genome.fa.s8716.2.7.7.80.10.50.1000.17.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: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5677467

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   

This is table  17  of  24  ( 2813 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)
4265250--4265382	41	3.2	41	74	13	137	31	16	20	31	1.95
4265216--4265400	83	2.2	83	82	5	214	31	14	19	35	1.91
4266830--4267220	42	9.3	42	90	0	577	34	16	21	26	1.95
4271123--4271170	21	2.3	22	78	10	64	45	14	39	0	1.45
4271132--4271194	21	3.0	21	83	0	81	42	17	38	1	1.59
4271551--4271699	44	3.4	44	79	7	158	26	14	21	38	1.91
4271526--4271695	88	1.9	88	80	2	198	30	15	19	34	1.93
4272643--4272681	17	2.2	17	86	13	53	61	2	0	35	1.10
4272814--4272904	34	2.7	34	87	0	128	27	18	23	30	1.98
4272862--4273041	83	2.2	84	91	2	299	36	8	22	32	1.85
4272980--4273025	21	2.2	21	84	0	56	30	2	28	39	1.69
4276986--4277043	24	2.4	24	100	0	116	29	8	27	34	1.87
4277449--4277533	27	3.1	27	77	0	89	24	29	14	31	1.94
4277589--4277675	33	2.6	33	89	3	131	28	17	33	20	1.95
4277745--4277798	27	2.0	27	96	0	99	29	16	29	24	1.97
4290272--4290466	98	2.0	98	97	0	372	27	16	17	38	1.91
4291070--4291103	5	6.8	5	100	0	68	20	0	20	58	1.39
4301683--4301717	2	18.0	2	88	5	54	54	0	0	45	0.99
4314156--4314218	33	1.9	33	100	0	126	28	15	39	15	1.89
4321709--4321781	31	2.3	32	79	11	80	30	4	6	58	1.43
4322714--4323033	126	2.5	126	81	4	376	27	30	20	22	1.98
4323755--4323807	21	2.5	21	93	0	88	28	30	22	18	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4323822--4323929	21	5.3	20	73	8	103	20	18	25	35	1.95
4323822--4323943	40	3.0	40	92	2	208	21	18	23	36	1.95
4323822--4323920	19	5.0	19	73	7	90	21	18	25	35	1.95
4324028--4324052	6	4.2	6	100	0	50	36	48	16	0	1.46
4324694--4324812	62	1.9	62	89	3	186	28	15	22	32	1.95
4325947--4326002	25	2.2	26	84	9	71	58	3	1	35	1.26
4325981--4326024	23	1.9	23	86	9	63	63	4	0	31	1.14
4326027--4326067	2	20.5	2	100	0	82	48	0	0	51	1.00
4326221--4326289	27	2.5	28	83	9	88	43	4	5	46	1.47
4333338--4333375	20	2.0	19	90	10	60	52	10	18	18	1.73
4341069--4341093	5	5.0	5	100	0	50	20	60	0	20	1.37
4347478--4347509	15	2.0	17	88	11	50	50	6	12	31	1.65
4347750--4347794	17	2.4	20	78	21	69	28	0	42	28	1.56
4347754--4347792	17	2.3	17	100	0	78	30	0	38	30	1.58
4360928--4360970	22	2.0	22	90	9	70	37	0	2	60	1.10
4361931--4361976	19	2.4	19	96	0	83	6	28	26	39	1.81
4363847--4363971	62	2.0	62	100	0	250	33	16	26	24	1.95
4365418--4365529	50	2.2	50	85	1	143	16	30	33	19	1.94
4367143--4367179	19	2.0	19	89	5	58	45	0	24	29	1.53
4367316--4367417	48	2.1	48	83	3	125	18	34	31	15	1.93
4369015--4369058	20	2.2	20	87	0	61	63	15	0	20	1.31
4370870--4370932	23	2.7	23	80	7	74	33	23	23	19	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4378712--4378804	21	4.5	21	78	4	100	39	18	24	17	1.91
4378712--4378804	41	2.3	41	100	0	186	39	18	24	17	1.91
4378835--4378887	20	2.7	20	93	0	88	24	28	20	26	1.99
4379403--4379469	19	3.5	19	85	2	89	47	25	16	10	1.78
4379479--4379566	33	2.6	33	92	1	140	11	25	25	38	1.89
4379534--4379591	20	2.9	20	80	10	64	13	24	18	43	1.87
4381592--4381661	21	3.4	21	65	9	54	22	38	18	20	1.93
4382978--4383013	14	2.6	14	95	0	63	30	0	25	44	1.54
4383189--4383284	33	3.0	31	80	8	111	16	19	19	43	1.88
4383258--4383302	19	2.4	19	100	0	90	15	20	17	46	1.84
4383269--4383322	19	2.8	19	85	2	63	18	20	20	40	1.91
4385583--4385607	12	2.1	12	100	0	50	0	28	0	72	0.86
4385781--4385833	24	2.2	24	89	0	79	37	20	16	24	1.93
4386915--4386968	14	3.5	14	77	22	63	11	20	20	48	1.80
4386897--4386967	33	2.2	33	84	0	88	19	19	21	39	1.93
4386910--4386987	33	2.4	33	91	0	120	12	23	21	42	1.87
4387075--4387111	14	2.6	14	86	0	56	48	21	0	29	1.50
4388974--4389040	19	3.5	19	83	4	89	38	23	22	14	1.92
4388955--4389091	39	3.9	37	77	10	105	43	24	18	12	1.85
4389029--4389086	14	3.9	14	79	16	71	48	25	17	8	1.75
4389013--4389091	32	2.4	33	95	2	142	46	24	18	10	1.80
4389120--4389177	14	3.9	14	75	16	62	12	17	22	48	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4389103--4389193	32	2.8	33	91	3	157	13	18	20	47	1.82
4389178--4389232	20	2.8	19	83	8	65	16	23	23	36	1.94
4389713--4389757	18	2.5	18	88	0	72	13	15	44	26	1.83
4391073--4391131	20	3.0	20	82	0	64	44	20	16	18	1.87
4391394--4391437	22	2.0	22	100	0	88	18	13	45	22	1.84
4391625--4391675	20	2.5	20	93	0	84	27	19	23	29	1.98
4391645--4391722	41	1.9	41	81	5	95	24	16	20	38	1.93
4391708--4391800	20	4.5	21	78	4	100	17	24	18	39	1.91
4391708--4391800	41	2.3	41	100	0	150	17	24	18	39	1.91
4393351--4393513	65	2.5	64	84	3	220	26	15	26	30	1.96
4393461--4393511	19	2.7	19	85	8	70	25	15	35	23	1.94
4393355--4393562	65	3.2	65	81	12	207	26	17	25	29	1.97
4395179--4395241	21	3.0	21	78	0	72	42	15	38	3	1.63
4395583--4395667	44	1.9	44	95	0	152	32	16	17	32	1.93
4395750--4395873	42	2.9	42	84	2	149	33	25	15	25	1.95
4395708--4395848	43	3.3	43	80	3	142	36	23	17	23	1.95
4395708--4395873	85	1.9	86	81	3	201	33	24	16	25	1.96
4396119--4396283	2	78.0	2	65	20	61	45	4	5	44	1.48
4396124--4396165	9	4.4	9	78	21	50	45	0	7	47	1.30
4396124--4396283	20	8.4	19	66	19	93	45	4	5	44	1.47
4396152--4396315	31	5.1	32	66	25	78	44	6	6	43	1.53
4396118--4396192	22	3.6	21	78	15	84	45	2	5	46	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4396230--4396446	75	2.9	70	77	16	231	42	7	8	40	1.65
4396228--4396783	33	15.3	33	72	20	182	42	7	8	41	1.64
4396235--4396526	150	2.0	148	81	8	351	42	6	9	41	1.63
4396400--4396563	80	2.1	75	85	5	211	42	7	9	41	1.64
4396472--4396815	86	4.0	90	82	13	456	41	7	8	42	1.63
4396280--4397040	166	4.6	166	92	3	1184	41	7	8	41	1.65
4396715--4396791	33	2.5	31	86	12	113	38	7	9	44	1.65
4396508--4396996	133	3.8	133	79	15	453	41	7	8	41	1.65
4396937--4397077	33	4.2	33	81	11	137	42	4	8	43	1.56
4396301--4397037	18	39.8	18	68	23	260	41	7	8	41	1.65
4397038--4397111	20	3.5	20	76	16	76	51	1	6	40	1.37
4397054--4397100	13	3.6	13	78	18	53	53	2	6	38	1.39
4397334--4397433	50	2.0	50	96	0	182	30	15	7	48	1.71
4397122--4397648	265	2.0	265	93	0	912	28	14	7	48	1.71
4397384--4397836	215	2.1	216	93	2	770	28	12	8	49	1.70
4407260--4407697	84	5.2	84	78	3	384	27	18	20	32	1.97
4407325--4407712	168	2.3	168	83	3	485	27	19	20	32	1.97
4408068--4408178	43	2.6	44	81	4	136	23	16	30	29	1.96
4408408--4408547	43	3.3	43	85	0	181	23	16	29	30	1.96
4408718--4408874	64	2.5	64	83	3	174	28	14	23	33	1.93
4409105--4409193	32	2.8	32	85	0	106	33	24	11	30	1.90
4409320--4409387	23	3.0	23	72	12	68	42	2	14	39	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4412779--4413067	144	2.0	145	99	0	571	44	14	12	28	1.81
4421443--4421599	43	3.8	42	72	16	139	47	3	20	28	1.67
4421520--4421778	93	2.8	95	86	4	300	49	5	16	28	1.68
4421613--4421848	42	5.4	42	72	17	158	48	5	16	28	1.69
4421564--4421783	93	2.4	92	90	3	343	48	5	17	28	1.70
4421706--4421848	43	3.4	41	75	15	130	48	5	16	29	1.69
4435107--4435229	54	2.3	54	88	1	176	22	24	30	21	1.99
4435850--4435891	17	2.7	15	82	13	57	57	28	0	14	1.38
4435854--4435887	17	2.0	17	94	0	59	55	32	0	11	1.36
4437821--4437860	21	1.9	21	89	0	62	10	25	40	25	1.86

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