{
 "about": {
  "generatedBy": "pipeline/plasmid-map/assembly-cut-refusals.py",
  "scriptSha256": "83e671170414b0bb2a27053a89e18824f2063aefa1e2ee98643678679a031258",
  "oracle": "Biopython 1.88 Bio.Restriction",
  "recordedOn": "2026-10-11"
 },
 "cases": [
  {
   "id": "coincident-top-distinct-bottom",
   "sequence": "AAAAAAAAGGTCTCCCGCAAAAAAAAA",
   "circular": true,
   "enzymes": [
    "BsaI",
    "AciI"
   ],
   "cuts": [
    {
     "enzyme": "BsaI",
     "topAfter": 15,
     "bottomAfter": 19,
     "strandOffset": 4
    },
    {
     "enzyme": "AciI",
     "topAfter": 15,
     "bottomAfter": 17,
     "strandOffset": 2
    }
   ],
   "reason": "overlapping-cuts",
   "notes": "Distinct physical cuts share one top-strand cut but differ on the opposite strand. Neither interval is a full circuit; this paired-core model refuses."
  }
 ]
}