Search for SINE repeats in the rice genome using correlation-based position weight matrices

BMC Bioinformatics

Table 2 The statistics of the SINE copies found in the rice genome by the programs HDRSM and RepeatMasker

(1) Family name	(2) HDRSM	(3) RM	HDRSM			RM
(1) Family name	(2) HDRSM	(3) RM	(4) Overlap, same family	(5) Overlap, other family	(6) Not found	(7) Overlap, same family	(8) Overlap, other family	(9) Not found
Os0006	854	323	69	668	117	69	121	133
Os0106	716	945	648	10	58	649	241	55
Os0277	261	133	17	157	87	17	59	57
Os0358	76	220	18	0	58	18	0	202
Os0509	418	407	281	0	137	281	2	124
Os0580	155	104	19	75	61	20	13	71
Os0604	55	53	24	7	24	25	14	14
Os0642	201	136	22	17	162	22	26	88
Os0660	171	179	51	1	119	51	2	126
Os0751	942	1292	641	10	291	648	30	614
Os1022	160	135	80	4	76	81	4	50
Os1374	507	364	139	40	328	139	32	193
Os1424	188	141	32	31	125	32	20	89
Os1427	144	131	98	0	46	98	1	32
Os1605	54	37	10	0	44	10	0	27
Os1611	86	91	63	2	21	63	1	27
Os1635	372	511	216	2	154	217	0	294
Os1661	55	75	15	7	33	15	16	44
Os1716	613	401	222	4	387	245	4	152
Os1815	1441	458	225	1	1215	230	2	226
Os1867	152	70	14	79	59	14	5	51
Os1922	391	289	92	2	297	92	0	197
Os2220	493	524	193	17	283	195	57	272
Os2338	325	351	46	52	227	48	15	288
Os2393	272	297	42	42	188	42	43	212
Os3050	329	284	115	3	211	127	0	157
RST-Osativa-Cluster_0	380	78	14	297	69	14	51	13
RST-Osativa-Cluster_1	137	291	6	98	33	6	259	26
RST-Osativa-Cluster_10	527	648	395	11	121	397	141	110
RST-Osativa-Cluster_11	174	21	4	137	33	4	3	14
RST-Osativa-Cluster_12	299	30	14	237	48	15	9	6
RST-Osativa-Cluster_2	1676	2991	1302	91	283	1359	1039	593
RST-Osativa-Cluster_3	305	117	9	249	47	9	87	21
RST-Osativa-Cluster_4	209	189	7	162	40	7	136	46
RST-Osativa-Cluster_5	147	331	35	73	39	35	232	64
RST-Osativa-Cluster_6	235	201	51	129	55	52	99	50
RST-Osativa-Cluster_7	241	323	50	139	52	50	206	67
RST-Osativa-Cluster_8	238	102	8	175	55	8	45	49
RST-Osativa-Cluster_9	31	29	0	10	21	0	8	21
Total	14,030	13,302	5287	3039	5704	5404	3023	4875

Column 1—family name; Column 2—the number of copies of the family found by HDRSM; Column 3—the number of copies of the family found by RepeatMasker; Column 4—the number of copies of the family found by HDRSM that intersected with the result of RepeatMasker, and family names match; Column 5—the number of copies of the family found by HDRSM that intersected with RepeatMasker, but the family names do not match; Column 6—the number of copies of the family found by HDRSM but missed by RepeatMasker; Column 7—the number of copies of the family found by RepeatMasker that intersected with the HDRSM, and family names match; Column 8—the number of copies of the family found by RepeatMasker that intersected with the HDRSM, but the family names do not match; Column 9—number of copies of the family found by RepeatMasker but missed by HDRSM

ISSN: 1471-2105