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In-silico PCR amplification on complete genomes

Home Page: https://www.gear-genomics.com/silica

License: GNU General Public License v3.0

Python 20.97% HTML 32.69% CSS 6.57% JavaScript 39.77%
gear-genomics pcr in-silico primer-design primer sanger-sequencing amplicon

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silica's Issues

Understanding the -k parameter

I am trying to understand how to adjust -k since it seems to impact the results dramatically.
For example with primers of length 25 and a -k of 15 I get no amplicons.
I think this is the same as changing the Number of bp from the 3' End of the Primer Used to Seach for Matches (>14) param on the Silica website.
https://www.gear-genomics.com/silica/index.html?UUID=0101f455-249c-4e7f-beb5-63f2f50a7501
image

If I change this to -k 20 or the same param on the website I get an amplicon
https://www.gear-genomics.com/silica/index.html?UUID=c40f28ba-5abd-420a-8d45-6667d72de0fe
image

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