@opencloning/ui 1.2.0 → 1.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (31) hide show
  1. package/CHANGELOG.md +17 -0
  2. package/package.json +4 -3
  3. package/src/components/assembler/Assembler.cy.jsx +364 -0
  4. package/src/components/assembler/Assembler.jsx +298 -205
  5. package/src/components/assembler/AssemblerPart.cy.jsx +52 -0
  6. package/src/components/assembler/AssemblerPart.jsx +51 -79
  7. package/src/components/assembler/ExistingSyntaxDialog.cy.jsx +194 -0
  8. package/src/components/assembler/ExistingSyntaxDialog.jsx +65 -0
  9. package/src/components/assembler/PlasmidSyntaxTable.jsx +83 -0
  10. package/src/components/assembler/assembler_utils.js +134 -0
  11. package/src/components/assembler/assembler_utils.test.js +193 -0
  12. package/src/components/assembler/assembly_component.module.css +1 -1
  13. package/src/components/assembler/graph_utils.js +153 -0
  14. package/src/components/assembler/graph_utils.test.js +239 -0
  15. package/src/components/assembler/index.js +9 -0
  16. package/src/components/assembler/useAssembler.js +59 -22
  17. package/src/components/assembler/useCombinatorialAssembly.js +76 -0
  18. package/src/components/assembler/usePlasmidsLogic.js +82 -0
  19. package/src/components/eLabFTW/utils.js +0 -9
  20. package/src/components/index.js +2 -0
  21. package/src/components/navigation/SelectTemplateDialog.jsx +0 -1
  22. package/src/components/primers/DownloadPrimersButton.jsx +0 -1
  23. package/src/components/primers/PrimerList.jsx +4 -3
  24. package/src/components/primers/import_primers/ImportPrimersButton.jsx +0 -1
  25. package/src/version.js +1 -1
  26. package/vitest.config.js +2 -4
  27. package/src/components/DraggableDialogPaper.jsx +0 -16
  28. package/src/components/assembler/AssemblePartWidget.jsx +0 -252
  29. package/src/components/assembler/StopIcon.jsx +0 -34
  30. package/src/components/assembler/assembler_data2.json +0 -50
  31. package/src/components/assembler/moclo.json +0 -110
package/src/components/assembler/StopIcon.jsx DELETED
@@ -1,34 +0,0 @@
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- import React from 'react'
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-
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- function StopIcon({ color = 'currentColor', size = 24, ...props }) {
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- return (
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- <svg xmlns="http://www.w3.org/2000/svg"
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- viewBox="0 0 24 24"
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- width={size} height={size}
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- role="img"
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- aria-label="Stop sign icon"
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- {...props}
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- >
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- <mask id="stop-mask">
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- {/* Octagon area (visible part) */}
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- <polygon fill="white"
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- points="7.07,2 16.93,2 22,7.07 22,16.93 16.93,22 7.07,22 2,16.93 2,7.07" />
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- {/* Text area (cut out) */}
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- <text x="12" y="12.3"
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- fill="black"
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- fontFamily="Arial, Helvetica, sans-serif"
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- fontWeight="700"
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- fontSize="7.2"
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- textAnchor="middle"
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- dominantBaseline="middle">STOP</text>
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- </mask>
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-
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- {/* Octagon using mask */}
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- <rect width="24" height="24" fill={color} mask="url(#stop-mask)" />
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- </svg>
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- )
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- }
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-
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- export default StopIcon
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-
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-
package/src/components/assembler/assembler_data2.json DELETED
@@ -1,50 +0,0 @@
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- [
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- {
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- "name": "A",
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- "overhang": "GGAG"
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- },
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- {
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- "name": "B",
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- "overhang": "TACT"
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- },
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- {
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- "name": "T1",
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- "overhang": "CCAT"
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- },
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- {
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- "name": "T2",
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- "overhang": "GTCA"
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- },
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- {
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- "name": "T3",
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- "overhang": "TCCA"
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- },
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- {
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- "name": "C",
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- "overhang": "AATG"
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- },
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- {
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- "name": "D",
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- "overhang": "AGGT"
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- },
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- {
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- "name": "T4",
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- "overhang": "TTCG"
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- },
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- {
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- "name": "T5",
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- "overhang": "CGGC"
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- },
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- {
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- "name": "E",
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- "overhang": "GCTT"
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- },
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- {
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- "name": "F",
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- "overhang": "CGCT"
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- },
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- {
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- "name": "backbone",
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- "overhang": "GGAG"
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- }
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- ]
package/src/components/assembler/moclo.json DELETED
@@ -1,110 +0,0 @@
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- [
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- {
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- "header": "Assembly connector",
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- "body": "",
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- "glyph": "three-prime-sticky-restriction-site",
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- "left_overhang": "CCCT",
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- "right_overhang": "AACG",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#92C3DC"
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- },
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- {
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- "header": "Promoter",
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- "body": "",
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- "glyph": "promoter",
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- "left_overhang": "AACG",
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- "right_overhang": "TATG",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#B2D06E"
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- },
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- {
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- "header": "Coding sequence",
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- "body": "You can use the ATG from the fusion site as translation start. If possible omit STOP codon and make your protein in frame with the Ser.",
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- "glyph": "cds",
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- "left_overhang": "TATG",
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- "right_overhang": "ATCC",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": 2,
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- "right_codon_start": 2,
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- "color": "#F1EC9B"
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- },
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- {
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- "header": "Terminator",
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- "body": "",
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- "glyph": "terminator",
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- "left_overhang": "ATCC",
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- "right_overhang": "GCTG",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#E2929E"
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- },
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- {
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- "header": "Assembly connector",
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- "body": "",
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- "glyph": "three-prime-sticky-restriction-site",
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- "left_overhang": "GCTG",
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- "right_overhang": "TACA",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#7C6AA9"
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- },
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- {
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- "header": "Yeast marker",
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- "body": "",
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- "glyph": "engineered-region",
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- "left_overhang": "TACA",
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- "right_overhang": "GAGT",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#EFD198"
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- },
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- {
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- "header": "Yeast plasmid origin of replication",
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- "body": "",
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- "glyph": "origin-of-replication",
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- "left_overhang": "GAGT",
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- "right_overhang": "CCGA",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#85643E"
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- },
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- {
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- "header": "Bacterial marker and origin",
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- "body": "",
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- "glyph": "engineered-region",
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- "left_overhang": "CCGA",
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- "right_overhang": "CCCT",
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- "left_inside": "",
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- "right_inside": "",
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- "left_codon_start": null,
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- "right_codon_start": null,
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- "color": "#7F7F7F"
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- },
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- {
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- "header": "Dummy",
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- "body": "promoter text",
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- "glyph": "cds-stop",
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- "left_overhang": "CATG",
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- "right_overhang": "TATG",
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- "left_inside": "AAAATA",
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- "right_inside": "AATG",
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- "left_codon_start": 2,
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- "right_codon_start": 1,
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- "color": "greenyellow"
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- }
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- ]