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Fig. 8D summarizes the results obtained with the ten most frequent sequence patterns.
We defined the typical repeat sequence as the most frequent sequence within a particular CRISPR locus.
In all these cases, the consensus sequence corresponds to the most frequent sequence within a particular CRISPR.
A consensus sequence (the most frequent sequence) for each conserved sequence in the alignments was generated for each of the 6 subgroups.
The two most frequent sequence patterns are HDWWW (16.4% of the 10,000 low-energy sequences, or 1640 sequences) and DLWWL (9.6% of the sequences).
Adding ST2, the second most frequent sequence type (8 isolates), and ST3 (1 isolate), both of which differed from ST1 by a single base pair, accounted for 97% of the isolates (see Table 1).
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The recommendations are nothing more than the most frequent sequences found by the sequence mining algorithm, which in practice are the most common paths found in the workflows.
In particular, we developed a new graphical tool that permits discrimination between the most frequent sequences in the parasites.
Mononucleotide repeat motifs were discarded since monomer runs are known to be the most frequent sequencing errors in Roche/454 data.
Numbers of low frequency single nt mismatch sequences for the 20 most frequent sequences in each sequencing cohort were tallied for each cutoff value.
The second main result is that, although the most frequent sequences are quite similar among species, there are some species-specific differences.
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