genome.fa.s9605.2.7.7.80.10.50.1000.17.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: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9158330

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   30   31   32   
          33   34   35   

This is table  17  of  35  ( 4090 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)
3781645--3781683	21	1.9	20	89	5	60	56	0	30	12	1.37
3783336--3783928	293	2.0	293	97	0	1105	30	15	25	28	1.96
3787006--3787056	24	2.1	24	96	0	93	27	5	7	58	1.49
3789735--3789762	6	4.7	6	100	0	56	17	50	0	32	1.47
3795537--3795578	23	2.0	22	86	13	61	35	0	14	50	1.43
3795663--3795744	20	3.9	21	88	4	105	23	36	25	14	1.93
3795675--3795766	22	4.2	21	80	10	71	22	41	22	13	1.88
3800022--3800066	20	2.2	20	80	7	56	17	0	35	46	1.49
3802964--3803120	65	2.4	65	89	4	228	29	21	19	29	1.97
3803105--3803158	19	2.8	19	97	0	99	22	29	22	25	1.99
3803143--3803267	54	2.3	54	93	2	216	32	14	16	36	1.89
3808949--3809028	23	3.6	22	76	6	90	25	26	23	25	2.00
3808930--3808997	23	3.2	20	74	13	57	29	25	22	23	1.99
3808930--3809025	44	2.2	43	87	5	131	27	26	21	25	2.00
3809485--3809519	12	2.8	13	82	8	54	37	14	2	45	1.59
3811640--3811796	65	2.4	65	85	0	215	31	20	17	30	1.95
3826929--3826972	9	5.1	9	89	10	74	77	0	22	0	0.77
3826929--3826985	17	3.5	17	88	11	93	75	0	24	0	0.80
3826929--3826985	8	7.1	8	90	9	82	75	0	24	0	0.80
3827069--3827112	17	2.6	17	81	0	52	77	2	6	13	1.07
3828688--3829233	85	6.4	85	81	4	643	24	19	22	33	1.97
3828689--3829233	170	3.2	170	88	1	797	24	19	22	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3829194--3829267	34	2.2	34	87	0	103	25	10	22	40	1.87
3830246--3830432	99	1.9	99	89	0	293	30	19	17	32	1.95
3830795--3831300	252	2.0	253	91	2	820	34	14	15	34	1.88
3831466--3831490	10	2.5	10	100	0	50	92	0	8	0	0.40
3833279--3833327	3	16.7	3	87	12	75	71	0	0	28	0.86
3833186--3833295	40	2.8	38	77	9	114	66	4	6	22	1.33
3834638--3834880	43	5.7	43	79	8	262	33	19	18	28	1.95
3834638--3834921	129	2.2	128	78	8	283	33	18	18	29	1.95
3834645--3834921	86	3.2	86	78	10	282	33	18	18	28	1.95
3839292--3839530	41	5.8	41	81	7	191	37	17	17	27	1.93
3839307--3839535	123	1.9	123	82	5	293	38	17	17	26	1.92
3839345--3839542	41	4.8	41	84	5	240	37	18	17	26	1.93
3839519--3839566	23	2.0	24	88	4	71	33	22	16	27	1.96
3839543--3839662	39	3.0	40	75	3	116	36	19	13	30	1.90
3847243--3847272	15	2.0	15	100	0	60	33	13	6	46	1.69
3849376--3849401	3	8.7	3	100	0	52	65	0	34	0	0.93
3859238--3859286	2	24.5	2	95	0	89	48	2	0	48	1.12
3866157--3866310	43	3.6	43	76	9	138	24	16	23	36	1.94
3874151--3874180	15	2.0	15	93	0	51	53	6	16	23	1.66
3875385--3875642	83	3.1	83	65	22	232	30	20	15	32	1.94
3875375--3875776	166	2.4	167	93	3	677	28	20	16	34	1.94
3875468--3875726	83	3.1	84	65	24	204	28	21	16	33	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3880323--3880378	21	2.7	21	91	0	85	46	0	0	53	1.00
3880331--3880376	19	2.4	19	85	0	65	50	0	0	50	1.00
3880339--3880379	2	21.0	2	90	5	57	46	0	0	53	1.00
3884771--3884844	37	2.0	36	84	7	96	44	1	5	48	1.34
3886804--3886976	88	2.0	88	100	0	346	33	23	17	26	1.96
3887949--3888010	3	21.7	3	77	12	60	66	0	3	30	1.08
3887949--3888006	13	4.3	14	75	12	50	65	0	3	31	1.09
3887949--3888010	19	3.2	20	77	8	67	66	0	3	30	1.08
3888185--3888492	134	2.3	134	84	2	395	27	15	22	34	1.95
3889634--3889704	16	4.6	16	70	19	53	9	12	0	77	0.99
3889654--3889692	17	2.4	16	86	4	51	12	10	0	76	1.01
3896094--3896125	16	2.0	16	100	0	64	50	6	12	31	1.65
3897588--3897854	133	2.0	134	99	0	527	27	8	32	30	1.88
3898542--3898600	23	2.6	23	91	2	93	18	27	30	23	1.98
3909895--3909932	16	2.3	16	86	4	58	63	0	5	31	1.17
3914332--3914480	72	2.1	72	100	0	298	36	17	16	29	1.92
3915128--3915153	13	2.0	13	100	0	52	30	0	0	69	0.89
3922520--3923289	256	3.0	255	85	2	1001	35	20	14	29	1.92
3923176--3923411	79	3.0	79	84	1	303	36	23	13	26	1.91
3926397--3926424	2	14.0	2	100	0	56	50	0	0	50	1.00
3930104--3930142	19	2.1	19	85	4	53	46	15	2	35	1.60
3943065--3943145	30	2.6	31	79	13	112	45	3	3	46	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3944499--3944553	23	2.4	23	93	3	94	52	10	0	36	1.37
3957055--3957080	2	13.0	2	100	0	52	50	0	0	50	1.00
3957358--3957398	13	3.1	13	82	6	55	43	0	0	56	0.99
3957360--3957405	14	3.4	13	82	8	56	36	0	2	60	1.09
3967906--3968097	36	5.3	36	89	0	303	35	23	22	18	1.96
3967906--3968120	72	3.0	71	88	6	321	36	22	22	18	1.95
3969764--3969823	26	2.3	27	85	8	79	43	0	6	50	1.28
3972199--3972239	22	1.9	21	90	5	64	51	7	9	31	1.62
3975415--3975462	19	2.6	19	87	9	64	2	18	6	72	1.15
3976167--3976216	21	2.5	21	90	6	77	48	8	12	32	1.69
3977028--3977061	17	2.0	17	94	0	59	44	0	17	38	1.49
3978303--3978387	15	5.7	15	66	18	52	43	2	1	52	1.21
3978395--3978463	15	4.6	15	75	13	52	49	1	0	49	1.09
3978400--3978539	31	4.8	29	72	15	103	50	1	0	48	1.09
3978395--3978486	36	2.8	33	79	15	102	48	1	0	50	1.08
3978400--3978470	7	10.3	7	74	17	60	49	1	0	49	1.09
3978476--3978516	9	4.2	10	90	9	59	56	0	0	43	0.99
3978535--3978593	18	3.3	18	72	13	50	45	3	1	49	1.28
3978546--3978610	29	2.2	29	78	13	71	44	3	1	50	1.26
3978639--3978674	15	2.4	15	100	0	72	38	0	0	61	0.96
3982760--3982795	18	1.9	19	88	5	56	77	0	8	13	0.98
3983890--3984098	7	30.6	7	65	20	61	53	4	3	37	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3983893--3983938	24	1.9	24	86	8	67	54	0	4	41	1.20
3983896--3983988	40	2.4	37	81	15	109	52	2	4	40	1.33
3983906--3983986	21	3.9	19	78	18	83	51	2	3	41	1.32
3983890--3984020	63	2.1	63	79	14	139	53	3	4	38	1.40
4005506--4005598	40	2.3	40	81	3	107	31	9	18	40	1.83
4005594--4005680	41	2.1	41	85	4	113	28	14	16	40	1.88
4006111--4006145	17	2.1	18	89	10	56	51	0	0	48	1.00
4009332--4009785	42	10.6	42	76	6	299	25	20	18	34	1.96
4011918--4012158	35	7.0	35	78	8	271	44	3	9	41	1.55
4011937--4012142	69	3.1	64	79	8	234	44	3	10	41	1.55
4012098--4012231	35	3.9	33	80	10	119	47	2	8	41	1.49
4012356--4012396	20	2.0	20	85	9	55	17	2	4	75	1.08
4018565--4018626	21	3.1	19	80	13	70	25	38	24	11	1.88
4018567--4018606	20	2.0	20	90	5	62	25	37	25	12	1.91
4030012--4030117	50	2.1	50	87	0	158	27	23	26	22	2.00
4030892--4031127	35	6.9	35	77	10	245	44	2	11	41	1.55
4030908--4031111	66	3.1	65	81	5	194	44	2	11	41	1.55
4030953--4031141	104	1.9	99	86	5	270	44	3	10	41	1.57
4031108--4031216	37	2.9	36	86	8	137	40	2	9	47	1.50
4031332--4031383	6	8.3	6	78	16	52	19	1	1	76	0.97
4044838--4044916	30	2.6	31	83	2	106	31	17	8	41	1.80
4045637--4045693	31	1.9	30	89	7	89	31	29	3	35	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4049302--4049430	64	2.0	64	100	0	258	30	12	29	27	1.93
4055696--4055913	34	6.4	34	79	10	225	44	1	9	44	1.47
4055729--4055793	29	2.2	30	88	2	96	46	1	7	44	1.41
4055675--4055913	35	7.0	35	78	9	244	43	3	9	43	1.53
4055859--4056004	76	1.9	77	82	2	186	43	2	8	45	1.46
4055894--4056004	41	2.9	37	85	9	134	42	1	9	46	1.45
4056120--4056171	6	8.3	6	78	16	52	19	3	0	76	0.93
4056805--4056895	42	2.2	42	95	0	164	30	0	43	25	1.55
4066006--4066052	11	4.2	11	79	12	51	4	19	0	76	0.95
4066003--4066054	21	2.5	20	75	6	59	3	19	0	76	0.93

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   30   31   32   
          33   34   35