TABLE 5.

List of new spacers found in CRISPR1 and the corresponding region in phages 2972, 858, and DT1

Spacer	Phagea	5′ positionb	Spacer length (pb)	Proto-spacer sequencec	3′ flanking regiond	Strand/modulee	ORF/function in the genome of the phage used in the challenge
S1	858	31378	30	CAACACATTCAACAGATTAATGAAGAATAC	AAAGAAAAAA	(+)/E	ORF40/primase
S2	2972*	25432	30	TCCACTCACGTACAAATAGTGAGCGTACTC	CTAAAAGGAT	(-)/L	ORF27/unknown
S3	2972*	17202	30	TTACGTTTGAAAAGAATATCAAATCAATGA	CGAGAAAGAT	(+)/L	ORF20/receptor-binding protein
S4	2972	31582	30	CTCAGTCGTTACTGGTGAACCAGTTTCAAT	TGAGAAAAAA	(+)/E	ORF38/primase
S5	2972	22075	30	AGTTTCTTTGTCAGACTCTAACACAGCCGC	TCAGAAAGTT	(+)/L	ORF21/tail protein
S6	2972*	34521	30	GCCCTTCTAATTGGATTACCTTCCGAGGTG	TTAGAATTCC	(-)/E	ORF44/unknown
S7	2972*	10299	30	AAGCAAGTTGATATATTTCTCTTTCTTTAT	TAAGAAAACG	(-)/L	ORF17/unknown
S8	2972	30016	29	CGTTTTCAGTCATTGGTGGTTTGTCAGCG	AAAGAAATAA	(-)/E	ORF37/replication
S9	2972*	7874	30	TTACTAGAGCGTGTCGTTAACCACTTTAAA	TCAGAATATG	(+)/M	ORF11/unknown
S10	2972*	20650	30	TTCGTTAAAGTCACCTCGTGCTAGCGTTGC	ATAGAAAGTT	(-)/L	ORF20/receptor-binding protein
S11	2972*	8360	30	ATAACGGTAGCAAATATAAACCTGTTACTG	TCAGAAGCTA	(+)/M	ORF12/unknown
S12	2972a	18998	30	GAAGTAGCCATACAAGAAGATGGATCAGCA	CCAGAAATTG	(+)/L	ORF20/receptor-binding protein
S13	2972*	33602	30	GATGTCACTGAGTGTCTAAGCATTGCGTAC	GAGGAAATCA	(+)/E	ORF42/DNA binding
S14	2972*	4830	30	TGAATAAGCAGTTCTTGACGACCAACCGAC	ATAGAAAAGT	(-)/M	ORF6/capsid protein
S15	2972*	34444	29	CAATTAACACAGCAATTAACACAGTATAT	ACAGAAATTG	(+)/E	ORF44/unknown
S16	2972*	6799	30	ATGCCATTCTTTAAAGAGGCTTTACTCGTT	AAAGAAAACG	(+)/M	ORF9/capsid protein
S17	2972	30547	30	GTTGGCGGACTACTCCTTCGAGGGGTTGAT	CCAGAAATTA	(+)/E	ORF37/replication
S18	2972	30370	29	GAAGCACCTCTTGCGTTGATAAAAGTATT	GCAGAAAATG	(+)/E	ORF37/replication
S19	2972	31709	29	ACATATCGACGTATCGTGATTATCCCATT	CAAGAAAACA	(+)/E	ORF38/primase
S20	2972*	1113	30	TTATATCGAAGAACGACTGAAAGAGCTTGA	GAAGAAAAAA	(+)/M	ORF2/small terminase
S21	2972*	19188	30	AAATCAACGTACATCCCGATATAGGCACGA	TTAGAATCAG	(-)/L	ORF20/receptor-binding protein
S22	2972	31708	30	GACATATCGACGTATCGTGATTATCCCATT	CAAGAAAACA	(+)/E	ORF38/primase
S23	2972	26529	31	TGAAGTATTAGGTCTCTCAAAAGATGATATT	GTAGAATACT	(+)/E	ORF31/Cro-like repressor
S24	2972	29923	30	AGTTGATTGCGTAATCAACCATCTCCATAA	TTAGAATGGA	(-)/E	ORF37/replication
S25	2972*	441	30	GCAACACTCAAACGTTGCAAACGCAAGCTT	CGAGAATATC	(+)/E	ORF1/unknown
S26	2972	31606	31	CTCAGTCGTTACTGGTGAACCAGTT*TCAAT	TGAGAAAAAA	(+)/E	ORF38/primase
S27	2972*	27032	30	TTTCATCGTCAATTTCCATGTTATAAATCT	CTAGAAACTG	(-)/E	ORF33/unknown
S28	2972	26530	30	GAAGTATTAGGTCTCTCAAAAGATGATATT	GTAGAATACT	(+)/E	ORF31/cro-like repressor
S29	2972	32136	29	ATTGGCATGATTTCAATTTTAATTGGGAT	GTAGAAAAAG	(+)/E	ORF38/primase
S30	2972*	33968	30	TCCAAGTTATTTGAGGAGTTATTAAGACAT	GAAGAAATAT	(+)/E	ORF43/unknown
S31	2972	30803	30	TACCGAAACGACTGGTTTGAAAAATTCAAG	GAAGAAAATC	(+)/E	ORF38/primase
S32	2972*	33044	30	ATTGTCTATTACGACAACATGGAAGATGAT	GTAGAAATTT	(+)/E	ORF41/unknown
S33	858	30335	30	CTTCAAATGTACTGCAAGGCTGCAAAAGTA	CCAGAAAATA	(+)/E	ORF38/unknown
S34	DT1	14535	30	GCTACTGAAAGCTACGAGGTTGGTAATCCT	AAAGAATGGG	(+)/L	ORF17/tail protein
S35	DT1	13255	30	GTAGTTAGAGCGCTTGAAGCTAACGGTATA	GAACCAAACA	(+)/L	ORF15/tail protein
S36	DT1	29132	30	TTAGATCTCATGAGTGGCGACAGTGAGCTT	GTAGAATTAC	(+)/E	ORF36/primase
S37	DT1	20837	30	AACGATGAGGAACTCTTGGCAAAACTTACA	CAAGAATAGC	(+)/L	ORF22/unknown
S38	DT1	9893	30	GCATTCATGGTTTGTTGGTATTTAACGTAT	TCGGAACTGG	(-)/L	ORF15/tail protein
S39	DT1	2603	30	TATTTTATCAGTCATCATGGCGTCATAGCC	GAAGAAAACG	(-)/M	ORF4/Large terminase

^a*, DNA regions that are 100% identical between phages 858 and 2972.

^bThat is, the 5′ position of the proto-spacer in the phage genome.

^cUnderlined and italicized nucleotides indicate a mismatch between the phage and the spacer. An asterisk indicates a deletion.

^dThat is, the 3′ flanking sequence in the phage genome. A mismatch in the AGAAW motif is boldfaced.

^eTranscription module: E, early expressed genes; M, middle expressed genes; L, late expressed genes.