genome.fa.s8428.2.7.7.80.10.50.1000.16.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: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6915314

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   

This is table  16  of  30  ( 3508 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)
3904485--3904515	13	2.4	13	100	0	62	12	16	22	48	1.80
3912831--3912862	16	1.9	17	93	6	57	56	15	3	25	1.54
3914999--3915072	32	2.3	32	79	9	89	17	31	27	24	1.97
3921182--3921222	15	2.7	14	85	14	55	53	0	0	46	1.00
3921460--3921491	16	1.9	17	93	6	57	71	0	6	21	1.07
3921480--3922475	498	2.0	497	99	0	1974	46	14	12	26	1.80
3923822--3923855	18	1.9	17	88	5	50	50	14	2	32	1.58
3927147--3927176	11	2.7	11	94	0	51	60	10	30	0	1.30
3928673--3928723	2	25.5	2	91	0	84	0	3	45	50	1.20
3929214--3929275	24	2.5	25	81	2	63	53	20	1	24	1.55
3929238--3929313	25	3.0	25	88	0	107	51	17	0	31	1.45
3929240--3929316	13	6.1	13	76	11	79	48	18	0	33	1.48
3929454--3929505	17	2.9	17	80	13	52	59	1	3	34	1.27
3932504--3932561	21	2.8	21	84	10	66	70	3	0	25	1.03
3932506--3932545	12	3.5	11	86	10	53	75	2	0	22	0.93
3932674--3932763	30	3.0	29	73	9	92	44	13	4	37	1.64
3932726--3933053	36	9.3	35	86	4	437	42	10	3	42	1.58
3932726--3933053	107	3.1	107	93	2	538	42	10	3	42	1.58
3933340--3933401	24	2.5	25	81	2	63	53	20	1	24	1.55
3933364--3933439	25	3.0	25	88	0	107	51	17	0	31	1.45
3933366--3933442	13	6.1	13	76	11	79	48	18	0	33	1.48
3936218--3936326	25	4.3	24	70	17	71	70	0	5	22	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3936223--3936278	12	4.6	12	80	10	51	73	0	3	23	0.99
3938268--3938451	84	2.2	84	88	0	260	23	17	25	34	1.96
3938448--3938551	33	2.9	36	83	9	151	30	10	17	41	1.83
3938518--3938732	66	3.2	66	78	10	181	37	12	18	31	1.88
3938813--3938991	36	5.1	36	69	14	115	37	12	20	30	1.89
3938792--3938984	101	1.9	102	93	1	334	38	11	20	29	1.88
3939001--3939149	72	2.1	72	94	0	262	36	10	20	32	1.87
3939003--3939117	36	3.2	36	66	9	90	36	10	20	33	1.86
3945862--3946672	81	10.0	80	87	2	1052	31	21	10	36	1.87
3946833--3947081	57	4.4	57	89	0	356	36	18	9	35	1.83
3947947--3947997	20	2.4	22	84	12	63	29	25	15	29	1.96
3949923--3949984	24	2.5	25	81	2	63	53	20	1	24	1.55
3949947--3950022	25	3.0	25	88	0	107	51	17	0	31	1.45
3949949--3950025	13	6.1	13	76	11	79	48	18	0	33	1.48
3950163--3950214	17	2.9	17	80	13	52	59	1	3	34	1.27
3953234--3953291	21	2.8	21	84	10	66	70	3	0	25	1.03
3953236--3953275	12	3.5	11	86	10	53	75	2	0	22	0.93
3953329--3953785	71	6.6	71	76	13	312	42	11	3	42	1.58
3953404--3953493	30	3.0	29	73	9	92	44	13	4	37	1.64
3953456--3953785	36	9.3	35	87	3	455	42	10	3	42	1.58
3953456--3953785	107	3.1	107	94	1	556	42	10	3	42	1.58
3954075--3954136	24	2.5	25	81	2	63	53	20	1	24	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3954099--3954174	25	3.0	25	88	0	107	51	17	0	31	1.45
3954101--3954177	13	6.1	13	76	11	79	48	18	0	33	1.48
3956955--3957063	25	4.3	24	70	17	71	70	0	4	23	1.11
3956960--3957015	12	4.6	12	80	10	51	73	0	3	23	0.99
3957058--3957120	33	1.9	33	87	9	94	60	1	9	28	1.37
3959011--3959194	84	2.2	84	88	0	260	22	17	25	34	1.96
3959191--3959295	33	2.9	37	80	12	146	30	10	17	41	1.83
3959182--3959305	33	3.8	32	79	14	119	32	11	17	38	1.85
3959262--3959458	66	3.0	66	80	8	172	37	12	19	30	1.89
3959557--3959735	36	5.1	36	68	14	115	37	11	20	30	1.88
3959536--3959728	101	1.9	102	93	1	334	38	11	20	30	1.87
3959746--3959894	72	2.1	72	94	0	262	36	10	20	32	1.87
3959748--3959862	36	3.2	36	66	9	90	36	10	20	33	1.86
3964735--3964809	37	2.0	37	100	0	150	52	13	8	26	1.68
3965748--3965776	2	14.5	2	100	0	58	51	0	0	48	1.00
3965971--3966011	2	20.5	2	94	0	73	48	0	0	51	1.00
3966672--3966810	51	2.7	51	89	2	154	32	9	2	55	1.47
3966706--3966788	26	3.2	26	67	16	82	32	9	3	54	1.50
3966700--3966815	51	2.3	50	96	1	187	30	11	3	55	1.52
3970346--3970393	21	2.2	21	85	3	60	77	8	12	2	1.08
3970324--3970393	22	3.1	22	79	8	70	77	5	14	2	1.07
3970347--3970399	22	2.5	20	77	14	54	75	7	15	1	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3971001--3971044	22	2.0	22	91	8	72	38	22	11	27	1.88
3971463--3971498	18	2.0	18	88	0	54	19	8	30	41	1.81
3971993--3972117	36	3.4	36	83	2	169	26	20	13	39	1.90
3972075--3972249	65	2.6	65	84	4	224	33	21	9	36	1.85
3972853--3973302	105	4.3	104	90	3	683	32	27	18	22	1.97
3974580--3974718	51	2.7	51	89	2	154	32	9	2	55	1.47
3974614--3974696	26	3.2	26	67	16	82	32	9	3	54	1.50
3974608--3974723	51	2.3	50	96	1	187	30	11	3	55	1.52
3974846--3974879	16	2.1	16	88	0	50	32	5	0	61	1.20
3976748--3977557	81	10.0	80	87	3	1070	31	21	10	36	1.87
3977718--3977966	57	4.4	57	90	0	365	36	18	9	35	1.83
3978833--3978883	20	2.4	22	84	12	63	29	25	15	29	1.96
3980302--3980341	2	20.0	2	89	0	62	45	0	5	50	1.23
3980303--3980341	14	2.8	14	100	0	78	43	0	5	51	1.24
3980831--3980892	24	2.5	25	81	2	63	53	20	1	24	1.55
3980855--3980930	25	3.0	25	88	0	107	51	17	0	31	1.45
3980857--3980933	13	6.1	13	76	11	79	48	18	0	33	1.48
3981071--3981122	17	2.9	17	80	13	52	59	1	3	34	1.27
3983718--3983811	11	8.1	11	74	17	57	70	0	6	23	1.10
3983858--3983888	2	15.5	2	93	0	53	48	0	0	51	1.00
3984510--3984637	25	5.0	24	70	17	80	71	0	7	21	1.15
3984588--3984637	19	2.5	20	81	12	59	74	0	12	14	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3984510--3984619	6	17.3	6	72	20	55	70	0	5	22	1.13
3984666--3984712	2	23.5	2	91	0	76	51	0	0	48	1.00
3986586--3986769	84	2.2	84	88	0	260	23	17	25	33	1.97
3986766--3986870	33	2.9	37	80	12	146	30	10	17	41	1.83
3986757--3986880	33	3.8	32	79	14	119	32	11	17	38	1.85
3986837--3987051	67	3.2	66	77	11	165	36	13	18	31	1.89
3987132--3987217	36	2.4	36	84	0	100	39	11	22	26	1.88
3987111--3987303	101	1.9	102	91	1	316	38	11	19	30	1.87
3987235--3987310	36	2.1	37	87	7	111	39	13	17	30	1.87
3987320--3987468	72	2.1	72	90	0	235	38	11	18	31	1.86
3987315--3987436	36	3.4	36	67	13	97	40	11	16	31	1.84
3987358--3987477	36	3.3	35	71	17	102	39	12	18	30	1.87
3995975--3996032	19	2.8	20	84	10	64	17	25	32	24	1.96
3995954--3996031	41	1.9	41	82	10	97	16	24	33	25	1.96
3998458--3998489	16	1.9	17	93	6	57	71	0	6	21	1.07
3998565--3998596	4	8.0	4	100	0	64	75	0	0	25	0.81
3999481--4000211	81	9.0	81	87	1	982	31	20	11	36	1.88
4000372--4000620	57	4.4	57	89	0	356	35	17	10	36	1.84
4001486--4001536	20	2.4	22	84	12	63	31	23	17	27	1.97
4002491--4002717	114	2.0	114	89	3	350	25	31	10	33	1.90
4006293--4006539	123	2.0	124	99	0	487	26	17	23	31	1.97
4006896--4006999	33	3.0	35	84	8	149	30	10	18	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4006887--4007009	33	3.8	32	81	13	144	32	10	18	38	1.85
4006966--4007180	67	3.2	67	80	7	224	38	12	18	31	1.87
4007261--4007383	36	3.4	36	86	0	156	39	11	21	27	1.88
4007481--4007599	36	3.3	36	64	4	96	37	12	18	31	1.88
4007484--4007621	72	1.9	72	96	0	258	35	11	20	32	1.88
4012847--4012936	5	17.2	5	70	19	51	72	0	8	18	1.10
4013692--4014016	161	2.0	164	98	1	629	31	17	16	34	1.93
4013967--4014081	56	2.1	56	100	0	230	28	13	17	40	1.88
4015450--4015491	19	2.2	19	95	0	75	21	11	35	30	1.90
4018741--4018830	30	3.0	31	80	4	85	43	15	3	37	1.63

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