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Only 23 of 255 identified unique repeat sequences matched repeats from the CRISPRdb database.
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All matched repeats originated from the JPN metagenome and corresponded to 17 repeat clusters.
Approximately 20% of all scaffolds matched known repeat sequences deposited in the RepBase database that includes sequences derived from the Tc genome (fig. 4 A).
Relatively few reads matched the repeat database for Arabidopsis.
Sequences matching known repeats were masked as N and repeat masked sequences were further used to identify novel repeats.
To remove false positive matches from Blast versus Repbase results, all matches that covered by repeats from Repbase less than 80% were discarded.
Sequences matching known repeats were masked with an "X".
As repeats identified by Stern et al. were not available, we checked whether HMP contigs matched by the Stern spacers contained repeats from the HMP repeat set (identified here) and/or known CRISPR repeats from CRISPRdb [ 58].
BES from 13,166 clones matched rDNA homologues from both Repbase and TIGR plant repeat databases, indicating their significant presence in the flax genome.
Only the best matching repeat copies would be merged.
Fifty-five of the repeats matched (with an e-value of 10-10 or less) 46 passerine microsatellites isolated from 25 different species.
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