PrimedRPA_Parameters.txt

This parameters file will guide the PrimedRPA-based primer and probe design process. Please follow the instructions outlined below:

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Important Note - Do not remove any of the “>” and write your input directly after this symbol.
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Please define the reference name for this PrimedRPA run:
>Installation_Validation_Run

Please indicate if you would like to use a previously generated Alignment File: [NO or File path]
>NO

Please indicate if you would like to use the previously generated Binding Sites: [NO or File path]
>NO

Please enter the path, from your current working directory, to the input fasta file:
>Validation/Validation_1_Input.fasta

Please classify the contents of the input fasta file as one of the following options: [SS, MS, AMS]. Whereby:
 SS = Single sequence
 MS = Multiple unaligned sequences
 MAS = Multiple aligned sequences

>MS

If multiple sequences are present in the input fasta file (Classification of MS or MAS), please indicate below the
percentage identity required for the primers and probes target binding sites:
>99

Please indicate if a primer identity anchor is required. [NO or length of anchor]
>NO

Desired primer length (This can be a range: 28-32 or fixed value: 32):
>28-32

Please state if you require a probe to be designed and if so what type [NO,EXO,NFO]
>NO

Desired probe length (This can be a range: 45-50 or fixed value: 50):
>50

Below please define your max amplicon length.
>300

Below please state the repeat nucleotide cut-off in bp (e.g. 5bp will exclude sequences containing GGGGG).

>5

Below please insert the minimum percentage GC content for primer/probe:
>40

Below please insert the maximum percentage GC content for primer/probe:
>60

Below please indicate the percentage match tolerance for primer-probe dimerisation and secondary structure formation:
>60

Please enter [No or Path to Background file] below to identify if you want to perform a background DNA binding check:
>Validation/Validation_1_Background.fasta

Below please insert the percentage background cross reactivity threshold:
>65

Below please indicate if you would like to implement a Background Hard Fail Filter [NO,YES]:
>NO

Please define the maximum number of sets you would like to identify:
>5

Please define the number of threads available:
>1

Blastn Cross Reactivity Search Settings [Basic or Advanced or Fast]
>Fast

Blastn Evalue
>1000