genome.fa.s9643.2.7.7.80.10.50.1000.23.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: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8859806

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   

This is table  23  of  41  ( 4862 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)
4878871--4881883	973	3.1	977	97	1	5677	40	12	7	39	1.71
4880994--4881053	23	2.6	23	89	0	84	38	20	6	35	1.79
4881477--4881539	23	2.7	23	87	0	90	38	19	4	38	1.73
4881557--4881602	22	2.1	22	87	0	65	41	10	8	39	1.71
4881882--4881947	25	2.6	25	80	0	87	42	13	9	34	1.76
4884407--4884749	183	1.9	183	91	2	564	33	16	14	35	1.89
4885106--4885168	23	2.7	23	92	0	99	38	20	4	36	1.74
4885596--4885654	23	2.6	23	88	0	82	40	16	5	37	1.71
4884929--4885929	486	2.1	477	95	1	1506	40	12	7	39	1.70
4887207--4887286	9	8.6	9	72	8	61	22	33	6	37	1.79
4887210--4887298	12	7.4	12	87	0	97	21	33	7	37	1.82
4887206--4887286	6	13.5	6	82	0	81	23	33	6	37	1.80
4887222--4887298	36	2.1	36	92	0	127	20	33	9	36	1.85
4887210--4887301	6	15.3	6	81	0	76	20	33	7	38	1.81
4888767--4890324	199	7.9	199	97	1	2931	30	17	15	36	1.91
4890442--4890490	19	2.6	19	93	0	80	57	10	2	30	1.43
4892257--4892322	33	2.0	33	87	0	96	22	46	1	28	1.61
4892356--4892399	21	2.1	21	91	0	70	15	31	11	40	1.83
4894612--4894659	20	2.4	20	82	6	53	20	12	8	58	1.60
4894783--4894827	19	2.4	19	85	7	65	17	17	11	53	1.72
4894785--4894836	19	2.7	18	85	8	50	19	17	13	50	1.78
4894876--4895594	229	3.1	229	95	2	1279	39	8	7	44	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4909021--4909052	10	3.3	10	91	8	57	37	9	9	43	1.69
4909501--4909559	24	2.5	24	88	0	100	33	20	25	20	1.97
4910189--4910218	15	2.0	15	93	0	51	43	3	26	26	1.70
4910427--4910461	18	1.9	18	94	0	61	20	20	34	25	1.96
4928085--4928118	12	2.8	12	90	0	50	55	29	0	14	1.40
4928244--4928297	24	2.2	24	86	0	72	22	18	16	42	1.89
4931175--4931224	24	2.1	24	88	7	75	28	0	14	58	1.37
4936799--4936848	24	2.1	24	88	7	75	26	2	14	58	1.47
4937799--4937834	18	2.0	18	94	0	63	55	25	2	16	1.55
4938165--4938222	20	2.9	20	86	0	80	41	22	18	17	1.90
4938356--4938405	25	2.0	25	96	0	91	26	8	22	44	1.80
4938779--4938865	39	2.2	39	89	4	131	50	18	12	18	1.77
4939530--4939565	16	2.3	16	95	4	65	50	22	0	27	1.50
4940711--4940829	21	5.7	21	75	6	98	21	20	34	24	1.96
4940731--4940829	42	2.4	42	77	6	110	21	20	33	25	1.97
4941237--4941286	21	2.4	21	82	0	64	38	30	14	18	1.89
4943424--4943528	20	5.2	20	91	0	165	20	19	22	37	1.95
4943552--4943607	20	2.8	20	76	12	71	28	14	26	30	1.95
4945018--4945126	58	1.9	55	94	5	191	35	22	20	22	1.96
4959238--4959262	13	1.9	13	100	0	50	8	8	8	76	1.18
4959526--4959588	11	5.9	11	69	14	51	57	3	1	38	1.24
4960134--4960208	21	3.6	21	74	0	60	41	26	1	30	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4960589--4960620	3	11.0	3	93	6	57	65	0	0	34	0.93
4961993--4962144	23	6.6	23	89	0	214	32	23	19	25	1.97
4962025--4962114	12	7.8	12	71	7	78	34	26	17	21	1.95
4962701--4962742	22	1.9	22	85	9	59	52	11	14	21	1.73
4962727--4962810	23	3.7	23	79	4	89	45	13	13	28	1.80
4970539--4970602	9	6.9	9	77	13	67	15	25	31	28	1.96
4970535--4970602	19	3.7	19	88	3	95	17	26	29	26	1.98
4970609--4970657	7	7.6	7	78	17	61	16	34	28	20	1.94
4970609--4970662	13	4.2	13	92	2	83	18	33	27	20	1.96
4970609--4970662	19	2.8	19	78	15	58	18	33	27	20	1.96
4977047--4977094	19	2.5	20	86	3	62	16	22	31	29	1.96
4977129--4977165	7	5.4	7	93	6	67	16	29	29	24	1.96
4977129--4977161	13	2.5	13	95	5	57	15	30	30	24	1.95
4979233--4979314	2	41.0	2	100	0	164	50	0	0	50	1.00
4981077--4981106	3	10.3	3	92	7	53	70	0	0	30	0.88
4981111--4981174	31	2.1	31	82	8	78	46	3	0	50	1.17
4981127--4981267	31	4.4	31	73	15	92	43	6	3	46	1.46
4981221--4981383	39	4.2	38	87	3	229	42	7	1	48	1.41
4981233--4981382	77	1.9	77	91	2	248	42	7	1	48	1.39
4981331--4981451	62	1.9	65	84	5	167	43	6	1	47	1.39
4981481--4981526	2	23.0	2	100	0	92	50	0	0	50	1.00
4981995--4982536	164	3.3	162	81	5	628	25	19	25	29	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4981993--4982557	248	2.3	246	85	5	730	25	19	25	29	1.99
4981995--4982560	84	6.9	82	78	6	545	25	19	25	29	1.99
4984293--4984448	31	5.0	31	94	1	260	37	23	19	19	1.95
4985379--4985423	21	2.1	21	91	0	72	17	24	26	31	1.97
4991673--4991709	19	1.9	19	88	0	56	70	0	8	21	1.13
4991749--4992098	38	9.6	37	75	14	252	44	7	2	45	1.43
4991843--4991992	77	1.9	77	91	2	248	42	6	2	48	1.40
4991977--4992098	39	3.3	35	77	18	122	46	9	0	42	1.42
4992896--4992945	2	25.0	2	92	8	84	48	2	0	50	1.12
5004665--5004797	65	2.0	65	86	0	185	35	6	18	39	1.76
5005024--5005076	15	3.4	15	81	5	61	47	11	7	33	1.68
5005499--5005597	33	3.0	33	94	1	164	45	15	7	32	1.73
5005592--5005631	21	1.9	21	94	0	71	47	7	15	30	1.72
5007935--5007965	12	2.6	12	94	0	53	16	19	19	45	1.86
5009955--5009982	14	2.0	14	100	0	56	57	0	0	42	0.99
5012972--5013009	18	2.2	17	86	13	51	42	0	0	57	0.98
5018405--5018489	44	1.9	44	95	0	152	27	25	8	38	1.84
5019290--5019393	42	2.5	42	88	0	154	24	19	21	35	1.96
5019286--5019361	21	3.6	21	69	13	66	19	21	23	35	1.96
5020197--5020492	21	14.3	21	72	19	155	35	23	19	21	1.96
5020193--5020413	42	5.3	42	88	1	320	34	23	19	21	1.97
5020260--5020478	103	2.1	103	87	5	316	33	24	21	21	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5020426--5020492	19	3.3	19	72	12	62	38	20	19	20	1.93
5020488--5020540	21	2.5	21	87	0	79	16	18	32	32	1.94
5022400--5022456	28	2.0	28	100	0	114	38	14	3	43	1.62
5022708--5022751	17	2.6	17	85	7	63	56	29	0	13	1.38
5024255--5024295	19	2.2	19	83	16	50	53	17	0	29	1.44
5024708--5024788	21	3.8	21	79	9	67	16	24	37	22	1.93
5032320--5032363	21	2.1	21	86	0	61	18	27	15	38	1.91
5032415--5032541	20	6.3	20	84	6	168	25	22	17	34	1.95
5032382--5032536	81	1.9	80	82	5	195	27	21	18	31	1.97
5032415--5032541	61	2.1	60	85	5	168	25	22	17	34	1.95
5032401--5032547	20	7.3	20	82	6	156	27	22	17	31	1.97
5035993--5036064	14	4.8	14	77	15	72	45	19	25	9	1.80
5036007--5036085	33	2.4	33	95	0	140	45	18	25	10	1.81
5036248--5036284	14	2.6	14	91	0	65	45	21	0	32	1.52
5037649--5037729	21	3.9	21	69	6	65	24	22	32	20	1.98
5038146--5038202	19	2.9	19	81	5	69	47	21	19	12	1.81
5038170--5038208	19	2.1	19	90	0	60	48	25	17	7	1.74
5038352--5038653	94	3.2	93	97	0	550	48	19	12	20	1.81
5038563--5038715	78	1.9	79	92	5	254	43	18	13	24	1.86
5040390--5040463	20	3.8	19	84	7	103	45	18	22	12	1.83
5041039--5041132	20	4.7	20	82	2	125	22	20	18	39	1.92
5041021--5041132	20	5.6	20	80	4	118	22	20	19	37	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5041039--5041132	41	2.3	40	87	1	125	22	20	18	39	1.92
5041122--5041196	21	3.6	21	80	3	89	38	17	22	21	1.93
5041140--5041207	21	3.4	20	82	6	84	41	19	22	17	1.91
5041115--5041207	41	2.3	40	87	3	132	37	18	21	22	1.94
5041217--5041267	20	2.5	20	90	0	84	19	21	23	35	1.96
5041264--5041309	21	2.2	21	92	0	74	34	17	30	17	1.93
5041835--5041874	21	2.0	21	90	5	64	30	2	0	67	1.04
5042771--5042797	2	13.5	2	100	0	54	51	0	0	48	1.00
5044686--5044712	2	13.5	2	100	0	54	51	0	0	48	1.00
5045119--5045162	2	22.5	2	95	4	81	47	0	0	52	1.00

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