A QUICK GUIDE
Which input should I use?
Enter one array per line, with its name followed by comma-separated spacer IDs, for example Array_1 1,2,3,4. You can also upload CRISPRPrep CSV, CRISPRCasFinder JSON or spacer FASTA files. Use Load example for a prepared input, then click Commit to generate the first figure.
What do the colors and triangles mean?
Each block represents one spacer occurrence. The same spacer ID uses the same color throughout the figure. A triangle (▲) marks a spacer found in only one array across the current input. If that spacer appears several times within that one array, every copy is marked. Uniqueness is determined by the number of arrays containing the spacer.
How do Alignment and Clustering change the figure?
Choose Left, Right or Justify (both ends) for alignment. The defaults are Right alignment and Shared spacer clustering. Justify assigns columns using repeated spacer IDs while preserving the order within each array; when no spacer ID is repeated, it uses right alignment. Shared spacer groups connect arrays sharing at least two spacer IDs; Ancestral spacer groups use the rightmost spacer ID. After the first figure is generated, changing Alignment or Clustering updates the current preview automatically, without another Commit.
What are the input and occurrence chart limits?
Direct JSON imports retain only evidence levels 3 and 4. Arrays whose orientation remains ND after checking CRISPRDirection are excluded. If any extracted spacer contains N, all extracted rows with that organism name are excluded. To choose evidence and filtering settings, process the JSON in CRISPRPrep first and import its processed CSV.
The occurrence chart requires 1–50 distinct spacer IDs. With more than 50, the chart is unavailable; spacer counts and the complete statistics CSV remain available.
How do I inspect and export results?
Drag the preview to pan and use Ctrl / ⌘ + scroll to zoom. Choose an export format and, for raster images, a DPI value. Spacer occurrence counts the arrays containing each spacer, with repeated copies within one array counted once. Download the statistics CSV for all spacer counts. Download numbered file provides a tab-separated Spacer_ID / Spacer_Sequence table; negative-strand spacers use the reverse-complement sequences used for numbering. Sequence variants assigned to the same ID are retained as separate rows. Inputs containing only IDs have no sequence mapping; older saved results need to be rerun from the original sequence input. For detailed instructions, read the SpacerMap documentation.