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Frequently Asked Questions

Here you can find answers to questions tend to recur, for example what are common fail reasons, what should be next steps, etc.

Why did my GapmeR design fail?

The most common reasons are repetitive sequences or low-complexity regions, GC content outside the optimal range (40-60%), strong RNA secondary structure blocking target accessibility, or too many off-target sites in the genome. Any of these can prevent the algorithm from finding a specific, effective GapmerS candidate.

My sequence contains repeats - can I still design a GapmeR?

Unfortunately no. Sequences with repetitive elements (e.g. simple repeats like CA/GT, or genomic repeats like SINE/LINE) generate too many off-target hits and cannot meet specificity requirements. We recommend submitting a unique region of your transcript, for example an exon-exon junction or a non-repetitive region of the 3'UTR.

How do I choose which part of my sequence to submit?

The best candidates come from regions that are unique to your target isoform, have 40-60% GC content, and are not predicted to form strong secondary structures. Free tools like RNAfold can help you identify accessible windows before submission.

What is the minimum sequence length required?

We recommend submitting at least 100 nucleotides. This gives the algorithm enough window to evaluate multiple candidate sites and select the optimal GapmeR.

My target is a lncRNA or non-coding RNA - does that affect design success?

Yes. lncRNAs often contain repetitive elements, poorly characterized isoforms, and complex secondary structures, all of which can cause design failure. If your design fails, try submitting a specific exon or a known functional region rather than the full transcript sequence.

What should I do if my design keeps failing?

Contact our team using the option at the top of the page. Include your Design ID (shown on the results page) so we can jump straight into your case. Our team can manually review your sequence and suggest alternatives, including custom LNA oligos.
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