{ "about": { "method": "pcr-product-exact-pair (exact-pair-v1, src/lib/seq/pcr.ts)", "generatedBy": "pipeline/sequence-toolkit/exact_matches.py", "recordedOn": "2026-10-10", "oracle": "An independent Python derivation; reverse complements by Biopython 1.88 (Bio.Seq.reverse_complement), every site and hit found by testing each window directly", "conventions": [ "Input: template, topology (linear or circular), and for each primer its annealing part and an optional 5' tail, all 5' to 3'. Whitespace is removed and letters upper-cased; nothing else is removed.", "Checks in this order, the first failure refused with its reason and field: template empty, template over 50,000 bases, template not A/C/G/T; then the forward primer (annealing not A/C/G/T, annealing outside 8 to 200 bases, tail not A/C/G/T, tail over 200 bases), then the reverse primer the same way.", "A site is an exact match of the annealing part on the top strand ('+') or of its reverse complement ('-'). On a circular template a site may cross the origin and each of the n start positions is read once; on a linear one it may not. A palindromic annealing part gives a '+' and a '-' site at the same place.", "A site's start is the primer's 5' end and its end the primer's 3' end, 1-based on the top strand, so a '-' site has start > end unless it crosses the origin. Sites are listed by start, '+' before '-' at the same start.", "More than 100 sites for one primer (both strands together) refuses with site-limit, forward primer first.", "A pair is a forward site and a reverse site on opposite strands. The template arc runs from the forward primer's 5' end towards the reverse primer's 5' end, inclusive; on a linear template it must not run backwards. If the arc is shorter than the two annealing lengths together the footprints overlap: the pair is counted in overlappingPairs and builds no product.", "The product is the arc's top strand when the forward site is '+', else the arc's reverse complement, with the forward tail before it and the reverse complement of the reverse tail after it. templateSpan is the arc's length; crossesOrigin is whether the arc passes from base n to base 1.", "Candidates are listed for each forward site in site order, then each reverse site in site order. More than 100 candidates refuses with candidate-limit. No candidate but at least one overlapping pair refuses with overlapping-sites. Otherwise status is none (0), unique (1) or ambiguous (2 or more).", "A candidate's id is '::|::'." ], "inputs": "A long input is stored as {\"parts\": [[unit, times], ...]}, the units concatenated in order.", "ruling": "CSO, 10 October 2026 (docs/board/memos/2026-10-10-cso-wave2-cloning.md ยง2.4): independent, published, hashed; never generated by the engine under test.", "handWorked": "pcr-hand-unique, written out base by base in the script's HAND_WORKED block; the script refuses to write if its derivation disagrees." }, "cases": [ { "id": "pcr-hand-unique", "note": "A unique product on a linear template, worked by hand base by base (HAND_WORKED in the script).", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:7:16|-:31:22", "sequence": "AGCTTGACCTTTAGCACTTGGATCC", "length": 25, "templateLength": 34, "templateSpan": 25, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 7, "end": 16, "length": 10 }, "reverse": { "strand": "-", "start": 31, "end": 22, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 7, "end": 16, "length": 10 } ], "reverse": [ { "strand": "-", "start": 31, "end": 22, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-two-forward-sites", "note": "Two forward sites before one reverse site: two products, status ambiguous, both kept.", "input": { "template": "GATCAAAGCTTGACCTTTAGCAGCTTGACCTGGACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "ambiguous", "candidates": [ { "id": "+:7:16|-:43:34", "sequence": "AGCTTGACCTTTAGCAGCTTGACCTGGACTTGGATCC", "length": 37, "templateLength": 46, "templateSpan": 37, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 7, "end": 16, "length": 10 }, "reverse": { "strand": "-", "start": 43, "end": 34, "length": 10 } }, { "id": "+:22:31|-:43:34", "sequence": "AGCTTGACCTGGACTTGGATCC", "length": 22, "templateLength": 46, "templateSpan": 22, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 22, "end": 31, "length": 10 }, "reverse": { "strand": "-", "start": 43, "end": 34, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 7, "end": 16, "length": 10 }, { "strand": "+", "start": 22, "end": 31, "length": 10 } ], "reverse": [ { "strand": "-", "start": 43, "end": 34, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-reverse-template", "note": "The hand case's template reverse complemented: the same product, the forward primer on the bottom strand.", "input": { "template": "TGGGGATCCAAGTGCTAAAGGTCAAGCTTTGATC", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "-:28:19|+:4:13", "sequence": "AGCTTGACCTTTAGCACTTGGATCC", "length": 25, "templateLength": 34, "templateSpan": 25, "orientation": "-", "crossesOrigin": false, "forward": { "strand": "-", "start": 28, "end": 19, "length": 10 }, "reverse": { "strand": "+", "start": 4, "end": 13, "length": 10 } } ], "sites": { "forward": [ { "strand": "-", "start": 28, "end": 19, "length": 10 } ], "reverse": [ { "strand": "+", "start": 4, "end": 13, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-circular-origin", "note": "The hand case rotated so the product crosses the origin of a circular template.", "input": { "template": "CACTTGGATCCCCAGATCAAAGCTTGACCTTTAG", "topology": "circular", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:21:30|-:11:2", "sequence": "AGCTTGACCTTTAGCACTTGGATCC", "length": 25, "templateLength": 34, "templateSpan": 25, "orientation": "+", "crossesOrigin": true, "forward": { "strand": "+", "start": 21, "end": 30, "length": 10 }, "reverse": { "strand": "-", "start": 11, "end": 2, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 21, "end": 30, "length": 10 } ], "reverse": [ { "strand": "-", "start": 11, "end": 2, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-linear-no-wrap", "note": "The same rotated template read as linear: no product, since a linear template has no origin to cross.", "input": { "template": "CACTTGGATCCCCAGATCAAAGCTTGACCTTTAG", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "none", "candidates": [], "sites": { "forward": [ { "strand": "+", "start": 21, "end": 30, "length": 10 } ], "reverse": [ { "strand": "-", "start": 11, "end": 2, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-site-across-origin", "note": "A circular template whose forward site itself crosses the origin.", "input": { "template": "TGACCTTTAGCACTTGGATCCCCAGATCAAAGCT", "topology": "circular", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:31:6|-:21:12", "sequence": "AGCTTGACCTTTAGCACTTGGATCC", "length": 25, "templateLength": 34, "templateSpan": 25, "orientation": "+", "crossesOrigin": true, "forward": { "strand": "+", "start": 31, "end": 6, "length": 10 }, "reverse": { "strand": "-", "start": 21, "end": 12, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 31, "end": 6, "length": 10 } ], "reverse": [ { "strand": "-", "start": 21, "end": 12, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-palindromic-pair", "note": "One palindromic primer (GGAATTCC) as both primers, twice on the template: each site on both strands, two products in opposite orientations and four overlapping pairs.", "input": { "template": "TTGGAATTCCAAACCCGGAATTCCTT", "topology": "linear", "forward": { "annealing": "GGAATTCC" }, "reverse": { "annealing": "GGAATTCC" } }, "expected": { "ok": true, "status": "ambiguous", "candidates": [ { "id": "+:3:10|-:24:17", "sequence": "GGAATTCCAAACCCGGAATTCC", "length": 22, "templateLength": 26, "templateSpan": 22, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 3, "end": 10, "length": 8 }, "reverse": { "strand": "-", "start": 24, "end": 17, "length": 8 } }, { "id": "-:24:17|+:3:10", "sequence": "GGAATTCCGGGTTTGGAATTCC", "length": 22, "templateLength": 26, "templateSpan": 22, "orientation": "-", "crossesOrigin": false, "forward": { "strand": "-", "start": 24, "end": 17, "length": 8 }, "reverse": { "strand": "+", "start": 3, "end": 10, "length": 8 } } ], "sites": { "forward": [ { "strand": "+", "start": 3, "end": 10, "length": 8 }, { "strand": "-", "start": 10, "end": 3, "length": 8 }, { "strand": "+", "start": 17, "end": 24, "length": 8 }, { "strand": "-", "start": 24, "end": 17, "length": 8 } ], "reverse": [ { "strand": "+", "start": 3, "end": 10, "length": 8 }, { "strand": "-", "start": 10, "end": 3, "length": 8 }, { "strand": "+", "start": 17, "end": 24, "length": 8 }, { "strand": "-", "start": 24, "end": 17, "length": 8 } ] }, "overlappingPairs": 4 } }, { "id": "pcr-tails", "note": "The hand case with 5' tails: the tails are in the product once, the reverse tail reverse complemented, and excluded from the annealing lengths.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGACCT", "tail": "GCGGCCGC" }, "reverse": { "annealing": "GGATCCAAGT", "tail": "TTAATTAA" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:7:16|-:31:22", "sequence": "GCGGCCGCAGCTTGACCTTTAGCACTTGGATCCTTAATTAA", "length": 41, "templateLength": 34, "templateSpan": 25, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 7, "end": 16, "length": 10 }, "reverse": { "strand": "-", "start": 31, "end": 22, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 7, "end": 16, "length": 10 } ], "reverse": [ { "strand": "-", "start": 31, "end": 22, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-tail-not-inferred", "note": "A tail pasted into the annealing field is not inferred: the longer annealing part has no exact site, so no product.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "GCGGCCGCAGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "none", "candidates": [], "sites": { "forward": [], "reverse": [ { "strand": "-", "start": 31, "end": 22, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-normalised-input", "note": "Lower case, spaces and line breaks in every field are read as the same bases.", "input": { "template": "gatcaa agcttgacct\nttagc\tacttggatcc cca", "topology": "linear", "forward": { "annealing": "agct tgacct" }, "reverse": { "annealing": "ggatcc\naagt" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:7:16|-:31:22", "sequence": "AGCTTGACCTTTAGCACTTGGATCC", "length": 25, "templateLength": 34, "templateSpan": 25, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 7, "end": 16, "length": 10 }, "reverse": { "strand": "-", "start": 31, "end": 22, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 7, "end": 16, "length": 10 } ], "reverse": [ { "strand": "-", "start": 31, "end": 22, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-overlap-only", "note": "The two footprints overlap and nothing else matches: refused as overlapping-sites, which does not mean amplification is impossible.", "input": { "template": "CCAGCTTGACCTAGGTT", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "CCTAGGTC" } }, "expected": { "ok": false, "reason": "overlapping-sites" } }, { "id": "pcr-adjacent", "note": "Adjacent, non-overlapping footprints make a product of exactly the two annealing lengths.", "input": { "template": "AGCTTGACCTACTTGGATCC", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:1:10|-:20:11", "sequence": "AGCTTGACCTACTTGGATCC", "length": 20, "templateLength": 20, "templateSpan": 20, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 20, "end": 11, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 1, "end": 10, "length": 10 } ], "reverse": [ { "strand": "-", "start": 20, "end": 11, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-primer-longer-than-template", "note": "A primer longer than the template has no site: status none.", "input": { "template": "AGCTTGACC", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "none", "candidates": [], "sites": { "forward": [], "reverse": [] }, "overlappingPairs": 0 } }, { "id": "pcr-mismatch", "note": "One mismatch in the forward primer: no exact site, status none.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "TGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "none", "candidates": [], "sites": { "forward": [], "reverse": [ { "strand": "-", "start": 31, "end": 22, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-refuse-invalid-input", "note": "A primer that is not text refuses.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": 42 }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "invalid-input" } }, { "id": "pcr-refuse-topology", "note": "An unknown topology refuses.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "unknown", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "invalid-topology" } }, { "id": "pcr-refuse-empty", "note": "A template of spaces only refuses as empty.", "input": { "template": " ", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "empty-template", "field": "template" } }, { "id": "pcr-accept-template-limit", "note": "A template of exactly 50,000 bases is read (no site: status none).", "input": { "template": { "parts": [ [ "ACCA", 12500 ] ] }, "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "none", "candidates": [], "sites": { "forward": [], "reverse": [] }, "overlappingPairs": 0 } }, { "id": "pcr-refuse-template-limit", "note": "A template of 50,001 bases refuses.", "input": { "template": { "parts": [ [ "ACCA", 12500 ], [ "A", 1 ] ] }, "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "template-limit", "field": "template" } }, { "id": "pcr-refuse-template-base", "note": "An N in the template refuses; no base is removed.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCAN", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "invalid-bases", "field": "template" } }, { "id": "pcr-refuse-primer-base", "note": "A U in the forward annealing part refuses.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCUUGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "invalid-bases", "field": "forward.annealing" } }, { "id": "pcr-refuse-tail-base", "note": "A digit in the reverse tail refuses.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT", "tail": "AC1" } }, "expected": { "ok": false, "reason": "invalid-bases", "field": "reverse.tail" } }, { "id": "pcr-refuse-min-annealing", "note": "A 7-base annealing part refuses (the limit is 8).", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGA" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "primer-length", "field": "forward.annealing" } }, { "id": "pcr-accept-min-annealing", "note": "An 8-base annealing part is read.", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGAC" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "unique", "candidates": [ { "id": "+:7:14|-:31:22", "sequence": "AGCTTGACCTTTAGCACTTGGATCC", "length": 25, "templateLength": 34, "templateSpan": 25, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 7, "end": 14, "length": 8 }, "reverse": { "strand": "-", "start": 31, "end": 22, "length": 10 } } ], "sites": { "forward": [ { "strand": "+", "start": 7, "end": 14, "length": 8 } ], "reverse": [ { "strand": "-", "start": 31, "end": 22, "length": 10 } ] }, "overlappingPairs": 0 } }, { "id": "pcr-refuse-max-annealing", "note": "A 201-base annealing part refuses (the limit is 200).", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": { "parts": [ [ "A", 201 ] ] } }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "primer-length", "field": "forward.annealing" } }, { "id": "pcr-refuse-tail-limit", "note": "A 201-base forward tail refuses (the limit is 200).", "input": { "template": "GATCAAAGCTTGACCTTTAGCACTTGGATCCCCA", "topology": "linear", "forward": { "annealing": "AGCTTGACCT", "tail": { "parts": [ [ "A", 201 ] ] } }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "tail-limit", "field": "forward.tail" } }, { "id": "pcr-accept-site-limit", "note": "Exactly 100 sites for the forward primer are read.", "input": { "template": { "parts": [ [ "A", 107 ] ] }, "topology": "linear", "forward": { "annealing": "AAAAAAAA" }, "reverse": { "annealing": "GATTCCAG" } }, "expected": { "ok": true, "status": "none", "candidates": [], "sites": { "forward": [ { "strand": "+", "start": 1, "end": 8, "length": 8 }, { "strand": "+", "start": 2, "end": 9, "length": 8 }, { "strand": "+", "start": 3, "end": 10, "length": 8 }, { "strand": "+", "start": 4, "end": 11, "length": 8 }, { "strand": "+", "start": 5, "end": 12, "length": 8 }, { "strand": "+", "start": 6, "end": 13, "length": 8 }, { "strand": "+", "start": 7, "end": 14, "length": 8 }, { "strand": "+", "start": 8, "end": 15, "length": 8 }, { "strand": "+", "start": 9, "end": 16, "length": 8 }, { "strand": "+", "start": 10, "end": 17, "length": 8 }, { "strand": "+", "start": 11, "end": 18, "length": 8 }, { "strand": "+", "start": 12, "end": 19, "length": 8 }, { "strand": "+", "start": 13, "end": 20, "length": 8 }, { "strand": "+", "start": 14, "end": 21, "length": 8 }, { "strand": "+", "start": 15, "end": 22, "length": 8 }, { "strand": "+", "start": 16, "end": 23, "length": 8 }, { "strand": "+", "start": 17, "end": 24, "length": 8 }, { "strand": "+", "start": 18, "end": 25, "length": 8 }, { "strand": "+", "start": 19, "end": 26, "length": 8 }, { "strand": "+", "start": 20, "end": 27, "length": 8 }, { "strand": "+", "start": 21, "end": 28, "length": 8 }, { "strand": "+", "start": 22, "end": 29, "length": 8 }, { "strand": "+", "start": 23, "end": 30, "length": 8 }, { "strand": "+", "start": 24, "end": 31, "length": 8 }, { "strand": "+", "start": 25, "end": 32, "length": 8 }, { "strand": "+", "start": 26, "end": 33, "length": 8 }, { "strand": "+", "start": 27, "end": 34, "length": 8 }, { "strand": "+", "start": 28, "end": 35, "length": 8 }, { "strand": "+", "start": 29, "end": 36, "length": 8 }, { "strand": "+", "start": 30, "end": 37, "length": 8 }, { "strand": "+", "start": 31, "end": 38, "length": 8 }, { "strand": "+", "start": 32, "end": 39, "length": 8 }, { "strand": "+", "start": 33, "end": 40, "length": 8 }, { "strand": "+", "start": 34, "end": 41, "length": 8 }, { "strand": "+", "start": 35, "end": 42, "length": 8 }, { "strand": "+", "start": 36, "end": 43, "length": 8 }, { "strand": "+", "start": 37, "end": 44, "length": 8 }, { "strand": "+", "start": 38, "end": 45, "length": 8 }, { "strand": "+", "start": 39, "end": 46, "length": 8 }, { "strand": "+", "start": 40, "end": 47, "length": 8 }, { "strand": "+", "start": 41, "end": 48, "length": 8 }, { "strand": "+", "start": 42, "end": 49, "length": 8 }, { "strand": "+", "start": 43, "end": 50, "length": 8 }, { "strand": "+", "start": 44, "end": 51, "length": 8 }, { "strand": "+", "start": 45, "end": 52, "length": 8 }, { "strand": "+", "start": 46, "end": 53, "length": 8 }, { "strand": "+", "start": 47, "end": 54, "length": 8 }, { "strand": "+", "start": 48, "end": 55, "length": 8 }, { "strand": "+", "start": 49, "end": 56, "length": 8 }, { "strand": "+", "start": 50, "end": 57, "length": 8 }, { "strand": "+", "start": 51, "end": 58, "length": 8 }, { "strand": "+", "start": 52, "end": 59, "length": 8 }, { "strand": "+", "start": 53, "end": 60, "length": 8 }, { "strand": "+", "start": 54, "end": 61, "length": 8 }, { "strand": "+", "start": 55, "end": 62, "length": 8 }, { "strand": "+", "start": 56, "end": 63, "length": 8 }, { "strand": "+", "start": 57, "end": 64, "length": 8 }, { "strand": "+", "start": 58, "end": 65, "length": 8 }, { "strand": "+", "start": 59, "end": 66, "length": 8 }, { "strand": "+", "start": 60, "end": 67, "length": 8 }, { "strand": "+", "start": 61, "end": 68, "length": 8 }, { "strand": "+", "start": 62, "end": 69, "length": 8 }, { "strand": "+", "start": 63, "end": 70, "length": 8 }, { "strand": "+", "start": 64, "end": 71, "length": 8 }, { "strand": "+", "start": 65, "end": 72, "length": 8 }, { "strand": "+", "start": 66, "end": 73, "length": 8 }, { "strand": "+", "start": 67, "end": 74, "length": 8 }, { "strand": "+", "start": 68, "end": 75, "length": 8 }, { "strand": "+", "start": 69, "end": 76, "length": 8 }, { "strand": "+", "start": 70, "end": 77, "length": 8 }, { "strand": "+", "start": 71, "end": 78, "length": 8 }, { "strand": "+", "start": 72, "end": 79, "length": 8 }, { "strand": "+", "start": 73, "end": 80, "length": 8 }, { "strand": "+", "start": 74, "end": 81, "length": 8 }, { "strand": "+", "start": 75, "end": 82, "length": 8 }, { "strand": "+", "start": 76, "end": 83, "length": 8 }, { "strand": "+", "start": 77, "end": 84, "length": 8 }, { "strand": "+", "start": 78, "end": 85, "length": 8 }, { "strand": "+", "start": 79, "end": 86, "length": 8 }, { "strand": "+", "start": 80, "end": 87, "length": 8 }, { "strand": "+", "start": 81, "end": 88, "length": 8 }, { "strand": "+", "start": 82, "end": 89, "length": 8 }, { "strand": "+", "start": 83, "end": 90, "length": 8 }, { "strand": "+", "start": 84, "end": 91, "length": 8 }, { "strand": "+", "start": 85, "end": 92, "length": 8 }, { "strand": "+", "start": 86, "end": 93, "length": 8 }, { "strand": "+", "start": 87, "end": 94, "length": 8 }, { "strand": "+", "start": 88, "end": 95, "length": 8 }, { "strand": "+", "start": 89, "end": 96, "length": 8 }, { "strand": "+", "start": 90, "end": 97, "length": 8 }, { "strand": "+", "start": 91, "end": 98, "length": 8 }, { "strand": "+", "start": 92, "end": 99, "length": 8 }, { "strand": "+", "start": 93, "end": 100, "length": 8 }, { "strand": "+", "start": 94, "end": 101, "length": 8 }, { "strand": "+", "start": 95, "end": 102, "length": 8 }, { "strand": "+", "start": 96, "end": 103, "length": 8 }, { "strand": "+", "start": 97, "end": 104, "length": 8 }, { "strand": "+", "start": 98, "end": 105, "length": 8 }, { "strand": "+", "start": 99, "end": 106, "length": 8 }, { "strand": "+", "start": 100, "end": 107, "length": 8 } ], "reverse": [] }, "overlappingPairs": 0 } }, { "id": "pcr-refuse-site-limit", "note": "101 sites for the forward primer refuse: the search would be incomplete.", "input": { "template": { "parts": [ [ "A", 108 ] ] }, "topology": "linear", "forward": { "annealing": "AAAAAAAA" }, "reverse": { "annealing": "GATTCCAG" } }, "expected": { "ok": false, "reason": "site-limit", "field": "forward.annealing" } }, { "id": "pcr-refuse-candidate-limit", "note": "More than 100 products refuse: the list would be incomplete.", "input": { "template": { "parts": [ [ "AGCTTGACCTCC", 11 ], [ "ACTTGGATCCCC", 10 ] ] }, "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": false, "reason": "candidate-limit" } }, { "id": "pcr-accept-candidate-limit", "note": "Exactly 100 products are all listed.", "input": { "template": { "parts": [ [ "AGCTTGACCTCC", 10 ], [ "ACTTGGATCCCC", 10 ] ] }, "topology": "linear", "forward": { "annealing": "AGCTTGACCT" }, "reverse": { "annealing": "GGATCCAAGT" } }, "expected": { "ok": true, "status": "ambiguous", "candidates": [ { "id": "+:1:10|-:130:121", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCC", "length": 130, "templateLength": 240, "templateSpan": 130, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 130, "end": 121, "length": 10 } }, { "id": "+:1:10|-:142:133", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCC", "length": 142, "templateLength": 240, "templateSpan": 142, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 142, "end": 133, "length": 10 } }, { "id": "+:1:10|-:154:145", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 154, "templateLength": 240, "templateSpan": 154, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 154, "end": 145, "length": 10 } }, { "id": "+:1:10|-:166:157", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 166, "templateLength": 240, "templateSpan": 166, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 166, "end": 157, "length": 10 } }, { "id": "+:1:10|-:178:169", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 178, "templateLength": 240, "templateSpan": 178, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 178, "end": 169, "length": 10 } }, { "id": "+:1:10|-:190:181", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 190, "templateLength": 240, "templateSpan": 190, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 190, "end": 181, "length": 10 } }, { "id": "+:1:10|-:202:193", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 202, "templateLength": 240, "templateSpan": 202, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 202, "end": 193, "length": 10 } }, { "id": "+:1:10|-:214:205", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 214, "templateLength": 240, "templateSpan": 214, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 214, "end": 205, "length": 10 } }, { "id": "+:1:10|-:226:217", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 226, "templateLength": 240, "templateSpan": 226, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 226, "end": 217, "length": 10 } }, { "id": "+:1:10|-:238:229", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 238, "templateLength": 240, "templateSpan": 238, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 1, "end": 10, "length": 10 }, "reverse": { "strand": "-", "start": 238, "end": 229, "length": 10 } }, { "id": "+:13:22|-:130:121", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCC", "length": 118, "templateLength": 240, "templateSpan": 118, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 130, "end": 121, "length": 10 } }, { "id": "+:13:22|-:142:133", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCC", "length": 130, "templateLength": 240, "templateSpan": 130, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 142, "end": 133, "length": 10 } }, { "id": "+:13:22|-:154:145", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 142, "templateLength": 240, "templateSpan": 142, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 154, "end": 145, "length": 10 } }, { "id": "+:13:22|-:166:157", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 154, "templateLength": 240, "templateSpan": 154, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 166, "end": 157, "length": 10 } }, { "id": "+:13:22|-:178:169", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 166, "templateLength": 240, "templateSpan": 166, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 178, "end": 169, "length": 10 } }, { "id": "+:13:22|-:190:181", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 178, "templateLength": 240, "templateSpan": 178, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 190, "end": 181, "length": 10 } }, { "id": "+:13:22|-:202:193", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 190, "templateLength": 240, "templateSpan": 190, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 202, "end": 193, "length": 10 } }, { "id": "+:13:22|-:214:205", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 202, "templateLength": 240, "templateSpan": 202, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 214, "end": 205, "length": 10 } }, { "id": "+:13:22|-:226:217", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 214, "templateLength": 240, "templateSpan": 214, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 226, "end": 217, "length": 10 } }, { "id": "+:13:22|-:238:229", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 226, "templateLength": 240, "templateSpan": 226, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 13, "end": 22, "length": 10 }, "reverse": { "strand": "-", "start": 238, "end": 229, "length": 10 } }, { "id": "+:25:34|-:130:121", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCC", "length": 106, "templateLength": 240, "templateSpan": 106, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 130, "end": 121, "length": 10 } }, { "id": "+:25:34|-:142:133", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCC", "length": 118, "templateLength": 240, "templateSpan": 118, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 142, "end": 133, "length": 10 } }, { "id": "+:25:34|-:154:145", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 130, "templateLength": 240, "templateSpan": 130, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 154, "end": 145, "length": 10 } }, { "id": "+:25:34|-:166:157", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 142, "templateLength": 240, "templateSpan": 142, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 166, "end": 157, "length": 10 } }, { "id": "+:25:34|-:178:169", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 154, "templateLength": 240, "templateSpan": 154, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 178, "end": 169, "length": 10 } }, { "id": "+:25:34|-:190:181", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 166, "templateLength": 240, "templateSpan": 166, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 190, "end": 181, "length": 10 } }, { "id": "+:25:34|-:202:193", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 178, "templateLength": 240, "templateSpan": 178, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 202, "end": 193, "length": 10 } }, { "id": "+:25:34|-:214:205", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 190, "templateLength": 240, "templateSpan": 190, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 214, "end": 205, "length": 10 } }, { "id": "+:25:34|-:226:217", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 202, "templateLength": 240, "templateSpan": 202, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 226, "end": 217, "length": 10 } }, { "id": "+:25:34|-:238:229", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCCCCACTTGGATCC", "length": 214, "templateLength": 240, "templateSpan": 214, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 25, "end": 34, "length": 10 }, "reverse": { "strand": "-", "start": 238, "end": 229, "length": 10 } }, { "id": "+:37:46|-:130:121", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCC", "length": 94, "templateLength": 240, "templateSpan": 94, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 37, "end": 46, "length": 10 }, "reverse": { "strand": "-", "start": 130, "end": 121, "length": 10 } }, { "id": "+:37:46|-:142:133", "sequence": "AGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCAGCTTGACCTCCACTTGGATCCCCACTTGGATCC", "length": 106, "templateLength": 240, "templateSpan": 106, "orientation": "+", "crossesOrigin": false, "forward": { "strand": "+", "start": 37, "end": 46, "length": 10 }, "reverse": { "strand": "-", "start": 142, "end": 133, "length": 10 } }, { "id": "+:37:46|-:154:145", "sequence": 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