DNA Pattern Find

Search for patterns in DNA sequences with support for IUPAC ambiguous nucleotides. Find restriction sites, motifs, and sequence patterns.

IUPAC codes: R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=C/G/T, D=A/G/T, H=A/C/T, V=A/C/G, N=any

What is DNA Pattern Find?

DNA Pattern Find is a tool for searching specific patterns within DNA sequences. It supports IUPAC ambiguous nucleotide codes, making it ideal for finding restriction enzyme sites, consensus sequences, motifs, and degenerate patterns. The tool searches all positions and reports every match with its location.

How to Use This Tool

Search for DNA patterns:

  1. Enter your search pattern using IUPAC codes
  2. Paste your DNA sequence(s)
  3. Results appear automatically with positions
  4. Download or copy the matches

When to Use

This tool is useful for:

  • Finding restriction enzyme sites
  • Searching for consensus sequences
  • Locating transcription factor binding sites
  • Identifying sequence motifs
  • Finding degenerate patterns in DNA

IUPAC Nucleotide Codes

A = Adenine
C = Cytosine
G = Guanine
T = Thymine
R = A or G (puRine)
Y = C or T (pYrimidine)
S = G or C (Strong)
W = A or T (Weak)
K = G or T (Keto)
M = A or C (aMino)
B = C, G, or T (not A)
D = A, G, or T (not C)
H = A, C, or T (not G)
V = A, C, or G (not T)
N = any nucleotide

Example Patterns

Common restriction sites and motifs:

GAATTC - EcoRI site
GGATCC - BamHI site
GCGGCCGC - NotI site
GANTC - HinfI site
RGATCY - BstYI site
TATAWAW - TATA box

Use the Example button to see it in action.

FAQ

Q: Can I search multiple sequences at once?
A: Yes, paste multiple FASTA sequences and all will be searched.

Q: Is the search case-sensitive?
A: No, the tool automatically handles both uppercase and lowercase DNA.