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  CLONEIT — KEY FEATURES
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  Plasmid map editor compatible with plasmid-map / AngularPlasmid formats.
  Version reference: see VERSION in app.py
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PLASMID MAPS
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  • Circular and linear topology with a customizable main track (radius, ticks,
    numbering, double track option).
  • Manual features: start/end positions, name, color, strand (+ / - / neutral).
  • Features can be dragged on the map; style presets and saved styles.
  • Plasmid name, length, and description; optional center label.
  • Text boxes on the map with connectors and layout options.
  • Zoom, pan, and arc selection for regions of interest.


SEQUENCES & IMPORT
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  • Load DNA from FASTA, plain sequence, GenBank (NCBI fetch), SnapGene (.dna),
    and CloneIt / JSON project files.
  • Auto-detect common features from reference sequences (FASTA library).
  • Sequence length drives the map; topology matches circular or linear design.


DNA SEQUENCE VIEWER
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  • Multi-line and single-line sequence views for selected arcs.
  • Sense strand with optional antisense; 5' and 3' end labels on strands.
  • Amino acid translation with auto frame (ATG-based ORF) or fixed frame.
  • Search highlights on the sequence; optional mutations display.
  • Base numbering aligned with monospace layout.


RESTRICTION ENZYMES
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  • Detect restriction sites from a pattern library (CSV / built-in MCS set).
  • Show sites on the plasmid map and in the sequence viewer.
  • Cut positions indicated between bases in multi-line view.


TFBS (TRANSCRIPTION FACTOR BINDING SITES)
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  • Scan sequence with PWM motifs from bundled MEME-format libraries.
  • Adjustable score threshold and result limits.


PCR PRIMERS
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  • Primer library (database + CSV) with search and CRUD via the UI.
  • Search primer sequences against the plasmid; show matches as features.


SEQUENCE ALIGNMENTS
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  • Receive alignments from the companion Sequence Aligner tool (or API).
  • View match lines and chromatogram-style traces when trace data is present.
  • Save and list alignments in the project.


PLASMID LIBRARY (OPTIONAL)
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  • Index a “Plasmid” folder of .json/.cloneit projects.
  • Search by name, description, or DNA substring; open or delete entries.


EXPORT & PROJECT
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  • Export the map as SVG or JPG.
  • Save and load projects in CloneIt-compatible JSON.
  • Portable Windows .exe (PyInstaller) and optional Setup installer — no
    separate Python required for end users who use the built package.


TECHNICAL NOTE
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  • Runs locally in the browser (e.g. http://127.0.0.1:8080) with a small
    Flask server started from app.py or the packaged executable.

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