genome.fa.s7800.2.7.7.80.10.50.1000.20.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: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4652821

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   

This is table  20  of  23  ( 2671 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)
3897244--3897273	15	2.0	15	100	0	60	53	20	0	26	1.46
3899963--3900129	90	1.9	90	94	0	298	46	5	11	36	1.65
3905569--3905623	12	4.7	12	90	2	85	30	0	40	29	1.57
3910117--3910160	12	3.7	12	87	0	70	36	0	36	27	1.57
3918697--3918737	8	5.2	8	82	5	57	34	0	29	36	1.58
3918808--3919436	128	4.9	128	94	1	1084	22	24	19	33	1.97
3919837--3919937	34	3.0	34	85	0	139	38	2	3	54	1.34
3920830--3920868	20	2.0	20	90	9	64	15	20	23	41	1.90
3922675--3922741	20	3.3	20	87	0	80	44	23	14	16	1.85
3923163--3923213	22	2.3	22	93	0	84	19	13	45	21	1.85
3923388--3923533	20	7.2	20	79	7	152	26	19	24	28	1.99
3923388--3923553	40	4.1	40	79	6	165	26	19	23	30	1.98
3923487--3923555	20	3.5	20	78	7	77	26	17	18	37	1.93
3923966--3924054	33	2.7	31	75	13	81	43	1	0	55	1.07
3923969--3924064	30	3.3	31	76	11	78	41	1	0	57	1.06
3924052--3924086	17	2.1	17	89	5	54	20	0	8	71	1.11
3924200--3924259	26	2.3	27	81	13	72	41	0	3	55	1.16
3926389--3926483	36	2.8	33	81	13	120	32	13	26	27	1.94
3926418--3926490	36	2.0	36	94	0	128	34	13	24	27	1.93
3933084--3933152	21	3.3	21	80	8	77	18	28	24	27	1.98
3933661--3933733	34	2.1	34	89	0	110	50	6	5	36	1.52
3933923--3934050	63	2.0	63	92	0	211	37	22	1	38	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3934005--3934047	23	1.9	22	86	13	61	34	13	2	48	1.56
3934188--3934671	138	3.5	138	93	1	785	33	21	22	22	1.97
3937200--3937270	22	3.5	21	68	22	53	47	0	0	52	1.00
3937230--3937271	21	2.0	21	85	0	57	50	0	0	50	1.00
3938906--3938947	16	2.6	16	82	17	52	35	4	2	57	1.33
3950251--3950284	16	2.1	17	88	5	52	41	17	2	38	1.65
3950967--3951052	44	2.0	44	85	0	118	31	25	16	26	1.96
3950990--3951073	21	3.9	22	80	14	88	29	27	17	25	1.98
3952983--3953050	27	2.6	27	95	4	122	41	16	11	30	1.84
3956728--3956795	27	2.6	27	95	4	122	41	16	11	30	1.84
3958617--3958667	25	2.0	26	81	11	61	45	35	9	9	1.71
3959401--3959448	25	1.9	25	91	0	78	39	20	4	35	1.72
3959962--3960041	3	26.0	3	75	9	72	40	0	2	57	1.12
3959963--3960041	12	6.7	12	81	8	90	40	0	2	56	1.12
3966721--3966817	28	3.4	27	80	9	113	81	0	18	0	0.69
3966724--3966836	12	9.2	12	79	12	124	80	0	18	0	0.76
3968336--3968479	52	2.8	52	90	1	227	37	16	22	22	1.94
3970179--3970216	16	2.4	16	95	0	67	44	23	5	26	1.74
3970836--3971131	46	6.8	44	71	13	206	25	26	16	31	1.97
3970764--3971393	129	4.8	129	82	5	569	26	26	17	30	1.97
3971552--3971616	3	21.0	3	73	17	53	36	1	3	58	1.23
3973660--3973694	2	18.0	2	94	5	63	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3977179--3977207	11	2.6	11	100	0	58	37	0	37	24	1.56
3978324--3978422	12	8.2	12	76	15	82	80	0	17	2	0.80
3978326--3978418	21	4.2	21	80	17	84	80	0	17	2	0.81
3978321--3978422	24	4.2	23	79	15	100	80	0	17	1	0.81
3978324--3978422	34	2.9	33	85	10	121	80	0	17	2	0.80
3979924--3980067	52	2.8	52	90	1	227	36	15	23	23	1.94
3982395--3982625	46	5.3	44	74	11	190	26	26	17	29	1.97
3982371--3982931	129	4.3	129	82	5	530	26	26	16	30	1.97
3983143--3983207	3	21.0	3	75	12	60	38	0	3	58	1.14
3987538--3987607	36	1.9	36	85	0	95	34	17	20	28	1.95
3988023--3988775	405	1.9	405	89	0	1166	37	14	18	28	1.91
3988903--3988936	17	2.0	17	100	0	68	35	17	23	23	1.95
3988904--3988943	17	2.4	17	91	0	62	32	15	35	17	1.91
3993988--3994029	23	1.9	23	85	9	61	42	42	0	14	1.45
3993988--3994035	23	2.1	23	81	11	55	43	43	0	12	1.42
3995877--3995916	2	20.0	2	100	0	80	50	0	0	50	1.00
3995916--3995940	2	12.5	2	100	0	50	0	0	48	52	1.00
4008064--4008119	21	2.7	21	88	5	87	37	26	8	26	1.86
4008064--4008126	21	3.0	21	90	0	81	34	28	11	25	1.90
4017956--4018007	26	2.0	26	100	0	104	50	0	26	23	1.50
4019691--4019913	39	5.8	39	79	12	230	44	3	7	43	1.50
4019750--4019775	12	2.2	12	100	0	52	38	0	7	53	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4019698--4019952	76	3.4	74	84	9	291	43	3	7	45	1.48
4019972--4020031	3	19.3	3	89	3	84	31	1	0	66	1.01
4020728--4020770	22	2.0	22	86	9	61	13	48	27	9	1.73
4021179--4021279	42	2.3	45	77	11	109	19	10	0	68	1.25
4026623--4026921	84	3.6	84	79	8	333	29	26	20	24	1.99
4030800--4030834	3	11.7	3	100	0	70	34	0	0	65	0.93
4030964--4030994	15	2.1	15	93	0	53	25	29	22	22	1.99
4033485--4033521	18	2.0	19	89	5	58	13	5	13	67	1.39
4034408--4034463	21	2.7	21	88	0	94	48	21	14	16	1.81
4038353--4038724	125	3.0	124	86	3	498	33	16	25	25	1.96
4039993--4040151	37	4.3	37	84	4	198	35	22	18	23	1.95
4040003--4040151	73	2.0	73	87	5	212	34	22	18	24	1.96
4040530--4040793	54	4.9	54	83	1	332	34	17	25	21	1.96
4040530--4040834	108	2.8	108	82	3	355	34	16	24	24	1.96
4040797--4041370	55	10.9	54	80	9	483	31	15	23	28	1.96
4041075--4041170	45	2.1	45	92	0	156	29	16	25	29	1.97
4040812--4041312	54	9.6	51	78	13	382	32	15	23	27	1.96
4040968--4041276	151	2.0	150	82	6	374	30	15	24	29	1.96
4041497--4041536	3	12.7	3	84	10	53	37	2	0	60	1.11
4042891--4042932	20	2.0	20	82	13	50	23	9	2	64	1.35
4049967--4050305	172	2.0	166	94	5	592	42	16	7	34	1.75
4055657--4055695	19	2.1	19	95	0	69	23	23	33	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4056986--4057277	36	8.0	36	87	4	320	38	14	20	26	1.91
4057101--4057163	21	3.2	21	70	21	73	41	12	20	25	1.88
4056987--4057281	71	4.0	74	86	5	320	39	14	20	26	1.90
4056986--4057797	40	21.0	37	88	6	298	39	12	19	28	1.88
4057217--4057802	40	14.7	40	90	5	868	39	11	18	30	1.86
4057581--4057649	23	3.3	23	61	23	60	39	14	14	31	1.86
4057734--4057798	23	3.1	23	61	38	56	36	10	20	32	1.87
4058324--4058488	53	3.1	52	64	26	119	40	16	13	28	1.87
4058307--4058520	107	2.0	108	94	0	376	41	16	14	28	1.87
4058965--4059043	31	2.7	29	84	9	115	39	10	12	37	1.77
4067035--4067073	19	2.1	19	95	0	69	28	23	15	33	1.95
4067743--4067802	29	2.1	29	87	0	84	35	3	40	21	1.70
4069019--4069044	8	3.2	8	100	0	52	65	11	0	23	1.25
4069375--4069532	29	5.4	29	78	11	101	40	23	5	31	1.76
4069402--4069531	30	4.4	29	79	6	118	40	23	5	31	1.77
4076675--4076793	29	4.1	28	82	6	132	39	18	5	36	1.75
4076807--4076859	23	2.3	22	81	9	61	15	22	43	18	1.87
4077632--4077803	91	1.9	86	85	10	231	26	18	15	40	1.90
4077637--4077819	86	2.1	90	84	11	236	27	18	14	39	1.90
4077784--4078044	138	1.9	138	89	0	405	29	20	16	32	1.95
4078401--4078494	37	2.6	35	75	11	91	44	14	14	25	1.84
4078398--4078651	76	3.4	76	91	1	388	39	13	18	28	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4078521--4078645	36	3.4	36	69	12	117	40	14	16	28	1.88
4078653--4078710	28	2.0	29	93	3	100	41	17	12	29	1.85
4078682--4079096	36	11.4	36	85	4	455	37	13	20	27	1.91
4078624--4079033	72	5.9	64	80	11	248	39	13	19	27	1.90
4079034--4079676	40	16.0	40	91	2	977	39	11	17	30	1.85
4079034--4079676	119	5.3	119	89	2	953	39	11	17	30	1.85
4088611--4088648	18	2.1	18	90	0	58	21	10	36	31	1.87
4091796--4092025	117	2.0	117	99	0	451	28	19	14	37	1.91
4093469--4093548	30	2.8	28	80	5	88	57	1	11	30	1.41
4093469--4093549	29	2.8	28	77	7	81	56	1	11	30	1.42

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23