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The element searches primers against the input sequence.

Parameters in GUI

ParameterDescriptionDefault value
Annotate AsName of the result annotations.top primers
DirectionSee the description here.Any
Excluded regionsThe regions should be avoided for primer selection.No default value.
Max repeat misprimingThe maximum allowed weighted similarity with any sequence in Mispriming Library.12
Max template misprimingThe maximum allowed similarity to ectopic sites in the sequence from which you are designing the primers.12
Number to returnThe maximum number of primer pairs to return.5
Pair max repeat misprimingThe maximum allowed sum of similarities of a primer pair (one similarity for each primer) with any single sequence in Mispriming Library.24
Pair max template misprimingThe maximum allowed summed similarity of both primers to ectopic sites in the sequence from which you are designing the primers.24
Product size rangesList of product size ranges. Primer first tries to pick primers in the first range. If that is not possible, it goes to the next range and tries again. It continues in this way until it has either picked all necessary primers or until there are no more ranges.

150-200

100-300

301-400

401-500

501-600

601-700

701-850

851-1000

Max 3’ stabilityThe maximum stability for the last five 3’ bases of a left or right primer. Bigger numbers mean more stable 3’ ends.9
TargetsIf one or more Targets is specified then a legal primer pair must flank at least one of them.No default value.

 

Parameters in Schema File

Type: primer

ParameterParameter in the GUIType
keyAnnotate Asstring
excluded_regionsExcluded regionstring
max_misprimingMax repeat misprimingnumeric
max_template_misprimingMax template misprimingnumeric
num_returnNumber to returnnumeric
pair_max_misprimingPair max repeat misprimingnumeric
pair_max_template_misprimingPair max template misprimingnumeric
size_rangesProduct size rangestring
stabilityMax 3’ stabilitynumeric
targetsTargetsstring
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