genome.fa.s1279.2.7.7.80.10.50.1000.19.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: 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  19  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)
4377546--4377614	2	34.5	2	95	0	120	46	0	1	52	1.09
4379551--4379660	31	3.4	31	74	14	114	39	17	19	24	1.92
4396936--4396986	20	2.5	20	80	0	66	49	9	17	23	1.77
4397088--4397147	26	2.3	26	91	0	102	23	11	6	58	1.57
4397168--4397198	15	2.1	15	93	0	53	54	0	0	45	0.99
4399592--4399616	12	2.1	12	100	0	50	36	0	24	40	1.55
4399880--4399919	21	1.9	21	90	10	64	20	30	30	20	1.97
4400257--4400341	2	43.0	2	97	2	163	49	0	0	50	1.00
4400610--4400634	12	2.1	12	100	0	50	68	0	8	24	1.16
4401895--4402093	75	2.6	76	88	3	285	19	24	33	22	1.97
4402708--4402751	17	2.6	17	85	7	63	56	29	0	13	1.38
4402703--4402753	9	6.2	8	78	17	52	58	27	0	13	1.36
4410527--4410729	74	2.7	76	86	4	277	20	24	32	23	1.98
4411270--4411397	31	4.1	31	74	6	123	28	17	20	33	1.96
4412215--4412261	22	2.1	22	88	0	67	23	19	17	40	1.91
4412223--4412267	22	2.0	22	91	0	72	22	20	17	40	1.92
4413715--4413739	12	2.1	12	100	0	50	36	0	24	40	1.55
4414003--4414047	22	2.0	22	95	0	81	22	28	26	22	1.99
4415188--4415231	20	2.3	18	88	7	61	34	2	25	38	1.68
4415233--4415542	153	2.0	153	99	0	611	42	7	18	31	1.78
4416600--4416656	22	2.5	23	85	5	71	19	14	19	47	1.82
4416622--4416665	24	2.0	23	86	13	65	22	11	18	47	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4416623--4416684	21	2.9	21	81	11	56	22	14	14	48	1.80
4416633--4416684	21	2.6	20	79	8	61	23	15	13	48	1.80
4419205--4419295	27	3.4	27	82	10	91	43	1	1	53	1.15
4419253--4419318	16	4.4	16	66	24	54	42	0	3	54	1.15
4419349--4419386	19	2.0	20	85	15	53	60	0	10	28	1.30
4419371--4419485	33	3.6	31	74	14	99	54	2	6	35	1.41
4419455--4419518	27	2.4	27	86	5	85	54	1	1	42	1.19
4419476--4419539	27	2.5	27	85	9	82	53	0	4	42	1.22
4423379--4423444	27	2.4	27	100	0	132	42	12	34	10	1.77
4423379--4423444	12	4.8	15	78	21	90	42	12	34	10	1.77
4425712--4425759	20	2.5	19	83	9	62	35	14	25	25	1.94
4428956--4429144	94	2.0	94	100	0	378	39	17	20	22	1.93
4432637--4432665	6	4.8	6	100	0	58	17	17	65	0	1.27
4432676--4432712	12	3.0	12	92	4	56	18	54	16	10	1.71
4432713--4432809	32	3.0	32	79	10	101	53	0	0	46	1.00
4432811--4432865	24	2.3	24	90	0	83	25	47	14	12	1.80
4432811--4432865	12	4.6	12	81	0	65	25	47	14	12	1.80
4439166--4439206	3	14.0	3	80	14	50	36	0	0	63	0.95
4448278--4448583	84	3.7	84	92	3	510	28	13	21	37	1.91
4451152--4451206	22	2.5	22	90	0	92	34	12	14	38	1.84
4451609--4452278	113	6.0	113	89	3	931	38	13	18	29	1.89
4452685--4453324	76	8.4	76	96	0	1145	22	20	21	36	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4453753--4453794	20	2.0	21	81	9	50	76	9	11	2	1.12
4462995--4463034	19	2.1	19	100	0	80	0	40	10	50	1.36
4463843--4463994	53	2.9	53	84	0	205	22	26	19	30	1.98
4464038--4464147	20	5.2	21	64	15	66	35	21	17	25	1.95
4464029--4464157	42	3.1	41	88	1	177	34	22	17	25	1.96
4475247--4475279	7	4.7	7	100	0	66	84	0	0	15	0.61
4476180--4476215	18	2.0	18	88	0	54	30	8	30	30	1.87
4477093--4477198	30	3.5	30	80	5	106	33	22	18	24	1.97
4477106--4477198	30	3.1	30	80	6	107	33	21	18	26	1.96
4477333--4477368	17	2.0	19	89	10	58	38	11	5	44	1.63
4477855--4478014	64	2.5	64	84	4	198	26	20	19	34	1.96
4479742--4479814	31	2.4	31	84	9	87	41	8	8	42	1.64
4488086--4488162	38	2.0	38	87	0	109	23	14	18	44	1.86
4488387--4488596	105	2.0	105	100	0	420	46	9	20	22	1.80
4491481--4491514	2	17.0	2	93	0	59	50	2	0	47	1.16
4494523--4494650	56	2.3	56	82	2	150	39	16	16	27	1.90
4494890--4495118	55	4.2	55	85	2	291	39	10	16	34	1.82
4496134--4496483	183	1.9	183	89	3	544	45	8	3	43	1.49
4497814--4497856	20	2.0	22	86	8	63	34	16	2	46	1.60
4498137--4498173	3	12.0	3	94	5	65	32	0	0	67	0.91
4512293--4512356	28	2.3	28	94	0	110	26	23	14	35	1.93
4512376--4512440	22	3.0	22	83	0	85	18	44	16	20	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4512861--4512906	23	2.0	23	95	0	83	21	10	52	15	1.73
4513622--4513659	18	2.1	18	100	0	76	31	10	5	52	1.58
4514338--4514392	22	2.5	22	96	0	101	32	16	12	38	1.86
4514782--4515337	123	4.5	123	89	2	812	40	15	19	25	1.90
4514782--4515337	245	2.3	246	90	2	848	40	15	19	25	1.90
4515169--4515232	20	3.2	20	63	20	53	42	9	23	25	1.84
4515706--4515749	3	15.0	3	90	4	72	34	0	2	63	1.07
4515710--4515749	20	2.0	20	95	0	71	35	0	2	62	1.09
4516727--4516777	15	3.5	15	74	15	52	27	5	7	58	1.49
4517173--4517199	13	2.1	13	100	0	54	22	0	0	77	0.76
4518727--4518789	30	2.1	29	85	2	81	53	0	0	46	1.00
4518737--4518789	18	2.8	21	83	16	71	56	0	0	43	0.99
4521191--4521264	23	3.2	23	81	7	87	28	20	28	22	1.99
4521197--4521265	24	2.9	24	89	2	104	27	21	28	21	1.99
4521370--4521446	30	2.6	30	82	0	91	40	25	7	25	1.83
4521407--4521446	15	2.7	14	81	11	53	45	27	2	25	1.66
4523621--4523661	17	2.4	17	95	0	73	17	41	24	17	1.89
4523651--4523687	7	5.4	7	93	6	67	16	29	29	24	1.96
4523651--4523683	13	2.5	13	95	5	57	15	30	30	24	1.95
4530830--4530898	10	7.1	10	76	12	72	18	23	30	27	1.98
4530830--4530900	19	3.7	19	88	5	90	18	25	29	26	1.98
4530907--4530956	7	7.4	7	91	8	86	16	30	28	26	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4530907--4530956	20	2.5	20	93	6	84	16	30	28	26	1.96
4530907--4530953	13	3.5	13	91	2	76	14	29	27	27	1.96
4541312--4541380	23	2.9	24	82	8	79	36	24	21	17	1.95
4542892--4543123	112	2.1	110	90	1	365	28	15	19	36	1.93
4543166--4543207	20	2.1	19	86	8	57	57	2	19	21	1.52
4549874--4550082	112	1.9	112	87	1	312	29	18	17	34	1.94
4550722--4550795	15	5.1	15	67	9	55	41	25	6	25	1.80
4554066--4554121	18	3.1	18	84	2	76	46	0	0	53	1.00
4557654--4557795	47	3.0	47	97	0	266	26	23	14	34	1.94
4561276--4561327	24	2.2	23	83	13	61	50	1	0	48	1.12
4570466--4570511	22	2.1	22	87	0	65	26	23	15	34	1.94
4571628--4571666	21	1.9	21	94	5	71	30	10	20	38	1.86
4587779--4587839	20	2.9	21	87	7	79	18	26	34	21	1.96
4599957--4599981	11	2.3	11	100	0	50	28	8	12	52	1.66
4601206--4601256	26	2.0	26	96	0	93	21	17	29	31	1.96
4607868--4607903	12	3.0	12	92	8	56	66	8	25	0	1.19
4608691--4608718	2	14.0	2	100	0	56	50	0	0	50	1.00
4609572--4609636	2	32.5	2	100	0	130	49	0	0	50	1.00
4610114--4610235	64	1.9	63	90	5	192	28	0	14	56	1.39
4610855--4610919	18	3.5	18	76	19	55	26	4	0	69	1.08
4613708--4613801	5	19.0	5	77	10	77	24	5	1	69	1.16
4613708--4613777	14	4.9	14	87	3	95	21	7	0	71	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4613708--4613800	19	4.7	20	78	9	93	24	5	1	68	1.17
4615379--4615442	32	2.0	32	85	11	87	25	0	9	65	1.22
4616134--4616177	18	2.4	19	88	3	63	18	6	2	72	1.17
4618037--4618867	414	2.0	414	96	0	1527	37	14	14	33	1.86
4620610--4621287	54	12.6	54	85	3	814	31	18	16	33	1.93
4621629--4621682	22	2.6	22	78	18	62	29	18	16	35	1.93
4621631--4621682	19	2.5	22	77	20	58	28	19	17	34	1.94
4625146--4625196	20	2.5	20	84	6	68	41	17	7	33	1.79
4626613--4626660	13	3.7	13	88	5	71	41	0	0	58	0.98
4626613--4626660	3	15.0	3	79	12	51	41	0	0	58	0.98

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