genome.fa.s8747.2.7.7.80.10.50.1000.15.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: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12616935

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   

This is table  15  of  51  ( 6054 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)
3818242--3818284	22	2.0	22	85	0	59	34	4	9	51	1.55
3838032--3838074	20	2.2	20	91	0	68	32	11	20	34	1.89
3843318--3843352	14	2.4	14	95	4	61	85	0	14	0	0.59
3843964--3844006	20	2.2	20	91	0	68	32	11	20	34	1.89
3848603--3848673	23	3.2	23	66	22	60	29	19	21	29	1.98
3848587--3848686	44	2.3	44	89	0	146	30	17	22	31	1.96
3852630--3852655	2	13.0	2	100	0	52	50	0	0	50	1.00
3854225--3854267	3	14.3	3	90	0	59	62	2	4	30	1.28
3866057--3866146	39	2.3	39	84	0	108	31	18	26	23	1.98
3868678--3868745	35	1.9	35	85	11	95	32	23	20	23	1.98
3868852--3868880	8	3.6	8	100	0	58	48	24	13	13	1.79
3891618--3891958	55	6.2	55	84	3	411	30	17	17	33	1.94
3892304--3892346	22	2.0	22	85	0	59	30	27	13	27	1.95
3893350--3893382	16	2.2	15	89	10	50	6	27	0	66	1.15
3894841--3894886	2	23.0	2	91	8	76	50	0	2	47	1.13
3894941--3894999	29	2.0	29	83	6	75	30	6	5	57	1.46
3897630--3897676	11	3.6	14	78	21	57	40	0	0	59	0.97
3902852--3902916	21	3.1	21	90	0	103	30	15	6	47	1.70
3904278--3904302	12	2.1	12	100	0	50	16	0	12	72	1.13
3904585--3904633	25	1.9	26	83	4	64	18	2	10	69	1.27
3906293--3906580	149	1.9	149	81	5	350	34	17	25	22	1.96
3909153--3909337	101	1.8	104	84	5	261	30	17	11	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3909153--3909362	101	2.0	104	81	6	250	30	16	12	40	1.85
3909395--3909575	65	2.8	65	85	0	238	29	19	11	39	1.86
3909951--3910067	37	3.2	37	72	7	121	29	22	11	35	1.90
3909916--3910035	37	3.4	34	71	10	105	28	21	13	36	1.91
3909916--3910042	36	3.5	35	72	7	112	27	21	13	37	1.91
3909654--3910068	73	5.6	75	80	7	458	29	22	12	35	1.91
3909654--3910087	148	2.9	146	80	8	348	30	22	12	35	1.91
3910341--3910801	91	5.1	91	88	2	633	36	17	21	24	1.94
3911110--3911149	21	2.0	20	85	5	53	17	5	2	75	1.10
3914096--3914125	14	2.1	14	93	0	51	46	3	10	40	1.54
3914882--3914934	24	2.2	24	83	6	63	18	3	15	62	1.47
3915833--3915863	15	2.0	16	93	6	55	38	0	9	51	1.35
3919180--3919238	24	2.5	24	88	0	91	25	11	16	45	1.82
3921631--3921860	75	3.0	75	81	12	268	53	12	2	30	1.52
3926325--3926374	22	2.3	22	92	0	82	38	8	14	40	1.75
3935609--3935942	178	1.9	178	81	5	415	32	13	19	35	1.90
3937728--3937766	21	2.0	20	90	10	62	23	35	25	15	1.94
3943809--3944428	308	2.0	307	99	0	1215	32	17	14	35	1.90
3944589--3944643	24	2.3	24	96	0	101	30	20	16	32	1.94
3946640--3946730	38	2.4	38	87	3	121	37	16	15	30	1.90
3951967--3952016	26	1.9	26	87	0	73	64	4	16	16	1.44
3952445--3952486	20	2.1	20	86	8	59	9	0	9	80	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3960989--3961050	23	2.8	22	77	13	65	24	32	20	22	1.98
3968492--3968553	23	2.8	22	77	13	65	24	32	20	22	1.98
3973520--3973664	61	2.3	64	84	5	188	29	16	27	26	1.97
3977127--3977214	3	30.7	3	91	8	148	34	0	0	65	0.93
3978348--3978476	30	4.4	28	75	13	118	17	13	9	59	1.59
3984020--3984082	32	2.0	32	90	6	101	26	14	28	30	1.95
3984152--3984293	61	2.2	63	84	8	173	26	11	15	45	1.81
3984377--3984757	130	2.9	128	82	3	422	26	31	16	25	1.96
3984585--3984944	180	2.0	180	100	0	720	26	31	15	27	1.96
3984602--3984890	88	3.2	88	72	16	313	26	31	14	26	1.95
3985151--3985249	3	32.7	3	91	6	164	34	0	0	65	0.93
3986671--3986763	30	3.1	29	72	11	89	16	11	12	59	1.62
3992462--3992540	32	2.5	31	85	6	95	55	2	1	40	1.21
3995167--3995191	12	2.1	12	100	0	50	32	16	8	44	1.76
3998139--3998187	21	2.3	21	96	0	89	34	20	20	24	1.96
4000769--4000793	13	1.9	13	100	0	50	36	0	0	64	0.94
4002998--4003042	17	2.5	17	85	7	54	71	4	4	20	1.21
4003178--4003220	16	2.7	16	85	0	59	30	2	32	34	1.71
4003184--4003253	16	4.5	16	72	13	56	34	4	28	32	1.77
4003184--4003272	46	1.9	46	90	0	142	33	4	28	33	1.77
4003401--4003485	28	3.1	28	60	27	65	51	10	14	23	1.72
4003375--4003497	53	2.3	53	97	0	228	51	8	14	25	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4008219--4008295	34	2.2	34	90	2	118	12	11	11	63	1.52
4012761--4012821	27	2.2	28	94	2	106	27	8	19	44	1.79
4012822--4013193	55	6.8	55	84	1	440	30	19	16	34	1.93
4013521--4013570	20	2.5	20	96	0	91	26	32	14	28	1.94
4013650--4013705	20	2.8	20	94	0	103	19	30	16	33	1.94
4014017--4014049	16	2.1	16	100	0	66	27	24	6	42	1.78
4019567--4019596	15	1.9	16	93	6	53	50	16	6	26	1.70
4019775--4020164	55	7.1	54	87	3	492	28	20	16	33	1.95
4020494--4020564	20	3.5	19	77	19	72	29	22	15	32	1.95
4031476--4031546	36	2.0	36	83	5	90	33	15	18	32	1.92
4048125--4048761	318	2.0	318	99	0	1265	35	18	8	37	1.81
4050403--4050472	26	2.8	25	79	8	81	44	4	5	45	1.47
4054397--4054447	21	2.4	21	93	0	84	49	25	5	19	1.71
4054397--4054455	21	2.8	21	89	0	73	49	25	5	20	1.69
4054624--4055244	306	2.0	306	88	2	908	36	19	11	32	1.87
4060145--4060203	16	3.7	16	76	0	55	25	27	13	33	1.93
4060746--4060814	21	3.3	21	77	4	68	23	0	31	44	1.53
4060767--4060814	14	3.4	14	83	11	62	27	0	27	45	1.54
4060748--4060814	28	2.4	28	85	5	82	23	0	29	46	1.53
4060993--4061603	4	152.8	4	97	0	1060	47	24	2	25	1.65
4061838--4061885	19	2.5	20	89	3	71	27	31	0	41	1.56
4062009--4062061	2	26.5	2	100	0	106	50	0	0	49	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4062531--4062560	13	2.3	13	94	0	51	50	0	0	50	1.00
4062522--4062560	11	3.5	11	86	6	53	46	0	2	51	1.14
4064668--4064781	41	2.8	41	67	16	99	35	17	17	28	1.93
4064627--4064781	82	1.9	83	83	4	206	34	18	17	30	1.94
4064809--4064999	83	2.3	83	78	7	217	28	17	20	32	1.96
4066342--4066381	2	20.0	2	100	0	80	50	0	0	50	1.00
4066376--4066403	13	2.2	13	100	0	56	46	7	14	32	1.71
4069009--4069051	18	2.4	18	84	7	52	23	9	2	65	1.34
4072989--4073032	18	2.4	19	84	3	54	18	6	4	70	1.27
4078708--4078746	18	2.1	19	85	4	53	20	7	5	66	1.36
4082727--4082772	17	2.6	17	86	3	56	58	8	19	13	1.60
4087021--4087092	31	2.3	31	100	0	144	37	5	22	34	1.77
4093773--4093848	23	3.3	23	71	14	75	19	18	14	47	1.83
4093713--4094288	46	12.6	46	84	4	727	23	20	14	41	1.89
4098053--4098159	48	2.3	47	81	7	123	42	9	17	30	1.81
4100042--4100081	20	2.0	20	100	0	80	25	10	15	50	1.74
4103018--4103139	23	5.3	23	65	18	83	20	22	13	43	1.87
4102958--4103538	46	12.6	46	87	1	743	23	19	13	43	1.87
4121044--4121093	21	2.5	20	83	6	64	22	34	14	30	1.93
4122681--4122825	60	2.5	55	90	6	227	37	8	13	40	1.74
4122695--4122792	33	3.2	33	65	24	86	40	7	11	40	1.68
4122784--4122866	41	2.0	41	95	0	148	32	8	15	43	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4122838--4123423	308	1.9	308	97	0	1102	43	4	12	40	1.61
4123493--4123596	33	3.2	33	66	15	97	41	5	10	42	1.63
4123588--4123670	41	2.0	41	95	0	148	32	8	15	43	1.77
4122078--4123919	794	2.3	793	97	1	3472	42	5	11	41	1.63
4123676--4124180	262	1.9	257	94	2	893	44	4	10	40	1.60
4128404--4128435	16	1.9	17	93	6	57	40	18	3	37	1.67
4132402--4132436	10	3.6	10	92	3	54	11	0	5	82	0.82
4133378--4133423	14	2.9	16	75	15	51	43	10	13	32	1.78
4139222--4139295	29	2.6	29	82	8	105	27	24	13	35	1.93
4140359--4140417	28	2.1	28	100	0	118	32	13	13	40	1.84

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