Extended Data Table 3a. Adaptation experiments with E. coli BL21-AI ΔrecB, ΔrecC, ΔrecD and ydhQ::I-SceI cells.

Following overnight growth without induction of Cas1+2, the CRISPR array was amplified and sequenced to determine the fraction of cells that acquired a new spacer. In addition, gel-separated expanded arrays were amplified and sequenced, to study the identity of newly acquired spacers in high resolution.

		Sequencing of the CRISPR array PCR product				Direct sequencing of expanded arrays
Sample	rep	# of reads spanning the CRISPR array	# of reads supporting unmodified parental array	# of reads supporting acquisition of a new spacer	% expanded arrays	# new spacers sequenced	# spacers from chromosome	# spacers from plasmid	% spacers from plasmid	% spacers from genome
BL21-AI ΔrecB, no ara	1	35,060	34,615	445	1.27%	663,470	107,260	556,210	83.83%	16.17%
BL21-AI ΔrecB, no ara	2	36,116	35,778	338	0.94%	441,290	75,260	366,030	82.95%	17.05%
BL21-AI ΔrecC, no ara	1	116,840	115,012	1,828	1.56%	704,870	96,707	608,163	86.28%	13.72%
BL21-AI ΔrecC, no ara	2	132,549	130,724	1,825	1.38%	507,844	55,057	452,787	89.16%	10.84%
BL21-AI ΔrecD, no ara	1	85,877	85,253	624	0.73%	2,938,455	353,353	2,585,102	87.97%	12.03%
BL21-AI ΔrecD, no ara	2	90,498	89,802	696	0.77%	4,437,733	1,405,158	3,032,575	68.34%	31.66%
BL21-AI ydhQ-l-SceI site/pCasl2-IPTG/pBAD-I-SceI, no ara	1	87,419	83,625	3,794	4.34%	221,721	16,906	204,815	92.38%	7.62%
BL21-AI ydhQ-I-SceI site/pCasl2-IPTG/pBAD-I-SceI, no ara	2	89,357	86,745	2,612	2.92%	192,597	15,995	176,642	91.72%	8.28%