VARVAMP log

MODE = qpcr


ARG SETTINGS

THRESHOLD = 0.7
PRIMER_ALLOWED_N_AMB = 1
PROBE_ALLOWED_N_AMB = 1
TEST_DELTAG_N_AMPLICONS = 10
DELTAG_CUTOFF = -15

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
QPROBE_TMP = (64, 70, 67)
QPROBE_SIZES = (20, 30, 25)
QPROBE_GC_RANGE = (40, 80, 60)
QPROBE_GC_END = (0, 4)
QPRIMER_DIFF = 2
QPROBE_TEMP_DIFF = (5, 10)
QPROBE_DISTANCE = (4, 15)
QAMPLICON_LENGTH = (70, 200)
QAMPLICON_GC = (40, 60)
QAMPLICON_DEL_CUTOFF = 4