgtga tagccacact gcagttaccg aaggcgattt
+ 4261 tatactaccc tgataagtgc tcgcagcccc tcctccctaa taatgtaacg acgagcatta
+ 4321 acccaggagt atttctcacg ttgctcgtgc ccagccaagg cgatcaacgc agaccggata
+ 4381 gcgttagcta gcccacgggt aaaagcgatt gttgtactct ttcatatgaa tacagcactc
+ 4441 gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc acactggagg cgatgatcta
+ 4501 gcccgtcttt caccccgtac ctttatactc ggccgcgtat ttctccaccg ggagctctgc
+ 4561 ctaccaaagc gtcgtacgcc caggaagccg tttcctttat cctccctcat gtctcaacgc
+ 4621 gcgagcatcg gagagtacgc gaaatcgact gtctggccaa cactggacag acgcgcgaga
+ 4681 cactgataaa cccccatttt cgtggggtta gtaaatcggt ggcttcaaac ggttcgatcg
+ 4741 ctcgcacgag cattagtcag gagtatgatt gcgcatcatc tctactccgt actaggttct
+ 4801 gtagctcagg atctccgggg ggatcaagct tttatgtccc gcgggattag aagatatcca
+ 4861 tccatatgtt tactttgatg cgggtccgag ctctctatga tgctgctttg acaaaatgtg
+ 4921 gaaagcctca gcgaccgctc tggggtcaaa gctctacgac acgttgatgc taaacaagtt
+ 4981 ggactactaa gcaaatgaag cggaagagat actgagcgct ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/receptor.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_2/provided_parts_records/receptor.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,75 @@
+LOCUS Exported 3022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION receptor
+VERSION receptor
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 3022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..3022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ CDS 523..1222
+ /label="KanR"
+ misc_feature 2023..2522
+ /label="RepO_2"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 attgagagac gcgtctcagg cactttcgct atatggcgac gtgcgaaaaa cgcgatttgg
+ 61 ccgaaatctc aaataataat gcaatgtgtt ggctaagctc gggcaaactc aggatgtgac
+ 121 ctagtaccct ctgccccgtg agtacccata cccaatcaag ccagcccaat tcgcgatagg
+ 181 tacagataag ccttactcgt cccgatcctt gactaaaaca ctcatcctcg atagtacgtg
+ 241 ccttgtagag tccgacggcc ataggtaaac gaccagttag tgtcgtaggg tcctccactt
+ 301 tagctacgat tgcaactccc ttaccttcgt gccggcgcgc tcctcttgct accatcacgc
+ 361 ttcaaatcgg gtggaagacc aactgatgaa tgagggtgca gaccccagtg gagcataata
+ 421 cgatgcgccc acgatactct agagccacgc gtcgacgttc gtaagatgtc ccgggcccgt
+ 481 gggtggccac atcggccgcc catccttgtg tcttccgata agtactccct ttcaaggact
+ 541 ctccgatacc ggcttagaac acgaacggac aacgctttca gcgctgagaa atgacggctg
+ 601 cttcaaccag aacgatacag ccttctttgc tagatagcct ctagtgtcag ccaccaagtc
+ 661 cgccacctaa tccttcgccg agggtcaaag cttctgacca tccaattgtt aggcactctt
+ 721 ggaaccttgc aagtacctga tcatgcagaa aatggacttg cccggagcat attcattata
+ 781 agtaccattc acggcaggtt atagtatgcg ttgacgcggg gtgatacggt aatgcaagta
+ 841 accatcgggc cgcggtatgc acatagaagg gtgtttgact tggtttctta cagtgcaact
+ 901 gcatatgtgg accgccattc caagtgaaag gatacgaagg gaggtttcgg actgctatcc
+ 961 agagcatgga aagccttcaa ggtggtgcgc actggaatag tgactcgggg attgtatgtc
+ 1021 gagccgcgtc cagtctttcc tatacttatg cgagcaaata gaccgagtgg aacttgattg
+ 1081 catcagccga atcacgatga aaactcagct tacaattcgt aagcacttca aatatatgcc
+ 1141 cggaaaatcg ccgtccagtg acttgtaata gctccagggt cagtagcgct gccctggccg
+ 1201 aaccaggtga cggttacgtg gacctcacag tatcaatgtt gcagtgcgcc accagattaa
+ 1261 gctggccgtg tcatggtgaa caaccgtgat aaaagaacgg gagtatgaga gtgccaccca
+ 1321 agagtggtac tccaggattc ggaaagggga gggggctttt cctgcttaac aaccttcctc
+ 1381 ggcacggtct aagggtctca ctcgtcctaa actctaccat catgcagcta ggcgaaagta
+ 1441 taactttagg gtctctcagg atgagctatc tgtaccacgg tgatgagata agtagggggt
+ 1501 gcgctagggt cgttcgtgtt ttcatcgtct atagtaccta tttctcgtct tccattagcg
+ 1561 catacggcca tctcgcggcg gctacgtcag ccagcgtcaa ccccaagtca ctaatttccg
+ 1621 ttattatagg tgtagctcat aacttcttct gccgaccaag ccaaaagctt tgcggcagct
+ 1681 gcaaggccac gttaggctct cggacggcag atatttatta ataacaccac tgggttccag
+ 1741 ctcttaacgc acttcccttc actggatcac ctgtacgccc ataagctaag cctgaagcca
+ 1801 cggcctcaat cgtggacatt actcttagca aatccacatt accatgtcac caatccccga
+ 1861 accccgcgcc gacctaaggc ggggtacctc gtgcacggca gcatcgaggg aaatatatta
+ 1921 caaaagacgc ggcgatccaa cggttgataa aaacagttcc gtggaaggcg gacgtgtgct
+ 1981 tagcgcatgc ttctcaccga gtgacagcac cgattccatc tcgctagcac gccgatgagc
+ 2041 ctcgctgtgg gactatggtc cagcctatgc ttaactaggc agaacagaga gtatggtggt
+ 2101 cctcggtaag gtcgatttgg tggcactcgc aagatacgcg ggttattagt agagcgcagt
+ 2161 cagggcccat cgccagcatt tgcatgctcg ccgtacgcta tccttgtact acggttcctc
+ 2221 agtggctata aaggaatgtc acaactccat tagccccttt tgttcagcgc ttagtcatgg
+ 2281 tgggactgac tcaccgagac tacatacgga ttgtgcccgc agagacctgc ctttcatgct
+ 2341 ggggttttgt aagcagctcc acggggtagt gtcaccatgc cttcgaccta tgcttatgaa
+ 2401 acccgaggta atgcggcagg atcccgtgga tcctacgctt agcctgttta agccatcgtt
+ 2461 ctcctcggcc cccagccagc gcgtattccg cgcattcctc cgagtgcgta tcgcgcaaac
+ 2521 cacaagatac ctctcaacga ctagcggtga accaccaagc ttgacatacg tgccccttcg
+ 2581 gaaacgttat tagtggtcct gagtggtacg tcccgagtat acggggcagc gatagtaacg
+ 2641 ctacaaatag ctaggcgagg ttgcgatacc tgaatgaata tccaacagtg gcaacgaggc
+ 2701 gcttagaaag ggaaactaca taccagttca atccgggatg acttcaaaag ggtatgtttg
+ 2761 ttttgaagcg aagctttggt tgtcattcag ttcctagagt ttacggcgct gatatggctc
+ 2821 taggagtcca gtgaattcgt cagcataagc cccacatcgt aggaaattgc ccggtcgtcg
+ 2881 gtctagcaaa tgctcggtaa actgggagtg tactaacacc atgtcgtggt aacccggtgg
+ 2941 accggctact agagacatat ttattcatgc tcagttgaac ctgtttcgag ggggccgagt
+ 3001 taacataaag tgattagtca ca
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/construct_3_connections_graph.pdf
Binary file test-data/init/example_assembly_plan_simulation/construct_3/construct_3_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/error.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_3/error.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+assembly_name;message;suggestion;data
+construct_3;Wrong number of constructs;expected_: 1,found: 0
+construct_3;Some parts are unused;unused_parts: partA & partA2 & partB & partC & receptor
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/fragments_in_construct_3_homology_mix/partA2_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_plots/partB.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_plots/partC.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_plots/receptor.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partA.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partA.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,95 @@
+LOCUS Exported 4022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partA
+VERSION partA
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 4022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..4022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..1001
+ /label="pA"
+ /label="nonstandard type: annotation"
+ CDS 1123..2022
+ /label="AmpR"
+ misc_feature 3023..3522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaatt gtaagataga acagggatat agctcgttgc atccataaat tgcccaccgt
+ 61 agggagaacg ccgttggaaa atgagagtta ggcgatgagc ggttgtcgcc cgcacagaca
+ 121 aaggatgcct ttataaatag tagcggcctt gtctgcacca gacgtttgtg ggtcgacgtg
+ 181 ctattctagc caaaagcaaa atgtatcata ctacaggcaa taggccctat gctgaccaaa
+ 241 cttggggacc cttgcgcctt ctctcttacg cataacatgc ataggtacct ctactcatca
+ 301 ggcagggcgg cgtgaggtca ctatggctca agatgtgtac gactaaagaa aggtttatgc
+ 361 tccttcccca aggacgcatt tgggactgct acttgcccct agcgaattca ctaggatttt
+ 421 tgtagaacca tgagcgccct atccgatagc acagagacaa tgctacaagc aactgtgcat
+ 481 gcgctcgatc gccgtgcatt aatacgtatt atagcgtatc gtgtacgcta atatcttagt
+ 541 gcaccgcacg ctggttggat acaattccgt gaaataattc ctgcttacac aggggctttc
+ 601 tggcgcatgg ctgtgtctgg atgtttgtga taagaggctc catgaacccg gcgggaaatg
+ 661 aggggaaacc ccggggagca acgacactaa gcctggcagt tgttcagata ggacgctttt
+ 721 gtcagtgggc ggttttgcat ccactaacta tcataaacga cacaacgtcg aatgatcatc
+ 781 ggcggtttgc atgtagagac agctcctgca acaccatacc ggctcgtgga attacgctgt
+ 841 gcgccggccc tcattcgatt gtgtccagcg tcggcgcgaa tgatgattga gatgtgcttc
+ 901 ggctcagagc gtgcacaggt agttctcccc ccttacctag ctgatccagc aattccacgc
+ 961 tggcccgcgc gtccttgggt aacactggat ctgtacccaa atacaccgtc gggctagaga
+ 1021 cgctccacct gcgtctatcg tacagtgcta aaatggcagc agatagtgaa acttccgcta
+ 1081 agctagcccc tcagggtaca ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt
+ 1141 tgtcggggac ctgccgtcac gcttccgagt gtatatccgg atttagttga cgtcatacag
+ 1201 aggcactaag aagaataaac gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct
+ 1261 cccttgcgcc gttcggcaag cgtccggtgt cgggctgcaa ggaataaatc tttatggacc
+ 1321 agaggggctt gtttcctcat atgggtgcgt gcacttatac gattcaaagg tggatatggc
+ 1381 cgcataacac gtagccaggc tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg
+ 1441 tttttgtttt tcctttacga cacgaaccgc tctaacctgc tctatttcgc cacgttccag
+ 1501 tgaacctctt agcctaccgc ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg
+ 1561 gagaaatcgt tcaatattag aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc
+ 1621 cgtttaacgg ctgccgtggt cataccgtga ggcaccacga ggggatgcta cgcaacatgc
+ 1681 gaggtgtaat cagcagggaa gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat
+ 1741 atgcataagg tgtcatttat attacaccta cgacactggt accggctcac agccaaatgc
+ 1801 acagtctcaa gatagaattc gcaaaaatta ggcttatcgg gcgcttactc tttgttacac
+ 1861 ttctggtctg tgagtgacgc cctgtgtccc atcactgcat gtgaggatgc gtgtactgca
+ 1921 cctgtgaatt acagacgttt ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc
+ 1981 tctatagggt gatctcgaca taccactatg gtttgcgcgt ttcgggtgct tttggcgagg
+ 2041 gccaggtacg gcggtgagac agcgtatttt gcgaataggg tattcggacg cacggtgtat
+ 2101 agctcttgga aaacgactct tcgacgggcg tgtagaagta gccaagcagt tcggttgtta
+ 2161 tcactaaatg cggaccatgt gcagccgttt aggagaggag tctgcaatgg atcagctggt
+ 2221 cagattgtac cactcggttg agcctaaggc acttcaggtg ctcggattgt aatgaaccct
+ 2281 caggttacgc cgttgcgctg agatcccaca agccataagc aatgagaatc gagcagctat
+ 2341 cgaattacgc agcacttgct gatgaactgg gtgcacctaa agcgcccgat aaaacggagg
+ 2401 gagtgaggta actactacat tgcgagtagt gcgaggggcc tccgagacta cattagagca
+ 2461 gccatgccga atacgacaaa atctatagcc ttgcgaacgt aggggactga tttatggaca
+ 2521 acaggaccga aacaagttgg agccacaacg gagctatgga cgttttcact attgatgggt
+ 2581 ggcttgcgtc cgcatcccag gtttctctgg ttaattttca tgacgattct ttgtggtacg
+ 2641 atccaggcat aagatagggc acctaacccg atactgtgaa cttatatgac ggctgaacat
+ 2701 gccctaatag tctgccaaaa gggaaaccta taacggctct aaacgggccc cgggtacgta
+ 2761 acagcaatgt tcctgtccac caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat
+ 2821 tccgttttac gccccagatc gcagctccct tgacagtgtc agttgaatcc ccattctagg
+ 2881 tttcctgata aaactaagta cggggacgca tcagtcgaaa gcaatcacag ataatagata
+ 2941 tcttgagcag aaagacgtct tcacgaatca ggagcgagtg tcccctttga aagtgcgggc
+ 3001 aacaataggt gtgaggtttc acggttgctt gatcagtagc tgttcactct ctcgcaggcc
+ 3061 tacatagtga ggtggtgaga ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc
+ 3121 gggcacgcta acaaggacag gaattcgggt cgtcaaataa caatttacgt catcgcatcc
+ 3181 ctcaagggta aggcgtgatc tccatctcgg ttcccaattg gtcattgtga tagccacact
+ 3241 gcagttaccg aaggcgattt tatactaccc tgataagtgc tcgcagcccc tcctccctaa
+ 3301 taatgtaacg acgagcatta acccaggagt atttctcacg ttgctcgtgc ccagccaagg
+ 3361 cgatcaacgc agaccggata gcgttagcta gcccacgggt aaaagcgatt gttgtactct
+ 3421 ttcatatgaa tacagcactc gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc
+ 3481 acactggagg cgatgatcta gcccgtcttt caccccgtac ctttatactc ggccgcgtat
+ 3541 ttctccaccg ggagctctgc ctaccaaagc gtcgtacgcc caggaagccg tttcctttat
+ 3601 cctccctcat gtctcaacgc gcgagcatcg gagagtacgc gaaatcgact gtctggccaa
+ 3661 cactggacag acgcgcgaga cactgataaa cccccatttt cgtggggtta gtaaatcggt
+ 3721 ggcttcaaac ggttcgatcg ctcgcacgag cattagtcag gagtatgatt gcgcatcatc
+ 3781 tctactccgt actaggttct gtagctcagg atctccgggg ggatcaagct tttatgtccc
+ 3841 gcgggattag aagatatcca tccatatgtt tactttgatg cgggtccgag ctctctatga
+ 3901 tgctgctttg acaaaatgtg gaaagcctca gcgaccgctc tggggtcaaa gctctacgac
+ 3961 acgttgatgc taaacaagtt ggactactaa gcaaatgaag cggaagagat actgagcgct
+ 4021 ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partA2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partA2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,95 @@
+LOCUS Exported 4022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partA2
+VERSION partA2
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 4022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..4022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..1001
+ /label="pA2"
+ /label="nonstandard type: annotation"
+ CDS 1123..2022
+ /label="AmpR"
+ misc_feature 3023..3522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaatt gtaagataga acagggatat agctcgttgc atccataaat tgcccaccgt
+ 61 agggagaacg ccgttggaaa atgagagtta ggcgatgagc ggttgtcgcc cgcacagaca
+ 121 aaggatgcct ttataaatag tagcggcctt gtctgcacca gacgtttgtg ggtcgacgtg
+ 181 ctattctagc caaaagcaaa atgtatcata ctacaggcaa taggccctat gctgaccaaa
+ 241 cttggggacc cttgcgcctt ctctcttacg cataacatgc ataggtacct ctactcatca
+ 301 ggcagggcgg cgtgaggtca ctatggctca agatgtgtac gactaaagaa aggtttatgc
+ 361 tccttcccca aggacgcatt tgggactgct acttgcccct agcgaattca ctaggatttt
+ 421 tgtagaacca tgagcgccct atccgatagc acagagacaa tgctacaagc aactgtgcat
+ 481 gcgctcgatc gccgtgcatt aatacgtatt atagagtatc gtgtacgcta atatcttagt
+ 541 gcaccgcacg ctggttggat acaattccgt gaaataattc ctgcttacac aggggctttc
+ 601 tggcgcatgg ctgtgtctgg atgtttgtga taagaggctc caagaacccg gcgggaaatg
+ 661 aggggaaacc ccggggagca acgacactaa gcctggcagt tgttcagata ggacgctttt
+ 721 gtcagtgggc ggttttgcat ccactaacta tcataaacga cacaacgtcg aatgatcatc
+ 781 ggcggtttgc atgtagagac agctcctgca acaccatacc ggctcgtgga attacgctgt
+ 841 gcgccggccc tcattcgatt gtgtccagcg tcggcgcgaa tgatgattga gatgtgcttc
+ 901 ggctcagagc gtgcacaggt agttctcccc ccttacctag ctaatccagc aattccacgc
+ 961 tggcccgcgc gtccttgggt aacactggat ctgtacccaa atacaccgtc gggctagaga
+ 1021 cgctccacct gcgtctatcg tacagtgcta aaatggcagc agatagtgaa acttccgcta
+ 1081 agctagcccc tcagggtaca ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt
+ 1141 tgtcggggac ctgccgtcac gcttccgagt gtatatccgg atttagttga cgtcatacag
+ 1201 aggcactaag aagaataaac gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct
+ 1261 cccttgcgcc gttcggcaag cgtccggtgt cgggctgcaa ggaataaatc tttatggacc
+ 1321 agaggggctt gtttcctcat atgggtgcgt gcacttatac gattcaaagg tggatatggc
+ 1381 cgcataacac gtagccaggc tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg
+ 1441 tttttgtttt tcctttacga cacgaaccgc tctaacctgc tctatttcgc cacgttccag
+ 1501 tgaacctctt agcctaccgc ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg
+ 1561 gagaaatcgt tcaatattag aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc
+ 1621 cgtttaacgg ctgccgtggt cataccgtga ggcaccacga ggggatgcta cgcaacatgc
+ 1681 gaggtgtaat cagcagggaa gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat
+ 1741 atgcataagg tgtcatttat attacaccta cgacactggt accggctcac agccaaatgc
+ 1801 acagtctcaa gatagaattc gcaaaaatta ggcttatcgg gcgcttactc tttgttacac
+ 1861 ttctggtctg tgagtgacgc cctgtgtccc atcactgcat gtgaggatgc gtgtactgca
+ 1921 cctgtgaatt acagacgttt ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc
+ 1981 tctatagggt gatctcgaca taccactatg gtttgcgcgt ttcgggtgct tttggcgagg
+ 2041 gccaggtacg gcggtgagac agcgtatttt gcgaataggg tattcggacg cacggtgtat
+ 2101 agctcttgga aaacgactct tcgacgggcg tgtagaagta gccaagcagt tcggttgtta
+ 2161 tcactaaatg cggaccatgt gcagccgttt aggagaggag tctgcaatgg atcagctggt
+ 2221 cagattgtac cactcggttg agcctaaggc acttcaggtg ctcggattgt aatgaaccct
+ 2281 caggttacgc cgttgcgctg agatcccaca agccataagc aatgagaatc gagcagctat
+ 2341 cgaattacgc agcacttgct gatgaactgg gtgcacctaa agcgcccgat aaaacggagg
+ 2401 gagtgaggta actactacat tgcgagtagt gcgaggggcc tccgagacta cattagagca
+ 2461 gccatgccga atacgacaaa atctatagcc ttgcgaacgt aggggactga tttatggaca
+ 2521 acaggaccga aacaagttgg agccacaacg gagctatgga cgttttcact attgatgggt
+ 2581 ggcttgcgtc cgcatcccag gtttctctgg ttaattttca tgacgattct ttgtggtacg
+ 2641 atccaggcat aagatagggc acctaacccg atactgtgaa cttatatgac ggctgaacat
+ 2701 gccctaatag tctgccaaaa gggaaaccta taacggctct aaacgggccc cgggtacgta
+ 2761 acagcaatgt tcctgtccac caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat
+ 2821 tccgttttac gccccagatc gcagctccct tgacagtgtc agttgaatcc ccattctagg
+ 2881 tttcctgata aaactaagta cggggacgca tcagtcgaaa gcaatcacag ataatagata
+ 2941 tcttgagcag aaagacgtct tcacgaatca ggagcgagtg tcccctttga aagtgcgggc
+ 3001 aacaataggt gtgaggtttc acggttgctt gatcagtagc tgttcactct ctcgcaggcc
+ 3061 tacatagtga ggtggtgaga ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc
+ 3121 gggcacgcta acaaggacag gaattcgggt cgtcaaataa caatttacgt catcgcatcc
+ 3181 ctcaagggta aggcgtgatc tccatctcgg ttcccaattg gtcattgtga tagccacact
+ 3241 gcagttaccg aaggcgattt tatactaccc tgataagtgc tcgcagcccc tcctccctaa
+ 3301 taatgtaacg acgagcatta acccaggagt atttctcacg ttgctcgtgc ccagccaagg
+ 3361 cgatcaacgc agaccggata gcgttagcta gcccacgggt aaaagcgatt gttgtactct
+ 3421 ttcatatgaa tacagcactc gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc
+ 3481 acactggagg cgatgatcta gcccgtcttt caccccgtac ctttatactc ggccgcgtat
+ 3541 ttctccaccg ggagctctgc ctaccaaagc gtcgtacgcc caggaagccg tttcctttat
+ 3601 cctccctcat gtctcaacgc gcgagcatcg gagagtacgc gaaatcgact gtctggccaa
+ 3661 cactggacag acgcgcgaga cactgataaa cccccatttt cgtggggtta gtaaatcggt
+ 3721 ggcttcaaac ggttcgatcg ctcgcacgag cattagtcag gagtatgatt gcgcatcatc
+ 3781 tctactccgt actaggttct gtagctcagg atctccgggg ggatcaagct tttatgtccc
+ 3841 gcgggattag aagatatcca tccatatgtt tactttgatg cgggtccgag ctctctatga
+ 3901 tgctgctttg acaaaatgtg gaaagcctca gcgaccgctc tggggtcaaa gctctacgac
+ 3961 acgttgatgc taaacaagtt ggactactaa gcaaatgaag cggaagagat actgagcgct
+ 4021 ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partB.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partB.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,111 @@
+LOCUS Exported 5022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partB
+VERSION partB
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 5022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..5022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..2001
+ /label="pB"
+ /label="nonstandard type: annotation"
+ CDS 2123..3022
+ /label="AmpR"
+ misc_feature 4023..4522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaggc ttgattgtta actaccgtat ggcggttacg atcgagtgac actattatta
+ 61 gaccgctact ccaagtccca acttttcatc gccatacaga agagaacgag aaagtcgaag
+ 121 agttatagcg tgtacacttc tgattagcta acgaatcgat gcgtacagca tactcgagca
+ 181 actttatggg tcgtctgtct ccttgtaccc cgcttgacga ggatgtgttt gtaggcggct
+ 241 tggatatcgg cagtgtatcc gcatggtcaa acactttagc ccgaccggtg ctcaaggtcg
+ 301 aaatcctaat atagattggg ataggacccg tccattacta ggcgacattc gcagtcacga
+ 361 gcccgcacgg ggtgcctcaa cacggtgaca ctcaattcgc cggcactgag tacgacgatc
+ 421 gtgattgcca taccgtcatg ttttgtgtta cccctgataa gaagcgcaga tatggcacgg
+ 481 gggcagaggg cggagtagac ccatgcaaaa ctctagcctc tgggcagcat gatcgacgta
+ 541 gaacgccgtt gtgactcact agtttcagtt atgatgttca gccaagaatc ctccattttg
+ 601 acgtgaacct tctcccttta caccttgaag ctgcaatatt aagtcgaccc tttaagttgc
+ 661 cttgtcttgg tctagagccc gcagctcacc gataaaatga gcagtcaatt ttagcggcgg
+ 721 ttgtccaggt tacatgcact ttgggctgga accgcgttac gtttggagta cttagaagtg
+ 781 tcgtaggcat aggagagccg aaacttgata ttgggtctag ttagtgctct accccgcttc
+ 841 ggatccgtaa tagtgatgtt gcataagacg cttgcctcaa ggcgacatac ggtggcggtt
+ 901 gctggaaatg acgccccacc ccgtgataat ttggggacga gccgcacgat aacttctgcc
+ 961 agcgaccgcc cctcccacgt ccgatggtga ttccgaattt tgattacatg ccagacacgc
+ 1021 tttaatctcg ccaccacatt ggcaccccca ccaagtaatg tatgtaagaa gcagctgcgc
+ 1081 cccaagttac gtgccgtttc cgatgggagc agcaataatg tcgatagcaa ccacccccct
+ 1141 ctctactgac gaagcaacac cggggacacc gtcaccttgg cttcatttcg tattcattca
+ 1201 cctacgcaca accgcctgac cgttcgttat cacgagccta tccccttcaa gcaatttccc
+ 1261 ccccttgttc agcagcctac actatacgtt ggtacactgt gtgcgacaga tatttggtgc
+ 1321 ccgtcttatt ctattctgag agagtttaat agccaaaaga tatgagtagg aacgggaggt
+ 1381 acccgactcg cgttgaagca ctcttaagac ctctcttagc acttcgaagg gtaggtgcgt
+ 1441 tcaaagaacc tctgctttta actaagatca aaaggattgc gtacaacttc cccgttaact
+ 1501 ctccagagga tccgtagaag tctacaccaa aatacgtttg gtttcgccaa ggtgactatc
+ 1561 ggtacttgtg cacgtaacag ggtaaagaat tgaaagcctc aaattgtacg acgttacgcc
+ 1621 cggacggtcg ccggtgatag ggtgacgcat ttgcgtttgt catatcattt gggattagac
+ 1681 ggagctggtg tacctctatg gacgttacaa aaccttgtgg taacagcctg ggtgccatcc
+ 1741 acctagtccg aagtttcctt ctaaccgcgg catcagatgg atatgtacct tatggcgctt
+ 1801 cccgggaagt ccaattcttc gtgttgaagg gacagctcta caggcctggc cacttgtggc
+ 1861 gcatctaagt agtctaggtg catgattctc tcccttgggg gcgctgtcgt gggtcctgcc
+ 1921 gagccacacc ctaacctcac gtcgcaagac ttggtaaata gctttttttt ttatgcccaa
+ 1981 tctatttacg taacaatcga catcagagga ggggcagaga cgctccacct gcgtctatcg
+ 2041 tacagtgcta aaatggcagc agatagtgaa acttccgcta agctagcccc tcagggtaca
+ 2101 ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt tgtcggggac ctgccgtcac
+ 2161 gcttccgagt gtatatccgg atttagttga cgtcatacag aggcactaag aagaataaac
+ 2221 gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct cccttgcgcc gttcggcaag
+ 2281 cgtccggtgt cgggctgcaa ggaataaatc tttatggacc agaggggctt gtttcctcat
+ 2341 atgggtgcgt gcacttatac gattcaaagg tggatatggc cgcataacac gtagccaggc
+ 2401 tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg tttttgtttt tcctttacga
+ 2461 cacgaaccgc tctaacctgc tctatttcgc cacgttccag tgaacctctt agcctaccgc
+ 2521 ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg gagaaatcgt tcaatattag
+ 2581 aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc cgtttaacgg ctgccgtggt
+ 2641 cataccgtga ggcaccacga ggggatgcta cgcaacatgc gaggtgtaat cagcagggaa
+ 2701 gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat atgcataagg tgtcatttat
+ 2761 attacaccta cgacactggt accggctcac agccaaatgc acagtctcaa gatagaattc
+ 2821 gcaaaaatta ggcttatcgg gcgcttactc tttgttacac ttctggtctg tgagtgacgc
+ 2881 cctgtgtccc atcactgcat gtgaggatgc gtgtactgca cctgtgaatt acagacgttt
+ 2941 ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc tctatagggt gatctcgaca
+ 3001 taccactatg gtttgcgcgt ttcgggtgct tttggcgagg gccaggtacg gcggtgagac
+ 3061 agcgtatttt gcgaataggg tattcggacg cacggtgtat agctcttgga aaacgactct
+ 3121 tcgacgggcg tgtagaagta gccaagcagt tcggttgtta tcactaaatg cggaccatgt
+ 3181 gcagccgttt aggagaggag tctgcaatgg atcagctggt cagattgtac cactcggttg
+ 3241 agcctaaggc acttcaggtg ctcggattgt aatgaaccct caggttacgc cgttgcgctg
+ 3301 agatcccaca agccataagc aatgagaatc gagcagctat cgaattacgc agcacttgct
+ 3361 gatgaactgg gtgcacctaa agcgcccgat aaaacggagg gagtgaggta actactacat
+ 3421 tgcgagtagt gcgaggggcc tccgagacta cattagagca gccatgccga atacgacaaa
+ 3481 atctatagcc ttgcgaacgt aggggactga tttatggaca acaggaccga aacaagttgg
+ 3541 agccacaacg gagctatgga cgttttcact attgatgggt ggcttgcgtc cgcatcccag
+ 3601 gtttctctgg ttaattttca tgacgattct ttgtggtacg atccaggcat aagatagggc
+ 3661 acctaacccg atactgtgaa cttatatgac ggctgaacat gccctaatag tctgccaaaa
+ 3721 gggaaaccta taacggctct aaacgggccc cgggtacgta acagcaatgt tcctgtccac
+ 3781 caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat tccgttttac gccccagatc
+ 3841 gcagctccct tgacagtgtc agttgaatcc ccattctagg tttcctgata aaactaagta
+ 3901 cggggacgca tcagtcgaaa gcaatcacag ataatagata tcttgagcag aaagacgtct
+ 3961 tcacgaatca ggagcgagtg tcccctttga aagtgcgggc aacaataggt gtgaggtttc
+ 4021 acggttgctt gatcagtagc tgttcactct ctcgcaggcc tacatagtga ggtggtgaga
+ 4081 ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc gggcacgcta acaaggacag
+ 4141 gaattcgggt cgtcaaataa caatttacgt catcgcatcc ctcaagggta aggcgtgatc
+ 4201 tccatctcgg ttcccaattg gtcattgtga tagccacact gcagttaccg aaggcgattt
+ 4261 tatactaccc tgataagtgc tcgcagcccc tcctccctaa taatgtaacg acgagcatta
+ 4321 acccaggagt atttctcacg ttgctcgtgc ccagccaagg cgatcaacgc agaccggata
+ 4381 gcgttagcta gcccacgggt aaaagcgatt gttgtactct ttcatatgaa tacagcactc
+ 4441 gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc acactggagg cgatgatcta
+ 4501 gcccgtcttt caccccgtac ctttatactc ggccgcgtat ttctccaccg ggagctctgc
+ 4561 ctaccaaagc gtcgtacgcc caggaagccg tttcctttat cctccctcat gtctcaacgc
+ 4621 gcgagcatcg gagagtacgc gaaatcgact gtctggccaa cactggacag acgcgcgaga
+ 4681 cactgataaa cccccatttt cgtggggtta gtaaatcggt ggcttcaaac ggttcgatcg
+ 4741 ctcgcacgag cattagtcag gagtatgatt gcgcatcatc tctactccgt actaggttct
+ 4801 gtagctcagg atctccgggg ggatcaagct tttatgtccc gcgggattag aagatatcca
+ 4861 tccatatgtt tactttgatg cgggtccgag ctctctatga tgctgctttg acaaaatgtg
+ 4921 gaaagcctca gcgaccgctc tggggtcaaa gctctacgac acgttgatgc taaacaagtt
+ 4981 ggactactaa gcaaatgaag cggaagagat actgagcgct ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partC.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/partC.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,111 @@
+LOCUS Exported 5022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION partC
+VERSION partC
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 5022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..5022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ misc_feature 22..2001
+ /label="pC"
+ /label="nonstandard type: annotation"
+ CDS 2123..3022
+ /label="AmpR"
+ misc_feature 4023..4522
+ /label="RepO_1"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 cgtctcaggg caaagattac gatagaaaaa cactcgacac agagtagtat gataaaagtt
+ 61 gggacggcat gctggactcg agaagtgtcg atccggcaat ccagatacgg caatggtacc
+ 121 ggtcacacct cattctaaga gcagtcaggg gctgtcaggt ctacagggca ccggccctga
+ 181 ggcccttggg ctagggtctg tcacccctat ctgcactgac tttaaagtaa ccgagcaata
+ 241 agacaatcaa tcgcagggct ctggatcggg gtccgaaggc ggggtgcagt gtctccctaa
+ 301 ttgttaagct caaaagagca gccactcgtt ctcgatcctt agtccatcgc cgtgaggtac
+ 361 aagcagtaca cccacggaag gcccggcatt gaagatgcaa gaaatagagc actggggtga
+ 421 cgacggcatg ctaaggtaag aaggcaaatt ctggaggact gacttcccca caagcggcgt
+ 481 aagctcggat aagattggga taaacggacc acggcggctg gatcttcacc cctttgcacg
+ 541 gtatgaaaac ggatcaggat tctcttccac ctattgcacc tgctgagaag agagcgctgg
+ 601 ggggacgtta cttatcccaa tcgcgacgtc acggacaaca tcgtgttaca ggtcaggctc
+ 661 gaaatcctag gcagctggta tccgacgcgc aagttatcta ccaaataagt taggcgatcg
+ 721 aaatcatagg ctgtttagtg cttttcttgg tatcatcctg aacttctgtc acctccgagg
+ 781 ccgaagcaac tattatgagg acgactcgat gattgtccgg agatgttgca ccccggcaag
+ 841 cctagaaaac cccggtcctt tgagttttaa tctaatagta gaagttctcg gaaatcagag
+ 901 ctggagactc ggtgacgtta tagaaatgtt cgcacgaaga gcgcgacatg tcctacttca
+ 961 caagatgctt tctaggaggg gatctggatt ctcaagccct acacatggtc cgtggtgtat
+ 1021 gttggatcgt agtgctttta ccgactatgt cgcgttaaat tgtctttcat ttctacaatt
+ 1081 cggggagcat ggggccatgt gacttaggtt cagaaggtgc gagcgggcgt actacgtttg
+ 1141 gtggtcgtgt ataatcagaa gaatcggcga tatccgctag caagcaaagt gtccttgacg
+ 1201 cttgtggaaa tccaactatt tcctgcctct caagtgttta gaaaaatatc ccctggagga
+ 1261 gatatcgctc ctctcttctg cgaccaacac cagttcaatt ccgcagtgca gcagtcctat
+ 1321 tccgcatgga tcacgctgac gagatgcggg gttgagacta ccccaaaaga tatgttgaga
+ 1381 taaattacca ggatggataa tctggtaccg gtgcgaaagg gtggttacac cagagtcgcc
+ 1441 tgatgagctt atgcgcaatt tcaagtccct atgttttact atgaaagtac gaccgagccg
+ 1501 ctagcctgag tcaaatagcg cagaatttgg gtcgtggaga tcgcgcttgt taacctggtc
+ 1561 taggcgcatc tgagtcataa cggggttata acgactgtca acgtgtgacc gcatatcctg
+ 1621 caaggcgaac aaataacgcc ccgcccaaaa tattacattt aagtagttat ctaactcccg
+ 1681 gcatgcgggg catttggggg cagcgtgccc attccgcccc tatgcctgtt tcaacacgca
+ 1741 accgtagaga ttggctagga tgggttttca cgagccaact gccacattag acatagaatt
+ 1801 ccgataagta taagagatat cagcgaggtt cagggtagtt tggaacgaca gccggttcag
+ 1861 aagttcagta tggtcattca tcatccgttg tgttgagtcc tttagatcgt ggctttatca
+ 1921 tgcatgtctc ccgccagccc tcaaactatg tcgtcacgcg catgtttaca ttatatggaa
+ 1981 caaaacgaga ggtagaagcc aatcactatc cggcaagaga cgctccacct gcgtctatcg
+ 2041 tacagtgcta aaatggcagc agatagtgaa acttccgcta agctagcccc tcagggtaca
+ 2101 ctgcaccgag gcgtgctgtc aatacttgat taagtcgggt tgtcggggac ctgccgtcac
+ 2161 gcttccgagt gtatatccgg atttagttga cgtcatacag aggcactaag aagaataaac
+ 2221 gcttacctcc agcaatcgtg tagtgtcagg tgtacgttct cccttgcgcc gttcggcaag
+ 2281 cgtccggtgt cgggctgcaa ggaataaatc tttatggacc agaggggctt gtttcctcat
+ 2341 atgggtgcgt gcacttatac gattcaaagg tggatatggc cgcataacac gtagccaggc
+ 2401 tatagtcccg cggcctaatt ccttcgagtg cgggtgcctg tttttgtttt tcctttacga
+ 2461 cacgaaccgc tctaacctgc tctatttcgc cacgttccag tgaacctctt agcctaccgc
+ 2521 ccacgtacgg tgggacgcgt cgagcagtta aggtactgtg gagaaatcgt tcaatattag
+ 2581 aaaacaggcg gtgtacgaat tactgtgtcc cggtgttgcc cgtttaacgg ctgccgtggt
+ 2641 cataccgtga ggcaccacga ggggatgcta cgcaacatgc gaggtgtaat cagcagggaa
+ 2701 gatcccgggg atcgaaagcg gtccgcgatt tgcgaccgat atgcataagg tgtcatttat
+ 2761 attacaccta cgacactggt accggctcac agccaaatgc acagtctcaa gatagaattc
+ 2821 gcaaaaatta ggcttatcgg gcgcttactc tttgttacac ttctggtctg tgagtgacgc
+ 2881 cctgtgtccc atcactgcat gtgaggatgc gtgtactgca cctgtgaatt acagacgttt
+ 2941 ccctaccagg gcgctacgtt ataatgttcg gttgcaaccc tctatagggt gatctcgaca
+ 3001 taccactatg gtttgcgcgt ttcgggtgct tttggcgagg gccaggtacg gcggtgagac
+ 3061 agcgtatttt gcgaataggg tattcggacg cacggtgtat agctcttgga aaacgactct
+ 3121 tcgacgggcg tgtagaagta gccaagcagt tcggttgtta tcactaaatg cggaccatgt
+ 3181 gcagccgttt aggagaggag tctgcaatgg atcagctggt cagattgtac cactcggttg
+ 3241 agcctaaggc acttcaggtg ctcggattgt aatgaaccct caggttacgc cgttgcgctg
+ 3301 agatcccaca agccataagc aatgagaatc gagcagctat cgaattacgc agcacttgct
+ 3361 gatgaactgg gtgcacctaa agcgcccgat aaaacggagg gagtgaggta actactacat
+ 3421 tgcgagtagt gcgaggggcc tccgagacta cattagagca gccatgccga atacgacaaa
+ 3481 atctatagcc ttgcgaacgt aggggactga tttatggaca acaggaccga aacaagttgg
+ 3541 agccacaacg gagctatgga cgttttcact attgatgggt ggcttgcgtc cgcatcccag
+ 3601 gtttctctgg ttaattttca tgacgattct ttgtggtacg atccaggcat aagatagggc
+ 3661 acctaacccg atactgtgaa cttatatgac ggctgaacat gccctaatag tctgccaaaa
+ 3721 gggaaaccta taacggctct aaacgggccc cgggtacgta acagcaatgt tcctgtccac
+ 3781 caaggcgttt ttagtaaccg ccgatcgatc tcgatcgaat tccgttttac gccccagatc
+ 3841 gcagctccct tgacagtgtc agttgaatcc ccattctagg tttcctgata aaactaagta
+ 3901 cggggacgca tcagtcgaaa gcaatcacag ataatagata tcttgagcag aaagacgtct
+ 3961 tcacgaatca ggagcgagtg tcccctttga aagtgcgggc aacaataggt gtgaggtttc
+ 4021 acggttgctt gatcagtagc tgttcactct ctcgcaggcc tacatagtga ggtggtgaga
+ 4081 ttgttcaggt ctgtctcctg cgcggttgtc gagccccgtc gggcacgcta acaaggacag
+ 4141 gaattcgggt cgtcaaataa caatttacgt catcgcatcc ctcaagggta aggcgtgatc
+ 4201 tccatctcgg ttcccaattg gtcattgtga tagccacact gcagttaccg aaggcgattt
+ 4261 tatactaccc tgataagtgc tcgcagcccc tcctccctaa taatgtaacg acgagcatta
+ 4321 acccaggagt atttctcacg ttgctcgtgc ccagccaagg cgatcaacgc agaccggata
+ 4381 gcgttagcta gcccacgggt aaaagcgatt gttgtactct ttcatatgaa tacagcactc
+ 4441 gcgaatgcaa gcctacgtcg gctcgattct cttcctcacc acactggagg cgatgatcta
+ 4501 gcccgtcttt caccccgtac ctttatactc ggccgcgtat ttctccaccg ggagctctgc
+ 4561 ctaccaaagc gtcgtacgcc caggaagccg tttcctttat cctccctcat gtctcaacgc
+ 4621 gcgagcatcg gagagtacgc gaaatcgact gtctggccaa cactggacag acgcgcgaga
+ 4681 cactgataaa cccccatttt cgtggggtta gtaaatcggt ggcttcaaac ggttcgatcg
+ 4741 ctcgcacgag cattagtcag gagtatgatt gcgcatcatc tctactccgt actaggttct
+ 4801 gtagctcagg atctccgggg ggatcaagct tttatgtccc gcgggattag aagatatcca
+ 4861 tccatatgtt tactttgatg cgggtccgag ctctctatga tgctgctttg acaaaatgtg
+ 4921 gaaagcctca gcgaccgctc tggggtcaaa gctctacgac acgttgatgc taaacaagtt
+ 4981 ggactactaa gcaaatgaag cggaagagat actgagcgct ct
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/receptor.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/construct_3/provided_parts_records/receptor.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,75 @@
+LOCUS Exported 3022 bp DNA circular UNK 01-JAN-1980
+DEFINITION natural circular DNA.
+ACCESSION receptor
+VERSION receptor
+KEYWORDS .
+SOURCE natural DNA sequence
+ ORGANISM unspecified
+ .
+REFERENCE 1 (bases 1 to 3022)
+ AUTHORS .
+ TITLE Direct Submission
+ JOURNAL Exported Thursday, Oct 17, 2019 from SnapGene Viewer 4.3.11
+ https://www.snapgene.com
+FEATURES Location/Qualifiers
+ source 1..3022
+ /organism="unspecified"
+ /mol_type="genomic DNA"
+ CDS 523..1222
+ /label="KanR"
+ misc_feature 2023..2522
+ /label="RepO_2"
+ /label="nonstandard type: rep._origin"
+ORIGIN
+ 1 attgagagac gcgtctcagg cactttcgct atatggcgac gtgcgaaaaa cgcgatttgg
+ 61 ccgaaatctc aaataataat gcaatgtgtt ggctaagctc gggcaaactc aggatgtgac
+ 121 ctagtaccct ctgccccgtg agtacccata cccaatcaag ccagcccaat tcgcgatagg
+ 181 tacagataag ccttactcgt cccgatcctt gactaaaaca ctcatcctcg atagtacgtg
+ 241 ccttgtagag tccgacggcc ataggtaaac gaccagttag tgtcgtaggg tcctccactt
+ 301 tagctacgat tgcaactccc ttaccttcgt gccggcgcgc tcctcttgct accatcacgc
+ 361 ttcaaatcgg gtggaagacc aactgatgaa tgagggtgca gaccccagtg gagcataata
+ 421 cgatgcgccc acgatactct agagccacgc gtcgacgttc gtaagatgtc ccgggcccgt
+ 481 gggtggccac atcggccgcc catccttgtg tcttccgata agtactccct ttcaaggact
+ 541 ctccgatacc ggcttagaac acgaacggac aacgctttca gcgctgagaa atgacggctg
+ 601 cttcaaccag aacgatacag ccttctttgc tagatagcct ctagtgtcag ccaccaagtc
+ 661 cgccacctaa tccttcgccg agggtcaaag cttctgacca tccaattgtt aggcactctt
+ 721 ggaaccttgc aagtacctga tcatgcagaa aatggacttg cccggagcat attcattata
+ 781 agtaccattc acggcaggtt atagtatgcg ttgacgcggg gtgatacggt aatgcaagta
+ 841 accatcgggc cgcggtatgc acatagaagg gtgtttgact tggtttctta cagtgcaact
+ 901 gcatatgtgg accgccattc caagtgaaag gatacgaagg gaggtttcgg actgctatcc
+ 961 agagcatgga aagccttcaa ggtggtgcgc actggaatag tgactcgggg attgtatgtc
+ 1021 gagccgcgtc cagtctttcc tatacttatg cgagcaaata gaccgagtgg aacttgattg
+ 1081 catcagccga atcacgatga aaactcagct tacaattcgt aagcacttca aatatatgcc
+ 1141 cggaaaatcg ccgtccagtg acttgtaata gctccagggt cagtagcgct gccctggccg
+ 1201 aaccaggtga cggttacgtg gacctcacag tatcaatgtt gcagtgcgcc accagattaa
+ 1261 gctggccgtg tcatggtgaa caaccgtgat aaaagaacgg gagtatgaga gtgccaccca
+ 1321 agagtggtac tccaggattc ggaaagggga gggggctttt cctgcttaac aaccttcctc
+ 1381 ggcacggtct aagggtctca ctcgtcctaa actctaccat catgcagcta ggcgaaagta
+ 1441 taactttagg gtctctcagg atgagctatc tgtaccacgg tgatgagata agtagggggt
+ 1501 gcgctagggt cgttcgtgtt ttcatcgtct atagtaccta tttctcgtct tccattagcg
+ 1561 catacggcca tctcgcggcg gctacgtcag ccagcgtcaa ccccaagtca ctaatttccg
+ 1621 ttattatagg tgtagctcat aacttcttct gccgaccaag ccaaaagctt tgcggcagct
+ 1681 gcaaggccac gttaggctct cggacggcag atatttatta ataacaccac tgggttccag
+ 1741 ctcttaacgc acttcccttc actggatcac ctgtacgccc ataagctaag cctgaagcca
+ 1801 cggcctcaat cgtggacatt actcttagca aatccacatt accatgtcac caatccccga
+ 1861 accccgcgcc gacctaaggc ggggtacctc gtgcacggca gcatcgaggg aaatatatta
+ 1921 caaaagacgc ggcgatccaa cggttgataa aaacagttcc gtggaaggcg gacgtgtgct
+ 1981 tagcgcatgc ttctcaccga gtgacagcac cgattccatc tcgctagcac gccgatgagc
+ 2041 ctcgctgtgg gactatggtc cagcctatgc ttaactaggc agaacagaga gtatggtggt
+ 2101 cctcggtaag gtcgatttgg tggcactcgc aagatacgcg ggttattagt agagcgcagt
+ 2161 cagggcccat cgccagcatt tgcatgctcg ccgtacgcta tccttgtact acggttcctc
+ 2221 agtggctata aaggaatgtc acaactccat tagccccttt tgttcagcgc ttagtcatgg
+ 2281 tgggactgac tcaccgagac tacatacgga ttgtgcccgc agagacctgc ctttcatgct
+ 2341 ggggttttgt aagcagctcc acggggtagt gtcaccatgc cttcgaccta tgcttatgaa
+ 2401 acccgaggta atgcggcagg atcccgtgga tcctacgctt agcctgttta agccatcgtt
+ 2461 ctcctcggcc cccagccagc gcgtattccg cgcattcctc cgagtgcgta tcgcgcaaac
+ 2521 cacaagatac ctctcaacga ctagcggtga accaccaagc ttgacatacg tgccccttcg
+ 2581 gaaacgttat tagtggtcct gagtggtacg tcccgagtat acggggcagc gatagtaacg
+ 2641 ctacaaatag ctaggcgagg ttgcgatacc tgaatgaata tccaacagtg gcaacgaggc
+ 2701 gcttagaaag ggaaactaca taccagttca atccgggatg acttcaaaag ggtatgtttg
+ 2761 ttttgaagcg aagctttggt tgtcattcag ttcctagagt ttacggcgct gatatggctc
+ 2821 taggagtcca gtgaattcgt cagcataagc cccacatcgt aggaaattgc ccggtcgtcg
+ 2881 gtctagcaaa tgctcggtaa actgggagtg tactaacacc atgtcgtggt aacccggtgg
+ 2941 accggctact agagacatat ttattcatgc tcagttgaac ctgtttcgag ggggccgagt
+ 3001 taacataaag tgattagtca ca
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/example_assembly_plan_all_required_parts.txt
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/example_assembly_plan_errors.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/example_assembly_plan_errors.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,7 @@
+assembly_name;message;suggestion;data;used_in
+construct_1;Wrong number of constructs;expected_: 1,found: 0;
+construct_1;Some parts are unused;unused_parts: partA & partB & partC & receptor;
+construct_2;Wrong number of constructs;expected_: 1,found: 0;
+construct_2;Some parts are unused;unused_parts: partA2 & partB2 & partC & receptor;
+construct_3;Wrong number of constructs;expected_: 1,found: 0;
+construct_3;Some parts are unused;unused_parts: partA & partA2 & partB & partC & receptor;
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/example_assembly_plan_simulation_stats.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/example_assembly_plan_simulation_stats.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+cancelled_assemblies: 0
+errored_assemblies: 3
+valid_assemblies: 0
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/example_assembly_plan_simulation/example_assembly_plan_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/example_assembly_plan_simulation/example_assembly_plan_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,1 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,parts
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/Report.pdf
Binary file test-data/init/gibson_assembly_simulation/Report.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/all_construct_records/construct_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/all_construct_records/construct_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,191 @@
+LOCUS construct_1 8000 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_1
+VERSION construct_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1781..1800
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1781..3581
+ /source="Frag_3"
+ /indicates_part=True
+ /note="From Frag_3"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3582..3599
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3582..4781
+ /source="Frag_4"
+ /indicates_part=True
+ /note="From Frag_4"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4782..4799
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4782..6190
+ /source="Frag_5"
+ /indicates_part=True
+ /note="From Frag_5"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6191..8000
+ /source="Frag_1"
+ /indicates_part=True
+ /note="From Frag_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6191..6209
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 8021..9800
+ /source="Frag_2"
+ /indicates_part=True
+ /note="From Frag_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cccagatcgc agctcccttg acagtgtcag ttgaatcccc attctaggtt tcctgataaa
+ 61 actaagtacg gggacgcatc agtcgaaagc aatcacagat aatagatatc ttgagcagaa
+ 121 agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa gtgcgggcaa caataggtgt
+ 181 gaggtttcac ggttgcttga tcagtagctg ttcactctct cgcaggccta catagtgagg
+ 241 tggtgagatt gttcaggtct gtctcctgcg cggttgtcga gccccgtcgg gcacgctaac
+ 301 aaggacagga attcgggtcg tcaaataaca atttacgtca tcgcatccct caagggtaag
+ 361 gcgtgatctc catctcggtt cccaattggt cattgtgata gccacactgc agttaccgaa
+ 421 ggcgatttta tactaccctg ataagtgctc gcagcccctc ctccctaata atgtaacgac
+ 481 gagcattaac ccaggagtat ttctcacgtt gctcgtgccc agccaaggcg atcaacgcag
+ 541 accggatagc gttagctagc ccacgggtaa aagcgattgt tgtactcttt catatgaata
+ 601 cagcactcgc gaatgcaagc ctacgtcggc tcgattctct tcctcaccac actggaggcg
+ 661 atgatctagc ccgtctttca ccccgtacct ttatactcgg ccgcgtattt ctccaccggg
+ 721 agctctgcct accaaagcgt cgtacgccca ggaagccgtt tcctttatcc tccctcatgt
+ 781 ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt ctggccaaca ctggacagac
+ 841 gcgcgagacg ctgataaacc cccattttcg tggggttagt aaatcggtgg cttcaaacgg
+ 901 ttcgatcgct cgcacgagca ttagtcagga gtatgattgc gcatcatctc tactccgtac
+ 961 taggttctgt agctcaggat ctccgggggg atcaagcttt tatgtcccgc gggattagaa
+ 1021 gatatccatc catatgttta ctttgatgcg ggtccgagct ctctatgatg ctgctttgac
+ 1081 aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc tctacgacac gttgatgcta
+ 1141 aacaagttgg actactaagc aaatgaagcg gaagagatac tgagcgctct ctctatgact
+ 1201 ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga aatctcaaat aataatgcaa
+ 1261 tgtgttggct aagctcgggc aaactcagga tgtgacctag taccctctgc cccgtgagta
+ 1321 cccataccca atcaagccag cccaattcgc gataggtaca gataagcctt actcgtcccg
+ 1381 atccttgact aaaacactca tcctcgatag tacgtgcctt gtagagtccg acggccatag
+ 1441 gtaaacgacc agttagtgtc gtagggtcct ccactttagc tacgattgca actcccttac
+ 1501 cttcgtgccg gcgcgctcct cttgctacca tcacgcttca aatcgggtgg aagaccaact
+ 1561 gatgaatgag ggtgcagacc ccagtggagc ataatacgat gcgcccacga tactctagag
+ 1621 ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt ggccacatcg gccgcccatc
+ 1681 cttgtgtctt ccgataagta ctccctttca aggactctcc gataccggct tagaacacga
+ 1741 acggacaacg ctttcagcgc tgagaaatga cggctgcttc aaccagaacg atacagcctt
+ 1801 ctttgctaga tagcctctag tgtcagccac caagtccgcc acctaatcct tcgccgaggg
+ 1861 tcaaagcttc tgaccatcca attgttaggc actcttggaa ccttgcaagt acctgatcat
+ 1921 gcagaaaatg gacttgcccg gagcatattc attataagta ccattcacgg caggttatag
+ 1981 tatgcgttga cgcggggtga tacggtaatg caagtaacca tcgggccgcg gtatgcacat
+ 2041 agaagggtgt ttgacttggt ttcttacagt gcaactgcat atgtggaccg ccattccaag
+ 2101 tgaaaggata cgaagggagg tttcggactg ctatccagag catggaaagc cttcaaggtg
+ 2161 gtgcgcactg gaatagtgac tcggggattg tatgtcgagc cgcgtccagt ctttcctata
+ 2221 cttatgcgag caaatagacc gagtggaact tgattgcatc agccgaatca cgatgaaaac
+ 2281 tcagcttaca attcgtaagc acttcaaata tatgcccgga aaatcgccgt ccagtgactt
+ 2341 gtaatagctc cagggtcagt agcgctgccc tggccgaacc aggtgacggt tacgtggacc
+ 2401 tcacagtatc aatgttgcag tgcgccacca gattaagctg gccgtgtcat ggtgaacaac
+ 2461 cgtgataaaa gaacgggagt atgagagtgc cacccaagag tggtactcca ggattcggaa
+ 2521 aggggagggg gcttttcctg cttaacaacc ttcctcggca cggtctaagc gtctcactcg
+ 2581 tcctaaactc taccatcatg cagctaggcg aaagtataac tttagggtct atcaggatga
+ 2641 gctatctgta ccacggtgat gagataagta gggggtgcgc tagggtcgtt cgtgttttca
+ 2701 tcgtctatag tacctatttc tcgtcttcca ttagcgcata cggccatctc gcggcggcta
+ 2761 cgtcagccag cgtcaacccc aagtcactaa tttccgttat tataggtgta gctcataact
+ 2821 tcttctgccg accaagccaa aagctttgcg gcagctgcaa ggccacgtta ggctctcgga
+ 2881 cggcagatat ttattaataa caccactggg ttccagctct taacgcactt cccttcactg
+ 2941 gatcacctgt acgcccataa gctaagcctg aagccacggc ctcaatcgtg gacattactc
+ 3001 ttagcaaatc cacattacca tgtcaccaat ccccgaaccc cgcgccgacc taaggcgggg
+ 3061 tacctcgtgc acggcagcat cgagggaaat atattacaaa agacgcggcg atccaacggt
+ 3121 tgataaaaac agttccgtgg aaggcggacg tgtgcttagc gcatgcttct caccgagtga
+ 3181 cagcaccgat tccatctcgc tagcacgccg atgagcctcg ctgtgggact atggtccagc
+ 3241 ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc ggtaaggtcg atttggtggc
+ 3301 actcgcaaga tacgcgggtt attagtagag cgcagtcagg gcccatcgcc agcatttgca
+ 3361 tgctcgccgt acgctatcct tgtactacgg ttcctcagtg gctataaagg aatgtcacaa
+ 3421 ctccattagc cccttttgtt cagcgcttag tcatggtggg actgactcac cgagactaca
+ 3481 tacggattgt gcccgcagag acatgccttt catgctgggg ttttgtaagc agctccacgg
+ 3541 ggtagtgtca ccatgccttc gacctatgct tatgaaaccc gaggtaatgc ggcaggatcc
+ 3601 cgtggatcct acgcttagcc tgtttaagcc atcgttctcc tcggccccca gccagcgcgt
+ 3661 attccgcgca ttcctccgag tgcgtatcgc gcaaaccaca agatacctct caacgactag
+ 3721 cggtgaacca ccaagcttga catacgtgcc ccttcggaaa cgttattagt ggtcctgagt
+ 3781 ggtacgtccc gagtatacgg ggcagcgata gtaacgctac aaatagctag gcgaggttgc
+ 3841 gatacctgaa tgaatatcca acagtggcaa cgagacgctt agaaagggaa actacatacc
+ 3901 agttcaatcc gggatgactt caaaagggta tgtttgtttt gaagcgaagc tttggttgtc
+ 3961 attcagttcc tagagtttac ggcgctgata tggctctagg agtccagtga attcgtcagc
+ 4021 ataagcccca catcgtagga aattgcccgg tcgtcggtct agcaaatgct cggtaaactg
+ 4081 ggagtgtact aacaccatgt cgtggtaacc cggtggaccg gctactagag acatatttat
+ 4141 tcatgctcag ttgaacctgt ttcgaggggg ccgagttaac ataaagtgat tagtcacagc
+ 4201 gcattaagat agaacaggga tatagctcgt tgcatccata aattgcccac cgtagggaga
+ 4261 acgccgttgg aaaatgagag ttaggcgatg agcggttgtc gcccgcacag acaaaggatg
+ 4321 cctttataaa tagtagcggc cttgtctgca ccagacgttt gtgggtcgac gtgctattct
+ 4381 agccaaaagc aaaatgtatc atactacagg caataggccc tatgctgacc aaacttgggg
+ 4441 acccttgcgc cttctctctt acgcataaca tgcataggta cctctactca tcaggcaggg
+ 4501 cggcgtgagg tcactatggc tcaagatgtg tacgactaaa gaaaggttta tgctccttcc
+ 4561 ccaaggacgc atttgggact gctacttgcc cctagcgaat tcactaggat ttttgtagaa
+ 4621 ccatgagcgc cctatccgat agcacagaga caatgctaca agcaactgtg catgcgctcg
+ 4681 atcgccgtgc attaatacgt attatagcgt atcgtgtacg ctaatatctt agtgcaccgc
+ 4741 acgctggttg gatacaattc cgtgaaataa ttcctgctta cacaggggct ttctggcgca
+ 4801 tggctgtgtc tggatgtttg tgataagagg ctccatgaac ccggcgggaa atgaggggaa
+ 4861 accccgggga gcaacgacac taagcctggc agttgttcag ataggacgct tttgtcagtg
+ 4921 ggcggttttg catccactaa ctatcataaa cgacacaacg tcgaatgatc atcggcggtt
+ 4981 tgcatgtaga gacagctcct gcaacaccat accggctcgt ggaattacgc tgtgcgccgg
+ 5041 ccctcattcg attgtgtcca gcgtcggcgc gaatgatgat tgagatgtgc ttcggctcag
+ 5101 agcgtgcaca ggtagttctc cccccttacc tagctgatcc agcaattcca cgctggcccg
+ 5161 cgcgtccttg ggtaacactg gatctgtacc caaatacacc gtcgtgattg ttaactaccg
+ 5221 tatggcggtt acgatcgagt gacactatta ttagaccgct actccaagtc ccaacttttc
+ 5281 atcgccatac agaagagaac gagaaagtcg aagagttata gcgtgtacac ttctgattag
+ 5341 ctaacgaatc gatgcgtaca gcatactcga gcaactttat gggtcgtctg tctccttgta
+ 5401 ccccgcttga cgaggatgtg tttgtaggcg gcttggatat cggcagtgta tccgcatggt
+ 5461 caaacacttt agcccgaccg gtgctcaagg tcgaaatcct aatatagatt gggataggac
+ 5521 ccgtccatta ctaggcgaca ttcgcagtca cgagcccgca cggggtgcct caacacggtg
+ 5581 acactcaatt cgccggcact gagtacgacg atcgtgattg ccataccgtc atgttttgtg
+ 5641 ttacccctga taagaagcgc agatatggca cgggggcaga gggcggagta gacccatgca
+ 5701 aaactctagc ctctgggcag catgatcgac gtagaacgcc gttgtgactc actagtttca
+ 5761 gttatgatgt tcagccaaga atcctccatt ttgacgtgaa ccttctccct ttacaccttg
+ 5821 aagctgcaat attaagtcga ccctttaagt tgccttgtct tggtctagag cccgcagctc
+ 5881 accgataaaa tgagcagtca attttagcgg cggttgtcca ggttacatgc actttgggct
+ 5941 ggaaccgcgt tacgtttgga gtacttagaa gtgtcgtagg cataggagag ccgaaacttg
+ 6001 atattgggtc tagttagtgc tctaccccgc ttcggatccg taatagtgat gttgcatgag
+ 6061 acgcttgcct caaggcgaca tacggtggcg gttgctggaa atgacgcccc accccgtgat
+ 6121 aatttgggga cgagccgcac gataacttct gccagcgacc gcccctccca cgtccgatgg
+ 6181 tgattccgaa ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac
+ 6241 ttccgctaag ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta
+ 6301 agtcgggttg tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg
+ 6361 tcatacagag gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg
+ 6421 tacgttctcc cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt
+ 6481 tatggaccag aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg
+ 6541 gatatggccg cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg
+ 6601 ggtgcctgtt tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca
+ 6661 cgttccagtg aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag
+ 6721 gtactgtgga gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg
+ 6781 gtgttgcccg tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg
+ 6841 caacatgcga ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg
+ 6901 cgaccgatat gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag
+ 6961 ccaaatgcac agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt
+ 7021 tgttacactt ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt
+ 7081 gtactgcacc tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt
+ 7141 tgcaaccctc tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt
+ 7201 tggcgagggc caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca
+ 7261 cggtgtatag ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc
+ 7321 ggttgttatc actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat
+ 7381 cagctggtca gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa
+ 7441 tgaaccctca ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga
+ 7501 gcagctatcg aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa
+ 7561 aacggaggga gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca
+ 7621 ttagagcagc catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt
+ 7681 tatggacaac aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat
+ 7741 tgatgggtgg cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt
+ 7801 gtggtacgat ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg
+ 7861 ctgaacatgc cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg
+ 7921 ggtacgtaac agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc
+ 7981 gatcgaattc cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/all_construct_records/construct_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/all_construct_records/construct_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,191 @@
+LOCUS construct_2 8000 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_2
+VERSION construct_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1781..1800
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1781..3581
+ /source="Frag_3"
+ /indicates_part=True
+ /note="From Frag_3"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3582..3599
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3582..4781
+ /source="Frag_4b"
+ /indicates_part=True
+ /note="From Frag_4b"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4782..4799
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4782..6190
+ /source="Frag_5"
+ /indicates_part=True
+ /note="From Frag_5"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6191..8000
+ /source="Frag_1"
+ /indicates_part=True
+ /note="From Frag_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6191..6209
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 8021..9800
+ /source="Frag_2"
+ /indicates_part=True
+ /note="From Frag_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cccagatcgc agctcccttg acagtgtcag ttgaatcccc attctaggtt tcctgataaa
+ 61 actaagtacg gggacgcatc agtcgaaagc aatcacagat aatagatatc ttgagcagaa
+ 121 agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa gtgcgggcaa caataggtgt
+ 181 gaggtttcac ggttgcttga tcagtagctg ttcactctct cgcaggccta catagtgagg
+ 241 tggtgagatt gttcaggtct gtctcctgcg cggttgtcga gccccgtcgg gcacgctaac
+ 301 aaggacagga attcgggtcg tcaaataaca atttacgtca tcgcatccct caagggtaag
+ 361 gcgtgatctc catctcggtt cccaattggt cattgtgata gccacactgc agttaccgaa
+ 421 ggcgatttta tactaccctg ataagtgctc gcagcccctc ctccctaata atgtaacgac
+ 481 gagcattaac ccaggagtat ttctcacgtt gctcgtgccc agccaaggcg atcaacgcag
+ 541 accggatagc gttagctagc ccacgggtaa aagcgattgt tgtactcttt catatgaata
+ 601 cagcactcgc gaatgcaagc ctacgtcggc tcgattctct tcctcaccac actggaggcg
+ 661 atgatctagc ccgtctttca ccccgtacct ttatactcgg ccgcgtattt ctccaccggg
+ 721 agctctgcct accaaagcgt cgtacgccca ggaagccgtt tcctttatcc tccctcatgt
+ 781 ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt ctggccaaca ctggacagac
+ 841 gcgcgagacg ctgataaacc cccattttcg tggggttagt aaatcggtgg cttcaaacgg
+ 901 ttcgatcgct cgcacgagca ttagtcagga gtatgattgc gcatcatctc tactccgtac
+ 961 taggttctgt agctcaggat ctccgggggg atcaagcttt tatgtcccgc gggattagaa
+ 1021 gatatccatc catatgttta ctttgatgcg ggtccgagct ctctatgatg ctgctttgac
+ 1081 aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc tctacgacac gttgatgcta
+ 1141 aacaagttgg actactaagc aaatgaagcg gaagagatac tgagcgctct ctctatgact
+ 1201 ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga aatctcaaat aataatgcaa
+ 1261 tgtgttggct aagctcgggc aaactcagga tgtgacctag taccctctgc cccgtgagta
+ 1321 cccataccca atcaagccag cccaattcgc gataggtaca gataagcctt actcgtcccg
+ 1381 atccttgact aaaacactca tcctcgatag tacgtgcctt gtagagtccg acggccatag
+ 1441 gtaaacgacc agttagtgtc gtagggtcct ccactttagc tacgattgca actcccttac
+ 1501 cttcgtgccg gcgcgctcct cttgctacca tcacgcttca aatcgggtgg aagaccaact
+ 1561 gatgaatgag ggtgcagacc ccagtggagc ataatacgat gcgcccacga tactctagag
+ 1621 ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt ggccacatcg gccgcccatc
+ 1681 cttgtgtctt ccgataagta ctccctttca aggactctcc gataccggct tagaacacga
+ 1741 acggacaacg ctttcagcgc tgagaaatga cggctgcttc aaccagaacg atacagcctt
+ 1801 ctttgctaga tagcctctag tgtcagccac caagtccgcc acctaatcct tcgccgaggg
+ 1861 tcaaagcttc tgaccatcca attgttaggc actcttggaa ccttgcaagt acctgatcat
+ 1921 gcagaaaatg gacttgcccg gagcatattc attataagta ccattcacgg caggttatag
+ 1981 tatgcgttga cgcggggtga tacggtaatg caagtaacca tcgggccgcg gtatgcacat
+ 2041 agaagggtgt ttgacttggt ttcttacagt gcaactgcat atgtggaccg ccattccaag
+ 2101 tgaaaggata cgaagggagg tttcggactg ctatccagag catggaaagc cttcaaggtg
+ 2161 gtgcgcactg gaatagtgac tcggggattg tatgtcgagc cgcgtccagt ctttcctata
+ 2221 cttatgcgag caaatagacc gagtggaact tgattgcatc agccgaatca cgatgaaaac
+ 2281 tcagcttaca attcgtaagc acttcaaata tatgcccgga aaatcgccgt ccagtgactt
+ 2341 gtaatagctc cagggtcagt agcgctgccc tggccgaacc aggtgacggt tacgtggacc
+ 2401 tcacagtatc aatgttgcag tgcgccacca gattaagctg gccgtgtcat ggtgaacaac
+ 2461 cgtgataaaa gaacgggagt atgagagtgc cacccaagag tggtactcca ggattcggaa
+ 2521 aggggagggg gcttttcctg cttaacaacc ttcctcggca cggtctaagc gtctcactcg
+ 2581 tcctaaactc taccatcatg cagctaggcg aaagtataac tttagggtct atcaggatga
+ 2641 gctatctgta ccacggtgat gagataagta gggggtgcgc tagggtcgtt cgtgttttca
+ 2701 tcgtctatag tacctatttc tcgtcttcca ttagcgcata cggccatctc gcggcggcta
+ 2761 cgtcagccag cgtcaacccc aagtcactaa tttccgttat tataggtgta gctcataact
+ 2821 tcttctgccg accaagccaa aagctttgcg gcagctgcaa ggccacgtta ggctctcgga
+ 2881 cggcagatat ttattaataa caccactggg ttccagctct taacgcactt cccttcactg
+ 2941 gatcacctgt acgcccataa gctaagcctg aagccacggc ctcaatcgtg gacattactc
+ 3001 ttagcaaatc cacattacca tgtcaccaat ccccgaaccc cgcgccgacc taaggcgggg
+ 3061 tacctcgtgc acggcagcat cgagggaaat atattacaaa agacgcggcg atccaacggt
+ 3121 tgataaaaac agttccgtgg aaggcggacg tgtgcttagc gcatgcttct caccgagtga
+ 3181 cagcaccgat tccatctcgc tagcacgccg atgagcctcg ctgtgggact atggtccagc
+ 3241 ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc ggtaaggtcg atttggtggc
+ 3301 actcgcaaga tacgcgggtt attagtagag cgcagtcagg gcccatcgcc agcatttgca
+ 3361 tgctcgccgt acgctatcct tgtactacgg ttcctcagtg gctataaagg aatgtcacaa
+ 3421 ctccattagc cccttttgtt cagcgcttag tcatggtggg actgactcac cgagactaca
+ 3481 tacggattgt gcccgcagag acatgccttt catgctgggg ttttgtaagc agctccacgg
+ 3541 ggtagtgtca ccatgccttc gacctatgct tatgaaaccc gaggtaatgc ggcaggatcc
+ 3601 cgtggatcct acgcttagcc tgttaccccc cccgttctcc tcggccccca gccagcgcgt
+ 3661 attccgcgca ttcctccgag tgcgtatcgc gcaaaccaca agatacctct caacgactag
+ 3721 cggtgaacca ccaagcttga catacgtgcc ccttcggaaa cgttattagt ggtcctgagt
+ 3781 ggtacgtccc gagtatacgg ggcagcgata gtaacgctac aaatagctag accgacgaca
+ 3841 aacacagcac tgaatatcca acagtggcaa cgagacgctt agaaagggaa actacatacc
+ 3901 agttcaatcc gggatgactt caaaagggta tgtttgtttt gaagcgaagc tttggttgtc
+ 3961 attcagttcc tagagtttac ggcgctgata tggctctagg agtccagtga attcgtcagc
+ 4021 ataagcccca catcgtagga aattgcccgg tcgtcggtct agcaaatgct cggtaaactg
+ 4081 ggagtgtact aacaccatgt cgtggtaacc cggtggaccg gctactagag acatatttat
+ 4141 tcatgctcag ttgaacctgt ttcgaggggg ccgagttaac ataaagtgat tagtcacagc
+ 4201 gcattaagat agaacaggga tatagctcgt tgcatccata aattgcccac cgtagggaga
+ 4261 acgccgttgg aaaatgagag ttaggcgatg agcggttgtc gcccgcacag acaaaggatg
+ 4321 cctttataaa tagtagcggc cttgtctgca ccagacgttt gtgggtcgac gtgctattct
+ 4381 agccaaaagc aaaatgtatc atactacagg caataggccc tatgctgacc aaacttgggg
+ 4441 acccttgcgc cttctctctt acgcataaca tgcataggta cctctactca tcaggcaggg
+ 4501 cggcgtgagg tcactatggc tcaagatgtg tacgactaaa gaaaggttta tgctccttcc
+ 4561 ccaaggacgc atttgggact gctacttgcc cctagcgaat tcactaggat ttttgtagaa
+ 4621 ccatgagcgc cctatccgat agcacagaga caatgctaca agcaactgtg catgcgctcg
+ 4681 atcgccgtgc attaatacgt attatagcgt atcgtgtacg ctaatatctt agtgcaccgc
+ 4741 acgctggttg gatacaattc cgtgaaataa ttcctgctta cacaggggct ttctggcgca
+ 4801 tggctgtgtc tggatgtttg tgataagagg ctccatgaac ccggcgggaa atgaggggaa
+ 4861 accccgggga gcaacgacac taagcctggc agttgttcag ataggacgct tttgtcagtg
+ 4921 ggcggttttg catccactaa ctatcataaa cgacacaacg tcgaatgatc atcggcggtt
+ 4981 tgcatgtaga gacagctcct gcaacaccat accggctcgt ggaattacgc tgtgcgccgg
+ 5041 ccctcattcg attgtgtcca gcgtcggcgc gaatgatgat tgagatgtgc ttcggctcag
+ 5101 agcgtgcaca ggtagttctc cccccttacc tagctgatcc agcaattcca cgctggcccg
+ 5161 cgcgtccttg ggtaacactg gatctgtacc caaatacacc gtcgtgattg ttaactaccg
+ 5221 tatggcggtt acgatcgagt gacactatta ttagaccgct actccaagtc ccaacttttc
+ 5281 atcgccatac agaagagaac gagaaagtcg aagagttata gcgtgtacac ttctgattag
+ 5341 ctaacgaatc gatgcgtaca gcatactcga gcaactttat gggtcgtctg tctccttgta
+ 5401 ccccgcttga cgaggatgtg tttgtaggcg gcttggatat cggcagtgta tccgcatggt
+ 5461 caaacacttt agcccgaccg gtgctcaagg tcgaaatcct aatatagatt gggataggac
+ 5521 ccgtccatta ctaggcgaca ttcgcagtca cgagcccgca cggggtgcct caacacggtg
+ 5581 acactcaatt cgccggcact gagtacgacg atcgtgattg ccataccgtc atgttttgtg
+ 5641 ttacccctga taagaagcgc agatatggca cgggggcaga gggcggagta gacccatgca
+ 5701 aaactctagc ctctgggcag catgatcgac gtagaacgcc gttgtgactc actagtttca
+ 5761 gttatgatgt tcagccaaga atcctccatt ttgacgtgaa ccttctccct ttacaccttg
+ 5821 aagctgcaat attaagtcga ccctttaagt tgccttgtct tggtctagag cccgcagctc
+ 5881 accgataaaa tgagcagtca attttagcgg cggttgtcca ggttacatgc actttgggct
+ 5941 ggaaccgcgt tacgtttgga gtacttagaa gtgtcgtagg cataggagag ccgaaacttg
+ 6001 atattgggtc tagttagtgc tctaccccgc ttcggatccg taatagtgat gttgcatgag
+ 6061 acgcttgcct caaggcgaca tacggtggcg gttgctggaa atgacgcccc accccgtgat
+ 6121 aatttgggga cgagccgcac gataacttct gccagcgacc gcccctccca cgtccgatgg
+ 6181 tgattccgaa ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac
+ 6241 ttccgctaag ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta
+ 6301 agtcgggttg tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg
+ 6361 tcatacagag gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg
+ 6421 tacgttctcc cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt
+ 6481 tatggaccag aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg
+ 6541 gatatggccg cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg
+ 6601 ggtgcctgtt tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca
+ 6661 cgttccagtg aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag
+ 6721 gtactgtgga gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg
+ 6781 gtgttgcccg tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg
+ 6841 caacatgcga ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg
+ 6901 cgaccgatat gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag
+ 6961 ccaaatgcac agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt
+ 7021 tgttacactt ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt
+ 7081 gtactgcacc tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt
+ 7141 tgcaaccctc tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt
+ 7201 tggcgagggc caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca
+ 7261 cggtgtatag ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc
+ 7321 ggttgttatc actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat
+ 7381 cagctggtca gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa
+ 7441 tgaaccctca ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga
+ 7501 gcagctatcg aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa
+ 7561 aacggaggga gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca
+ 7621 ttagagcagc catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt
+ 7681 tatggacaac aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat
+ 7741 tgatgggtgg cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt
+ 7801 gtggtacgat ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg
+ 7861 ctgaacatgc cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg
+ 7921 ggtacgtaac agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc
+ 7981 gatcgaattc cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/all_construct_records/construct_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/all_construct_records/construct_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,191 @@
+LOCUS construct_3 8000 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_3
+VERSION construct_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1781..1800
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1781..3581
+ /source="Frag_3"
+ /indicates_part=True
+ /note="From Frag_3"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3582..3599
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3582..4781
+ /source="Frag_4c"
+ /indicates_part=True
+ /note="From Frag_4c"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4782..4799
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4782..6190
+ /source="Frag_5b"
+ /indicates_part=True
+ /note="From Frag_5b"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6191..8000
+ /source="Frag_1"
+ /indicates_part=True
+ /note="From Frag_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6191..6209
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 8021..9800
+ /source="Frag_2"
+ /indicates_part=True
+ /note="From Frag_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cccagatcgc agctcccttg acagtgtcag ttgaatcccc attctaggtt tcctgataaa
+ 61 actaagtacg gggacgcatc agtcgaaagc aatcacagat aatagatatc ttgagcagaa
+ 121 agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa gtgcgggcaa caataggtgt
+ 181 gaggtttcac ggttgcttga tcagtagctg ttcactctct cgcaggccta catagtgagg
+ 241 tggtgagatt gttcaggtct gtctcctgcg cggttgtcga gccccgtcgg gcacgctaac
+ 301 aaggacagga attcgggtcg tcaaataaca atttacgtca tcgcatccct caagggtaag
+ 361 gcgtgatctc catctcggtt cccaattggt cattgtgata gccacactgc agttaccgaa
+ 421 ggcgatttta tactaccctg ataagtgctc gcagcccctc ctccctaata atgtaacgac
+ 481 gagcattaac ccaggagtat ttctcacgtt gctcgtgccc agccaaggcg atcaacgcag
+ 541 accggatagc gttagctagc ccacgggtaa aagcgattgt tgtactcttt catatgaata
+ 601 cagcactcgc gaatgcaagc ctacgtcggc tcgattctct tcctcaccac actggaggcg
+ 661 atgatctagc ccgtctttca ccccgtacct ttatactcgg ccgcgtattt ctccaccggg
+ 721 agctctgcct accaaagcgt cgtacgccca ggaagccgtt tcctttatcc tccctcatgt
+ 781 ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt ctggccaaca ctggacagac
+ 841 gcgcgagacg ctgataaacc cccattttcg tggggttagt aaatcggtgg cttcaaacgg
+ 901 ttcgatcgct cgcacgagca ttagtcagga gtatgattgc gcatcatctc tactccgtac
+ 961 taggttctgt agctcaggat ctccgggggg atcaagcttt tatgtcccgc gggattagaa
+ 1021 gatatccatc catatgttta ctttgatgcg ggtccgagct ctctatgatg ctgctttgac
+ 1081 aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc tctacgacac gttgatgcta
+ 1141 aacaagttgg actactaagc aaatgaagcg gaagagatac tgagcgctct ctctatgact
+ 1201 ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga aatctcaaat aataatgcaa
+ 1261 tgtgttggct aagctcgggc aaactcagga tgtgacctag taccctctgc cccgtgagta
+ 1321 cccataccca atcaagccag cccaattcgc gataggtaca gataagcctt actcgtcccg
+ 1381 atccttgact aaaacactca tcctcgatag tacgtgcctt gtagagtccg acggccatag
+ 1441 gtaaacgacc agttagtgtc gtagggtcct ccactttagc tacgattgca actcccttac
+ 1501 cttcgtgccg gcgcgctcct cttgctacca tcacgcttca aatcgggtgg aagaccaact
+ 1561 gatgaatgag ggtgcagacc ccagtggagc ataatacgat gcgcccacga tactctagag
+ 1621 ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt ggccacatcg gccgcccatc
+ 1681 cttgtgtctt ccgataagta ctccctttca aggactctcc gataccggct tagaacacga
+ 1741 acggacaacg ctttcagcgc tgagaaatga cggctgcttc aaccagaacg atacagcctt
+ 1801 ctttgctaga tagcctctag tgtcagccac caagtccgcc acctaatcct tcgccgaggg
+ 1861 tcaaagcttc tgaccatcca attgttaggc actcttggaa ccttgcaagt acctgatcat
+ 1921 gcagaaaatg gacttgcccg gagcatattc attataagta ccattcacgg caggttatag
+ 1981 tatgcgttga cgcggggtga tacggtaatg caagtaacca tcgggccgcg gtatgcacat
+ 2041 agaagggtgt ttgacttggt ttcttacagt gcaactgcat atgtggaccg ccattccaag
+ 2101 tgaaaggata cgaagggagg tttcggactg ctatccagag catggaaagc cttcaaggtg
+ 2161 gtgcgcactg gaatagtgac tcggggattg tatgtcgagc cgcgtccagt ctttcctata
+ 2221 cttatgcgag caaatagacc gagtggaact tgattgcatc agccgaatca cgatgaaaac
+ 2281 tcagcttaca attcgtaagc acttcaaata tatgcccgga aaatcgccgt ccagtgactt
+ 2341 gtaatagctc cagggtcagt agcgctgccc tggccgaacc aggtgacggt tacgtggacc
+ 2401 tcacagtatc aatgttgcag tgcgccacca gattaagctg gccgtgtcat ggtgaacaac
+ 2461 cgtgataaaa gaacgggagt atgagagtgc cacccaagag tggtactcca ggattcggaa
+ 2521 aggggagggg gcttttcctg cttaacaacc ttcctcggca cggtctaagc gtctcactcg
+ 2581 tcctaaactc taccatcatg cagctaggcg aaagtataac tttagggtct atcaggatga
+ 2641 gctatctgta ccacggtgat gagataagta gggggtgcgc tagggtcgtt cgtgttttca
+ 2701 tcgtctatag tacctatttc tcgtcttcca ttagcgcata cggccatctc gcggcggcta
+ 2761 cgtcagccag cgtcaacccc aagtcactaa tttccgttat tataggtgta gctcataact
+ 2821 tcttctgccg accaagccaa aagctttgcg gcagctgcaa ggccacgtta ggctctcgga
+ 2881 cggcagatat ttattaataa caccactggg ttccagctct taacgcactt cccttcactg
+ 2941 gatcacctgt acgcccataa gctaagcctg aagccacggc ctcaatcgtg gacattactc
+ 3001 ttagcaaatc cacattacca tgtcaccaat ccccgaaccc cgcgccgacc taaggcgggg
+ 3061 tacctcgtgc acggcagcat cgagggaaat atattacaaa agacgcggcg atccaacggt
+ 3121 tgataaaaac agttccgtgg aaggcggacg tgtgcttagc gcatgcttct caccgagtga
+ 3181 cagcaccgat tccatctcgc tagcacgccg atgagcctcg ctgtgggact atggtccagc
+ 3241 ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc ggtaaggtcg atttggtggc
+ 3301 actcgcaaga tacgcgggtt attagtagag cgcagtcagg gcccatcgcc agcatttgca
+ 3361 tgctcgccgt acgctatcct tgtactacgg ttcctcagtg gctataaagg aatgtcacaa
+ 3421 ctccattagc cccttttgtt cagcgcttag tcatggtggg actgactcac cgagactaca
+ 3481 tacggattgt gcccgcagag acatgccttt catgctgggg ttttgtaagc agctccacgg
+ 3541 ggtagtgtca ccatgccttc gacctatgct tatgaaaccc gaggtaatgc ggcaggatcc
+ 3601 cgtggatcct acgcttagcc tgttaggggg ggggttctcc tcggccccca gccagcgcgt
+ 3661 attccgcgca ttcctccgag tgcgtatcgc gcaaaccaca agatacctct caacgactag
+ 3721 cggtgaacca ccaagcttga catacgtgcc ccttcggaaa cgttattagt ggtcctgagt
+ 3781 ggtacgtccc gagtatacgg ggcagcgata gtaacgctac aaatagctag accgacgaca
+ 3841 aacacagcac tgaatatcca acagtggcaa cgagacgctt agaaagggaa actacatacc
+ 3901 agttcaatcc gggatgactt caaaagggta tgtttgtttt gaagcgaagc tttggttgtc
+ 3961 attcagttcc tagagtttac ggcgctgata tggctctagg agtccagtga attcgtcagc
+ 4021 ataagcccca catcgtagga aattgcccgg tcgtcggtct agcaaatgct cggtaaactg
+ 4081 ggagtgtact aacaccatgt cgtggtaacc cggtggaccg gctactagag acatatttat
+ 4141 tcatgctcag ttgaacctgt ttcgaggggg ccgagttaac ataaagtgat tagtcacagc
+ 4201 gcattaagat agaacaggga tatagctcgt tgcatccata aattgcccac cgtagggaga
+ 4261 acgccgttgg aaaatgagag ttaggcgatg agcggttgtc gcccgcacag acaaaggatg
+ 4321 cctttataaa tagtagcggc cttgtctgca ccagacgttt gtgggtcgac gtgctattct
+ 4381 agccaaaagc aaaatgtatc atactacagg caataggccc tatgctgacc aaacttgggg
+ 4441 acccttgcgc cttctctctt acgcataaca tgcataggta cctctactca tcaggcaggg
+ 4501 cggcgtgagg tcactatggc tcaagatgtg tacgactaaa gaaaggttta tgctccttcc
+ 4561 ccaaggacgc atttgggact gctacttgcc cctagcgaat tcactaggat ttttgtagaa
+ 4621 ccatgagcgc cctatccgat agcacagaga caatgctaca agcaactgtg catgcgctcg
+ 4681 atcgccgtgc attaatacgt attatagcgt atcgtgtacg ctaatatctt agtgcaccgc
+ 4741 acgctggttg gatacaattc cgtgaaataa ttcctgctta cacaggggct ttctggcgca
+ 4801 tggctgtgtc tggaaaaaaa aaaaaaaaaa aaacatgaac ccggcgggaa atgaggggaa
+ 4861 accccgggga gcaacgacac taagcctggc agttgttcag ataggacgct tttgtcagtg
+ 4921 ggcggttttg catccactaa ctatcataaa cgacacaacg tcgaatgatc atcggcggtt
+ 4981 tgcatgtaga gacagctcct gcaacaccat accggctcgt ggaattacgc tgtgcgccgg
+ 5041 ccctcattcg attgtgtcca gcgtcggcgc gaatgatgat tgagatgtgc ttcggctcag
+ 5101 agcgtgcaca ggtagttctc cccccttacc tagctgatcc agcaattcca cgctggcccg
+ 5161 cgcgtccttg ggtaacactg gatctgtacc caaatacacc gtcgtgattg ttaactaccg
+ 5221 tatggcggtt acgatcgagt gacactatta ttagaccgct actccaagtc ccaacttttc
+ 5281 atcgccatac agaagagaac gagaaagtcg aagagttata gcgtgtacac ttctgattag
+ 5341 ctaacgaatc gatgcgtaca gcatactcga gcaactttat gggtcgtctg tctccttgta
+ 5401 ccccgcttga cgaggatgtg tttgtaggcg gcttggatat cggcagtgta tccgcatggt
+ 5461 caaacacttt agcccgaccg gtgctcaagg tcgaaatcct aatatagatt gggataggac
+ 5521 ccgtccatta ctaggcgaca ttcgcagtca cgagcccgca cggggtgcct caacacggtg
+ 5581 acactcaatt cgccggcact gagtacgacg atcgtgattg ccataccgtc atgttttgtg
+ 5641 ttacccctga taagaagcgc agatatggca cgggggcaga gggcggagta gacccatgca
+ 5701 aaactctagc ctctgggcag catgatcgac gtagaacgcc gttgtgactc actagtttca
+ 5761 gttatgatgt tcagccaaga atcctccatt ttgacgtgaa ccttctccct ttacaccttg
+ 5821 aagctgcaat attaagtcga ccctttaagt tgccttgtct tggtctagag cccgcagctc
+ 5881 accgataaaa tgagcagtca attttagcgg cggttgtcca ggttacatgc actttgggct
+ 5941 ggaaccgcgt tacgtttgga gtacttagaa gtgtcgtagg cataggagag ccgaaacttg
+ 6001 atattgggtc tagttagtgc tctaccccgc ttcggatccg taatagtgat gttgcatgag
+ 6061 acgcttgcct caaggcgaca tacggtggcg gttgctggaa atgacgcccc accccgtgat
+ 6121 aatttgggga cgagccgcac gataacttct gccagcgacc gcccctccca cgtccgatgg
+ 6181 tgattccgaa ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac
+ 6241 ttccgctaag ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta
+ 6301 agtcgggttg tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg
+ 6361 tcatacagag gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg
+ 6421 tacgttctcc cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt
+ 6481 tatggaccag aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg
+ 6541 gatatggccg cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg
+ 6601 ggtgcctgtt tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca
+ 6661 cgttccagtg aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag
+ 6721 gtactgtgga gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg
+ 6781 gtgttgcccg tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg
+ 6841 caacatgcga ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg
+ 6901 cgaccgatat gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag
+ 6961 ccaaatgcac agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt
+ 7021 tgttacactt ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt
+ 7081 gtactgcacc tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt
+ 7141 tgcaaccctc tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt
+ 7201 tggcgagggc caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca
+ 7261 cggtgtatag ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc
+ 7321 ggttgttatc actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat
+ 7381 cagctggtca gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa
+ 7441 tgaaccctca ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga
+ 7501 gcagctatcg aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa
+ 7561 aacggaggga gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca
+ 7621 ttagagcagc catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt
+ 7681 tatggacaac aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat
+ 7741 tgatgggtgg cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt
+ 7801 gtggtacgat ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg
+ 7861 ctgaacatgc cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg
+ 7921 ggtacgtaac agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc
+ 7981 gatcgaattc cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/construct_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/construct_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,191 @@
+LOCUS construct_1 8000 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_1
+VERSION construct_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1781..1800
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1781..3581
+ /source="Frag_3"
+ /indicates_part=True
+ /note="From Frag_3"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3582..3599
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3582..4781
+ /source="Frag_4"
+ /indicates_part=True
+ /note="From Frag_4"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4782..4799
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4782..6190
+ /source="Frag_5"
+ /indicates_part=True
+ /note="From Frag_5"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6191..8000
+ /source="Frag_1"
+ /indicates_part=True
+ /note="From Frag_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6191..6209
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 8021..9800
+ /source="Frag_2"
+ /indicates_part=True
+ /note="From Frag_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cccagatcgc agctcccttg acagtgtcag ttgaatcccc attctaggtt tcctgataaa
+ 61 actaagtacg gggacgcatc agtcgaaagc aatcacagat aatagatatc ttgagcagaa
+ 121 agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa gtgcgggcaa caataggtgt
+ 181 gaggtttcac ggttgcttga tcagtagctg ttcactctct cgcaggccta catagtgagg
+ 241 tggtgagatt gttcaggtct gtctcctgcg cggttgtcga gccccgtcgg gcacgctaac
+ 301 aaggacagga attcgggtcg tcaaataaca atttacgtca tcgcatccct caagggtaag
+ 361 gcgtgatctc catctcggtt cccaattggt cattgtgata gccacactgc agttaccgaa
+ 421 ggcgatttta tactaccctg ataagtgctc gcagcccctc ctccctaata atgtaacgac
+ 481 gagcattaac ccaggagtat ttctcacgtt gctcgtgccc agccaaggcg atcaacgcag
+ 541 accggatagc gttagctagc ccacgggtaa aagcgattgt tgtactcttt catatgaata
+ 601 cagcactcgc gaatgcaagc ctacgtcggc tcgattctct tcctcaccac actggaggcg
+ 661 atgatctagc ccgtctttca ccccgtacct ttatactcgg ccgcgtattt ctccaccggg
+ 721 agctctgcct accaaagcgt cgtacgccca ggaagccgtt tcctttatcc tccctcatgt
+ 781 ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt ctggccaaca ctggacagac
+ 841 gcgcgagacg ctgataaacc cccattttcg tggggttagt aaatcggtgg cttcaaacgg
+ 901 ttcgatcgct cgcacgagca ttagtcagga gtatgattgc gcatcatctc tactccgtac
+ 961 taggttctgt agctcaggat ctccgggggg atcaagcttt tatgtcccgc gggattagaa
+ 1021 gatatccatc catatgttta ctttgatgcg ggtccgagct ctctatgatg ctgctttgac
+ 1081 aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc tctacgacac gttgatgcta
+ 1141 aacaagttgg actactaagc aaatgaagcg gaagagatac tgagcgctct ctctatgact
+ 1201 ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga aatctcaaat aataatgcaa
+ 1261 tgtgttggct aagctcgggc aaactcagga tgtgacctag taccctctgc cccgtgagta
+ 1321 cccataccca atcaagccag cccaattcgc gataggtaca gataagcctt actcgtcccg
+ 1381 atccttgact aaaacactca tcctcgatag tacgtgcctt gtagagtccg acggccatag
+ 1441 gtaaacgacc agttagtgtc gtagggtcct ccactttagc tacgattgca actcccttac
+ 1501 cttcgtgccg gcgcgctcct cttgctacca tcacgcttca aatcgggtgg aagaccaact
+ 1561 gatgaatgag ggtgcagacc ccagtggagc ataatacgat gcgcccacga tactctagag
+ 1621 ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt ggccacatcg gccgcccatc
+ 1681 cttgtgtctt ccgataagta ctccctttca aggactctcc gataccggct tagaacacga
+ 1741 acggacaacg ctttcagcgc tgagaaatga cggctgcttc aaccagaacg atacagcctt
+ 1801 ctttgctaga tagcctctag tgtcagccac caagtccgcc acctaatcct tcgccgaggg
+ 1861 tcaaagcttc tgaccatcca attgttaggc actcttggaa ccttgcaagt acctgatcat
+ 1921 gcagaaaatg gacttgcccg gagcatattc attataagta ccattcacgg caggttatag
+ 1981 tatgcgttga cgcggggtga tacggtaatg caagtaacca tcgggccgcg gtatgcacat
+ 2041 agaagggtgt ttgacttggt ttcttacagt gcaactgcat atgtggaccg ccattccaag
+ 2101 tgaaaggata cgaagggagg tttcggactg ctatccagag catggaaagc cttcaaggtg
+ 2161 gtgcgcactg gaatagtgac tcggggattg tatgtcgagc cgcgtccagt ctttcctata
+ 2221 cttatgcgag caaatagacc gagtggaact tgattgcatc agccgaatca cgatgaaaac
+ 2281 tcagcttaca attcgtaagc acttcaaata tatgcccgga aaatcgccgt ccagtgactt
+ 2341 gtaatagctc cagggtcagt agcgctgccc tggccgaacc aggtgacggt tacgtggacc
+ 2401 tcacagtatc aatgttgcag tgcgccacca gattaagctg gccgtgtcat ggtgaacaac
+ 2461 cgtgataaaa gaacgggagt atgagagtgc cacccaagag tggtactcca ggattcggaa
+ 2521 aggggagggg gcttttcctg cttaacaacc ttcctcggca cggtctaagc gtctcactcg
+ 2581 tcctaaactc taccatcatg cagctaggcg aaagtataac tttagggtct atcaggatga
+ 2641 gctatctgta ccacggtgat gagataagta gggggtgcgc tagggtcgtt cgtgttttca
+ 2701 tcgtctatag tacctatttc tcgtcttcca ttagcgcata cggccatctc gcggcggcta
+ 2761 cgtcagccag cgtcaacccc aagtcactaa tttccgttat tataggtgta gctcataact
+ 2821 tcttctgccg accaagccaa aagctttgcg gcagctgcaa ggccacgtta ggctctcgga
+ 2881 cggcagatat ttattaataa caccactggg ttccagctct taacgcactt cccttcactg
+ 2941 gatcacctgt acgcccataa gctaagcctg aagccacggc ctcaatcgtg gacattactc
+ 3001 ttagcaaatc cacattacca tgtcaccaat ccccgaaccc cgcgccgacc taaggcgggg
+ 3061 tacctcgtgc acggcagcat cgagggaaat atattacaaa agacgcggcg atccaacggt
+ 3121 tgataaaaac agttccgtgg aaggcggacg tgtgcttagc gcatgcttct caccgagtga
+ 3181 cagcaccgat tccatctcgc tagcacgccg atgagcctcg ctgtgggact atggtccagc
+ 3241 ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc ggtaaggtcg atttggtggc
+ 3301 actcgcaaga tacgcgggtt attagtagag cgcagtcagg gcccatcgcc agcatttgca
+ 3361 tgctcgccgt acgctatcct tgtactacgg ttcctcagtg gctataaagg aatgtcacaa
+ 3421 ctccattagc cccttttgtt cagcgcttag tcatggtggg actgactcac cgagactaca
+ 3481 tacggattgt gcccgcagag acatgccttt catgctgggg ttttgtaagc agctccacgg
+ 3541 ggtagtgtca ccatgccttc gacctatgct tatgaaaccc gaggtaatgc ggcaggatcc
+ 3601 cgtggatcct acgcttagcc tgtttaagcc atcgttctcc tcggccccca gccagcgcgt
+ 3661 attccgcgca ttcctccgag tgcgtatcgc gcaaaccaca agatacctct caacgactag
+ 3721 cggtgaacca ccaagcttga catacgtgcc ccttcggaaa cgttattagt ggtcctgagt
+ 3781 ggtacgtccc gagtatacgg ggcagcgata gtaacgctac aaatagctag gcgaggttgc
+ 3841 gatacctgaa tgaatatcca acagtggcaa cgagacgctt agaaagggaa actacatacc
+ 3901 agttcaatcc gggatgactt caaaagggta tgtttgtttt gaagcgaagc tttggttgtc
+ 3961 attcagttcc tagagtttac ggcgctgata tggctctagg agtccagtga attcgtcagc
+ 4021 ataagcccca catcgtagga aattgcccgg tcgtcggtct agcaaatgct cggtaaactg
+ 4081 ggagtgtact aacaccatgt cgtggtaacc cggtggaccg gctactagag acatatttat
+ 4141 tcatgctcag ttgaacctgt ttcgaggggg ccgagttaac ataaagtgat tagtcacagc
+ 4201 gcattaagat agaacaggga tatagctcgt tgcatccata aattgcccac cgtagggaga
+ 4261 acgccgttgg aaaatgagag ttaggcgatg agcggttgtc gcccgcacag acaaaggatg
+ 4321 cctttataaa tagtagcggc cttgtctgca ccagacgttt gtgggtcgac gtgctattct
+ 4381 agccaaaagc aaaatgtatc atactacagg caataggccc tatgctgacc aaacttgggg
+ 4441 acccttgcgc cttctctctt acgcataaca tgcataggta cctctactca tcaggcaggg
+ 4501 cggcgtgagg tcactatggc tcaagatgtg tacgactaaa gaaaggttta tgctccttcc
+ 4561 ccaaggacgc atttgggact gctacttgcc cctagcgaat tcactaggat ttttgtagaa
+ 4621 ccatgagcgc cctatccgat agcacagaga caatgctaca agcaactgtg catgcgctcg
+ 4681 atcgccgtgc attaatacgt attatagcgt atcgtgtacg ctaatatctt agtgcaccgc
+ 4741 acgctggttg gatacaattc cgtgaaataa ttcctgctta cacaggggct ttctggcgca
+ 4801 tggctgtgtc tggatgtttg tgataagagg ctccatgaac ccggcgggaa atgaggggaa
+ 4861 accccgggga gcaacgacac taagcctggc agttgttcag ataggacgct tttgtcagtg
+ 4921 ggcggttttg catccactaa ctatcataaa cgacacaacg tcgaatgatc atcggcggtt
+ 4981 tgcatgtaga gacagctcct gcaacaccat accggctcgt ggaattacgc tgtgcgccgg
+ 5041 ccctcattcg attgtgtcca gcgtcggcgc gaatgatgat tgagatgtgc ttcggctcag
+ 5101 agcgtgcaca ggtagttctc cccccttacc tagctgatcc agcaattcca cgctggcccg
+ 5161 cgcgtccttg ggtaacactg gatctgtacc caaatacacc gtcgtgattg ttaactaccg
+ 5221 tatggcggtt acgatcgagt gacactatta ttagaccgct actccaagtc ccaacttttc
+ 5281 atcgccatac agaagagaac gagaaagtcg aagagttata gcgtgtacac ttctgattag
+ 5341 ctaacgaatc gatgcgtaca gcatactcga gcaactttat gggtcgtctg tctccttgta
+ 5401 ccccgcttga cgaggatgtg tttgtaggcg gcttggatat cggcagtgta tccgcatggt
+ 5461 caaacacttt agcccgaccg gtgctcaagg tcgaaatcct aatatagatt gggataggac
+ 5521 ccgtccatta ctaggcgaca ttcgcagtca cgagcccgca cggggtgcct caacacggtg
+ 5581 acactcaatt cgccggcact gagtacgacg atcgtgattg ccataccgtc atgttttgtg
+ 5641 ttacccctga taagaagcgc agatatggca cgggggcaga gggcggagta gacccatgca
+ 5701 aaactctagc ctctgggcag catgatcgac gtagaacgcc gttgtgactc actagtttca
+ 5761 gttatgatgt tcagccaaga atcctccatt ttgacgtgaa ccttctccct ttacaccttg
+ 5821 aagctgcaat attaagtcga ccctttaagt tgccttgtct tggtctagag cccgcagctc
+ 5881 accgataaaa tgagcagtca attttagcgg cggttgtcca ggttacatgc actttgggct
+ 5941 ggaaccgcgt tacgtttgga gtacttagaa gtgtcgtagg cataggagag ccgaaacttg
+ 6001 atattgggtc tagttagtgc tctaccccgc ttcggatccg taatagtgat gttgcatgag
+ 6061 acgcttgcct caaggcgaca tacggtggcg gttgctggaa atgacgcccc accccgtgat
+ 6121 aatttgggga cgagccgcac gataacttct gccagcgacc gcccctccca cgtccgatgg
+ 6181 tgattccgaa ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac
+ 6241 ttccgctaag ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta
+ 6301 agtcgggttg tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg
+ 6361 tcatacagag gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg
+ 6421 tacgttctcc cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt
+ 6481 tatggaccag aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg
+ 6541 gatatggccg cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg
+ 6601 ggtgcctgtt tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca
+ 6661 cgttccagtg aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag
+ 6721 gtactgtgga gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg
+ 6781 gtgttgcccg tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg
+ 6841 caacatgcga ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg
+ 6901 cgaccgatat gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag
+ 6961 ccaaatgcac agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt
+ 7021 tgttacactt ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt
+ 7081 gtactgcacc tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt
+ 7141 tgcaaccctc tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt
+ 7201 tggcgagggc caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca
+ 7261 cggtgtatag ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc
+ 7321 ggttgttatc actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat
+ 7381 cagctggtca gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa
+ 7441 tgaaccctca ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga
+ 7501 gcagctatcg aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa
+ 7561 aacggaggga gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca
+ 7621 ttagagcagc catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt
+ 7681 tatggacaac aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat
+ 7741 tgatgggtgg cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt
+ 7801 gtggtacgat ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg
+ 7861 ctgaacatgc cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg
+ 7921 ggtacgtaac agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc
+ 7981 gatcgaattc cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/construct_1.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_1/construct_1.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/construct_1_connections_graph.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_1/construct_1_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/construct_1_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/construct_1_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,homology_condition,used_in,parts
+construct_1,construct_1,1,8000,5,,"15-80bp, 0.0-+C Tm",,Frag_2 & Frag_3 & Frag_4 & Frag_5 & Frag_1
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_1 1810 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_1.
+ACCESSION Frag_1
+VERSION Frag_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac ttccgctaag
+ 61 ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta agtcgggttg
+ 121 tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg tcatacagag
+ 181 gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg tacgttctcc
+ 241 cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt tatggaccag
+ 301 aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg gatatggccg
+ 361 cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg ggtgcctgtt
+ 421 tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca cgttccagtg
+ 481 aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag gtactgtgga
+ 541 gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg gtgttgcccg
+ 601 tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg caacatgcga
+ 661 ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg cgaccgatat
+ 721 gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag ccaaatgcac
+ 781 agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt tgttacactt
+ 841 ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt gtactgcacc
+ 901 tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt tgcaaccctc
+ 961 tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt tggcgagggc
+ 1021 caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca cggtgtatag
+ 1081 ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc ggttgttatc
+ 1141 actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat cagctggtca
+ 1201 gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa tgaaccctca
+ 1261 ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga gcagctatcg
+ 1321 aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa aacggaggga
+ 1381 gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca ttagagcagc
+ 1441 catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt tatggacaac
+ 1501 aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat tgatgggtgg
+ 1561 cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt gtggtacgat
+ 1621 ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg ctgaacatgc
+ 1681 cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg ggtacgtaac
+ 1741 agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc gatcgaattc
+ 1801 cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_2 1820 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_2.
+ACCESSION Frag_2
+VERSION Frag_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 gatcgaattc cgttttacgc cccagatcgc agctcccttg acagtgtcag ttgaatcccc
+ 61 attctaggtt tcctgataaa actaagtacg gggacgcatc agtcgaaagc aatcacagat
+ 121 aatagatatc ttgagcagaa agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa
+ 181 gtgcgggcaa caataggtgt gaggtttcac ggttgcttga tcagtagctg ttcactctct
+ 241 cgcaggccta catagtgagg tggtgagatt gttcaggtct gtctcctgcg cggttgtcga
+ 301 gccccgtcgg gcacgctaac aaggacagga attcgggtcg tcaaataaca atttacgtca
+ 361 tcgcatccct caagggtaag gcgtgatctc catctcggtt cccaattggt cattgtgata
+ 421 gccacactgc agttaccgaa ggcgatttta tactaccctg ataagtgctc gcagcccctc
+ 481 ctccctaata atgtaacgac gagcattaac ccaggagtat ttctcacgtt gctcgtgccc
+ 541 agccaaggcg atcaacgcag accggatagc gttagctagc ccacgggtaa aagcgattgt
+ 601 tgtactcttt catatgaata cagcactcgc gaatgcaagc ctacgtcggc tcgattctct
+ 661 tcctcaccac actggaggcg atgatctagc ccgtctttca ccccgtacct ttatactcgg
+ 721 ccgcgtattt ctccaccggg agctctgcct accaaagcgt cgtacgccca ggaagccgtt
+ 781 tcctttatcc tccctcatgt ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt
+ 841 ctggccaaca ctggacagac gcgcgagacg ctgataaacc cccattttcg tggggttagt
+ 901 aaatcggtgg cttcaaacgg ttcgatcgct cgcacgagca ttagtcagga gtatgattgc
+ 961 gcatcatctc tactccgtac taggttctgt agctcaggat ctccgggggg atcaagcttt
+ 1021 tatgtcccgc gggattagaa gatatccatc catatgttta ctttgatgcg ggtccgagct
+ 1081 ctctatgatg ctgctttgac aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc
+ 1141 tctacgacac gttgatgcta aacaagttgg actactaagc aaatgaagcg gaagagatac
+ 1201 tgagcgctct ctctatgact ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga
+ 1261 aatctcaaat aataatgcaa tgtgttggct aagctcgggc aaactcagga tgtgacctag
+ 1321 taccctctgc cccgtgagta cccataccca atcaagccag cccaattcgc gataggtaca
+ 1381 gataagcctt actcgtcccg atccttgact aaaacactca tcctcgatag tacgtgcctt
+ 1441 gtagagtccg acggccatag gtaaacgacc agttagtgtc gtagggtcct ccactttagc
+ 1501 tacgattgca actcccttac cttcgtgccg gcgcgctcct cttgctacca tcacgcttca
+ 1561 aatcgggtgg aagaccaact gatgaatgag ggtgcagacc ccagtggagc ataatacgat
+ 1621 gcgcccacga tactctagag ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt
+ 1681 ggccacatcg gccgcccatc cttgtgtctt ccgataagta ctccctttca aggactctcc
+ 1741 gataccggct tagaacacga acggacaacg ctttcagcgc tgagaaatga cggctgcttc
+ 1801 aaccagaacg atacagcctt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_3 1819 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_3.
+ACCESSION Frag_3
+VERSION Frag_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aaccagaacg atacagcctt ctttgctaga tagcctctag tgtcagccac caagtccgcc
+ 61 acctaatcct tcgccgaggg tcaaagcttc tgaccatcca attgttaggc actcttggaa
+ 121 ccttgcaagt acctgatcat gcagaaaatg gacttgcccg gagcatattc attataagta
+ 181 ccattcacgg caggttatag tatgcgttga cgcggggtga tacggtaatg caagtaacca
+ 241 tcgggccgcg gtatgcacat agaagggtgt ttgacttggt ttcttacagt gcaactgcat
+ 301 atgtggaccg ccattccaag tgaaaggata cgaagggagg tttcggactg ctatccagag
+ 361 catggaaagc cttcaaggtg gtgcgcactg gaatagtgac tcggggattg tatgtcgagc
+ 421 cgcgtccagt ctttcctata cttatgcgag caaatagacc gagtggaact tgattgcatc
+ 481 agccgaatca cgatgaaaac tcagcttaca attcgtaagc acttcaaata tatgcccgga
+ 541 aaatcgccgt ccagtgactt gtaatagctc cagggtcagt agcgctgccc tggccgaacc
+ 601 aggtgacggt tacgtggacc tcacagtatc aatgttgcag tgcgccacca gattaagctg
+ 661 gccgtgtcat ggtgaacaac cgtgataaaa gaacgggagt atgagagtgc cacccaagag
+ 721 tggtactcca ggattcggaa aggggagggg gcttttcctg cttaacaacc ttcctcggca
+ 781 cggtctaagc gtctcactcg tcctaaactc taccatcatg cagctaggcg aaagtataac
+ 841 tttagggtct atcaggatga gctatctgta ccacggtgat gagataagta gggggtgcgc
+ 901 tagggtcgtt cgtgttttca tcgtctatag tacctatttc tcgtcttcca ttagcgcata
+ 961 cggccatctc gcggcggcta cgtcagccag cgtcaacccc aagtcactaa tttccgttat
+ 1021 tataggtgta gctcataact tcttctgccg accaagccaa aagctttgcg gcagctgcaa
+ 1081 ggccacgtta ggctctcgga cggcagatat ttattaataa caccactggg ttccagctct
+ 1141 taacgcactt cccttcactg gatcacctgt acgcccataa gctaagcctg aagccacggc
+ 1201 ctcaatcgtg gacattactc ttagcaaatc cacattacca tgtcaccaat ccccgaaccc
+ 1261 cgcgccgacc taaggcgggg tacctcgtgc acggcagcat cgagggaaat atattacaaa
+ 1321 agacgcggcg atccaacggt tgataaaaac agttccgtgg aaggcggacg tgtgcttagc
+ 1381 gcatgcttct caccgagtga cagcaccgat tccatctcgc tagcacgccg atgagcctcg
+ 1441 ctgtgggact atggtccagc ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc
+ 1501 ggtaaggtcg atttggtggc actcgcaaga tacgcgggtt attagtagag cgcagtcagg
+ 1561 gcccatcgcc agcatttgca tgctcgccgt acgctatcct tgtactacgg ttcctcagtg
+ 1621 gctataaagg aatgtcacaa ctccattagc cccttttgtt cagcgcttag tcatggtggg
+ 1681 actgactcac cgagactaca tacggattgt gcccgcagag acatgccttt catgctgggg
+ 1741 ttttgtaagc agctccacgg ggtagtgtca ccatgccttc gacctatgct tatgaaaccc
+ 1801 gaggtaatgc ggcaggatc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_4.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_4.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4.
+ACCESSION Frag_4
+VERSION Frag_4
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gtttaagcca tcgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctagg cgaggttgcg atacctgaat gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_5.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_1/provided_parts_records/Frag_5.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,35 @@
+LOCUS Frag_5 1428 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_5.
+ACCESSION Frag_5
+VERSION Frag_5
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 acaggggctt tctggcgcat ggctgtgtct ggatgtttgt gataagaggc tccatgaacc
+ 61 cggcgggaaa tgaggggaaa ccccggggag caacgacact aagcctggca gttgttcaga
+ 121 taggacgctt ttgtcagtgg gcggttttgc atccactaac tatcataaac gacacaacgt
+ 181 cgaatgatca tcggcggttt gcatgtagag acagctcctg caacaccata ccggctcgtg
+ 241 gaattacgct gtgcgccggc cctcattcga ttgtgtccag cgtcggcgcg aatgatgatt
+ 301 gagatgtgct tcggctcaga gcgtgcacag gtagttctcc ccccttacct agctgatcca
+ 361 gcaattccac gctggcccgc gcgtccttgg gtaacactgg atctgtaccc aaatacaccg
+ 421 tcgtgattgt taactaccgt atggcggtta cgatcgagtg acactattat tagaccgcta
+ 481 ctccaagtcc caacttttca tcgccataca gaagagaacg agaaagtcga agagttatag
+ 541 cgtgtacact tctgattagc taacgaatcg atgcgtacag catactcgag caactttatg
+ 601 ggtcgtctgt ctccttgtac cccgcttgac gaggatgtgt ttgtaggcgg cttggatatc
+ 661 ggcagtgtat ccgcatggtc aaacacttta gcccgaccgg tgctcaaggt cgaaatccta
+ 721 atatagattg ggataggacc cgtccattac taggcgacat tcgcagtcac gagcccgcac
+ 781 ggggtgcctc aacacggtga cactcaattc gccggcactg agtacgacga tcgtgattgc
+ 841 cataccgtca tgttttgtgt tacccctgat aagaagcgca gatatggcac gggggcagag
+ 901 ggcggagtag acccatgcaa aactctagcc tctgggcagc atgatcgacg tagaacgccg
+ 961 ttgtgactca ctagtttcag ttatgatgtt cagccaagaa tcctccattt tgacgtgaac
+ 1021 cttctccctt tacaccttga agctgcaata ttaagtcgac cctttaagtt gccttgtctt
+ 1081 ggtctagagc ccgcagctca ccgataaaat gagcagtcaa ttttagcggc ggttgtccag
+ 1141 gttacatgca ctttgggctg gaaccgcgtt acgtttggag tacttagaag tgtcgtaggc
+ 1201 ataggagagc cgaaacttga tattgggtct agttagtgct ctaccccgct tcggatccgt
+ 1261 aatagtgatg ttgcatgaga cgcttgcctc aaggcgacat acggtggcgg ttgctggaaa
+ 1321 tgacgcccca ccccgtgata atttggggac gagccgcacg ataacttctg ccagcgaccg
+ 1381 cccctcccac gtccgatggt gattccgaac tccacctgcg tctatcgt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/construct_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/construct_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,191 @@
+LOCUS construct_2 8000 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_2
+VERSION construct_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1781..1800
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1781..3581
+ /source="Frag_3"
+ /indicates_part=True
+ /note="From Frag_3"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3582..3599
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3582..4781
+ /source="Frag_4b"
+ /indicates_part=True
+ /note="From Frag_4b"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4782..4799
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4782..6190
+ /source="Frag_5"
+ /indicates_part=True
+ /note="From Frag_5"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6191..8000
+ /source="Frag_1"
+ /indicates_part=True
+ /note="From Frag_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6191..6209
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 8021..9800
+ /source="Frag_2"
+ /indicates_part=True
+ /note="From Frag_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cccagatcgc agctcccttg acagtgtcag ttgaatcccc attctaggtt tcctgataaa
+ 61 actaagtacg gggacgcatc agtcgaaagc aatcacagat aatagatatc ttgagcagaa
+ 121 agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa gtgcgggcaa caataggtgt
+ 181 gaggtttcac ggttgcttga tcagtagctg ttcactctct cgcaggccta catagtgagg
+ 241 tggtgagatt gttcaggtct gtctcctgcg cggttgtcga gccccgtcgg gcacgctaac
+ 301 aaggacagga attcgggtcg tcaaataaca atttacgtca tcgcatccct caagggtaag
+ 361 gcgtgatctc catctcggtt cccaattggt cattgtgata gccacactgc agttaccgaa
+ 421 ggcgatttta tactaccctg ataagtgctc gcagcccctc ctccctaata atgtaacgac
+ 481 gagcattaac ccaggagtat ttctcacgtt gctcgtgccc agccaaggcg atcaacgcag
+ 541 accggatagc gttagctagc ccacgggtaa aagcgattgt tgtactcttt catatgaata
+ 601 cagcactcgc gaatgcaagc ctacgtcggc tcgattctct tcctcaccac actggaggcg
+ 661 atgatctagc ccgtctttca ccccgtacct ttatactcgg ccgcgtattt ctccaccggg
+ 721 agctctgcct accaaagcgt cgtacgccca ggaagccgtt tcctttatcc tccctcatgt
+ 781 ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt ctggccaaca ctggacagac
+ 841 gcgcgagacg ctgataaacc cccattttcg tggggttagt aaatcggtgg cttcaaacgg
+ 901 ttcgatcgct cgcacgagca ttagtcagga gtatgattgc gcatcatctc tactccgtac
+ 961 taggttctgt agctcaggat ctccgggggg atcaagcttt tatgtcccgc gggattagaa
+ 1021 gatatccatc catatgttta ctttgatgcg ggtccgagct ctctatgatg ctgctttgac
+ 1081 aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc tctacgacac gttgatgcta
+ 1141 aacaagttgg actactaagc aaatgaagcg gaagagatac tgagcgctct ctctatgact
+ 1201 ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga aatctcaaat aataatgcaa
+ 1261 tgtgttggct aagctcgggc aaactcagga tgtgacctag taccctctgc cccgtgagta
+ 1321 cccataccca atcaagccag cccaattcgc gataggtaca gataagcctt actcgtcccg
+ 1381 atccttgact aaaacactca tcctcgatag tacgtgcctt gtagagtccg acggccatag
+ 1441 gtaaacgacc agttagtgtc gtagggtcct ccactttagc tacgattgca actcccttac
+ 1501 cttcgtgccg gcgcgctcct cttgctacca tcacgcttca aatcgggtgg aagaccaact
+ 1561 gatgaatgag ggtgcagacc ccagtggagc ataatacgat gcgcccacga tactctagag
+ 1621 ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt ggccacatcg gccgcccatc
+ 1681 cttgtgtctt ccgataagta ctccctttca aggactctcc gataccggct tagaacacga
+ 1741 acggacaacg ctttcagcgc tgagaaatga cggctgcttc aaccagaacg atacagcctt
+ 1801 ctttgctaga tagcctctag tgtcagccac caagtccgcc acctaatcct tcgccgaggg
+ 1861 tcaaagcttc tgaccatcca attgttaggc actcttggaa ccttgcaagt acctgatcat
+ 1921 gcagaaaatg gacttgcccg gagcatattc attataagta ccattcacgg caggttatag
+ 1981 tatgcgttga cgcggggtga tacggtaatg caagtaacca tcgggccgcg gtatgcacat
+ 2041 agaagggtgt ttgacttggt ttcttacagt gcaactgcat atgtggaccg ccattccaag
+ 2101 tgaaaggata cgaagggagg tttcggactg ctatccagag catggaaagc cttcaaggtg
+ 2161 gtgcgcactg gaatagtgac tcggggattg tatgtcgagc cgcgtccagt ctttcctata
+ 2221 cttatgcgag caaatagacc gagtggaact tgattgcatc agccgaatca cgatgaaaac
+ 2281 tcagcttaca attcgtaagc acttcaaata tatgcccgga aaatcgccgt ccagtgactt
+ 2341 gtaatagctc cagggtcagt agcgctgccc tggccgaacc aggtgacggt tacgtggacc
+ 2401 tcacagtatc aatgttgcag tgcgccacca gattaagctg gccgtgtcat ggtgaacaac
+ 2461 cgtgataaaa gaacgggagt atgagagtgc cacccaagag tggtactcca ggattcggaa
+ 2521 aggggagggg gcttttcctg cttaacaacc ttcctcggca cggtctaagc gtctcactcg
+ 2581 tcctaaactc taccatcatg cagctaggcg aaagtataac tttagggtct atcaggatga
+ 2641 gctatctgta ccacggtgat gagataagta gggggtgcgc tagggtcgtt cgtgttttca
+ 2701 tcgtctatag tacctatttc tcgtcttcca ttagcgcata cggccatctc gcggcggcta
+ 2761 cgtcagccag cgtcaacccc aagtcactaa tttccgttat tataggtgta gctcataact
+ 2821 tcttctgccg accaagccaa aagctttgcg gcagctgcaa ggccacgtta ggctctcgga
+ 2881 cggcagatat ttattaataa caccactggg ttccagctct taacgcactt cccttcactg
+ 2941 gatcacctgt acgcccataa gctaagcctg aagccacggc ctcaatcgtg gacattactc
+ 3001 ttagcaaatc cacattacca tgtcaccaat ccccgaaccc cgcgccgacc taaggcgggg
+ 3061 tacctcgtgc acggcagcat cgagggaaat atattacaaa agacgcggcg atccaacggt
+ 3121 tgataaaaac agttccgtgg aaggcggacg tgtgcttagc gcatgcttct caccgagtga
+ 3181 cagcaccgat tccatctcgc tagcacgccg atgagcctcg ctgtgggact atggtccagc
+ 3241 ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc ggtaaggtcg atttggtggc
+ 3301 actcgcaaga tacgcgggtt attagtagag cgcagtcagg gcccatcgcc agcatttgca
+ 3361 tgctcgccgt acgctatcct tgtactacgg ttcctcagtg gctataaagg aatgtcacaa
+ 3421 ctccattagc cccttttgtt cagcgcttag tcatggtggg actgactcac cgagactaca
+ 3481 tacggattgt gcccgcagag acatgccttt catgctgggg ttttgtaagc agctccacgg
+ 3541 ggtagtgtca ccatgccttc gacctatgct tatgaaaccc gaggtaatgc ggcaggatcc
+ 3601 cgtggatcct acgcttagcc tgttaccccc cccgttctcc tcggccccca gccagcgcgt
+ 3661 attccgcgca ttcctccgag tgcgtatcgc gcaaaccaca agatacctct caacgactag
+ 3721 cggtgaacca ccaagcttga catacgtgcc ccttcggaaa cgttattagt ggtcctgagt
+ 3781 ggtacgtccc gagtatacgg ggcagcgata gtaacgctac aaatagctag accgacgaca
+ 3841 aacacagcac tgaatatcca acagtggcaa cgagacgctt agaaagggaa actacatacc
+ 3901 agttcaatcc gggatgactt caaaagggta tgtttgtttt gaagcgaagc tttggttgtc
+ 3961 attcagttcc tagagtttac ggcgctgata tggctctagg agtccagtga attcgtcagc
+ 4021 ataagcccca catcgtagga aattgcccgg tcgtcggtct agcaaatgct cggtaaactg
+ 4081 ggagtgtact aacaccatgt cgtggtaacc cggtggaccg gctactagag acatatttat
+ 4141 tcatgctcag ttgaacctgt ttcgaggggg ccgagttaac ataaagtgat tagtcacagc
+ 4201 gcattaagat agaacaggga tatagctcgt tgcatccata aattgcccac cgtagggaga
+ 4261 acgccgttgg aaaatgagag ttaggcgatg agcggttgtc gcccgcacag acaaaggatg
+ 4321 cctttataaa tagtagcggc cttgtctgca ccagacgttt gtgggtcgac gtgctattct
+ 4381 agccaaaagc aaaatgtatc atactacagg caataggccc tatgctgacc aaacttgggg
+ 4441 acccttgcgc cttctctctt acgcataaca tgcataggta cctctactca tcaggcaggg
+ 4501 cggcgtgagg tcactatggc tcaagatgtg tacgactaaa gaaaggttta tgctccttcc
+ 4561 ccaaggacgc atttgggact gctacttgcc cctagcgaat tcactaggat ttttgtagaa
+ 4621 ccatgagcgc cctatccgat agcacagaga caatgctaca agcaactgtg catgcgctcg
+ 4681 atcgccgtgc attaatacgt attatagcgt atcgtgtacg ctaatatctt agtgcaccgc
+ 4741 acgctggttg gatacaattc cgtgaaataa ttcctgctta cacaggggct ttctggcgca
+ 4801 tggctgtgtc tggatgtttg tgataagagg ctccatgaac ccggcgggaa atgaggggaa
+ 4861 accccgggga gcaacgacac taagcctggc agttgttcag ataggacgct tttgtcagtg
+ 4921 ggcggttttg catccactaa ctatcataaa cgacacaacg tcgaatgatc atcggcggtt
+ 4981 tgcatgtaga gacagctcct gcaacaccat accggctcgt ggaattacgc tgtgcgccgg
+ 5041 ccctcattcg attgtgtcca gcgtcggcgc gaatgatgat tgagatgtgc ttcggctcag
+ 5101 agcgtgcaca ggtagttctc cccccttacc tagctgatcc agcaattcca cgctggcccg
+ 5161 cgcgtccttg ggtaacactg gatctgtacc caaatacacc gtcgtgattg ttaactaccg
+ 5221 tatggcggtt acgatcgagt gacactatta ttagaccgct actccaagtc ccaacttttc
+ 5281 atcgccatac agaagagaac gagaaagtcg aagagttata gcgtgtacac ttctgattag
+ 5341 ctaacgaatc gatgcgtaca gcatactcga gcaactttat gggtcgtctg tctccttgta
+ 5401 ccccgcttga cgaggatgtg tttgtaggcg gcttggatat cggcagtgta tccgcatggt
+ 5461 caaacacttt agcccgaccg gtgctcaagg tcgaaatcct aatatagatt gggataggac
+ 5521 ccgtccatta ctaggcgaca ttcgcagtca cgagcccgca cggggtgcct caacacggtg
+ 5581 acactcaatt cgccggcact gagtacgacg atcgtgattg ccataccgtc atgttttgtg
+ 5641 ttacccctga taagaagcgc agatatggca cgggggcaga gggcggagta gacccatgca
+ 5701 aaactctagc ctctgggcag catgatcgac gtagaacgcc gttgtgactc actagtttca
+ 5761 gttatgatgt tcagccaaga atcctccatt ttgacgtgaa ccttctccct ttacaccttg
+ 5821 aagctgcaat attaagtcga ccctttaagt tgccttgtct tggtctagag cccgcagctc
+ 5881 accgataaaa tgagcagtca attttagcgg cggttgtcca ggttacatgc actttgggct
+ 5941 ggaaccgcgt tacgtttgga gtacttagaa gtgtcgtagg cataggagag ccgaaacttg
+ 6001 atattgggtc tagttagtgc tctaccccgc ttcggatccg taatagtgat gttgcatgag
+ 6061 acgcttgcct caaggcgaca tacggtggcg gttgctggaa atgacgcccc accccgtgat
+ 6121 aatttgggga cgagccgcac gataacttct gccagcgacc gcccctccca cgtccgatgg
+ 6181 tgattccgaa ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac
+ 6241 ttccgctaag ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta
+ 6301 agtcgggttg tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg
+ 6361 tcatacagag gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg
+ 6421 tacgttctcc cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt
+ 6481 tatggaccag aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg
+ 6541 gatatggccg cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg
+ 6601 ggtgcctgtt tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca
+ 6661 cgttccagtg aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag
+ 6721 gtactgtgga gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg
+ 6781 gtgttgcccg tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg
+ 6841 caacatgcga ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg
+ 6901 cgaccgatat gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag
+ 6961 ccaaatgcac agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt
+ 7021 tgttacactt ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt
+ 7081 gtactgcacc tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt
+ 7141 tgcaaccctc tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt
+ 7201 tggcgagggc caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca
+ 7261 cggtgtatag ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc
+ 7321 ggttgttatc actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat
+ 7381 cagctggtca gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa
+ 7441 tgaaccctca ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga
+ 7501 gcagctatcg aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa
+ 7561 aacggaggga gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca
+ 7621 ttagagcagc catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt
+ 7681 tatggacaac aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat
+ 7741 tgatgggtgg cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt
+ 7801 gtggtacgat ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg
+ 7861 ctgaacatgc cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg
+ 7921 ggtacgtaac agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc
+ 7981 gatcgaattc cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/construct_2.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_2/construct_2.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/construct_2_connections_graph.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_2/construct_2_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/construct_2_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/construct_2_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,homology_condition,used_in,parts
+construct_2,construct_2,1,8000,5,,"15-80bp, 0.0-+C Tm",,Frag_2 & Frag_3 & Frag_4b & Frag_5 & Frag_1
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_1 1810 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_1.
+ACCESSION Frag_1
+VERSION Frag_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac ttccgctaag
+ 61 ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta agtcgggttg
+ 121 tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg tcatacagag
+ 181 gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg tacgttctcc
+ 241 cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt tatggaccag
+ 301 aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg gatatggccg
+ 361 cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg ggtgcctgtt
+ 421 tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca cgttccagtg
+ 481 aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag gtactgtgga
+ 541 gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg gtgttgcccg
+ 601 tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg caacatgcga
+ 661 ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg cgaccgatat
+ 721 gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag ccaaatgcac
+ 781 agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt tgttacactt
+ 841 ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt gtactgcacc
+ 901 tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt tgcaaccctc
+ 961 tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt tggcgagggc
+ 1021 caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca cggtgtatag
+ 1081 ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc ggttgttatc
+ 1141 actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat cagctggtca
+ 1201 gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa tgaaccctca
+ 1261 ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga gcagctatcg
+ 1321 aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa aacggaggga
+ 1381 gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca ttagagcagc
+ 1441 catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt tatggacaac
+ 1501 aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat tgatgggtgg
+ 1561 cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt gtggtacgat
+ 1621 ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg ctgaacatgc
+ 1681 cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg ggtacgtaac
+ 1741 agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc gatcgaattc
+ 1801 cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_2 1820 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_2.
+ACCESSION Frag_2
+VERSION Frag_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 gatcgaattc cgttttacgc cccagatcgc agctcccttg acagtgtcag ttgaatcccc
+ 61 attctaggtt tcctgataaa actaagtacg gggacgcatc agtcgaaagc aatcacagat
+ 121 aatagatatc ttgagcagaa agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa
+ 181 gtgcgggcaa caataggtgt gaggtttcac ggttgcttga tcagtagctg ttcactctct
+ 241 cgcaggccta catagtgagg tggtgagatt gttcaggtct gtctcctgcg cggttgtcga
+ 301 gccccgtcgg gcacgctaac aaggacagga attcgggtcg tcaaataaca atttacgtca
+ 361 tcgcatccct caagggtaag gcgtgatctc catctcggtt cccaattggt cattgtgata
+ 421 gccacactgc agttaccgaa ggcgatttta tactaccctg ataagtgctc gcagcccctc
+ 481 ctccctaata atgtaacgac gagcattaac ccaggagtat ttctcacgtt gctcgtgccc
+ 541 agccaaggcg atcaacgcag accggatagc gttagctagc ccacgggtaa aagcgattgt
+ 601 tgtactcttt catatgaata cagcactcgc gaatgcaagc ctacgtcggc tcgattctct
+ 661 tcctcaccac actggaggcg atgatctagc ccgtctttca ccccgtacct ttatactcgg
+ 721 ccgcgtattt ctccaccggg agctctgcct accaaagcgt cgtacgccca ggaagccgtt
+ 781 tcctttatcc tccctcatgt ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt
+ 841 ctggccaaca ctggacagac gcgcgagacg ctgataaacc cccattttcg tggggttagt
+ 901 aaatcggtgg cttcaaacgg ttcgatcgct cgcacgagca ttagtcagga gtatgattgc
+ 961 gcatcatctc tactccgtac taggttctgt agctcaggat ctccgggggg atcaagcttt
+ 1021 tatgtcccgc gggattagaa gatatccatc catatgttta ctttgatgcg ggtccgagct
+ 1081 ctctatgatg ctgctttgac aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc
+ 1141 tctacgacac gttgatgcta aacaagttgg actactaagc aaatgaagcg gaagagatac
+ 1201 tgagcgctct ctctatgact ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga
+ 1261 aatctcaaat aataatgcaa tgtgttggct aagctcgggc aaactcagga tgtgacctag
+ 1321 taccctctgc cccgtgagta cccataccca atcaagccag cccaattcgc gataggtaca
+ 1381 gataagcctt actcgtcccg atccttgact aaaacactca tcctcgatag tacgtgcctt
+ 1441 gtagagtccg acggccatag gtaaacgacc agttagtgtc gtagggtcct ccactttagc
+ 1501 tacgattgca actcccttac cttcgtgccg gcgcgctcct cttgctacca tcacgcttca
+ 1561 aatcgggtgg aagaccaact gatgaatgag ggtgcagacc ccagtggagc ataatacgat
+ 1621 gcgcccacga tactctagag ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt
+ 1681 ggccacatcg gccgcccatc cttgtgtctt ccgataagta ctccctttca aggactctcc
+ 1741 gataccggct tagaacacga acggacaacg ctttcagcgc tgagaaatga cggctgcttc
+ 1801 aaccagaacg atacagcctt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_3 1819 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_3.
+ACCESSION Frag_3
+VERSION Frag_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aaccagaacg atacagcctt ctttgctaga tagcctctag tgtcagccac caagtccgcc
+ 61 acctaatcct tcgccgaggg tcaaagcttc tgaccatcca attgttaggc actcttggaa
+ 121 ccttgcaagt acctgatcat gcagaaaatg gacttgcccg gagcatattc attataagta
+ 181 ccattcacgg caggttatag tatgcgttga cgcggggtga tacggtaatg caagtaacca
+ 241 tcgggccgcg gtatgcacat agaagggtgt ttgacttggt ttcttacagt gcaactgcat
+ 301 atgtggaccg ccattccaag tgaaaggata cgaagggagg tttcggactg ctatccagag
+ 361 catggaaagc cttcaaggtg gtgcgcactg gaatagtgac tcggggattg tatgtcgagc
+ 421 cgcgtccagt ctttcctata cttatgcgag caaatagacc gagtggaact tgattgcatc
+ 481 agccgaatca cgatgaaaac tcagcttaca attcgtaagc acttcaaata tatgcccgga
+ 541 aaatcgccgt ccagtgactt gtaatagctc cagggtcagt agcgctgccc tggccgaacc
+ 601 aggtgacggt tacgtggacc tcacagtatc aatgttgcag tgcgccacca gattaagctg
+ 661 gccgtgtcat ggtgaacaac cgtgataaaa gaacgggagt atgagagtgc cacccaagag
+ 721 tggtactcca ggattcggaa aggggagggg gcttttcctg cttaacaacc ttcctcggca
+ 781 cggtctaagc gtctcactcg tcctaaactc taccatcatg cagctaggcg aaagtataac
+ 841 tttagggtct atcaggatga gctatctgta ccacggtgat gagataagta gggggtgcgc
+ 901 tagggtcgtt cgtgttttca tcgtctatag tacctatttc tcgtcttcca ttagcgcata
+ 961 cggccatctc gcggcggcta cgtcagccag cgtcaacccc aagtcactaa tttccgttat
+ 1021 tataggtgta gctcataact tcttctgccg accaagccaa aagctttgcg gcagctgcaa
+ 1081 ggccacgtta ggctctcgga cggcagatat ttattaataa caccactggg ttccagctct
+ 1141 taacgcactt cccttcactg gatcacctgt acgcccataa gctaagcctg aagccacggc
+ 1201 ctcaatcgtg gacattactc ttagcaaatc cacattacca tgtcaccaat ccccgaaccc
+ 1261 cgcgccgacc taaggcgggg tacctcgtgc acggcagcat cgagggaaat atattacaaa
+ 1321 agacgcggcg atccaacggt tgataaaaac agttccgtgg aaggcggacg tgtgcttagc
+ 1381 gcatgcttct caccgagtga cagcaccgat tccatctcgc tagcacgccg atgagcctcg
+ 1441 ctgtgggact atggtccagc ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc
+ 1501 ggtaaggtcg atttggtggc actcgcaaga tacgcgggtt attagtagag cgcagtcagg
+ 1561 gcccatcgcc agcatttgca tgctcgccgt acgctatcct tgtactacgg ttcctcagtg
+ 1621 gctataaagg aatgtcacaa ctccattagc cccttttgtt cagcgcttag tcatggtggg
+ 1681 actgactcac cgagactaca tacggattgt gcccgcagag acatgccttt catgctgggg
+ 1741 ttttgtaagc agctccacgg ggtagtgtca ccatgccttc gacctatgct tatgaaaccc
+ 1801 gaggtaatgc ggcaggatc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_4b.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_4b.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4b 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4b.
+ACCESSION Frag_4b
+VERSION Frag_4b
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gttacccccc ccgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctaga ccgacgacaa acacagcact gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_5.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_2/provided_parts_records/Frag_5.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,35 @@
+LOCUS Frag_5 1428 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_5.
+ACCESSION Frag_5
+VERSION Frag_5
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 acaggggctt tctggcgcat ggctgtgtct ggatgtttgt gataagaggc tccatgaacc
+ 61 cggcgggaaa tgaggggaaa ccccggggag caacgacact aagcctggca gttgttcaga
+ 121 taggacgctt ttgtcagtgg gcggttttgc atccactaac tatcataaac gacacaacgt
+ 181 cgaatgatca tcggcggttt gcatgtagag acagctcctg caacaccata ccggctcgtg
+ 241 gaattacgct gtgcgccggc cctcattcga ttgtgtccag cgtcggcgcg aatgatgatt
+ 301 gagatgtgct tcggctcaga gcgtgcacag gtagttctcc ccccttacct agctgatcca
+ 361 gcaattccac gctggcccgc gcgtccttgg gtaacactgg atctgtaccc aaatacaccg
+ 421 tcgtgattgt taactaccgt atggcggtta cgatcgagtg acactattat tagaccgcta
+ 481 ctccaagtcc caacttttca tcgccataca gaagagaacg agaaagtcga agagttatag
+ 541 cgtgtacact tctgattagc taacgaatcg atgcgtacag catactcgag caactttatg
+ 601 ggtcgtctgt ctccttgtac cccgcttgac gaggatgtgt ttgtaggcgg cttggatatc
+ 661 ggcagtgtat ccgcatggtc aaacacttta gcccgaccgg tgctcaaggt cgaaatccta
+ 721 atatagattg ggataggacc cgtccattac taggcgacat tcgcagtcac gagcccgcac
+ 781 ggggtgcctc aacacggtga cactcaattc gccggcactg agtacgacga tcgtgattgc
+ 841 cataccgtca tgttttgtgt tacccctgat aagaagcgca gatatggcac gggggcagag
+ 901 ggcggagtag acccatgcaa aactctagcc tctgggcagc atgatcgacg tagaacgccg
+ 961 ttgtgactca ctagtttcag ttatgatgtt cagccaagaa tcctccattt tgacgtgaac
+ 1021 cttctccctt tacaccttga agctgcaata ttaagtcgac cctttaagtt gccttgtctt
+ 1081 ggtctagagc ccgcagctca ccgataaaat gagcagtcaa ttttagcggc ggttgtccag
+ 1141 gttacatgca ctttgggctg gaaccgcgtt acgtttggag tacttagaag tgtcgtaggc
+ 1201 ataggagagc cgaaacttga tattgggtct agttagtgct ctaccccgct tcggatccgt
+ 1261 aatagtgatg ttgcatgaga cgcttgcctc aaggcgacat acggtggcgg ttgctggaaa
+ 1321 tgacgcccca ccccgtgata atttggggac gagccgcacg ataacttctg ccagcgaccg
+ 1381 cccctcccac gtccgatggt gattccgaac tccacctgcg tctatcgt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/construct_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/construct_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,191 @@
+LOCUS construct_3 8000 bp DNA circular UNK 01-JAN-1980
+DEFINITION .
+ACCESSION construct_3
+VERSION construct_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ homology 1781..1800
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 1781..3581
+ /source="Frag_3"
+ /indicates_part=True
+ /note="From Frag_3"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 3582..3599
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 3582..4781
+ /source="Frag_4c"
+ /indicates_part=True
+ /note="From Frag_4c"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 4782..4799
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 4782..6190
+ /source="Frag_5b"
+ /indicates_part=True
+ /note="From Frag_5b"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ misc_feature 6191..8000
+ /source="Frag_1"
+ /indicates_part=True
+ /note="From Frag_1"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ homology 6191..6209
+ /label="homology"
+ /color="#f7e8f7"
+ /ApEinfo_fwdcolor="#f7e8f7"
+ misc_feature 8021..9800
+ /source="Frag_2"
+ /indicates_part=True
+ /note="From Frag_2"
+ /color="white"
+ /ApEinfo_fwdcolor="white"
+ORIGIN
+ 1 cccagatcgc agctcccttg acagtgtcag ttgaatcccc attctaggtt tcctgataaa
+ 61 actaagtacg gggacgcatc agtcgaaagc aatcacagat aatagatatc ttgagcagaa
+ 121 agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa gtgcgggcaa caataggtgt
+ 181 gaggtttcac ggttgcttga tcagtagctg ttcactctct cgcaggccta catagtgagg
+ 241 tggtgagatt gttcaggtct gtctcctgcg cggttgtcga gccccgtcgg gcacgctaac
+ 301 aaggacagga attcgggtcg tcaaataaca atttacgtca tcgcatccct caagggtaag
+ 361 gcgtgatctc catctcggtt cccaattggt cattgtgata gccacactgc agttaccgaa
+ 421 ggcgatttta tactaccctg ataagtgctc gcagcccctc ctccctaata atgtaacgac
+ 481 gagcattaac ccaggagtat ttctcacgtt gctcgtgccc agccaaggcg atcaacgcag
+ 541 accggatagc gttagctagc ccacgggtaa aagcgattgt tgtactcttt catatgaata
+ 601 cagcactcgc gaatgcaagc ctacgtcggc tcgattctct tcctcaccac actggaggcg
+ 661 atgatctagc ccgtctttca ccccgtacct ttatactcgg ccgcgtattt ctccaccggg
+ 721 agctctgcct accaaagcgt cgtacgccca ggaagccgtt tcctttatcc tccctcatgt
+ 781 ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt ctggccaaca ctggacagac
+ 841 gcgcgagacg ctgataaacc cccattttcg tggggttagt aaatcggtgg cttcaaacgg
+ 901 ttcgatcgct cgcacgagca ttagtcagga gtatgattgc gcatcatctc tactccgtac
+ 961 taggttctgt agctcaggat ctccgggggg atcaagcttt tatgtcccgc gggattagaa
+ 1021 gatatccatc catatgttta ctttgatgcg ggtccgagct ctctatgatg ctgctttgac
+ 1081 aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc tctacgacac gttgatgcta
+ 1141 aacaagttgg actactaagc aaatgaagcg gaagagatac tgagcgctct ctctatgact
+ 1201 ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga aatctcaaat aataatgcaa
+ 1261 tgtgttggct aagctcgggc aaactcagga tgtgacctag taccctctgc cccgtgagta
+ 1321 cccataccca atcaagccag cccaattcgc gataggtaca gataagcctt actcgtcccg
+ 1381 atccttgact aaaacactca tcctcgatag tacgtgcctt gtagagtccg acggccatag
+ 1441 gtaaacgacc agttagtgtc gtagggtcct ccactttagc tacgattgca actcccttac
+ 1501 cttcgtgccg gcgcgctcct cttgctacca tcacgcttca aatcgggtgg aagaccaact
+ 1561 gatgaatgag ggtgcagacc ccagtggagc ataatacgat gcgcccacga tactctagag
+ 1621 ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt ggccacatcg gccgcccatc
+ 1681 cttgtgtctt ccgataagta ctccctttca aggactctcc gataccggct tagaacacga
+ 1741 acggacaacg ctttcagcgc tgagaaatga cggctgcttc aaccagaacg atacagcctt
+ 1801 ctttgctaga tagcctctag tgtcagccac caagtccgcc acctaatcct tcgccgaggg
+ 1861 tcaaagcttc tgaccatcca attgttaggc actcttggaa ccttgcaagt acctgatcat
+ 1921 gcagaaaatg gacttgcccg gagcatattc attataagta ccattcacgg caggttatag
+ 1981 tatgcgttga cgcggggtga tacggtaatg caagtaacca tcgggccgcg gtatgcacat
+ 2041 agaagggtgt ttgacttggt ttcttacagt gcaactgcat atgtggaccg ccattccaag
+ 2101 tgaaaggata cgaagggagg tttcggactg ctatccagag catggaaagc cttcaaggtg
+ 2161 gtgcgcactg gaatagtgac tcggggattg tatgtcgagc cgcgtccagt ctttcctata
+ 2221 cttatgcgag caaatagacc gagtggaact tgattgcatc agccgaatca cgatgaaaac
+ 2281 tcagcttaca attcgtaagc acttcaaata tatgcccgga aaatcgccgt ccagtgactt
+ 2341 gtaatagctc cagggtcagt agcgctgccc tggccgaacc aggtgacggt tacgtggacc
+ 2401 tcacagtatc aatgttgcag tgcgccacca gattaagctg gccgtgtcat ggtgaacaac
+ 2461 cgtgataaaa gaacgggagt atgagagtgc cacccaagag tggtactcca ggattcggaa
+ 2521 aggggagggg gcttttcctg cttaacaacc ttcctcggca cggtctaagc gtctcactcg
+ 2581 tcctaaactc taccatcatg cagctaggcg aaagtataac tttagggtct atcaggatga
+ 2641 gctatctgta ccacggtgat gagataagta gggggtgcgc tagggtcgtt cgtgttttca
+ 2701 tcgtctatag tacctatttc tcgtcttcca ttagcgcata cggccatctc gcggcggcta
+ 2761 cgtcagccag cgtcaacccc aagtcactaa tttccgttat tataggtgta gctcataact
+ 2821 tcttctgccg accaagccaa aagctttgcg gcagctgcaa ggccacgtta ggctctcgga
+ 2881 cggcagatat ttattaataa caccactggg ttccagctct taacgcactt cccttcactg
+ 2941 gatcacctgt acgcccataa gctaagcctg aagccacggc ctcaatcgtg gacattactc
+ 3001 ttagcaaatc cacattacca tgtcaccaat ccccgaaccc cgcgccgacc taaggcgggg
+ 3061 tacctcgtgc acggcagcat cgagggaaat atattacaaa agacgcggcg atccaacggt
+ 3121 tgataaaaac agttccgtgg aaggcggacg tgtgcttagc gcatgcttct caccgagtga
+ 3181 cagcaccgat tccatctcgc tagcacgccg atgagcctcg ctgtgggact atggtccagc
+ 3241 ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc ggtaaggtcg atttggtggc
+ 3301 actcgcaaga tacgcgggtt attagtagag cgcagtcagg gcccatcgcc agcatttgca
+ 3361 tgctcgccgt acgctatcct tgtactacgg ttcctcagtg gctataaagg aatgtcacaa
+ 3421 ctccattagc cccttttgtt cagcgcttag tcatggtggg actgactcac cgagactaca
+ 3481 tacggattgt gcccgcagag acatgccttt catgctgggg ttttgtaagc agctccacgg
+ 3541 ggtagtgtca ccatgccttc gacctatgct tatgaaaccc gaggtaatgc ggcaggatcc
+ 3601 cgtggatcct acgcttagcc tgttaggggg ggggttctcc tcggccccca gccagcgcgt
+ 3661 attccgcgca ttcctccgag tgcgtatcgc gcaaaccaca agatacctct caacgactag
+ 3721 cggtgaacca ccaagcttga catacgtgcc ccttcggaaa cgttattagt ggtcctgagt
+ 3781 ggtacgtccc gagtatacgg ggcagcgata gtaacgctac aaatagctag accgacgaca
+ 3841 aacacagcac tgaatatcca acagtggcaa cgagacgctt agaaagggaa actacatacc
+ 3901 agttcaatcc gggatgactt caaaagggta tgtttgtttt gaagcgaagc tttggttgtc
+ 3961 attcagttcc tagagtttac ggcgctgata tggctctagg agtccagtga attcgtcagc
+ 4021 ataagcccca catcgtagga aattgcccgg tcgtcggtct agcaaatgct cggtaaactg
+ 4081 ggagtgtact aacaccatgt cgtggtaacc cggtggaccg gctactagag acatatttat
+ 4141 tcatgctcag ttgaacctgt ttcgaggggg ccgagttaac ataaagtgat tagtcacagc
+ 4201 gcattaagat agaacaggga tatagctcgt tgcatccata aattgcccac cgtagggaga
+ 4261 acgccgttgg aaaatgagag ttaggcgatg agcggttgtc gcccgcacag acaaaggatg
+ 4321 cctttataaa tagtagcggc cttgtctgca ccagacgttt gtgggtcgac gtgctattct
+ 4381 agccaaaagc aaaatgtatc atactacagg caataggccc tatgctgacc aaacttgggg
+ 4441 acccttgcgc cttctctctt acgcataaca tgcataggta cctctactca tcaggcaggg
+ 4501 cggcgtgagg tcactatggc tcaagatgtg tacgactaaa gaaaggttta tgctccttcc
+ 4561 ccaaggacgc atttgggact gctacttgcc cctagcgaat tcactaggat ttttgtagaa
+ 4621 ccatgagcgc cctatccgat agcacagaga caatgctaca agcaactgtg catgcgctcg
+ 4681 atcgccgtgc attaatacgt attatagcgt atcgtgtacg ctaatatctt agtgcaccgc
+ 4741 acgctggttg gatacaattc cgtgaaataa ttcctgctta cacaggggct ttctggcgca
+ 4801 tggctgtgtc tggaaaaaaa aaaaaaaaaa aaacatgaac ccggcgggaa atgaggggaa
+ 4861 accccgggga gcaacgacac taagcctggc agttgttcag ataggacgct tttgtcagtg
+ 4921 ggcggttttg catccactaa ctatcataaa cgacacaacg tcgaatgatc atcggcggtt
+ 4981 tgcatgtaga gacagctcct gcaacaccat accggctcgt ggaattacgc tgtgcgccgg
+ 5041 ccctcattcg attgtgtcca gcgtcggcgc gaatgatgat tgagatgtgc ttcggctcag
+ 5101 agcgtgcaca ggtagttctc cccccttacc tagctgatcc agcaattcca cgctggcccg
+ 5161 cgcgtccttg ggtaacactg gatctgtacc caaatacacc gtcgtgattg ttaactaccg
+ 5221 tatggcggtt acgatcgagt gacactatta ttagaccgct actccaagtc ccaacttttc
+ 5281 atcgccatac agaagagaac gagaaagtcg aagagttata gcgtgtacac ttctgattag
+ 5341 ctaacgaatc gatgcgtaca gcatactcga gcaactttat gggtcgtctg tctccttgta
+ 5401 ccccgcttga cgaggatgtg tttgtaggcg gcttggatat cggcagtgta tccgcatggt
+ 5461 caaacacttt agcccgaccg gtgctcaagg tcgaaatcct aatatagatt gggataggac
+ 5521 ccgtccatta ctaggcgaca ttcgcagtca cgagcccgca cggggtgcct caacacggtg
+ 5581 acactcaatt cgccggcact gagtacgacg atcgtgattg ccataccgtc atgttttgtg
+ 5641 ttacccctga taagaagcgc agatatggca cgggggcaga gggcggagta gacccatgca
+ 5701 aaactctagc ctctgggcag catgatcgac gtagaacgcc gttgtgactc actagtttca
+ 5761 gttatgatgt tcagccaaga atcctccatt ttgacgtgaa ccttctccct ttacaccttg
+ 5821 aagctgcaat attaagtcga ccctttaagt tgccttgtct tggtctagag cccgcagctc
+ 5881 accgataaaa tgagcagtca attttagcgg cggttgtcca ggttacatgc actttgggct
+ 5941 ggaaccgcgt tacgtttgga gtacttagaa gtgtcgtagg cataggagag ccgaaacttg
+ 6001 atattgggtc tagttagtgc tctaccccgc ttcggatccg taatagtgat gttgcatgag
+ 6061 acgcttgcct caaggcgaca tacggtggcg gttgctggaa atgacgcccc accccgtgat
+ 6121 aatttgggga cgagccgcac gataacttct gccagcgacc gcccctccca cgtccgatgg
+ 6181 tgattccgaa ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac
+ 6241 ttccgctaag ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta
+ 6301 agtcgggttg tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg
+ 6361 tcatacagag gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg
+ 6421 tacgttctcc cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt
+ 6481 tatggaccag aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg
+ 6541 gatatggccg cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg
+ 6601 ggtgcctgtt tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca
+ 6661 cgttccagtg aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag
+ 6721 gtactgtgga gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg
+ 6781 gtgttgcccg tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg
+ 6841 caacatgcga ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg
+ 6901 cgaccgatat gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag
+ 6961 ccaaatgcac agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt
+ 7021 tgttacactt ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt
+ 7081 gtactgcacc tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt
+ 7141 tgcaaccctc tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt
+ 7201 tggcgagggc caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca
+ 7261 cggtgtatag ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc
+ 7321 ggttgttatc actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat
+ 7381 cagctggtca gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa
+ 7441 tgaaccctca ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga
+ 7501 gcagctatcg aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa
+ 7561 aacggaggga gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca
+ 7621 ttagagcagc catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt
+ 7681 tatggacaac aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat
+ 7741 tgatgggtgg cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt
+ 7801 gtggtacgat ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg
+ 7861 ctgaacatgc cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg
+ 7921 ggtacgtaac agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc
+ 7981 gatcgaattc cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/construct_3.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_3/construct_3.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/construct_3_connections_graph.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_3/construct_3_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/construct_3_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/construct_3_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,homology_condition,used_in,parts
+construct_3,construct_3,1,8000,5,,"15-80bp, 0.0-+C Tm",,Frag_2 & Frag_3 & Frag_4c & Frag_5b & Frag_1
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_1 1810 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_1.
+ACCESSION Frag_1
+VERSION Frag_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac ttccgctaag
+ 61 ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta agtcgggttg
+ 121 tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg tcatacagag
+ 181 gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg tacgttctcc
+ 241 cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt tatggaccag
+ 301 aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg gatatggccg
+ 361 cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg ggtgcctgtt
+ 421 tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca cgttccagtg
+ 481 aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag gtactgtgga
+ 541 gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg gtgttgcccg
+ 601 tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg caacatgcga
+ 661 ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg cgaccgatat
+ 721 gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag ccaaatgcac
+ 781 agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt tgttacactt
+ 841 ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt gtactgcacc
+ 901 tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt tgcaaccctc
+ 961 tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt tggcgagggc
+ 1021 caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca cggtgtatag
+ 1081 ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc ggttgttatc
+ 1141 actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat cagctggtca
+ 1201 gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa tgaaccctca
+ 1261 ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga gcagctatcg
+ 1321 aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa aacggaggga
+ 1381 gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca ttagagcagc
+ 1441 catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt tatggacaac
+ 1501 aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat tgatgggtgg
+ 1561 cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt gtggtacgat
+ 1621 ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg ctgaacatgc
+ 1681 cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg ggtacgtaac
+ 1741 agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc gatcgaattc
+ 1801 cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_2 1820 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_2.
+ACCESSION Frag_2
+VERSION Frag_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 gatcgaattc cgttttacgc cccagatcgc agctcccttg acagtgtcag ttgaatcccc
+ 61 attctaggtt tcctgataaa actaagtacg gggacgcatc agtcgaaagc aatcacagat
+ 121 aatagatatc ttgagcagaa agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa
+ 181 gtgcgggcaa caataggtgt gaggtttcac ggttgcttga tcagtagctg ttcactctct
+ 241 cgcaggccta catagtgagg tggtgagatt gttcaggtct gtctcctgcg cggttgtcga
+ 301 gccccgtcgg gcacgctaac aaggacagga attcgggtcg tcaaataaca atttacgtca
+ 361 tcgcatccct caagggtaag gcgtgatctc catctcggtt cccaattggt cattgtgata
+ 421 gccacactgc agttaccgaa ggcgatttta tactaccctg ataagtgctc gcagcccctc
+ 481 ctccctaata atgtaacgac gagcattaac ccaggagtat ttctcacgtt gctcgtgccc
+ 541 agccaaggcg atcaacgcag accggatagc gttagctagc ccacgggtaa aagcgattgt
+ 601 tgtactcttt catatgaata cagcactcgc gaatgcaagc ctacgtcggc tcgattctct
+ 661 tcctcaccac actggaggcg atgatctagc ccgtctttca ccccgtacct ttatactcgg
+ 721 ccgcgtattt ctccaccggg agctctgcct accaaagcgt cgtacgccca ggaagccgtt
+ 781 tcctttatcc tccctcatgt ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt
+ 841 ctggccaaca ctggacagac gcgcgagacg ctgataaacc cccattttcg tggggttagt
+ 901 aaatcggtgg cttcaaacgg ttcgatcgct cgcacgagca ttagtcagga gtatgattgc
+ 961 gcatcatctc tactccgtac taggttctgt agctcaggat ctccgggggg atcaagcttt
+ 1021 tatgtcccgc gggattagaa gatatccatc catatgttta ctttgatgcg ggtccgagct
+ 1081 ctctatgatg ctgctttgac aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc
+ 1141 tctacgacac gttgatgcta aacaagttgg actactaagc aaatgaagcg gaagagatac
+ 1201 tgagcgctct ctctatgact ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga
+ 1261 aatctcaaat aataatgcaa tgtgttggct aagctcgggc aaactcagga tgtgacctag
+ 1321 taccctctgc cccgtgagta cccataccca atcaagccag cccaattcgc gataggtaca
+ 1381 gataagcctt actcgtcccg atccttgact aaaacactca tcctcgatag tacgtgcctt
+ 1441 gtagagtccg acggccatag gtaaacgacc agttagtgtc gtagggtcct ccactttagc
+ 1501 tacgattgca actcccttac cttcgtgccg gcgcgctcct cttgctacca tcacgcttca
+ 1561 aatcgggtgg aagaccaact gatgaatgag ggtgcagacc ccagtggagc ataatacgat
+ 1621 gcgcccacga tactctagag ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt
+ 1681 ggccacatcg gccgcccatc cttgtgtctt ccgataagta ctccctttca aggactctcc
+ 1741 gataccggct tagaacacga acggacaacg ctttcagcgc tgagaaatga cggctgcttc
+ 1801 aaccagaacg atacagcctt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_3 1819 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_3.
+ACCESSION Frag_3
+VERSION Frag_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aaccagaacg atacagcctt ctttgctaga tagcctctag tgtcagccac caagtccgcc
+ 61 acctaatcct tcgccgaggg tcaaagcttc tgaccatcca attgttaggc actcttggaa
+ 121 ccttgcaagt acctgatcat gcagaaaatg gacttgcccg gagcatattc attataagta
+ 181 ccattcacgg caggttatag tatgcgttga cgcggggtga tacggtaatg caagtaacca
+ 241 tcgggccgcg gtatgcacat agaagggtgt ttgacttggt ttcttacagt gcaactgcat
+ 301 atgtggaccg ccattccaag tgaaaggata cgaagggagg tttcggactg ctatccagag
+ 361 catggaaagc cttcaaggtg gtgcgcactg gaatagtgac tcggggattg tatgtcgagc
+ 421 cgcgtccagt ctttcctata cttatgcgag caaatagacc gagtggaact tgattgcatc
+ 481 agccgaatca cgatgaaaac tcagcttaca attcgtaagc acttcaaata tatgcccgga
+ 541 aaatcgccgt ccagtgactt gtaatagctc cagggtcagt agcgctgccc tggccgaacc
+ 601 aggtgacggt tacgtggacc tcacagtatc aatgttgcag tgcgccacca gattaagctg
+ 661 gccgtgtcat ggtgaacaac cgtgataaaa gaacgggagt atgagagtgc cacccaagag
+ 721 tggtactcca ggattcggaa aggggagggg gcttttcctg cttaacaacc ttcctcggca
+ 781 cggtctaagc gtctcactcg tcctaaactc taccatcatg cagctaggcg aaagtataac
+ 841 tttagggtct atcaggatga gctatctgta ccacggtgat gagataagta gggggtgcgc
+ 901 tagggtcgtt cgtgttttca tcgtctatag tacctatttc tcgtcttcca ttagcgcata
+ 961 cggccatctc gcggcggcta cgtcagccag cgtcaacccc aagtcactaa tttccgttat
+ 1021 tataggtgta gctcataact tcttctgccg accaagccaa aagctttgcg gcagctgcaa
+ 1081 ggccacgtta ggctctcgga cggcagatat ttattaataa caccactggg ttccagctct
+ 1141 taacgcactt cccttcactg gatcacctgt acgcccataa gctaagcctg aagccacggc
+ 1201 ctcaatcgtg gacattactc ttagcaaatc cacattacca tgtcaccaat ccccgaaccc
+ 1261 cgcgccgacc taaggcgggg tacctcgtgc acggcagcat cgagggaaat atattacaaa
+ 1321 agacgcggcg atccaacggt tgataaaaac agttccgtgg aaggcggacg tgtgcttagc
+ 1381 gcatgcttct caccgagtga cagcaccgat tccatctcgc tagcacgccg atgagcctcg
+ 1441 ctgtgggact atggtccagc ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc
+ 1501 ggtaaggtcg atttggtggc actcgcaaga tacgcgggtt attagtagag cgcagtcagg
+ 1561 gcccatcgcc agcatttgca tgctcgccgt acgctatcct tgtactacgg ttcctcagtg
+ 1621 gctataaagg aatgtcacaa ctccattagc cccttttgtt cagcgcttag tcatggtggg
+ 1681 actgactcac cgagactaca tacggattgt gcccgcagag acatgccttt catgctgggg
+ 1741 ttttgtaagc agctccacgg ggtagtgtca ccatgccttc gacctatgct tatgaaaccc
+ 1801 gaggtaatgc ggcaggatc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_4c.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_4c.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4c 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4c.
+ACCESSION Frag_4c
+VERSION Frag_4c
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gttagggggg gggttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctaga ccgacgacaa acacagcact gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_5b.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_3/provided_parts_records/Frag_5b.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,35 @@
+LOCUS Frag_5b 1428 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_5b.
+ACCESSION Frag_5b
+VERSION Frag_5b
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 acaggggctt tctggcgcat ggctgtgtct ggaaaaaaaa aaaaaaaaaa aacatgaacc
+ 61 cggcgggaaa tgaggggaaa ccccggggag caacgacact aagcctggca gttgttcaga
+ 121 taggacgctt ttgtcagtgg gcggttttgc atccactaac tatcataaac gacacaacgt
+ 181 cgaatgatca tcggcggttt gcatgtagag acagctcctg caacaccata ccggctcgtg
+ 241 gaattacgct gtgcgccggc cctcattcga ttgtgtccag cgtcggcgcg aatgatgatt
+ 301 gagatgtgct tcggctcaga gcgtgcacag gtagttctcc ccccttacct agctgatcca
+ 361 gcaattccac gctggcccgc gcgtccttgg gtaacactgg atctgtaccc aaatacaccg
+ 421 tcgtgattgt taactaccgt atggcggtta cgatcgagtg acactattat tagaccgcta
+ 481 ctccaagtcc caacttttca tcgccataca gaagagaacg agaaagtcga agagttatag
+ 541 cgtgtacact tctgattagc taacgaatcg atgcgtacag catactcgag caactttatg
+ 601 ggtcgtctgt ctccttgtac cccgcttgac gaggatgtgt ttgtaggcgg cttggatatc
+ 661 ggcagtgtat ccgcatggtc aaacacttta gcccgaccgg tgctcaaggt cgaaatccta
+ 721 atatagattg ggataggacc cgtccattac taggcgacat tcgcagtcac gagcccgcac
+ 781 ggggtgcctc aacacggtga cactcaattc gccggcactg agtacgacga tcgtgattgc
+ 841 cataccgtca tgttttgtgt tacccctgat aagaagcgca gatatggcac gggggcagag
+ 901 ggcggagtag acccatgcaa aactctagcc tctgggcagc atgatcgacg tagaacgccg
+ 961 ttgtgactca ctagtttcag ttatgatgtt cagccaagaa tcctccattt tgacgtgaac
+ 1021 cttctccctt tacaccttga agctgcaata ttaagtcgac cctttaagtt gccttgtctt
+ 1081 ggtctagagc ccgcagctca ccgataaaat gagcagtcaa ttttagcggc ggttgtccag
+ 1141 gttacatgca ctttgggctg gaaccgcgtt acgtttggag tacttagaag tgtcgtaggc
+ 1201 ataggagagc cgaaacttga tattgggtct agttagtgct ctaccccgct tcggatccgt
+ 1261 aatagtgatg ttgcatgaga cgcttgcctc aaggcgacat acggtggcgg ttgctggaaa
+ 1321 tgacgcccca ccccgtgata atttggggac gagccgcacg ataacttctg ccagcgaccg
+ 1381 cccctcccac gtccgatggt gattccgaac tccacctgcg tctatcgt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/construct_4_connections_graph.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/construct_4_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/error.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_4/error.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+assembly_name;message;suggestion;data
+construct_4;Wrong number of constructs;expected_: 1,found: 0
+construct_4;Some parts are unused;unused_parts: Frag_1 & Frag_2 & Frag_3 & Frag_4
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_1_01.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_1_01.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_2_01.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_2_01.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_3_01.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_3_01.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_4_01.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_4_01.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_1.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_1.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_2.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_2.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_3.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_3.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_4.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_4/provided_parts_plots/Frag_4.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_1 1810 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_1.
+ACCESSION Frag_1
+VERSION Frag_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac ttccgctaag
+ 61 ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta agtcgggttg
+ 121 tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg tcatacagag
+ 181 gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg tacgttctcc
+ 241 cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt tatggaccag
+ 301 aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg gatatggccg
+ 361 cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg ggtgcctgtt
+ 421 tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca cgttccagtg
+ 481 aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag gtactgtgga
+ 541 gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg gtgttgcccg
+ 601 tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg caacatgcga
+ 661 ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg cgaccgatat
+ 721 gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag ccaaatgcac
+ 781 agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt tgttacactt
+ 841 ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt gtactgcacc
+ 901 tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt tgcaaccctc
+ 961 tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt tggcgagggc
+ 1021 caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca cggtgtatag
+ 1081 ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc ggttgttatc
+ 1141 actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat cagctggtca
+ 1201 gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa tgaaccctca
+ 1261 ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga gcagctatcg
+ 1321 aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa aacggaggga
+ 1381 gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca ttagagcagc
+ 1441 catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt tatggacaac
+ 1501 aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat tgatgggtgg
+ 1561 cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt gtggtacgat
+ 1621 ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg ctgaacatgc
+ 1681 cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg ggtacgtaac
+ 1741 agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc gatcgaattc
+ 1801 cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_2 1820 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_2.
+ACCESSION Frag_2
+VERSION Frag_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 gatcgaattc cgttttacgc cccagatcgc agctcccttg acagtgtcag ttgaatcccc
+ 61 attctaggtt tcctgataaa actaagtacg gggacgcatc agtcgaaagc aatcacagat
+ 121 aatagatatc ttgagcagaa agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa
+ 181 gtgcgggcaa caataggtgt gaggtttcac ggttgcttga tcagtagctg ttcactctct
+ 241 cgcaggccta catagtgagg tggtgagatt gttcaggtct gtctcctgcg cggttgtcga
+ 301 gccccgtcgg gcacgctaac aaggacagga attcgggtcg tcaaataaca atttacgtca
+ 361 tcgcatccct caagggtaag gcgtgatctc catctcggtt cccaattggt cattgtgata
+ 421 gccacactgc agttaccgaa ggcgatttta tactaccctg ataagtgctc gcagcccctc
+ 481 ctccctaata atgtaacgac gagcattaac ccaggagtat ttctcacgtt gctcgtgccc
+ 541 agccaaggcg atcaacgcag accggatagc gttagctagc ccacgggtaa aagcgattgt
+ 601 tgtactcttt catatgaata cagcactcgc gaatgcaagc ctacgtcggc tcgattctct
+ 661 tcctcaccac actggaggcg atgatctagc ccgtctttca ccccgtacct ttatactcgg
+ 721 ccgcgtattt ctccaccggg agctctgcct accaaagcgt cgtacgccca ggaagccgtt
+ 781 tcctttatcc tccctcatgt ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt
+ 841 ctggccaaca ctggacagac gcgcgagacg ctgataaacc cccattttcg tggggttagt
+ 901 aaatcggtgg cttcaaacgg ttcgatcgct cgcacgagca ttagtcagga gtatgattgc
+ 961 gcatcatctc tactccgtac taggttctgt agctcaggat ctccgggggg atcaagcttt
+ 1021 tatgtcccgc gggattagaa gatatccatc catatgttta ctttgatgcg ggtccgagct
+ 1081 ctctatgatg ctgctttgac aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc
+ 1141 tctacgacac gttgatgcta aacaagttgg actactaagc aaatgaagcg gaagagatac
+ 1201 tgagcgctct ctctatgact ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga
+ 1261 aatctcaaat aataatgcaa tgtgttggct aagctcgggc aaactcagga tgtgacctag
+ 1321 taccctctgc cccgtgagta cccataccca atcaagccag cccaattcgc gataggtaca
+ 1381 gataagcctt actcgtcccg atccttgact aaaacactca tcctcgatag tacgtgcctt
+ 1441 gtagagtccg acggccatag gtaaacgacc agttagtgtc gtagggtcct ccactttagc
+ 1501 tacgattgca actcccttac cttcgtgccg gcgcgctcct cttgctacca tcacgcttca
+ 1561 aatcgggtgg aagaccaact gatgaatgag ggtgcagacc ccagtggagc ataatacgat
+ 1621 gcgcccacga tactctagag ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt
+ 1681 ggccacatcg gccgcccatc cttgtgtctt ccgataagta ctccctttca aggactctcc
+ 1741 gataccggct tagaacacga acggacaacg ctttcagcgc tgagaaatga cggctgcttc
+ 1801 aaccagaacg atacagcctt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_3 1819 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_3.
+ACCESSION Frag_3
+VERSION Frag_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aaccagaacg atacagcctt ctttgctaga tagcctctag tgtcagccac caagtccgcc
+ 61 acctaatcct tcgccgaggg tcaaagcttc tgaccatcca attgttaggc actcttggaa
+ 121 ccttgcaagt acctgatcat gcagaaaatg gacttgcccg gagcatattc attataagta
+ 181 ccattcacgg caggttatag tatgcgttga cgcggggtga tacggtaatg caagtaacca
+ 241 tcgggccgcg gtatgcacat agaagggtgt ttgacttggt ttcttacagt gcaactgcat
+ 301 atgtggaccg ccattccaag tgaaaggata cgaagggagg tttcggactg ctatccagag
+ 361 catggaaagc cttcaaggtg gtgcgcactg gaatagtgac tcggggattg tatgtcgagc
+ 421 cgcgtccagt ctttcctata cttatgcgag caaatagacc gagtggaact tgattgcatc
+ 481 agccgaatca cgatgaaaac tcagcttaca attcgtaagc acttcaaata tatgcccgga
+ 541 aaatcgccgt ccagtgactt gtaatagctc cagggtcagt agcgctgccc tggccgaacc
+ 601 aggtgacggt tacgtggacc tcacagtatc aatgttgcag tgcgccacca gattaagctg
+ 661 gccgtgtcat ggtgaacaac cgtgataaaa gaacgggagt atgagagtgc cacccaagag
+ 721 tggtactcca ggattcggaa aggggagggg gcttttcctg cttaacaacc ttcctcggca
+ 781 cggtctaagc gtctcactcg tcctaaactc taccatcatg cagctaggcg aaagtataac
+ 841 tttagggtct atcaggatga gctatctgta ccacggtgat gagataagta gggggtgcgc
+ 901 tagggtcgtt cgtgttttca tcgtctatag tacctatttc tcgtcttcca ttagcgcata
+ 961 cggccatctc gcggcggcta cgtcagccag cgtcaacccc aagtcactaa tttccgttat
+ 1021 tataggtgta gctcataact tcttctgccg accaagccaa aagctttgcg gcagctgcaa
+ 1081 ggccacgtta ggctctcgga cggcagatat ttattaataa caccactggg ttccagctct
+ 1141 taacgcactt cccttcactg gatcacctgt acgcccataa gctaagcctg aagccacggc
+ 1201 ctcaatcgtg gacattactc ttagcaaatc cacattacca tgtcaccaat ccccgaaccc
+ 1261 cgcgccgacc taaggcgggg tacctcgtgc acggcagcat cgagggaaat atattacaaa
+ 1321 agacgcggcg atccaacggt tgataaaaac agttccgtgg aaggcggacg tgtgcttagc
+ 1381 gcatgcttct caccgagtga cagcaccgat tccatctcgc tagcacgccg atgagcctcg
+ 1441 ctgtgggact atggtccagc ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc
+ 1501 ggtaaggtcg atttggtggc actcgcaaga tacgcgggtt attagtagag cgcagtcagg
+ 1561 gcccatcgcc agcatttgca tgctcgccgt acgctatcct tgtactacgg ttcctcagtg
+ 1621 gctataaagg aatgtcacaa ctccattagc cccttttgtt cagcgcttag tcatggtggg
+ 1681 actgactcac cgagactaca tacggattgt gcccgcagag acatgccttt catgctgggg
+ 1741 ttttgtaagc agctccacgg ggtagtgtca ccatgccttc gacctatgct tatgaaaccc
+ 1801 gaggtaatgc ggcaggatc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_4.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_4/provided_parts_records/Frag_4.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4.
+ACCESSION Frag_4
+VERSION Frag_4
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gtttaagcca tcgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctagg cgaggttgcg atacctgaat gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_4/warnings.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_4/warnings.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,2 @@
+assembly_name;message;suggestion;data
+construct_4;Part(s) with single-sided sticky end;parts: Frag_1 & Frag_4
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/construct_5_connections_graph.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_5/construct_5_connections_graph.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/error.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/error.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+assembly_name;message;suggestion;data
+construct_5;Wrong number of constructs;expected_: 1,found: 0
+construct_5;Some parts are unused;unused_parts: Frag_1 & Frag_2 & Frag_3 & Frag_4 & Frag_4b
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_1_01.pdf
Binary file test-data/init/gibson_assembly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_1_01.pdf has changed
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_2_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_3_01.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_plots/Frag_4.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_plots/Frag_4b.pdf
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diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_1 1810 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_1.
+ACCESSION Frag_1
+VERSION Frag_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac ttccgctaag
+ 61 ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta agtcgggttg
+ 121 tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg tcatacagag
+ 181 gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg tacgttctcc
+ 241 cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt tatggaccag
+ 301 aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg gatatggccg
+ 361 cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg ggtgcctgtt
+ 421 tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca cgttccagtg
+ 481 aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag gtactgtgga
+ 541 gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg gtgttgcccg
+ 601 tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg caacatgcga
+ 661 ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg cgaccgatat
+ 721 gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag ccaaatgcac
+ 781 agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt tgttacactt
+ 841 ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt gtactgcacc
+ 901 tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt tgcaaccctc
+ 961 tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt tggcgagggc
+ 1021 caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca cggtgtatag
+ 1081 ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc ggttgttatc
+ 1141 actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat cagctggtca
+ 1201 gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa tgaaccctca
+ 1261 ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga gcagctatcg
+ 1321 aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa aacggaggga
+ 1381 gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca ttagagcagc
+ 1441 catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt tatggacaac
+ 1501 aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat tgatgggtgg
+ 1561 cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt gtggtacgat
+ 1621 ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg ctgaacatgc
+ 1681 cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg ggtacgtaac
+ 1741 agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc gatcgaattc
+ 1801 cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_2 1820 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_2.
+ACCESSION Frag_2
+VERSION Frag_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 gatcgaattc cgttttacgc cccagatcgc agctcccttg acagtgtcag ttgaatcccc
+ 61 attctaggtt tcctgataaa actaagtacg gggacgcatc agtcgaaagc aatcacagat
+ 121 aatagatatc ttgagcagaa agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa
+ 181 gtgcgggcaa caataggtgt gaggtttcac ggttgcttga tcagtagctg ttcactctct
+ 241 cgcaggccta catagtgagg tggtgagatt gttcaggtct gtctcctgcg cggttgtcga
+ 301 gccccgtcgg gcacgctaac aaggacagga attcgggtcg tcaaataaca atttacgtca
+ 361 tcgcatccct caagggtaag gcgtgatctc catctcggtt cccaattggt cattgtgata
+ 421 gccacactgc agttaccgaa ggcgatttta tactaccctg ataagtgctc gcagcccctc
+ 481 ctccctaata atgtaacgac gagcattaac ccaggagtat ttctcacgtt gctcgtgccc
+ 541 agccaaggcg atcaacgcag accggatagc gttagctagc ccacgggtaa aagcgattgt
+ 601 tgtactcttt catatgaata cagcactcgc gaatgcaagc ctacgtcggc tcgattctct
+ 661 tcctcaccac actggaggcg atgatctagc ccgtctttca ccccgtacct ttatactcgg
+ 721 ccgcgtattt ctccaccggg agctctgcct accaaagcgt cgtacgccca ggaagccgtt
+ 781 tcctttatcc tccctcatgt ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt
+ 841 ctggccaaca ctggacagac gcgcgagacg ctgataaacc cccattttcg tggggttagt
+ 901 aaatcggtgg cttcaaacgg ttcgatcgct cgcacgagca ttagtcagga gtatgattgc
+ 961 gcatcatctc tactccgtac taggttctgt agctcaggat ctccgggggg atcaagcttt
+ 1021 tatgtcccgc gggattagaa gatatccatc catatgttta ctttgatgcg ggtccgagct
+ 1081 ctctatgatg ctgctttgac aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc
+ 1141 tctacgacac gttgatgcta aacaagttgg actactaagc aaatgaagcg gaagagatac
+ 1201 tgagcgctct ctctatgact ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga
+ 1261 aatctcaaat aataatgcaa tgtgttggct aagctcgggc aaactcagga tgtgacctag
+ 1321 taccctctgc cccgtgagta cccataccca atcaagccag cccaattcgc gataggtaca
+ 1381 gataagcctt actcgtcccg atccttgact aaaacactca tcctcgatag tacgtgcctt
+ 1441 gtagagtccg acggccatag gtaaacgacc agttagtgtc gtagggtcct ccactttagc
+ 1501 tacgattgca actcccttac cttcgtgccg gcgcgctcct cttgctacca tcacgcttca
+ 1561 aatcgggtgg aagaccaact gatgaatgag ggtgcagacc ccagtggagc ataatacgat
+ 1621 gcgcccacga tactctagag ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt
+ 1681 ggccacatcg gccgcccatc cttgtgtctt ccgataagta ctccctttca aggactctcc
+ 1741 gataccggct tagaacacga acggacaacg ctttcagcgc tgagaaatga cggctgcttc
+ 1801 aaccagaacg atacagcctt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_3 1819 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_3.
+ACCESSION Frag_3
+VERSION Frag_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aaccagaacg atacagcctt ctttgctaga tagcctctag tgtcagccac caagtccgcc
+ 61 acctaatcct tcgccgaggg tcaaagcttc tgaccatcca attgttaggc actcttggaa
+ 121 ccttgcaagt acctgatcat gcagaaaatg gacttgcccg gagcatattc attataagta
+ 181 ccattcacgg caggttatag tatgcgttga cgcggggtga tacggtaatg caagtaacca
+ 241 tcgggccgcg gtatgcacat agaagggtgt ttgacttggt ttcttacagt gcaactgcat
+ 301 atgtggaccg ccattccaag tgaaaggata cgaagggagg tttcggactg ctatccagag
+ 361 catggaaagc cttcaaggtg gtgcgcactg gaatagtgac tcggggattg tatgtcgagc
+ 421 cgcgtccagt ctttcctata cttatgcgag caaatagacc gagtggaact tgattgcatc
+ 481 agccgaatca cgatgaaaac tcagcttaca attcgtaagc acttcaaata tatgcccgga
+ 541 aaatcgccgt ccagtgactt gtaatagctc cagggtcagt agcgctgccc tggccgaacc
+ 601 aggtgacggt tacgtggacc tcacagtatc aatgttgcag tgcgccacca gattaagctg
+ 661 gccgtgtcat ggtgaacaac cgtgataaaa gaacgggagt atgagagtgc cacccaagag
+ 721 tggtactcca ggattcggaa aggggagggg gcttttcctg cttaacaacc ttcctcggca
+ 781 cggtctaagc gtctcactcg tcctaaactc taccatcatg cagctaggcg aaagtataac
+ 841 tttagggtct atcaggatga gctatctgta ccacggtgat gagataagta gggggtgcgc
+ 901 tagggtcgtt cgtgttttca tcgtctatag tacctatttc tcgtcttcca ttagcgcata
+ 961 cggccatctc gcggcggcta cgtcagccag cgtcaacccc aagtcactaa tttccgttat
+ 1021 tataggtgta gctcataact tcttctgccg accaagccaa aagctttgcg gcagctgcaa
+ 1081 ggccacgtta ggctctcgga cggcagatat ttattaataa caccactggg ttccagctct
+ 1141 taacgcactt cccttcactg gatcacctgt acgcccataa gctaagcctg aagccacggc
+ 1201 ctcaatcgtg gacattactc ttagcaaatc cacattacca tgtcaccaat ccccgaaccc
+ 1261 cgcgccgacc taaggcgggg tacctcgtgc acggcagcat cgagggaaat atattacaaa
+ 1321 agacgcggcg atccaacggt tgataaaaac agttccgtgg aaggcggacg tgtgcttagc
+ 1381 gcatgcttct caccgagtga cagcaccgat tccatctcgc tagcacgccg atgagcctcg
+ 1441 ctgtgggact atggtccagc ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc
+ 1501 ggtaaggtcg atttggtggc actcgcaaga tacgcgggtt attagtagag cgcagtcagg
+ 1561 gcccatcgcc agcatttgca tgctcgccgt acgctatcct tgtactacgg ttcctcagtg
+ 1621 gctataaagg aatgtcacaa ctccattagc cccttttgtt cagcgcttag tcatggtggg
+ 1681 actgactcac cgagactaca tacggattgt gcccgcagag acatgccttt catgctgggg
+ 1741 ttttgtaagc agctccacgg ggtagtgtca ccatgccttc gacctatgct tatgaaaccc
+ 1801 gaggtaatgc ggcaggatc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_4.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_4.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4.
+ACCESSION Frag_4
+VERSION Frag_4
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gtttaagcca tcgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctagg cgaggttgcg atacctgaat gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_4b.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/provided_parts_records/Frag_4b.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4b 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4b.
+ACCESSION Frag_4b
+VERSION Frag_4b
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gttacccccc ccgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctaga ccgacgacaa acacagcact gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/construct_5/warnings.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/construct_5/warnings.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+assembly_name;message;suggestion;data
+construct_5;Part(s) with single-sided sticky end;parts: Frag_1 & Frag_4 & Frag_4b
+construct_5;Warning: parts at graph forking positions;parts: Frag_3
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/gibson_assembly_all_required_parts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/gibson_assembly_all_required_parts.txt Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,8 @@
+Frag_1
+Frag_2
+Frag_3
+Frag_4
+Frag_4b
+Frag_4c
+Frag_5
+Frag_5b
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/gibson_assembly_assembly_plan.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/gibson_assembly_assembly_plan.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,4 @@
+construct,parts
+construct_1,Frag_2,Frag_3,Frag_4,Frag_5,Frag_1
+construct_2,Frag_2,Frag_3,Frag_4b,Frag_5,Frag_1
+construct_3,Frag_2,Frag_3,Frag_4c,Frag_5b,Frag_1
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/gibson_assembly_errors.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/gibson_assembly_errors.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,5 @@
+assembly_name;message;suggestion;data;used_in
+construct_4;Wrong number of constructs;expected_: 1,found: 0;
+construct_4;Some parts are unused;unused_parts: Frag_1 & Frag_2 & Frag_3 & Frag_4;
+construct_5;Wrong number of constructs;expected_: 1,found: 0;
+construct_5;Some parts are unused;unused_parts: Frag_1 & Frag_2 & Frag_3 & Frag_4 & Frag_4b;
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/gibson_assembly_simulation_stats.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/gibson_assembly_simulation_stats.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,3 @@
+cancelled_assemblies: 0
+errored_assemblies: 2
+valid_assemblies: 3
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/gibson_assembly_summary.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/gibson_assembly_summary.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,4 @@
+assembly_name,construct_id,assembly_level,construct_size,number_of_parts,depends_on,homology_condition,used_in,parts
+construct_1,construct_1,1,8000,5,,"15-80bp, 0.0-+C Tm",,Frag_2 & Frag_3 & Frag_4 & Frag_5 & Frag_1
+construct_2,construct_2,1,8000,5,,"15-80bp, 0.0-+C Tm",,Frag_2 & Frag_3 & Frag_4b & Frag_5 & Frag_1
+construct_3,construct_3,1,8000,5,,"15-80bp, 0.0-+C Tm",,Frag_2 & Frag_3 & Frag_4c & Frag_5b & Frag_1
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/gibson_assembly_warnings.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/gibson_assembly_warnings.csv Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,4 @@
+assembly_name;message;suggestion;data;used_in
+construct_4;Part(s) with single-sided sticky end;parts: Frag_1 & Frag_4;
+construct_5;Part(s) with single-sided sticky end;parts: Frag_1 & Frag_4 & Frag_4b;
+construct_5;Warning: parts at graph forking positions;parts: Frag_3;
\ No newline at end of file
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_1.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_1.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_1 1810 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_1.
+ACCESSION Frag_1
+VERSION Frag_1
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 ctccacctgc gtctatcgta cagtgctaaa atggcagcag atagtgaaac ttccgctaag
+ 61 ctagcccctc agggtacact gcaccgaggc gtgctgtcaa tacttgatta agtcgggttg
+ 121 tcggggacct gccgtcacgc ttccgagtgt atatccggat ttagttgacg tcatacagag
+ 181 gcactaagaa gaataaacgc ttacctccag caatcgtgta gtgtcaggtg tacgttctcc
+ 241 cttgcgccgt tcggcaagcg tccggtgtcg ggctgcaagg aataaatctt tatggaccag
+ 301 aggggcttgt ttcctcatat gggtgcgtgc acttatacga ttcaaaggtg gatatggccg
+ 361 cataacacgt agccaggcta tagtcccgcg gcctaattcc ttcgagtgcg ggtgcctgtt
+ 421 tttgtttttc ctttacgaca cgaaccgctc taacctgctc tatttcgcca cgttccagtg
+ 481 aacctcttag cctaccgccc acgtacggtg ggacgcgtcg agcagttaag gtactgtgga
+ 541 gaaatcgttc aatattagaa aacaggcggt gtacgaatta ctgtgtcccg gtgttgcccg
+ 601 tttaacggct gccgtggtca taccgtgagg caccacgagg ggatgctacg caacatgcga
+ 661 ggtgtaatca gcagggaaga tcccggggat cgaaagcggt ccgcgatttg cgaccgatat
+ 721 gcataaggtg tcatttatat tacacctacg acactggtac cggctcacag ccaaatgcac
+ 781 agtctcaaga tagaattcgc aaaaattagg cttatcgggc gcttactctt tgttacactt
+ 841 ctggtctgtg agtgacgccc tgtgtcccat cactgcatgt gaggatgcgt gtactgcacc
+ 901 tgtgaattac agacgtttcc ctaccagggc gctacgttat aatgttcggt tgcaaccctc
+ 961 tatagggtga tctcgacata ccactatggt ttgcgcgtct cgggtgcttt tggcgagggc
+ 1021 caggtacggc ggtgagacag cgtattttgc gaatagggta ttcggacgca cggtgtatag
+ 1081 ctcttggaaa acgactcttc gacgggcgtg tagaagtagc caagcagttc ggttgttatc
+ 1141 actaaatgcg gaccatgtgc agccgtttag gagaggagtc tgcaatggat cagctggtca
+ 1201 gattgtacca ctcggttgag cctaaggcac ttcaggtgct cggattgtaa tgaaccctca
+ 1261 ggttacgccg ttgcgctgag atcccacaag ccataagcaa tgagaatcga gcagctatcg
+ 1321 aattacgcag cacttgctga tgaactgggt gcacctaaag cgcccgataa aacggaggga
+ 1381 gtgaggtaac tactacattg cgagtagtgc gaggggcctc cgagactaca ttagagcagc
+ 1441 catgccgaat acgacaaaat ctatagcctt gcgaacgtag gggactgatt tatggacaac
+ 1501 aggaccgaaa caagttggag ccacaacgga gctatggacg ttttcactat tgatgggtgg
+ 1561 cttgcgtccg catcccaggt ttctctggtt aattttcatg acgattcttt gtggtacgat
+ 1621 ccaggcataa gatagggcac ctaacccgat actgtgaact tatatgacgg ctgaacatgc
+ 1681 cctaatagtc tgccaaaagg gaaacctata acggctctaa acgggccccg ggtacgtaac
+ 1741 agcaatgttc ctgtccacca aggcgttttt agtaaccgcc gatcgatctc gatcgaattc
+ 1801 cgttttacgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_2.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_2.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_2 1820 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_2.
+ACCESSION Frag_2
+VERSION Frag_2
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 gatcgaattc cgttttacgc cccagatcgc agctcccttg acagtgtcag ttgaatcccc
+ 61 attctaggtt tcctgataaa actaagtacg gggacgcatc agtcgaaagc aatcacagat
+ 121 aatagatatc ttgagcagaa agacgtcttc acgaatcagg agcgagtgtc ccctttgaaa
+ 181 gtgcgggcaa caataggtgt gaggtttcac ggttgcttga tcagtagctg ttcactctct
+ 241 cgcaggccta catagtgagg tggtgagatt gttcaggtct gtctcctgcg cggttgtcga
+ 301 gccccgtcgg gcacgctaac aaggacagga attcgggtcg tcaaataaca atttacgtca
+ 361 tcgcatccct caagggtaag gcgtgatctc catctcggtt cccaattggt cattgtgata
+ 421 gccacactgc agttaccgaa ggcgatttta tactaccctg ataagtgctc gcagcccctc
+ 481 ctccctaata atgtaacgac gagcattaac ccaggagtat ttctcacgtt gctcgtgccc
+ 541 agccaaggcg atcaacgcag accggatagc gttagctagc ccacgggtaa aagcgattgt
+ 601 tgtactcttt catatgaata cagcactcgc gaatgcaagc ctacgtcggc tcgattctct
+ 661 tcctcaccac actggaggcg atgatctagc ccgtctttca ccccgtacct ttatactcgg
+ 721 ccgcgtattt ctccaccggg agctctgcct accaaagcgt cgtacgccca ggaagccgtt
+ 781 tcctttatcc tccctcatgt ctcaacgcgc gagcatcgga gagtacgcga aatcgactgt
+ 841 ctggccaaca ctggacagac gcgcgagacg ctgataaacc cccattttcg tggggttagt
+ 901 aaatcggtgg cttcaaacgg ttcgatcgct cgcacgagca ttagtcagga gtatgattgc
+ 961 gcatcatctc tactccgtac taggttctgt agctcaggat ctccgggggg atcaagcttt
+ 1021 tatgtcccgc gggattagaa gatatccatc catatgttta ctttgatgcg ggtccgagct
+ 1081 ctctatgatg ctgctttgac aaaatgtgga aagcctcagc gaccgctctg gggtcaaagc
+ 1141 tctacgacac gttgatgcta aacaagttgg actactaagc aaatgaagcg gaagagatac
+ 1201 tgagcgctct ctctatgact ttcgctatat ggcgacgtgc gaaaaacgcg atttggccga
+ 1261 aatctcaaat aataatgcaa tgtgttggct aagctcgggc aaactcagga tgtgacctag
+ 1321 taccctctgc cccgtgagta cccataccca atcaagccag cccaattcgc gataggtaca
+ 1381 gataagcctt actcgtcccg atccttgact aaaacactca tcctcgatag tacgtgcctt
+ 1441 gtagagtccg acggccatag gtaaacgacc agttagtgtc gtagggtcct ccactttagc
+ 1501 tacgattgca actcccttac cttcgtgccg gcgcgctcct cttgctacca tcacgcttca
+ 1561 aatcgggtgg aagaccaact gatgaatgag ggtgcagacc ccagtggagc ataatacgat
+ 1621 gcgcccacga tactctagag ccacgcgtcg acgttcgtaa gatgtcccgg gcccgtgggt
+ 1681 ggccacatcg gccgcccatc cttgtgtctt ccgataagta ctccctttca aggactctcc
+ 1741 gataccggct tagaacacga acggacaacg ctttcagcgc tgagaaatga cggctgcttc
+ 1801 aaccagaacg atacagcctt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_3.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_3.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,42 @@
+LOCUS Frag_3 1819 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_3.
+ACCESSION Frag_3
+VERSION Frag_3
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aaccagaacg atacagcctt ctttgctaga tagcctctag tgtcagccac caagtccgcc
+ 61 acctaatcct tcgccgaggg tcaaagcttc tgaccatcca attgttaggc actcttggaa
+ 121 ccttgcaagt acctgatcat gcagaaaatg gacttgcccg gagcatattc attataagta
+ 181 ccattcacgg caggttatag tatgcgttga cgcggggtga tacggtaatg caagtaacca
+ 241 tcgggccgcg gtatgcacat agaagggtgt ttgacttggt ttcttacagt gcaactgcat
+ 301 atgtggaccg ccattccaag tgaaaggata cgaagggagg tttcggactg ctatccagag
+ 361 catggaaagc cttcaaggtg gtgcgcactg gaatagtgac tcggggattg tatgtcgagc
+ 421 cgcgtccagt ctttcctata cttatgcgag caaatagacc gagtggaact tgattgcatc
+ 481 agccgaatca cgatgaaaac tcagcttaca attcgtaagc acttcaaata tatgcccgga
+ 541 aaatcgccgt ccagtgactt gtaatagctc cagggtcagt agcgctgccc tggccgaacc
+ 601 aggtgacggt tacgtggacc tcacagtatc aatgttgcag tgcgccacca gattaagctg
+ 661 gccgtgtcat ggtgaacaac cgtgataaaa gaacgggagt atgagagtgc cacccaagag
+ 721 tggtactcca ggattcggaa aggggagggg gcttttcctg cttaacaacc ttcctcggca
+ 781 cggtctaagc gtctcactcg tcctaaactc taccatcatg cagctaggcg aaagtataac
+ 841 tttagggtct atcaggatga gctatctgta ccacggtgat gagataagta gggggtgcgc
+ 901 tagggtcgtt cgtgttttca tcgtctatag tacctatttc tcgtcttcca ttagcgcata
+ 961 cggccatctc gcggcggcta cgtcagccag cgtcaacccc aagtcactaa tttccgttat
+ 1021 tataggtgta gctcataact tcttctgccg accaagccaa aagctttgcg gcagctgcaa
+ 1081 ggccacgtta ggctctcgga cggcagatat ttattaataa caccactggg ttccagctct
+ 1141 taacgcactt cccttcactg gatcacctgt acgcccataa gctaagcctg aagccacggc
+ 1201 ctcaatcgtg gacattactc ttagcaaatc cacattacca tgtcaccaat ccccgaaccc
+ 1261 cgcgccgacc taaggcgggg tacctcgtgc acggcagcat cgagggaaat atattacaaa
+ 1321 agacgcggcg atccaacggt tgataaaaac agttccgtgg aaggcggacg tgtgcttagc
+ 1381 gcatgcttct caccgagtga cagcaccgat tccatctcgc tagcacgccg atgagcctcg
+ 1441 ctgtgggact atggtccagc ctatgcttaa ctaggcagaa cagagagtat ggtggtcctc
+ 1501 ggtaaggtcg atttggtggc actcgcaaga tacgcgggtt attagtagag cgcagtcagg
+ 1561 gcccatcgcc agcatttgca tgctcgccgt acgctatcct tgtactacgg ttcctcagtg
+ 1621 gctataaagg aatgtcacaa ctccattagc cccttttgtt cagcgcttag tcatggtggg
+ 1681 actgactcac cgagactaca tacggattgt gcccgcagag acatgccttt catgctgggg
+ 1741 ttttgtaagc agctccacgg ggtagtgtca ccatgccttc gacctatgct tatgaaaccc
+ 1801 gaggtaatgc ggcaggatc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_4.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_4.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4.
+ACCESSION Frag_4
+VERSION Frag_4
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gtttaagcca tcgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctagg cgaggttgcg atacctgaat gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_4b.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_4b.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4b 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4b.
+ACCESSION Frag_4b
+VERSION Frag_4b
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gttacccccc ccgttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctaga ccgacgacaa acacagcact gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_4c.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_4c.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,32 @@
+LOCUS Frag_4c 1218 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_4c.
+ACCESSION Frag_4c
+VERSION Frag_4c
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 aggtaatgcg gcaggatccc gtggatccta cgcttagcct gttagggggg gggttctcct
+ 61 cggcccccag ccagcgcgta ttccgcgcat tcctccgagt gcgtatcgcg caaaccacaa
+ 121 gatacctctc aacgactagc ggtgaaccac caagcttgac atacgtgccc cttcggaaac
+ 181 gttattagtg gtcctgagtg gtacgtcccg agtatacggg gcagcgatag taacgctaca
+ 241 aatagctaga ccgacgacaa acacagcact gaatatccaa cagtggcaac gagacgctta
+ 301 gaaagggaaa ctacatacca gttcaatccg ggatgacttc aaaagggtat gtttgttttg
+ 361 aagcgaagct ttggttgtca ttcagttcct agagtttacg gcgctgatat ggctctagga
+ 421 gtccagtgaa ttcgtcagca taagccccac atcgtaggaa attgcccggt cgtcggtcta
+ 481 gcaaatgctc ggtaaactgg gagtgtacta acaccatgtc gtggtaaccc ggtggaccgg
+ 541 ctactagaga catatttatt catgctcagt tgaacctgtt tcgagggggc cgagttaaca
+ 601 taaagtgatt agtcacagcg cattaagata gaacagggat atagctcgtt gcatccataa
+ 661 attgcccacc gtagggagaa cgccgttgga aaatgagagt taggcgatga gcggttgtcg
+ 721 cccgcacaga caaaggatgc ctttataaat agtagcggcc ttgtctgcac cagacgtttg
+ 781 tgggtcgacg tgctattcta gccaaaagca aaatgtatca tactacaggc aataggccct
+ 841 atgctgacca aacttgggga cccttgcgcc ttctctctta cgcataacat gcataggtac
+ 901 ctctactcat caggcagggc ggcgtgaggt cactatggct caagatgtgt acgactaaag
+ 961 aaaggtttat gctccttccc caaggacgca tttgggactg ctacttgccc ctagcgaatt
+ 1021 cactaggatt tttgtagaac catgagcgcc ctatccgata gcacagagac aatgctacaa
+ 1081 gcaactgtgc atgcgctcga tcgccgtgca ttaatacgta ttatagcgta tcgtgtacgc
+ 1141 taatatctta gtgcaccgca cgctggttgg atacaattcc gtgaaataat tcctgcttac
+ 1201 acaggggctt tctggcgc
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_5.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_5.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,35 @@
+LOCUS Frag_5 1428 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_5.
+ACCESSION Frag_5
+VERSION Frag_5
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 acaggggctt tctggcgcat ggctgtgtct ggatgtttgt gataagaggc tccatgaacc
+ 61 cggcgggaaa tgaggggaaa ccccggggag caacgacact aagcctggca gttgttcaga
+ 121 taggacgctt ttgtcagtgg gcggttttgc atccactaac tatcataaac gacacaacgt
+ 181 cgaatgatca tcggcggttt gcatgtagag acagctcctg caacaccata ccggctcgtg
+ 241 gaattacgct gtgcgccggc cctcattcga ttgtgtccag cgtcggcgcg aatgatgatt
+ 301 gagatgtgct tcggctcaga gcgtgcacag gtagttctcc ccccttacct agctgatcca
+ 361 gcaattccac gctggcccgc gcgtccttgg gtaacactgg atctgtaccc aaatacaccg
+ 421 tcgtgattgt taactaccgt atggcggtta cgatcgagtg acactattat tagaccgcta
+ 481 ctccaagtcc caacttttca tcgccataca gaagagaacg agaaagtcga agagttatag
+ 541 cgtgtacact tctgattagc taacgaatcg atgcgtacag catactcgag caactttatg
+ 601 ggtcgtctgt ctccttgtac cccgcttgac gaggatgtgt ttgtaggcgg cttggatatc
+ 661 ggcagtgtat ccgcatggtc aaacacttta gcccgaccgg tgctcaaggt cgaaatccta
+ 721 atatagattg ggataggacc cgtccattac taggcgacat tcgcagtcac gagcccgcac
+ 781 ggggtgcctc aacacggtga cactcaattc gccggcactg agtacgacga tcgtgattgc
+ 841 cataccgtca tgttttgtgt tacccctgat aagaagcgca gatatggcac gggggcagag
+ 901 ggcggagtag acccatgcaa aactctagcc tctgggcagc atgatcgacg tagaacgccg
+ 961 ttgtgactca ctagtttcag ttatgatgtt cagccaagaa tcctccattt tgacgtgaac
+ 1021 cttctccctt tacaccttga agctgcaata ttaagtcgac cctttaagtt gccttgtctt
+ 1081 ggtctagagc ccgcagctca ccgataaaat gagcagtcaa ttttagcggc ggttgtccag
+ 1141 gttacatgca ctttgggctg gaaccgcgtt acgtttggag tacttagaag tgtcgtaggc
+ 1201 ataggagagc cgaaacttga tattgggtct agttagtgct ctaccccgct tcggatccgt
+ 1261 aatagtgatg ttgcatgaga cgcttgcctc aaggcgacat acggtggcgg ttgctggaaa
+ 1321 tgacgcccca ccccgtgata atttggggac gagccgcacg ataacttctg ccagcgaccg
+ 1381 cccctcccac gtccgatggt gattccgaac tccacctgcg tctatcgt
+//
diff -r 32e44a646b68 -r 3171db614963 test-data/init/gibson_assembly_simulation/part_records/Frag_5b.gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/init/gibson_assembly_simulation/part_records/Frag_5b.gb Fri May 16 11:32:06 2025 +0000
@@ -0,0 +1,35 @@
+LOCUS Frag_5b 1428 bp DNA circular UNK 01-JAN-1980
+DEFINITION Frag_5b.
+ACCESSION Frag_5b
+VERSION Frag_5b
+KEYWORDS .
+SOURCE .
+ ORGANISM .
+ .
+FEATURES Location/Qualifiers
+ORIGIN
+ 1 acaggggctt tctggcgcat ggctgtgtct ggaaaaaaaa aaaaaaaaaa aacatgaacc
+ 61 cggcgggaaa tgaggggaaa ccccggggag caacgacact aagcctggca gttgttcaga
+ 121 taggacgctt ttgtcagtgg gcggttttgc atccactaac tatcataaac gacacaacgt
+ 181 cgaatgatca tcggcggttt gcatgtagag acagctcctg caacaccata ccggctcgtg
+ 241 gaattacgct gtgcgccggc cctcattcga ttgtgtccag cgtcggcgcg aatgatgatt
+ 301 gagatgtgct tcggctcaga gcgtgcacag gtagttctcc ccccttacct agctgatcca
+ 361 gcaattccac gctggcccgc gcgtccttgg gtaacactgg atctgtaccc aaatacaccg
+ 421 tcgtgattgt taactaccgt atggcggtta cgatcgagtg acactattat tagaccgcta
+ 481 ctccaagtcc caacttttca tcgccataca gaagagaacg agaaagtcga agagttatag
+ 541 cgtgtacact tctgattagc taacgaatcg atgcgtacag catactcgag caactttatg
+ 601 ggtcgtctgt ctccttgtac cccgcttgac gaggatgtgt ttgtaggcgg cttggatatc
+ 661 ggcagtgtat ccgcatggtc aaacacttta gcccgaccgg tgctcaaggt cgaaatccta
+ 721 atatagattg ggataggacc cgtccattac taggcgacat tcgcagtcac gagcccgcac
+ 781 ggggtgcctc aacacggtga cactcaattc gccggcactg agtacgacga tcgtgattgc
+ 841 cataccgtca tgttttgtgt tacccctgat aagaagcgca gatatggcac gggggcagag
+ 901 ggcggagtag acccatgcaa aactctagcc tctgggcagc atgatcgacg tagaacgccg
+ 961 ttgtgactca ctagtttcag ttatgatgtt cagccaagaa tcctccattt tgacgtgaac
+ 1021 cttctccctt tacaccttga agctgcaata ttaagtcgac cctttaagtt gccttgtctt
+ 1081 ggtctagagc ccgcagctca ccgataaaat gagcagtcaa ttttagcggc ggttgtccag
+ 1141 gttacatgca ctttgggctg gaaccgcgtt acgtttggag tacttagaag tgtcgtaggc
+ 1201 ataggagagc cgaaacttga tattgggtct agttagtgct ctaccccgct tcggatccgt
+ 1261 aatagtgatg ttgcatgaga cgcttgcctc aaggcgacat acggtggcgg ttgctggaaa
+ 1321 tgacgcccca ccccgtgata atttggggac gagccgcacg ataacttctg ccagcgaccg
+ 1381 cccctcccac gtccgatggt gattccgaac tccacctgcg tctatcgt
+//