Raw CR1/2 and 3 array sequences were assembled using the Geneious program version 11 (Biomatters, Auckland, New Zealand) and Benchling Life Sciences RandD Cloud (Benchling, San Fransisco, USA). CRISPR array spacers and DRs patterns were generated with resource to CRISPRs finder tool (https://crispr.i2bc.paris-saclay.fr/). Both spacers and DRs of the CR1/2 and 3 arrays were further assessed by BLASTn for existing homology in GenBank database (http://blast.ncbi.nlm.nih.gov/Blast.cgi). To identify novel spacers and patterns, the CRISPR array patterns of the 36 E. amylovora isolates, together with the E. amylovora type strain LMG 2024, and the North American reference strain ATCC 49946, were compared with CRISPR array patterns previously described [39, 40, 49].

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