genome.fa.s7999.2.7.7.80.10.50.1000.20.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: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11700749

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   44   45   46   47   48   
          49   50   

This is table  20  of  50  ( 5918 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)
5326879--5327115	108	2.2	108	96	0	438	27	24	7	40	1.82
5327427--5327507	23	3.5	23	81	9	94	13	17	20	48	1.81
5328302--5328425	35	3.5	35	89	0	185	26	20	16	36	1.94
5328409--5328503	42	2.3	42	84	0	118	29	15	20	34	1.93
5328409--5328526	42	2.8	42	79	7	107	26	19	17	36	1.94
5335850--5336044	35	5.5	35	82	1	219	22	24	20	33	1.97
5335850--5336042	71	2.7	70	84	0	233	21	24	19	34	1.97
5337595--5337649	26	2.2	25	86	3	74	41	1	1	54	1.21
5337597--5337644	23	2.1	23	84	0	60	39	2	2	56	1.23
5338403--5338427	12	2.1	12	100	0	50	36	40	0	24	1.55
5338973--5339009	15	2.4	16	86	8	51	32	0	0	67	0.91
5341364--5341443	20	4.1	19	79	9	81	16	12	7	63	1.50
5341368--5341450	26	3.2	26	75	14	73	18	10	6	65	1.44
5343475--5343569	3	32.0	3	95	4	167	67	0	31	1	0.98
5345658--5345760	54	1.9	54	91	0	170	36	13	21	28	1.91
5347114--5347185	20	3.5	20	66	7	54	23	23	18	34	1.96
5346732--5347384	216	3.0	218	84	5	786	28	16	21	33	1.95
5347341--5347439	42	2.4	42	81	3	110	21	20	21	37	1.95
5348011--5348061	26	1.9	27	88	4	77	45	1	0	52	1.12
5348832--5348896	28	2.3	28	94	0	112	29	18	24	27	1.98
5349537--5349569	2	16.5	2	100	0	66	48	0	0	51	1.00
5351020--5351070	18	2.8	20	80	14	56	78	0	15	5	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5351037--5351075	10	3.9	11	87	12	50	79	0	15	5	0.90
5352169--5352358	36	5.5	35	75	15	164	47	5	1	45	1.34
5352183--5352350	36	5.0	33	77	18	177	49	5	1	43	1.34
5352364--5352472	2	57.5	2	80	13	106	51	0	0	46	1.13
5352327--5352444	48	2.4	47	85	13	150	47	4	1	46	1.32
5353143--5353590	36	12.8	36	74	13	346	40	12	18	27	1.87
5353365--5353416	17	3.1	17	71	18	54	42	13	21	23	1.88
5353153--5353590	172	2.5	173	91	3	720	41	12	18	27	1.87
5353356--5353601	138	1.8	134	86	5	359	39	12	19	29	1.87
5357936--5357977	20	2.1	20	82	8	50	71	2	7	19	1.20
5357959--5358017	22	2.7	21	84	7	64	74	3	8	13	1.17
5359193--5359231	3	13.0	3	84	10	53	64	0	2	33	1.08
5359265--5359307	11	3.6	12	78	12	52	51	4	0	44	1.22
5359307--5359547	39	6.4	38	79	7	233	49	7	2	41	1.43
5359256--5359377	61	2.0	61	80	6	138	53	4	0	40	1.28
5359551--5360458	4	229.5	4	95	3	1624	49	25	0	24	1.56
5361689--5361770	43	1.9	42	85	2	110	26	15	17	40	1.89
5361688--5361785	43	2.3	42	80	5	108	29	16	15	38	1.89
5364650--5364674	13	1.9	13	100	0	50	24	16	24	36	1.94
5374080--5374130	3	16.7	3	77	18	52	68	0	3	27	1.07
5374080--5374127	18	2.6	19	90	6	73	68	0	4	27	1.07
5374246--5374933	134	5.1	134	80	6	709	30	14	22	32	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5374248--5374933	268	2.6	267	83	5	836	30	14	22	32	1.94
5375984--5376070	29	3.0	29	86	6	124	35	18	18	27	1.94
5376767--5376915	65	2.3	65	79	3	158	31	22	17	28	1.97
5381117--5381179	26	2.4	26	94	0	108	17	14	20	47	1.82
5384159--5384202	21	2.0	22	91	4	72	38	0	2	59	1.10
5391201--5391353	64	2.4	64	84	3	182	30	19	22	27	1.98
5392005--5392036	2	16.0	2	100	0	64	50	0	0	50	1.00
5393898--5393982	21	4.0	21	73	10	66	28	18	24	28	1.98
5403542--5403589	21	2.3	21	100	0	96	56	4	4	35	1.38
5404140--5404663	277	1.9	277	91	0	850	39	7	11	41	1.70
5409846--5409934	32	2.8	32	79	1	99	26	29	28	15	1.96
5415524--5415688	82	2.0	82	98	0	321	33	27	12	26	1.93
5421529--5421558	3	10.0	3	100	0	60	33	0	0	66	0.92
5421983--5422126	46	3.3	44	70	20	133	22	22	12	42	1.87
5421984--5422141	83	1.9	83	92	2	264	21	22	13	42	1.88
5422278--5422566	140	2.1	140	91	1	463	26	21	15	37	1.93
5422501--5422649	45	3.5	44	68	16	116	22	22	15	39	1.91
5423357--5423412	22	2.4	24	77	14	64	35	10	14	39	1.81
5434891--5434934	22	2.0	22	100	0	88	54	18	4	22	1.61
5435835--5435860	13	2.0	13	100	0	52	30	15	7	46	1.74
5437670--5437735	16	4.1	16	72	20	66	65	1	1	31	1.11
5439277--5439480	110	1.9	110	85	0	282	24	19	21	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5451089--5451136	18	2.7	17	81	9	53	72	4	4	18	1.17
5452638--5452740	42	2.3	43	82	17	115	61	1	1	34	1.18
5452653--5452716	26	2.5	26	76	16	71	64	3	1	31	1.19
5452695--5452775	30	2.8	29	69	12	76	56	1	1	40	1.15
5453435--5453480	13	3.4	14	82	14	60	17	4	0	78	0.91
5453435--5453491	26	2.1	27	81	9	64	19	3	1	75	1.04
5453777--5453824	13	3.8	13	75	5	53	29	10	2	58	1.43
5453777--5453832	25	2.2	25	100	0	112	28	10	3	57	1.49
5454731--5454800	29	2.4	29	76	4	70	21	22	5	50	1.70
5455288--5455347	3	20.0	3	100	0	120	66	0	0	33	0.92
5455346--5455388	3	14.3	3	95	0	77	34	0	0	65	0.93
5456204--5456263	27	2.3	26	82	5	75	53	5	1	40	1.33
5456947--5457438	85	5.9	85	86	4	658	26	18	19	36	1.94
5456947--5457438	163	2.9	166	86	5	668	26	18	19	36	1.94
5463292--5463328	14	2.8	14	84	12	51	78	0	8	13	0.96
5463337--5463395	21	2.7	21	87	12	75	76	3	10	10	1.13
5463371--5463448	25	3.0	26	77	11	70	73	2	10	14	1.20
5463381--5463438	26	2.2	27	84	9	75	75	0	10	13	1.04
5463465--5463508	10	4.2	10	80	11	52	84	0	2	13	0.73
5463467--5463504	17	2.2	17	90	9	60	84	0	2	13	0.73
5463465--5463517	22	2.5	22	84	9	65	79	1	1	16	0.92
5469175--5469219	18	2.5	18	85	7	56	62	2	8	26	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5469790--5469836	22	2.1	23	88	4	69	70	8	6	14	1.32
5472152--5472192	16	2.6	16	96	0	73	29	12	29	29	1.93
5473825--5473892	19	3.5	19	70	7	57	27	7	0	64	1.20
5474045--5474088	16	2.7	16	86	10	54	18	6	0	75	1.02
5474053--5474092	19	2.0	20	85	4	55	15	10	0	75	1.05
5474101--5474161	26	2.2	26	86	13	79	29	4	1	63	1.24
5474256--5474312	16	3.4	16	74	13	53	17	8	0	73	1.07
5474250--5474296	16	2.6	17	80	16	51	17	8	0	74	1.05
5474289--5474323	14	2.4	14	90	4	52	20	5	0	74	1.02
5474267--5474337	24	3.1	24	67	18	62	18	8	0	73	1.08
5481351--5481489	75	1.9	75	83	10	187	60	9	20	10	1.56
5481454--5481501	19	2.5	20	80	6	64	81	0	16	2	0.79
5482308--5482745	124	3.6	124	87	2	597	32	23	17	27	1.96
5484534--5484563	2	15.5	2	93	6	53	46	0	0	53	1.00
5484530--5484584	10	5.5	11	78	20	59	40	0	0	60	0.97
5484533--5484596	15	4.5	14	81	12	60	37	1	0	60	1.06
5484530--5484588	19	3.2	17	78	19	57	38	0	0	61	0.96
5493727--5493758	4	7.8	4	96	3	55	78	0	0	21	0.76
5493813--5494064	127	2.0	128	88	4	373	47	14	15	22	1.82
5494671--5494700	2	15.0	2	100	0	60	50	0	0	50	1.00
5495375--5495734	132	2.7	130	80	3	324	23	18	30	27	1.98
5495818--5495876	20	2.9	21	84	5	84	37	16	25	20	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5495749--5495937	86	2.2	86	84	2	245	38	13	23	24	1.91
5496072--5496163	36	2.5	37	91	1	141	36	14	19	29	1.91
5495966--5496287	138	2.3	137	79	6	339	37	13	17	31	1.89
5497312--5497344	16	2.1	16	94	0	57	18	15	24	42	1.88
5497432--5497495	30	2.2	29	86	5	85	6	12	6	75	1.19
5498610--5498844	114	2.1	114	88	1	346	30	19	22	27	1.98
5501677--5501745	33	2.1	34	89	8	106	31	2	7	57	1.40
5502159--5502237	21	3.7	22	81	6	74	16	30	18	34	1.94
5502178--5502238	22	2.8	22	82	7	72	16	36	18	29	1.92
5505019--5505077	29	2.0	29	87	6	84	61	6	1	30	1.32

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   44   45   46   47   48   
          49   50