genome.fa.s9175.2.7.7.80.10.50.1000.19.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: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  10629029

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   

This is table  19  of  51  ( 6037 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)
3705322--3705374	25	2.1	25	89	0	79	33	20	7	37	1.81
3708312--3708356	18	2.5	18	85	7	56	26	4	0	68	1.08
3718974--3718999	13	2.0	13	100	0	52	92	0	7	0	0.39
3719556--3719588	1	33.0	1	100	0	66	100	0	0	0	0.00
3719938--3720511	105	5.6	105	89	5	827	33	26	18	21	1.96
3719938--3720511	209	2.8	209	89	4	909	33	26	18	21	1.96
3728419--3728465	16	2.9	16	100	0	94	38	6	19	36	1.77
3729020--3729058	16	2.4	16	91	0	60	20	28	17	33	1.96
3729889--3729938	26	1.9	26	87	0	73	36	18	22	24	1.95
3730372--3730412	19	2.1	20	86	4	57	29	9	0	60	1.28
3731026--3731072	23	2.1	23	88	4	69	36	23	10	29	1.89
3731156--3731206	20	2.5	20	87	0	66	58	15	11	13	1.63
3734595--3734682	24	3.7	24	73	4	70	47	13	13	25	1.79
3739888--3740033	6	24.3	6	68	5	62	10	3	37	47	1.56
3739923--3740033	18	6.1	18	71	12	75	9	4	37	48	1.55
3740215--3740423	113	1.9	113	85	7	291	33	7	28	30	1.84
3740650--3740790	61	2.3	60	86	3	210	34	9	6	49	1.62
3740818--3740915	26	3.5	26	74	23	83	46	4	5	43	1.44
3740847--3740997	32	4.6	32	84	8	180	43	5	5	45	1.53
3740849--3740997	33	4.5	33	83	9	173	42	6	6	44	1.53
3740969--3741007	13	3.0	13	84	0	51	35	5	5	53	1.45
3740994--3741048	18	2.8	18	86	10	65	43	5	9	41	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3741011--3741154	18	8.5	17	66	26	60	43	9	5	40	1.61
3741248--3741389	18	7.2	18	71	20	97	38	10	9	40	1.73
3741290--3741527	60	4.1	57	78	15	231	38	6	8	46	1.61
3741348--3741469	27	4.7	26	71	18	83	40	6	7	45	1.58
3741494--3741600	20	5.0	20	68	18	54	45	4	6	42	1.50
3741515--3741570	27	2.1	27	86	0	76	48	5	7	39	1.54
3741522--3741585	27	2.4	27	86	2	94	46	4	7	40	1.53
3741914--3741967	9	6.2	9	73	14	51	51	3	0	44	1.19
3741929--3742030	11	9.9	10	68	26	54	47	2	1	48	1.28
3741973--3742010	11	3.5	11	88	0	58	44	2	2	50	1.30
3742100--3742266	2	81.5	2	76	13	153	46	3	2	47	1.32
3741847--3742266	22	19.7	20	67	22	132	46	4	3	45	1.40
3742366--3742870	216	2.3	216	96	0	929	29	10	8	51	1.67
3743854--3743899	16	2.8	16	86	3	56	45	2	2	50	1.26
3744267--3744312	23	2.0	24	82	4	58	21	2	10	65	1.35
3747422--3747584	88	1.9	88	92	0	272	44	7	9	38	1.66
3748318--3748389	3	24.0	3	100	0	144	66	0	0	33	0.92
3748548--3748627	27	3.0	27	76	15	69	60	2	1	36	1.18
3752055--3752089	13	2.7	13	95	0	61	25	37	20	17	1.94
3752427--3752481	23	2.5	23	76	5	60	20	18	40	21	1.92
3762997--3763788	137	5.8	137	83	2	899	34	25	15	25	1.94
3762994--3763789	277	2.9	272	81	5	920	34	25	14	25	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3764222--3764257	3	12.0	3	100	0	72	66	0	0	33	0.92
3764390--3764461	25	2.8	24	83	8	72	61	0	5	33	1.19
3764405--3764461	8	6.8	8	76	7	51	63	0	1	35	1.05
3764420--3764481	27	2.3	25	79	15	70	59	1	1	37	1.17
3766204--3766236	2	16.5	2	100	0	66	51	0	0	48	1.00
3767777--3767802	3	8.7	3	100	0	52	34	0	0	65	0.93
3768817--3768866	15	3.4	15	78	13	59	28	0	0	72	0.86
3768815--3768897	23	3.6	23	72	18	73	28	2	1	67	1.11
3768818--3768864	14	3.3	14	80	14	60	27	0	0	72	0.85
3768813--3768871	15	3.8	17	78	17	51	28	0	0	71	0.87
3768945--3768984	2	20.0	2	100	0	80	50	0	0	50	1.00
3785498--3785763	20	13.5	19	84	6	184	34	24	14	27	1.94
3785656--3785763	19	5.7	19	93	2	173	37	22	10	30	1.87
3785616--3785763	57	2.6	57	82	8	174	36	22	12	27	1.91
3786571--3786624	24	2.2	24	90	0	81	22	18	18	40	1.91
3788906--3788987	20	4.1	20	79	0	92	20	18	20	40	1.92
3788996--3789037	20	2.1	20	90	0	66	14	23	19	42	1.87
3789098--3789147	25	2.0	25	96	0	91	26	8	22	44	1.80
3789539--3789575	18	2.1	18	89	0	56	32	5	10	51	1.60
3789531--3789583	24	2.2	24	86	0	70	35	3	13	47	1.61
3789842--3789928	39	2.2	39	97	0	165	47	20	14	17	1.83
3790167--3790251	20	4.2	20	95	1	143	15	18	22	43	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3794059--3794102	20	2.2	20	91	0	70	54	20	15	9	1.68
3794386--3794436	22	2.3	22	86	0	75	23	11	41	23	1.87
3794572--3794665	20	4.7	20	69	12	66	26	15	25	31	1.96
3795501--3795611	21	5.4	21	66	4	82	23	15	25	36	1.94
3795496--3795634	41	3.4	41	93	0	233	20	16	24	38	1.93
3795518--3795631	20	5.6	20	67	4	84	19	18	23	38	1.93
3795644--3795710	19	3.5	19	91	0	107	19	19	17	43	1.89
3795492--3795732	82	3.0	81	79	8	215	21	17	21	39	1.92
3795701--3795754	22	2.5	22	87	0	81	18	16	24	40	1.90
3796029--3796076	19	2.5	19	100	0	96	41	18	20	18	1.90
3796067--3796187	22	5.7	22	74	13	103	38	23	21	17	1.93
3797126--3797172	16	2.9	16	75	15	51	38	0	2	59	1.09
3797362--3797403	20	2.1	20	91	8	68	35	4	16	42	1.69
3798228--3798260	17	2.0	17	88	5	50	6	12	21	60	1.53
3800257--3800303	23	2.0	23	84	8	60	42	6	2	48	1.40
3801459--3801508	22	2.3	21	80	10	57	56	2	2	40	1.22
3801489--3801586	15	6.3	15	68	24	60	56	0	3	40	1.15
3801535--3801595	14	4.4	14	73	20	56	62	0	1	36	1.05
3801529--3801589	28	2.2	27	80	11	70	63	0	0	36	0.94
3815976--3816064	23	4.0	23	80	5	101	22	15	24	37	1.93
3815895--3816057	21	7.6	21	72	11	107	23	16	23	36	1.94
3816710--3816743	16	2.1	17	88	5	52	38	0	17	44	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3819322--3819357	18	2.0	18	94	0	63	47	0	0	52	1.00
3824546--3824575	6	5.0	6	91	0	51	33	13	50	3	1.58
3826016--3826072	3	19.3	3	96	3	107	35	0	0	64	0.93
3826220--3826256	16	2.3	16	95	0	65	16	45	24	13	1.83
3827797--3827852	29	1.9	28	85	7	76	42	0	0	57	0.99
3827811--3827861	26	2.0	26	84	7	68	43	0	0	56	0.99
3833417--3834201	84	9.6	82	78	7	713	29	25	20	25	1.99
3833504--3834184	165	4.2	164	81	6	742	29	25	20	24	1.99
3833898--3834048	77	2.0	77	85	2	205	31	23	19	25	1.98
3833408--3834216	249	3.3	239	81	6	863	29	24	20	24	1.99
3836895--3836952	29	2.0	30	83	10	75	62	5	1	31	1.27
3839733--3839767	18	1.9	18	94	0	61	48	0	17	34	1.47
3845838--3845869	2	16.0	2	100	0	64	50	0	0	50	1.00
3847770--3847950	92	2.0	89	84	5	238	39	12	11	37	1.79
3849001--3849057	22	2.6	22	83	8	71	47	3	0	49	1.18
3851109--3851158	18	2.6	19	78	6	57	46	2	14	38	1.56
3853421--3853480	14	4.3	14	74	20	54	23	0	0	76	0.78
3853421--3853480	20	2.9	20	85	5	84	23	0	0	76	0.78
3853421--3853478	6	8.4	7	80	19	52	22	0	0	77	0.77
3853436--3853479	14	2.9	16	86	13	58	20	0	0	79	0.73
3861096--3861170	39	1.9	39	83	5	98	29	13	12	45	1.79
3861116--3861198	37	2.2	39	78	10	91	32	16	10	39	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3861274--3861395	36	3.3	35	84	6	120	30	18	13	38	1.88
3861299--3861410	36	3.1	36	88	3	154	28	18	15	37	1.91
3861353--3861737	67	5.6	67	79	5	367	30	18	13	38	1.89
3861702--3861744	22	2.0	22	90	0	68	32	18	9	39	1.83
3861674--3861788	54	2.1	55	93	4	198	32	18	10	39	1.84
3862070--3862127	3	18.7	3	82	7	71	36	0	3	60	1.14
3862072--3862108	19	1.9	19	100	0	74	32	0	0	67	0.91
3862070--3862127	22	2.6	22	88	0	80	36	0	3	60	1.14
3870002--3870044	18	2.4	17	92	7	68	53	6	9	30	1.59
3870245--3870274	15	2.0	15	93	0	51	6	13	3	76	1.11

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