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There are the following parameters:
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3' perfect match - specify the number of nucleotides at the 3' end that must not have mismatches.
Maximum product size - the maximum size of the amplified sequence. Use ambiguous bases - search for ambiguous bases (as \"N\") if checked.
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- Value Inner is selected by default. When this value is selected, the extracted PCR product contains annotations from the original sequence, located within the extracted region.
- Value All intersected specifies that all annotations of the original sequence that intersect the extracted region must be extracted as well.
- Value None specifies that annotations from the original sequence must not be extracted.
Melting temperature - see the corresponding page for details.
Choosing primers
Type two primers for running In Silico PCR. If the primers pair is invalid for running the PCR process then the warning is shown. Also, primers for the running In silico PCR can be chosen from a primer library. Click the following button to choose a primer from the primers library:
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When you run the process, the predicted PCR products appear in the products table.
Melting temperature
Click the Melting tempeature link for choosing temperature calculation algorithm: Rough or Primer 3.
More information about the temperature options see here: Melting tempeature
Products table
There are three columns in the table:
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