{ "about": { "generatedBy": "pipeline/sequence-toolkit/reference.py", "scriptSha256": "1bc66633d1a780a7f255b02743e9258652769ed35b770f193c5d74e0070410d6", "recordedOn": "2026-10-06", "python": "3.11.15", "oracle": "Biopython 1.88 Bio.Seq.Seq.translate", "oracleLicence": "Biopython Licence Agreement or BSD-3-Clause", "rule": "No value in this file comes from the Drybench engine under test.", "fixture": "Translation, three sequences x tables 1, 2, 11 x six frames x full and to_stop (brief section 4.3 (4))", "tolerance": "Brief: translation exact", "frames": "+1, +2, +3 read the given strand from position 1, 2, 3; -1, -2, -3 read the reverse complement from its position 1, 2, 3; a trailing partial codon is dropped", "modes": "full: every codon, stops as '*'; to_stop: up to (not including) the first in-frame stop", "cds": "Annotated CDS features translated with alternative initiation codons off (first codon read as its amino acid; to_stop) and on (Biopython cds=True: an alternative start of that table reads as M), checked against the record's /translation qualifier.", "sequences": [ { "id": "ins-mrna", "accession": "NM_000207.3", "range": null, "description": "Homo sapiens insulin (INS), transcript variant 1, mRNA (RefSeq), whole record", "why": "Teaching example (insulin); a nuclear mRNA read with the standard code; AGA/AGG codons make table 2 cut the CDS short.", "length": 465, "sequence": "AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAGACGCAGCCCGCAGGCAGCCCCACACCCGCCGCCTCCTGCACCGAGAGAGATGGAATAAAGCCCTTGAACCAGC", "sha256": "2132509911c26572e7dfcaea140a3c893ab2cb6ec1d71cfe23b91fcf09ae4ff1", "file": "pipeline/sequence-toolkit/inputs/nucleotide/NM_000207.3.gb", "retrieved": "2026-10-06T02:24:10Z", "naturalTable": 1, "licence": "NCBI: no restrictions placed by NCBI on GenBank/RefSeq data (submitter rights may apply)" }, { "id": "mt-atp8-atp6-cox3", "accession": "NC_012920.1", "range": [ 8295, 9990 ], "description": "Homo sapiens mitochondrion (rCRS), positions 8295-9990: tRNA-Lys, ATP8, ATP6 and COX3", "why": "Vertebrate mitochondrial code: TGA is Trp and AGA/AGG are stops; ATP8 and ATP6 overlap in different frames; COX3 ends with an incomplete stop (T, completed by polyadenylation), so its ORF is not stop-terminated in the DNA.", "length": 1696, "sequence": "CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTT", "sha256": "27920863d5c2e03f14784ddf0a553d59643e759b8cef3ddac95ff8fbf8c19e5c", "file": "pipeline/sequence-toolkit/inputs/nucleotide/NC_012920.1_8295-9990.gb", "retrieved": "2026-10-06T02:24:11Z", "naturalTable": 2, "licence": "NCBI: no restrictions placed by NCBI on GenBank/RefSeq data (submitter rights may apply)" }, { "id": "ecoli-lacI", "accession": "J01636.1", "range": [ 1, 1500 ], "description": "Escherichia coli lactose operon, positions 1-1500: lacI (GTG start) and the start of lacZ", "why": "Bacterial code: lacI starts with GTG (Met only with alternative initiation codons on); lacZ runs off the end of the region, so it is not stop-terminated.", "length": 1500, "sequence": "GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGTCAATTCAGGGTGGTGAATGTGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGGATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAA", "sha256": "3866d793146ad0a0c8c75011f117b5b4ee6a341a971e61f00d9fe85fc1a227b8", "file": "pipeline/sequence-toolkit/inputs/nucleotide/J01636.1_1-1500.gb", "retrieved": "2026-10-06T02:24:12Z", "naturalTable": 11, "licence": "NCBI: no restrictions placed by NCBI on GenBank/RefSeq data (submitter rights may apply)" } ], "geneticCodes": { "file": "pipeline/sequence-toolkit/ncbi/gc.prt", "version": "4.6", "retrieved": "2026-10-06T02:24:29Z", "sha256": "2aecbdd09ecc5e0d233c105090a593737298ef93d88f6bc0c1bef26df6051a04", "tables": { "1": { "name": "Standard", "stops": [ "TAA", "TAG", "TGA" ], "starts": [ "ATG", "CTG", "TTG" ], "biopythonEqualsGcPrt": true }, "2": { "name": "Vertebrate Mitochondrial", "stops": [ "AGA", "AGG", "TAA", "TAG" ], "starts": [ "ATA", "ATC", "ATG", "ATT", "GTG" ], "biopythonEqualsGcPrt": true }, "11": { "name": "Bacterial, Archaeal and Plant Plastid", "stops": [ "TAA", "TAG", "TGA" ], "starts": [ "ATA", "ATC", "ATG", "ATT", "CTG", "GTG", "TTG" ], "biopythonEqualsGcPrt": true } } } }, "cases": [ { "id": "ins-mrna.t1.f+1.full", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "SPPGQAASEEAIKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPL*TNTCAAHTWWKLST*CAGNEASSTHPRPAGRQRTCRWGRWSWAGALVQAACSPWPWRGPCRSVALWNNAVPASAPSTSWRTTATRRSPQAAPHPPPPAPREME*SP*TS", "length": 155 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f+1.to_stop", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "SPPGQAASEEAIKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPL", "length": 45 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f+2.full", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "ALQDRLHQKRPSSRSLSFCHGPVDAPPAPAGAAGPLGT*PSRSLCEPTPVRLTPGGSSLPSVRGTRLLLHTQDPPGGRGPAGGAGGAGRGPWCRQPAALGPGGVPAEAWHCGTMLYQHLLPLPAGELLQLDAARRQPHTRRLLHRERWNKALEP", "length": 154 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f+2.to_stop", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "ALQDRLHQKRPSSRSLSFCHGPVDAPPAPAGAAGPLGT", "length": 38 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f+3.full", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "PSRTGCIRRGHQADHCPSAMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*TQPAGSPTPAASCTERDGIKPLNQ", "length": 154 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f+3.to_stop", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "PSRTGCIRRGHQADHCPSAMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN", "length": 129 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f-1.full", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "AGSRALFHLSRCRRRRVWGCLRAASSCSSSPAGRGSRCWYSIVPQCHASAGTPPGPRAAGCLHQGPRPAPPAPPAGPLPPGGSWVCRRSLVPRTLGRELPPGVSRTGVGSQRLRLGQVPRGPAAPAGAGGASTGPWQKDSDLLDGLF*CSLSWRA", "length": 155 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f-1.to_stop", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "AGSRALFHLSRCRRRRVWGCLRAASSCSSSPAGRGSRCWYSIVPQCHASAGTPPGPRAAGCLHQGPRPAPPAPPAGPLPPGGSWVCRRSLVPRTLGRELPPGVSRTGVGSQRLRLGQVPRGPAAPAGAGGASTGPWQKDSDLLDGLF", "length": 147 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f-2.full", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACTRAPAQLHLPHLQVLCLPAGLGCVEEASFPAH*VESFHQV*AAQVLVHKGCGWVRSPEGQQRQQGQEAHPQGHGRRTVICLMASSDAACPGG", "length": 154 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f-2.to_stop", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACTRAPAQLHLPHLQVLCLPAGLGCVEEASFPAH", "length": 94 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f-3.full", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "WFKGFIPSLSVQEAAGVGLPAGCV*LQ*FSSW*REQMLVQHCSTMPRFCRDPSRAKGCRLPAPGPPPSSTCPTCRSSASRRVLGV*KKPRSPHTR*RASTRCEPHRCWFTKAAAGSGPQRASSASRGRRRIHRAMAEGQ*SA*WPLLMQPVLEG", "length": 154 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t1.f-3.to_stop", "input": { "sequenceId": "ins-mrna", "table": 1, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "WFKGFIPSLSVQEAAGVGLPAGCV", "length": 24 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f+1.full", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "SPPGQAASEEAIKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPLWTNTCAAHTWWKLST*CAGNEASSTHP*PAG*Q*TC*WG*WSWAGALVQAACSPWPW*GPC*SVALWNNAVPASAPSTSW*TTAT*RSPQAAPHPPPPAP*EME*SPWTS", "length": 155 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f+1.to_stop", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "SPPGQAASEEAIKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPLWTNTCAAHTWWKLST", "length": 60 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f+2.full", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "ALQD*LHQK*PSS*SLSFCHGPVDAPPAPAGAAGPLGTWPSRSLCEPTPVRLTPGGSSLPSVRGT*LLLHTQDPPGG*GPAGGAGGAGRGPWC*QPAALGPGGVPAEAWHCGTMLYQHLLPLPAGELLQLDAAR*QPHTRRLLHRE*WNKALEP", "length": 154 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f+2.to_stop", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "ALQD", "length": 4 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f+3.full", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "PS*TGCI**GHQADHCPSAMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*TQPAGSPTPAASCTE*DGMKPLNQ", "length": 154 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f+3.to_stop", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "PS", "length": 2 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f-1.full", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "AGS*ALFHLSRC**RRVWGCLRAASSCSSSPAG*GS*CWYSIVPQCHASAGTPPGP*AAGCLHQGPRPAPPAPPAGPLPPGGSWVC**SLVPRTLG*ELPPGVSRTGVGSQ*LRLGQVP*GPAAPAGAGGASTGPWQKDSDLLDGLFWCSLSW*A", "length": 155 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f-1.to_stop", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "AGS", "length": 3 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f-2.full", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACT*APAQLHLPHLQVLCLPAGLGCVEEASFPAH*VESFHQVWAAQVLVHKGCGWV*SPEGQQRQQGQEAHPQGHG**TVICLMASSDAACPGG", "length": 154 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f-2.to_stop", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACT", "length": 63 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f-3.full", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "WFKGFIPSLSVQEAAGVGLPAGCV*LQ*FSSW**EQMLVQHCSTMPRFC*DPS*AKGC*LPAPGPPPSSTCPTC*SSASRRVLGV*KKPRSPHT***AST*CEPH*CWFTKAAAGSGPQ*ASSAS*G**RIH*AMAEGQWSAWWPLLMQPVLEG", "length": 154 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t2.f-3.to_stop", "input": { "sequenceId": "ins-mrna", "table": 2, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "WFKGFIPSLSVQEAAGVGLPAGCV", "length": 24 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f+1.full", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "SPPGQAASEEAIKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPL*TNTCAAHTWWKLST*CAGNEASSTHPRPAGRQRTCRWGRWSWAGALVQAACSPWPWRGPCRSVALWNNAVPASAPSTSWRTTATRRSPQAAPHPPPPAPREME*SP*TS", "length": 155 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f+1.to_stop", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "SPPGQAASEEAIKQITVLLPWPCGCASCPCWRCWPSGDLTQPQPL", "length": 45 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f+2.full", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "ALQDRLHQKRPSSRSLSFCHGPVDAPPAPAGAAGPLGT*PSRSLCEPTPVRLTPGGSSLPSVRGTRLLLHTQDPPGGRGPAGGAGGAGRGPWCRQPAALGPGGVPAEAWHCGTMLYQHLLPLPAGELLQLDAARRQPHTRRLLHRERWNKALEP", "length": 154 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f+2.to_stop", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "ALQDRLHQKRPSSRSLSFCHGPVDAPPAPAGAAGPLGT", "length": 38 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f+3.full", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "PSRTGCIRRGHQADHCPSAMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*TQPAGSPTPAASCTERDGIKPLNQ", "length": 154 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f+3.to_stop", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "PSRTGCIRRGHQADHCPSAMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN", "length": 129 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f-1.full", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "AGSRALFHLSRCRRRRVWGCLRAASSCSSSPAGRGSRCWYSIVPQCHASAGTPPGPRAAGCLHQGPRPAPPAPPAGPLPPGGSWVCRRSLVPRTLGRELPPGVSRTGVGSQRLRLGQVPRGPAAPAGAGGASTGPWQKDSDLLDGLF*CSLSWRA", "length": 155 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f-1.to_stop", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (465 nt)" }, "expected": { "protein": "AGSRALFHLSRCRRRRVWGCLRAASSCSSSPAGRGSRCWYSIVPQCHASAGTPPGPRAAGCLHQGPRPAPPAPPAGPLPPGGSWVCRRSLVPRTLGRELPPGVSRTGVGSQRLRLGQVPRGPAAPAGAGGASTGPWQKDSDLLDGLF", "length": 147 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f-2.full", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACTRAPAQLHLPHLQVLCLPAGLGCVEEASFPAH*VESFHQV*AAQVLVHKGCGWVRSPEGQQRQQGQEAHPQGHGRRTVICLMASSDAACPGG", "length": 154 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f-2.to_stop", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "LVQGLYSISLGAGGGGCGAACGLRLVAVVLQLVEGADAGTALFHNATLLQGPLQGQGLQAACTRAPAQLHLPHLQVLCLPAGLGCVEEASFPAH", "length": 94 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f-3.full", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "WFKGFIPSLSVQEAAGVGLPAGCV*LQ*FSSW*REQMLVQHCSTMPRFCRDPSRAKGCRLPAPGPPPSSTCPTCRSSASRRVLGV*KKPRSPHTR*RASTRCEPHRCWFTKAAAGSGPQRASSASRGRRRIHRAMAEGQ*SA*WPLLMQPVLEG", "length": 154 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ins-mrna.t11.f-3.to_stop", "input": { "sequenceId": "ins-mrna", "table": 11, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (462 nt)" }, "expected": { "protein": "WFKGFIPSLSVQEAAGVGLPAGCV", "length": 24 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f+1.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "HCKANLALTF*VKD*ENQHLFTVKCPN*ILPYGPP*LPPYSLHYSSSPN*KY*TQTTTYLPHQSP*K*KIITNPENQNERKSVRFIHCPHNPRPTRRSTDHSISPSIDPHLQISHQQPTNHHPTMTNQTNLKTNDNHTQH*RTNLISYTSILNHFYCHN*PPRTPASLIYTNHPTIYKPSHGHPLMSGHSDYRLSL*D*KCPSPLLTTRHTYTPYPHTSYYRNHQPTHSTNSPGRTPNR*HYCRPPTHAPNWKRHPSNINH*PSLYTYHLHNSNSTDYPRNRCRLNPSLRFHTSSKPLPARQHIMTHQSHAYHIVKPSP*PLTGALSALLMTSGLAM*FHFHSITLLILGLLTNTLTIYQ*WRDVTRESTYQGHHTPPVQKGLRYGIILFITSEVFFFAGFF*AFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSIT*AHHSLIENNRNQIIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLIFHFTSKHHFGFEAAA*YWHFVDVV*LFLYVSIY**GS", "length": 565 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f+1.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "HCKANLALTF", "length": 10 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f+2.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "TVKLT*H*PFKLKIKRTNTSLQ*NAPTKYYRMAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL*QTLRTKMNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQ*LIKLTSKQMITIHNTKGRT*SLILVSLIIFIATTNLLGLLPHSFTPTTQLSINLAMAIPL*AGTVIIGFRSKIKNALAHFLPQGTPTPLIPILVIIETISLLIQPIALAVRLTANITAGHLLMHLIGSATLAISTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT**PTNHMPII**NPAHDP*QGPSQPS**PPA*PCDFTSTP*RSSY*AY*PTH*PYTNDGAM*HEKAHTKATTHHLSKKAFDTG*SYLLPQKFFSSQDFSEPFTTPA*PLPPN*EGTGPQQASPR*IP*KSHS*THPYYSHQEYQSPELTIV**KTTETK*FKHCLLQFYWVSILPSYKPQSTSSLPSPFPTASTAQHFL*PQASTDFTSLLAQLSSLSASSAN*YFTLHPNITLASKPPPDTGIL*MWFDYFCMSPSIDEGL", "length": 565 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f+2.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "TVKLT", "length": 5 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f+3.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "L*S*LSINLLS*RLREPTPLYSEMPQLNTTVWPTIITPILLTLFLITQLKILNTNYHLPPSPKPIKIKNYNKP*EPK*TKICSLHSLPPQS*AYPPQY*SFYFPLY*SPPPNISSTTD*SPPNND*SN*PQNK**PYTTLKDEPDLLY*YP*SFLLPQLTSSDSCLTHLHQPPNYL*T*PWPSPYERAQ*L*AFALRLKMP*PTSYHKAHLHPLSPY*LLSKPSAYSFNQ*PWPYA*PLTLLQATYSCT*LEAPP*QYQPLTFPLHLSSSQF*FY*LS*KSLSP*SKPTFSHF**ASTCTTTHNDPPITCLSYSKTQPMTPNRGPLSPPNDLRPSHVISLPLHNAPHTRPTNQHTNHIPMMARCNTRKHIPRPPHTTCPKRPSIRDNPIYYLRSFFLRRIFLSLLPLQPSPYPPIRRALAPNRHHPAKSPRSPTPKHIRITRIRSINHLSSP*SNRKQPKPNNSSTAYYNFTGSLFYPPTSLRVLRVSLHHFRRHLRLNIFCSHRLPRTSRHYWLNFPHYLLHPPTNISLYIQTSLWLRSRRLILAFCRCGLTISVCLHLLMRV", "length": 564 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f+3.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "L", "length": 1 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f-1.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "KTLINRWRHTEIVKPHLQNASIRRRLRSQSDVWM*SEILVGG*SR**GKLSQ**REVRGSLWLQKMLSRRCRRKW*RETRSTLRLVGG*NRDPVKL**AVLELFGFGCFLLDYGELR*LILLMRVIRMCLGVGLLGDLAG*CLLGASALLIGG*GLGWSGKRLRKILRRKKLLR**IGLSRIEGLFGQVVCGGLGMCFLVLHRAIIGIWLVCWLVGLV*GALWSGSEITWLGRRSLGGLRGPLLGVMGWVLLYDRHVIGGSLCVVVQVEAY*KCENVGLD*GDSDF*DSQ*N*NCEDDKCRGKVNG*YC*GGASN*VHE*VACSNVSG*AYGQGYWLNE*ADGFDNN*YGDKGCRCALW*EVG*GIFNLRAKAYNHCARS*GDGHG*VYR*LGGWCK*VRQESEEVSCGNKND*GY*YKRSGSSFSVVYGYHLF*G*FD*SLLGGD*SVVDEIFGGGDQ*RGK*NDQYCGG*A*DCGGNE*SEQIFVHFGSQGLL*FFIFMGFGEGGRW*FVFNIFSWVMRNSVRSMGVIMVGHTVVFSWGISL*RGVGSLNL*LKRLMLS*LYS", "length": 565 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f-1.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "KTLINRWRHTEIVKPHLQNASIRRRLRSQSDVWM", "length": 34 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f-2.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "RPSSIDGDIQK*SNHIYKMPVSGGGFEAKVMFGCKVKY*LADEADSEES*ANNDVKSVEACGYKKC*AVDAVGNGEGRLEVL*GL*EGKIETQ*NCNKQCLNYLVSVVFY*TMVSSGD*YS*CE*YGCV*EWDF*GI*RGDACWGPVPS*LGGRG*AGVVKGSEKSCEEKNF*GNK*DYPVSKAFLDRWCVVALVCAFSCYIAPSLVYG*CVG**A*YEERYGVEVKSHG*AGGH*EG*EGPC*GSWAGFYYMIGM*LVGHYVLSCR*RLTRSVKT*AWIKATAISRIVSRIRIVKMISVEGRLMVDIARVALPIRCMSRWPAVMLAVRRTARAIG*MSRLMVSIITSMGIRGVGVPCGKKWARAFLILERKPIITVPAHKGMAMARFIDSWVVGVNE*GRSPRRLVVAIKMIKDTSIRDQVRPLVLCMVIICFEVSLISHCWVVISRLLMRYLEVGINRGGNRMISTAAGRPRIVGAMNEANRFSFILVLRVCYNFLFLWALVREVGGSLCLIFLVG**GIV*GVWG*LWWAIR*YLVGAFHCKEVLVLLIFNLKG*C*VSFTV", "length": 565 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f-2.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "RPSSIDGDIQK", "length": 11 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f-3.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "DPHQ*METYRNSQTTSTKCQYQAAASKPK*CLDVK*NISWRMKQIVRKVEPIMT*SPWKPVATKNVEP*MPSEMVKGDSKYSEACRRVK*RPSKIVISSA*IIWFRLFSIRLW*AQVIDTPDASNTDVFRSGTSRGFSGVMPVGGQCPPNWGVGARLEW*KAQKNPAKKKTSEVINRIIPYRRPFWTGGVWWPWYVLSRVTSRHHWYMVSVLVSRPSMRSVMEWK*NHMARPEVIRRAERAPVRGHGLGFTI**ACDWWVIMCCRAGRGLLEV*KRRLGLRRQRFLG*SVELEL*R**V*REG*WLILLGWRFQLGA*VGGLQ*C*RLGVRPGLLVE*VG*WFR**LVWG*GV*VCLVVRSGLGHF*S*SESL*SLCPLIRGWPWLGL*IVGWLV*MSEAGVRGG*LWQ*K*LRILV*EIRFVL*CCVWLSFVLRLV*LVIVGW*LVGC**DIWRWGSIEGEIE*SVLRRVGLGLWGQ*MKRTDFRSFWFSGFVIIFYFYGLW*GR*VVVCV*YF*LGDEE*CKEYGGNYGGPYGSI*LGHFTVKRCWFS*SLT*KVNAKLALQ", "length": 564 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t1.f-3.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 1, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "DPHQ", "length": 4 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f+1.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "HCKANLALTF*VKD*ENQHLFTVKCPN*MLPYGPP*LPPYSLHYSSSPN*KY*TQTTTYLPHQSP*K*KIMTNPENQNERKSVRFIHCPHNP*PTRRSTDHSISPSIDPHLQMSHQQPTNHHPTMTNQTNLKTNDNHTQH**TNLISYTSILNHFYCHN*PPRTPASLIYTNHPTIYKPSHGHPLMSGHSDY*LSL*D*KCPSPLLTT*HTYTPYPHTSYYRNHQPTHSTNSPGRTPNR*HYC*PPTHAPNWKRHPSNINH*PSLYTYHLHNSNSTDYP*NRCRLNPSLRFHTSSKPLPARQHMMTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS", "length": 565 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f+1.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "HCKANLALTF", "length": 10 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f+2.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "TVKLT*H*PFKLKIK*TNTSLQWNAPTKYYRMAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL*QTL*TKMNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQWLIKLTSKQMMTMHNTKGRTWSLMLVSLIIFIATTNLLGLLPHSFTPTTQLSMNLAMAIPLWAGTVIMGFRSKIKNALAHFLPQGTPTPLIPMLVIIETISLLIQPMALAVRLTANITAGHLLMHLIGSATLAMSTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT*WPTNHMPIM**NPAHDP*QGPSQPS*WPPA*PCDFTSTP*RSSY*AY*PTH*PYTNDGAM*HEKAHTKATTHHLSKKAFDTG*SYLLPQKFFSSQDFSEPFTTPA*PLPPN*EGTGPQQASPR*IP*KSHS*THPYYSHQEYQSPELTMV**KTTETK*FKHCLLQFYWVSILPSYKPQSTSSLPSPFPTASTAQHFL*PQASTDFTSLLAQLSSLSASSAN*YFTLHPNITLASKPPPDTGIL*MWFDYFCMSPSIDEGL", "length": 565 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f+2.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "TVKLT", "length": 5 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f+3.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "L*S*LSINLLS**L*EPTPLYSEMPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS*AYPPQYWSFYFPLYWSPPPNISSTTD*SPPNND*SN*PQNKW*PYTTLKDEPDLLY*YP*SFLLPQLTSSDSCLTHLHQPPNYL*T*PWPSPYERAQWL*AFAL*LKMP*PTSYHKAHLHPLSPY*LLSKPSAYSFNQ*PWPYA*PLTLLQATYSCT*LEAPP*QYQPLTFPLHLSSSQF*FYWLS*KSLSP*SKPTFSHF**ASTCTTTHNDPPITCLSYSKTQPMTPN*GPLSPPNDLRPSHVISLPLHNAPHT*PTNQHTNHMPMMARCNT*KHMP*PPHTTCPK*PSMRDNPIYYL*SFFLR*IFLSLLPLQPSPYPPI**ALAPN*HHPAKSP*SPTPKHIRITRI*SINHLSSP*SN*KQPKPNNSSTAYYNFTGSLFYPPTSL*VLRVSLHHFRRHLRLNIFCSH*LPRTSRHYWLNFPHYLLHPPTNISLYIQTSLWLRSRRLMLAFC*CGLTISVCLHLLM*V", "length": 564 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f+3.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "L", "length": 1 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f-1.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "KTLIN*W*HTEMVKPHLQNASI*RRLRSQSDVWM*SEMLVGGWS**WGKLSQ*WREVRGSLWLQKMLSR*CRRKWW*ETRSTL*LVGG*N*DPVKL**AVLELFGFGCFLLDYGEL*WLMLLMRVMRMCLGVGLLGDLAGWCLLGASALLIGG*GLGWSGK*L*KILR*KKLL***MGLSRIEGLFGQVVCGGLGMCFLVLHRAIIGMWLVCWLVGLVWGALWSGSEITWLGR*SLGGL*GPLLGVMGWVLLYD*HVIGGSLCVVVQVEAY*KCENVGLD*GDSDF*DSQ*N*NCEDDKC*GKVNGWYC*GGASN*VHE*VACSNVSG*AYGQGYWLNE*ADGFDNN*YGDKGC*CALW*EVG*GIFNL*AKAYNHCARS*GDGHG*VY**LGGWCKWV*QESEEVSCGNKND*GY*YK*SGSSFSVVYGYHLFWG*FD*SLLGGD*SVVDEMFGGGDQ**GK*NDQYCGG*A*DCGGNEWSEQIFVHFGSQGLL*FFIFMGFGEGG*W*FVFNIFSWVM*NSV*SMGVIMVGHTVVFSWGISL**GVGSLNL*LK*LMLS*LYS", "length": 565 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f-1.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "KTLIN", "length": 5 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f-2.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "*PSSMDGDMQK*SNHIYKMPVSGGGFEAKVMFGCKVKY*LADEADSEESWANNDVKSVEACGYKKCWAVDAVGNGEG*LEVLWGL*EGKMETQ*NCNKQCLNYLVSVVFY*TMVSSGDWYSWCE*YGCV*EWDF*GI*RGDACWGPVPS*LGG*G*AGVVKGSEKSCEEKNFWGNK*DYPVSKAFLD*WCVVALVCAFSCYIAPSLVYG*CVG**A*YEERYGVEVKSHG*AGGH*EGWEGPC*GSWAGFYYMMGMWLVGHYVLSC***LT*SVKT*AWIKATAIS*MVS*I*IVKMMSVEG*LMVDIA*VALPI*CMS*WPAVMLAV*RTA*AIGWMS*LMVSMMTSMGM*GVGVPCGKKWA*AFLILERKPMITVPAHKGMAMA*FMDSWVVGVNEWG*SP**LVVAMKMIKDTSM*DQVRPLVLCMVIICFEVSLISHCWVVISRLLM*YLEVGIN*GGN*MISTAAG*P*IVGAMNEAN*FSFILVL*VCYNFLFLWALV*EVGGSLCLMFLVGWWGMV*GVWG*LWWAMR*YLVGAFHCKEVLVLLIFNLKG*C*VSFTV", "length": 565 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f-2.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "", "length": 0 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f-3.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "DPHQ*METY*NSQTTSTKCQYQAAASKPKWCLDVKWNISWRMKQMV*KVEPMMTWSPWKPVATKNVEP*MPSEMVKGDSKYSEAC**VK**PSKIVMSSAWIIWFRLFSI*LWWAQVIDTPDASNTDVF*SGTS*GFSGVMPVGGQCPPNWGVGA*LEW*KAQKNPAKKKTSEVMN*IIPYR*PFWTGGVWWPWYVLSRVTSRHHWYMVSVLVS*PSM*SVMEWKWNHMA*PEVI**AE*APV*GHGLGFTMW*ACDWWVIMCCRAG*GLLEVWKR*LGL*RQRFLG*SVELELW*W*V**EG*WLMLLGWRFQLGAWVGGLQ*C*RLGVRPGLLVEWVGWWFR**LVWG*GV*VCLVV*SGLGHF*S*SESL*SLCPLM*GWPWLGL*MVGWLV*MSEAGVRGG*LWQ*KWL*MLV*EI*FVL*CCVWLSFVL*LVWLVIVGWWLVGCWWDIW*WGSMEGEMEWSVLRRVGLGLWGQWMKRTDFRSFWFSGFVMIFYFYGLWWG**VVVCV*YF*LGDEE*CKEYGGNYGGPYGSI*LGHFTVK*CWFS*SLT*KVNAKLALQ", "length": 564 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t2.f-3.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 2, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "DPHQ", "length": 4 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f+1.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "HCKANLALTF*VKD*ENQHLFTVKCPN*ILPYGPP*LPPYSLHYSSSPN*KY*TQTTTYLPHQSP*K*KIITNPENQNERKSVRFIHCPHNPRPTRRSTDHSISPSIDPHLQISHQQPTNHHPTMTNQTNLKTNDNHTQH*RTNLISYTSILNHFYCHN*PPRTPASLIYTNHPTIYKPSHGHPLMSGHSDYRLSL*D*KCPSPLLTTRHTYTPYPHTSYYRNHQPTHSTNSPGRTPNR*HYCRPPTHAPNWKRHPSNINH*PSLYTYHLHNSNSTDYPRNRCRLNPSLRFHTSSKPLPARQHIMTHQSHAYHIVKPSP*PLTGALSALLMTSGLAM*FHFHSITLLILGLLTNTLTIYQ*WRDVTRESTYQGHHTPPVQKGLRYGIILFITSEVFFFAGFF*AFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSIT*AHHSLIENNRNQIIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLIFHFTSKHHFGFEAAA*YWHFVDVV*LFLYVSIY**GS", "length": 565 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f+1.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "HCKANLALTF", "length": 10 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f+2.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "TVKLT*H*PFKLKIKRTNTSLQ*NAPTKYYRMAHHNYPHTPYTIPHHPTKNIKHKLPPTSLTKAHKNKKL*QTLRTKMNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQ*LIKLTSKQMITIHNTKGRT*SLILVSLIIFIATTNLLGLLPHSFTPTTQLSINLAMAIPL*AGTVIIGFRSKIKNALAHFLPQGTPTPLIPILVIIETISLLIQPIALAVRLTANITAGHLLMHLIGSATLAISTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT**PTNHMPII**NPAHDP*QGPSQPS**PPA*PCDFTSTP*RSSY*AY*PTH*PYTNDGAM*HEKAHTKATTHHLSKKAFDTG*SYLLPQKFFSSQDFSEPFTTPA*PLPPN*EGTGPQQASPR*IP*KSHS*THPYYSHQEYQSPELTIV**KTTETK*FKHCLLQFYWVSILPSYKPQSTSSLPSPFPTASTAQHFL*PQASTDFTSLLAQLSSLSASSAN*YFTLHPNITLASKPPPDTGIL*MWFDYFCMSPSIDEGL", "length": 565 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f+2.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "TVKLT", "length": 5 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f+3.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "L*S*LSINLLS*RLREPTPLYSEMPQLNTTVWPTIITPILLTLFLITQLKILNTNYHLPPSPKPIKIKNYNKP*EPK*TKICSLHSLPPQS*AYPPQY*SFYFPLY*SPPPNISSTTD*SPPNND*SN*PQNK**PYTTLKDEPDLLY*YP*SFLLPQLTSSDSCLTHLHQPPNYL*T*PWPSPYERAQ*L*AFALRLKMP*PTSYHKAHLHPLSPY*LLSKPSAYSFNQ*PWPYA*PLTLLQATYSCT*LEAPP*QYQPLTFPLHLSSSQF*FY*LS*KSLSP*SKPTFSHF**ASTCTTTHNDPPITCLSYSKTQPMTPNRGPLSPPNDLRPSHVISLPLHNAPHTRPTNQHTNHIPMMARCNTRKHIPRPPHTTCPKRPSIRDNPIYYLRSFFLRRIFLSLLPLQPSPYPPIRRALAPNRHHPAKSPRSPTPKHIRITRIRSINHLSSP*SNRKQPKPNNSSTAYYNFTGSLFYPPTSLRVLRVSLHHFRRHLRLNIFCSHRLPRTSRHYWLNFPHYLLHPPTNISLYIQTSLWLRSRRLILAFCRCGLTISVCLHLLMRV", "length": 564 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f+3.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "L", "length": 1 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f-1.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "KTLINRWRHTEIVKPHLQNASIRRRLRSQSDVWM*SEILVGG*SR**GKLSQ**REVRGSLWLQKMLSRRCRRKW*RETRSTLRLVGG*NRDPVKL**AVLELFGFGCFLLDYGELR*LILLMRVIRMCLGVGLLGDLAG*CLLGASALLIGG*GLGWSGKRLRKILRRKKLLR**IGLSRIEGLFGQVVCGGLGMCFLVLHRAIIGIWLVCWLVGLV*GALWSGSEITWLGRRSLGGLRGPLLGVMGWVLLYDRHVIGGSLCVVVQVEAY*KCENVGLD*GDSDF*DSQ*N*NCEDDKCRGKVNG*YC*GGASN*VHE*VACSNVSG*AYGQGYWLNE*ADGFDNN*YGDKGCRCALW*EVG*GIFNLRAKAYNHCARS*GDGHG*VYR*LGGWCK*VRQESEEVSCGNKND*GY*YKRSGSSFSVVYGYHLF*G*FD*SLLGGD*SVVDEIFGGGDQ*RGK*NDQYCGG*A*DCGGNE*SEQIFVHFGSQGLL*FFIFMGFGEGGRW*FVFNIFSWVMRNSVRSMGVIMVGHTVVFSWGISL*RGVGSLNL*LKRLMLS*LYS", "length": 565 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f-1.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "KTLINRWRHTEIVKPHLQNASIRRRLRSQSDVWM", "length": 34 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f-2.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "RPSSIDGDIQK*SNHIYKMPVSGGGFEAKVMFGCKVKY*LADEADSEES*ANNDVKSVEACGYKKC*AVDAVGNGEGRLEVL*GL*EGKIETQ*NCNKQCLNYLVSVVFY*TMVSSGD*YS*CE*YGCV*EWDF*GI*RGDACWGPVPS*LGGRG*AGVVKGSEKSCEEKNF*GNK*DYPVSKAFLDRWCVVALVCAFSCYIAPSLVYG*CVG**A*YEERYGVEVKSHG*AGGH*EG*EGPC*GSWAGFYYMIGM*LVGHYVLSCR*RLTRSVKT*AWIKATAISRIVSRIRIVKMISVEGRLMVDIARVALPIRCMSRWPAVMLAVRRTARAIG*MSRLMVSIITSMGIRGVGVPCGKKWARAFLILERKPIITVPAHKGMAMARFIDSWVVGVNE*GRSPRRLVVAIKMIKDTSIRDQVRPLVLCMVIICFEVSLISHCWVVISRLLMRYLEVGINRGGNRMISTAAGRPRIVGAMNEANRFSFILVLRVCYNFLFLWALVREVGGSLCLIFLVG**GIV*GVWG*LWWAIR*YLVGAFHCKEVLVLLIFNLKG*C*VSFTV", "length": 565 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f-2.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1695 nt)" }, "expected": { "protein": "RPSSIDGDIQK", "length": 11 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f-3.full", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "DPHQ*METYRNSQTTSTKCQYQAAASKPK*CLDVK*NISWRMKQIVRKVEPIMT*SPWKPVATKNVEP*MPSEMVKGDSKYSEACRRVK*RPSKIVISSA*IIWFRLFSIRLW*AQVIDTPDASNTDVFRSGTSRGFSGVMPVGGQCPPNWGVGARLEW*KAQKNPAKKKTSEVINRIIPYRRPFWTGGVWWPWYVLSRVTSRHHWYMVSVLVSRPSMRSVMEWK*NHMARPEVIRRAERAPVRGHGLGFTI**ACDWWVIMCCRAGRGLLEV*KRRLGLRRQRFLG*SVELEL*R**V*REG*WLILLGWRFQLGA*VGGLQ*C*RLGVRPGLLVE*VG*WFR**LVWG*GV*VCLVVRSGLGHF*S*SESL*SLCPLIRGWPWLGL*IVGWLV*MSEAGVRGG*LWQ*K*LRILV*EIRFVL*CCVWLSFVLRLV*LVIVGW*LVGC**DIWRWGSIEGEIE*SVLRRVGLGLWGQ*MKRTDFRSFWFSGFVIIFYFYGLW*GR*VVVCV*YF*LGDEE*CKEYGGNYGGPYGSI*LGHFTVKRCWFS*SLT*KVNAKLALQ", "length": 564 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "mt-atp8-atp6-cox3.t11.f-3.to_stop", "input": { "sequenceId": "mt-atp8-atp6-cox3", "table": 11, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1692 nt)" }, "expected": { "protein": "DPHQ", "length": 4 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f+1.full", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "DTIEWRKTFRGMA**RPEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ*AQRN*CELAHSLGTPGFTLYASGSYVVWNCERITISHRKQL*P*LRIHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVIAKRPAPIALPNSCAA*MANGALPGFRHQKRCRK", "length": 500 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f+1.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "DTIEWRKTFRGMA", "length": 13 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f+2.full", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "TPSNGAKPFAVWHDSARKRVNSGW*M*NQ*RYTMSQSMPVSLIRPFPAW*TRPATFLRKRGKKWKRRWRS*ITFPTAWHNNWRANSRC*LALPPPVWPCTRRRKLSRRLNLAPINWVPAWWCRW*NEAASKPVKRRCTIFSRNASVG*SLTIRWMTRMPLLWKLPALMFRRYFLMSLTRHPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC*RAH*VLSRRVCVWLAGINISLAIKFSR*RNGKATGVPCPVFNKPCKC*MRASFPLRCWLPTIRWRWAQCAPLPSPGCALVRISR*WDTTIPKTAHVISRRQPPSNRIFACWGKPAWTACCNSLRARR*RAISCCPSHW*KEKPPWRPIRKPPLPARWPIH*CSWHDRFPDWKAGSERNAINVS*LTH*APQALHFMLPARMLCGIVSG*QFHTGNSYDHDYGFTGRRFTTS*LGKPWRYPT*SPCSTSPFRQLA**RRGPHRSPFPTVAQPEWRMALCLVSGTRSGAG", "length": 499 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f+2.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "TPSNGAKPFAVWHDSARKRVNSGW", "length": 24 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f+3.full", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "HHRMAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD*ISRRSTGCQRGGVDGRTKRRRSL*SGGAQSSRATRQWADH*LSAG*PGCHCCGSCLH*CSGVIS*CL*PDTHQQYYFLP*RRYATGRGASGRIGSPANRAVSGPIKFCLGASASGWLA*ISHSQSNSADSGTGRRLECHVRFSTNHANAE*GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLM*VSSLIRHPRLYTLCFRLVCCVEL*ADNNFTQETAMTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE", "length": 499 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f+3.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "HHRMAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD", "length": 108 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f-1.full", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "FPAPLLVPETRQSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD*VG*RQGFPSHDVVKRRPVNP*SWS*LFPV*NCYPLTIPHNIRAGSIKCKAWGA**VS*LTLIALRSLPAFQSGNLSCQLH**IGQRAGRGGLRIGRQGGFSFHQ*DGQQLIALHRLALRELQQAVHAGLPQQAKILFDGG*RRDIT*AVFGIVVSHYRDIRTNAQPGLGNGAHCAQRHLIVGNQHRSGNDALIQHLHGLLKTGHGTPVAFPFRYRLNLIASEIFMPASQTQTRRDRT*WAR*QRDLLVTQCDQMLHAQSRTVFMGENNTVDGCLVRDIKK*RRNISAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGARFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGLVHHAGNGLIRDTGILCDIV*RYWFHIHHPELTLFRALSCHTAKGFAPFDGV", "length": 500 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f-1.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "FPAPLLVPETRQSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD", "length": 47 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f-2.full", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "FRHRFWCRKPGKAPFAIQAAQLLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL*NDGQ*IRNHGHSCFLCEIVIRSQFHTTYEPEA*SVKPGVPNE*ANSH*LRCAHCPLSSRETCRASCINESANARGEAVCVLGARVVFLFTSETGNS*LPFTAWP*ESCSKRSTLVCPSRRKSCLMVVDGGI*HELSSVSSYPTTEISAPTRSPDSVMARIAPSAI*SLATSIAVGTMPSFSICMVC*KPDMALQSPSRSAIG*I*LRVRYLCQPARRRRAETELNGPANSAICW*PNATRCSTPSRVPSSWEKIILLMGVWSETSRNNAGTLVQAASTAMASWSSSG*LMISPLTRCARRLCTAALQASTPLRSTIDTTTLAPS*SARDLIAATICDGACRARLEVATPISNDCLPASCCATRLGM*FSSAIAASTFSRVFAETWLAWFTTRETV**ETPAYSATSYNVTGFTFTTLN*LSSGRYHAIPRKVLRHSMV", "length": 499 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f-2.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "FRHRFWCRKPGKAPFAIQAAQLLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL", "length": 60 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f-3.full", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "SGTASGAGNQAKRHSPFRLRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASESVIMVIAVSCVKLLSAHNSTQHTSRKHKV*SLGCLMSELTHINCVALTARFPVGKPVVPAALMNRPTRGERRFAYWAPGWFFFSPVRRATADCPSPPGPERVAASGPRWFAPAGENPV*WWLTAGYNMSCLRYRRIPLPRYPHQRAARTR*WRALRPAPSDRWQPASQWERCPHSAFAWFVENRTWHSSRLPVPLSAEFDCE*DIYASQPDADAPRQNLMGPLTARFAGDPMRPDAPRPVAYRLHGRK*YC*WVSGQRHQEITPEH*CRQLPQQWHPGHPADS**SAH*RVAREDCAPPLYRLRRRFVLPSTPPRWHPVDRREI*SPRQFATARAGPDWRWQRQSATTVCPPVVVPRGWECNSAPPSPLPLFPAFSQKRGWPGSPRGKRSDKRHRHTLRHRITLLVSHSPP*IDSLPGAIMPYRERFCAIRWC", "length": 499 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t1.f-3.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 1, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "SGTASGAGNQAKRHSPFRLRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASESVIMVIAVSCVKLLSAHNSTQHTSRKHKV", "length": 95 }, "method": "NCBI genetic code table 1 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=1, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f+1.full", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "DTIEWRKTFRGMAW*RPEESQF*VVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPMAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVK*KTTLAPNTQTASPRALADSLMQLARQVSRLESGQWAQRN*CELAHSLGTPGFTLYASGSYVVWNCERMTISH*KQLWPWLRIHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVMAK*PAPIALPNSCAAWMANGALPGFRHQKRCRK", "length": 500 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f+1.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "DTIEWRKTFRGMAW", "length": 14 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f+2.full", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "TPSNGAKPFAVWHDSARK*VNSGWWMWNQ*RYTMSQSMPVSLI*PFPAWWT*PATFLRKRGKKWKRRWRSWITFPTAWHNNWRANSRCWLALPPPVWPCTRRRKLSRRLNLAPINWVPAWWCRW*NEAASKPVKRRCTIFSRNASVGWSLTIRWMT*MPLLWKLPALMFRRYFLMSLT*HPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC*RAH*VLSRRVCVWLAGMNISLAIKFSR*RNGKATGVPCPVFNKPCKCWM*ASFPLRCWLPTI*WRWAQCAPLPSPGCALVRMSR*WDTTMPKTAHVMSRRQPPSN*IFACWGKPAWTACCNSL*A*RW*AISCCPSHWWKEKPPWRPMRKPPLPARWPIH*CSWHD*FPDWKAGSERNAINVS*LTH*APQALHFMLPARMLCGIVSG*QFHTGNSYDHDYGFTGRRFTTSWLGKPWRYPT*SPCSTSPFRQLA**R*GPHRSPFPTVAQPEWRMALCLVSGT*SGAG", "length": 499 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f+2.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "TPSNGAKPFAVWHDSARK", "length": 18 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f+3.full", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "HHRMAQNLSRYGMMAPG*ESIQGGECETSNVMRCR*VCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD*ISRRSTGCQRGGVDG*TKRRRSL*SGGAQSSRATRQWADH*LSAGWPGCHCCGSCLH*CSGVISWCLWPDTHQQYYFLPW*RYATGRGASGRIGSPANRAVSGPIKFCLGASASGWLA*MSHSQSNSADSGTG*RLECHVRFSTNHANAEWGHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGMRRYR*QLMLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLMWVSSLI*HP*LYTLCFRLVCCVELWADNNFTQETAMTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE", "length": 499 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f+3.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "HHRMAQNLSRYGMMAPG", "length": 17 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f-1.full", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "FPAPLLVPET*QSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD*VG*RQGFPSHDVVKRRPVNP*SWS*LFPVWNCYPLTIPHNMRAGSMKCKAWGA*WVS*LTLIALRSLPAFQSGNLSCQLH*WIGQRAG*GGLRIGRQGGFSFHQWDGQQLIALHRLAL*ELQQAVHAGLPQQAKILFDGGWRRDMTWAVFGIVVSHYRDIRTNAQPGLGNGAHCAQRHLIVGNQHRSGNDALIQHLHGLLKTGHGTPVAFPFRYRLNLIASEMFMPASQTQTRRD*T*WAR*QRDLLVTQCDQMLHAQSRTVFMGENNTVDGCLV*DIKK*RRNISAGSFHSNGILVIQRMVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGA*FNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFR*NVAGLVHHAGNGLM*DTGMLCDIV*RYWFHIHHPELTLFRALSCHTAKGFAPFDGV", "length": 500 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f-1.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "FPAPLLVPET", "length": 10 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f-2.full", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "FRHRFWCRKPGKAPFAIQAAQLLG*AIGAGLFAITPAGE*GMCCKAIKLGNA*VFPVTTL*NDGQWIRNHGHSCFLCEIVIRSQFHTTYEPEA*SVKPGVPNEWANSH*LRCAHCPLSSRETCRASCINESANARGEAVCVLGA*VVFLFTSETGNSWLPFTAWPWESCSKRSTLVCPS*RKSCLMVVDGGM*HELSSVSSYPTTEMSAPTRSPDSVMARIAPSAIWSLATSIAVGTMPSFSICMVCWKPDMALQSPSRSAIGWIWLRV*YLCQPA*R*RAETELNGPANSAICWWPNAT*CSTPSRVPSSWEKMMLLMGVWSETS*NNAGTLVQAASTAMASWSSSG*LMISPLTRCA**LCTAALQASTPLRSTIDTTTLAPSWSARDLIAATICDGAC*A*LEVATPISNDCLPASCCATRLGM*FSSAIAASTFSRVFAETWLAWFTTRETVW*ETPAYSATSYNVTGFTFTTLNWLSSGRYHAMPRKVLRHSMV", "length": 499 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f-2.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "FRHRFWCRKPGKAPFAIQAAQLLG", "length": 24 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f-3.full", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "SGTASGAGNQAKRHSPF*LRNCWEGRSVRASSLLRQLAKGGCAA*RLSWVTPGFSQSRRCKTTASESVIMVMAVSCVKLLSAHNSTQHTSRKHKV*SLGCLMSELTHINCVALTARFPVGKPVVPAALMNRPTRGE*RFAYWAPGWFFFSPV*RATADCPSPPGPE*VAASGPRWFAPAGENPVWWWLTAGYNMSCLRYRRIPLP*YPHQRAARTR*WRALRPAPSDRWQPASQWERCPHSAFAWFVENRTWHSSRLPVPLSAEFDCEWDIYASQPDADAP*QNLMGPLTARFAGDPMRPDAPRPVAYRLHG*K*YCWWVSGQ*HQEMTPEH*C*QLPQQWHPGHPADS*WSAHWRVAREDCAPPLY*LRRRFVLPSTPPRWHPVDRREI*SPRQFATARAGPDW*WQRQSATTVCPPVVVPRGWECNSAPPSPLPLFPAFSQKRGWPGSPRGKRSDK*HRHTLRHRMTLLVSHSPPWIDSLPGAIMPYRE*FCAIRWC", "length": 499 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t2.f-3.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 2, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "SGTASGAGNQAKRHSPF", "length": 17 }, "method": "NCBI genetic code table 2 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=2, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f+1.full", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "+1", "mode": "full", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "DTIEWRKTFRGMA**RPEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ*AQRN*CELAHSLGTPGFTLYASGSYVVWNCERITISHRKQL*P*LRIHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVIAKRPAPIALPNSCAA*MANGALPGFRHQKRCRK", "length": 500 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f+1.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "+1", "mode": "to_stop", "nucleotides": "plus strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "DTIEWRKTFRGMA", "length": 13 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f+2.full", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "+2", "mode": "full", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "TPSNGAKPFAVWHDSARKRVNSGW*M*NQ*RYTMSQSMPVSLIRPFPAW*TRPATFLRKRGKKWKRRWRS*ITFPTAWHNNWRANSRC*LALPPPVWPCTRRRKLSRRLNLAPINWVPAWWCRW*NEAASKPVKRRCTIFSRNASVG*SLTIRWMTRMPLLWKLPALMFRRYFLMSLTRHPSTVLFSPMKTVRDWAWSIWSHWVTSKSRC*RAH*VLSRRVCVWLAGINISLAIKFSR*RNGKATGVPCPVFNKPCKC*MRASFPLRCWLPTIRWRWAQCAPLPSPGCALVRISR*WDTTIPKTAHVISRRQPPSNRIFACWGKPAWTACCNSLRARR*RAISCCPSHW*KEKPPWRPIRKPPLPARWPIH*CSWHDRFPDWKAGSERNAINVS*LTH*APQALHFMLPARMLCGIVSG*QFHTGNSYDHDYGFTGRRFTTS*LGKPWRYPT*SPCSTSPFRQLA**RRGPHRSPFPTVAQPEWRMALCLVSGTRSGAG", "length": 499 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f+2.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "+2", "mode": "to_stop", "nucleotides": "plus strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "TPSNGAKPFAVWHDSARKRVNSGW", "length": 24 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f+3.full", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "+3", "mode": "full", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "HHRMAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD*ISRRSTGCQRGGVDGRTKRRRSL*SGGAQSSRATRQWADH*LSAG*PGCHCCGSCLH*CSGVIS*CL*PDTHQQYYFLP*RRYATGRGASGRIGSPANRAVSGPIKFCLGASASGWLA*ISHSQSNSADSGTGRRLECHVRFSTNHANAE*GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSPAGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFPTGKRAVSATQLM*VSSLIRHPRLYTLCFRLVCCVEL*ADNNFTQETAMTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPE", "length": 499 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f+3.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "+3", "mode": "to_stop", "nucleotides": "plus strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "HHRMAQNLSRYGMIAPGRESIQGGECETSNVIRCRRVCRCLLSDRFPRGEPGQPRFCENAGKSGSGDGGAELHSQPRGTTTGGQTVVADWRCHLQSGPARAVANCRGD", "length": 108 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f-1.full", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "-1", "mode": "full", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "FPAPLLVPETRQSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD*VG*RQGFPSHDVVKRRPVNP*SWS*LFPV*NCYPLTIPHNIRAGSIKCKAWGA**VS*LTLIALRSLPAFQSGNLSCQLH**IGQRAGRGGLRIGRQGGFSFHQ*DGQQLIALHRLALRELQQAVHAGLPQQAKILFDGG*RRDIT*AVFGIVVSHYRDIRTNAQPGLGNGAHCAQRHLIVGNQHRSGNDALIQHLHGLLKTGHGTPVAFPFRYRLNLIASEIFMPASQTQTRRDRT*WAR*QRDLLVTQCDQMLHAQSRTVFMGENNTVDGCLVRDIKK*RRNISAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGARFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGLVHHAGNGLIRDTGILCDIV*RYWFHIHHPELTLFRALSCHTAKGFAPFDGV", "length": 500 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f-1.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "-1", "mode": "to_stop", "nucleotides": "reverse complement strand from position 1, trailing partial codon dropped (1500 nt)" }, "expected": { "protein": "FPAPLLVPETRQSAIRHSGCATVGKGDRCGPLRYYASWRKGDVLQGD", "length": 47 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f-2.full", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "-2", "mode": "full", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "FRHRFWCRKPGKAPFAIQAAQLLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL*NDGQ*IRNHGHSCFLCEIVIRSQFHTTYEPEA*SVKPGVPNE*ANSH*LRCAHCPLSSRETCRASCINESANARGEAVCVLGARVVFLFTSETGNS*LPFTAWP*ESCSKRSTLVCPSRRKSCLMVVDGGI*HELSSVSSYPTTEISAPTRSPDSVMARIAPSAI*SLATSIAVGTMPSFSICMVC*KPDMALQSPSRSAIG*I*LRVRYLCQPARRRRAETELNGPANSAICW*PNATRCSTPSRVPSSWEKIILLMGVWSETSRNNAGTLVQAASTAMASWSSSG*LMISPLTRCARRLCTAALQASTPLRSTIDTTTLAPS*SARDLIAATICDGACRARLEVATPISNDCLPASCCATRLGM*FSSAIAASTFSRVFAETWLAWFTTRETV**ETPAYSATSYNVTGFTFTTLN*LSSGRYHAIPRKVLRHSMV", "length": 499 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f-2.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "-2", "mode": "to_stop", "nucleotides": "reverse complement strand from position 2, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "FRHRFWCRKPGKAPFAIQAAQLLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL", "length": 60 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f-3.full", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "-3", "mode": "full", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "SGTASGAGNQAKRHSPFRLRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASESVIMVIAVSCVKLLSAHNSTQHTSRKHKV*SLGCLMSELTHINCVALTARFPVGKPVVPAALMNRPTRGERRFAYWAPGWFFFSPVRRATADCPSPPGPERVAASGPRWFAPAGENPV*WWLTAGYNMSCLRYRRIPLPRYPHQRAARTR*WRALRPAPSDRWQPASQWERCPHSAFAWFVENRTWHSSRLPVPLSAEFDCE*DIYASQPDADAPRQNLMGPLTARFAGDPMRPDAPRPVAYRLHGRK*YC*WVSGQRHQEITPEH*CRQLPQQWHPGHPADS**SAH*RVAREDCAPPLYRLRRRFVLPSTPPRWHPVDRREI*SPRQFATARAGPDWRWQRQSATTVCPPVVVPRGWECNSAPPSPLPLFPAFSQKRGWPGSPRGKRSDKRHRHTLRHRITLLVSHSPP*IDSLPGAIMPYRERFCAIRWC", "length": 499 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11)", "source": "pipeline/sequence-toolkit/reference.py (translation)" }, { "id": "ecoli-lacI.t11.f-3.to_stop", "input": { "sequenceId": "ecoli-lacI", "table": 11, "frame": "-3", "mode": "to_stop", "nucleotides": "reverse complement strand from position 3, trailing partial codon dropped (1497 nt)" }, "expected": { "protein": "SGTASGAGNQAKRHSPFRLRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASESVIMVIAVSCVKLLSAHNSTQHTSRKHKV", "length": 95 }, "method": "NCBI genetic code table 11 (gc.prt version 4.6)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "call": "Seq(frame_nt).translate(table=11, to_stop=True)", "source": "pipeline/sequence-toolkit/reference.py (translation)" } ], "cdsCases": [ { "id": "ins-mrna.cds.INS", "input": { "sequenceId": "ins-mrna", "feature": "CDS INS 60..392 (record coordinates)", "table": 1, "firstCodon": "ATG", "lastCodon": "TAG", "length": 333 }, "method": "NCBI genetic code table 1; alternative initiation codons off (to_stop) and on (cds=True)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "source": "pipeline/sequence-toolkit/reference.py (translation, CDS)", "expected": { "alternativeStartsOff": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN", "alternativeStartsOn": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN" }, "crossCheck": { "ncbiTranslationQualifier": "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN", "equalsAlternativeStartsOn": true, "equalsToStop": true }, "call": "Seq(cds_nt).translate(table=1, to_stop=True) and .translate(table=1, cds=True)" }, { "id": "mt-atp8-atp6-cox3.cds.ATP8", "input": { "sequenceId": "mt-atp8-atp6-cox3", "feature": "CDS ATP8 72..278 (record coordinates)", "table": 2, "firstCodon": "ATG", "lastCodon": "TAG", "length": 207 }, "method": "NCBI genetic code table 2; alternative initiation codons off (to_stop) and on (cds=True)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "source": "pipeline/sequence-toolkit/reference.py (translation, CDS)", "expected": { "alternativeStartsOff": "MPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS", "alternativeStartsOn": "MPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS" }, "crossCheck": { "ncbiTranslationQualifier": "MPQLNTTVWPTMITPMLLTLFLITQLKMLNTNYHLPPSPKPMKMKNYNKPWEPKWTKICSLHSLPPQS", "equalsAlternativeStartsOn": true, "equalsToStop": true }, "call": "Seq(cds_nt).translate(table=2, to_stop=True) and .translate(table=2, cds=True)" }, { "id": "mt-atp8-atp6-cox3.cds.ATP6", "input": { "sequenceId": "mt-atp8-atp6-cox3", "feature": "CDS ATP6 233..913 (record coordinates)", "table": 2, "firstCodon": "ATG", "lastCodon": "TAA", "length": 681 }, "method": "NCBI genetic code table 2; alternative initiation codons off (to_stop) and on (cds=True)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "source": "pipeline/sequence-toolkit/reference.py (translation, CDS)", "expected": { "alternativeStartsOff": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQWLIKLTSKQMMTMHNTKGRTWSLMLVSLIIFIATTNLLGLLPHSFTPTTQLSMNLAMAIPLWAGTVIMGFRSKIKNALAHFLPQGTPTPLIPMLVIIETISLLIQPMALAVRLTANITAGHLLMHLIGSATLAMSTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT", "alternativeStartsOn": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQWLIKLTSKQMMTMHNTKGRTWSLMLVSLIIFIATTNLLGLLPHSFTPTTQLSMNLAMAIPLWAGTVIMGFRSKIKNALAHFLPQGTPTPLIPMLVIIETISLLIQPMALAVRLTANITAGHLLMHLIGSATLAMSTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT" }, "crossCheck": { "ncbiTranslationQualifier": "MNENLFASFIAPTILGLPAAVLIILFPPLLIPTSKYLINNRLITTQQWLIKLTSKQMMTMHNTKGRTWSLMLVSLIIFIATTNLLGLLPHSFTPTTQLSMNLAMAIPLWAGTVIMGFRSKIKNALAHFLPQGTPTPLIPMLVIIETISLLIQPMALAVRLTANITAGHLLMHLIGSATLAMSTINLPSTLIIFTILILLTILEIAVALIQAYVFTLLVSLYLHDNT", "equalsAlternativeStartsOn": true, "equalsToStop": true }, "call": "Seq(cds_nt).translate(table=2, to_stop=True) and .translate(table=2, cds=True)" }, { "id": "mt-atp8-atp6-cox3.cds.COX3", "input": { "sequenceId": "mt-atp8-atp6-cox3", "feature": "CDS COX3 913..1696 (record coordinates)", "table": 2, "firstCodon": "ATG", "lastCodon": "T", "length": 784 }, "method": "NCBI genetic code table 2; alternative initiation codons off (to_stop) and on (cds=True)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "source": "pipeline/sequence-toolkit/reference.py (translation, CDS)", "expected": { "alternativeStartsOff": "MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS", "cdsTranslation": null, "note": "784 nt is not a multiple of three (incomplete stop codon completed by polyadenylation, /transl_except (pos:9990,aa:TERM)); Biopython's cds=True raises, so only the to_stop translation of the complete codons is recorded" }, "crossCheck": { "ncbiTranslationQualifier": "MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS", "equalsAlternativeStartsOn": false, "equalsToStop": true }, "call": "Seq(cds_nt).translate(table=2, to_stop=True) and .translate(table=2, cds=True)" }, { "id": "ecoli-lacI.cds.lacI", "input": { "sequenceId": "ecoli-lacI", "feature": "CDS lacI 79..1161 (record coordinates)", "table": 11, "firstCodon": "GTG", "lastCodon": "TGA", "length": 1083 }, "method": "NCBI genetic code table 11; alternative initiation codons off (to_stop) and on (cds=True)", "oracle": "Biopython Bio.Seq.Seq.translate", "oracleVersion": "1.88", "recordedOn": "2026-10-06", "source": "pipeline/sequence-toolkit/reference.py (translation, CDS)", "expected": { "alternativeStartsOff": "VKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ", "alternativeStartsOn": "MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ" }, "crossCheck": { "ncbiTranslationQualifier": "MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ", "equalsAlternativeStartsOn": true, "equalsToStop": false }, "call": "Seq(cds_nt).translate(table=11, to_stop=True) and .translate(table=11, cds=True)" } ], "skippedFeatures": [ { "sequenceId": "ecoli-lacI", "feature": "CDS lacZ 1284..>1500 (record coordinates)", "reason": "partial in this record (the region cuts it), so its /translation is not the region's to compare" } ] }