genome.fa.s1465.2.7.7.80.10.50.1000.28.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

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   51   52   53   54   55   

This is table  28  of  55  ( 6520 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)
5496666--5496710	9	4.8	9	81	8	54	2	20	0	77	0.87
5496664--5496776	6	18.5	6	70	20	65	6	17	0	76	0.99
5496699--5496793	37	2.6	35	77	12	93	7	18	0	73	1.06
5498050--5498178	50	2.6	50	96	0	240	17	17	27	37	1.91
5498302--5498344	23	1.9	23	85	4	61	13	13	4	67	1.38
5505455--5505499	24	1.9	23	86	4	63	33	13	33	20	1.91
5512101--5512159	29	2.0	29	100	0	118	49	13	13	23	1.78
5516791--5516847	29	2.0	29	96	0	105	43	14	17	24	1.86
5519575--5519620	2	23.5	2	95	4	85	47	0	0	52	1.00
5521684--5521733	20	2.5	20	80	3	64	4	14	2	80	0.95
5524843--5524926	23	3.7	23	85	0	123	28	23	26	21	1.99
5526391--5526552	64	2.5	64	80	5	184	26	24	17	31	1.97
5530023--5530106	23	3.7	23	91	0	141	29	26	26	17	1.98
5532660--5532686	13	2.1	13	100	0	54	37	0	0	62	0.95
5533186--5533216	14	2.2	14	94	0	53	41	6	19	32	1.77
5536314--5536375	2	31.0	2	100	0	124	50	0	0	50	1.00
5539568--5539609	17	2.5	17	84	3	50	33	16	19	30	1.94
5543428--5543632	37	5.5	36	75	18	131	44	5	4	45	1.46
5543622--5543709	41	2.2	40	81	8	97	43	3	6	46	1.47
5543437--5543725	71	3.9	72	78	12	250	43	4	5	46	1.48
5543720--5543768	9	5.0	10	81	16	50	34	0	2	63	1.06
5543739--5543790	20	2.5	20	82	11	61	25	0	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5543752--5543792	16	2.6	16	81	14	57	19	0	0	80	0.71
5549914--5550010	50	1.9	50	87	0	140	25	9	36	28	1.87
5554505--5554556	15	3.5	15	79	10	54	42	0	1	55	1.10
5562476--5562516	14	2.9	14	82	13	57	14	17	19	48	1.81
5562628--5562803	60	3.0	60	88	3	252	22	18	22	36	1.95
5564155--5564204	22	2.3	22	92	0	82	24	6	12	58	1.56
5567653--5567689	3	13.0	3	83	11	51	64	0	2	32	1.07
5568488--5568589	42	2.5	41	79	3	132	34	22	19	23	1.97
5567821--5569842	233	8.7	233	87	1	2719	34	16	16	32	1.92
5567821--5569842	465	4.3	463	87	2	2730	34	16	16	32	1.92
5571463--5571505	2	22.0	2	95	4	79	48	0	0	51	1.00
5596045--5596092	24	1.9	25	83	8	62	37	0	0	62	0.95
5597649--5597724	33	2.2	37	86	9	106	52	0	2	44	1.14
5597732--5597789	17	3.4	17	88	9	75	55	1	0	43	1.10
5597744--5597793	8	6.2	8	86	9	75	60	0	0	40	0.97
5597745--5597791	15	3.0	15	90	6	67	61	0	0	38	0.96
5597745--5597802	17	3.9	14	84	15	64	60	0	1	37	1.07
5597853--5597896	23	1.9	23	81	9	54	38	2	0	59	1.10
5597885--5597931	23	2.0	23	84	8	60	46	0	4	48	1.21
5600885--5601137	140	1.8	140	85	1	364	26	8	15	49	1.74
5602761--5602870	24	4.5	24	80	4	114	51	16	12	19	1.75
5602761--5602845	12	7.1	12	68	9	57	49	17	12	20	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5605060--5605088	6	4.8	6	100	0	58	48	17	17	17	1.82
5605209--5605238	13	2.3	13	94	0	51	50	23	10	16	1.75
5610986--5611020	2	17.5	2	100	0	70	48	0	0	51	1.00
5612834--5612886	19	2.8	19	72	11	54	43	0	1	54	1.11
5614738--5614767	11	2.7	11	100	0	60	33	6	40	20	1.78
5615964--5616053	30	3.0	30	98	0	171	51	0	0	48	1.00
5615941--5616230	54	5.9	47	78	12	200	41	0	6	51	1.28
5615964--5616096	15	8.5	15	80	11	151	45	0	2	51	1.13
5616076--5616224	32	5.3	31	67	29	118	34	0	9	55	1.32
5616076--5617079	54	18.4	55	75	15	484	34	0	11	53	1.41
5616151--5616195	22	2.0	22	95	0	81	37	0	11	51	1.38
5616198--5616245	22	2.4	18	73	23	51	33	0	14	52	1.42
5616254--5616361	32	3.7	31	73	23	108	33	1	12	52	1.49
5616287--5616329	22	2.0	22	100	0	86	34	0	13	51	1.42
5616388--5616473	32	2.7	32	92	0	136	32	2	10	54	1.47
5616309--5617015	112	6.5	109	75	18	568	34	0	12	52	1.41
5616444--5616494	22	2.4	22	71	15	52	35	0	11	52	1.38
5616125--5617015	134	6.6	137	84	9	734	34	0	12	52	1.42
5616500--5616607	32	3.7	31	75	23	110	35	0	12	51	1.40
5616537--5616584	22	2.2	22	100	0	96	35	0	10	54	1.35
5616577--5616650	22	3.2	21	75	21	60	28	0	18	52	1.46
5616634--5616741	32	3.7	32	76	23	146	35	0	12	51	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5616671--5616807	22	5.8	22	79	17	132	37	0	10	51	1.37
5616721--5616807	44	2.0	44	95	0	156	36	0	11	51	1.38
5616667--5616953	98	2.8	100	81	13	346	35	0	11	52	1.38
5616791--5616848	18	3.4	18	65	26	54	37	0	5	56	1.21
5616796--5616848	14	3.5	14	72	18	52	37	0	5	56	1.23
5616787--5616870	32	2.6	32	96	0	150	35	0	9	54	1.33
5616842--5616889	22	2.4	19	75	21	53	31	0	14	54	1.41
5616901--5617024	14	7.9	15	64	20	58	37	0	9	53	1.34
5616922--5617042	18	7.4	18	64	23	70	33	0	13	52	1.40
5616908--5617047	32	4.4	32	96	0	262	35	0	11	52	1.37
5617094--5617153	31	1.9	31	93	0	102	43	6	6	43	1.57
5617996--5618027	2	16.0	2	100	0	64	50	0	0	50	1.00
5620537--5620628	39	2.4	39	92	0	148	17	31	20	30	1.96
5621399--5621441	20	2.2	20	86	0	59	39	20	16	23	1.92
5622062--5622099	20	1.9	20	94	0	67	57	15	13	13	1.65
5622102--5622154	20	2.7	19	80	8	61	15	13	20	50	1.76
5623568--5623623	3	18.7	3	96	0	103	33	1	0	64	1.04
5623622--5623679	20	3.1	19	80	9	57	67	1	0	31	1.01
5625021--5625056	19	1.9	19	94	5	65	22	0	5	72	1.05
5636457--5636501	7	6.6	7	85	14	67	84	0	15	0	0.62
5636457--5636501	13	3.3	13	85	11	63	84	0	15	0	0.62
5636829--5636867	19	2.0	20	90	5	62	30	5	12	51	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5637436--5638215	81	9.5	81	91	2	1204	29	13	21	35	1.92
5637436--5638215	164	4.8	164	92	1	1255	29	13	21	35	1.92
5638949--5639459	113	4.5	113	95	0	898	37	15	18	29	1.91
5639704--5639747	3	14.7	3	95	0	79	34	2	0	63	1.07
5639746--5639790	20	2.3	19	84	3	54	62	2	0	35	1.08
5641919--5642015	42	2.3	42	89	0	140	29	36	17	16	1.92
5642130--5642179	21	2.4	21	82	0	64	18	14	36	32	1.90
5642605--5642698	21	4.5	21	90	0	152	21	41	19	18	1.90
5644234--5644279	20	2.3	20	84	0	56	15	21	15	47	1.81
5644264--5644320	29	2.0	29	100	0	114	31	28	15	24	1.96
5647051--5647084	12	2.8	12	90	0	50	14	0	29	55	1.40
5647849--5647900	18	2.7	20	73	11	63	34	9	21	34	1.86
5647893--5647962	20	3.5	19	74	14	61	35	12	22	28	1.91
5649587--5649620	2	17.0	2	100	0	68	50	0	0	50	1.00
5653279--5653329	24	2.1	24	92	0	84	52	3	29	13	1.58
5657137--5657189	21	2.5	21	100	0	106	33	18	15	32	1.92
5660665--5660821	65	2.4	64	88	5	219	29	17	22	29	1.97
5669414--5669573	65	2.5	64	87	7	227	28	19	23	28	1.98
5676264--5676299	2	18.0	2	94	0	63	47	2	0	50	1.15
5681104--5681130	5	5.4	5	100	0	54	81	18	0	0	0.69
5681486--5681665	52	3.5	52	92	0	306	27	32	14	25	1.94
5698427--5698460	9	3.8	9	100	0	68	82	0	8	8	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5701651--5701751	51	2.0	51	90	0	157	34	17	16	30	1.93
5703836--5703888	24	2.2	24	96	0	97	32	15	20	32	1.93
5704505--5704587	40	2.1	38	86	4	112	34	25	16	22	1.95
5711519--5711552	17	2.1	16	88	5	50	76	0	8	14	1.01
5715355--5715398	20	2.2	20	84	4	63	65	0	15	18	1.27
5721734--5721767	17	2.1	16	88	5	50	76	0	8	14	1.01
5730707--5730799	20	5.0	20	72	15	83	34	3	16	46	1.63
5730691--5730798	53	2.0	53	96	0	198	30	2	15	50	1.58
5735307--5735374	33	2.1	33	91	5	111	25	2	13	58	1.49
5737465--5737496	5	6.6	5	92	7	57	81	0	0	18	0.70

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   51   52   53   54   55