{ "about": { "generatedBy": "pipeline/plasmid-map/reference.py", "scriptSha256": "6d99ac2790c5d6b6791dbd91a6d49db4a4cbfdf63424fe7465b11e85e74744a5", "recordedOn": "2026-10-17", "oracle": "Biopython 1.88", "oracleLicence": "Biopython Licence Agreement or BSD-3-Clause", "text": "What the map must show where two entries of the annotation library reach their thresholds at one place (the CSO, 17 October 2026). Each case puts one entry's own bases between 300-base seeded random flanks and records the calls the oracle makes there, then applies the published cross-check's rule for each pair: an identity pair shows the best-scoring call and names the others; a containment pair marked different-element shows both, the contained call drawn inside its container; a pair marked same-element or shared-subsequence, and any unmarked pair, shows one call and names the other, a shared-subsequence pair over the shared span alone. `offsets` counts how many times each entry is called in the target, which is how the doubled containment of dTomato inside tdTomato is published without being drawn twice. Nothing here is read from the engine.", "seed": 20261018, "coextensiveRatio": "9/10" }, "cases": [ { "id": "D1", "label": "containment marked different-element: both shown, the contained call drawn inside", "target": "sv40Promoter", "targetLength": 417, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCGCAGCACCATGGCCTGAAATAACCTCTGAAAGAGGAACTTGGTTAGGTACCTTCTGAGGCGGAAAGAACCAGCTGTGGAATGTGTGTCAGTTAGGGTGTGGAAAGTCCCCAGGCTCCCCAGCAGGCAGAAGTATGCAAAGCATGCATCTCAATTAGTCAGCAACCAGGTGTGGAAAGTCCCCAGGCTCCCCAGCAGGCAGAAGTATGCAAAGCATGCATCTCAATTAGTCAGCAACCATAGTCCCGCCCCTAACTCCGCCCATCCCGCCCCTAACTCCGCCCAGTTCCGCCCATTCTCCGCCCCATGGCTGACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCGGCCTCTGAGCTATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGCTTTTGCAAAAAGCTTCACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "ba575727e193c36b9d23d65ad6711210f669731e67ae818f808a1a686ac2ceda", "expected": { "shown": [ "sv40Ori", "sv40Promoter" ], "alsoWithinThresholds": [], "inside": { "sv40Ori@615": [ "sv40Promoter" ] }, "offsets": { "sv40Promoter": 1, "sv40Ori": 1 } }, "pairs": [ "containment (different-element)" ] }, { "id": "D2", "label": "identity: one best call, the other named", "target": "lucPlus", "targetLength": 1653, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCATGGAAGACGCCAAAAACATAAAGAAAGGCCCGGCGCCATTCTATCCGCTGGAAGATGGAACCGCTGGAGAGCAACTGCATAAGGCTATGAAGAGATACGCCCTGGTTCCTGGAACAATTGCTTTTACAGATGCACATATCGAGGTGGACATCACTTACGCTGAGTACTTCGAAATGTCCGTTCGGTTGGCAGAAGCTATGAAACGATATGGGCTGAATACAAATCACAGAATCGTCGTATGCAGTGAAAACTCTCTTCAATTCTTTATGCCGGTGTTGGGCGCGTTATTTATCGGAGTTGCAGTTGCGCCCGCGAACGACATTTATAATGAACGTGAATTGCTCAACAGTATGGGCATTTCGCAGCCTACCGTGGTGTTCGTTTCCAAAAAGGGGTTGCAAAAAATTTTGAACGTGCAAAAAAAGCTCCCAATCATCCAAAAAATTATTATCATGGATTCTAAAACGGATTACCAGGGATTTCAGTCGATGTACACGTTCGTCACATCTCATCTACCTCCCGGTTTTAATGAATACGATTTTGTGCCAGAGTCCTTCGATAGGGACAAGACAATTGCACTGATCATGAACTCCTCTGGATCTACTGGTCTGCCTAAAGGTGTCGCTCTGCCTCATAGAACTGCCTGCGTGAGATTCTCGCATGCCAGAGATCCTATTTTTGGCAATCAAATCATTCCGGATACTGCGATTTTAAGTGTTGTTCCATTCCATCACGGTTTTGGAATGTTTACTACACTCGGATATTTGATATGTGGATTTCGAGTCGTCTTAATGTATAGATTTGAAGAAGAGCTGTTTCTGAGGAGCCTTCAGGATTACAAGATTCAAAGTGCGCTGCTGGTGCCAACCCTATTCTCCTTCTTCGCCAAAAGCACTCTGATTGACAAATACGATTTATCTAATTTACACGAAATTGCTTCTGGTGGCGCTCCCCTCTCTAAGGAAGTCGGGGAAGCGGTTGCCAAGAGGTTCCATCTGCCAGGTATCAGGCAAGGATATGGGCTCACTGAGACTACATCAGCTATTCTGATTACACCCGAGGGGGATGATAAACCGGGCGCGGTCGGTAAAGTTGTTCCATTTTTTGAAGCGAAGGTTGTGGATCTGGATACCGGGAAAACGCTGGGCGTTAATCAAAGAGGCGAACTGTGTGTGAGAGGTCCTATGATTATGTCCGGTTATGTAAACAATCCGGAAGCGACCAACGCCTTGATTGACAAGGATGGATGGCTACATTCTGGAGACATAGCTTACTGGGACGAAGACGAACACTTCTTCATCGTTGACCGCCTGAAGTCTCTGATTAAGTACAAAGGCTATCAGGTGGCTCCCGCTGAATTGGAATCCATCTTGCTCCAACACCCCAACATCTTCGACGCAGGTGTCGCAGGTCTTCCCGACGATGACGCCGGTGAACTTCCCGCCGCCGTTGTTGTTTTGGAGCACGGAAAGACGATGACGGAAAAAGAGATCGTGGATTACGTCGCCAGTCAAGTAACAACCGCGAAAAAGTTGCGCGGAGGAGTTGTGTTTGTGGACGAAGTACCGAAAGGTCTTACCGGAAAACTCGACGCAAGAAAAATCAGAGAGATCCTCATAAAGGCCAAGAAGGGCGGAAAGATCGCCGTGTAACACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "540452224ac19d46186ab571ce1f88539d477a2be51a6dc00d5bb4025bfdc619", "expected": { "shown": [ "lucPlus" ], "alsoWithinThresholds": [], "inside": {}, "offsets": { "lucPlus": 1 } }, "pairs": [] }, { "id": "D3", "label": "containment marked same-element, doubled: one call at the locus, dTomato named, two offsets published", "target": "tdTomato", "targetLength": 1431, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCATGGTGAGCAAGGGCGAGGAGGTCATCAAAGAGTTCATGCGCTTCAAGGTGCGCATGGAGGGCTCCATGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGCGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCCCAGTTCATGTACGGCTCCAAGGCGTACGTGAAGCACCCCGCCGACATCCCCGATTACAAGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGTCTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCACGCTGATCTACAAGGTGAAGATGCGCGGCACCAACTTCCCCCCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCACCGAGCGCCTGTACCCCCGCGACGGCGTGCTGAAGGGCGAGATCCACCAGGCCCTGAAGCTGAAGGACGGCGGCCACTACCTGGTGGAGTTCAAGACCATCTACATGGCCAAGAAGCCCGTGCAACTGCCCGGCTACTACTACGTGGACACCAAGCTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAGCGCTCCGAGGGCCGCCACCACCTGTTCCTGGGGCATGGCACCGGCAGCACCGGCAGCGGCAGCTCCGGCACCGCCTCCTCCGAGGACAACAACATGGCCGTCATCAAAGAGTTCATGCGCTTCAAGGTGCGCATGGAGGGCTCCATGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGCGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCCCAGTTCATGTACGGCTCCAAGGCGTACGTGAAGCACCCCGCCGACATCCCCGATTACAAGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGTCTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCACGCTGATCTACAAGGTGAAGATGCGCGGCACCAACTTCCCCCCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCACCGAGCGCCTGTACCCCCGCGACGGCGTGCTGAAGGGCGAGATCCACCAGGCCCTGAAGCTGAAGGACGGCGGCCACTACCTGGTGGAGTTCAAGACCATCTACATGGCCAAGAAGCCCGTGCAACTGCCCGGCTACTACTACGTGGACACCAAGCTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAGCGCTCCGAGGGCCGCCACCACCTGTTCCTGTACGGCATGGACGAGCTGTACAAGTAACACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "23080eb5bb3570a7f21bcd61d667448bee9a15d162a6c1adb9b3263f9adf78ac", "expected": { "shown": [ "tdTomato" ], "alsoWithinThresholds": [ { "feature": "dTomato", "call": "match", "exact": false, "identity": "684/684", "coverage": "684/705", "start": 1048, "end": 1731, "strand": "+", "score": 1368.0, "drawnInstead": "tdTomato" }, { "feature": "mCherry", "call": "partial", "exact": false, "identity": "642/705", "coverage": "697/711", "start": 1029, "end": 1731, "strand": "+", "score": 1099.0, "drawnInstead": "dTomato" }, { "feature": "mHoneydew", "call": "partial", "exact": false, "identity": "606/660", "coverage": "658/678", "start": 315, "end": 970, "strand": "+", "score": 1047.0, "drawnInstead": "mRfp1" }, { "feature": "mRfp1", "call": "partial", "exact": false, "identity": "609/660", "coverage": "658/678", "start": 315, "end": 970, "strand": "+", "score": 1062.0, "drawnInstead": "tdTomato" }, { "feature": "mStrawberry", "call": "partial", "exact": false, "identity": "637/707", "coverage": "697/711", "start": 1029, "end": 1731, "strand": "+", "score": 1066.0, "drawnInstead": "dTomato" }, { "feature": "mTangerine", "call": "partial", "exact": false, "identity": "607/661", "coverage": "658/678", "start": 315, "end": 970, "strand": "+", "score": 1045.0, "drawnInstead": "mRfp1" } ], "inside": {}, "offsets": { "dTomato": 2, "mCherry": 2, "tdTomato": 1, "mHoneydew": 2, "mRfp1": 2, "mTangerine": 2, "mStrawberry": 1 } }, "pairs": [ "containment (unsettled)", "containment (same-element)", "containment (unsettled)", "containment (unsettled)", "containment (unsettled)", "containment (unsettled)" ] }, { "id": "D4", "label": "nothing reported between the phage promoters", "target": "t7Promoter", "targetLength": 19, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCTAATACGACTCACTATAGGCACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "998cc2d38d17ac5f0ef46591870ddc64ca6fd1486866062e9d34b5bc95d9d382", "expected": { "shown": [ "t7Promoter" ], "alsoWithinThresholds": [], "inside": {}, "offsets": { "t7Promoter": 1 } }, "pairs": [] }, { "id": "D5", "label": "an unmarked containment pair: the container alone, the contained entry named", "target": "pucOri", "targetLength": 668, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACCACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "ee5d15f6cbe346d7c6e76c02f14a35d4c0ae5233ec7d8ac18467c2e4bd9e0b90", "expected": { "shown": [ "pucOri", "rnaI" ], "alsoWithinThresholds": [], "inside": { "rnaI@799": [ "pucOri" ] }, "offsets": { "pucOri": 1, "rnaI": 1 } }, "pairs": [ "containment (different-element)" ] }, { "id": "D6", "label": "the lac neighbourhood: the operator and the CAP site drawn inside the promoter", "target": "lacPromoter", "targetLength": 122, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTCACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "010043fff43d68f1b0f3cd151928405c1eb39263bef5b91fabcafabdcb85f153", "expected": { "shown": [ "capSite", "lacO", "lacPromoter" ], "alsoWithinThresholds": [], "inside": { "capSite@301": [ "lacPromoter" ], "lacO@385": [ "lacPromoter" ] }, "offsets": { "capSite": 1, "lacPromoter": 1, "lacO": 1 } }, "pairs": [ "containment (different-element)", "containment (different-element)", "partial overlap (unsettled)" ] }, { "id": "D7", "label": "a three-way identity: one best call and a two-entry also-within list", "target": "ebfp2", "targetLength": 720, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGAGGGGCGAGGGCGAGGGCGATGCCACCAACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGAGCCACGGCGTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCACCTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCGTCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTTCAACAGCCACAACATCTATATCATGGCCGTCAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACGTGGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAGCCACTACCTGAGCACCCAGTCCGTGCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCCGCACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "09266a5031d7c8e656dadb789ce989a4a15997386fbcb349c12492d41c72a107", "expected": { "shown": [ "ebfp2" ], "alsoWithinThresholds": [ { "feature": "egfp", "call": "partial", "exact": false, "identity": "699/720", "coverage": "720/720", "start": 301, "end": 1020, "strand": "+", "score": 1335.0, "drawnInstead": "ebfp2" }, { "feature": "mKalama1", "call": "partial", "exact": false, "identity": "675/723", "coverage": "720/720", "start": 301, "end": 1020, "strand": "+", "score": 1206.0, "drawnInstead": "egfp" } ], "inside": {}, "offsets": { "ebfp2": 1, "egfp": 1, "mKalama1": 1 } }, "pairs": [ "identity (identity)", "identity (identity)" ] }, { "id": "D8", "label": "a parent and its variant at 95 percent of each other's length: identity, not containment", "target": "mCherry", "targetLength": 711, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGTAACACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "548c432c8a884a2dcfcc25c390fcfabe9290c9cceaad873673b190d8994937c0", "expected": { "shown": [ "mCherry" ], "alsoWithinThresholds": [ { "feature": "dTomato", "call": "partial", "exact": false, "identity": "648/719", "coverage": "705/705", "start": 301, "end": 1011, "strand": "+", "score": 1096.0, "drawnInstead": "mTangerine" }, { "feature": "mApple", "call": "partial", "exact": false, "identity": "678/711", "coverage": "711/711", "start": 301, "end": 1011, "strand": "+", "score": 1257.0, "drawnInstead": "mStrawberry" }, { "feature": "mBanana", "call": "partial", "exact": false, "identity": "677/712", "coverage": "711/711", "start": 301, "end": 1011, "strand": "+", "score": 1245.0, "drawnInstead": "mStrawberry" }, { "feature": "mBlueberry2", "call": "partial", "exact": false, "identity": "685/712", "coverage": "711/711", "start": 301, "end": 1011, "strand": "+", "score": 1285.0, "drawnInstead": "mStrawberry" }, { "feature": "mHoneydew", "call": "partial", "exact": false, "identity": "634/654", "coverage": "654/678", "start": 335, "end": 988, "strand": "+", "score": 1208.0, "drawnInstead": "mTangerine" }, { "feature": "mOrange", "call": "partial", "exact": false, "identity": "693/711", "coverage": "711/711", "start": 301, "end": 1011, "strand": "+", "score": 1332.0, "drawnInstead": "mStrawberry" }, { "feature": "mOrange2", "call": "partial", "exact": false, "identity": "691/711", "coverage": "711/711", "start": 301, "end": 1011, "strand": "+", "score": 1322.0, "drawnInstead": "mStrawberry" }, { "feature": "mRfp1", "call": "partial", "exact": false, "identity": "639/654", "coverage": "654/678", "start": 335, "end": 988, "strand": "+", "score": 1233.0, "drawnInstead": "mStrawberry" }, { "feature": "mStrawberry", "call": "partial", "exact": false, "identity": "696/711", "coverage": "711/711", "start": 301, "end": 1011, "strand": "+", "score": 1347.0, "drawnInstead": "mCherry" }, { "feature": "mTangerine", "call": "partial", "exact": false, "identity": "639/655", "coverage": "654/678", "start": 335, "end": 988, "strand": "+", "score": 1226.0, "drawnInstead": "mRfp1" } ], "inside": {}, "offsets": { "dTomato": 1, "mApple": 1, "mBanana": 1, "mBlueberry2": 1, "mCherry": 1, "mOrange": 1, "mOrange2": 1, "mStrawberry": 1, "mHoneydew": 1, "mRfp1": 1, "mTangerine": 1 } }, "pairs": [ "containment (unsettled)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)", "identity (identity)" ] }, { "id": "D9", "label": "containment across two records, marked different-element: both shown", "target": "pucOri", "targetLength": 668, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACCACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "ee5d15f6cbe346d7c6e76c02f14a35d4c0ae5233ec7d8ac18467c2e4bd9e0b90", "expected": { "shown": [ "pucOri", "rnaI" ], "alsoWithinThresholds": [], "inside": { "rnaI@799": [ "pucOri" ] }, "offsets": { "pucOri": 1, "rnaI": 1 } }, "pairs": [ "containment (different-element)" ] }, { "id": "D10", "label": "a shared subsequence: best call per locus, the other named over the shared span, neither nested", "target": "hiv1Ltr5", "targetLength": 634, "sequence": "CGATACAGGCACCAACCAATAAACAAAGAGAAATCTTTCATCCACAGTCAAGGTCAACCCAGCTTCTTCGTTGAACCAGCGTATTTTCGATCCCATCCCAATCGGTGTGTCACGGAGATCCCCGTACGGGGTAGACCAAAAGGCATTTCCCTCCCATATAAGCAGGCAGATTATCCGACGGACCAATACGCTACCTAAGCAAGTATACTGCTACGATGTATGATGGTAGCGGCCTCTCTCATTCTTGCTCCTGGGCAATTCTTCGGATCCCCGAAAGACGGGCTAAAACAACGTGGCTGCTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGGTAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGATATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCACACCCGGCGTAAGGGTATTCCGCCCCACAAAACCAGCGGAACGGCGTTACTGTCGATGCTGTTACGGCCAGCGAGACGTGGATGCCTTATCCCATGTTTGACGTCACAACGTGATTCTTTTTTACAAAGCGCGCGAAGTTATACTGCCGGAGACGGGGCCAATAACATCTCCTGGGGGGGGGTGTGCGTGGTGATTGAACGGATTCAACTTCAATAGGGTCGAAGGCCCAGACCTCGTTAGGCGAATACTGTACGGTACGCCCTTTCAGATTGAACTTTTATTATTACGTTTTAAACGCT", "sha256": "a4610002b5082c24eec7baa0f7a92bfe6250290e70be9991060a343749780e48", "expected": { "shown": [ "hiv1Ltr5" ], "alsoWithinThresholds": [ { "feature": "hiv1Ltr3", "call": "partial", "exact": false, "identity": "198/199", "coverage": "199/235", "start": 736, "end": 934, "strand": "+", "score": 393.0, "drawnInstead": "hiv1Ltr5" } ], "inside": {}, "offsets": { "hiv1Ltr5": 1, "hiv1Ltr3": 1 } }, "pairs": [ "partial overlap (shared-subsequence)" ] } ], "lacCases": [ { "id": "L1", "label": "the lac promoter with the operator and the CAP site inside it, as siblings", "sequence": "GACTGGAGCAGTGGAATGCTACTGAGGCAGATAGGTGGGGACTTACCTAGGCACTGAGATCGAGCGTAGCGGCGTGAGAGTCATTGTCGCGCAAGCAGGGCCCGCCCTATACGGAAGAAAAATTCATTGTGCTCGCTCGGAACACCGGCCCCATTAAGAAATCTGTTAGTCGGCGGTGGGTCCAGCAGAGTGTCCTGGACAAGGTGGACGTACCTATGAGCAGTTAAGGGTAACTGGCTAAGACCTTTACTGTCCTGCTGGACAAAACTATCCGAATTAGCCTGCCTGCCGACTAGACTTGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTTGCTATACAGCACTACCCAACAGTTGCTAGCAACTCTGCGCAAGACATCATTCCTTCCGTGTTTTCCAACACGCAACTTCGAGGGTTCTTGCTAGTTAATTTACTCATGTTTATGAGTTCACACCGGCAGTACGACGTCGTGACTTCATGTGTATGCTTCCAAAAACCGGAAGAGACATAGACCGATGATTATCAAGCGAGGTTCAGGCAAGGGCCCATTAGGGTGGTCACGTCGGTCGCGCTCGTTAGCGGCCTGCAGTTGGTACATGTTTAAGCAGATGTTGTGAGCTTTGACCGCGC", "sha256": "2395fee47640f61aabb6a25406db85fc25c6e43dbbd6036c051fd320a31f3b16", "expected": { "calls": [ { "feature": "capSite", "start": 301, "end": 338, "call": "match" }, { "feature": "lacPromoter", "start": 301, "end": 422, "call": "match" }, { "feature": "lacO", "start": 385, "end": 405, "call": "match" } ], "inside": { "capSite@301": [ "lacPromoter" ], "lacO@385": [ "lacPromoter" ] } } }, { "id": "L2", "label": "the trc promoter region with the operator inside it", "sequence": "TATTGCTTTACAAAATTAAGGCCCAAAAGCGAGGACAGTAACTATTCACGGAAGCGGGCAGGAGACGCCAATCCCCTGCGTCTGTACTCGGCGTAGTGCCGACGGACCAGAACAATGTGGGGAAGATCTGCAGTAAACAACCAGTTCAGTCACTTCCTTCGACTGATCTGTACGTGCAGACATGGACCAATCGATGATGGACTCGGATCGTGTCGTAAGACGAGCGTTATGGTCGACCACAAAGTGTGTAACGGCTTTCCGGTCTGTCCGATAAATCATCTATACAAGGATCAATCTGGACGACTGCACGGTGCACCAATGCTTCTGGCGTCAGGCAGCCATCGGAAGCTGTGGTATGGCTGTGCAGGTCGTAAATCACTGCATAATTCGTGTCGCTCAAGGCGCACTCCCGTTCTGGATAATGTTTTTTGCGCCGACATCATAACGGTTCTGGCAAATATTCTGAAATGAGCTGTTGACAATTAATCATCCGGCTCGTATAATGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGGGCACCCACACCGACCACTAAGCGTAACCTAACGACTTATTACTCAAGAGCAAATCTTAAGATATACACGGAGTAAAGAAATGTATGCGTGGGTGGCCCTGTCAATGCATTCCTCATGACTGAGACAGGTTAACCTCTAACTCCTTGCTGGAAATCTCAGCTTTGTGACCCTTATACAATACGCGGCGGAAGCGCGGGACCTCGTGTCCACAGTGTGCGCGTAGATTAGGAGGATTGAGACCCAAGGAGGCCTAGAGATGCGGGAGGTAAGCGGGCGAACGCAGACTAAGCAACTTAAAG", "sha256": "794b2a65e10ce207bd08ad76295bd2f2115311fe49bf6c2b5c4a49c3e59f1c31", "expected": { "calls": [ { "feature": "trc", "start": 301, "end": 546, "call": "match" }, { "feature": "lacPromoter", "start": 476, "end": 546, "call": "partial" }, { "feature": "lacO", "start": 511, "end": 531, "call": "match" } ], "inside": { "lacO@511": [ "lacPromoter", "trc" ] } } }, { "id": "L3", "label": "both promoters at separate loci: each operator call names its own container", "sequence": "GGCGCGATATCGGGGGATACTTCGAGCTGGGAAGGCCGGGGAGCGCCAAGCACACACGGGATTTTTACGCCTGTTACATCGACCGTCGTACGCGTAATTAAAGTGAGCATGAGGAAGCCGGCACACGACATGAACCCAGCAGTGGAAGTCATTTTGACGCGTGCGGATCAGGGTTGAACTTCTGGTGTATTTAGAAATGTCAGCGAGAACTTGTAAGGAATTTCCACTTTTATCGGCTGATCCCGACAGGCCCTTGGGCTTCGGCGAAATTAGGAACTGGAGTCAATACCCGACCAGGGCGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTCAGACAAGGTCCTTTGGGGGAATACGCCGAGCAGGTAATCATTAATCGCAAATAGCCATCGTACGCCACTTGGCCCTACTCTGTTCGGTGGGGGACCAACTTAATACTAGTAGGAACTACAAATTTTGTGTCGGCGATGTCGTATGCTCAACAAAGCGCGACTGGCGCAGGACGTAAACACAAGCCGGGAAACGGGCCGCTTTAACACGGGGCCCGGTGACAGAGCGCCGGGAGGGTTAAGTCCCCTGTTTCGTTCGTACCGACAGGGTTGATCCCGGTCGCGGATTACCGTCTATCTACCGACTGCACGGTGCACCAATGCTTCTGGCGTCAGGCAGCCATCGGAAGCTGTGGTATGGCTGTGCAGGTCGTAAATCACTGCATAATTCGTGTCGCTCAAGGCGCACTCCCGTTCTGGATAATGTTTTTTGCGCCGACATCATAACGGTTCTGGCAAATATTCTGAAATGAGCTGTTGACAATTAATCATCCGGCTCGTATAATGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGTTCCTATGCCAGTTAGATAAAAGTTCTAAGCTTGGCCTTAGGCAGCGGTGGTAAAACTAGGTCCGTACACTTGGTCAATGCTCCCGCACCACCTGCTTTACTCCCACCGGCGCCGGGTGTTCGATTTAACCCGAAAAATTCTAAATACGGCGATAGCAAAACTTCCTTATAATACCTTCGGGGTTTGGGTTCCTGCAACAATTGGCGCTCGGGAATACAATTGGTACTCAAATCGTCGAAGACCGGCGGCGACTAGTTGGCAATCAGGTGGCGAAGACCTTTTATCCTTGAAGTGATTAC", "sha256": "27c529c8fb30c17320c55da413af86e69dc8539cf3bd699e32d5a139f1085f62", "expected": { "calls": [ { "feature": "capSite", "start": 301, "end": 338, "call": "match" }, { "feature": "lacPromoter", "start": 301, "end": 422, "call": "match" }, { "feature": "lacO", "start": 385, "end": 405, "call": "match" }, { "feature": "trc", "start": 723, "end": 968, "call": "match" }, { "feature": "lacPromoter", "start": 898, "end": 968, "call": "partial" }, { "feature": "lacO", "start": 933, "end": 953, "call": "match" } ], "inside": { "capSite@301": [ "lacPromoter" ], "lacO@385": [ "lacPromoter" ], "lacO@933": [ "lacPromoter", "trc" ] } } }, { "id": "L4", "label": "a bare operator, with no container call around it: no label", "sequence": "ACCTTAATGGGCGTGGACGTCTCTTGCTTGGAGGCTGGTGTGCACCCCTCATTATGACATCTCAGGAGAGGTATAGAGGAGAAAAGCTGTTACATGGTTCGGTTTTTACGGAATGGCGGGGCGGTTTCGTGCGTACTGTCTGTGCTCCCGGCCGTTGTAAGATTCCTAAACTCGACGGCAACCAAGTCAATTGTTAGTCTTTTACACAAAGAACTCTACGGTATGCTGACTGTCTTCCACTCCGAGTGGCCGCAAGTACTTCTCCCTTATAGTTAAGTCTGCAAATGCGCATTTCGAGGGAATTGTGAGCGGATAACAATTCACCCTACAATTTAATCTCGTCCTGTCGGGAAACGGCGAGCTGGATTGGTGCACTGGCAACATCCCGCGCTAGGTTTGATGGTAAACTGTACGAGCCACCCTGCTGCAGCGTCCACGGACTTACAGTAAGCGCCCTCGAGGCTCCTCCCTCCATTGAAAGCAGAAGTCCCGGATTTCTTAACAATCTACCTCTGGCACGCAGATCTGGGTTTCTTACATCACACTTCCACGGAGTATAAAGAATGAGAGTCGTTCTTGTCATGGCCGGGTCCCATGCACTAAATTCACGACACGTATAAA", "sha256": "ea14a17a13a2f1dc7cba04e14fd6ce727d4a29645bccdaeb7f3e3d7f57a3c1fd", "expected": { "calls": [ { "feature": "lacO", "start": 301, "end": 321, "call": "match" } ], "inside": {} } } ], "offsetCase": { "id": "O1", "label": "an identity pair whose two calls at one locus are offset, not coincident: one call drawn, the other named", "pair": [ "dTomato", "mHoneydew" ], "target": "dTomato", "sequence": "ACATCGATCCAACTTGCCTACAACTAGCCCTCCTCCGTTGGCCGAGTTAATGCAAGCGCGAAGTTGTGCGCAGCTTAGAAAACTCGGTGTGCTCCACGAATAGCCAGTCAAAAGCTTGCCACGTTCACAGTTCTCTGATACAGTGTATTGGTATAGACACATTTGTAAAGCCGGGTAGTTGACGGTGGCTGCCGATGGGCCTAGCCTGTAGGCAGATATCGGGTATCGAGGATGAGCGTAGCCTATTCAATTGCTCCCGGGCTCCTGACAGCTTGGTGTCAAACCCTGAACCCTCCTGAAATGGTGAGCAAGGGCGAGGAGGTCATCAAAGAGTTCATGCGCTTCAAGGTGCGCATGGAGGGCTCCATGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGCGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCCCAGTTCATGTACGGCTCCAAGGCGTACGTGAAGCACCCCGCCGACATCCCCGATTACAAGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGTCTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCACGCTGATCTACAAGGTGAAGATGCGCGGCACCAACTTCCCCCCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCACCGAGCGCCTGTACCCCCGCGACGGCGTGCTGAAGGGCGAGATCCACCAGGCCCTGAAGCTGAAGGACGGCGGCCACTACCTGGTGGAGTTCAAGACCATCTACATGGCCAAGAAGCCCGTGCAACTGCCCGGCTACTACTACGTGGACACCAAGCTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAGCGCTCCGAGGGCCGCCACCACCTGTTCCTGTACGGCATGGACGAGCTGTACAAGTAATCGTGCTTAGGCTCCGGACAGGCTTCCAACGACTGTCCTTTTTATAGTTGCTTGCGAGGGTTTTGTGCATCTGGGCGTCTCCTGATGACAACCAAGTTAGCCTGGAGAATCCAAGGCAGTACATCCTAGCAAATTCGTACCGGCTCCCAGTAGGAACAAAAGCTGAGCAACATACTAGAACATGTTCAAGGACTCTATTCTGCGAGAGTTTGTTCCGATACGTCCAAGAGTGTACCTGTCGCCCTCAACTCTCGCACGACTTTCCGTGTTTTGTCTGCAAGTAACTCACTTGCGACCGAT", "sha256": "74fe0032e34a3a68d58703287c032f2e6cf33f6fa3ea8f005921b13fbbac9bd1", "offsets": { "dTomato": { "start": 301, "end": 1005 }, "mHoneydew": { "start": 315, "end": 970 } }, "overlapOfShorterSpan": "656/656", "expected": { "shown": [ "dTomato" ], "named": [ "mHoneydew" ], "callsDrawnAtTheLocus": 1 } }, "repeatCase": { "id": "R1", "label": "a tandem repeat with five entries of one lineage within the thresholds at one locus", "how": "tdTomato with 12 substitutions at positions [716, 776, 836, 896, 956, 1016, 1076, 1136, 1196, 1256, 1316, 1376] of the entry, the first dTomato copy left perfect", "sequence": "CAACTATGACGTTTGTGTTTCCATTCGGGCCACCGGAATCCGTCGCCGTAGTGCCGTAATGGGTCAAAACCATTGGAACCTGTATTTGAAAGGAGTATAAGAGGCTCAAATCAGGGCTGTAGAGTTTGGACCACCAAGTTTGTCATCTTGGTGATATGCTTGACAATCGCCGACAATGGCGAGGAAGTATGTCGCAGCAGTGTGAGGTGGGCTCGAAGGGCCTTCCATATCTTAGAAGTCTCTTGTCTTTGCTGCTCGTCGTAGCCAGATTATCGGCCCATGAGGACGTCGTGATGATAGATGGTGAGCAAGGGCGAGGAGGTCATCAAAGAGTTCATGCGCTTCAAGGTGCGCATGGAGGGCTCCATGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGCGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCCCAGTTCATGTACGGCTCCAAGGCGTACGTGAAGCACCCCGCCGACATCCCCGATTACAAGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGTCTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCACGCTGATCTACAAGGTGAAGATGCGCGGCACCAACTTCCCCCCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCACCGAGCGCCTGTACCCCCGCGACGGCGTGCTGAAGGGCGAGATCCACCAGGCCCTGAAGCTGAAGGACGGCGGCCACTACCTGGTGGAGTTCAAGACCATCTACATGGCCAAGAAGCCCGTGCAACTGCCCGGCTACTACTACGTGGACACCAAGCTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAGCGCTCCGAGGGCCGCCACCACCTGTTCCTGGGGCATGGCACCGGCAGCACCGGCAGCGGCAGCTCCGTCACCGCCTCCTCCGAGGACAACAACATGGCCGTCATCAAAGAGTTCATGCGCTTCAAGGAGCGCATGGAGGGCTCCATGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCTCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGCGGCCCCCTGCCCTACGCCTGGGACATCCTGTCCCCCCAGTTCATGTACGGCTCCAAGGCGTACGTGAAGCACCGCGCCGACATCCCCGATTACAAGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGAGATGAACTTCGAGGACGGCGGTCTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGTCACGCTGATCTACAAGGTGAAGATGCGCGGCACCAACTTCCCCCCCGACGGCCCCGTAAAGCAGAAGAAGACCATGGGCTGGGAGGCCTCCACCGAGCGCCTGTACCCCCGCGACGGCGAGCTGAAGGGCGAGATCCACCAGGCCCTGAAGCTGAAGGACGGCGGCCACTACCTGGTGGCGTTCAAGACCATCTACATGGCCAAGAAGCCCGTGCAACTGCCCGGCTACTACTACGTGGCCACCAAGCTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAGCTCTCCGAGGGCCGCCACCACCTGTTCCTGTACGGCATGGACGAGCTGTACAAGTAAGGCTAGTAGCGGTATAGGATCATCAGGGATCGAGCGTACCAATGATATCGATTCGATAAATCGCGGGACTTTATCGCCGGTCGAGCTGGAACAAAAACCCAGCCATCTTTGTACACCGACCTTCAGGGTGCGTGAATAAAATTCTTTCTATAACCTAAGCTTATCGATCCGTCCTGCCTTGTGCGGGGTTGTTTTTGGGTCACTCGGTTTGGGGGCATCAGAGGGCCAGCCGCCTCACCCGAGTGCTTGCCCACATCCCTATAAAAAGGCCACTCTTATATACTAACAGATGTGCGACTG", "sha256": "f3e46f870bf73ff274a61d7aa4a191678d654146ec9f8d236b91ff672ca81871", "statedAs": [ "the repeat exposes the monomer twice, because the dimer carries two copies of it, so an entry reaching threshold against the monomer reaches it at both copies", "that five entries reach it rather than one is a shared-ancestry fact about engineered variants of one lineage", "neither asserts that any of the five describes the same element as the dimer" ], "expected": { "callsDrawnAtTheLocus": 1, "shown": "tdTomato", "alsoWithinThresholds": [ "dTomato", "mCherry", "mHoneydew", "mRfp1", "mTangerine" ], "eachNamedOnce": true, "identities": { "dTomato": "673/684", "mCherry": "622/684", "mHoneydew": "593/657", "mRfp1": "596/657", "mTangerine": "594/658", "tdTomato": "1419/1431" } } }, "suppressionCase": { "id": "S1", "label": "a longer partial call drawn over a shorter exact one, with the exact call named in full", "how": "pauseSite with substitutions at positions [54, 102, 150] of the entry, all outside the syntheticPA it contains", "sequence": "AGGCCCGATCGCGTGGGCACCGTTTGTACTTCCGTGTGTGGCATCTTTTGAATAGCTGACTGGTCTGACTCAGCCGGAAAGCCACCGCCTGGCTTGTTTCCAGGAGTGGAATATGACGAGACATTAAATGAGAATCGCCCTACACCTCAATGCAATTGAGTGTACCTATAGTAGAGTTGTAACAACATCTGTAGCGCGACACGGCTGGATTGCTACTGGGAAGCAGTGAGGGACGGAGCTACTACCCATGTCAGAGGTTGGTTCACAGTCCATGATGACGGTCTTTGGGAGCCTCAGCTGAATAAAATATCTTTATTTTCATTACATCTGTGTGTTGGTTTTTTGTGTGAATCTATAGTACTAACATACGCTCTCCATCAAAACAAAACGAAACAAAACAACCTAGCAAAATAGGCTGTCCCCAGTGCAAGTGCAGGTGCCAGAACATTACTCTGCATCCCAGAAGACATGAACACGAACACATGTTCCGAATAATGGAGGCAACATAGAGACACTTTAGGAACTATGAGGAGATTTAACGGGGTACGCGCGATGCGGCTCGTTGGCACCATTCATGTTGATAATTCTGGGCTCGGGAACCGGTAAAGTGCGTGCCCCCGTGCGGGCTACAGTCATGTAGGGTACCATACACTAGTTTCCTGGGGGTCAAATTTCCATGGAAACTTCGTAGATGGCAAAGCTATGATGTGTATATGCCGTATACCGGTAATCTCGTGAAAGTCTGTAGATTACA", "sha256": "1a600626a2a2cc08627aebe3bc41188e2cd4b7e685ec91ff810f721d9dfa8fd3", "scoresByHand": { "pauseSite": 293, "syntheticPA": 98, "how": "match times identical columns plus mismatch times differing columns, from SCORING; an exact call of an entry scores twice its length, since no column differs" }, "expected": { "drawn": "pauseSite", "drawnSpan": [ 301, 454 ], "alsoWithinThresholds": [ { "feature": "syntheticPA", "call": "match", "exact": true, "identity": "49/49", "coverage": "49/49", "start": 301, "end": 349, "strand": "+", "score": 98.0, "drawnInstead": "pauseSite" } ] } }, "tieCase": { "id": "T1", "label": "a partial call inside an exact call's span, equal scores: the exact call is drawn", "calls": [ { "featureId": "exactEntry", "identityExact": "100/100", "coverageExact": "100/100", "call": "match", "start": 201, "end": 300, "strand": "+", "score": 200.0 }, { "featureId": "partialEntry", "identityExact": "103/106", "coverageExact": "106/120", "call": "partial", "start": 211, "end": 290, "strand": "+", "score": 200.0 } ], "expected": { "drawn": "exactEntry", "why": "equal score, so the comparator's second step decides: exact before match before partial. A partial call wholly inside an exact call's span can at best tie, so preferring the exact one buys the reader a true word and costs no extent." } }, "partialOverlapCase": { "constructed": false, "why": "every marked different-element pair in this library is strictly nested, and a nested entry's remaining bases are its container's own continuation, so a cut that leaves the contained entry whole restores the container and the pair stays contained", "attempts": [ { "pair": [ "rnaI", "pucOri" ], "outcome": "the contained entry is not an exact substring of its container, so no cut point is known" }, { "pair": [ "sv40Ori", "sv40Promoter" ], "tail": 5, "spans": { "sv40Ori": [ 615, 680 ], "sv40Promoter": [ 301, 680 ] }, "coverage": { "sv40Ori": "66/66", "sv40Promoter": "380/417" }, "outcome": "still contained: the container's alignment ran through the appended remainder, which is its own sequence" }, { "pair": [ "lacO", "lacPromoter" ], "tail": 2, "spans": { "lacO": [ 385, 405 ], "lacPromoter": [ 301, 405 ] }, "coverage": { "lacO": "21/21", "lacPromoter": "105/122" }, "outcome": "still contained: the container's alignment ran through the appended remainder, which is its own sequence" } ], "testedInstead": "src/lib/seq/features/specificity-v2.test.ts, against a two-entry library built for the purpose" } }