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DNA Sequence Search Tool - no match with the database

You have received a message stating that your sequence is not consistent with any reference sequences in the database. Possible reasons for this message and alternatives are discussed below.

The DNA Search Sequence Tool performs an "exact matching" algorithm against sequences in the reference database. Failure to match any reference sequences could be due to one of the following reasons:

1. The search sequence is not formatted correctly

Search sequences must be properly trimmed between the primers. Three sets of primers are commonly used to generate COI barcode sequences (LepF1-LepR1, LCO1490-HCO2198, and TYJ1460-C1N2191). Sequences should be trimmed between these primer regions so that they are approximately 650bp long. Sequences should also be continuous strings of bases (letters) with no spaces, line breaks, or return characters, including at the end of the sequence.

2. The taxon is not included in the reference database

While the reference database contains more than 300 taxa, it does not contain representatives of all 9,500 described tortricid species. It is also possible that the search sequence is not from a tortricid.

3. The haplotype for the species is not in the reference database

Although the reference database contains more than 800 unique COI haplotypes, it does not contain all possible haplotypes for all species. Some species, such as Epiphyas postvittana, have more than 40 unique haplotypes for the COI DNA barcode region.

4. Sequencing or PCR errors exist in the search or reference sequences

It is possible that sequencing or PCR problems could have led to errors in the search or reference sequences. Without resampling all taxa these errors would be difficult or impossible to detect.

What to do next?

If you have access to the Internet, attempt your search on one of the following public DNA databases:

BOLD Data Systems

Genbank Standard Nucleotide BLAST

Be aware that matching algorithms and criteria are very different for the DNA sequence search tool, BOLD, and BLAST. Please interpret results carefully.

  Tortricids of Agricultural Importance by Todd M. Gilligan and Marc E. Epstein
   Interactive Keys developed in Lucid 3.5. Last updated August 2014.