Sequencing primer design

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Primo Sequencing 3.4: Sequencing Primer Design Click here for more PCR primer design tools.

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Primo Sequencing 3.4 --- Sequencing Primer Design

How to use Primo Sequencing 3.4 --- Sequencing Primer Design (beta-testing)

Input your DNA sequences by copy and paste. Click on the "Go" button to start. Numbers and blank spaces will be ignored. Degenerate nucleotide codes can be accepted. But sequencing primers will avoid any degenerate sequences.

For multiple sequences, please check the "Batch mode" checkbox, and input your sequences in the following formart:


>Name of Sequence 1

1 ggccgggcgc ggtggctcac gcctgtaatc ccagcacttt gggaggccga ggcgggtgga
61 tcacctgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc cgtctctact
121 aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
181 gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtgagc cgagatcgcg
241 ccactgcact ccagcctggg caacaagagc gaaactccgt ctcaaaaaaa a

>Name of Sequence 2
aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtgagc cgagatcgcg
ccactgcact ccagcctggg caacaagagc gaaactccgt ctcaaaaaaa a

>Name of Sequence 3
61 tcacctgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc cgtctctact
121 aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
181 gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtg

Warning: If the "Batch mode" checkbox is not checked, multiple sequences will be treated as one sequence.

There are four options for sequencing directions. The relative primer positions are shown in the figure below.

For melting temperature calculation, the nearest neighbor formula is suggested.

If no primers are found, try to lower the melting temperature.

Primers designed use this program has a GC-content of 40-60%.

In case your input sequence is not in the 5'->3' direction, you can change it to the 5'->3' direction by choosing one of the following: Complement, Reverse, or, Reverse and Complement.

For more PCR primer design tools, please visit Primo Home.

Thanks for using Primo Sequencing 3.4! Please let us know your suggestions and comments.

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