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PCR primers were designed for each spacer using the Primer3 software program (INFOBIOGEN, Evry, France).
For each spacer, three types of genetic events were observed, i.e. variation in the number of tandem repeats, deletions and point mutations.
A dot plot was constructed for each spacer in order to visualise the type of genetic events responsible for spacer sequence heterogeneity, i.e. tandem repeat, mutation, insertion or deletion.
For each spacer, the waiting time to get lost is exponentially distributed with rate μ.
(b) Draw the waiting times until the next deletion for each spacer or fragment.
For each spacer, differences among genotypes mainly consisted of nucleotide substitutions.
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Plots of CRISPR spacer comparisons for each CRISPR spacer type.
We binned the spacers from each sequence read according to their trinucleotide content to account for the potential for sequencing errors, and assigned each spacer a unique identifier (Fig. 6).
Using this mapping we can calculate the regression coefficients for each individual spacer in each domain.
For each intergenic spacer, a genotype was defined as a sequence exhibiting unique mutations, which were checked by sequencing the corresponding spacers 3 times.
For each unique spacer, the number of self-recombining reactions, non-self recombining reactions, and total interactions were stored in MySQL tables.
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