genome.fa.s2875.2.7.7.80.10.50.1000.4.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: VEPZ01002875.1 Hibiscus syriacus cultivar Beakdansim tig00005929_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1473696

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 570 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)
987631--987698	17	3.7	16	71	28	55	48	5	4	41	1.47
1003746--1003773	2	14.0	2	100	0	56	50	0	0	50	1.00
1009982--1010094	60	1.9	60	81	3	138	37	15	15	32	1.88
1023116--1023223	53	2.0	53	89	3	164	29	15	17	37	1.91
1027027--1027083	29	2.0	29	89	3	89	45	3	8	42	1.52
1036337--1036425	30	3.0	30	75	8	92	48	1	2	48	1.21
1039642--1039667	13	2.0	13	100	0	52	30	23	7	38	1.83
1043240--1043269	15	2.0	15	93	0	51	60	0	16	23	1.36
1043358--1043428	28	2.5	28	76	15	74	78	1	7	12	1.00
1043417--1043479	30	2.1	29	85	5	81	73	0	3	23	0.98
1043378--1043489	39	2.8	39	85	4	136	73	0	5	20	1.09
1043473--1043499	2	13.5	2	100	0	54	51	0	0	48	1.00
1043536--1043593	24	2.3	25	82	14	75	67	3	3	25	1.22
1043536--1043606	24	3.0	23	82	15	74	69	2	4	23	1.20
1043946--1044014	34	2.0	34	94	0	120	31	14	11	42	1.82
1044610--1044868	98	2.6	98	80	5	277	20	20	24	34	1.97
1045672--1045800	31	3.9	31	71	17	75	34	12	20	33	1.90
1045574--1045766	67	2.8	67	83	3	233	38	12	19	29	1.88
1045721--1045836	34	3.4	34	89	5	166	31	10	19	37	1.86
1046597--1046641	21	2.1	21	83	0	54	31	31	24	13	1.93
1047368--1047433	31	2.1	31	83	5	80	30	19	18	31	1.96
1047421--1047580	30	5.3	30	93	1	232	21	20	25	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1050798--1050842	21	2.1	21	83	0	54	31	31	24	13	1.93
1051622--1051776	30	5.1	30	93	1	240	21	21	25	30	1.99
1052450--1052795	36	10.1	36	69	18	140	39	11	18	30	1.86
1052569--1052627	30	2.0	30	83	6	75	33	10	15	40	1.81
1052582--1052884	102	3.0	102	89	3	450	37	12	18	31	1.89
1052713--1052795	37	2.3	36	83	6	98	39	12	20	27	1.88
1054073--1054426	183	1.9	183	96	0	654	29	21	21	27	1.98
1057226--1057331	53	2.0	53	100	0	212	41	20	15	22	1.89
1058239--1058268	15	2.0	15	100	0	60	60	0	20	20	1.37
1058242--1058276	15	2.3	15	90	0	52	65	0	17	17	1.27
1058367--1058422	21	2.8	20	78	10	60	80	1	7	10	0.97
1058361--1058436	38	2.0	39	85	12	104	76	1	6	15	1.06
1058356--1058467	13	9.1	12	71	13	59	75	0	4	19	1.03
1058521--1058578	24	2.3	25	80	14	66	67	5	3	24	1.27
1058543--1058604	23	2.8	22	75	20	58	67	4	6	20	1.32
1058919--1058987	34	2.0	34	91	5	113	31	13	11	43	1.79
1062756--1062814	11	5.2	11	74	8	55	57	0	6	35	1.25
1062755--1062825	35	2.0	35	97	0	133	54	0	9	35	1.33
1067501--1067571	26	2.6	27	80	12	74	61	5	1	30	1.27
1068767--1068837	3	23.3	3	82	5	81	60	0	0	39	0.97
1078956--1078986	16	1.9	16	93	0	53	16	12	9	61	1.56
1083219--1083274	29	1.9	29	92	0	94	37	7	7	48	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1087664--1087700	2	19.0	2	94	5	67	48	0	0	51	1.00
1096108--1096152	21	2.1	21	100	0	90	33	6	24	35	1.82
1097729--1097820	45	2.0	45	95	0	166	39	15	26	19	1.91
1104823--1104907	42	2.0	42	100	0	170	30	14	22	32	1.93
1113064--1113177	35	3.3	35	87	0	165	42	21	0	35	1.59
1113171--1113245	35	2.1	35	90	0	114	36	1	18	44	1.59
1113222--1113293	24	3.0	24	66	28	62	37	5	13	43	1.68
1113950--1114301	174	2.0	178	96	3	660	28	13	13	44	1.82
1114789--1114839	8	5.9	8	84	11	57	43	0	0	56	0.99
1114770--1114838	28	2.5	27	83	9	86	44	0	1	53	1.09
1114764--1114829	14	5.0	14	73	17	52	45	0	1	53	1.09
1114764--1114842	28	2.6	27	80	13	77	44	0	1	54	1.08
1117674--1117705	3	10.7	3	100	0	64	65	0	0	34	0.93
1123623--1123741	60	2.0	61	80	5	134	36	13	15	34	1.87
1123647--1123760	60	1.9	59	80	8	133	35	14	15	33	1.89
1124199--1124274	33	2.3	33	93	0	125	22	27	35	14	1.93
1124198--1124277	10	7.4	10	68	15	52	22	27	36	13	1.92
1124303--1124378	29	2.6	29	87	0	107	22	30	34	13	1.92
1124648--1124674	2	13.5	2	100	0	54	51	0	0	48	1.00
1135557--1135603	2	23.5	2	100	0	94	48	0	0	51	1.00
1135959--1136064	32	3.4	31	80	3	95	38	30	10	20	1.86
1136315--1136342	2	14.0	2	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1138534--1138675	8	17.8	8	91	0	221	26	11	23	38	1.88
1140791--1140824	14	2.4	14	95	0	59	32	20	0	47	1.51
1142174--1142244	33	2.2	33	94	0	124	47	16	23	11	1.79
1142624--1142795	20	8.6	20	87	3	240	20	19	27	33	1.96
1144386--1144434	2	25.5	2	87	8	75	53	0	0	46	1.00
1144604--1144633	15	2.0	15	93	0	51	53	6	3	36	1.44
1145792--1145856	3	22.0	3	75	9	62	56	0	0	43	0.99
1152450--1152482	16	2.0	17	88	5	50	69	0	6	24	1.10
1152543--1152732	96	2.0	96	100	0	380	32	14	21	32	1.93
1157343--1157413	27	2.8	25	81	14	74	42	5	0	52	1.25
1157365--1157413	24	2.0	26	88	8	75	38	4	0	57	1.18
1157605--1157631	13	2.1	13	100	0	54	40	0	37	22	1.54
1158216--1158247	6	5.3	6	100	0	64	0	18	46	34	1.49
1158323--1158418	41	2.6	34	78	20	120	39	20	18	20	1.92
1158353--1158422	19	3.5	19	74	11	77	40	21	20	18	1.92
1158343--1158443	19	4.9	20	68	11	71	37	23	19	18	1.94
1158343--1158463	41	2.9	41	93	3	199	38	23	20	17	1.93
1158435--1158589	20	7.6	20	74	4	148	38	24	20	16	1.92
1158432--1158614	41	4.5	41	97	0	339	37	24	19	18	1.94
1158432--1158611	20	8.8	21	71	4	143	37	24	19	18	1.94
1158391--1158614	82	2.7	82	91	4	346	37	24	19	18	1.93
1158350--1158614	123	2.1	122	85	9	344	38	23	19	18	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1159177--1159227	20	2.5	20	90	0	84	45	11	19	23	1.83
1159385--1159459	37	2.0	37	82	10	91	48	4	1	46	1.29
1160275--1160319	21	2.1	21	83	0	54	53	4	11	31	1.56
1161602--1161800	21	9.6	21	83	11	234	30	24	20	24	1.99
1161602--1161819	41	5.3	41	92	4	268	31	23	20	24	1.98
1161706--1161819	20	5.6	20	76	19	128	33	19	21	25	1.97
1161809--1161862	21	2.6	21	82	5	65	22	22	27	27	1.99
1161851--1161891	20	2.0	20	100	0	82	24	19	14	41	1.89
1161892--1162015	21	5.9	21	84	5	153	29	23	21	25	1.99
1162024--1162079	29	1.9	29	96	0	103	25	21	25	28	1.99
1162050--1162147	21	4.7	21	76	16	105	23	19	25	31	1.98
1171481--1171545	26	2.5	26	80	7	69	49	24	12	13	1.77
1177275--1177330	12	4.5	12	72	16	51	46	0	1	51	1.11
1182141--1182185	22	2.0	22	83	8	56	26	0	13	60	1.34
1182820--1182860	2	20.5	2	100	0	82	48	0	0	51	1.00
1183292--1183345	2	27.0	2	100	0	108	50	0	0	50	1.00
1195951--1196019	2	34.5	2	100	0	138	50	0	0	49	1.00
1198915--1198984	21	3.5	20	76	7	79	35	1	1	61	1.14
1211424--1211498	39	1.9	39	83	5	98	26	26	20	26	1.99
1214252--1214510	129	2.0	129	100	0	518	33	12	16	37	1.86
1215633--1215767	67	2.0	68	95	1	245	34	27	12	25	1.92
1219916--1220106	95	2.0	95	92	6	325	26	25	15	32	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1228762--1228866	19	5.4	18	72	13	84	50	0	0	49	1.00
1228762--1228844	23	4.0	22	73	20	88	51	0	0	48	1.00
1228798--1228874	15	5.3	15	73	17	56	50	0	0	49	1.00
1228775--1228872	40	2.5	38	87	6	142	51	0	0	48	1.00
1228780--1228866	40	2.2	40	95	0	156	50	0	0	49	1.00
1229615--1229673	32	1.9	31	82	6	75	28	1	11	57	1.44
1229685--1229709	2	12.5	2	100	0	50	48	0	0	52	1.00
1230521--1230831	156	2.0	156	100	0	622	25	16	22	35	1.95
1232087--1232227	69	2.0	70	86	1	194	23	21	17	38	1.93
1232353--1232434	41	2.0	41	100	0	164	29	9	29	31	1.89

Tables:   1   2   3   4   5