Table 4.

The size, position and integration sites of any prophage-like elements within all samples in this study. Also showing the percentage nucleotide similarity and coverage to the prophage-like elements found in Sakai

Prophage- like element	Gene 5’	Gene 3’	Size (bp) in sample A	Size (bp) in sample B	Size (bp) in sample C	Size (bp) in sample D	(% similarity /%coverage) to Sakai SpLE’s	Position in sample A	Position in sample B	Position in sample C	Position in sample D
PLE1	tRNA-Leu	int	9530	9530	9530	9530	SpLE5 (99 %/97 %)	650 711–660 241	650 730–660 260	650 601–660 131	650 715–660 245
PLE2	int	nanS	34 465	34 981	34 465	34 465	SpLE6 (99 %/100 %)	660 260–694 725	659 763–694 744	660 150–694 615	660 264–694 729
PLE3	ycdU	tRNA-Ser	85 906	85 906	85 906	85 911	SpLE1 (99 %/100 %)	2 112 819–2 198 725	2 113 064–2 198 970	2 112 913–2 198 819	2 113 028–2 198 939
PLE4	cobU	yeeB	15 044	15 045	15 044	15 046	SpLE2 (99 %/100 %)	3 439 339–3 454 383	3 439 883–3 454 928	3 439 719–3 454 763	3 377 102–3 392 148
PLE5	tRNA-Phe	pitB	23 334	23 333	23 333	23 332	SpLE3 (99 %/100 %)	4 664 210–4 687 544	4 664 345–4 687 678	4 664 588–4 687 921	4 601 991–4 625 323
PLE6	selC	yicL	50 390	50 389	50 390	50 390	SpLE4 (99 %/79 %)	5 392 598–5 442 988	5 392 972–5 443 361	5 393 215–5 443 605	5 330 617–5 381 007