genome.fa.s8094.2.7.7.80.10.50.1000.20.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: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9952466

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   38   39   40   41   42   43   

This is table  20  of  43  ( 5090 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)
3936907--3936971	9	6.8	9	72	19	51	15	7	1	75	1.10
3936910--3936971	22	2.8	20	83	16	70	14	8	1	75	1.10
3937590--3937632	22	2.0	22	86	9	61	39	16	13	30	1.87
3940439--3940486	23	2.1	22	88	3	69	41	4	0	54	1.20
3941008--3941044	14	2.6	14	91	0	56	8	8	16	67	1.40
3940922--3941031	47	2.3	47	78	6	116	14	8	15	61	1.55
3940922--3941044	24	5.2	24	75	10	110	13	8	15	62	1.53
3941113--3941176	28	2.3	28	94	0	110	9	14	26	50	1.73
3943596--3943622	14	1.9	14	100	0	54	29	14	7	48	1.71
3947954--3947983	2	15.0	2	100	0	60	50	0	0	50	1.00
3949365--3950051	233	2.9	234	90	0	1065	34	17	16	31	1.92
3949847--3949962	42	2.8	41	80	2	133	29	21	24	25	1.99
3956647--3956687	2	21.5	2	85	9	59	46	0	0	53	1.00
3956647--3956687	19	2.2	19	95	0	73	46	0	0	53	1.00
3956647--3956699	19	3.0	18	84	15	67	43	0	1	54	1.11
3961817--3962687	94	9.0	94	94	1	1274	33	25	18	22	1.96
3963542--3963583	2	22.5	2	81	13	54	45	0	0	54	0.99
3963543--3963583	7	5.9	7	91	8	66	43	0	0	56	0.99
3963545--3963583	20	2.0	20	94	0	69	43	0	0	56	0.99
3966486--3966517	2	16.0	2	100	0	64	50	0	0	50	1.00
3967049--3967077	2	14.5	2	100	0	58	48	0	0	51	1.00
3966272--3967400	563	2.0	563	99	0	2222	49	13	7	29	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3968714--3968765	27	1.9	27	100	0	104	11	17	38	32	1.85
3970039--3970095	7	8.1	7	100	0	114	70	0	29	0	0.88
3970476--3970525	22	2.3	23	83	13	61	34	6	4	56	1.43
3981622--3981664	22	1.9	23	85	4	61	25	20	27	25	1.99
3981628--3981700	37	2.0	37	94	0	128	24	19	30	26	1.98
3983071--3983110	19	2.2	19	90	4	64	37	17	0	45	1.49
3984729--3984769	15	2.7	15	88	0	64	56	14	12	17	1.68
3985158--3985199	22	1.9	22	90	0	66	26	21	26	26	1.99
3985166--3985234	36	1.9	36	90	0	111	27	20	23	28	1.99
3988189--3988239	19	2.7	18	76	11	50	13	13	1	70	1.25
3990877--3990995	24	5.0	24	85	6	143	37	19	16	26	1.93
3993445--3993479	18	1.9	18	94	0	61	14	20	45	20	1.85
3994950--3994980	10	3.2	10	95	4	55	22	16	12	48	1.80
3997265--3997325	20	3.0	20	76	4	68	31	13	29	26	1.93
3997526--3997563	20	1.9	20	94	0	67	26	23	13	36	1.91
4000758--4000801	22	2.0	22	82	4	54	36	22	6	34	1.81
4002760--4002806	4	11.5	4	95	4	85	48	25	0	25	1.51
4004421--4004478	20	2.6	22	89	10	84	25	22	20	31	1.98
4004466--4004606	64	2.2	63	81	7	160	24	22	19	33	1.97
4004661--4004692	12	2.7	12	100	0	64	25	25	0	50	1.50
4007895--4007951	18	3.0	19	80	7	71	24	33	19	22	1.97
4009171--4009311	64	2.2	63	82	7	169	25	23	19	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4011494--4011537	17	2.6	17	77	0	52	27	13	13	45	1.81
4011941--4012345	180	2.3	178	82	8	470	41	7	10	40	1.68
4012286--4012330	19	2.4	19	84	0	63	42	0	11	46	1.39
4014476--4014550	39	1.9	39	94	0	132	14	16	14	54	1.71
4015272--4015305	14	2.5	14	85	4	52	67	0	0	32	0.91
4015797--4015834	20	1.9	19	89	5	58	65	0	0	34	0.93
4015792--4015839	18	2.9	17	85	11	57	70	0	0	29	0.87
4015823--4015852	12	2.4	12	94	5	51	66	0	0	33	0.92
4016189--4016623	81	5.3	80	85	4	424	24	20	25	29	1.99
4016199--4016623	165	2.6	163	80	4	462	24	20	25	29	1.99
4016219--4016634	84	5.0	84	85	2	301	23	20	26	29	1.99
4016747--4017282	110	4.9	110	92	1	857	24	19	23	33	1.97
4018274--4018305	2	16.0	2	100	0	64	50	0	0	50	1.00
4018464--4018510	15	3.1	15	80	14	51	57	8	4	29	1.48
4018470--4018512	15	2.8	16	83	13	54	60	9	2	27	1.40
4018525--4018570	23	2.0	23	83	8	58	65	4	4	26	1.30
4021823--4021847	10	2.5	10	100	0	50	0	12	0	88	0.53
4021884--4021926	17	2.6	17	89	7	63	0	9	6	83	0.80
4032364--4032420	3	19.3	3	96	3	107	66	0	0	33	0.92
4032439--4032469	2	15.5	2	100	0	62	51	0	0	48	1.00
4032520--4032566	15	3.1	15	80	14	51	57	8	4	29	1.48
4032526--4032568	15	2.8	16	83	13	54	60	9	2	27	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4037012--4037102	39	2.3	39	77	15	98	69	1	3	26	1.11
4037433--4037519	33	2.6	34	89	5	126	27	11	20	40	1.87
4037586--4037612	6	4.5	6	100	0	54	51	0	0	48	1.00
4037612--4037653	4	10.5	4	85	10	59	71	0	0	28	0.86
4038568--4038619	17	3.1	17	80	0	59	38	15	5	40	1.71
4038812--4038836	12	2.1	12	100	0	50	36	24	8	32	1.84
4039312--4039355	22	2.0	22	82	4	54	43	22	4	29	1.73
4041331--4041505	90	2.0	89	90	1	278	44	8	11	36	1.70
4048073--4048239	90	1.9	90	92	0	280	45	6	11	35	1.67
4054483--4054538	19	3.3	17	75	22	55	44	1	0	53	1.11
4054505--4054543	19	2.0	20	95	5	71	46	0	0	53	1.00
4056334--4056403	21	3.3	21	70	7	61	22	28	22	25	1.99
4058081--4058133	17	3.1	17	88	0	79	41	5	15	37	1.70
4058723--4058760	18	2.2	18	85	4	51	39	2	7	50	1.46
4059048--4059090	19	2.2	19	87	8	59	41	9	9	39	1.69
4059177--4059549	137	2.7	137	84	2	444	35	21	19	23	1.96
4062737--4062862	26	4.9	26	71	6	87	39	34	1	24	1.65
4062737--4062855	51	2.3	51	86	2	159	38	35	1	24	1.66
4064278--4064430	60	2.6	61	78	8	161	41	5	19	33	1.76
4064275--4064456	60	3.0	60	77	7	147	42	7	18	32	1.77
4066325--4066355	2	15.5	2	100	0	62	48	0	0	51	1.00
4069651--4069705	22	2.5	23	85	8	71	30	23	10	34	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4075394--4075419	3	8.7	3	100	0	52	69	0	0	30	0.89
4075476--4075508	14	2.3	15	89	5	50	84	0	6	9	0.76
4075476--4075544	15	4.5	15	71	15	52	73	2	5	17	1.15
4075648--4075716	11	6.4	10	75	20	59	79	0	4	15	0.88
4075648--4075716	5	11.7	6	79	11	56	79	0	4	15	0.88
4075648--4075736	10	8.9	10	71	21	53	76	0	3	20	0.93
4075713--4075751	5	7.4	5	83	11	51	61	2	2	33	1.23
4078693--4078733	13	3.1	14	86	10	59	4	14	0	80	0.87
4088133--4088184	22	2.2	24	90	6	81	9	17	13	59	1.60
4090997--4091022	3	8.7	3	100	0	52	69	0	0	30	0.89
4091075--4091118	14	3.0	15	83	9	56	79	2	4	13	0.98
4091079--4091118	16	2.6	16	88	7	57	77	2	5	15	1.04
4091189--4091226	19	2.0	20	84	5	51	73	5	7	13	1.22
4091296--4091337	17	2.4	17	80	4	57	61	2	4	30	1.29
4095255--4095288	16	2.0	18	88	11	54	38	0	2	58	1.13
4095478--4095625	79	1.9	79	82	0	188	37	17	18	26	1.93
4114773--4114805	17	2.0	17	94	5	59	12	24	33	30	1.91
4122704--4122763	20	2.8	21	85	7	77	23	33	21	21	1.97
4122746--4122785	21	1.9	21	89	0	62	25	40	25	10	1.86
4124723--4124766	17	2.5	17	85	3	52	25	2	25	47	1.63
4126730--4126812	24	3.5	24	88	0	130	25	12	20	42	1.86
4126721--4126829	24	4.5	24	83	2	121	25	10	19	44	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4126718--4126835	48	2.5	48	84	0	164	25	9	19	45	1.80
4126996--4127025	2	15.0	2	100	0	60	50	0	0	50	1.00
4128920--4128958	20	2.0	20	85	10	53	15	30	25	28	1.96
4131232--4131314	24	3.5	24	88	0	121	26	10	20	42	1.85
4131222--4131339	48	2.5	48	80	0	128	24	9	20	45	1.80
4133155--4133197	21	2.0	21	100	0	86	27	4	34	32	1.78
4135863--4135893	7	4.4	7	100	0	62	70	0	12	16	1.16
4139916--4139940	12	2.1	12	100	0	50	40	8	52	0	1.31
4146066--4146105	21	1.9	21	100	0	80	42	37	0	20	1.52
4146068--4146125	7	8.4	7	75	3	55	43	37	0	18	1.51

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   38   39   40   41   42   43