CleanFinder

Forward primer

Reverse primer

Chromosome

Gene (optional)

Focus near genePad (kb)

Flanking bases (to include in amplicon)

Upstream

Downstream

Chunk size (bp)

Analyze FASTQ for Editing Outcomes

First, find an amplicon in Tab 1 or 5. The anchors and buffers will be set automatically. Then, upload one or more FASTQ files to analyze the reads.

FASTQ File(s)

HDR Donor Template (optional)

Other Known Alleles (optional)

Anchor Length (bp)

Max Anchor Mismatches

Upstream Buffer (bp)

Downstream Buffer (bp)

Per-Sample Chart Grouping Show Unclassified

Anchor Sequences

Allelic Dropout SNP Analyzer

Analyze long-read FASTQ data to detect heterozygous SNPs, which can be used to assess allelic dropout after CRISPR editing.

FASTQ File

No file selected

Stable Anchor Sequence

This should be a unique sequence far from the expected SNP.

Reference Amplicon Sequence

Max Reads

Scan Window

Min Coverage

Min Allele Freq (%)

Max Allele Freq (%)

DNA Sequence Manipulator

Paste a DNA sequence (A, C, G, T, N) below to instantly get its reverse and reverse complement.

Input DNA Sequence

Reverse Sequence

Reverse Complement

Find Amplicon on Transcripts (cDNA)

Enter a gene symbol and primers to check which transcripts will be amplified. This tool is ideal for checking qPCR primer specificity across different isoforms.

Gene Symbol

Forward Primer

Reverse Primer

In-Silico Genome PCR

Test a primer pair against the entire human genome to check for specificity and predict potential off-target amplicons. This is essential for validating qPCR primers.

Forward Primer

Reverse Primer

Max Product Size (bp)

CleanFinder Application Info (v1.5)

Recent Improvements

**Genome Viewer Upgrade:** The target site marker in the Genome Viewer is now a highly visible **highlighted box** that spans the entire gRNA sequence, making it easy to locate even when zoomed out.
**HTML Report Generation:** Added a feature to download the complete FASTQ analysis, including all charts and tables, as a single, self-contained HTML file for easy sharing and archiving.
**Enhanced Summary Chart:** The main summary chart now includes a "Top 10 Alleles (Stacked)" view, providing a more granular look at the most frequent editing outcomes across samples.
**UI Refinements:** The accent color has been reverted to a professional black, and the FASTQ results layout has been streamlined by integrating the reference length into the main summary and enlarging the indel distribution chart for better visibility.
**CRISPR Alignment Logic:** Implemented **dynamic alignment scoring** (match/mismatch/gap penalties) based on the selected CRISPR enzyme (Cas9 vs. Cas12a) for more biologically accurate allele analysis.

Application Goals

CleanFinder is designed to be a comprehensive suite of in-silico tools for modern molecular biology and genome engineering workflows, focusing on primer design validation, CRISPR outcome analysis, and quality control. It targets users requiring precision for qPCR, Sanger sequencing, and next-generation sequencing analysis related to genomic loci.

**Developed by Andrea Rossi**

Gene symbol

Use the buttons above to view gene data.