Extended Data Table 3b. Adaptation experiments with E. coli BL21-AI pCas1+2-Chi.

Following overnight growth without induction of Cas1+2 from the pChi plasmid (which contains a cluster of 4 counter clockwise Chi sites on a 50bp cassette inserted at position 1300 of the pCas plasmid) gel-separated expanded arrays were amplified and sequenced, to differentiate between spacers acquired from self and plasmid DNA. As a control a similar plasmid with a 50bp Chi-less insertion at the same position in the pCas plasmid was used.

		Direct sequencing of expanded arrays
Sample	rep	# new spacers sequenced	# spacers from chromosome	# spacers from plasmid	% spacers from plasmid	% spacers from genome
BL21-AI pCtrl-Chi, no ara	1	4,221,820	42,055	4,179,765	99%	1%
BL21-AI pCtrl-Chi, no ara	2	5,743,373	50,345	5,693,028	99.12%	0.88%
BL21-AI pChi, no ara	1	2,726,923	78,079	2,648,844	96.97%	2.86%
BL21-AI pChi, no ara	2	2,841,509	87,106	2,754,403	96.74%	3.06%