{ "about": { "generatedBy": "pipeline/sequence-toolkit/orf_circular.py", "scriptSha256": "7bf10cb3ce47900310b1bd04fd2aebd252a1315af18c97122fbbc2f0664bffaf", "recordedOn": "2026-10-14", "rules": "docs/board/memos/2026-10-12-cso-circular-orfs.md (R1 to R6); docs/board/memos/2026-10-12-cto-circular-orfs.md", "oracle": "O2 seven copies read as linear; O3 an explicit modular walk (agreeing exactly); O4 Biopython 1.88 translation; O5 the linear scan and NCBI ORFfinder 0.4.3 on each unrolled reading (see orffinder); O6 rotations; O7 locality against reference.py scan_orfs", "orffinder": { "state": "run", "version": "ORFfinder: 0.4.3", "binarySha256": "933cb6ff9eecdb64e650030c28c71c275e13a58aef8bb650d31cd8048e03f9a3", "gzSha256": "f30a0806b984931a967d8024066a53dbb811035ca14564f36f7f7045a6a509f2", "readings": 278, "agreed": 278, "outputs": "pipeline/sequence-toolkit/orffinder/circular-orffinder.fa", "index": "pipeline/sequence-toolkit/orffinder/circular-orffinder.json", "check": "on each unrolled reading, plus strand, nested shown, the ORFfinder ORF from the reading's ORF start to its end has the fixture's protein, and is partial exactly when the fixture's ORF has no stop" }, "checks": { "o3Agreement": 64, "o4": 296, "o5Readings": 278, "o6Rotations": 19197, "o7Local": 169, "crossing": 98, "r4": 18, "cut": 16, "o5Orffinder": 278 }, "refusedTables": [ 27, 28, 31 ], "sequences": [ { "id": "c1-r0-plus", "length": 300, "lengthMod3": 0, "cases": [ "C1", "C11" ], "note": "n = 300 (n mod 3 = 0): a 75-coding-nt ORF across the origin on the plus strand (kept) and a 72 (absent)", "sequence": "CCGGGGGCGGCCCGCGCCGCGGCGGCGGCGCGCCCGTAAGATGCCCGCGCGGCCGGGGCGCCCCCCGGCCCCGGGCCCCCGGCCGGGGGCCGCCCGGCGGGGGCGGCCCGCCTAAGCGCCGCCGCCGCGCCCCCCCCGGGATGCGCGGCCCCGCGCCCCCCCCCCGGCGGCGCGGGGCGGCCCGCCGCGCCCGCGGCCGCGCGCGCGCGCGCCCCGCCGCCCCCGCGGGCTAACGCCCCCGCGCGCCCCCCCGCCCCGCCGATGGCGCGGCGGGCGCGCGCCGGGCCGCCGGCGCCGGGC" }, { "id": "c1-r0-minus", "length": 300, "lengthMod3": 0, "cases": [ "C1", "C11" ], "note": "The reverse complement of c1-r0-plus: the same ORFs on the minus strand", "sequence": "GCCCGGCGCCGGCGGCCCGGCGCGCGCCCGCCGCGCCATCGGCGGGGCGGGGGGGCGCGCGGGGGCGTTAGCCCGCGGGGGCGGCGGGGCGCGCGCGCGCGCGGCCGCGGGCGCGGCGGGCCGCCCCGCGCCGCCGGGGGGGGGGCGCGGGGCCGCGCATCCCGGGGGGGGCGCGGCGGCGGCGCTTAGGCGGGCCGCCCCCGCCGGGCGGCCCCCGGCCGGGGGCCCGGGGCCGGGGGGCGCCCCGGCCGCGCGGGCATCTTACGGGCGCGCCGCCGCCGCGGCGCGGGCCGCCCCCGG" }, { "id": "c1-r1-plus", "length": 301, "lengthMod3": 1, "cases": [ "C1", "C11" ], "note": "n = 301 (n mod 3 = 1): a 75-coding-nt ORF across the origin on the plus strand (kept) and a 72 (absent)", "sequence": "CCCCGGCCGCGGGGCGGCGCGCCGCGGCGGCCCGCCTAAGATGCCGGCCGCGGGGGCGCCGGGGCGCCGCGCCCGGGGGGGCCCGCCGCGCCGCCCCGGGGGGCCCGCCGGCTAAGGGGGCGGCCCGCCCCCGGGGGGGGATGCGGGCGCGCCCGCCGGCCGGCCGCCGCGCCCGGGGCCCCGCCCCCCCCGGCGGCGCGCGGCCGCGGGGGGGGGCCCGCGCGCCGGCCTAACGGCGGCCCCCCGCGGCCGGCGCGCGCCGATGCGCCGCGCCCGGCCGGGCGCCCGGGCGCGCGGGGCC" }, { "id": "c1-r1-minus", "length": 301, "lengthMod3": 1, "cases": [ "C1", "C11" ], "note": "The reverse complement of c1-r1-plus: the same ORFs on the minus strand", "sequence": "GGCCCCGCGCGCCCGGGCGCCCGGCCGGGCGCGGCGCATCGGCGCGCGCCGGCCGCGGGGGGCCGCCGTTAGGCCGGCGCGCGGGCCCCCCCCCGCGGCCGCGCGCCGCCGGGGGGGGCGGGGCCCCGGGCGCGGCGGCCGGCCGGCGGGCGCGCCCGCATCCCCCCCCGGGGGCGGGCCGCCCCCTTAGCCGGCGGGCCCCCCGGGGCGGCGCGGCGGGCCCCCCCGGGCGCGGCGCCCCGGCGCCCCCGCGGCCGGCATCTTAGGCGGGCCGCCGCGGCGCGCCGCCCCGCGGCCGGGG" }, { "id": "c1-r2-plus", "length": 302, "lengthMod3": 2, "cases": [ "C1", "C11" ], "note": "n = 302 (n mod 3 = 2): a 75-coding-nt ORF across the origin on the plus strand (kept) and a 72 (absent)", "sequence": "CGGCCGCCCGGCCGGGGCCGGGCCCCGGCGCCGCGGTAAGATGGGCCCGCCGCGCGCCGGGCCCGCGGCCCGGGCGGGGGGGGCCCCGCGGCGCCGCCGGCCGGCCCCCGGCTAAGCCGGGGGGCCCGCCGCCCGGGCGGATGCGGGGGCGCGGCGCGCGGGGGCCCGGGGCGCGCCCCGCGGCCCGGCGCGCGCCGGGGCGGGGGGGGCCCCCGGCGCCGCCCCCCCGCTAAGGGGGGGGCGCGCGCGCCGCCCGGGCCGGGATGGCCGGCCCGCCCGCCGGGCGCCCGCGGCCCGCCCCC" }, { "id": "c1-r2-minus", "length": 302, "lengthMod3": 2, "cases": [ "C1", "C11" ], "note": "The reverse complement of c1-r2-plus: the same ORFs on the minus strand", "sequence": "GGGGGCGGGCCGCGGGCGCCCGGCGGGCGGGCCGGCCATCCCGGCCCGGGCGGCGCGCGCGCCCCCCCCTTAGCGGGGGGGCGGCGCCGGGGGCCCCCCCCGCCCCGGCGCGCGCCGGGCCGCGGGGCGCGCCCCGGGCCCCCGCGCGCCGCGCCCCCGCATCCGCCCGGGCGGCGGGCCCCCCGGCTTAGCCGGGGGCCGGCCGGCGGCGCCGCGGGGCCCCCCCCGCCCGGGCCGCGGGCCCGGCGCGCGGCGGGCCCATCTTACCGCGGCGCCGGGGCCCGGCCCCGGCCGGGCGGCCG" }, { "id": "c2-ends-and-starts", "length": 330, "lengthMod3": 0, "cases": [ "C2" ], "note": "An ORF ending at n and one starting at 1 (plus); its reverse complement is c2-ends-and-starts-minus", "sequence": "ATGGCCGCCGGCCGGGGGCGGCCGCCGCCCGGGGGCGGCCGGGCCCCCCGGCCGGGCGGGCCGCGGGCGGCGGGCCCCCCGGCGGCGCCCTAACCGGGCGCCGCCGCGCGGGGCCGGGGGCCCGCCGCGCGGGGCGGCGCGGCGCCCGGGGCCCGGGGGCCCCCCGCCGGCGGGGGGCGGCGGCCCGCCCGCCCCGCGGCCGCCCCGATGCGGCGGGGCCCCCGGCGGCCGGCGGGGCGGCGCCGGCCGCGGCGGCCGCGCCGCCGCCCCGCCGGCGGGGCCCCGCCCGGGGCCCCGCCCCCCCGGGGCCGGCGCCCCCCCCCCGCCTAA" }, { "id": "c2-ends-and-starts-minus", "length": 330, "lengthMod3": 0, "cases": [ "C2" ], "note": "The same on the minus strand", "sequence": "TTAGGCGGGGGGGGGGCGCCGGCCCCGGGGGGGCGGGGCCCCGGGCGGGGCCCCGCCGGCGGGGCGGCGGCGCGGCCGCCGCGGCCGGCGCCGCCCCGCCGGCCGCCGGGGGCCCCGCCGCATCGGGGCGGCCGCGGGGCGGGCGGGCCGCCGCCCCCCGCCGGCGGGGGGCCCCCGGGCCCCGGGCGCCGCGCCGCCCCGCGCGGCGGGCCCCCGGCCCCGCGCGGCGGCGCCCGGTTAGGGCGCCGCCGGGGGGCCCGCCGCCCGCGGCCCGCCCGGCCGGGGGGCCCGGCCGCCCCCGGGCGGCGGCCGCCCCCGGCCGGCGGCCAT" }, { "id": "c2-split-start-2-1", "length": 333, "lengthMod3": 0, "cases": [ "C2" ], "note": "A start codon split 2 + 1 by the origin (A T | G)", "sequence": "GCCCGGGCCGGGGCGGGGCCGCGCGGGGCCGCGGGCGCGGGGCGGCGCGGCGCCCCCGGCGCGCGCCGCGCGCGGGCCCGGGCCCGGCTAAGCCGGCCGGGCCCCCCGCCCGGGGGGCCCCCCGGCGCCCCCGGCCCGGCCCGGGCGCGCCGGGGGCCGCGGCGGCCCGCGCCGGCGGGCCGGGCCCGCGGGCGGGCCGCGGCCCCGCGCCGGGGCCCCGCCGGCCCCGCCGGGCCGCCGGGGGGCCCCCCGGCCCGCCGGCGGCGGGCGCGGCCCGGCCGGCCCGCCGGCCGGCCCGGGCGCGGCCCCCCCCCCCGCGGCGGGCCCCCGCAT" }, { "id": "c2-split-start-1-2", "length": 334, "lengthMod3": 1, "cases": [ "C2" ], "note": "A start codon split 1 + 2 by the origin (A | T G)", "sequence": "TGCCGGCGGCCGCGGCCCCGGCGCGCGCCCCGGCCCGGGGCGGGGGCGGGCCGCCGCGCCCCCCCCCGGGCCCGCGCGGGCGGGCCCCGTGACGGGCCCCCGGGCGCGCGGGGCGGGCCGCCGGGCCCGCCGGGCGCGCGGCCCCCCCCCGGCCGGCCGGCCGCGCGGGCGCCGGGGGGCCCGGCGCCCGCGCGGCCGCCGCGGGGCCCGCGCCGGGCCGCGGGGGCGCGGCGGCGGGGCCCGGGGGCCGCCCCCGCCCGCGGCCCCCGGGCCGGCCCGGGCGCCCGGCCCGCGCGCCCGCGGGCCCCCGGCGGCGCGCGGCGGCCGGGGGGCA" }, { "id": "c2-split-stop-2-1", "length": 335, "lengthMod3": 2, "cases": [ "C2" ], "note": "A stop codon split 2 + 1 by the origin (T A | G)", "sequence": "GCGGCCGGGCGCGCCGCGGCGCGCCGCCGGGCGGCCCCGGCCCCGCCGGGGCCCGGGGGCCGGGCCGCGGCCCGGGGGGGCGCCCCCCGGGGGGGGCCCGCGCCCCCCGCGGGGCCCCCCGCCCGGCGCCCGCGGGCCCCCGGGGCGGCGGGCGCCGGGCGGGCCGCCCCGCGCGGGGGGCCCGGCCCGCGGGCGGGGCCGCGGCGGCGCCGGCCCCCGGCCCCGCGGGCCGGCGGCCGGGGGATGCGCGGGCGGCCCCGGCCGGCGGCGGCCCGCCGGCCGGCGGCGGGCGCGGGCGCGGCCCCCGCCGCCGCGCGCGCCGGCCGCCCCCCCTA" }, { "id": "c2-split-stop-1-2", "length": 336, "lengthMod3": 0, "cases": [ "C2" ], "note": "A stop codon split 1 + 2 by the origin (T | A A)", "sequence": "AAGGCGGCCCGCCGCCCGGGGCGCCGGCGCGGCCCCGGCGCCCCGCCGGGGGCGCCGGGGGGCCCGCGGCGCCGGCGGGCGCGGCGGCGCCCGCCCGCCCGGGGCCGCGCGGCGGGGCCCCGCGCCGGCGCGGCCGGGGCCGGCCGGGCGCCGGCCCGGCGGCCGCCCGCGGCCGGCGCCGCCCCCCCGCGGGCGCCCCGCGGGCCGCCCGGGGGCCGGGGCGCGCCGGCCGGGCGGCGCGCCCGATGCCGGGCGGCGGCGGCCCCGCCCCGCGGGGCGGCCGCGGCGGGGCGCCGGGCGGCCCGGCGGCGCCCCCCCCCCCCGGGCGCCGCCCCT" }, { "id": "c2-split-start-2-1-minus", "length": 333, "lengthMod3": 0, "cases": [ "C2" ], "note": "The reverse complement of c2-split-start-2-1: the split codon on the minus strand", "sequence": "ATGCGGGGGCCCGCCGCGGGGGGGGGGGCCGCGCCCGGGCCGGCCGGCGGGCCGGCCGGGCCGCGCCCGCCGCCGGCGGGCCGGGGGGCCCCCCGGCGGCCCGGCGGGGCCGGCGGGGCCCCGGCGCGGGGCCGCGGCCCGCCCGCGGGCCCGGCCCGCCGGCGCGGGCCGCCGCGGCCCCCGGCGCGCCCGGGCCGGGCCGGGGGCGCCGGGGGGCCCCCCGGGCGGGGGGCCCGGCCGGCTTAGCCGGGCCCGGGCCCGCGCGCGGCGCGCGCCGGGGGCGCCGCGCCGCCCCGCGCCCGCGGCCCCGCGCGGCCCCGCCCCGGCCCGGGC" }, { "id": "c2-split-start-1-2-minus", "length": 334, "lengthMod3": 1, "cases": [ "C2" ], "note": "The reverse complement of c2-split-start-1-2: the split codon on the minus strand", "sequence": "TGCCCCCCGGCCGCCGCGCGCCGCCGGGGGCCCGCGGGCGCGCGGGCCGGGCGCCCGGGCCGGCCCGGGGGCCGCGGGCGGGGGCGGCCCCCGGGCCCCGCCGCCGCGCCCCCGCGGCCCGGCGCGGGCCCCGCGGCGGCCGCGCGGGCGCCGGGCCCCCCGGCGCCCGCGCGGCCGGCCGGCCGGGGGGGGGCCGCGCGCCCGGCGGGCCCGGCGGCCCGCCCCGCGCGCCCGGGGGCCCGTCACGGGGCCCGCCCGCGCGGGCCCGGGGGGGGGCGCGGCGGCCCGCCCCCGCCCCGGGCCGGGGCGCGCGCCGGGGCCGCGGCCGCCGGCA" }, { "id": "c2-split-stop-2-1-minus", "length": 335, "lengthMod3": 2, "cases": [ "C2" ], "note": "The reverse complement of c2-split-stop-2-1: the split codon on the minus strand", "sequence": "TAGGGGGGGCGGCCGGCGCGCGCGGCGGCGGGGGCCGCGCCCGCGCCCGCCGCCGGCCGGCGGGCCGCCGCCGGCCGGGGCCGCCCGCGCATCCCCCGGCCGCCGGCCCGCGGGGCCGGGGGCCGGCGCCGCCGCGGCCCCGCCCGCGGGCCGGGCCCCCCGCGCGGGGCGGCCCGCCCGGCGCCCGCCGCCCCGGGGGCCCGCGGGCGCCGGGCGGGGGGCCCCGCGGGGGGCGCGGGCCCCCCCCGGGGGGCGCCCCCCCGGGCCGCGGCCCGGCCCCCGGGCCCCGGCGGGGCCGGGGCCGCCCGGCGGCGCGCCGCGGCGCGCCCGGCCGC" }, { "id": "c2-split-stop-1-2-minus", "length": 336, "lengthMod3": 0, "cases": [ "C2" ], "note": "The reverse complement of c2-split-stop-1-2: the split codon on the minus strand", "sequence": "AGGGGCGGCGCCCGGGGGGGGGGGGCGCCGCCGGGCCGCCCGGCGCCCCGCCGCGGCCGCCCCGCGGGGCGGGGCCGCCGCCGCCCGGCATCGGGCGCGCCGCCCGGCCGGCGCGCCCCGGCCCCCGGGCGGCCCGCGGGGCGCCCGCGGGGGGGCGGCGCCGGCCGCGGGCGGCCGCCGGGCCGGCGCCCGGCCGGCCCCGGCCGCGCCGGCGCGGGGCCCCGCCGCGCGGCCCCGGGCGGGCGGGCGCCGCCGCGCCCGCCGGCGCCGCGGGCCCCCCGGCGCCCCCGGCGGGGCGCCGGGGCCGCGCCGGCGCCCCGGGCGGCGGGCCGCCTT" }, { "id": "c3-frame-start-gains-start", "length": 300, "lengthMod3": 0, "cases": [ "C3" ], "note": "A linear frame-start ORF whose start is found across the origin on the circle", "sequence": "CGGCGCCCGGCCCGGGGCCGGGCGCGGCGGGGGCGGCGCGGGCGCGGCGCGCCCCGGGGGGCCCGGCCCCCCGCGTAACTGCTACAACCATTTAGACCGCTTCACACGGCTCTTGTACATGCATATTCCGACGACTTAACGGTTCGGTCCTACTGTCAGAGACGGGAACGTATCGAGCCCACGCCTCATTCCACAGACGACTTATTCTCTGGTGATGAGTTAGGTCTCACTTCGGCGCCATAAATGGGGGCCGGCCCGCCGGCCCCGCCGCCGGGGGCCGCGCGGCGGGCCGCCGGCCGC" }, { "id": "c3-ctg-after-crossing-stop", "length": 306, "lengthMod3": 0, "cases": [ "C3", "C12" ], "note": "Anchored by a stop across the origin (TA | G); with table 11 alternative starts the ORF opens with CTG, read as M; with table 1 there is no ORF", "sequence": "GCTGGCGGGGCCGCCCCGCCGGGGGCCCGCGCGGCGCCCCGCCCCGCGGCCCCGCCGGGGCCCGCGGGGCCCGGGGCCGCCCCGCCCGCCGGGGTAGGGGGCGCCGCGGCCCGCGCGCGGCCCGCGGCGCCCCCCGGGGCGGGCGGCGGCGGGCGCGGCCCGGGCCGCGCCGCCGGCGGGGCCCCGCGGGGCGCGGCGGCGCGCCGGGCGGCCCGGCCGCCGCGCGGCGCGGGCGCGCGCGGGGCGGCGGGCGGCGCCGCCGGCCCCGGGGCCGCCCGCGCGGCGGGCCCGCCCGCCGCGGGGGTA" }, { "id": "c3-no-stop-ends-across", "length": 309, "lengthMod3": 0, "cases": [ "C3" ], "note": "A linear ORF with no stop that ends at a stop across the origin", "sequence": "ACGCCGGGGGGCGCGCGCGCCGCGGCGGCGCCCGCCCGGGGCGGCCCGCGCCGCCCCGGCCGGGGGGCCCGCCCCCCCCCCCCCCCCCGGCCGGCCCCCCCGCCGCCGGCGCGCCCGCCCGCGCGGCGGCCCGGGCCGCGGCCCCCGCGCGATGGGCCCGGGGCCGGCGCGGCCGGGCGCGGGGCGCCCGCCCGGCGCGCGCCCCGCCCGGGCCCCCGGGCGGCGGCCGCCCCGGCGCCCGGGGCCGGGCCGGGCCGCGCGGGCCCGGCGCGCGGGCGGCGGCGGGCCCCCGGCGCGCCGGCCCCGGTA" }, { "id": "c3-start-becomes-internal", "length": 312, "lengthMod3": 0, "cases": [ "C3" ], "note": "A linear ORF whose start becomes internal: on the circle its stretch's first start is before the origin", "sequence": "CGGGCGGGCCCCGCCGGCATGGCGCGGCCGGGCGGGCCGGCGCGGGGGGCCCCGGCCCCGGGGGGGGGGGCGCCGCGGGCCGGCGGCGGCCCGCCCTAACGGCCCGGGGGCGGGGCGCCCCGGCCCCGGGGGCCCCCCCGCCGCCGGCGCGCGCGCCCCGCGCCCCGGCGCCCGGGGCGGCGGGCGGCCGGCCGCCCGGGGCCGCGCGGCCGCCGCGCCCCCCGCGCCGCCCCCGGGGGGGGCGCCGCGCCGCGGGGCCGGCCGCGCGGCCGGCCGCGCTAAATGGCGGGGCGGCGCGGCCGCGCGGCGCGG" }, { "id": "c4-full-turn", "length": 150, "lengthMod3": 0, "cases": [ "C4" ], "note": "n = 150: two frames each with one stop and a start right after it (two full-turn ORFs of n bases, equal position sets, neither nested)", "sequence": "CCGCCCCCCCCGGCCGCCGCCGGCGCCCGGCCCCGCGGCGTAAATGCGGCCCCCGGCCCGCCGCCCCCCGGCCGGGGGCGGCCCGCCCCCGCTAGATGGCGCGGGGCGGCGGCGCCGCGCGCGCGGGGGGCGGCCGCGCCGCCGGCCGGC" }, { "id": "c5-stop-free-frame", "length": 153, "lengthMod3": 0, "cases": [ "C5", "C10" ], "note": "n = 153: a frame with no stop and a start (an R4 entry), a frame with no stop and no start (no entry), and a frame with one stop", "sequence": "GCGGGGGCGCCGGGGCGGGCCGCCGCGCCGGGCGCCGCGGCGGGGGGGCCGGGGGGGGGGATGCGGGGCCGGCGCGGGCGCCGCCGCCCGCCCCCCCGGCGTAACGCGCCCGGCGCGCGGCGGCGCCGGGCCGGGGGGGGGGCCGCGCCCCGC" }, { "id": "c6-stop-over-a-turn-upstream", "length": 301, "lengthMod3": 1, "cases": [ "C6" ], "note": "n = 301: the previous stop more than a turn upstream, the ORF within a turn of its closing stop: listed, read as M", "sequence": "TAACGGCGGGCGCCGGGGGGGGGGCCCGGGGCGCCGGCCCGCCCCGCCGCGCCCCCCCCGGGGGGCCCCCGGGCCGCCCCCCGGGCGCCCCCCGCCGGGGGGCGCCGGGCGGCCGCGGATGGGCCCGGCGGCCCGCGCCCGCCGCGCGCCGCGGCGCCCGCCGGCGCGGGCCGCGCCGGGGCCGGCCGCGCCGCGCGGCGGGCGGGGGCGGCGCCCGGCCGCGCCCCCGGGGCCGGGCCCGGGGCGCCCCCGCGGGGCGGGCGGCCCCGGCCCCGCCGCGCGGCGCCCCCGCCGGGCCGCG" }, { "id": "c7-cut-by-the-turn", "length": 301, "lengthMod3": 1, "cases": [ "C7" ], "note": "n = 301: the first start more than a turn from its stop: cut at W codons, and that stop ends no listed ORF", "sequence": "TAGGCGGCCGCGCGCCCGCCCGCCGCCGCCGCGGCCGCGGGGCGGGCGGGCGGCGCCGGCCGCCGGCGGGCGCCCGCCCCCCCCCCCGGGATGGGCCGGCCCCCCGCCGGCGCGGCGCCCCGGCGGCCCCGGGGGCCGGCCGGCCGCCCGGGGGGCGCGCCCGCCGGCGGGCGCCCGCGCCGGCGGCGCCGGGGGCGGCGCCGCGCGGGGCGCGGCGCGGCGCGGCGCGGGCCGCCCCCCCGGCGCCCCGGGGCCGCCCCCGGGGCGGGGGCGGCCCGGCCGGCCCCGCGGCGGCGCCGGG" }, { "id": "c8-ta-atg", "length": 302, "lengthMod3": 2, "cases": [ "C8" ], "note": "n = 302 (n mod 3 = 2): a cut reading whose next codon is TA|ATG, reading TAA", "sequence": "CGCGCCCCGGGCGCGCCGCCGGGCCGGGGCGGGGGCGCGCGGCGGCGGCCCGGCGCGGGGGGGCCGGCCGCCGGCGGGGGCGGGCCCCGGGGGGCGGCCGTAATGGGCGGGCGGGGGCCGCGGCCCCGCCCCGGCCGCCGGCGCCCGGGCGCGGCGCGGCCGCGGCCGGCCCGGCCGCCCGGGCCCCCGCGGCGCGCCGCGCCGCGGGGCGGGGGGCCCCCCGGGGCCCCGGCCCGCGGGGGGGCCGGGGGGCCGCCGGCCGCCCGCCCCCCCGGCGGGGCCGCCGCGCGCGGGCCCCCCCG" }, { "id": "c9-strand-without-stops", "length": 301, "lengthMod3": 1, "cases": [ "C9" ], "note": "n = 301: a strand with no stop anywhere and one start: one entry for the strand", "sequence": "GGGGGCCGCCCCCCCGCCCCCCCCGGCGGGGCGGGGGCGGCGGCGGCGGCGGCCCCCCCGCGCGGCGCGCCCGGGCGATGCGGGCGCGCGCCCGGCGCGGGGGGCGGCCGGGGGGCCGGCCCGGGCGCCGCGCGCCCCGGCGCCCCCGGGCGCGGGCCGCGCGGGCGCCCGCCGCGGGCCCGGCGGCGGGGCCCCGCCCCGCCCCGGGGGGCGGCGCGGCGCGCCCGCCCGGGGCGCGCCCCCCGGGGGGCCGGGGGCGGGGGCCGCCGGCCGGGCCGCCGCCCCCGGGGGCGCCGCCGGC" }, { "id": "c10-nesting", "length": 400, "lengthMod3": 1, "cases": [ "C10" ], "note": "A non-crossing ORF nested in a crossing one; nesting on either strand", "sequence": "GATGCCGGGGGCGCCCGCGGGCGGCGGGGGGCGGGGCGGGCGGCGCCGCCGCCCGCGCCCCGCGCCCCGCGCCGCCGCCGGGGGCGCGCCGTAACCGGGCCTTACCGCGGGCGCGCGGCCGGCCGGGGGGCCGCGGGGCCGGGGGCGGCGCGCCGGCCCCGCCGGGGCGGCGCGCGCGCGGGCGGGGCCGGCATCGGCGGTAACGGGGGCGGCCCGGCGCCGCCCGGGGCGGGGGGCGGCCGCGGCGCGCGGCGCCCGGGCGCCCGCCGCCCGGGCGGCGCCGCCGCGGCCCCGCCCGGCGGGCGGCCGGGCGCGGCGCGGGGGCCGGGGATGCGCCCGGCGGGGGGCCGGCCCCCCCGGGCCGCCGGGCGCGCCGGGGCGGGCGCGCGGGGCGGGGCGG" }, { "id": "c10-crossing-in-crossing", "length": 420, "lengthMod3": 0, "cases": [ "C10" ], "note": "A crossing ORF nested in a larger crossing ORF on the other strand", "sequence": "CGCCCGCGGCGGGGCCGGCGGGGGGGGCGGCGCCGCCGCCCGCGGGCCCGCCGGGTAAGCGGCGCGCGGCGCGGGCGCGCGCCGGGCGGCGGGCCCGCGGGGGGCCCGGCCGCCCCCGGGGCGCCGGCGGCCGCCGGCGGGCCCGCCGGGCATCGGGCCCCGGCGGGGGCCGGCCCGCCCCGGGCGGGCGGGCCCCCGCCCGGCCGGCCCGGCCGCCGCCCGGGCGGCGCGCGCGGGGCGTTACCGGGGCCGGGGCCGGGGCGCGGCCGCGCGCCGCCGGCGGGCCGCGCCGGCGCGGCCCCCCGGGCGCCGGCCGCGGCGGGGGCGGGCGCCGCCGGGCCGGGCGCGGGCGGCCCGCGCCCGGCCGCGGATGGGCCGGGGGCCCCGGCGCGCCGGCGGCGCCGCGCCCCGGCCGCCGCG" }, { "id": "c12-tga-across", "length": 303, "lengthMod3": 0, "cases": [ "C12" ], "note": "TGA across the origin: a stop in tables 1 and 11, Trp in table 2", "sequence": "AGGCCCGCCCGCCGCCGCCCCGGGGCCGGCCGGCGGGGCCCCGGGGGCGCCGCCGCCCCGCTAGGCCCCGCGCCCCCCCGGGGGGGCGGCGGGGCCCCCCGGCGGCGGGCGGCGGCCGGGCGCGCCCGGCGCGGGGCGGCCCCCGGGCGCGCGCGCGGCCCGCCGGGGCGCGGGGGCGCCGGGGATGCGGCCGCGCGCGGCGGCCCCCGGGGCGGCGGCGCCCGGCGCCGGGCGGGGGGGCGCGGCGCCCCGCGGGGGCGGCCGGCGCGCCCCCGGCCCGGCCCGCCCGGGCGCGCGGCCGTG" }, { "id": "l09137-2", "length": 2686, "lengthMod3": 1, "cases": [ "C13" ], "note": "pipeline/plasmid-map/records/L09137.2.gb read as circular (sha256 8a205af08518dae1b0045c7b098986dca18824ef654e75233603602ab89cad04)", "sequence": "TCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTC" }, { "id": "j01749-1", "length": 4361, "lengthMod3": 2, "cases": [ "C13" ], "note": "pipeline/plasmid-map/records/J01749.1.gb read as circular (sha256 536042a7485bdabdf49c4d21a306213a098d77d19bdba57a1c6adc76ce2b8372)", "sequence": "TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA" } ], "tolerance": "Exact: every field of every entry in main, noStopInTurn and nestedHidden, hiddenCount, and the absence of mustBeAbsent", "rule": "No value in this file comes from the Drybench engine under test.", "python": "3.13.16", "biopython": "1.88" }, "cases": [ { "id": "c1-r0-plus.t1.atg.min75", "input": { "sequenceId": "c1-r0-plus", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "+", "frame": 3, "start": 141, "end": 233, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MRGPAPPPRRRGAARRARGRARARPAAPAG", "id": "orf2" }, { "strand": "+", "frame": 1, "start": 262, "end": 39, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MARRARAGPPAPGPGAARAAAAARP", "id": "orf1" } ], "noStopInTurn": [], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [ { "strand": "+", "start": 41, "end": 115 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r0-plus.t11.alt.min75", "input": { "sequenceId": "c1-r0-plus", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "-", "frame": -1, "start": 42, "end": 112, "lengthNt": 231, "codingLengthNt": 228, "lengthAa": 76, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MLRARRRRGAGRPRARRRRPGARPPRHRRGGGARGGVSPRGRRGARARGRGRGGPPRAAGGGARGRASRGGRGGGA", "id": "orf4" }, { "strand": "-", "frame": -3, "start": 142, "end": 230, "lengthNt": 213, "codingLengthNt": 210, "lengthAa": 70, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MPGGARRRRLGGPPPPGGPRPGARGRGAPRPRGHLTGAPPPRRGPPPGPAPAARRAPAAPSAGRGGARGR", "id": "orf5" } ], "noStopInTurn": [ { "strand": "-", "frame": -2, "start": 263, "end": 264, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATC", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "noStopAround": "frame", "containedIn": [], "nested": false, "protein": "IGGAGGRAGALARGGGGARARAAAGAAGRPAPPGGGRGAAHPGGGAAAALRRAAPAGRPPAGGPGPGGAPAARASYGRAAAAARAAPGPGAGGPARARRA", "id": "orf3" } ], "nestedHidden": [ { "strand": "+", "frame": 3, "start": 141, "end": 233, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf4" ], "nested": true, "protein": "MRGPAPPPRRRGAARRARGRARARPAAPAG", "id": "orf2" }, { "strand": "+", "frame": 1, "start": 262, "end": 39, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [ "orf4", "orf5" ], "nested": true, "protein": "MARRARAGPPAPGPGAARAAAAARP", "id": "orf1" } ], "hiddenCount": 2, "mustBeAbsent": [ { "strand": "+", "start": 41, "end": 115 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r0-minus.t1.atg.min75", "input": { "sequenceId": "c1-r0-minus", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "-", "frame": -1, "start": 39, "end": 262, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MARRARAGPPAPGPGAARAAAAARP", "id": "orf1" }, { "strand": "-", "frame": -3, "start": 160, "end": 68, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MRGPAPPPRRRGAARRARGRARARPAAPAG", "id": "orf2" } ], "noStopInTurn": [], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [ { "strand": "-", "start": 260, "end": 186 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r0-minus.t11.alt.min75", "input": { "sequenceId": "c1-r0-minus", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "+", "frame": 3, "start": 159, "end": 71, "lengthNt": 213, "codingLengthNt": 210, "lengthAa": 70, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MPGGARRRRLGGPPPPGGPRPGARGRGAPRPRGHLTGAPPPRRGPPPGPAPAARRAPAAPSAGRGGARGR", "id": "orf3" }, { "strand": "+", "frame": 1, "start": 259, "end": 189, "lengthNt": 231, "codingLengthNt": 228, "lengthAa": 76, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MLRARRRRGAGRPRARRRRPGARPPRHRRGGGARGGVSPRGRRGARARGRGRGGPPRAAGGGARGRASRGGRGGGA", "id": "orf2" } ], "noStopInTurn": [ { "strand": "+", "frame": 2, "start": 38, "end": 37, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATC", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "noStopAround": "frame", "containedIn": [], "nested": false, "protein": "IGGAGGRAGALARGGGGARARAAAGAAGRPAPPGGGRGAAHPGGGAAAALRRAAPAGRPPAGGPGPGGAPAARASYGRAAAAARAAPGPGAGGPARARRA", "id": "orf1" } ], "nestedHidden": [ { "strand": "-", "frame": -1, "start": 39, "end": 262, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [ "orf2", "orf3" ], "nested": true, "protein": "MARRARAGPPAPGPGAARAAAAARP", "id": "orf4" }, { "strand": "-", "frame": -3, "start": 160, "end": 68, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf2" ], "nested": true, "protein": "MRGPAPPPRRRGAARRARGRARARPAAPAG", "id": "orf5" } ], "hiddenCount": 2, "mustBeAbsent": [ { "strand": "-", "start": 260, "end": 186 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r1-plus.t1.atg.min75", "input": { "sequenceId": "c1-r1-plus", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "+", "frame": 3, "start": 141, "end": 233, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MRARPPAGRRARGPAPPGGARPRGGARAPA", "id": "orf2" }, { "strand": "+", "frame": 2, "start": 263, "end": 39, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": 1, "containedIn": [], "nested": false, "protein": "MRRARPGARARGAPRPRGGAPRRPA", "id": "orf1" } ], "noStopInTurn": [], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [ { "strand": "+", "start": 41, "end": 115 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r1-plus.t11.alt.min75", "input": { "sequenceId": "c1-r1-plus", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "-", "frame": -2, "start": 264, "end": 112, "lengthNt": 153, "codingLengthNt": 150, "lengthAa": 50, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MGARRPRGAAVRPARGPPPAAARRRGGRGPGRGGRPAGAPASPPGGGPPP", "id": "orf4" } ], "noStopInTurn": [ { "strand": "-", "frame": -1, "start": 142, "end": 144, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATC", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": -3, "containedIn": [], "nested": false, "protein": "MPPRGRAAPLAGGPPGAARRAPPGAAPRRPRGRHLRRAAAARRPAAGGPRAPGRPAGRGASARAGRGGPPLGRRAGPPPRPRAAGGGGAPGAAAGRRARP", "id": "orf3" } ], "nestedHidden": [ { "strand": "-", "frame": -2, "start": 42, "end": 230, "lengthNt": 114, "codingLengthNt": 111, "lengthAa": 37, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": -1, "containedIn": [ "orf3" ], "nested": true, "protein": "MLGGPPRRAAPRPGGPARPGARPGAAHRRAPAAGGRR", "id": "orf5" }, { "strand": "+", "frame": 3, "start": 141, "end": 233, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf4" ], "nested": true, "protein": "MRARPPAGRRARGPAPPGGARPRGGARAPA", "id": "orf2" }, { "strand": "+", "frame": 2, "start": 263, "end": 39, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": 1, "containedIn": [ "orf3", "orf5" ], "nested": true, "protein": "MRRARPGARARGAPRPRGGAPRRPA", "id": "orf1" } ], "hiddenCount": 3, "mustBeAbsent": [ { "strand": "+", "start": 41, "end": 115 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r1-minus.t1.atg.min75", "input": { "sequenceId": "c1-r1-minus", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "-", "frame": -2, "start": 39, "end": 263, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": -1, "containedIn": [], "nested": false, "protein": "MRRARPGARARGAPRPRGGAPRRPA", "id": "orf1" }, { "strand": "-", "frame": -3, "start": 161, "end": 69, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MRARPPAGRRARGPAPPGGARPRGGARAPA", "id": "orf2" } ], "noStopInTurn": [], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [ { "strand": "-", "start": 261, "end": 187 } ] }, "cases": [ "C1", "C11" ], "rotations": "all" }, { "id": "c1-r1-minus.t11.alt.min75", "input": { "sequenceId": "c1-r1-minus", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "+", "frame": 2, "start": 38, "end": 190, "lengthNt": 153, "codingLengthNt": 150, "lengthAa": 50, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MGARRPRGAAVRPARGPPPAAARRRGGRGPGRGGRPAGAPASPPGGGPPP", "id": "orf2" } ], "noStopInTurn": [ { "strand": "+", "frame": 1, "start": 160, "end": 158, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATC", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": 3, "containedIn": [], "nested": false, "protein": "MPPRGRAAPLAGGPPGAARRAPPGAAPRRPRGRHLRRAAAARRPAAGGPRAPGRPAGRGASARAGRGGPPLGRRAGPPPRPRAAGGGGAPGAAAGRRARP", "id": "orf1" } ], "nestedHidden": [ { "strand": "-", "frame": -2, "start": 39, "end": 263, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": -1, "containedIn": [ "orf1", "orf3" ], "nested": true, "protein": "MRRARPGARARGAPRPRGGAPRRPA", "id": "orf4" }, { "strand": "-", "frame": -3, "start": 161, "end": 69, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf2" ], "nested": true, "protein": "MRARPPAGRRARGPAPPGGARPRGGARAPA", "id": "orf5" }, { "strand": "+", "frame": 2, "start": 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"orf2" } ], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [] }, "cases": [ "C6" ], "rotations": "all" }, { "id": "c7-cut-by-the-turn.t1.atg.min30", "input": { "sequenceId": "c7-cut-by-the-turn", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 30 }, "expected": { "main": [], "noStopInTurn": [ { "strand": "+", "frame": 1, "start": 91, "end": 89, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATG", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": 3, "containedIn": [], "nested": false, "protein": "MGRPPAGAAPRRPRGPAGRPGGAPAGGRPRRRRRGRRRAGRGAARRGPPPRRPGAAPGAGAARPAPRRRRVGGRAPARRRRGRGAGGRRRPPAGARPPPR", "id": "orf1" } ], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [] }, "cases": [ "C7" ], "rotations": "all" }, { "id": "c7-cut-by-the-turn.t11.alt.min30", "input": { "sequenceId": "c7-cut-by-the-turn", "topology": "circular", "table": 11, "alternativeStarts": true, 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"c8-ta-atg.t1.atg.min30", "input": { "sequenceId": "c8-ta-atg", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 30 }, "expected": { "main": [], "noStopInTurn": [ { "strand": "+", "frame": 1, "start": 103, "end": 100, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATG", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": 2, "containedIn": [], "nested": false, "protein": "MGGRGPRPRPGRRRPGAARPRPARPPGPPRRAAPRGGGPPGAPARGGAGGPPAARPPGGAAARGPPRAPRARRRAGAGARGGGPARGGRPPAGAGPGGRP", "id": "orf1" } ], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [] }, "cases": [ "C8" ], "rotations": "all" }, { "id": "c8-ta-atg.t11.alt.min30", "input": { "sequenceId": "c8-ta-atg", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 30 }, "expected": { "main": [], "noStopInTurn": [ { "strand": "+", "frame": 1, "start": 103, "end": 100, "lengthNt": 300, "codingLengthNt": 300, 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"minimumCodingNt": 30 }, "expected": { "main": [], "noStopInTurn": [ { "strand": "+", "frame": 3, "start": 78, "end": 76, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATG", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "noStopAround": "strand", "frameAfterOrigin": 2, "containedIn": [], "nested": false, "protein": "MRARARRGGRPGGRPGRRAPRRPRARAARAPAAGPAAGPRPAPGGGAARPPGARPPGGRGRGPPAGPPPPGAPPAGAAPPPPPAGRGRRRRRPPRAARPG", "id": "orf1" } ], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [] }, "cases": [ "C9" ], "rotations": "all" }, { "id": "c9-strand-without-stops.t11.alt.min30", "input": { "sequenceId": "c9-strand-without-stops", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 30 }, "expected": { "main": [], "noStopInTurn": [ { "strand": "+", "frame": 3, "start": 78, "end": 76, "lengthNt": 300, "codingLengthNt": 300, "lengthAa": 100, "startCodon": "ATG", "stopCodon": null, "startsAtFrameStart": 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"startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MPGAPAPRRAARAPGGRPAPGAPGRRPPPGGPAAPPGGRGA", "id": "orf3" } ], "noStopInTurn": [ { "strand": "+", "frame": 1, "start": 301, "end": 300, "lengthNt": 303, "codingLengthNt": 303, "lengthAa": 101, "startCodon": "GTG", "stopCodon": null, "startsAtFrameStart": false, "crossesOrigin": true, "noStopAround": "frame", "containedIn": [], "nested": false, "protein": "VRPARRRPGAGRRGPGGAAAPLGPAPPRGGGGAPRRRAAAGRARRGAAPGRARGPPGRGGAGDAAARGGPRGGGARRRAGGRGAPRGRPARPRPGPPGRAA", "id": "orf1" } ], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [] }, "cases": [ "C12" ], "rotations": "all" }, { "id": "c12-tga-across.t2.alt.min75", "input": { "sequenceId": "c12-tga-across", "topology": "circular", "table": 2, "alternativeStarts": true, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "+", "frame": 2, "start": 185, "end": 64, "lengthNt": 183, "codingLengthNt": 180, "lengthAa": 60, "startCodon": "ATG", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": true, "containedIn": [], "nested": false, "protein": "MRPRAAAPGAAAPGAGRGGAAPRGGGRRAPGPARPGARPWGPPAAAPGPAGGAPGAPPPR", "id": "orf1" }, { "strand": "-", "frame": -1, "start": 186, "end": 61, "lengthNt": 126, "codingLengthNt": 123, "lengthAa": 41, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MPGAPAPRRAARAPGGRPAPGAPGRRPPPGGPAAPPGGRGA", "id": "orf2" } ], "noStopInTurn": [], "nestedHidden": [], "hiddenCount": 0, "mustBeAbsent": [] }, "cases": [ "C12" ], "rotations": "all" }, { "id": "l09137-2.t1.atg.min75", "input": { "sequenceId": "l09137-2", "topology": "circular", "table": 1, "alternativeStarts": false, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "+", "frame": 1, "start": 16, "end": 174, "lengthNt": 159, "codingLengthNt": 156, "lengthAa": 52, "startCodon": "ATG", "stopCodon": "TGA", "startsAtFrameStart": 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"protein": "MTLTYKNRRITRPFRLARFGDDGENL", "id": "orf5" } ], "noStopInTurn": [], "nestedHidden": [ { "strand": "+", "frame": 2, "start": 209, "end": 382, "lengthNt": 174, "codingLengthNt": 171, "lengthAa": 57, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf8", "orf12" ], "nested": true, "protein": "MRKEKIPHQAPFAIQAAQLLGRAIGAGLFAITPAGERGMCCKAIKLGNARVFPVTTL", "id": "orf6" }, { "strand": "-", "frame": -3, "start": 242, "end": 156, "lengthNt": 87, "codingLengthNt": 84, "lengthAa": 28, "startCodon": "ATG", "stopCodon": "TGA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf12" ], "nested": true, "protein": "MAPDAVFSPYASVRYFTPHMVHSQYNLL", "id": "orf16" }, { "strand": "+", "frame": 2, "start": 443, "end": 535, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf8" ], "nested": true, 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2602, 2641, 2644, 2680 ] }, { "id": "l09137-2.t11.alt.min75", "input": { "sequenceId": "l09137-2", "topology": "circular", "table": 11, "alternativeStarts": true, "minimumCodingNt": 75 }, "expected": { "main": [ { "strand": "-", "frame": -3, "start": 104, "end": 2647, "lengthNt": 144, "codingLengthNt": 141, "lengthAa": 47, "startCodon": "CTG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": true, "frameAfterOrigin": -2, "containedIn": [], "nested": false, "protein": "MTGLSAPGIRLQTSCDRLRELHVSEVFTVITETRETKGPRDTPIFIG", "id": "orf45" }, { "strand": "+", "frame": 3, "start": 165, "end": 542, "lengthNt": 378, "codingLengthNt": 375, "lengthAa": 125, "startCodon": "ATT", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MVLRVHHMRCEIPHRCVRRKYRIRRHSPFRLRNCWEGRSVRASSLLRQLAKGGCAARRLSWVTPGFSQSRRCKTTASEFELGTRGSSRVDLQACKLGVIMVIAVSCVKLLSAHNSTQHTSRKHKV", "id": "orf21" }, { "strand": "-", "frame": -2, "start": 225, 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581, "end": 766, "lengthNt": 186, "codingLengthNt": 183, "lengthAa": 61, "startCodon": "TTG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MRCAHCPLSSRETCRASCINESANARGEAVCVLGALPLPRSLTRCARSFGCGERYQLTQRR", "id": "orf14" }, { "strand": "+", "frame": 1, "start": 643, "end": 813, "lengthNt": 171, "codingLengthNt": 168, "lengthAa": 56, "startCodon": "ATC", "stopCodon": "TGA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MGQRAGRGGLRIGRSSASSLTDSLRSVVRLRRAVSAHSKAVIRLSTESGDNAGKNM", "id": "orf2" }, { "strand": "+", "frame": 2, "start": 791, "end": 1192, "lengthNt": 402, "codingLengthNt": 399, "lengthAa": 133, "startCodon": "ATA", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": 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false, "containedIn": [], "nested": false, "protein": "MSVRPRRKDQRIFLRSFFSARNLLLANKKTTATSGGLFAGSRATNSFSEGNWLQQSADTKYCSSSVAVVRPPLQELCSTAYIPRSANPVTSGCCQWR", "id": "orf36" }, { "strand": "+", "frame": 3, "start": 2343, "end": 2555, "lengthNt": 213, "codingLengthNt": 210, "lengthAa": 70, "startCodon": "ATC", "stopCodon": "TGA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MQFDVTHSCTQLIFSIFYFHQRFWVSKNRKAKCRKKGNKGDTEMLNTHTLPFSILLKHLSGLLSHERIHI", "id": "orf26" }, { "strand": "-", "frame": -3, "start": 2486, "end": 1626, "lengthNt": 861, "codingLengthNt": 858, "lengthAa": 286, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": 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"MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHYGVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRIVAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPFLAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIMQLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAIIAGMAADALGYVLLAFATRGWMAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSLAALTSLTSITGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST", "id": "orf11" }, { "strand": "-", "frame": -2, "start": 220, "end": 56, "lengthNt": 165, "codingLengthNt": 162, "lengthAa": 54, "startCodon": "ATA", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MVTGDAVGMDDIPQEARQYRHNQAYAYSIQGDGAEDDDERIVRFHTRCLTALAI", "id": "orf59" }, { "strand": "+", "frame": 1, "start": 1099, "end": 1518, "lengthNt": 420, "codingLengthNt": 417, "lengthAa": 139, "startCodon": "ATC", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MARGSYQPNFDHWTADRHGDLCRLGEHMERVGMDCRRRPIPCLPPRVASRCMEPGHLDLNGSRRHLANGFTTPRIGANQFLRRTVNAQTNPWQNISIASAISSSRTRRISGSVGSWPRVRMIVLLSLRTRLGWRGCLTG", "id": "orf3" }, { "strand": "+", "frame": 3, "start": 1305, "end": 1526, "lengthNt": 222, "codingLengthNt": 219, "lengthAa": 73, "startCodon": "ATT", "stopCodon": "TGA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MHHSKNWSQSILAENCECANQPLAEHIHRVRHLQQPHAAHLGQRWVLATGAHDRAPVVEDPARLAGLPYWLAE", "id": "orf23" }, { "strand": "+", "frame": 2, "start": 1511, "end": 1723, "lengthNt": 213, "codingLengthNt": 210, "lengthAa": 70, "startCodon": "CTG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MVSRMNHRYASEREATAAAKRLRPEQQHEWSSVSVFRKVWKRGSQRPAPLCSGSASQDAAGYPVEHLHLY", "id": "orf14" }, { "strand": "-", "frame": -2, "start": 1645, "end": 1508, "lengthNt": 138, "codingLengthNt": 135, "lengthAa": 45, "startCodon": "CTG", "stopCodon": 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"strand": "+", "frame": 2, "start": 3161, "end": 3253, "lengthNt": 93, "codingLengthNt": 90, "lengthAa": 30, "startCodon": "GTG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MERKLTLRDFGHEIIKKDLHLDPFKLKMKF", "id": "orf17" }, { "strand": "-", "frame": -1, "start": 3161, "end": 2868, "lengthNt": 294, "codingLengthNt": 291, "lengthAa": 97, "startCodon": "CTG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MSVRPRRKDQRIFLRSFFSARNLLLANKKTTATSGGLFAGSRATNSFSEGNWLQQSADTKYCPSSVAVVRPPLQELCSTAYIPRSANPVTSGCCQWR", "id": "orf37" }, { "strand": "+", "frame": 2, "start": 4010, "end": 4222, "lengthNt": 213, "codingLengthNt": 210, "lengthAa": 70, "startCodon": "ATC", "stopCodon": "TGA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MQFDVTHSCTQLIFSIFYFHQRFWVSKNRKAKCRKKGNKGDTEMLNTHTLPFSILLKHLSGLLSHERIHI", "id": "orf19" }, { "strand": "-", "frame": -2, "start": 4153, "end": 3293, "lengthNt": 861, "codingLengthNt": 858, "lengthAa": 286, "startCodon": "ATG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW", "id": "orf49" }, { "strand": "-", "frame": -1, "start": 4244, "end": 4050, "lengthNt": 195, "codingLengthNt": 192, "lengthAa": 64, "startCodon": "TTG", "stopCodon": "TGA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [], "nested": false, "protein": "MFIFLNTFKYVSAHETITLINASIILKKEEYEYSTFPCRPYSLFCGILPSCFCSPRNAGESKRC", "id": "orf36" }, { 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138, "startCodon": "ATT", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf11" ], "nested": true, "protein": "MPNTASDRPIIVALQRKRSSPKMTQSAAGTCPTSCMIKKTVISAATIVMPRAHRKELTGLKALKGIGRRSPLCDSCIRKQPSSRLRPLSTAAARNGACKEMAPNSPPATGPATIPTPKQALMSPKWRARSSPSVMSAI", "id": "orf70" }, { "strand": "-", "frame": -3, "start": 1062, "end": 955, "lengthNt": 108, "codingLengthNt": 105, "lengthAa": 35, "startCodon": "CTG", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf2", "orf11", "orf57" ], "nested": true, "protein": "MDSMACNAGIPMPPEARRIIMGKAIQPRVANASKT", "id": "orf69" }, { "strand": "-", "frame": -2, "start": 1096, "end": 623, "lengthNt": 474, "codingLengthNt": 471, "lengthAa": 157, "startCodon": "TTG", "stopCodon": "TAG", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf11" ], "nested": true, "protein": "MKLSLMVVIYLPGQHGLQRGHPDAAGSEKNHNGEGHPASRRERQQDVAQRVGRHAGDNGLLLAETFGGGTSDEGLSEGVQDSEYRKRQADHRRAPAKAVLAENDPERCRHLSYELHDKEDSHKCGDDSHAPRPPEGADWVEGSQGHRSTLSLMRLLH", "id": "orf57" }, { "strand": "-", "frame": -1, "start": 1100, "end": 1002, "lengthNt": 99, "codingLengthNt": 96, "lengthAa": 32, "startCodon": "ATC", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf11" ], "nested": true, "protein": "MLEAVPDGRHLPAWTAWPATRASRCRRKREES", "id": "orf46" }, { "strand": "+", "frame": 3, "start": 1221, "end": 1301, "lengthNt": 81, "codingLengthNt": 78, "lengthAa": 26, "startCodon": "TTG", "stopCodon": "TAA", "startsAtFrameStart": false, "crossesOrigin": false, "containedIn": [ "orf3", "orf45", "orf68" ], "nested": true, "protein": "MSASPRCVAVHGAGPPRPEWKPAAPR", "id": "orf22" }, { "strand": "+", "frame": 2, "start": 1277, "end": 1354, "lengthNt": 78, "codingLengthNt": 75, "lengthAa": 25, "startCodon": "ATG", "stopCodon": "TGA", "startsAtFrameStart": false, 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