User Specified Parameters | Description |
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min_len_upstream | minimum length of conserved sequence upstream (5') of a SNP |
min_len_downstream | minimum length of conserved sequence downstream (3') of a SNP |
max_amplicon_length | maximum amplicon length allowed for PCR-RFLP analysis |
jump | the series of sequences input to primer3 for amplicon generation for PCR-RFLP analyses are chosen by sliding a window along the consensus gestalt. Each new window must start at least jump bases from the start of the previous window. |
precision | there must be at least one difference in fragment lengths among all input genomes that is at least this long for the given amplicon+enzyme combination to be considered variable enough for further PCR-RFLP examination. |
num_restriction_enzymes | number of restriction enzymes used in an PCR-RFLP analysis before a single electrophoretic determination of fragment length distributions is made. This number may range from 0–3. |
number_combinations_to_test | maximum number of haplotypes per combination tested in a multi-locus solution set to maximally discriminate all the input sequences. Thus, combinatorics are performed on number haplotypessCnumber_combinations_to_test total combinations. |