genome.fa.s9639.2.7.7.80.10.50.1000.19.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: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  15077257

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   56   57   58   59   60   61   62   

This is table  19  of  62  ( 7398 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)
4096705--4096744	18	2.3	18	83	8	57	25	5	2	67	1.23
4096814--4096846	2	16.5	2	100	0	66	48	0	0	51	1.00
4096942--4096978	19	1.9	19	88	0	56	43	5	0	51	1.24
4097027--4097055	2	14.5	2	100	0	58	48	0	0	51	1.00
4097405--4097473	9	7.8	8	75	22	50	18	7	0	73	1.05
4097405--4097473	13	5.2	13	80	16	70	18	7	0	73	1.05
4097413--4097473	9	6.8	9	77	22	58	18	6	0	75	1.01
4097405--4097489	18	4.8	17	76	11	64	17	9	1	71	1.18
4101837--4102031	102	1.9	102	84	4	259	46	14	12	26	1.80
4101837--4102014	51	3.5	52	78	9	188	48	15	11	25	1.78
4102163--4102192	2	15.0	2	100	0	60	50	0	0	50	1.00
4102383--4102601	117	1.9	118	81	7	275	30	19	16	32	1.94
4102364--4102608	40	6.1	41	75	12	195	29	18	16	35	1.93
4102364--4102569	81	2.6	77	81	6	227	29	18	17	33	1.95
4106088--4106121	16	2.1	16	100	0	68	26	5	17	50	1.69
4106337--4106589	117	2.2	117	88	2	382	32	20	20	26	1.97
4106484--4106623	76	1.9	75	86	1	199	33	18	20	27	1.96
4111574--4111617	23	2.0	23	86	4	63	13	13	4	68	1.36
4117476--4117506	2	15.5	2	100	0	62	48	0	0	51	1.00
4118121--4118170	22	2.2	23	86	10	68	32	0	2	66	1.03
4118194--4118263	14	5.1	14	72	19	58	41	0	2	55	1.14
4118195--4118260	26	2.4	28	87	12	109	39	0	3	57	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4118195--4118269	26	2.8	26	90	8	107	40	1	2	56	1.22
4118195--4118288	26	3.9	24	74	19	81	40	1	2	56	1.18
4118256--4118317	19	3.3	19	78	15	58	37	1	0	61	1.06
4119195--4119246	20	2.6	20	96	0	95	9	26	26	36	1.87
4119734--4119793	31	1.9	31	86	0	84	45	10	3	41	1.54
4121185--4121266	37	2.4	32	75	24	87	50	0	1	48	1.08
4126897--4126932	16	2.2	16	100	0	72	47	5	16	30	1.70
4127378--4127410	14	2.4	14	95	5	59	30	33	21	15	1.94
4128390--4128443	17	2.8	20	75	18	60	25	37	9	27	1.87
4129965--4129993	12	2.3	13	94	5	51	0	37	6	55	1.27
4130484--4130533	23	2.2	23	96	0	91	30	24	28	18	1.97
4135335--4135399	23	2.8	23	80	0	85	30	24	21	23	1.99
4136932--4136986	20	2.5	21	77	14	58	23	23	20	32	1.98
4136977--4137064	19	4.6	19	97	0	158	21	29	15	32	1.95
4138385--4138435	22	2.3	22	89	0	75	39	21	11	27	1.88
4138958--4139024	33	2.0	33	97	0	125	29	22	17	29	1.97
4139053--4139082	15	2.0	15	93	0	51	36	13	23	26	1.92
4138996--4139139	72	2.0	72	100	0	288	27	20	20	30	1.98
4148367--4148431	12	5.8	12	78	14	84	36	18	16	27	1.93
4148366--4148430	22	3.0	22	100	0	130	36	18	16	27	1.93
4148379--4148418	10	3.8	10	81	12	53	40	17	17	25	1.91
4148966--4149032	33	2.0	33	97	0	125	31	26	16	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4169019--4169080	31	2.0	31	100	0	124	25	35	16	22	1.94
4177273--4177345	2	36.5	2	100	0	146	49	0	0	50	1.00
4177538--4177860	68	4.8	68	89	1	463	30	24	14	30	1.95
4177538--4177860	135	2.4	135	91	2	497	30	24	14	30	1.95
4180564--4180593	16	1.9	16	93	6	53	56	13	3	26	1.52
4181930--4182301	184	2.0	185	92	2	615	45	9	3	41	1.54
4203761--4203785	2	12.5	2	100	0	50	52	0	0	48	1.00
4208605--4208658	28	1.9	28	85	7	74	55	0	5	38	1.23
4211334--4211385	18	2.9	18	72	11	52	55	11	5	26	1.58
4227782--4227864	23	3.8	21	80	10	78	25	31	22	20	1.98
4227783--4227848	23	2.9	22	86	6	87	22	30	24	22	1.99
4234455--4234508	26	2.1	26	100	0	108	11	38	7	42	1.68
4234874--4234936	31	2.1	31	87	3	92	49	1	12	36	1.51
4242259--4242288	14	2.1	14	93	0	51	13	30	0	56	1.37
4244497--4244588	30	3.1	30	91	0	157	33	22	17	26	1.96
4244497--4244616	60	2.0	60	85	0	159	34	24	18	23	1.96
4247233--4247302	2	35.0	2	100	0	140	50	0	0	50	1.00
4250008--4250110	30	3.4	30	82	0	134	33	22	18	26	1.97
4250014--4250127	60	1.9	60	81	0	138	35	21	18	23	1.95
4257949--4257982	14	2.3	15	85	10	52	67	0	8	23	1.18
4257981--4258013	17	1.9	17	93	0	57	60	3	9	27	1.42
4258471--4258572	47	2.1	48	96	3	197	31	16	7	44	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4258851--4259449	43	14.0	43	75	12	454	49	5	19	26	1.69
4258837--4259441	85	7.1	85	77	10	463	49	4	19	26	1.68
4259710--4259813	31	3.6	28	82	8	120	42	10	9	37	1.72
4263920--4263954	18	2.0	18	88	5	54	54	2	0	42	1.15
4270663--4270695	15	2.2	15	94	0	57	6	66	18	9	1.40
4278207--4278257	18	2.8	18	93	0	84	15	21	7	54	1.66
4280326--4280419	32	3.0	31	77	11	93	41	8	6	43	1.60
4280810--4280865	15	3.6	15	83	9	76	41	12	12	33	1.81
4280813--4280863	17	3.1	17	80	11	70	41	11	9	37	1.75
4281035--4281108	21	3.5	21	96	0	130	29	27	22	20	1.98
4281304--4281358	13	4.2	13	75	13	58	49	12	3	34	1.59
4281344--4281442	33	3.0	33	92	1	155	46	14	7	32	1.71
4281437--4281476	21	1.9	21	94	0	71	47	7	15	30	1.72
4284562--4284660	46	2.2	46	96	0	180	50	10	9	30	1.67
4284792--4284838	21	2.2	21	96	0	85	23	19	34	23	1.97
4288922--4288951	3	10.0	3	100	0	60	33	0	0	66	0.92
4289501--4289527	6	4.5	6	100	0	54	55	0	0	44	0.99
4289718--4289753	5	7.4	5	87	6	56	77	0	2	19	0.88
4291898--4291935	2	19.5	2	86	5	51	47	0	2	50	1.15
4292001--4292049	2	25.0	2	91	4	82	53	0	0	46	1.00
4302256--4302280	5	5.0	5	100	0	50	20	20	40	20	1.92
4302443--4302480	6	6.3	6	82	11	51	21	28	31	18	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4302443--4302480	13	3.2	12	88	7	51	21	28	31	18	1.97
4302473--4302518	12	3.9	12	77	5	58	19	19	21	39	1.93
4302474--4302525	23	2.3	23	93	0	86	21	21	21	36	1.95
4302474--4302525	11	4.5	12	76	7	54	21	21	21	36	1.95
4305337--4305374	20	1.9	20	100	0	76	28	15	21	34	1.94
4305424--4305600	20	9.5	20	74	16	130	18	18	21	41	1.90
4305403--4305600	40	5.4	38	73	15	145	17	18	21	42	1.89
4305396--4305589	107	1.8	107	90	0	316	17	19	20	43	1.88
4307486--4307555	20	3.5	20	90	0	86	41	25	17	15	1.89
4307485--4307598	33	3.2	34	75	13	88	42	24	19	13	1.86
4307923--4307988	22	3.0	22	90	0	105	21	15	39	24	1.91
4308196--4308502	20	15.3	20	78	12	206	24	18	22	34	1.96
4308294--4308339	21	2.2	21	88	0	65	36	17	28	17	1.92
4308207--4308623	201	2.1	201	96	0	773	26	18	23	31	1.97
4313976--4314014	13	3.0	13	88	0	60	28	23	17	30	1.97
4314214--4314275	26	2.3	27	94	5	108	45	12	9	32	1.75
4315466--4315492	2	13.5	2	100	0	54	51	0	0	48	1.00
4333229--4333261	15	2.2	15	94	0	57	51	6	0	42	1.26
4333915--4334001	31	2.9	30	79	5	104	60	8	12	18	1.55
4337895--4337955	23	2.7	23	92	2	97	21	27	26	24	1.99
4338147--4338207	21	2.9	21	78	9	54	47	1	19	31	1.59
4342815--4343112	149	2.0	145	88	3	445	25	15	22	36	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4343091--4343151	23	2.7	23	94	2	106	21	26	26	26	1.99
4344066--4344268	44	4.9	40	77	12	180	25	18	24	31	1.98
4344315--4344672	47	7.9	47	78	11	372	29	17	22	30	1.97
4344443--4344800	94	3.9	94	80	11	440	27	17	24	30	1.97
4344034--4344825	128	6.2	127	82	8	829	27	18	24	29	1.98
4345194--4345295	33	3.1	33	92	0	168	31	21	14	32	1.94
4346285--4346319	14	2.6	14	95	4	63	11	8	0	80	0.92
4351368--4351422	22	2.5	22	96	0	101	40	5	7	47	1.54
4351378--4351429	22	2.7	18	76	21	59	36	3	7	51	1.49
4351516--4351559	16	2.8	16	83	10	56	54	6	4	34	1.47

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   56   57   58   59   60   61   62