varvamp_log.txt

VARVAMP log 

MODE = qpcr

Automatic parameter selection set -pn 0.

ARG SETTINGS

THRESHOLD = 0.97
PRIMER_ALLOWED_N_AMB = 1
PROBE_ALLOWED_N_AMB = 0
TEST_DELTAG_N_AMPLICONS = 50
DELTAG_CUTOFF = -3

CONFIG SETTINGS

PRIMER_TMP = (57, 63, 60)
PRIMER_GC_RANGE = (35, 65, 50)
PRIMER_SIZES = (18, 24, 21)
PRIMER_HAIRPIN = 47
PRIMER_MAX_POLYX = 3
PRIMER_MAX_DINUC_REPEATS = 3
PRIMER_GC_END = (1, 3)
PRIMER_MAX_DIMER_TMP = 47
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 = 8
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1
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

PROGRESS

Job:	 Checking config. 
Result:	 config file passed

Job:	 Preprocessing alignment and cleaning gaps. 
Result:	 8 gaps with 113 nucleotides

Job:	 Creating consensus sequences. 
Result:	 length of the consensus is 7362 nt

Job:	 Finding primer regions. 
Result:	 42.9 % of the consensus sequence will be evaluated for primers

Job:	 Digesting into kmers. 
Result:	 10758 kmers

Job:	 Filtering for primers. 
Result:	 1556 fw and 1685 rw potential primers

Job:	 Finding qPCR probes. 
Result:	 340 potential qPCR probes

Job:	 Finding unique amplicons with probe. 
Result:	 32 unique amplicons with internal probe

Job:	 Filtering amplicons for deltaG. 
Result:	 5 non-overlapping qPCR schemes that passed deltaG cutoff

Job:	 Finalizing output. 
Result:	 all done 


varVAMP finished in 63.0 sec!
2023-04-26 18:16:02.482875