VARVAMP log

MODE = tiled

WARNING: your amplicon lengths might be to small. Consider increasing
WARNING: your min overlap is lower than your optimal length / 2 - 2 * min primer length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.

ARG SETTINGS

THRESHOLD = 0.6
PRIMER_ALLOWED_N_AMB = 2
AMPLICON_OPT_LENGTH = 150
AMPLICON_MAX_LENGTH = 300
MIN_OVERLAP = 40

CONFIG SETTINGS

PRIMER_TMP = (56, 63, 60)
PRIMER_GC_RANGE = (35, 65, 50)
PRIMER_SIZES = (18, 24, 21)
PRIMER_HAIRPIN = 47
PRIMER_MAX_POLYX = 4
PRIMER_MAX_DINUC_REPEATS = 4
PRIMER_GC_END = (1, 3)
PRIMER_MAX_DIMER_TMP = 35
PRIMER_MIN_3_WITHOUT_AMB = 3
PCR_MV_CONC = 100
PCR_DV_CONC = 2
PCR_DNTP_CONC = 0.8
PCR_DNA_CONC = 15
PRIMER_TM_PENALTY = 2
PRIMER_GC_PENALTY = 0.2
PRIMER_SIZE_PENALTY = 0.5
PRIMER_MAX_BASE_PENALTY = 10
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1
END_OVERLAP = 5