genome.fa.s2647.2.7.7.80.10.50.1000.16.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: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7027529

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   

This is table  16  of  26  ( 3011 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)
3799526--3799563	14	2.7	14	84	11	51	84	0	13	2	0.73
3801000--3801045	3	15.0	3	95	4	83	34	0	0	65	0.93
3801004--3801056	25	2.1	25	86	6	72	41	0	0	58	0.98
3802455--3802495	22	2.0	21	86	13	59	46	0	0	53	1.00
3802455--3802495	21	1.9	22	90	5	66	46	0	0	53	1.00
3805470--3805500	11	2.8	11	95	0	53	83	0	16	0	0.64
3807680--3807710	14	2.2	14	94	0	53	38	0	12	48	1.42
3814653--3814722	23	3.0	23	81	4	79	42	8	10	38	1.69
3817441--3817481	17	2.4	17	95	0	73	24	17	9	48	1.76
3823758--3823814	17	3.4	16	81	16	62	80	1	8	8	0.97
3823761--3823816	21	2.6	21	82	2	67	82	1	8	7	0.92
3824113--3824148	17	2.1	18	89	5	56	8	0	30	61	1.26
3832945--3832997	24	2.2	24	86	3	72	11	11	13	64	1.51
3838140--3838183	18	2.5	18	77	3	54	43	9	6	40	1.63
3844588--3844676	32	2.8	32	74	6	90	33	11	21	33	1.89
3846153--3846190	19	2.0	20	90	10	62	42	10	15	31	1.81
3854799--3855618	134	6.1	134	82	4	913	30	16	22	30	1.96
3854799--3855618	268	3.1	267	83	5	1012	30	16	22	30	1.96
3858919--3858959	19	2.1	20	90	4	66	63	2	17	17	1.42
3860266--3860296	12	2.6	12	94	0	53	19	16	22	41	1.89
3862704--3862741	16	2.4	16	100	0	76	44	5	31	18	1.72
3862782--3862898	59	2.0	59	84	3	155	39	23	11	25	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3867418--3867457	12	3.3	12	82	0	53	82	10	7	0	0.84
3867409--3867464	21	2.6	21	85	2	67	80	12	7	0	0.90
3875299--3875331	16	2.0	17	88	5	50	21	21	0	57	1.41
3883056--3883106	12	4.6	11	95	4	70	25	9	45	19	1.81
3884370--3884412	16	2.8	16	86	10	54	76	6	16	0	0.99
3886348--3886382	2	17.5	2	100	0	70	51	0	0	48	1.00
3889150--3889190	1	41.0	1	90	0	64	95	4	0	0	0.28
3889150--3889190	12	3.5	12	96	3	75	95	4	0	0	0.28
3897649--3897949	161	1.9	161	90	0	476	38	15	16	29	1.89
3898440--3898507	31	2.2	31	94	0	118	45	20	14	19	1.85
3908623--3908676	23	2.3	25	84	12	78	64	11	14	9	1.48
3908627--3908682	24	2.4	22	80	11	67	62	12	16	8	1.53
3915259--3915311	27	2.0	27	85	7	72	67	5	18	7	1.35
3919398--3919438	22	1.9	21	90	5	64	34	36	2	26	1.70
3919662--3920320	327	2.0	327	100	0	1318	28	25	9	35	1.88
3920766--3920825	26	2.3	26	91	0	102	28	26	21	23	1.99
3920962--3921023	31	2.0	31	100	0	124	41	9	6	41	1.63
3921270--3922102	422	2.0	422	90	0	1326	29	24	17	29	1.97
3923451--3923504	25	2.2	25	96	0	99	33	22	18	25	1.97
3925480--3926237	406	1.9	406	85	2	1074	29	23	16	30	1.96
3929493--3929534	15	2.6	16	88	7	59	16	9	2	71	1.23
3929889--3929913	9	2.8	9	100	0	50	92	8	0	0	0.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3929906--3929943	13	2.6	15	88	12	53	76	10	13	0	1.02
3929906--3929943	14	2.5	15	87	8	51	76	10	13	0	1.02
3934200--3934241	15	2.6	16	88	7	59	16	9	2	71	1.23
3939077--3939114	19	2.0	19	94	0	67	2	15	2	78	0.97
3942934--3942979	24	2.0	24	86	4	67	2	17	4	76	1.06
3944919--3945047	50	2.6	50	88	2	179	41	27	13	18	1.87
3953420--3953454	17	2.1	17	100	0	70	40	22	11	25	1.88
3954314--3954368	24	2.4	22	78	9	56	32	18	14	34	1.91
3965549--3965720	89	1.9	89	86	2	247	38	9	7	43	1.66
3966889--3966928	21	1.9	21	84	0	53	55	0	12	32	1.38
3971364--3971401	15	2.4	16	86	4	51	68	5	13	13	1.37
3975546--3975597	22	2.3	22	83	9	61	1	5	9	82	0.90
3977636--3977678	23	1.9	21	81	13	50	37	9	18	34	1.83
3983185--3983214	13	2.3	13	94	0	51	23	33	0	43	1.54
3983640--3983689	11	4.5	11	76	16	50	82	4	14	0	0.82
3983640--3983689	26	1.9	26	84	8	66	82	4	14	0	0.82
3983647--3983689	6	7.2	6	82	10	52	83	2	13	0	0.74
3983910--3983964	24	2.3	24	79	17	62	14	16	0	69	1.20
3999301--3999419	59	2.0	59	88	1	177	25	15	21	36	1.93
4003316--4003345	15	2.0	15	93	0	51	60	0	30	10	1.30
4004880--4004923	6	7.2	6	84	5	61	0	18	2	79	0.83
4004880--4004926	25	1.9	24	91	4	76	0	17	4	78	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4004880--4004923	19	2.4	18	84	3	61	0	18	2	79	0.83
4006433--4006481	16	2.9	17	79	14	57	69	0	16	14	1.19
4006610--4006652	5	8.4	5	80	14	52	0	20	2	76	0.89
4008216--4008257	16	2.6	16	81	7	50	69	0	16	14	1.20
4008441--4008502	7	9.1	7	83	10	76	0	22	1	75	0.88
4008441--4008514	10	7.7	9	71	17	51	0	20	2	77	0.90
4011415--4011482	36	1.9	35	90	3	109	35	2	35	26	1.72
4029433--4029475	23	1.9	21	81	13	50	32	18	13	34	1.90
4030228--4030287	25	2.4	25	91	0	93	13	18	21	46	1.83
4039119--4039163	20	2.3	20	84	3	56	8	4	11	75	1.17
4039127--4039164	20	1.9	20	88	0	58	7	5	10	76	1.15
4039146--4039178	12	2.6	13	85	9	50	0	9	9	81	0.87
4042141--4042183	10	4.3	10	78	0	50	2	2	11	83	0.83
4042141--4042200	9	6.3	9	76	14	50	5	1	10	83	0.87
4042158--4042201	17	2.5	17	81	3	52	9	2	6	81	0.94
4046740--4046779	15	2.6	17	74	25	52	20	30	12	37	1.89
4049000--4049046	24	2.0	24	86	0	67	51	19	14	14	1.77
4051241--4051278	15	2.5	16	83	12	53	65	0	18	15	1.27
4055493--4055546	11	4.7	11	75	24	58	0	14	1	83	0.73
4057092--4057138	24	2.0	23	87	4	67	57	4	0	38	1.18
4062791--4062836	15	2.9	15	81	18	58	8	30	0	60	1.26
4083656--4083719	11	5.6	11	79	3	56	0	6	10	82	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4083656--4083697	13	3.4	13	87	12	70	0	4	11	83	0.79
4083656--4083727	22	3.2	24	78	11	89	0	5	11	83	0.80
4083649--4083719	33	2.2	32	85	10	90	1	5	12	80	0.95
4083665--4083727	11	5.6	11	83	9	74	0	4	9	85	0.72
4099244--4099269	5	5.2	5	100	0	52	0	19	57	23	1.40
4104173--4104276	46	2.3	46	98	0	199	37	23	24	15	1.93
4106398--4106443	24	1.9	24	86	8	67	65	13	13	8	1.48
4107076--4107105	12	2.5	12	100	0	60	66	6	20	6	1.38
4121159--4121201	19	2.2	20	87	4	61	51	4	9	34	1.55
4129462--4129521	25	2.3	26	83	10	79	76	1	15	6	1.06
4132410--4132439	11	2.7	11	100	0	60	26	53	10	10	1.66
4140837--4142253	709	2.0	711	95	0	2577	35	16	16	31	1.91
4145943--4145973	13	2.4	13	94	0	53	45	0	32	22	1.53
4146317--4146359	19	2.2	20	87	4	61	48	6	9	34	1.62
4147064--4147102	20	1.9	21	84	5	53	48	7	17	25	1.74
4147340--4147378	20	2.0	19	85	5	51	46	10	12	30	1.75
4158507--4158556	1	50.0	1	79	0	55	90	0	8	2	0.54
4158485--4158555	16	5.0	14	78	20	67	84	0	7	8	0.78
4158507--4158555	8	5.9	8	86	9	62	89	0	8	2	0.55
4158485--4158556	28	2.5	28	84	10	85	84	0	6	8	0.77
4160442--4160521	35	2.2	37	88	4	119	27	3	36	32	1.75
4164501--4164580	35	2.2	37	88	4	119	27	3	36	32	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4171333--4171377	19	2.4	19	88	0	63	6	0	15	77	0.96
4171343--4171387	11	4.4	11	83	16	69	0	0	15	84	0.62
4171343--4171384	19	2.2	19	95	0	75	0	0	16	83	0.65
4173295--4173330	17	2.0	18	89	10	56	11	27	0	61	1.30
4175969--4176008	19	2.0	20	90	4	64	20	15	0	65	1.28
4179624--4179675	21	2.6	21	90	6	81	32	13	7	46	1.72
4180090--4180129	19	2.0	20	90	4	64	20	15	0	65	1.28
4181701--4181789	28	3.4	28	70	17	100	31	7	19	41	1.80
4181694--4181803	50	2.2	50	95	1	195	32	6	18	42	1.75
4181716--4181802	25	3.3	28	67	25	80	33	4	18	43	1.70

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