Sanger Trace Viewer & Clone Verification
Inspect chromatograms, compare a read with its reference, or screen a whole plate of clones.
View one trace, compare it with the sequence you expected, or screen a facility ZIP to decide which clone to grow. The same page carries your sequencing data between steps instead of asking you to upload it again.
What do you need to verify?
All three workflows are here. Choose a task now, or carry a trace result into the next step without entering it twice.
Assembly, mixed-peak and construct checks send the derived base calls, quality scores and dye-channel arrays to the server — and, for the construct check, the template and primers you give it.
The viewer decodes the raw ABIF (.ab1 / .abi) chromatogram: the four processed dye channels are drawn as an electropherogram (G black, A green, C blue, T red) with the called bases positioned over their peaks. Read length and mean Phred quality summarize the read; export the base calls as FASTA or the trace as an SVG/PNG figure. Low peaks, broad or overlapping peaks, and stretches of low quality near the ends are the usual signs to trim before downstream analysis.
Got the reverse read too? Assemble them
Two traces that overlap in the middle are one insert sequenced from both ends. This joins them into a single consensus without needing a reference: orientation comes from the overlaps, the ends are quality-trimmed, and every position the reads disagree on is listed rather than averaged away. Assembly is the feature that separates free Chromas from paid ChromasPro, and it is on this page.
Parsed in your browser — only the base calls and quality scores are sent. Pick the forward and reverse reads together.
0 pasted reads. A pasted read has no quality scores, so its ends are not trimmed. Pasted reads and uploaded traces are assembled together.
Upload two or more traces, or paste the reads, to assemble them into one contig.
Double peaks? Read what the basecaller did not report
A basecaller reports one base per position and stops early. This reads the same trace for the second dye under a called base — a heterozygote, or a mixed colony — and for the bases still visible in the scan past the point base calling gave up. Both are ordinary reasons a read looks wrong when the DNA is fine.
Second peak / first peak. The default is deliberately conservative.
Open a trace above, and this reads what is under its base calls.
No map of the finished plasmid? Check the read against the PCR
Comparing a read needs a reference. If what you have is the template and the two primers that made the insert, this rebuilds the insert from them, finds it in the read in either orientation, and reports identity, coverage and every mismatch — and, given the frame, whether a premature stop crept in.
The insert is re-derived from these three rather than taken from you, which is the point: if the primers you recorded do not produce what you think they produce, that shows up here instead of being assumed.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
How to use the Sanger Trace & Clone Verification tool
- 1Choose Inspect trace quality, Compare with a reference, or Screen clones or a plate.
- 2Upload AB1/ABI/SCF traces or a facility ZIP; comparison and screening also accept pasted reads.
- 3Add the expected reference sequence when you need coordinate-level differences or clone verdicts.
- 4Review the chromatogram, coverage and cited differences, then export or continue into the next Sanger task without re-entering the read.
Frequently asked questions
Which Sanger job should I choose?
Inspect trace quality when you need to see peaks, edit calls or trim one or more traces. Compare with a reference when one read should match a known sequence and you need coverage plus coordinate-level differences. Screen clones or a plate when several reads belong to several colonies and the real question is which clone to grow up.
Which files can I open?
The trace viewer and comparison workflow read ABIF traces (.ab1 / .abi) and Staden SCF traces (.scf). Clone screening also accepts a sequencing facility ZIP, FASTA or FASTQ reads, while references can be GenBank, FASTA or raw DNA.
How is a read-to-reference verdict decided?
Coverage is checked before identity: a clean match over too little of the requested reference is ambiguous, not a pass. With enough coverage, the read passes at 99% or higher identity with no indels; every mismatch, insertion and deletion is listed in reference coordinates for inspection against the trace.
How does plate screening know which reads belong to a clone?
It parses facility-style record names, sample names and wells, shows the confidence and reason for every grouping, and lets you correct them before running. Reads for each clone are then piled up in reference coordinates so one noisy base call is not automatically treated as a mutation.
Can I run this from code?
Yes — the underlying calculations are available through the REST API and MCP server.
More
Guides
Related tools
Align your reads to your own annotated reference and get what each difference DOES — silent, missense at a named codon, or a premature STOP that ends the protein — not just where it sits.
Paste what you got back and the PCR you say made the insert. It re-derives the insert, finds it in either orientation, and gives you the exact mismatch positions.
Drop in an unedited control trace and your edited pool's trace and get the indel spectrum, the unedited fraction, and the R² that says whether the decomposition means anything.