💡 Quick Summary
Primer Map displays restriction enzyme recognition sites and primer binding locations on a DNA sequence. Optionally translate all three reading frames. Useful for verifying primer placement, checking for restriction sites, and generating publication-ready annotated sequence figures.
📋 How to Use
- Paste a raw DNA sequence or one or more FASTA sequences into the first textarea. Input limit: 100,000,000 characters.
- Enter primers in the second textarea, one per line. Format:
(primer_name) sequence. Names in parentheses are optional; unnamed primers are labelled automatically. Primers must be ≥ 10 bases. - Set bases per line: how many bases to display on each line.
- Choose a reading frame: All three shows all three forward reading frames; Frame 1/2/3 shows a single frame; Uppercase only translates only uppercase runs (useful for GenBank exon/intron sequences); None suppresses translation.
- Select the genetic code used for translation (default: Standard).
- Choose whether to show restriction sites (standard enzyme set) above the sequence.
- Set topology to circular to detect sites and primer matches that wrap around the origin.
- Click Run. Restriction sites are coloured green (1 cut) or orange (2 cuts). Forward primer matches are blue (
>>name>>); reverse matches are red (<<name<<). Use Copy to copy the plain-text output.
🧮 Formulas & Logic
📊 Result Interpretation
Enzyme cuts the sequence exactly once — useful for linearisation or directional cloning.
Enzyme cuts twice. Check fragment sizes before using for cloning.
Enzyme cuts three or more times — usually not suitable for simple cloning steps.
Forward primer binding site; numbers show 1-based start and end positions in the sense strand.
Reverse primer binding site; positions shown on the sense strand.
🔬 Applications
- Verifying PCR primer placement and specificity on a cloning vector or gene
- Identifying restriction enzyme sites for cloning strategy design
- Checking reading frames and stop codons around an insertion site
- Generating annotated sequence figures for publications or lab notebooks
- Comparing primer binding positions across multiple sequence variants
⚠️ Common Mistakes & Warnings
Numbers, spaces, and non-letter characters are removed automatically. Only IUPAC nucleotide letters (A, T, G, C, R, Y, K, M, S, W, B, D, H, V, N, U) are retained.
Very short primers produce too many non-specific matches to be useful. Primers with fewer than 10 valid bases after stripping are silently skipped.
IUPAC degenerate bases (R, Y, K, M, S, W, B, D, H, V, N) in primer sequences are expanded to the corresponding nucleotide set during matching.
❓ Frequently Asked Questions
What primer format should I use?
(T7_fwd) TAATACGACTCACTATA. If you omit the name the primer is labelled Primer 1, Primer 2, etc. Enter the primer sequence in the 5′→3′ direction. Reverse primers should be entered as their actual 5′→3′ sequence — the tool automatically searches for both the forward and reverse complement.