CleanFinder

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Analysis Setup

1. Reference Sequence

Paste DNA Sequence

Species

Gene Symbol

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Species

Gene Symbol

OR LOAD INDIVIDUAL FASTA

5' Padding (bp)

3' Padding (bp)

Analysis window

Padding sets how much sequence is kept either side of the gRNA. A 20 bp anchor is added at each end to locate the window in your reads.

🎯 Target Sequences

gRNA Sequence (Required for Anchors)

Knock-in Oligo (Optional)

Expected inserted sequence for HDR/Knock-in detection.

2. Sequencing Reads

📁

Drag & drop files here or browse

3. Configuration

Analysis Mode

Advanced Alignment Parameters ▾

Preset Mode

Match

Mismatch

Gap Open

Gap Ext

Base Editing: Penalty -20 for Gaps (Prohibits Indels).
Prime Editing: Gap Ext -0.5 (Allows long insertions).

Anchor Search Settings

Max Mismatches: (0=Strict, >0=Fuzzy)

ONT Fast (K-mer Seeded)

Illumina Fast (K-mer Seeded)

Quality Filter (Pre-Analysis)

Min Phred Score:

Analysis Results

File Overview

Edit Distribution

Reads Analysed 0

Editing Efficiency (incl. SNPs) 0%

Out-of-Frame 0%

In-Frame 0%

Knock-in 0%

📊 Genotype Distribution

Group Indels

Collapse Reference

Type	Delta	Frame	Aligned Sequence lowercase: intronUPPERCASE: exon	REPAIRome	Reads	%

📈 Additional Charts (Indels, Frameshifts, RIMA) ▾

Indel Sizes

🔬 REPAIRome

📋 Clones Summary (Click to Toggle)

File Name	Total Reads	Efficiency	Knock-in %	In-Frame %	Out-of-Frame %	MMEJ % (of Deletions)

1. Reference Sequence

2. Sequencing Reads

3. Configuration

File Overview

Edit Distribution

📊 Genotype Distribution

Indel Sizes

🔬 REPAIRome

📖 Info & Resources

ℹ️ About

📜 License & Credits

📁 Datasets

📝 Changelog