genome.fa.s1279.2.7.7.80.10.50.1000.22.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

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   

This is table  22  of  29  ( 3433 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)
5059826--5059914	26	3.5	26	92	1	144	52	4	17	24	1.63
5060759--5060885	53	2.4	55	86	4	179	39	20	6	33	1.78
5060847--5060922	37	2.1	37	92	0	125	39	23	2	34	1.69
5063957--5063984	14	2.0	14	100	0	56	21	28	21	28	1.99
5066179--5066262	38	2.3	37	91	4	134	47	0	0	52	1.00
5066284--5066321	12	3.2	12	88	0	58	10	21	44	23	1.83
5066466--5066533	33	2.1	33	94	0	118	32	17	27	22	1.96
5069889--5070708	55	14.9	55	95	1	1396	31	24	15	28	1.95
5070712--5070821	37	3.0	37	87	2	141	22	20	18	39	1.93
5072082--5072153	34	2.2	33	78	14	76	5	18	0	76	0.97
5072100--5072138	15	2.4	16	87	8	53	7	17	0	74	1.05
5072088--5072234	26	5.8	24	72	19	88	6	19	0	73	1.10
5072094--5072251	9	18.0	9	67	25	56	6	18	0	74	1.08
5085298--5085458	36	4.5	36	85	3	191	49	8	12	29	1.70
5085509--5085667	44	3.6	44	81	2	158	32	17	21	28	1.96
5087052--5087106	18	3.1	18	78	7	67	47	1	5	45	1.36
5087052--5087114	19	3.4	18	76	14	58	50	1	4	42	1.32
5088316--5088347	6	5.3	6	100	0	64	18	18	0	62	1.33
5095766--5095801	2	18.5	2	88	5	56	50	0	0	50	1.00
5103403--5103432	7	4.3	7	91	0	51	46	36	0	16	1.47
5103403--5103456	21	2.6	21	81	0	72	46	31	0	22	1.52
5104408--5104472	34	1.9	33	93	3	112	20	35	12	32	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5107035--5107067	17	1.9	17	100	0	66	27	18	24	30	1.98
5107146--5107201	29	2.0	28	86	10	78	25	16	21	37	1.93
5109887--5109928	13	3.2	13	80	16	50	54	0	35	9	1.33
5120185--5120270	41	2.1	40	85	14	115	23	19	19	37	1.94
5120446--5120533	41	2.1	41	85	4	115	29	23	14	31	1.95
5120120--5120690	240	2.4	236	84	7	703	30	20	16	33	1.94
5121645--5121688	23	1.9	23	86	9	63	25	15	20	38	1.92
5126802--5126859	30	2.0	27	83	9	71	43	1	1	53	1.21
5126802--5126861	28	2.2	26	82	14	68	43	1	1	53	1.20
5132421--5132459	16	2.4	16	78	0	51	23	17	33	25	1.96
5132443--5132545	32	3.2	32	74	12	93	23	10	25	40	1.86
5132768--5132824	30	1.9	30	96	0	105	33	3	8	54	1.48
5132872--5132896	13	1.9	13	100	0	50	36	0	0	64	0.94
5133198--5133246	19	2.7	19	78	6	57	46	4	0	48	1.20
5133754--5133801	22	2.3	20	79	13	53	37	6	0	56	1.25
5136436--5136465	14	2.1	14	93	0	51	43	0	16	40	1.48
5142547--5142619	28	2.6	27	82	8	85	39	5	2	52	1.39
5142538--5142590	2	27.5	2	83	7	65	45	1	1	50	1.23
5146474--5146519	23	2.0	23	91	0	74	45	6	19	28	1.75
5154769--5154817	20	2.5	20	82	0	62	28	14	18	38	1.90
5156482--5156568	42	2.0	43	82	6	106	16	4	19	59	1.53
5157897--5157970	20	3.8	20	71	10	55	29	12	14	43	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5170284--5170329	20	2.3	19	85	14	58	50	8	15	26	1.73
5173293--5173434	63	2.3	63	79	4	144	34	17	19	28	1.94
5173324--5173469	42	3.5	41	80	7	134	34	17	19	28	1.95
5173367--5173470	21	5.0	21	77	8	104	34	14	20	30	1.92
5173893--5173927	18	1.9	18	94	0	61	22	22	25	28	1.99
5173913--5173971	21	2.7	23	87	7	79	35	18	16	28	1.93
5174941--5175881	467	2.0	472	97	2	1797	28	12	20	38	1.89
5175948--5176021	23	3.1	23	75	18	62	47	1	4	47	1.29
5175952--5176021	26	2.8	24	74	18	70	48	1	4	45	1.30
5176070--5176145	22	3.4	22	80	7	73	52	3	1	42	1.28
5177537--5177561	13	1.9	13	100	0	50	56	20	0	24	1.43
5178011--5178036	2	13.0	2	100	0	52	50	0	0	50	1.00
5179014--5179322	37	8.6	36	83	8	328	45	3	5	45	1.41
5179075--5179128	27	2.0	27	82	3	65	46	1	1	50	1.23
5179030--5179334	73	4.2	72	84	5	348	45	3	4	46	1.41
5179375--5179459	23	3.8	23	80	17	108	27	2	0	70	0.99
5179375--5179454	3	25.7	3	80	14	83	27	2	0	70	1.01
5179374--5179458	29	2.8	29	84	8	100	27	2	0	70	0.99
5181048--5181968	84	11.1	84	78	6	784	31	23	19	25	1.98
5181048--5181968	168	5.5	167	78	6	877	31	23	19	25	1.98
5181048--5181980	332	2.8	330	82	5	1056	31	23	19	25	1.98
5182782--5183115	37	9.1	37	83	9	364	44	3	6	45	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5182865--5182914	26	1.9	26	83	0	64	46	2	6	46	1.39
5182782--5183115	74	4.6	74	87	5	423	44	3	6	45	1.48
5183166--5183207	12	3.7	11	78	15	50	21	2	0	76	0.90
5183168--5183228	26	2.3	27	78	16	65	21	3	1	73	1.06
5183381--5183975	297	2.0	297	98	1	1149	42	27	17	12	1.86
5184736--5184786	16	3.3	16	74	15	54	19	5	0	74	1.02
5185349--5185374	13	2.0	13	100	0	52	38	15	15	30	1.88
5186877--5186903	3	9.0	3	100	0	54	66	0	33	0	0.92
5188848--5188872	11	2.3	11	100	0	50	16	0	16	68	1.22
5192530--5192604	21	3.8	21	80	18	97	37	13	13	36	1.84
5192527--5192605	39	2.1	38	92	2	131	39	12	12	35	1.81
5193984--5194051	35	2.0	35	97	2	129	47	2	0	50	1.16
5194008--5194051	24	1.9	22	86	9	61	45	2	0	52	1.13
5197353--5197387	14	2.5	14	100	0	70	31	22	8	37	1.85
5200761--5200800	21	1.9	21	89	0	62	55	7	7	30	1.56
5208227--5208289	22	3.0	21	90	4	99	25	23	26	23	2.00
5208864--5208922	21	2.8	21	92	5	93	25	23	32	18	1.97
5216181--5216221	21	2.0	21	90	0	64	24	24	24	26	2.00
5219525--5219602	22	3.6	22	91	1	113	26	20	29	23	1.99
5223557--5223617	17	3.5	17	84	8	79	19	44	22	13	1.85
5223620--5223897	29	9.6	29	85	4	328	37	3	19	39	1.69
5231180--5231339	29	5.6	28	83	7	196	36	5	21	36	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5231180--5231339	57	2.8	59	87	4	220	36	5	21	36	1.77
5234616--5235365	187	4.0	187	97	0	1380	33	13	16	36	1.88
5236408--5236680	139	2.0	140	86	3	381	42	16	14	27	1.86
5236415--5236716	139	2.2	140	83	4	369	41	16	13	28	1.86
5237126--5237183	30	1.9	30	86	6	82	62	5	6	25	1.42
5238265--5238323	22	2.7	21	73	17	57	54	3	18	23	1.59
5248984--5249780	252	3.2	252	88	6	1195	27	12	20	40	1.88
5253230--5253269	2	21.0	2	90	10	66	50	0	0	50	1.00
5256835--5256880	15	3.3	15	76	14	53	56	0	2	41	1.11
5258212--5258298	3	29.7	3	77	9	90	60	0	0	39	0.97
5258542--5259338	227	3.5	226	93	0	1306	31	18	14	35	1.91
5258542--5259338	340	2.3	340	92	0	1308	31	18	14	35	1.91
5258542--5259338	113	7.0	113	94	0	1306	31	18	14	35	1.91
5260148--5260508	83	4.4	83	90	3	579	37	21	12	28	1.90
5260148--5260508	161	2.2	163	91	2	573	37	21	12	28	1.90
5261641--5261686	10	4.5	10	91	5	65	0	15	0	84	0.62
5265648--5265690	20	2.1	20	83	12	52	11	27	4	55	1.55
5274364--5274435	3	24.7	3	72	10	51	58	0	0	41	0.98
5274364--5274423	18	3.2	18	83	4	75	55	0	0	45	0.99
5275595--5275620	2	13.0	2	100	0	52	50	0	0	50	1.00
5287039--5287092	23	2.3	23	96	0	99	50	11	9	29	1.69
5305882--5305924	20	2.2	20	86	0	59	30	11	20	37	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5314450--5314492	20	2.2	20	86	0	59	30	11	20	37	1.89
5316053--5316244	96	2.0	96	93	0	330	30	22	14	33	1.93
5317051--5317451	189	2.1	191	86	5	564	44	10	5	39	1.62
5320809--5320876	24	2.8	25	86	8	95	30	25	26	17	1.97
5324191--5324568	188	2.0	192	82	8	461	46	10	5	38	1.62
5326602--5326658	27	2.1	28	90	3	89	40	21	14	24	1.90
5327847--5327919	32	2.3	32	87	0	101	15	32	26	26	1.95
5342336--5342398	14	4.5	14	91	0	99	25	26	20	26	1.99
5342407--5342436	13	2.2	14	94	5	53	16	20	20	43	1.88
5352187--5352226	21	1.9	21	89	0	62	25	20	22	32	1.98

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