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The spacer deletions at the very first and last positions of CRISPR arrays deviate from a symmetric boundary effect. The reconstructed deletion rate is higher at the first positions compared to the losses at the last positions. This might have multiple reasons ...

Consistent with this mechanism, we observe a “boundary effect”: Spacer deletions are less frequent near the leader and trailer ends of the array, potentially due to fewer neighboring repeats for alignment, while the middle of the array sees the most deletions.

Interestingly, besides the loss of a single spacer, deletions occur often in blocks, involving an average of 2.7 spacers per event. This block deletion aligns with theories of replication slippage, where nearby repeats misalign, leading to multiple spacer deletions.