genome.fa.s1279.2.7.7.80.10.50.1000.23.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: 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  23  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)
5353772--5353817	20	2.3	19	85	14	58	50	8	15	26	1.73
5357681--5357713	2	16.5	2	100	0	66	48	0	0	51	1.00
5358587--5358611	6	4.2	6	100	0	50	16	0	0	84	0.63
5365900--5365933	15	2.3	15	89	0	50	17	32	23	26	1.97
5368396--5368476	24	3.4	24	85	0	117	22	17	20	39	1.92
5368396--5368486	24	3.8	24	84	5	94	23	15	20	40	1.90
5378150--5378367	103	2.1	103	93	0	373	25	13	23	37	1.91
5378383--5378451	23	3.0	23	93	0	111	20	26	26	27	1.99
5382160--5382219	31	2.0	30	83	9	77	36	3	23	36	1.71
5382442--5382533	46	2.0	46	93	0	157	20	23	25	30	1.99
5382442--5382533	23	4.0	23	91	0	139	20	23	25	30	1.99
5387082--5387139	23	2.4	25	75	11	59	39	22	3	34	1.71
5393339--5393387	17	2.7	18	87	9	64	53	0	12	34	1.39
5395839--5395890	22	2.4	22	90	6	79	9	21	44	25	1.82
5395837--5395880	22	2.0	22	100	0	88	9	22	45	22	1.80
5398177--5398393	3	72.7	3	85	8	291	63	0	2	34	1.07
5398644--5399426	114	6.7	114	90	4	1212	28	19	13	38	1.90
5398644--5399426	233	3.4	228	91	3	1212	28	19	13	38	1.90
5398644--5399431	347	2.3	346	94	2	1409	28	19	13	38	1.90
5400056--5401053	52	19.2	52	96	1	1833	35	24	15	24	1.94
5400056--5401053	261	3.8	260	96	0	1833	35	24	15	24	1.94
5412328--5412364	15	2.7	15	88	12	53	62	8	5	24	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5413162--5413208	20	2.3	21	78	10	62	63	8	2	25	1.34
5414073--5414144	35	2.1	35	82	14	89	0	22	16	61	1.35
5414524--5414772	3	82.0	3	88	2	372	63	0	2	34	1.09
5415387--5415430	23	1.9	23	90	0	70	18	43	15	22	1.88
5421890--5421931	21	2.0	22	86	13	61	40	0	7	52	1.29
5425201--5425227	12	2.2	12	100	0	54	48	7	14	29	1.71
5435649--5435750	44	2.4	42	85	6	125	67	6	5	19	1.35
5435649--5435750	42	2.4	44	86	3	136	67	6	5	19	1.35
5447945--5448004	31	1.9	31	89	0	93	33	0	8	58	1.28
5476330--5476361	2	16.0	2	100	0	64	50	0	0	50	1.00
5476480--5476550	24	3.0	24	95	0	124	53	0	0	46	1.00
5476834--5476880	21	2.2	22	85	7	71	21	25	19	34	1.96
5476872--5476925	20	2.7	19	83	8	63	37	18	20	24	1.94
5476895--5477023	20	6.4	20	84	1	150	28	25	18	27	1.98
5476895--5477023	61	2.1	60	84	1	159	28	25	18	27	1.98
5480363--5480602	20	12.6	20	76	10	218	34	21	18	25	1.96
5480371--5480513	74	1.9	74	92	0	241	34	23	18	23	1.96
5480363--5480602	114	2.1	114	85	2	322	34	21	18	25	1.96
5480596--5480634	20	2.0	20	94	0	69	7	20	25	46	1.77
5482254--5482420	65	2.6	64	82	1	217	28	16	25	30	1.96
5482258--5482466	65	3.2	62	81	7	195	27	17	23	31	1.97
5482634--5482673	20	2.0	21	85	14	57	45	7	5	42	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5484993--5485046	20	2.7	20	82	5	65	22	18	25	33	1.97
5488855--5488894	21	1.9	21	85	10	55	35	10	2	52	1.48
5490841--5491004	65	2.5	64	85	1	229	27	15	26	30	1.96
5490955--5491001	19	2.5	19	83	10	62	25	17	31	25	1.97
5490845--5491051	65	3.2	62	80	12	204	27	16	24	30	1.97
5491221--5491260	20	2.0	21	85	14	57	45	7	5	42	1.54
5492021--5492065	21	2.3	18	81	11	54	24	11	42	22	1.86
5492572--5492638	20	3.5	18	84	11	80	35	26	17	19	1.94
5492583--5492638	20	2.8	20	91	0	85	35	25	17	21	1.95
5492683--5492724	20	2.1	20	90	0	66	19	19	23	38	1.93
5494523--5494629	20	5.4	20	83	3	110	45	22	16	14	1.84
5495607--5495656	20	2.5	20	100	0	100	38	0	0	62	0.96
5498627--5498665	15	2.4	17	83	8	55	38	2	28	30	1.70
5498798--5498872	36	2.0	38	82	10	93	50	2	0	46	1.15
5502632--5502740	42	2.6	42	94	2	186	23	11	19	45	1.82
5503610--5503670	23	2.7	23	84	0	77	37	26	19	16	1.93
5510844--5510895	24	2.2	24	100	0	104	42	3	15	38	1.65
5517009--5517060	24	2.2	24	100	0	104	42	3	15	38	1.65
5522724--5522772	24	2.0	25	84	4	64	36	6	24	32	1.80
5525326--5525352	14	1.9	14	100	0	54	22	3	29	44	1.70
5525474--5526031	157	3.5	157	83	5	687	28	17	5	48	1.69
5527444--5527492	24	2.0	24	81	14	57	28	14	20	36	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5527714--5527749	17	2.1	17	100	0	72	50	11	5	33	1.61
5530045--5530424	46	8.3	46	92	0	627	23	22	9	44	1.82
5530045--5530423	183	2.1	184	93	0	652	23	22	9	44	1.82
5531460--5531505	17	2.7	17	93	0	83	34	21	0	43	1.53
5538870--5538912	20	2.2	20	91	0	68	34	20	11	32	1.89
5538979--5539057	20	3.7	20	70	18	68	22	22	8	45	1.80
5538998--5539074	26	3.2	26	68	21	76	23	19	10	46	1.80
5538979--5539129	46	3.3	46	85	3	205	21	22	9	45	1.81
5539042--5539238	26	8.1	25	66	18	130	22	22	10	44	1.82
5539045--5539206	77	2.2	73	83	11	206	21	23	9	45	1.82
5538999--5539238	123	2.0	118	84	7	313	22	22	9	45	1.81
5539121--5539239	51	2.4	49	86	6	154	21	23	10	44	1.82
5549247--5549764	117	4.4	117	90	0	761	19	13	32	33	1.91
5556871--5556920	21	2.4	21	96	0	91	20	12	28	40	1.87
5557402--5557428	9	3.0	9	100	0	54	55	11	11	22	1.66
5560026--5560072	22	2.1	22	84	0	58	6	6	10	76	1.15
5561614--5562360	117	6.5	117	92	3	1201	19	14	33	32	1.92
5561626--5562360	342	2.1	346	92	2	1219	20	14	33	31	1.92
5565263--5565387	20	5.7	20	68	20	79	23	24	8	43	1.82
5565448--5565526	20	3.6	20	69	21	59	24	21	8	45	1.80
5565263--5565538	46	6.0	45	88	4	399	23	21	9	45	1.80
5576282--5576328	20	2.4	21	86	10	64	25	10	0	63	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5586173--5586211	19	2.0	20	85	14	55	17	10	17	53	1.71
5586406--5586475	35	2.0	36	88	8	108	30	21	17	31	1.96
5586688--5586758	35	2.0	35	97	0	133	19	15	29	35	1.93
5587741--5587774	2	17.0	2	100	0	68	50	0	0	50	1.00
5588554--5588592	16	2.3	17	91	8	62	61	2	0	35	1.10
5588606--5588661	14	3.6	15	78	11	60	51	1	1	44	1.22
5588956--5588981	12	2.2	12	100	0	52	34	0	23	42	1.54
5589026--5589084	32	1.9	32	82	6	77	33	1	8	55	1.40
5590614--5590663	22	2.2	22	80	13	57	44	0	2	54	1.11
5590826--5591069	124	2.0	124	99	0	479	41	8	10	39	1.70
5592114--5592190	27	3.0	26	83	12	97	46	11	7	33	1.69
5597679--5597732	27	2.0	27	88	0	81	48	7	9	35	1.63
5608852--5608927	22	3.6	21	71	15	66	26	19	22	31	1.98
5608848--5609235	42	9.4	42	79	8	411	27	20	22	29	1.98
5609039--5609237	20	9.6	20	65	16	84	25	22	22	29	1.99
5609633--5609787	53	2.9	53	86	0	202	31	20	24	23	1.98
5615567--5615627	25	2.4	25	97	0	113	32	13	3	50	1.57
5615564--5615826	33	8.5	33	79	12	283	33	10	4	51	1.56
5615597--5615826	65	3.6	65	82	8	321	33	9	4	52	1.55
5615561--5615826	123	2.2	123	99	0	523	33	10	4	51	1.57
5615690--5615750	25	2.4	25	97	0	113	32	13	3	50	1.57
5615625--5615813	90	2.1	90	87	2	263	33	9	5	51	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5616044--5616104	28	2.1	29	82	14	74	19	18	8	54	1.68
5616043--5616105	29	2.2	28	78	18	67	19	17	7	55	1.66
5616838--5616864	13	2.1	13	100	0	54	37	0	0	62	0.95
5618473--5618534	21	3.0	21	92	0	106	41	6	0	51	1.27
5628629--5629118	62	7.9	62	86	2	583	28	20	15	35	1.93
5629301--5629830	36	14.7	36	85	3	719	35	20	23	19	1.96
5630034--5630074	3	13.7	3	85	10	57	34	0	0	65	0.93
5631216--5631273	20	2.6	22	86	10	75	31	18	22	27	1.97
5639107--5639146	21	1.9	21	85	10	55	35	10	2	52	1.48
5641095--5641300	65	3.2	63	80	12	206	26	18	23	31	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