genome.fa.s1444.2.7.7.80.10.50.1000.5.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2564052

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   

This is table  5  of  12  ( 1400 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1100382--1100532	29	5.1	30	82	10	179	52	0	5	41	1.29
1100377--1100513	60	2.3	60	93	1	231	51	0	5	43	1.26
1100987--1101111	21	6.0	21	70	14	96	25	20	19	34	1.96
1100991--1101104	42	2.7	42	88	0	174	25	20	19	35	1.96
1101201--1101252	6	9.2	6	87	12	83	34	48	17	0	1.48
1101201--1101247	15	2.9	15	90	9	67	34	48	17	0	1.47
1101210--1101252	21	2.0	21	100	0	86	34	46	18	0	1.50
1101991--1102181	19	9.3	19	73	16	148	35	22	19	22	1.96
1101994--1102182	42	4.5	42	83	8	242	35	22	19	21	1.96
1102187--1102237	21	2.4	21	86	0	75	19	17	31	31	1.95
1111088--1111140	27	2.0	27	100	0	106	24	18	22	33	1.97
1112352--1112404	2	27.0	2	96	3	99	50	0	0	49	1.00
1114115--1114180	27	2.4	28	75	12	75	57	0	9	33	1.30
1114644--1114698	4	13.8	4	81	7	67	27	49	23	0	1.51
1116264--1116514	124	2.0	124	100	0	502	33	19	16	31	1.94
1118252--1118298	21	2.2	21	96	0	85	38	12	42	6	1.69
1118252--1118311	21	2.9	21	89	0	75	36	15	40	8	1.77
1119327--1119390	21	2.9	23	82	15	89	29	23	18	28	1.98
1119327--1119428	45	2.3	45	83	6	127	29	20	20	29	1.98
1125209--1125367	64	2.5	64	78	13	150	28	16	22	32	1.96
1125564--1126019	241	1.9	241	98	0	885	41	7	14	36	1.73
1128411--1128537	31	4.1	31	74	5	121	30	16	17	35	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1129371--1129418	25	1.9	25	95	0	87	35	4	14	45	1.64
1132237--1132281	16	2.8	17	80	10	58	28	4	24	42	1.74
1134644--1134724	28	3.1	28	60	23	68	33	6	28	32	1.82
1134628--1134724	49	2.0	49	100	0	194	30	6	25	37	1.81
1138450--1138510	2	29.5	2	78	15	54	47	1	4	45	1.34
1141013--1141070	20	2.6	22	86	10	75	31	18	22	27	1.97
1141958--1142085	31	4.1	31	76	8	125	28	17	19	33	1.95
1147245--1147295	20	2.5	20	87	0	66	13	11	15	58	1.63
1148066--1148125	18	3.2	18	72	23	52	55	5	0	40	1.22
1148132--1148222	17	5.4	17	68	15	71	47	6	2	43	1.41
1148117--1148213	51	1.9	51	97	0	185	49	5	3	42	1.40
1148183--1148223	17	2.4	17	95	0	73	46	7	0	46	1.30
1154204--1154287	18	4.5	19	77	15	77	45	1	0	53	1.08
1154223--1154289	3	22.3	3	81	6	73	41	1	0	56	1.08
1154205--1154284	15	5.8	14	73	16	60	45	1	0	53	1.08
1160248--1160292	21	2.1	21	87	0	63	28	24	17	28	1.97
1164803--1164845	20	2.1	21	87	8	63	18	13	0	67	1.23
1164802--1164851	20	2.5	20	75	15	59	18	18	0	64	1.30
1169200--1169449	76	3.3	75	88	1	356	34	15	22	28	1.94
1169642--1169775	54	2.5	54	85	0	160	38	12	22	26	1.90
1170142--1170196	22	2.5	22	90	0	83	32	14	10	41	1.81
1170918--1171021	45	2.3	45	88	0	145	27	18	20	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1171039--1171140	45	2.3	45	86	3	136	27	20	18	33	1.96
1170865--1171216	119	2.9	120	92	1	553	25	20	21	32	1.97
1171082--1171300	76	2.9	76	91	2	336	24	20	21	33	1.97
1171158--1171587	121	3.6	121	90	1	686	23	20	21	33	1.97
1171234--1171321	45	2.0	45	97	0	167	22	23	20	32	1.98
1170963--1171421	197	2.4	194	90	2	724	24	20	21	33	1.97
1171355--1171468	45	2.5	45	84	5	131	24	21	20	34	1.97
1171476--1171634	45	3.5	45	92	1	246	23	23	22	30	1.99
1171355--1171667	166	1.9	166	90	1	502	23	21	20	34	1.97
1171400--1171542	76	1.9	74	89	2	223	24	20	20	34	1.97
1170865--1171542	316	2.1	315	90	2	1063	24	20	21	33	1.97
1171824--1171882	3	19.7	3	85	0	82	40	0	0	59	0.97
1174313--1174534	111	2.0	111	98	0	426	33	8	10	47	1.68
1175288--1175332	22	2.0	22	95	0	81	20	13	35	31	1.91
1196913--1197355	82	5.4	82	85	3	515	34	14	16	33	1.89
1196913--1197355	162	2.7	162	85	3	550	34	14	16	33	1.89
1196916--1197355	244	1.8	244	84	2	614	35	14	16	33	1.89
1199139--1199176	20	1.9	20	84	10	51	10	2	18	68	1.30
1199250--1199304	18	3.1	18	100	0	110	32	10	16	40	1.83
1200123--1200172	12	4.1	12	74	23	50	14	10	10	66	1.46
1200454--1202066	807	2.0	805	98	0	3093	34	17	19	28	1.95
1205684--1205722	20	1.9	20	84	5	51	10	2	17	69	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1208931--1208976	22	2.0	22	83	4	56	43	6	2	47	1.41
1212094--1212192	21	4.7	21	67	9	67	20	18	27	34	1.95
1212206--1212269	33	2.1	31	88	11	96	18	28	26	26	1.98
1212284--1212331	20	2.4	20	96	0	87	45	22	22	8	1.79
1212254--1212360	21	5.2	21	80	2	101	38	26	17	17	1.92
1214829--1214853	11	2.3	11	100	0	50	40	40	0	20	1.52
1223817--1223875	27	2.1	28	96	3	111	42	10	16	30	1.82
1224420--1224444	13	1.9	13	100	0	50	44	8	8	40	1.63
1230505--1230568	20	3.2	20	88	2	67	21	32	28	17	1.96
1230519--1230568	20	2.5	20	96	3	93	20	38	24	18	1.93
1232796--1232854	16	3.9	16	74	17	72	38	0	37	23	1.55
1232805--1232861	28	2.0	28	100	0	114	38	0	36	24	1.56
1235031--1235071	20	2.1	19	90	4	64	36	0	12	51	1.40
1236072--1236125	23	2.3	23	100	0	108	12	25	22	38	1.90
1236085--1236136	23	2.3	23	82	0	59	19	23	28	28	1.98
1236178--1236273	14	7.4	14	69	25	77	40	13	1	44	1.51
1236178--1236242	23	2.9	23	90	2	105	41	13	0	44	1.44
1245253--1245385	65	2.1	64	94	1	230	17	12	16	54	1.71
1245435--1245469	15	2.2	16	90	5	54	8	5	17	68	1.35
1248581--1248694	59	1.9	59	82	3	140	38	0	20	40	1.58
1251357--1251447	44	2.1	44	100	0	182	32	13	4	49	1.61
1252021--1252058	19	2.1	19	85	5	51	26	2	5	65	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1253709--1253791	25	3.6	25	68	25	83	18	2	8	71	1.23
1256747--1256784	13	3.0	13	80	3	51	57	0	0	42	0.98
1263048--1263356	156	2.0	156	94	0	537	33	13	24	29	1.93
1264783--1264812	13	2.3	13	100	0	60	13	13	23	50	1.77
1268635--1268668	2	17.5	2	87	6	52	55	0	0	44	0.99
1269170--1269271	50	2.0	50	80	10	111	40	7	5	46	1.57
1271589--1271787	109	1.8	109	84	2	274	18	24	17	40	1.91
1278462--1278525	31	2.1	31	85	5	85	31	10	9	48	1.70
1278474--1278536	31	2.0	31	87	0	90	25	12	12	49	1.76
1278693--1278753	26	2.4	27	84	12	78	57	0	4	37	1.20
1278708--1278777	25	2.8	23	80	10	68	51	1	5	41	1.34
1283409--1283992	189	3.1	188	83	2	677	34	15	18	31	1.92
1283955--1284040	42	2.0	42	90	0	136	32	15	20	31	1.94
1289374--1289487	43	2.6	43	80	10	124	31	24	11	32	1.91
1291697--1291759	31	2.0	31	96	0	117	19	33	15	31	1.93
1293994--1294018	2	12.5	2	100	0	50	52	0	0	48	1.00
1296573--1296602	15	1.9	16	93	6	53	80	3	0	16	0.85
1296805--1296876	25	3.0	25	80	17	98	43	8	4	44	1.53
1296775--1296948	36	4.5	36	70	25	117	44	7	4	43	1.53
1296805--1296884	22	3.6	21	86	10	97	43	8	3	43	1.53
1304158--1304216	21	2.8	21	100	0	118	52	18	8	20	1.71
1306202--1306241	21	1.9	21	84	0	53	75	7	10	7	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1306855--1306983	40	3.1	40	79	12	136	35	16	20	27	1.94
1306871--1307044	41	4.2	41	75	7	131	35	17	18	29	1.94
1313462--1313497	17	2.1	18	89	5	56	58	0	0	41	0.98
1314806--1314835	2	15.0	2	100	0	60	50	0	0	50	1.00
1314856--1314902	19	2.4	19	85	3	58	44	0	0	55	0.99
1316176--1316238	32	2.0	31	87	3	90	38	17	9	34	1.82
1324251--1324390	20	6.8	21	72	7	90	33	22	16	27	1.95
1324285--1324404	41	2.9	40	85	2	150	34	20	16	28	1.95
1324333--1324410	20	3.9	20	75	5	68	33	17	19	29	1.95
1327218--1327292	21	3.7	20	81	12	89	29	28	21	21	1.98

Tables:   1   2   3   4   5   6   7   8   9   10   11   12