genome.fa.s1465.2.7.7.80.10.50.1000.20.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

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   52   53   54   55   

This is table  20  of  55  ( 6520 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)
3786670--3787025	43	8.4	44	73	12	198	24	17	7	49	1.73
3786768--3786929	79	2.1	79	83	6	204	26	18	6	48	1.71
3787210--3787334	60	2.1	57	91	4	196	15	17	24	42	1.88
3788925--3788962	19	2.0	19	100	0	76	36	10	21	31	1.87
3791143--3791197	27	2.0	27	82	6	67	36	7	10	45	1.67
3791464--3791494	11	2.8	11	95	0	53	12	6	61	19	1.53
3804496--3804520	2	12.5	2	100	0	50	48	0	0	52	1.00
3813688--3813740	17	3.1	17	86	0	70	39	15	3	41	1.65
3813691--3813750	17	3.6	17	81	2	68	40	15	1	43	1.56
3816452--3816554	36	2.9	35	78	4	116	36	19	19	24	1.94
3816702--3816793	17	5.4	17	76	5	78	61	6	11	19	1.51
3816704--3816813	34	3.3	33	75	5	94	60	6	14	19	1.56
3816753--3816829	34	2.2	35	81	6	86	59	2	18	19	1.49
3816828--3816877	17	2.9	17	78	3	55	56	8	20	16	1.65
3819774--3819883	56	2.0	56	83	3	141	39	12	14	33	1.84
3834067--3834142	35	2.2	35	90	0	116	42	21	1	35	1.61
3835063--3835146	27	3.0	27	72	17	64	45	7	3	44	1.48
3835200--3835313	35	3.3	34	86	4	156	35	0	21	42	1.60
3839062--3839138	20	3.8	20	100	0	154	24	31	24	19	1.98
3840655--3840713	24	2.4	24	88	2	82	20	23	23	32	1.98
3840652--3840735	25	3.4	25	83	9	84	23	23	21	30	1.99
3849462--3849530	2	37.5	2	79	16	69	44	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3849466--3849567	34	2.8	34	84	14	116	42	0	0	56	1.05
3849480--3849567	35	2.5	36	94	5	155	40	1	0	57	1.06
3850191--3850248	23	2.5	23	82	0	71	6	25	15	51	1.68
3851845--3851878	16	2.1	17	88	5	52	64	0	0	35	0.94
3851846--3851902	21	2.7	21	76	13	62	63	0	0	36	0.95
3851850--3851899	16	3.3	16	78	13	61	64	0	0	36	0.94
3851996--3852142	5	29.4	5	100	0	294	39	0	20	40	1.53
3852448--3852538	46	2.0	46	89	2	139	27	26	19	26	1.99
3858360--3858453	22	4.3	22	87	4	136	24	23	24	27	2.00
3861164--3861488	160	2.0	160	97	0	614	29	21	17	31	1.96
3866460--3866490	2	16.0	2	93	6	55	48	0	0	51	1.00
3866673--3866841	20	8.3	20	75	8	135	27	22	19	30	1.98
3866720--3866841	60	2.0	60	84	3	156	31	22	18	27	1.97
3867445--3867531	20	4.4	20	86	4	106	11	14	22	50	1.75
3869437--3869484	20	2.4	20	92	0	78	33	27	20	18	1.96
3869527--3869570	20	2.2	20	87	0	61	20	20	22	36	1.95
3870083--3870187	21	5.0	21	76	3	104	20	36	19	23	1.95
3871584--3871645	14	4.3	14	77	6	61	38	0	14	46	1.45
3871744--3871797	20	2.7	20	85	0	72	44	25	18	11	1.83
3871791--3871833	20	2.2	20	83	4	52	25	20	25	27	1.99
3871842--3872084	20	12.8	20	74	13	181	27	16	21	34	1.95
3871842--3872084	54	4.2	60	81	5	215	27	16	21	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3872059--3872324	140	1.9	140	97	0	505	42	15	13	28	1.84
3872384--3872414	12	2.6	12	94	0	53	16	6	29	48	1.70
3874017--3874074	31	1.9	31	89	10	93	50	6	15	27	1.70
3874618--3875303	226	3.0	225	85	1	919	41	12	14	32	1.82
3875143--3875372	108	2.1	108	82	2	264	41	10	13	35	1.77
3875179--3875440	108	2.4	105	77	9	240	43	10	9	36	1.73
3875953--3876016	23	2.8	23	86	9	78	32	9	20	37	1.85
3875964--3876024	23	2.7	23	84	0	77	29	14	19	36	1.92
3875998--3876256	75	3.5	75	81	0	275	34	13	11	39	1.82
3876758--3876801	21	2.1	21	83	4	54	38	4	0	56	1.20
3887122--3887383	125	2.0	129	84	7	345	28	9	18	43	1.81
3898133--3898185	23	2.4	21	79	14	63	64	0	0	35	0.94
3900817--3900846	15	2.0	15	100	0	60	13	40	26	20	1.89
3905764--3905793	15	2.0	15	100	0	60	13	40	26	20	1.89
3908506--3908573	30	2.2	31	84	7	84	66	4	4	25	1.29
3911011--3911055	19	2.4	19	100	0	90	51	20	0	28	1.48
3913137--3913199	31	2.1	30	82	8	74	34	15	4	44	1.68
3924990--3925097	3	35.0	3	87	5	153	37	0	0	62	1.02
3925515--3925541	14	1.9	14	100	0	54	74	11	14	0	1.08
3925810--3925838	13	2.2	13	100	0	58	0	31	62	6	1.22
3926382--3926482	53	1.9	53	81	4	123	27	5	4	61	1.40
3926454--3926529	35	2.2	35	78	4	82	34	6	1	57	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3933764--3934194	83	5.2	83	93	0	729	28	12	20	38	1.90
3936392--3936443	22	2.4	22	96	0	95	36	9	15	38	1.80
3937111--3938132	76	13.5	76	97	1	1899	21	20	22	35	1.96
3938258--3938368	3	36.0	3	87	5	159	36	0	0	62	1.02
3938786--3938818	15	2.2	15	100	0	66	72	12	15	0	1.12
3939643--3939743	53	1.9	53	81	4	123	27	5	4	61	1.40
3939715--3939790	35	2.2	35	78	4	82	34	6	1	57	1.33
3942682--3942722	22	1.9	21	90	5	64	24	0	4	70	1.06
3944898--3944952	23	2.4	22	82	11	58	49	3	0	47	1.19
3945195--3945248	26	2.1	26	86	6	74	40	1	11	46	1.50
3948616--3948721	31	3.4	31	79	8	108	30	17	17	33	1.94
3952488--3952607	31	3.8	31	78	5	100	30	17	20	31	1.95
3952488--3952607	63	1.9	62	83	8	154	30	17	20	31	1.95
3954243--3954338	31	3.1	31	82	5	115	35	22	17	23	1.95
3956275--3956321	16	2.8	17	83	6	51	21	19	0	59	1.38
3959170--3959257	30	2.9	30	76	10	88	36	17	17	29	1.92
3959512--3959590	2	39.0	2	92	7	133	49	2	0	48	1.14
3963579--3963642	33	1.9	33	90	0	101	29	7	17	45	1.76
3964989--3965060	25	3.0	25	72	10	69	15	9	5	69	1.34
3972125--3972164	21	1.9	21	90	10	64	42	22	2	32	1.67
3973612--3973702	13	7.5	13	68	27	58	71	0	25	3	1.01
3973622--3973752	22	6.0	22	72	15	94	71	0	22	5	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3973625--3973754	44	3.0	43	80	17	160	72	0	22	5	1.05
3973651--3973754	7	14.6	7	71	18	65	73	0	21	5	1.04
3973624--3973755	15	8.6	15	73	21	80	72	0	21	5	1.04
3973635--3973754	29	4.2	28	75	19	99	72	0	22	5	1.04
3976194--3976244	2	25.5	2	91	0	84	50	45	0	3	1.20
3976739--3976861	42	3.0	42	78	5	126	25	21	22	30	1.99
3977087--3977518	134	3.2	133	83	4	539	33	20	16	28	1.95
3977691--3977723	3	11.0	3	93	0	57	30	0	0	69	0.88
3979550--3979609	31	2.0	30	87	9	86	38	0	25	36	1.56
3979833--3979892	23	2.6	23	83	0	84	15	28	30	26	1.96
3988652--3988703	19	2.9	17	82	8	50	61	1	3	32	1.25
3994690--3994749	30	2.0	30	90	0	93	36	8	11	43	1.71
3996437--3996472	18	2.0	18	88	0	54	44	11	11	33	1.75
3997005--3997066	31	2.0	32	84	9	83	30	1	9	58	1.40
4000164--4000253	3	31.0	3	80	6	105	62	0	1	36	1.03
4000163--4000253	26	3.5	25	89	4	110	61	0	1	37	1.03
4000638--4000692	20	2.8	20	94	0	92	29	21	27	21	1.99
4001182--4001257	20	3.7	20	72	6	62	36	19	19	23	1.95
4000661--4001516	260	3.3	260	90	1	1288	32	20	17	28	1.96
4004109--4004157	7	6.9	7	77	13	55	2	14	0	83	0.73
4004111--4004161	13	4.0	12	80	12	57	1	15	0	82	0.76
4004108--4004157	21	2.3	22	86	13	77	2	14	0	84	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4004110--4004161	26	2.0	26	85	11	70	1	15	0	82	0.75
4004108--4004159	16	3.5	15	77	12	54	1	13	0	84	0.70
4009732--4009756	2	12.5	2	100	0	50	48	0	0	52	1.00
4011261--4011333	3	25.0	3	75	5	69	58	0	4	36	1.17
4011273--4011324	23	2.2	23	89	3	77	59	0	1	38	1.08
4011637--4011677	20	2.0	20	100	0	82	56	4	14	24	1.58
4013273--4013321	25	1.9	25	87	4	71	12	6	30	51	1.64
4013273--4013329	24	2.4	25	77	8	66	17	5	28	49	1.68
4013323--4013392	8	8.4	8	75	13	61	54	0	1	44	1.09
4013323--4013389	22	3.0	23	76	8	75	53	0	1	44	1.09

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   52   53   54   55