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PrimerDesign-M

Purpose: To find primers for PCR, sequencing (including NGS), and other uses. Primers are based a multiple alignment and optimized to user-defined criteria. See PrimerDesign-M Explanation.

Alignment
Paste your alignment icon

[Sample Input]
Or upload alignment file
Or use premade HIV or SIV sequence alignment icon
Gap stripping icon Remove columns having greater than % gaps
Sequence, Adaptor, and Barcode Options
Region of Interest icon Start    Stop
Multiple fragments icon Single fragment Multiple fragments
Adaptor to use icon
Read length icon
Tag/barcode generation icon
Primer Options
Minimum Primer Length icon 10 ≤ X ≤ 40
Maximum Primer Length icon 10 ≤ X ≤ 40
Detection Limit icon %, 0≤ X ≤ 20
Complexity Limit icon 1≤ X ≤ 128
Max Difference in Tm icon °C
Dimer Window Size icon
Dimer Max Ratio icon
G/C Clamp icon Foward Reverse
Email
Always email results icon

References

Please cite these papers when using PrimerDesign-M:

last modified: Thu Jan 21 15:20 2016


Questions or comments? Contact us at seq-info@lanl.gov.

 
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