See also
PCR amplicon prediction
search_pcr command
Extract segments between matches to a primer pair. The input file can be in FASTA or FASTQ format. If both strands are searched, the output is oriented to be on the strand matching the pair.
To search for matches to single primers or probes, use search_oligodb.
The -fwdprimer option specifies the forward primer sequence.
The -revprimer option specifies the reverse primer sequence.
Wildcard letters (e.g., N for any letter) are supported in primer sequences.
The -strand option must be specified.
The -maxdiffs option specifies the maximum allowed number of mismatches with a primer. Default 2.
The -minamp option specifies the minimum length of the segment between the primers.
The -maxamp option specifies the maximum length of the segment between the primers.
The -tabbedout option specifies a tabbed text output file giving results for all input sequences.
The -notmatched option specifies a FASTA format file to contain input sequences which did not match.
The -notmatchedfq option specifies a FASTQ format file to contain input sequences which did not match. The input file must be in FASTQ format.
The -fastaout option is a FASTA format file containing segments between the primers.
The -fastaout option is a FASTQ format file containing segments between the primers. The input file must be in FASTQ format.
Example
usearch -search_pcr2 reads.fq -fwdprimer
CCGTCAATTCMTTTRAGT \
-revprimer GGACTACHVGGGTWTCTAAT -minamp 250
-maxamp 350 \
-strand both -fastaout v5_hits.fa