genome.fa.s1465.2.7.7.80.10.50.1000.27.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

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   52   53   54   55   

This is table  27  of  55  ( 6520 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)
5259319--5259374	25	2.1	27	75	18	64	41	1	7	50	1.40
5259484--5259532	20	2.6	19	78	15	57	24	2	2	71	1.07
5259482--5259534	19	2.5	20	76	17	54	24	1	1	71	1.06
5264529--5264572	21	2.1	21	82	0	52	31	38	13	15	1.87
5271165--5271448	112	2.5	111	82	4	349	44	2	7	45	1.47
5271166--5271510	37	9.5	37	74	11	295	42	2	7	46	1.45
5271166--5271445	73	3.8	74	84	4	332	43	2	7	46	1.45
5271359--5271549	104	1.8	104	84	8	264	40	3	9	46	1.53
5271617--5271666	19	2.7	18	78	9	55	22	2	2	74	1.03
5271614--5271669	24	2.3	23	84	6	67	21	1	1	75	0.99
5272787--5272830	19	2.4	19	84	3	63	15	4	2	77	1.04
5273085--5273111	6	4.5	6	100	0	54	44	0	0	55	0.99
5273396--5273553	64	2.5	63	82	5	167	32	22	12	31	1.92
5279330--5279386	21	2.7	21	100	0	114	26	26	14	33	1.94
5282076--5282233	64	2.5	63	77	7	160	33	21	12	32	1.91
5290272--5290349	26	2.7	27	84	13	95	38	19	23	19	1.93
5292034--5292078	23	2.0	23	86	0	63	44	0	2	53	1.13
5292197--5292283	23	3.7	23	83	4	95	52	1	2	43	1.21
5300454--5300512	29	2.0	29	96	0	109	25	13	11	49	1.76
5305142--5305200	29	2.0	29	100	0	118	23	13	13	49	1.78
5307934--5307958	12	2.1	12	100	0	50	52	0	8	40	1.31
5307956--5307995	20	2.0	20	90	0	62	57	22	12	7	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5307955--5307994	10	4.0	10	83	0	53	60	22	10	7	1.54
5308300--5308349	14	3.9	13	77	20	52	58	16	12	14	1.64
5308287--5308386	24	4.2	24	77	10	98	54	16	13	17	1.72
5329995--5330022	14	2.0	14	100	0	56	42	0	7	50	1.30
5331830--5331886	24	2.4	24	100	0	114	24	38	0	36	1.56
5334474--5334500	12	2.2	12	100	0	54	62	7	0	29	1.22
5334598--5334656	27	2.3	25	82	11	66	69	0	1	28	0.98
5334595--5334658	4	15.2	4	75	18	51	70	0	1	28	0.97
5335036--5335106	33	2.2	33	97	0	133	25	9	22	42	1.84
5335155--5335230	3	25.3	3	82	15	79	69	0	0	30	0.88
5336764--5336839	24	3.0	25	77	9	75	43	6	0	50	1.28
5337349--5337400	24	2.1	25	85	3	70	55	0	1	42	1.10
5337359--5337440	24	3.4	24	79	9	87	59	0	2	37	1.11
5338263--5338302	16	2.5	16	95	0	71	35	10	17	37	1.83
5338655--5338832	89	2.0	89	100	0	356	33	13	15	37	1.87
5342423--5342465	18	2.4	18	84	0	59	46	2	18	32	1.62
5349752--5349810	31	1.9	31	89	0	91	23	23	11	40	1.88
5349752--5349934	82	2.4	77	81	9	203	22	21	14	40	1.90
5349785--5349936	82	1.9	82	88	0	232	22	19	15	42	1.89
5349783--5349942	42	3.9	42	80	6	173	21	20	16	41	1.90
5349783--5349961	42	4.3	41	78	7	146	24	20	16	39	1.92
5352902--5352990	36	2.5	36	94	1	153	38	16	16	28	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5354327--5354445	56	2.1	59	82	7	147	42	24	13	20	1.88
5354390--5354686	41	7.2	40	82	6	301	34	20	18	26	1.96
5354390--5354686	83	3.6	83	84	4	368	34	20	18	26	1.96
5359940--5360008	30	2.2	30	82	15	86	37	5	15	40	1.72
5359949--5360008	29	2.0	31	90	6	97	36	6	15	41	1.73
5360169--5360210	21	2.0	21	100	0	84	23	19	28	28	1.98
5360494--5360563	34	2.1	32	86	5	95	31	15	30	22	1.95
5362720--5362779	29	2.0	31	90	6	97	36	6	15	41	1.73
5362997--5363038	21	2.0	21	95	0	75	23	21	28	26	1.99
5365964--5366020	12	4.8	12	74	8	53	52	17	12	17	1.74
5365959--5366046	24	3.7	24	76	3	88	48	17	13	20	1.80
5365950--5366043	48	2.0	48	87	4	136	50	14	13	21	1.78
5367762--5367843	36	2.2	36	89	2	119	32	15	7	43	1.75
5368481--5368510	7	4.1	7	91	8	51	26	30	30	13	1.94
5368481--5368510	15	2.1	14	93	6	51	26	30	30	13	1.94
5368520--5368566	18	2.3	22	68	31	57	23	12	46	17	1.82
5368526--5368572	18	2.6	18	96	0	85	21	10	44	23	1.83
5372599--5372628	7	4.3	7	95	0	51	53	0	0	46	1.00
5375465--5375558	21	4.4	21	95	1	170	59	24	4	11	1.50
5382769--5382799	15	2.1	15	93	0	53	45	0	0	54	0.99
5388787--5389114	44	7.5	44	89	2	477	17	25	24	32	1.97
5402364--5402994	53	11.7	53	88	5	858	26	28	14	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5402364--5403051	108	6.4	107	89	5	955	27	28	14	29	1.96
5402364--5402998	161	3.9	161	91	2	963	27	28	14	29	1.95
5402996--5403449	51	8.8	50	87	3	523	22	24	19	33	1.97
5402996--5403450	206	2.2	206	90	1	698	23	23	19	33	1.97
5402996--5403449	155	2.9	153	87	4	612	22	24	19	33	1.97
5403865--5404091	36	6.3	36	90	2	339	18	21	23	36	1.95
5403831--5404092	108	2.4	108	84	3	339	20	20	22	36	1.95
5418515--5418631	57	2.1	57	95	0	207	33	28	17	21	1.95
5424650--5424686	13	2.8	14	88	8	51	56	2	10	29	1.47
5424863--5424892	15	1.9	16	93	6	53	80	0	3	16	0.85
5424975--5425272	129	2.3	129	90	1	463	40	16	17	25	1.89
5429324--5429362	16	2.3	16	86	8	51	76	5	7	10	1.13
5450097--5450144	8	6.4	7	95	4	53	47	0	0	52	1.00
5450102--5450145	2	22.5	2	95	4	81	50	0	0	50	1.00
5450240--5450308	35	1.9	36	94	2	122	20	34	13	31	1.91
5451670--5451699	2	15.0	2	100	0	60	50	0	0	50	1.00
5452393--5452470	38	2.0	39	87	2	113	50	8	3	37	1.52
5452408--5452470	21	3.2	20	69	17	51	50	7	1	39	1.41
5452468--5452494	13	2.1	13	100	0	54	22	7	0	70	1.12
5452616--5452680	33	2.0	33	87	6	96	40	18	12	29	1.87
5454109--5454168	31	2.0	32	83	9	81	51	0	1	46	1.10
5454224--5454265	20	2.2	19	86	4	57	64	2	0	33	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5454440--5454469	3	10.0	3	92	0	51	63	0	3	33	1.11
5455766--5455834	3	23.7	3	77	11	72	60	0	0	39	0.97
5455743--5455833	40	2.3	37	75	17	94	60	0	1	38	1.04
5456175--5456849	113	6.0	113	90	1	982	28	19	15	37	1.91
5456175--5456849	337	2.0	338	94	1	1185	28	19	15	37	1.91
5456176--5456834	224	2.9	224	89	2	964	28	19	14	37	1.91
5458365--5458421	15	3.9	15	84	13	82	0	14	0	85	0.59
5458364--5458422	29	2.0	30	93	3	102	0	15	0	84	0.62
5458374--5458440	29	2.3	28	82	10	80	2	16	0	80	0.83
5461954--5461984	9	3.6	9	91	8	55	54	0	22	22	1.44
5465743--5465774	15	2.1	15	94	0	55	46	9	18	25	1.79
5469612--5469671	31	2.0	32	83	9	81	51	0	1	46	1.10
5469727--5469768	20	2.2	19	86	4	57	64	0	0	35	0.94
5469640--5469872	120	2.0	120	82	5	294	45	9	7	37	1.64
5471262--5471330	3	23.7	3	74	11	63	59	1	0	39	1.06
5472760--5472873	60	1.9	60	83	3	149	35	9	16	38	1.82
5473204--5473271	28	2.4	29	81	13	79	60	1	2	35	1.21
5473608--5473659	26	2.0	26	85	7	70	46	0	1	51	1.12
5473622--5473662	16	2.4	18	88	8	59	48	0	0	51	1.00
5474377--5474424	2	24.0	2	100	0	96	50	0	0	50	1.00
5474852--5474880	5	5.8	5	100	0	58	82	0	0	17	0.66
5489282--5489345	29	2.2	28	81	13	76	32	12	6	48	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5491314--5491354	16	2.6	16	88	3	57	56	0	14	29	1.39
5492258--5492299	2	21.0	2	100	0	84	50	0	0	50	1.00
5492610--5492647	15	2.5	15	100	0	76	52	10	28	7	1.64
5493398--5494168	242	3.2	236	85	5	985	35	15	16	31	1.91
5493849--5493955	42	2.6	40	78	11	117	33	19	19	27	1.96
5494140--5494188	22	2.2	22	88	0	80	40	16	18	24	1.90
5494325--5494904	55	10.6	55	84	3	652	41	15	9	33	1.79
5494339--5494828	218	2.2	218	86	2	676	42	14	9	33	1.78
5494327--5494833	273	1.9	274	86	1	730	42	14	9	32	1.78
5496664--5496793	12	10.6	11	69	24	50	6	19	0	74	1.02

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   52   53   54   55