Table 2.

Percentage of genes detected using sequence alignment.

Reference Genome		Terminase		Portal		Head		Tail		Tape measure		Prohead protease		Lysin		Holin		Integrase
	E-value cutoff	0.01	0.1	0.01	0.1	0.01	0.1	0.01	0.1	0.01	0.1	0.01	0.1	0.01	0.1	0.01	0.1	0.01	0.1
Bacteriophage bIL285		31	37	33	50	-	-	4	19	-	-	46	49	16	18	11	23	57	64
Lactococcus phage TP901-1		8	22	13	19	12	27	7	22	96	98	-	-	30	48	13	13	3	15
Enterobacteria phage HK97		29	40	35	43	4	26	12	19	83	96	54	64	0	4	5	24	54	73
Bacteriophage phi LC3		19	42	9	25	14	24	4	25	63	83	-	-	36	48	13	14	58	65
Staphylococcus aureus phage phi 13		12	25	40	56	9	19	-	-	77	94	36	38	-	-	13	26	62	71

The percentages are calculated by dividing the number of significantly similar sequences by the total number of sequences found by using regular expression. Sequence similarity is determined by BLAST (bl2seq) [33] using BLOSUM45 with indicated E-value cutoffs. Each sequence is "blasted" against its corresponding gene in the reference genome. The best cases are highlighted in bold.