Table 3.

The size, position and integration sites of all 16 prophages within all samples in this study, also included is the percentage nucleotide similarity to any Sakai prophages

Prophage detected	Gene 5′ to prophage	Gene 3′ to prophage	Size (bp) in sample A	Size (bp) in sample B	Size (bp) in sample C	Size (bp) in sample D	(% similarity /%coverage) to Sakai prophages	Position in sample A	Position in sample B	Position in sample C	Position in sample D
1	lexA	aphA	22 035	22 035	22 034	22 036	/	403 708–425 743	403 729–425 764	4 03 712–4 25 746	403 708–425 744
2∗	tRNA-Thr (cgt)†	prgR	26 826	26 823	26 823	26 821	/	1 101 413–1 128 239	1 101 440–1 128 263	1 101 421–1 128 244	1 101 414–1 128 235
3	ybhC†	ybhB	38 095	38 095	38 096	38 095	Sp3 (99 %/100 %)	1 697 277–1 735 372	1 697 420–1 735 515	1 697 397–1 735 493	1 697 388–1 735 483
4	yccA†	tRNA-Ser (tga)	48 257	48 277	48 265	48 263	Sp4 (99 %/100 %)	1 967 370–2 015 627	1 967 513–2 015 790	1 967 491–2 015 756	1 967 481–2 015 744
5	potC†	potB	47 889	47 679	47 879	47 896	Sp6 (99 %/100 %)	2 283 891–2 331 780	2 284 054–2 331 733	2 284 019–2 331 898	2 284 012–2 331 908
6	roxA†	phoQ	10 436	10 436	10 436	10 436	/	2 337 022–2 347 458	2 336 975–2 347 411	2 337 140–2 347 576	2 337 150–2 347 586
7	icd†	caeB	40 992	40 991	40 992	40 991	Sp8 (99 %/100 %)	2 356 230–2 397 222	2 356 183–2 397 174	2 356,348–2 397 340	2 356 358–2 397 349
8∗	ompW†	rspR	145 151	144 981	145 040	53 636	/	2 495 566–2 640 717	2 495 518–2 640 499	2 495 685–2 640 725	2 495 693–2 549 329
A	hipA	ydeP	/	/	/	28 513	/	/	/	/	2 589 222–2 617 735
9	trpA	rspA	59 339	59 340	59 322	59 863	/	2 918 047–2 977 386	2 917 834–2 977 174	2 918 061–2 977 383	2 855 169–2 915 032
10	yodB	tRNA-Ser (cga)†	43 681	43 694	43 684	43 690	Sp14 (99 %/98 %)	3 370 042–3 413 723	3 369 847–3 413 541	3 370 056–3 413 740	3 307 170–3 350 860
11 (stx2c)	yeeA	tnpA†	55 650	56 910	55 652	55 655	/	3 457 661–3 513 311	3 456 222–3 513 132	3 457 677–3 513 329	3 394 797–3 450 452
12	yehV	yehV†	45 720	45 725	45 732	45 719	/	3 654 766–3 700 486	3 654 584–3 700 309	3 654 782–3 700 514	3 591 904–3 637 623
13 (stx2a)	yfdC	argW†	60 239	60 237	60 239	60 242	/	3 948 563–4 008 802	3 948 386–4 008 623	3 948 591–4 008 830	3 885 700–3 945 942
14	argW†	lacY	8233	8233	8233	8233	Sp16 (100 %/100 %)	4 009 234–4 017 467	4 009 055–4 017 288	4 009 262–4 017 495	3 946 374–3 954 607
15	ssrA	alpA†	22 107	22 103	22 098	22 106	Sp17 (99 %/99 %)	4 294,770–4 316 877	4,294,584–4 316 687	4 294 801–4 316 899	4 231 915–4 254 021

∗Refers to prophages that appear to be compound prophages (i.e. two or more prophages that are sequential, with intact integrase genes).

†Refers to the end in which the Integrase gene (IntA) is located.