Markup | Genome Research

Table 2.

Analysis of the Avoidance of Palindromes and RS of Length 4 and 6 in the Genomes of Phages

Phage		Host		Length (bp)		Type		%G + C		Length 4	Length 6
Phage		Host		Length (bp)		Type		%G + C		Palindromes	RMS	Palindromes	RMS
					bias	O/E	bias	bias	O/E	bias
PBSX	Basu	27614	dsDNA	44.9	—	0.63	0	0	0.91	0
SPβc3	Basu	134416	dsDNA	34.6	—	0.63	0	0	0.89	0
PZA	Basu	19366	dsDNA	39.7	-	0.67	0	—	0.57	0
α3	Esco	6087	ssDNA	45.2	—	0.59	1^*	0	0.94	0
f1	Esco	6407	ssDNA	40.9	—	0.59	1^*	—	0.56	0
fd	Esco	6408	ssDNA	40.9	-	0.65	1^*	—	0.56	-
fr	Esco	3575	ssRNA	51.4	0	1.01	7^*	0	1.00	0
G4	Esco	5577	ssRNA	45.7	-	0.68	1^*	0	0.92	0
GA	Esco	3466	ssRNA	47.9	0	0.84	16^*	0	0.90	0
I2-2	Esco	6744	ssDNA	42.7	—	0.57	4^*	—	0.65	0
If1	Esco	8454	ssDNA	43.7	—	0.44	2^*	—	0.67	-
Ike	Esco	6883	ssDNA	39.5	-	0.72	3^*	—	0.69	-
λ	Esco	48502	dsDNA	49.9	—	0.42	1^*	—	0.38	—
MS2	Esco	3569	ssRNA	52.1	0	0.83	14^*	0	1.04	0
MX1	Esco	4215	ssRNA	28.6	0	0.89	6^*	0	1.03	0
Mu	Esco	36717	dsDNA	52.1	—	0.46	1^*	—	0.51	—
N15	Esco	46375	dsDNA	51.2	—	0.60	1^*	—	0.70	-
NL95	Esco	4248	ssRNA	50.8	0	1.01	1^*	0	1.06	0
P2	Esco	33593	dsDNA	51.2	-	0.70	1^*	—	0.66	-
P4	Esco	11624	dsDNA	49.5	-	0.70	1^*	—	0.77	—
φK	Esco	6089	ssDNA	45.0	—	0.54	1^*	0	0.85	0
φX174	Esco	5386	ssDNA	44.8	—	0.38	1^*	—	0.67	0
PRD1	Esco	14925	dsDNA	47.1	—	0.42	1^*	—	0.46	—
S13	Esco	5386	ssDNA	44.3	—	0.41	1^*	0	0.64	-
T3	Esco	19680	dsDNA	50.6	—	0.51	1^*	—	0.44	-
T4	Esco	168900	dsDNA	35.3	—	0.55	1^*	—	0.78	0
T7	Esco	39937	dsDNA	48.4	—	0.33	1^*	—	0.53	-
HP1	Hain	32355	dsDNA	40.0	—	0.24	-	—	0.63	0
PsiM2	Meth	26111	dsDNA	46.3	0	1.08	0	0	0.87	NA
D29	Mytu	49136	dsDNA	63.5	0	0.95	NA	—	0.36	NA
I5	Mytu	52297	dsDNA	62.2	0	0.92	NA	—	0.46	NA
PF1	Psae	7349	ssDNA	61.5	0	1.03	NA	—	0.74	0
Pf3	Psae	5833	ssDNA	45.4	+	1.29	NA	—	0.69	0
φCTX	Psae	35559	dsDNA	62.6	0	1.08	NA	-	0.84	0
PP7	Psae	3588	ssRNA	54.2	0	1.12	NA	0	1.02	0

[i] Palindrome bias is the test that palindromes are more biased than the remaining words. O/E displays the ratio observed/expected of the mean rank of palindromes sorted by decreasing avoidance. RMS avoidance is the result of the Wilcoxon test that RS are more biased than the remained palindromes.

[ii] Abbreviations: NA, unknown RMS on the species; n*, rank of the sole RS known in the species for 4-palindromes (not enough elements for nonparametric statistics); —, underrepresentation (P-value <0.001); -, underrepresentation (P-value <0.05); 0, no bias. See Methods for species abbreviations.