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varvamp_log.txt
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varvamp_log.txt
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VARVAMP log
MODE = qpcr
WARNING: The following sequences are considerably smaller than the alignment mean (7439 nt) and might cause alignment trimming:
MT432082.1/1-7251 (7282 nt)
MT432083.1/1-7251 (7282 nt)
MT432086.1/1-7251 (7282 nt)
MT432088.1/1-7252 (7283 nt)
MT432089.1/1-7247 (7278 nt)
MT432090.1/1-7252 (7283 nt)
MT432091.1/1-7251 (7282 nt)
MT432092.1/1-7251 (7282 nt)
MT432093.1/1-7249 (7280 nt)
MT432094.1/1-7251 (7282 nt)
MT432095.1/1-7251 (7281 nt)
MT432096.1/1-7252 (7283 nt)
MT432098.1/1-7253 (7284 nt)
MT432100.1/1-7248 (7279 nt)
MT432101.1/1-7256 (7287 nt)
MT432112.1/1-7250 (7281 nt)
MT432116.1/1-7254 (7285 nt)
MT432117.1/1-7251 (7282 nt)
MT432118.1/1-7251 (7282 nt)
MT432120.1/1-7251 (7282 nt)
MT432122.1/1-7258 (7289 nt)
MT432126.1/1-7251 (7282 nt)
MT432128.1/1-7252 (7283 nt)
MT432134.1/1-7247 (7278 nt)
MT432135.1/1-7247 (7278 nt)
MT432136.1/1-7252 (7283 nt)
MT432138.1/1-7250 (7281 nt)
MT432140.1/1-7250 (7281 nt)
MT432142.1/1-7251 (7282 nt)
MT432143.1/1-7250 (7281 nt)
MT432147.1/1-7252 (7283 nt)
MT432149.1/1-7249 (7281 nt)
MT432150.1/1-7212 (7243 nt)
MT432151.1/1-7250 (7281 nt)
OQ286209.1/1-7231 (7272 nt)
OQ286210.1/1-7231 (7272 nt)
Automatic parameter selection set -pa 3.
WARNING: setting the degeneracy of probes higher than 2 can result in variable probe design. Consider reducing!
ARG SETTINGS
THRESHOLD = 0.87
PRIMER_ALLOWED_N_AMB = 4
PROBE_ALLOWED_N_AMB = 3
TEST_DELTAG_N_AMPLICONS = 50
DELTAG_CUTOFF = -4
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: 28 gaps with 196 nucleotides
Job: Creating consensus sequences.
Result: length of the consensus is 7365 nt
Job: Finding primer regions.
Result: 58.6 % of the consensus sequence will be evaluated for primers
Job: Digesting into kmers.
Result: 11819 kmers
Job: Filtering for primers.
Result: 718 fw and 834 rw potential primers
Job: Finding qPCR probes.
Result: 271 potential qPCR probes
Job: Finding unique amplicons with probe.
Result: 35 unique amplicons with internal probe
Job: Filtering amplicons for deltaG.
Result: 4 non-overlapping qPCR schemes that passed deltaG cutoff
Job: Finalizing output.
Result: all done
varVAMP 0.9.3 finished in 55.253312 sec!
2023-09-18 12:39:05.268170