5) Report

Primrose's Report page considers in more detail the range of our chosen oligonucleotide, and how that range changes as the number of mismatches allowed between oligonucleotide and sequence increases. 

Running the search, with the default settings of three maximum mismatches allowed, generates the following output:



The graph shows us that whilst all members of the target group have been hit (as expected) very few non-target records have been hit.  A look at the graph data (by selecting 'show data' from the Options menu ) gives the exact figures:



In other words, three mismatches are required between oligo and sequence before 0.8% of the non-target records are successfully hit.  We now turn to the colour-coded database to determine which non-target records have been targeted.  Our novel taxon icon is coloured green signifying that all records within were successfully targeted (as expected).  The Archaeal domain is coloured red, indicating that no Archaeal record within the RDP database was targeted.  However the Bacterial domain is coloured yellow indicating some successful hits when up to three mismatches are allowed.  Expanding this group shows that these hits occur only in the Flexibacter-cytophaga-bacteroides division (or Bacteroidetes phylum) and within the Proteobacteria.



Exploring the Flexibacter-Cytophaga-Bacteroides taxon further, we find that records within two taxa are being hit; Cytophaga groups I and II.



Expanding Cytophaga group I identifies the Psh. burtonensis subgroup as the sole sub-taxon that contains successfully targeted records.



And when this taxon is expanded, we see that only one record, within the Psh. burtonensis subgroup is hit; Cytophaga sp. str. BD2-17.



Refering to the adjacent table display we see that bases 74 to 93, inclusive, of this record matches the oligonucleotide when three mismatches are allowed.







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