genome.fa.s761.2.7.7.80.10.50.1000.20.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: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5609167

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   

This is table  20  of  23  ( 2686 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)
4839536--4839601	25	2.6	26	78	9	73	66	12	3	18	1.36
4841772--4841824	16	3.2	17	81	10	56	66	3	0	30	1.10
4841795--4841827	17	1.9	17	100	0	66	60	9	0	30	1.27
4843950--4843974	3	8.3	3	100	0	50	64	0	0	36	0.94
4844046--4844113	31	2.2	31	86	0	91	29	13	10	47	1.75
4844287--4844363	26	3.1	24	81	14	77	51	0	2	45	1.14
4844287--4844351	22	2.7	24	86	9	80	52	0	3	44	1.16
4844325--4844384	26	2.3	27	82	2	68	48	0	5	46	1.24
4854057--4854112	23	2.5	22	85	5	67	33	26	17	21	1.96
4854219--4854259	14	2.9	15	82	7	50	31	26	12	29	1.92
4854735--4854775	20	2.0	20	85	0	55	31	14	12	41	1.83
4854966--4855047	41	2.0	41	100	0	164	29	26	7	36	1.83
4857511--4857559	20	2.6	19	83	6	55	34	10	26	28	1.89
4858077--4858312	49	4.8	49	93	0	391	36	14	22	27	1.93
4865116--4865352	49	4.8	49	93	0	393	38	15	19	26	1.92
4866946--4867379	215	2.0	217	98	1	845	33	22	12	32	1.91
4870369--4870440	23	3.3	22	83	13	78	33	27	13	25	1.94
4871064--4871103	20	2.0	20	85	0	53	35	15	10	40	1.80
4873865--4874140	141	2.0	141	96	3	515	21	27	14	36	1.93
4874759--4874831	31	2.4	31	88	0	101	31	17	20	30	1.96
4874814--4874885	31	2.3	31	85	4	92	30	30	12	26	1.93
4878225--4878250	3	8.7	3	100	0	52	0	34	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4881102--4881136	14	2.5	14	100	0	70	5	57	31	5	1.46
4881452--4881485	9	3.9	9	84	7	52	32	0	2	64	1.08
4883728--4883775	13	3.6	13	83	5	60	16	2	12	68	1.29
4889733--4891193	243	6.0	246	97	1	2752	33	23	16	26	1.95
4889733--4891185	728	2.0	731	97	1	2756	33	23	16	26	1.95
4891347--4891411	34	1.9	34	100	0	130	32	24	15	27	1.95
4893827--4893913	29	3.0	29	86	3	122	22	26	34	16	1.95
4894013--4894066	12	4.7	11	80	8	63	20	22	16	40	1.91
4894012--4894093	23	3.6	22	83	8	110	21	21	14	41	1.89
4894323--4894445	39	3.2	39	97	1	230	39	2	16	42	1.61
4894506--4894558	28	1.9	27	88	3	79	32	1	16	49	1.57
4895219--4895277	19	3.2	19	69	26	63	45	16	11	25	1.82
4895221--4895292	36	2.0	36	94	0	126	41	15	12	30	1.84
4898917--4898979	28	2.2	30	88	5	94	57	12	0	30	1.36
4898956--4898999	21	2.1	21	95	0	79	54	13	0	31	1.39
4898921--4898986	28	2.4	28	82	10	89	56	12	0	31	1.36
4899564--4899617	28	1.9	28	96	0	99	27	33	16	22	1.95
4899631--4899674	23	1.9	23	95	0	79	20	31	29	18	1.96
4903356--4903548	45	4.3	45	89	0	278	21	20	11	45	1.83
4910176--4910458	45	6.3	45	90	0	413	22	22	11	43	1.84
4919628--4919717	44	2.0	44	93	0	153	31	18	8	41	1.82
4925792--4925929	23	6.0	23	89	0	177	31	22	24	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4927557--4927612	20	2.8	20	86	5	78	17	28	23	30	1.97
4931469--4931525	30	1.9	30	89	7	89	29	17	8	43	1.79
4932400--4932448	23	2.1	23	96	0	89	48	0	4	46	1.20
4932803--4933006	31	6.4	30	74	20	166	49	3	4	42	1.39
4932810--4932856	24	1.9	25	82	4	60	55	4	2	38	1.31
4932866--4932927	14	4.4	14	76	15	56	45	1	6	46	1.38
4932893--4932981	15	5.6	15	69	19	56	50	3	3	42	1.35
4932846--4933029	21	8.5	21	68	19	85	47	3	5	42	1.46
4932808--4933065	131	2.0	131	82	9	321	48	4	5	41	1.47
4933072--4933139	22	3.1	21	82	12	84	45	5	7	41	1.56
4933088--4933213	39	3.2	40	73	13	116	42	7	8	41	1.63
4933113--4933152	17	2.4	17	87	4	55	42	10	7	40	1.67
4933236--4933283	14	3.4	14	79	0	51	20	2	27	50	1.60
4933419--4933458	20	2.0	20	90	0	62	40	10	5	45	1.60
4933669--4933704	7	5.0	7	86	6	54	33	0	0	66	0.92
4933667--4933701	15	2.4	15	90	4	54	37	0	0	62	0.95
4933734--4933773	17	2.4	17	86	0	53	52	2	0	45	1.14
4933757--4933830	21	3.6	21	77	10	64	47	5	2	44	1.40
4933709--4933958	20	12.3	20	69	15	95	47	4	3	45	1.39
4933842--4933959	10	11.3	11	70	13	63	46	3	5	44	1.42
4933922--4933963	2	21.5	2	95	4	77	50	0	0	50	1.00
4935250--4935357	20	5.5	20	73	13	82	29	23	11	36	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4936254--4936323	24	2.9	24	80	0	77	30	17	14	38	1.89
4938274--4938371	21	4.7	21	87	6	137	24	18	35	21	1.95
4938668--4938707	21	1.9	21	94	0	71	37	32	12	17	1.87
4938789--4938828	21	1.9	21	94	0	71	37	35	10	17	1.83
4938947--4939045	42	2.4	42	87	0	144	18	17	35	29	1.93
4940546--4940611	20	3.3	20	82	0	87	51	19	13	15	1.76
4940541--4940626	40	2.2	39	85	4	118	51	18	12	17	1.76
4940628--4940679	20	2.6	20	87	0	77	13	15	21	50	1.78
4941013--4941085	22	3.3	22	88	0	92	28	17	36	16	1.92
4941572--4941619	22	2.2	23	77	11	55	41	0	6	52	1.27
4941578--4941620	22	2.0	21	86	4	59	44	0	6	48	1.29
4952141--4952725	85	6.9	85	85	2	710	27	18	20	34	1.96
4952786--4953244	86	5.3	86	90	0	720	19	21	27	31	1.98
4954411--4954638	95	2.6	87	79	10	239	30	21	17	30	1.96
4954460--4954648	95	2.0	95	88	4	283	28	20	16	34	1.94
4958605--4958648	19	2.4	19	92	7	74	79	0	2	18	0.83
4959639--4959684	14	3.3	14	93	0	83	6	15	26	52	1.67
4960491--4960553	11	5.6	11	94	3	99	26	12	26	33	1.93
4960491--4960553	23	2.8	22	90	4	99	26	12	26	33	1.93
4960788--4960837	16	3.1	16	94	0	82	12	12	22	54	1.69
4961968--4962087	60	2.0	60	100	0	240	35	25	20	20	1.96
4968026--4968394	183	2.0	180	96	2	686	36	17	13	31	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4972998--4973129	54	2.4	53	82	5	156	31	18	14	36	1.90
4973098--4973225	54	2.4	54	78	10	145	24	17	21	35	1.95
4974840--4974900	30	2.0	30	93	0	104	54	9	9	26	1.64
4975972--4976002	13	2.4	13	100	0	62	19	0	32	48	1.49
4978807--4978901	29	3.3	29	92	2	156	27	10	10	51	1.69
4980164--4980194	15	2.1	15	93	0	53	29	0	16	54	1.42
4980644--4980675	16	2.0	16	93	0	55	34	6	25	34	1.81
4983947--4983976	15	2.0	15	93	0	51	30	6	16	46	1.73
4991369--4991394	2	13.0	2	100	0	52	50	0	0	50	1.00
4991551--4991589	13	2.9	14	84	7	53	35	2	0	61	1.10
5001315--5001341	12	2.2	12	100	0	54	14	25	40	18	1.89
5001339--5001376	9	4.1	9	86	6	58	13	21	44	21	1.85
5001322--5001374	19	2.9	19	88	5	74	11	22	45	20	1.83
5001376--5001444	10	7.1	9	73	15	57	28	27	28	14	1.95
5001376--5001444	20	3.5	20	79	14	74	28	27	28	14	1.95
5007887--5007939	20	2.7	19	82	8	61	30	24	26	18	1.98
5012191--5012244	2	27.0	2	100	0	108	50	0	0	50	1.00
5013030--5013063	6	5.7	6	92	0	59	0	50	0	50	1.00
5018718--5018800	39	2.1	39	100	0	166	45	7	2	44	1.44
5021290--5021347	25	2.3	25	96	0	107	5	37	0	56	1.21
5021979--5022042	30	2.1	31	85	8	87	48	7	14	29	1.71
5025115--5025174	19	3.2	19	84	11	79	15	23	30	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5025121--5025168	9	5.1	9	75	9	51	14	25	31	29	1.95
5025176--5025211	17	2.1	17	100	0	72	16	50	22	11	1.77
5028844--5028933	32	2.9	30	85	6	126	30	23	21	25	1.99
5037496--5037826	118	2.8	118	93	0	554	24	12	21	41	1.87
5038584--5038615	2	16.0	2	100	0	64	50	0	0	50	1.00
5049481--5049565	22	3.9	22	96	0	152	36	12	23	27	1.91
5049535--5049702	81	2.1	81	89	2	257	38	11	22	27	1.89
5049681--5049725	23	2.0	23	100	0	90	44	0	26	28	1.55
5049595--5049807	104	2.0	104	88	1	320	38	11	22	27	1.89
5049525--5050061	185	2.9	185	93	0	869	36	12	22	28	1.90

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23