genome.fa.s8087.2.7.7.80.10.50.1000.17.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: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8279816

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   36   37   

This is table  17  of  37  ( 4336 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)
3921402--3921443	22	1.9	22	100	0	84	38	19	9	33	1.84
3921402--3921456	22	2.6	21	85	8	58	43	18	9	29	1.80
3922168--3922209	22	1.9	22	100	0	84	38	19	9	33	1.84
3922168--3922222	22	2.6	21	85	8	58	43	18	9	29	1.80
3922899--3923066	75	2.3	76	86	5	229	36	6	2	53	1.42
3925475--3925519	6	7.5	6	82	9	56	0	20	0	80	0.72
3925475--3925519	17	2.5	19	85	7	58	0	20	0	80	0.72
3926718--3926744	1	27.0	1	100	0	54	0	0	0	100	0.00
3927886--3927937	14	3.6	14	81	2	50	51	7	17	23	1.70
3929363--3929437	31	2.3	32	84	13	109	73	0	0	26	0.84
3929355--3929435	25	3.1	26	84	10	94	71	0	0	28	0.86
3930511--3930543	10	3.3	10	87	12	50	72	0	0	27	0.85
3930939--3930963	13	1.9	13	100	0	50	8	64	24	4	1.38
3931643--3931733	3	29.7	3	82	8	112	61	1	0	37	1.03
3931637--3931745	19	5.9	18	78	8	103	60	0	0	38	1.03
3931871--3932053	75	2.5	75	91	4	293	35	20	21	22	1.96
3932285--3932479	88	2.3	84	90	7	304	25	18	19	36	1.94
3932506--3932764	110	2.3	112	90	5	393	29	20	12	37	1.89
3932666--3932836	72	2.4	73	95	3	301	34	16	11	38	1.84
3932587--3932943	181	2.0	179	94	2	626	32	17	12	37	1.87
3932506--3933055	291	1.9	291	90	4	876	30	18	12	37	1.89
3932739--3933433	112	6.2	112	88	6	932	29	19	13	37	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3932739--3933431	221	3.1	224	87	6	966	29	19	13	37	1.90
3933812--3933866	22	2.5	22	96	0	101	36	14	14	34	1.87
3936282--3936488	52	4.0	52	92	2	353	39	21	14	24	1.91
3938553--3938597	6	7.5	6	82	9	56	0	20	0	80	0.72
3938553--3938597	17	2.5	19	85	7	58	0	20	0	80	0.72
3939807--3939839	1	33.0	1	100	0	66	0	0	0	100	0.00
3941061--3941112	14	3.6	14	81	2	50	51	7	17	23	1.70
3942547--3942625	13	6.2	12	70	21	54	70	0	1	27	0.95
3942548--3942643	33	2.8	34	81	10	117	70	0	2	27	0.98
3942550--3942602	23	2.3	23	87	6	72	73	0	0	26	0.83
3942550--3942638	30	3.0	29	87	6	117	70	0	2	26	0.99
3943751--3943783	10	3.3	10	87	12	50	72	0	0	27	0.85
3944186--3944210	13	1.9	13	100	0	50	8	64	24	4	1.38
3944896--3945017	3	39.7	3	85	4	163	61	0	0	37	1.02
3951872--3951933	20	2.8	23	79	16	78	30	16	20	32	1.95
3952997--3953045	25	1.9	26	83	4	64	34	4	22	38	1.73
3957278--3957353	31	2.5	31	82	0	80	30	15	22	31	1.95
3961072--3961199	31	4.1	31	73	6	105	29	17	19	32	1.95
3964346--3964384	2	19.5	2	100	0	78	51	0	0	48	1.00
3972911--3972997	41	2.1	41	93	0	147	29	10	24	35	1.88
3975202--3975249	24	2.0	25	87	4	71	66	0	0	33	0.92
3982482--3982537	21	2.7	21	97	0	103	46	0	1	51	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3985458--3985553	31	3.1	30	79	4	95	40	13	9	36	1.77
3985458--3985553	30	3.1	29	77	7	93	40	13	9	36	1.77
3986269--3986350	29	2.8	29	85	9	105	57	3	8	30	1.46
3987075--3987124	25	2.0	25	88	0	73	32	6	4	58	1.41
3990274--3990320	20	2.3	20	100	0	94	36	19	0	44	1.51
3992438--3992475	20	1.9	20	88	0	58	42	2	0	55	1.14
3992440--3992489	20	2.5	19	81	15	57	40	6	0	54	1.25
3993799--3993824	13	2.0	13	100	0	52	61	0	0	38	0.96
4006115--4006144	2	15.0	2	92	0	51	46	0	3	50	1.18
4006195--4006227	17	1.9	17	93	0	57	69	6	0	24	1.10
4011817--4011844	12	2.3	12	100	0	56	17	42	25	14	1.87
4019071--4019105	17	2.1	17	100	0	70	17	48	22	11	1.79
4027454--4027499	16	2.9	16	93	0	74	28	10	34	26	1.90
4030880--4032061	297	4.0	297	89	1	1767	23	29	14	32	1.94
4033813--4033969	62	2.5	62	98	0	305	17	13	28	40	1.87
4034280--4034359	31	2.6	31	78	9	94	30	18	7	43	1.78
4034758--4034841	42	2.0	42	92	0	141	17	16	17	47	1.83
4034793--4034883	28	3.2	28	63	17	71	16	18	17	47	1.83
4034822--4034855	14	2.4	14	95	0	59	26	17	14	41	1.88
4034780--4034886	56	1.9	56	96	0	196	18	16	18	45	1.85
4034764--4034852	42	2.1	42	82	0	106	21	14	17	46	1.84
4035059--4035121	23	2.6	24	78	19	60	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4035148--4035251	29	3.5	29	77	17	99	46	0	1	51	1.12
4035393--4035430	18	2.0	20	85	10	53	60	0	0	39	0.97
4035608--4035687	15	5.4	15	81	3	99	36	17	5	41	1.71
4035608--4035687	30	2.7	30	90	1	117	36	17	5	41	1.71
4035608--4035695	45	2.0	44	90	2	140	34	18	4	43	1.70
4035725--4035766	14	3.0	14	82	0	57	40	7	21	30	1.80
4035775--4035810	14	2.6	14	90	0	54	33	13	22	30	1.93
4036127--4036168	19	2.3	18	91	4	66	61	4	0	33	1.17
4036201--4036245	23	2.0	23	86	0	63	55	0	0	44	0.99
4036199--4036249	17	3.1	16	78	10	59	56	0	0	43	0.99
4036452--4036548	42	2.3	42	87	0	131	50	14	15	19	1.78
4038386--4038423	19	2.0	19	89	0	58	21	5	0	73	1.02
4041673--4041720	21	2.3	21	96	0	87	27	18	12	41	1.86
4046327--4046371	21	2.1	21	91	0	72	31	15	8	44	1.77
4048977--4049028	25	2.1	25	82	13	63	55	3	1	38	1.29
4049769--4049959	20	9.4	20	86	3	256	35	17	27	19	1.94
4049748--4049951	63	3.3	63	88	6	310	35	17	27	19	1.94
4049644--4049961	20	15.6	20	78	9	198	38	19	24	17	1.93
4049948--4049991	20	2.2	20	91	0	70	54	15	18	11	1.70
4050067--4050114	6	8.5	6	97	2	75	29	54	16	0	1.43
4050222--4050277	26	2.2	26	100	0	112	32	17	21	28	1.96
4050861--4050986	6	20.8	6	93	1	207	1	13	52	32	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4050840--4050985	18	8.3	17	86	6	89	1	11	55	31	1.44
4050818--4050986	30	5.7	31	85	8	176	1	12	56	30	1.44
4051094--4051223	20	6.5	20	92	0	206	18	28	18	34	1.95
4051258--4051311	20	2.7	20	91	0	81	11	20	18	50	1.77
4051298--4051346	18	2.5	20	87	6	57	16	18	24	40	1.90
4051963--4052039	21	3.9	19	79	5	66	7	11	54	25	1.63
4051960--4052027	21	3.2	21	87	0	100	7	13	55	23	1.62
4056822--4056855	17	1.9	18	88	5	52	50	17	0	32	1.47
4066783--4067216	37	12.1	37	69	21	112	45	6	3	43	1.47
4066883--4066958	34	2.2	35	86	6	111	47	6	3	42	1.48
4066907--4067216	36	8.5	36	72	17	185	44	7	3	44	1.49
4067019--4067074	27	2.2	25	90	6	85	50	7	3	39	1.47
4067019--4067074	25	2.1	27	87	12	82	50	7	3	39	1.47
4066967--4067177	77	3.0	65	76	19	203	45	6	4	44	1.49
4067036--4067258	77	2.9	74	83	11	222	43	6	4	44	1.52
4073723--4073765	22	2.0	22	90	0	68	51	11	2	34	1.51
4076958--4077000	20	2.3	20	84	11	56	55	6	2	34	1.39
4089966--4090005	21	1.9	21	94	0	71	32	27	15	25	1.95
4090031--4090069	19	2.1	19	95	0	69	20	38	15	25	1.92
4089987--4090177	64	3.0	64	82	8	212	31	25	15	27	1.96
4095968--4096047	24	3.5	22	78	14	92	22	26	23	27	2.00
4098575--4098614	21	1.9	21	94	0	71	32	27	15	25	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4098639--4098678	19	2.1	19	90	0	62	22	40	12	25	1.89
4105909--4105940	16	2.0	16	100	0	64	37	12	18	31	1.88
4106078--4106164	42	2.1	42	93	0	147	27	18	22	31	1.97
4106217--4106466	42	6.1	42	71	11	203	28	19	21	30	1.98
4106069--4106391	177	1.8	177	90	0	520	30	19	20	28	1.97
4106845--4107200	53	6.8	53	85	3	407	30	19	26	23	1.98
4106846--4107207	106	3.4	105	86	3	462	30	19	26	23	1.98
4106845--4107207	159	2.3	159	85	3	466	30	19	26	23	1.98
4119050--4119115	34	1.9	34	96	0	123	45	3	13	37	1.59
4119247--4119296	19	2.8	19	82	17	63	38	0	0	62	0.96

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   36   37