genome.fa.s1279.2.7.7.80.10.50.1000.18.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   

This is table  18  of  29  ( 3433 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)
4039158--4039209	20	2.6	20	93	0	95	36	15	17	30	1.91
4039890--4039933	11	4.0	11	96	0	79	27	20	0	52	1.47
4042998--4043027	2	15.5	2	93	6	53	46	0	0	53	1.00
4042945--4043031	32	2.6	33	78	8	97	34	2	1	62	1.16
4043026--4043059	17	1.9	18	88	5	52	20	5	0	73	1.04
4043230--4043275	20	2.3	20	88	0	65	17	6	0	76	1.00
4043241--4043284	11	4.3	11	86	13	67	15	4	0	79	0.89
4043240--4043321	20	4.4	19	73	13	64	14	6	4	74	1.18
4043241--4043284	20	2.2	20	95	4	79	15	4	0	79	0.89
4046382--4046541	45	3.6	45	90	0	230	43	10	15	31	1.80
4047985--4048161	94	1.9	94	83	6	234	39	10	22	27	1.87
4048583--4048720	46	3.0	46	91	0	222	45	12	19	22	1.83
4048595--4048740	20	6.7	20	72	17	112	43	11	21	22	1.85
4048642--4048786	66	2.2	66	93	0	245	44	11	22	22	1.84
4048707--4048837	46	2.8	46	87	0	190	43	10	22	22	1.84
4048595--4048832	112	2.1	112	90	0	368	44	10	22	22	1.84
4055598--4055713	46	2.5	46	85	0	160	42	13	21	22	1.88
4055626--4055720	26	3.9	26	72	16	103	41	14	24	20	1.89
4057034--4057111	38	2.1	38	100	0	156	37	10	12	39	1.78
4067652--4067691	21	2.0	21	90	5	64	40	17	17	25	1.91
4079551--4079615	34	1.9	33	84	3	85	52	10	12	24	1.71
4092333--4092361	15	1.9	15	100	0	58	51	6	13	27	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4092328--4092363	15	2.5	14	86	8	54	52	5	11	30	1.59
4094421--4094455	15	2.3	15	90	0	52	37	8	0	54	1.31
4095689--4095791	3	34.7	3	85	9	140	35	0	0	63	1.01
4096576--4096604	13	2.2	13	100	0	58	0	31	62	6	1.22
4097045--4097069	13	1.9	13	100	0	50	84	0	0	16	0.63
4097138--4097171	17	2.0	17	94	0	59	26	0	5	67	1.13
4108392--4108488	21	4.6	21	76	10	99	82	0	17	0	0.67
4108392--4108488	30	3.5	26	79	18	106	82	0	17	0	0.67
4108398--4108487	36	2.6	33	83	13	119	82	0	17	0	0.68
4109422--4109872	51	8.8	51	99	0	857	24	13	23	38	1.91
4110294--4111795	328	4.6	334	86	8	2088	37	13	19	29	1.90
4111295--4111337	22	1.9	23	85	4	61	48	9	27	13	1.73
4112077--4112184	3	37.0	3	89	5	168	35	0	0	63	1.01
4112949--4112977	13	2.2	13	100	0	58	0	31	62	6	1.22
4113522--4113557	19	1.9	19	94	5	65	22	0	5	72	1.05
4113586--4113625	19	2.0	20	85	4	55	37	2	2	57	1.26
4125460--4125484	2	12.5	2	100	0	50	48	0	0	52	1.00
4129174--4129219	18	2.6	17	83	10	56	50	0	0	50	1.00
4128869--4129289	227	1.9	219	87	7	622	34	18	10	36	1.85
4130405--4130444	18	2.2	19	90	4	64	45	0	0	55	0.99
4130868--4130937	2	38.5	2	78	18	73	45	0	0	54	0.99
4130973--4130997	6	4.2	6	100	0	50	0	16	48	36	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4135601--4135632	17	1.9	16	93	6	55	53	3	12	31	1.54
4142957--4143025	34	2.0	34	100	0	138	42	26	11	20	1.86
4151023--4151062	4	9.8	4	84	15	55	72	0	2	25	0.97
4151023--4151062	18	2.2	19	90	4	64	72	0	2	25	0.97
4151056--4151102	25	1.9	24	82	4	58	74	2	12	10	1.16
4151155--4151199	2	22.5	2	100	0	90	51	0	0	48	1.00
4151183--4151470	134	2.1	132	84	7	375	46	13	12	27	1.78
4151218--4151510	135	2.2	129	80	8	336	48	12	12	26	1.77
4153442--4153527	34	2.5	34	94	0	145	23	18	23	34	1.96
4153681--4153805	43	2.9	43	84	0	169	23	16	29	31	1.96
4156102--4156157	21	2.7	21	94	0	103	19	25	28	26	1.99
4156962--4157042	23	3.7	22	82	11	87	25	22	30	20	1.98
4160793--4160832	21	1.9	21	90	10	64	32	7	5	55	1.50
4162786--4162825	21	1.9	21	100	0	80	10	25	37	27	1.88
4166987--4167043	26	2.2	26	100	0	114	28	14	19	38	1.90
4172331--4172466	4	32.2	4	76	16	91	75	0	5	18	1.05
4172320--4172451	22	6.0	21	72	15	83	75	0	7	16	1.08
4172316--4172477	21	8.0	20	72	16	95	75	0	7	16	1.06
4172334--4172473	14	10.2	13	71	18	81	75	0	6	17	1.05
4172331--4172466	25	5.2	26	69	20	88	75	0	5	18	1.05
4172331--4172477	29	5.0	28	75	15	113	75	0	6	17	1.04
4172313--4172454	74	2.0	70	83	8	178	75	0	7	16	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4172399--4172477	5	16.4	5	74	19	62	78	0	5	16	0.92
4172313--4172454	70	2.0	70	81	13	164	75	0	7	16	1.07
4172387--4172477	18	4.9	19	71	22	52	78	0	6	15	0.95
4172331--4172490	43	3.9	41	72	18	120	74	0	6	18	1.08
4172488--4172524	2	18.5	2	100	0	74	51	0	0	48	1.00
4172487--4172574	14	6.7	13	73	19	67	55	3	1	39	1.24
4172514--4172804	134	2.1	135	91	5	471	46	14	12	26	1.80
4172783--4172857	33	2.3	32	82	11	89	61	5	1	32	1.27
4172539--4172838	134	2.2	131	84	9	397	48	14	12	25	1.78
4174294--4174447	47	3.3	47	91	0	238	28	10	18	42	1.83
4174280--4174475	93	2.1	94	84	2	252	29	11	17	42	1.84
4176456--4176542	44	2.0	44	86	4	122	41	1	2	55	1.20
4186305--4186344	20	2.0	20	100	0	80	35	0	30	35	1.58
4187238--4187272	17	2.1	17	88	0	52	57	0	0	42	0.99
4189517--4189563	20	2.3	20	100	0	94	40	17	12	29	1.86
4190512--4190545	17	2.0	17	94	0	59	23	44	17	14	1.86
4196393--4196473	32	2.5	32	95	0	144	38	13	17	30	1.88
4199653--4199716	25	2.6	24	78	11	67	23	4	1	70	1.15
4199685--4199845	36	4.4	37	73	16	106	22	6	0	70	1.13
4199711--4199768	27	2.1	28	84	9	75	24	3	0	72	1.00
4199685--4199756	34	2.1	36	84	10	96	22	2	0	75	0.94
4211771--4211905	37	3.7	37	80	9	143	42	2	11	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4211957--4212026	24	3.0	24	82	2	79	40	1	7	51	1.38
4211897--4212011	60	1.9	59	82	3	142	36	3	6	53	1.45
4212007--4212064	10	6.2	10	72	22	54	34	0	0	65	0.93
4213270--4213313	20	2.2	20	80	4	54	27	0	0	72	0.85
4230289--4230338	26	1.9	26	91	0	82	48	8	8	36	1.62
4231019--4231132	47	2.4	46	86	5	165	28	23	18	29	1.98
4239233--4239331	49	2.0	48	90	5	155	42	10	4	43	1.57
4241062--4241110	13	3.6	13	78	10	53	10	12	2	75	1.13
4241062--4241115	28	1.9	28	88	0	81	11	12	1	74	1.16
4248034--4248110	21	3.6	21	74	10	66	27	22	16	33	1.95
4257226--4257299	36	2.1	36	100	0	148	32	25	18	22	1.97
4261448--4261544	51	1.9	51	86	0	140	28	21	23	25	1.99
4266828--4266882	22	2.5	22	90	0	83	29	29	25	16	1.97
4271571--4271605	18	1.9	18	88	0	52	28	31	20	20	1.97
4278788--4278821	18	1.9	18	88	5	52	17	26	29	26	1.98
4285537--4285600	2	32.0	2	93	6	112	48	0	1	50	1.10
4288690--4288762	24	3.0	24	88	6	76	35	0	21	42	1.54
4288705--4288762	24	2.4	24	97	0	107	31	0	22	46	1.52
4296846--4296931	45	1.9	45	85	0	118	27	12	40	18	1.87
4315378--4315407	2	15.0	2	100	0	60	50	0	0	50	1.00
4316532--4316582	20	2.5	20	100	0	102	25	23	15	35	1.94
4322130--4322203	33	2.2	33	90	0	112	24	25	14	35	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4324154--4324274	2	64.5	2	80	15	125	48	1	0	48	1.17
4325146--4325331	74	2.5	73	82	3	232	20	23	21	34	1.96
4325146--4325359	73	2.9	74	80	3	227	21	22	20	35	1.96
4335182--4336379	6	205.3	6	90	8	1944	32	0	17	49	1.48
4343468--4343544	34	2.2	36	80	15	92	46	0	0	53	1.00
4343468--4343553	38	2.3	37	82	7	111	47	0	0	52	1.00
4351068--4351118	2	25.5	2	92	7	86	50	1	0	47	1.12
4351123--4351161	17	2.3	17	90	0	60	41	12	5	41	1.65
4353608--4353843	110	2.1	110	98	0	454	47	13	12	26	1.79
4370314--4370692	187	2.0	190	95	4	689	41	9	11	37	1.74

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29