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Table 2
W-chromosome-specific repeats of S. mansoni
GenBank accession number	Name	Length (bp)	Percentage female hits	Repeat family^a	Transcription evidence	FISH localization	Copy number estimate^b	Reference

U12442	SMAlphafem-1	338	99.86	SMAlpha retroposon	RT-PCR	p-arm	60,000 - 70,000	[61,62]
J04665	W1	482	100	Retro		Middle of q-arm at frontier between heterochromatin and euchromatin as satellite, middle of q-arm	500	[26,27]
U10109	W2	715	100				400	[62]
HQ880214	W3	786	100	LTR, highly similar to W2, highly similar to R = 407	No transcription (RT-PCR)	As satellite in the middle of q-arm at frontier between heterochromatin and euchromatin or also in the pericentromeric region	200
HQ880209	W4	1132	99.52	Highly similar to R = 879	RT-PCR	Same location as W1	800
HQ880217	W5	1129	99.27	LTR, similar to Perere-2, identical to R = 564	EST and RT-PCR	Either at the frontier of heterochromatin and euchromatin of the q-arm or in the pericentromeric region, or at both locations
HQ880215	W6	310	99.88	Retro	EST	In the pericentromeric region
HQ880210	W7	1000	100	DNA transposon, 97% identical to GenBank accession number XP_002570219 (hypothetical protein Smp_186230)		In the pericentromeric region
HQ880218	W8	266	99.97	Tandem repeat (previously described as TR266), DNA transposon		Either at the frontier of heterochromatin and euchromatin of the q-arm or in the pericentromeric region
HQ880211	W9	803	100	LINE2, similar to SjR2 retrotransposon	EST
HQ880212	W10	682	100	LTR
HQ880213	W11	376	100	LINE, similar to R = 170
HQ880216	W12	264	100	Retro, 97 to 100% identical to several hypothetical S.m. proteins
HQ880219	W13	258	100	Retro		In the middle of the heterochromatic part of the q-arm as satellite
HQ880220	W14	209	100	DNA transposon, similar to R = 170
HQ880221	W15	185	96.62	DNA transposon
HQ880222	W16	164	100	Similar to R = 116
HQ880223	W17	160	100	LTR
HQ880224	W18	160	100	LTR	EST
HQ880225	W19	139	100	Retro, 100% identical to GenBank accession number XP_002569391 (hypothetical protein Smp_181820)	EST
HQ880226	W20	138	100
HQ880227	W21	138	99.84	DNA transposon, similar to R = 116
HQ880228	W22	132	100	DNA transposon
HQ880229	W23	125	100	DNA transposon
HQ880230	W24	115	99.56	Retro, similar to Sh122 repeat and R = 31
HQ880231	W25	112	99.65	LTR
HQ880232	W26	111	100	DNA transposon
HQ880233	W27	110	100	DNA transposon, similar to R = 133 and Sh microsatellite C2
HQ880234	W28	108	100	Similar to Sh microsatellite C140
HQ880235	W29	97	100	Similar to Sb Sbov20 repeat
HQ880236	W30	96	99.05	LTR
HQ880237	W31	92	100	LTR
HQ880238	W32	89	96.88	DNA transposon
HQ880239	W33	86	99.86	LTR
HQ880240	W34	82	100	DNA transposon
HQ880241	W35	80	100	Retro	EST

Because of the WZ-type chromosome set of females, these repeats are female-specific. ^aCombined Censor, Blast, Teclass results. ^bqPCR based. LINE, long interspersed element; LTR, long terminal repeat.
Lepesant et al. Genome Biology 2012 13:R14 doi:10.1186/gb-2012-13-2-r14

Table 2