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HIV sequence database

Primer Design

Purpose: This tool finds primers for PCR, sequencing (including NGS) and other molecular biology uses. It uses a multiple alignment and optimizes the primers to several user-defined criteria. See Primer Design Explanation.

Input Query
Title of analysis
Paste your alignment
[Sample Input]
Or upload your alignment file
Primer Options
Region of Interest:    Start Stop
Minimum Primer Length: 10 ≤ X ≤ 40
Maximum Primer Length: 10 ≤ X ≤ 40
Detection Limit: %
Max Difference in Tm: °C
Dimer Window Size:
Dimer Max Ratio:
Forward Primer Options: G/C on the 3' end
G/C on the 5' end
Reverse Primer Options: G/C on the 3' end
G/C on the 5' end
Adaptor Options
Adaptor to use
Tag Options
Tag/barcode generation
Always email results


Please cite this paper when using Primer Design:


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