genome.fa.s9587.2.7.7.80.10.50.1000.18.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: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6483253

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   

This is table  18  of  29  ( 3457 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)
3931860--3931979	47	2.6	44	82	13	136	25	1	21	50	1.58
3939529--3939678	81	1.9	81	84	0	201	30	23	12	34	1.91
3940127--3940156	13	2.3	13	94	0	51	73	0	3	23	0.98
3941944--3942970	105	9.8	105	87	4	1346	23	18	25	32	1.97
3941988--3943002	421	2.4	422	86	5	1436	22	19	25	32	1.97
3954218--3954247	13	2.3	13	94	0	51	73	0	3	23	0.98
3955872--3956385	55	9.4	55	90	2	775	34	19	11	35	1.88
3958816--3959727	303	3.0	302	91	3	1438	36	15	6	41	1.73
3959694--3959752	25	2.4	25	100	0	118	33	3	3	59	1.31
3967359--3967399	18	2.3	18	95	0	73	19	48	21	9	1.77
3967381--3967435	8	7.5	8	76	19	66	14	36	25	23	1.93
3967332--3967407	13	5.5	13	79	14	80	17	46	21	15	1.84
3967346--3967407	31	2.0	31	93	0	106	17	46	20	14	1.83
3967397--3967436	7	5.4	7	85	8	53	12	32	27	27	1.93
3967397--3967435	15	2.6	15	91	0	69	12	33	25	28	1.93
3968731--3968766	18	2.0	18	88	0	54	52	0	16	30	1.44
3969920--3969993	23	3.2	23	83	9	96	24	17	21	36	1.95
3969926--3970000	24	3.2	24	88	1	116	25	17	21	36	1.95
3972218--3972258	18	2.3	18	95	0	73	19	48	21	9	1.77
3972205--3972266	31	2.0	31	93	0	106	17	46	20	14	1.83
3972240--3972294	8	7.5	8	76	19	66	14	36	25	23	1.93
3972192--3972266	13	5.5	13	77	16	71	17	45	21	16	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3972256--3972295	7	5.4	7	85	8	53	12	32	27	27	1.93
3972256--3972294	15	2.6	15	91	0	69	12	33	25	28	1.93
3973590--3973625	18	2.0	18	88	0	54	52	0	16	30	1.44
3974779--3974852	23	3.2	23	83	9	96	24	17	21	36	1.95
3974785--3974859	24	3.2	24	88	1	116	25	17	21	36	1.95
3979244--3979318	35	2.1	35	87	0	105	44	22	0	33	1.53
3981908--3981967	28	2.2	28	90	3	95	53	10	5	31	1.56
3989716--3989763	23	2.1	23	92	0	78	37	6	16	39	1.74
3990381--3990835	182	2.5	182	92	0	730	27	15	13	43	1.84
3993624--3994297	220	3.3	197	86	7	834	28	14	14	42	1.85
3994047--3994102	21	2.7	21	88	0	94	33	14	10	41	1.80
3997207--3998702	199	7.5	199	94	0	2564	27	15	15	41	1.88
3999047--3999095	19	2.6	19	90	3	73	57	10	2	30	1.43
4000559--4000597	18	2.2	18	90	0	60	7	38	0	53	1.30
4001268--4001324	24	2.5	21	76	17	60	49	8	1	40	1.44
4002191--4003394	182	6.6	182	87	1	1684	26	15	13	44	1.83
4002212--4003375	545	2.1	546	88	1	1719	26	15	13	44	1.83
4003323--4003361	20	1.9	21	94	5	71	12	15	25	46	1.81
4003791--4003839	21	2.4	19	84	15	71	63	0	4	32	1.13
4004804--4005154	112	3.1	112	90	1	535	45	12	14	26	1.81
4006032--4006085	21	2.6	21	100	0	108	14	24	46	14	1.83
4008601--4008663	20	2.9	21	79	9	65	15	25	34	23	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4015148--4015195	23	2.1	23	84	0	60	39	8	6	45	1.59
4022441--4022488	19	2.5	20	82	3	62	29	12	6	52	1.63
4023348--4023417	34	2.1	32	86	5	95	21	31	14	32	1.93
4023855--4023895	19	2.1	20	90	4	66	12	24	39	24	1.89
4030368--4030565	76	2.6	76	94	0	333	28	0	12	58	1.38
4031142--4031187	4	11.8	4	80	13	51	21	2	0	76	0.90
4031212--4031257	16	2.6	18	77	16	51	34	2	0	63	1.07
4036912--4036946	16	2.4	14	90	9	52	62	14	8	14	1.53
4037017--4037081	10	6.7	10	73	19	66	56	21	12	9	1.63
4037037--4037075	16	2.4	16	91	0	69	56	23	12	7	1.62
4037021--4037065	22	2.0	22	95	0	81	55	24	13	6	1.62
4042715--4042798	11	7.3	11	71	19	55	59	2	3	34	1.28
4043214--4043314	36	2.8	37	86	6	134	30	15	14	38	1.88
4043775--4044228	106	4.3	106	82	8	500	22	19	24	33	1.97
4043775--4044228	206	2.2	209	81	10	534	22	19	24	33	1.97
4044819--4044989	68	2.5	67	84	4	229	36	9	21	32	1.86
4044819--4045015	65	2.9	67	82	5	229	38	9	21	31	1.85
4044965--4045245	36	8.0	35	78	12	254	40	13	19	26	1.89
4044913--4045226	138	2.3	137	85	1	432	40	13	19	27	1.88
4045001--4045189	102	1.9	103	86	2	274	40	13	17	28	1.87
4045107--4045279	36	4.8	36	84	4	145	39	15	20	24	1.91
4046790--4046849	22	2.7	22	84	7	68	1	10	10	78	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4046777--4046841	16	4.2	15	70	14	51	3	9	12	75	1.15
4046800--4046851	23	2.3	22	83	3	59	1	7	9	80	0.97
4058193--4058355	28	5.6	28	69	15	82	50	1	0	47	1.13
4058193--4058353	31	5.4	30	74	19	110	49	1	0	48	1.13
4058303--4058346	22	2.0	23	86	4	63	54	0	0	45	0.99
4058545--4058734	42	4.6	42	91	2	294	47	18	15	17	1.82
4058545--4058734	82	2.3	83	90	1	292	47	18	15	17	1.82
4073218--4073323	52	2.0	52	94	3	187	33	11	24	31	1.91
4074420--4074447	2	14.0	2	100	0	56	50	0	0	50	1.00
4074493--4074520	2	14.0	2	100	0	56	50	0	0	50	1.00
4074980--4075036	17	3.3	17	97	2	105	24	0	5	70	1.08
4075006--4075108	27	3.7	26	73	14	89	29	2	4	63	1.30
4076123--4076177	25	2.2	25	100	0	110	52	7	12	27	1.65
4076123--4076164	13	3.3	13	73	6	50	57	4	11	26	1.54
4076704--4076771	34	2.0	34	100	0	136	32	11	20	35	1.89
4076714--4076768	17	3.2	17	70	10	58	32	10	21	34	1.89
4077209--4077269	23	2.7	23	92	0	104	18	27	27	26	1.98
4079385--4079428	21	2.1	21	100	0	88	20	29	13	36	1.91
4082223--4082322	49	2.0	49	98	0	191	45	11	9	35	1.71
4089484--4089512	14	2.0	15	93	6	51	34	10	34	20	1.87
4098692--4098735	16	2.6	17	89	7	63	45	0	2	52	1.13
4104158--4104262	25	4.3	24	78	20	112	38	19	0	41	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4104391--4104422	15	2.2	15	94	5	57	31	9	28	31	1.88
4104484--4104520	19	2.0	20	84	10	51	32	18	16	32	1.93
4104852--4105261	188	2.2	188	84	2	520	34	22	16	26	1.95
4107560--4107600	17	2.4	18	88	11	61	39	0	4	56	1.21
4108075--4108117	12	3.5	12	79	17	52	79	0	9	11	0.95
4108111--4108140	4	7.2	4	92	7	51	73	0	3	23	0.98
4108144--4108168	2	12.5	2	100	0	50	52	0	0	48	1.00
4108390--4108434	2	23.5	2	82	8	58	57	0	0	42	0.98
4108392--4108434	17	2.5	17	92	0	68	58	0	0	41	0.98
4108375--4108510	21	6.3	21	71	17	75	60	2	3	33	1.27
4109803--4111183	106	13.0	106	92	0	2192	23	18	24	33	1.96
4112028--4112081	22	2.5	21	88	8	81	31	7	25	35	1.84
4112688--4112737	20	2.5	20	87	6	66	6	10	6	78	1.10
4113971--4114000	15	2.1	14	93	6	51	63	10	13	13	1.52
4115740--4115826	4	21.2	4	74	15	63	73	0	8	18	1.07
4115901--4115968	29	2.4	29	74	16	70	72	7	0	20	1.09
4116700--4116789	37	2.4	37	90	0	135	30	12	16	41	1.85
4121662--4121710	22	2.2	22	88	0	71	36	18	20	24	1.94
4123356--4123398	10	4.2	10	82	14	52	41	11	6	39	1.68
4123687--4123734	18	2.8	17	78	6	51	31	2	0	66	1.03
4123696--4123733	11	3.4	11	92	3	58	28	0	0	71	0.87
4123694--4123734	12	3.5	12	86	6	57	29	0	0	70	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4125491--4125564	29	2.6	28	87	6	105	43	25	20	10	1.84
4127347--4127580	117	2.0	117	98	0	450	34	24	15	25	1.95
4132653--4132711	29	2.0	29	83	6	75	35	22	28	13	1.92
4132710--4132734	13	1.9	13	100	0	50	16	24	44	16	1.86
4136560--4136615	28	2.0	28	85	0	76	46	1	1	50	1.22
4156321--4156350	15	2.0	15	93	0	51	13	0	30	56	1.37
4161176--4161231	28	2.0	28	100	0	112	28	32	10	28	1.90
4162648--4162711	30	2.2	28	78	10	74	57	12	6	23	1.57
4162699--4162767	28	2.5	28	92	0	120	46	20	1	31	1.60
4163825--4163862	20	1.9	20	89	10	60	52	10	0	36	1.36

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