genome.fa.s8027.2.7.7.80.10.50.1000.16.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: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7662336

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   

This is table  16  of  38  ( 4505 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)
3475154--3475184	9	3.3	9	95	4	53	19	0	0	80	0.71
3475153--3475185	14	2.3	15	94	5	59	18	0	0	81	0.68
3475152--3475194	15	2.9	15	86	10	61	20	0	0	79	0.74
3475154--3475194	19	2.2	19	86	8	57	21	0	0	78	0.76
3475082--3475401	120	2.6	121	84	6	421	24	18	14	43	1.87
3475284--3475308	12	2.1	12	100	0	50	16	0	0	84	0.63
3475418--3475512	32	2.9	32	71	11	84	26	13	4	55	1.56
3476218--3476275	16	3.7	16	79	6	57	13	6	1	77	1.05
3476251--3476284	10	3.1	11	87	12	52	17	2	0	79	0.86
3478754--3478818	23	2.8	23	90	0	103	40	7	16	35	1.78
3478920--3479597	198	3.4	198	87	2	878	30	14	15	39	1.87
3480688--3480863	90	2.0	90	90	0	280	38	9	7	44	1.65
3487533--3487710	90	2.0	90	92	0	293	36	11	7	44	1.68
3490715--3490762	19	2.5	19	96	0	87	52	6	6	35	1.52
3492331--3493082	200	3.8	197	83	4	933	31	15	14	38	1.87
3492329--3493082	397	1.9	399	85	4	1065	31	15	14	38	1.87
3495667--3495695	13	2.2	13	100	0	58	41	6	6	44	1.58
3496980--3497015	14	2.6	14	90	0	54	38	13	0	47	1.44
3499440--3500107	331	2.0	331	97	0	1264	29	23	6	40	1.79
3501751--3501795	23	2.0	23	86	0	63	26	28	24	20	1.99
3501774--3502077	149	2.0	149	99	0	599	35	20	16	27	1.94
3502246--3502317	29	2.5	29	90	0	108	37	12	9	40	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3502587--3502623	13	2.8	14	88	8	51	0	24	0	75	0.80
3508480--3508524	23	2.0	23	86	0	63	26	28	24	20	1.99
3508503--3508806	149	2.0	149	98	0	590	35	19	17	27	1.94
3508975--3509046	29	2.5	29	90	0	108	37	12	9	40	1.76
3512271--3512307	13	2.8	14	88	8	51	0	24	0	75	0.80
3514096--3514164	19	3.6	19	90	0	111	21	36	13	28	1.91
3517231--3517263	13	2.4	14	90	5	50	24	27	6	42	1.78
3517958--3518004	19	2.5	19	96	0	85	23	36	14	25	1.93
3520070--3520103	16	2.1	17	88	5	52	41	17	2	38	1.65
3520939--3520992	18	3.0	18	86	0	72	35	33	14	16	1.90
3524805--3524853	18	2.7	19	90	6	75	32	34	20	12	1.90
3526059--3527015	201	4.8	198	85	3	1186	32	14	13	39	1.85
3526050--3527015	399	2.4	400	86	3	1331	33	14	13	39	1.85
3527357--3527405	19	2.6	19	96	0	89	55	10	2	32	1.45
3529657--3529712	24	2.4	23	80	8	69	50	7	0	42	1.30
3531703--3532301	182	3.3	182	88	0	903	26	15	14	43	1.85
3535517--3535589	3	24.7	3	86	8	69	56	0	0	43	0.99
3535520--3535588	15	4.6	15	82	7	86	55	0	0	44	0.99
3536007--3536117	42	2.7	40	80	12	118	23	19	35	21	1.96
3535748--3536272	134	3.9	134	85	2	660	24	18	31	26	1.97
3535748--3536270	267	2.0	269	84	2	685	24	18	31	26	1.98
3536785--3537193	106	3.8	104	82	7	464	39	11	15	33	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3536988--3537193	110	1.9	110	91	3	342	38	10	15	34	1.82
3537167--3537268	36	3.0	34	81	4	107	34	12	18	34	1.89
3544527--3544623	18	5.3	18	72	23	69	53	0	1	45	1.07
3544537--3544622	3	28.7	3	86	9	77	55	0	0	44	0.99
3544537--3544608	13	5.5	13	83	8	92	56	0	0	43	0.99
3548635--3548667	2	16.5	2	100	0	66	51	0	0	48	1.00
3553101--3553150	20	2.5	20	93	0	82	20	16	26	38	1.92
3555232--3555304	32	2.3	32	100	0	146	28	38	19	13	1.90
3555452--3555502	27	1.9	26	84	11	68	47	1	3	47	1.32
3555521--3555603	18	4.6	18	73	11	71	33	2	4	59	1.32
3556213--3556268	23	2.5	23	82	2	69	33	25	12	28	1.92
3556355--3556432	20	3.9	21	80	9	92	60	16	7	15	1.57
3556368--3556422	10	5.5	10	73	16	51	61	18	3	16	1.48
3558778--3558851	24	3.0	24	84	6	85	52	18	4	24	1.63
3558797--3558961	59	2.9	59	80	15	213	53	23	3	20	1.59
3558867--3558956	24	3.6	25	79	7	110	52	26	3	17	1.60
3558853--3558968	51	2.2	52	92	1	189	52	25	2	18	1.58
3558853--3558984	52	2.6	51	85	6	194	53	25	3	18	1.59
3560284--3560342	12	5.1	12	73	22	54	33	6	1	57	1.35
3560311--3560369	24	2.5	24	78	8	66	35	5	1	57	1.31
3560345--3560626	7	36.5	8	68	18	75	36	6	2	53	1.41
3560388--3560535	39	3.6	37	75	19	127	37	7	1	53	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3560384--3561113	88	8.0	93	71	19	257	34	9	2	52	1.49
3560440--3560537	25	4.1	25	69	20	75	38	6	1	54	1.32
3560670--3560978	22	13.9	22	70	16	111	34	11	2	52	1.50
3560633--3561092	112	4.1	112	76	12	388	33	11	2	52	1.50
3560798--3561189	43	8.7	43	82	10	439	34	9	3	53	1.49
3560794--3561136	88	3.8	88	86	8	494	33	9	3	53	1.49
3560633--3561160	8	70.4	8	65	18	149	33	10	2	53	1.50
3560965--3561189	22	10.2	22	75	8	163	34	8	3	53	1.48
3561066--3561175	30	3.7	29	73	12	82	33	7	3	55	1.45
3560722--3561150	139	3.1	131	79	13	443	33	10	2	53	1.49
3560388--3561148	8	101.8	8	67	24	134	34	9	2	52	1.49
3561003--3561189	22	8.5	22	77	5	173	34	7	4	54	1.48
3561178--3561214	2	18.0	2	88	5	56	51	2	0	45	1.15
3561180--3561244	14	4.9	13	81	9	78	52	4	3	40	1.38
3561178--3561287	14	8.4	14	72	21	71	54	2	4	38	1.35
3561282--3561358	17	4.8	16	78	16	79	37	9	2	50	1.48
3561281--3561358	32	2.4	34	83	10	101	38	8	2	50	1.48
3561281--3561365	15	5.3	16	75	19	72	38	8	2	50	1.45
3561314--3561372	8	7.6	8	78	14	70	37	8	0	54	1.31
3561314--3561470	22	7.2	22	73	15	89	40	8	0	50	1.38
3561392--3561456	4	16.2	4	87	6	78	47	6	0	46	1.27
3561392--3561456	6	10.8	6	81	6	78	47	6	0	46	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3562379--3562427	21	2.3	21	89	0	71	28	24	22	24	1.99
3569125--3569330	42	4.8	42	90	2	295	33	23	24	17	1.96
3569263--3569329	21	3.2	21	68	16	66	34	26	23	14	1.94
3570150--3570218	29	2.4	29	87	4	95	47	17	2	31	1.62
3570238--3570284	18	2.6	18	93	0	76	10	23	46	19	1.80
3572346--3572388	21	2.0	21	86	0	59	30	27	25	16	1.97
3572928--3573145	103	2.1	103	99	0	427	25	13	24	37	1.92
3573162--3573224	23	2.7	23	85	4	83	22	26	25	25	2.00
3579280--3579322	21	2.0	21	86	0	59	30	27	25	16	1.97
3579998--3580042	23	2.0	23	90	0	72	20	31	24	24	1.98
3585350--3585555	42	4.8	42	87	3	288	32	22	26	18	1.97
3586390--3586458	29	2.4	29	90	4	104	49	17	1	31	1.56
3591912--3591959	25	1.9	25	95	0	87	20	43	25	10	1.83
3591912--3591977	22	2.8	24	86	6	91	19	42	25	12	1.86
3596192--3596233	2	21.0	2	100	0	84	50	0	0	50	1.00
3597366--3597396	2	15.0	2	93	6	53	48	0	3	48	1.17
3605981--3606040	29	2.1	29	87	3	86	10	23	0	66	1.21
3606022--3606069	25	1.9	25	86	0	69	8	39	0	52	1.32
3606428--3606482	21	2.6	21	100	0	110	27	21	21	29	1.99
3609773--3609810	3	12.7	3	94	0	67	68	2	0	28	1.03
3617436--3617489	16	3.3	16	94	2	90	31	18	12	37	1.89
3619979--3620036	23	2.5	23	74	20	66	39	15	10	34	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3629407--3629452	20	2.3	20	100	0	92	8	54	0	36	1.32
3636581--3636605	2	12.5	2	100	0	50	52	0	0	48	1.00
3640422--3640469	24	2.0	24	95	0	87	12	39	0	47	1.41
3641747--3641828	29	2.9	28	88	3	119	19	37	26	15	1.92
3641985--3642019	11	3.1	11	84	8	52	22	20	20	37	1.95
3642356--3642448	29	2.9	31	73	18	84	44	0	8	47	1.34
3642408--3642462	18	3.4	18	65	31	52	38	0	9	52	1.33
3642726--3642802	29	2.6	29	88	12	104	42	2	9	45	1.49
3642776--3642824	22	2.2	22	96	0	89	44	2	14	38	1.56
3645110--3645245	59	2.3	59	77	17	156	49	8	3	38	1.50

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