genome.fa.s8128.2.7.7.80.10.50.1000.16.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: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4987688

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

This is table  16  of  20  ( 2387 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)
3794543--3794574	16	2.0	16	100	0	64	25	0	43	31	1.55
3797311--3797429	22	5.2	22	69	21	68	47	0	6	44	1.35
3797304--3797414	22	4.5	25	73	21	92	49	0	6	43	1.34
3797311--3797423	46	2.4	46	78	11	115	47	0	7	44	1.36
3797508--3797558	2	25.5	2	100	0	102	50	0	0	49	1.00
3797574--3797613	20	2.0	21	90	5	64	15	0	10	75	1.05
3798829--3798887	21	2.9	21	70	17	52	22	8	0	69	1.15
3806355--3806386	16	2.0	16	93	0	55	31	15	6	46	1.71
3816014--3816116	26	3.8	26	78	17	95	47	1	7	42	1.43
3816044--3816116	28	2.7	28	87	8	98	47	1	5	45	1.34
3816088--3816159	17	4.1	17	79	13	67	43	2	8	45	1.48
3816124--3816218	44	2.2	43	79	9	102	44	3	7	45	1.47
3817595--3817625	13	2.4	13	94	0	53	22	6	3	67	1.28
3820561--3820667	56	1.9	56	84	1	144	34	7	10	47	1.66
3820528--3820665	29	4.9	28	75	3	116	31	6	10	50	1.63
3820495--3820668	29	6.1	28	72	4	107	32	6	10	51	1.61
3823893--3823917	13	1.9	13	100	0	50	36	8	0	56	1.29
3837429--3837543	61	1.9	61	88	0	176	28	26	18	26	1.98
3838502--3838565	20	3.2	20	79	0	74	26	7	12	53	1.66
3838497--3838578	40	2.0	40	85	0	110	24	7	13	54	1.64
3838502--3838585	20	4.2	21	77	7	70	27	7	11	53	1.63
3841656--3841688	16	2.1	16	88	11	50	48	18	3	30	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3860964--3861006	17	2.5	17	88	0	59	25	11	20	41	1.86
3860975--3861008	17	2.0	17	100	0	68	23	17	17	41	1.90
3862588--3862923	59	5.7	59	85	4	464	38	19	9	32	1.84
3862588--3862923	117	2.9	118	87	3	482	38	19	9	32	1.84
3863259--3863329	19	3.6	19	76	10	79	29	26	14	29	1.95
3868811--3868880	19	3.5	20	84	11	97	28	25	14	31	1.95
3875557--3875589	16	2.1	16	88	11	50	48	18	3	30	1.63
3878537--3878591	21	2.5	22	77	11	60	50	7	0	41	1.30
3902197--3902301	37	2.8	37	85	0	138	40	14	16	28	1.87
3902740--3902772	2	16.5	2	93	0	57	48	3	0	48	1.17
3902854--3902896	12	3.6	12	83	0	59	27	4	0	67	1.10
3902911--3902959	25	1.9	26	88	12	75	28	0	2	69	1.00
3902969--3903015	11	4.2	11	86	5	58	21	6	4	68	1.30
3902864--3903027	72	2.2	74	79	14	178	23	6	2	67	1.27
3903237--3903273	2	18.5	2	100	0	74	48	0	0	51	1.00
3904266--3904296	2	15.5	2	100	0	62	48	0	0	51	1.00
3908838--3908904	27	2.5	27	78	9	75	53	1	7	37	1.38
3909899--3909951	21	2.5	21	96	0	97	18	32	30	18	1.96
3909899--3909951	10	5.1	10	88	8	79	18	32	30	18	1.96
3912785--3912832	20	2.4	20	96	0	87	43	0	43	12	1.42
3917998--3918039	21	2.0	21	86	9	59	59	2	14	23	1.47
3924068--3924095	14	2.0	14	100	0	56	28	7	28	35	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3924196--3924510	149	2.1	149	95	1	560	27	16	21	34	1.95
3924478--3924522	23	2.0	23	90	0	72	22	26	26	24	2.00
3927797--3927841	21	2.1	21	87	0	63	31	28	24	15	1.96
3929220--3929247	14	2.0	14	100	0	56	28	7	28	35	1.84
3929348--3929662	149	2.1	149	95	1	569	27	17	21	34	1.95
3929630--3929674	23	2.0	23	90	0	72	22	26	26	24	2.00
3932798--3932825	11	2.5	11	100	0	56	92	7	0	0	0.37
3935152--3935192	17	2.3	19	91	8	68	46	0	0	53	1.00
3935480--3935526	2	23.5	2	100	0	94	51	0	0	48	1.00
3938548--3938800	54	4.7	54	88	2	328	33	16	16	33	1.92
3938549--3938760	108	2.0	108	93	0	361	32	16	16	33	1.92
3944239--3944290	22	2.5	21	75	6	52	36	11	28	23	1.90
3944595--3944863	54	5.0	54	82	0	322	31	17	18	33	1.94
3970169--3970229	16	3.5	16	71	26	52	40	4	11	42	1.62
3970168--3970241	37	2.1	36	87	5	105	41	5	10	41	1.63
3970180--3970326	20	7.2	20	71	16	97	41	6	8	42	1.62
3970248--3970290	17	2.4	19	81	18	56	41	6	6	44	1.58
3970232--3970307	36	2.1	37	82	7	93	42	7	6	43	1.60
3970232--3970326	38	2.4	37	79	11	100	43	7	6	43	1.58
3970365--3970417	21	2.5	21	84	0	70	39	7	7	45	1.61
3970457--3970615	34	4.9	33	76	17	129	48	1	1	47	1.23
3970497--3970622	6	20.3	6	75	18	59	49	0	1	48	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3970488--3970569	27	3.2	26	74	20	75	48	2	1	47	1.22
3970435--3970612	15	12.4	14	71	21	104	46	2	2	49	1.26
3970499--3970612	21	5.3	20	70	24	72	49	0	0	49	1.13
3970504--3970624	43	2.8	42	81	15	115	49	0	1	47	1.17
3970499--3970628	14	9.6	14	72	22	93	50	0	1	47	1.16
3970557--3970634	15	5.5	14	77	18	72	52	0	1	46	1.08
3971323--3971389	6	11.0	6	80	3	62	34	37	14	13	1.86
3971337--3971414	12	6.5	12	78	0	57	37	42	11	8	1.73
3971324--3971433	18	6.0	18	76	2	85	40	40	10	9	1.70
3971386--3971433	6	7.8	6	81	4	60	47	45	2	4	1.33
3971398--3971430	13	2.6	13	90	4	50	54	42	0	3	1.15
3971692--3971923	102	2.3	102	95	0	410	21	8	19	51	1.72
3971833--3972034	86	2.3	86	94	1	352	23	9	17	49	1.76
3974748--3974778	12	2.7	12	95	5	55	19	0	0	80	0.71
3975089--3975140	23	2.2	24	93	3	88	46	3	0	50	1.20
3975386--3975460	16	4.7	16	79	0	78	38	13	29	18	1.89
3976127--3976154	13	2.2	13	100	0	56	21	14	32	32	1.93
3980696--3980723	13	2.2	13	100	0	56	21	14	32	32	1.93
3983231--3983277	2	23.5	2	100	0	94	48	0	0	51	1.00
3984690--3985266	81	7.1	81	88	1	843	30	22	11	35	1.89
3991756--3992251	81	6.1	81	89	0	733	30	21	11	35	1.90
3991756--3992251	242	2.0	243	89	1	753	30	21	11	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3996401--3996441	12	3.5	12	77	16	50	48	0	0	51	1.00
3998817--3998864	23	2.1	23	84	0	60	35	10	18	35	1.85
3999272--3999343	23	3.1	23	89	2	99	40	22	4	33	1.73
3998929--3999980	428	2.5	430	95	3	1907	38	12	7	40	1.72
3999709--3999771	23	2.7	23	92	0	99	38	20	4	36	1.74
4000190--4000275	39	2.2	39	93	0	145	18	13	18	48	1.80
4000530--4000566	18	2.1	18	89	0	56	51	10	5	32	1.60
4000995--4001047	22	2.3	23	87	6	81	41	16	5	35	1.73
4003525--4004693	182	6.4	183	96	1	2102	33	16	13	35	1.88
4006158--4006232	3	25.0	3	73	0	60	22	34	6	36	1.81
4006162--4006244	12	6.9	12	83	0	94	20	34	8	36	1.83
4006166--4006244	36	2.2	36	90	0	122	20	35	8	35	1.84
4006186--4006247	18	3.4	18	79	0	79	17	35	9	37	1.83
4006162--4006247	6	14.3	6	77	0	64	19	34	8	37	1.82
4007705--4008784	196	5.5	197	97	0	1961	32	16	14	36	1.90
4008909--4008954	19	2.5	18	86	6	65	54	10	4	30	1.55
4008917--4008956	19	2.1	19	95	0	71	52	10	2	35	1.48
4010745--4010810	33	2.0	33	90	0	105	22	48	0	28	1.51
4010843--4010907	21	3.1	21	80	6	69	15	29	15	40	1.88
4013140--4013186	20	2.4	19	79	10	58	21	17	8	53	1.70
4013307--4013352	20	2.3	20	89	10	76	17	17	10	54	1.70
4016038--4016071	16	2.1	16	94	0	59	32	8	26	32	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4022517--4022595	26	3.0	26	90	3	131	60	3	11	24	1.47
4023114--4023193	31	2.6	30	77	11	74	43	1	16	38	1.56
4030563--4030597	17	2.1	17	94	0	61	37	14	11	37	1.82
4033339--4033389	23	2.2	23	100	0	102	41	17	7	33	1.79
4033679--4033719	19	2.0	21	90	9	68	19	14	26	39	1.90
4034449--4034499	21	2.4	21	87	6	68	39	9	7	43	1.67
4035230--4035321	43	2.1	43	100	0	184	44	27	21	6	1.77
4037256--4037299	17	2.6	17	96	0	79	31	11	13	43	1.80
4039951--4040008	28	2.2	26	81	6	62	67	1	1	29	1.11
4040811--4040857	21	2.3	20	85	3	58	19	10	23	46	1.80

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