Online plastome diversity analysis

MarkerSeek Analyzer

Upload annotated GenBank plastomes, tune nucleotide-diversity parameters, and generate publication-ready hotspot and similarity outputs through a reproducible web workflow.

Pi sliding-window analysis
Hotspot annotation
mVISTA-style tracks

Upload plastomes Provide annotated GenBank files from comparable chloroplast genomes.

Configure analysis Set Pi windows, hotspot labeling, and similarity-track parameters.

Export results Retrieve figures and tables by job ID for downstream manuscript use.

Input files

Upload 2-20 annotated GenBank files. Drag-and-drop is supported in modern browsers.

GenBank files

Accepted formats: .gb, .gbk, and .genbank. The selected files will also populate the reference-file selector below.

Selected 0/20 files

Maximum 20 files. For robust comparative inference, use consistently annotated plastomes.

Analysis parameters

Core settings used by the MarkerSeek command-line workflow.

Window size Step size

Defaults suit plastome Pi plots and support finer or smoother hotspot detection.

Hotspot labeling

Repeated labels are collapsed so each gene or spacer is annotated once in the plot.

Hotspot mode Hotspot value

Use top-percent for exploratory screening, top-N for concise marker panels, or threshold mode for predefined Pi cutoffs.

Similarity plot

Configure mVISTA-style identity tracks generated for non-reference samples.

Reference file Similarity window Similarity step Skip similarity plot

The reference file can be selected after upload. If left unchanged, MarkerSeek uses the first sorted input file.

Primer design

Optional primer screening for candidate hotspot regions.

Primer parameters

Length min Length max Mismatch Amplicon min Amplicon max Pairs returned

Skip primer design

Uses conserved flanks, primer3, and in-silico PCR to report primer availability.

View existing results