primers1e

Input section

-sequence seqall

The sequence from which to choose primers. The sequence must be presented 5' -> 3'

Additional section

-targetregion range

If one or more Targets is specified then a legal primer pair must flank at least one of them. A Target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism. The value should be a space-separated list of <start>,<end> pairs where <start> is the index of the first base of a Target, and <end> is the last E.g. 50,51 requires primers to surround the 2 bases at positions 50 and 51.

-minsize integer

Minimum acceptable length of a primer. Must be greater than 0 and less than or equal to MAX-SIZE. Default value: 18

-maxsize integer

Maximum acceptable length (in bases) of a primer. Currently this parameter cannot be larger than 35. This limit is governed by the maximum oligo size for which Primer3's melting-temperature is valid. Default value: 27

-maxdifftm float

Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers. Default value: 100.0

Output section

-explainflag boolean

If this flag is non-0, produce LEFT-EXPLAIN and RIGHT-EXPLAIN, output, which are intended to provide information on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons. Default value: N

-numreturn integer

The maximum number of primer pairs to return. Primer pairs returned are sorted by their 'quality', in other words by the value of the objective function (where a lower number indicates a better primer pair). Caution: setting this parameter to a large value will increase running time. Default value: 5

-outfile outfile