GC Content Plotter

Visualize GC content distribution along DNA sequences with sliding window analysis and identify compositional domains

Show Average Line
Identify GC Islands

What is GC Content Plot?

GC content plotting visualizes the percentage of guanine (G) and cytosine (C) nucleotides across a DNA sequence using a sliding window approach. This reveals compositional heterogeneity, identifies CpG islands, highlights horizontally transferred genes, and detects AT-rich or GC-rich regions in genomes.

How to Use This GC Content Plotter

  1. Paste your DNA sequence (FASTA or plain text)
  2. Adjust window size (100bp default) and step size
  3. Select visualization type (line, area, bar, heatmap)
  4. View interactive plot with zoom controls
  5. Analyze identified GC-rich and AT-rich regions

When to Use

This tool is useful when you need to:

  • Identify CpG islands in promoter regions
  • Detect horizontally transferred genes
  • Analyze isochore structures in eukaryotes
  • Find compositionally biased regions
  • Compare genomic segments

Example Input

DNA sequence with variable GC content:

GCGCGCGCGCGCATATATATATA...

Use the Example button for a demonstration sequence.

Example Output

GC content analysis:

Position 1-100: GC = 75.0%
Position 51-150: GC = 60.5%
CpG island detected: 1-500 bp

FAQ

Q: What window size should I use?
A: 100-200bp for detailed analysis, 1000-10000bp for genome-wide patterns.

Q: What indicates a CpG island?
A: Regions >200bp with GC% >50% and observed/expected CpG ratio >0.6.