SpacerTarget
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Details
Matches and associations
| Strain / spacer | Target sequence | Type | Identity | Coverage | Mismatch / gap | Target coordinates | E-value | Alignment |
|---|---|---|---|---|---|---|---|---|
| Run a search to explore candidate spacer targets. | ||||||||
One row represents one spacer occurrence matched to one target site.
Strain–target network
Connected associations form clusters
Strain associations will appear after a search.
Click a node or link to filter matches. Drag nodes to arrange; scroll to zoom. The table provides the same evidence without requiring graph interaction.
A QUICK GUIDE
Input formats and strain mapping
FASTA: >strain_A|CRISPR1|spacer_1 followed by 15–100 A/C/G/T bases. Alternatively use >spacer_1 strain=strain_A array=CRISPR1 source=NC_000000.1. Tables need sequence (or Spacer_Sequence) and should include strain_id, array_id and spacer_id. CRISPRPrep CSV fields are accepted, with Folder as the strain ID. JSON sample IDs use the uploaded filename without its extension. Files uploaded with the same name share a sample ID, even when selected from different folders. Use distinct filenames to keep samples separate. Unmapped records appear in the table but not in the strain graph.
What does a match mean?
These are candidate sequence associations, not experimentally verified targets or infection relationships. Strict and exact presets require full-length spacer coverage. PAMs are not evaluated. Unknown directions remain searchable. Source-accession matching flags the same source record only; it does not automatically detect all self-targets or array-region matches.
Search limits, metadata and recovery
NCBI is a shared service: BLAST search requests are spaced by at least 10 seconds and each search ID is checked at most once per minute. Upload up to 100 files with a combined size of 100 MB, or paste up to 2 MB of text. Add files or drag additional files to append selections from different folders; Reset clears them. A task accepts up to 10,000 spacer occurrences and 100 distinct spacer sequences. Each BLAST batch contains at most 10 sequences and 1,000 bases. Inputs are deleted when the task ends. Results are retained for seven days from completion and automatically removed, even when the site is idle. Keep the task link or download the report; anyone with the link can access that task. Closing this tab does not cancel the worker. Cancel stops future work; an already submitted NCBI search may continue. To run a task again, submit your input again.
Target types are based on available GenBank source annotations and taxonomy. Missing annotations stay unknown. core_nt and the configured hit limit do not provide an exhaustive phage/plasmid search. No hits means no matches returned under this search configuration.