Table 2.

Summary of highly repetitive sequences in the genome of T. vaginalis. The 31 unclassified repeat families have been collapsed into one group.

Repeat name	Putative identity	Copy no.	Length (bp)	Cumulative length (bp)	Average pairwise difference (%)
Viral
R128b	Poxvirus D5 protein	203	2348	370,658	1.2
R169a	Phage tail fiber prot	903	752	607,929	3.9
R1794	Hypothetical	2243	1037	1,879,762	3.0
R299a	KilA-N terminal domain	867	873	655,984	6.6
R3a	Poxvirus D5 protein	954	2637	1,721,187	4.6
R9a	KilA-N terminal domain	831	663	503,959	3.6
R947a	KilA-N terminal domain	518	669	298,778	3.1
Average (total)		931	1283	(6,038,257)	3.7
Transposon
R8	Mariner transposase	982	1304	1,158,473	0.5
R107	Integrase	384	2246	518,936	0.9
R119	Mutator-like profile	282	2954	303,256	1.1
R11b	Integrase	1842	981	1,634,764	2.1
R128a	HNH endonuclease	200	800	131,491	1.5
R130a	Mutator-like profile	173	1129	137,526	0.7
R165	Mutator-like profile	365	2410	368,152	1.1
R178	Integrase	580	2433	636,901	1.5
R204	Integrase	51	1323	51,185	1.6
R210	Mutator-like profile	75	2127	118,581	0.9
R2375	Endonuclease	566	765	329,717	5.4
R242b	Integrase	49	1151	45,564	2.5
R26b	Integrase	1148	1141	1,175,921	2.6
R289a	Integrase	54	1250	53,674	2.2
R309b	Integrase	56	1601	73,737	1.4
R414a	Integrase	37	909	27,708	1.4
R41b	Integrase	927	1184	807,711	2.5
R473	Integrase	19	1124	15,254	1.3
Integ.a95313	Integrase	68	1301	22,023	2.3
Average (total)		414	1481	(7,610,574)	1.8
Retrotransposon
R1407.RT	Reverse transcriptase	6	2349	6,833	1.0
copia.a38393	Copia-like profile	7	11001	16,504	7.5
Average (total)		6.5	6675	(23,337)	4.3
31 unclassified families
Average (total)		793	1131	(24,617,704)	2.6
Total all				38,289,872
Average all		660	1450		2.5