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Job ID: MSK-EXAMPLE-DEMO

Salvia plastome demo

Created 2026-05-05T00:36:18Z
Updated 2026-05-05T05:58:35Z
Expires Never
Reference Salvia_chinensis.gb
Samples 18
Genome length 151458
Windows 756
Hotspot windows 23

Estimated Runtime

Based on current queue, server load, and uploaded data size.

Actual runtime about 5.4 h
Input data 18 files, 4.6 MB uploaded
Queue 0 jobs ahead

Parameters

hotspot_mode
top-percent
hotspot_value
3.0
hotspot_window
600
hotspot_step
200
similarity_window
200
similarity_step
60
primer_design
True
primer_length_min
18
primer_length_max
27
primer_amplicon_min
80
primer_amplicon_max
3000
primer_mismatch
1
primer_pairs_returned
5
no_similarity_plot
False

Figures

PNG previews are shown below; publication files are available in the downloads.

Nucleotide diversity plot
Pi diversity plot
Similarity plot
Similarity plot

Candidate markers

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 969 0.0366 0.57 62.0 yes View details
psbK-psbI LSC 396 0.0383 0.98 62.9 yes View details
psaA-ycf3 LSC 783 0.0342 0.97 70.1 yes View details
ndhF SSC 2217 0.0215 1.00 52.4 yes View details
rpl32-trnL-UAG SSC 703 0.0510 0.98 74.6 yes View details
ccsA-ndhD SSC 230 0.0754 0.97 65.7 yes View details
rps15-ycf1 SSC 425 0.0460 0.93 65.1 yes View details
ycf1 SSC 5508 0.0306 1.00 58.0 yes View details
trnE-UUC-trnT-GGU LSC 538 0.0340 1.00 74.3 yes View details
atpH-atpI LSC 969 0.0311 0.99 73.0 yes View details
trnK-UUU-rps16 LSC 569 0.0325 0.97 71.3 yes View details
rps4-trnT-UGU LSC 373 0.0302 0.94 71.1 yes View details
ndhC-trnV-UAC LSC 948 0.0264 0.99 70.4 yes View details
petN-psbM LSC 967 0.0305 0.99 70.2 yes View details
trnH-GUG-psbA LSC 307 0.0524 0.96 69.2 yes View details
ndhG-ndhI SSC 376 0.0465 0.98 69.0 yes View details
petA-psbJ LSC 1058 0.0333 0.96 67.4 yes View details
ndhF-rpl32 SSC 451 0.0410 0.98 67.4 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Downloads

Download all results candidate_marker_features.tsv haplotype_assignments.tsv pi_plot.pdf pi_windows.tsv primers.tsv sample_metadata.tsv similarity_plot.pdf