Quick Start

Get from a DNA/RNA sequence to ranked guide RNAs in under a minute.

The Finder walks you through a four-step wizard. Open it from the header navigation and follow along.

1. Enzyme & PAM

Select your CRISPR enzyme family — Cas12 (DNA-targeting, PAM-dependent) or Cas13 (RNA-targeting, PAM-independent). For Cas12, choose a PAM recognition sequence (e.g., TTTV, TTTN). Cas13 does not require a PAM.

2. Sequence

Paste your target nucleic acid sequence or upload a FASTA file (drag-and-drop or file picker). If your FASTA contains multiple sequences, you can select one or concatenate all of them. You can also give the job a name for easier identification later.

Tip

For Cas13, you can provide either DNA or RNA — SPACER automatically handles in-silico transcription when needed.

3. Configuration

Toggle optional analysis features — all are enabled by default for the best results:

AI Activity Prediction — predicts guide cleavage activity (EasyDesign for Cas12, ADAPT for Cas13)
Structure Prediction — RNA secondary structure analysis via Vienna RNA
Primer Design — generates flanking RPA primers via Primer3

You can also adjust the spacer length (constrained automatically when ML is enabled — see why) and select a direct repeat preset for crRNA assembly.

4. Review & Submit

Verify all your settings on the summary screen. You can adjust toggles and parameters directly here, or go back to any previous step. When ready, click Find Guides to submit.

Viewing Results

After the analysis completes, you are redirected to the results page with four tabs:

Spacers — ranked table with scores, tiers, quality flags, and detail sheets
Statistics — histograms of score distributions, GC content, and activity
Primers — designed primer pairs grouped by cluster (when enabled)
Export — download results in CSV, TSV, JSON, or FASTA format

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