genome.fa.s9634.2.7.7.80.10.50.1000.20.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   

This is table  20  of  78  ( 9351 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)
4376194--4376321	31	4.1	31	76	9	134	29	17	21	32	1.96
4377558--4377601	22	2.0	22	100	0	88	31	27	18	22	1.97
4377862--4378246	184	2.1	184	90	2	596	41	3	9	46	1.53
4382625--4382692	23	3.0	23	73	0	64	33	26	22	17	1.96
4383345--4383385	20	2.1	20	86	4	57	39	21	12	26	1.89
4386704--4386736	17	1.9	17	93	0	57	48	12	0	39	1.40
4386926--4386950	10	2.5	10	100	0	50	32	0	20	48	1.50
4388228--4388302	35	2.1	35	82	0	87	29	13	10	46	1.76
4390418--4390539	31	3.9	31	82	3	147	28	19	27	23	1.98
4390409--4390536	62	2.1	62	85	2	168	30	21	25	21	1.99
4393981--4394009	15	1.9	15	100	0	58	31	13	13	41	1.84
4397092--4397326	130	1.8	129	83	4	312	45	8	8	37	1.63
4397533--4397619	11	7.5	11	73	23	72	65	1	2	31	1.12
4397532--4397619	23	3.8	23	78	15	92	65	1	2	30	1.12
4399346--4399691	139	2.5	139	88	2	482	26	19	14	40	1.89
4399620--4400289	113	5.7	123	85	7	490	26	19	15	38	1.92
4399863--4400312	113	4.0	113	94	0	744	26	19	16	37	1.92
4399863--4400312	225	2.0	225	92	1	742	26	19	16	37	1.92
4400713--4400767	22	2.5	22	90	0	92	38	14	12	34	1.84
4401139--4401339	54	3.8	54	84	6	236	24	20	14	39	1.91
4401139--4401339	104	1.9	104	84	6	269	24	20	14	39	1.91
4403302--4403584	103	2.6	107	90	6	430	33	19	14	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4411733--4411839	11	9.3	11	73	21	78	66	1	1	29	1.13
4411732--4411819	23	3.8	23	78	15	92	65	1	2	30	1.12
4414082--4414129	13	3.7	13	82	0	60	35	14	16	33	1.89
4418129--4418175	13	3.6	13	88	0	67	36	12	17	34	1.87
4418122--4418175	26	2.1	26	85	0	72	37	12	18	31	1.89
4424724--4424769	20	2.3	20	92	0	74	19	23	26	30	1.98
4424725--4424766	10	4.3	10	80	14	52	16	23	26	33	1.96
4424780--4424837	29	2.0	29	89	0	89	29	3	20	46	1.67
4425786--4426030	42	5.9	41	85	5	298	19	22	23	35	1.96
4425786--4426030	124	1.9	126	85	8	338	19	22	23	35	1.96
4427882--4427980	44	2.2	44	92	1	162	32	26	16	25	1.96
4429910--4429949	21	1.9	21	89	0	62	17	25	22	35	1.95
4431889--4431971	44	1.9	43	85	2	112	31	25	15	27	1.96
4433705--4433738	17	2.1	16	88	5	50	58	5	20	14	1.57
4436057--4436140	44	1.9	44	83	9	109	54	4	3	36	1.39
4444739--4444783	22	2.1	22	88	12	67	31	31	20	17	1.96
4444767--4444861	21	4.4	21	77	5	64	36	24	17	21	1.94
4444796--4444861	21	3.2	20	80	8	69	34	24	18	22	1.96
4448964--4449102	21	6.5	22	73	5	70	35	23	17	23	1.95
4449005--4449083	21	3.8	21	77	12	90	39	20	13	26	1.90
4449007--4449099	21	4.4	21	75	0	78	37	23	13	24	1.92
4449314--4449362	20	2.5	20	93	0	80	36	20	4	38	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4450183--4450225	18	2.3	18	84	8	50	37	23	2	37	1.68
4450188--4450225	18	2.1	19	85	5	51	36	23	2	36	1.69
4451483--4451626	67	2.1	69	79	5	159	25	16	19	38	1.92
4458371--4458417	20	2.3	20	85	0	67	42	8	23	25	1.82
4458563--4458640	37	2.1	37	81	11	88	44	3	3	47	1.39
4459865--4460056	43	4.6	43	71	14	134	50	5	17	27	1.68
4461663--4461692	2	15.0	2	100	0	60	50	0	0	50	1.00
4468429--4468518	23	3.9	23	77	17	71	50	2	0	47	1.13
4468985--4469039	22	2.5	22	82	2	67	41	34	0	23	1.55
4473763--4473793	16	2.0	16	93	6	55	41	6	25	25	1.79
4478939--4478981	22	2.0	22	81	9	52	53	0	0	46	1.00
4478947--4479034	22	3.9	22	78	12	97	52	5	0	42	1.25
4479050--4479090	21	2.0	21	95	0	73	53	12	0	34	1.38
4478939--4479116	52	3.5	53	82	11	210	52	8	0	38	1.36
4479200--4479307	32	3.7	31	75	23	126	50	12	0	36	1.46
4479130--4480016	54	16.2	54	73	15	650	52	11	0	34	1.44
4479232--4479274	22	2.0	22	95	0	77	51	11	0	37	1.39
4479331--4479403	32	2.3	31	86	9	94	52	8	1	38	1.40
4479548--4479604	18	3.4	18	72	18	68	57	7	0	35	1.26
4479543--4479622	32	2.5	32	100	0	160	56	6	0	37	1.25
4479566--4479618	14	3.5	14	72	18	52	58	3	0	37	1.16
4479609--4479657	22	2.2	22	85	3	62	57	10	2	30	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4479629--4480099	32	16.4	32	70	21	250	52	12	0	34	1.43
4479661--4479703	22	2.0	22	95	0	77	51	11	0	37	1.39
4479666--4479816	80	1.9	80	91	2	250	52	12	0	34	1.44
4479827--4479909	22	4.0	22	73	17	95	53	15	0	31	1.43
4479666--4480070	206	2.0	206	93	1	697	52	12	0	34	1.45
4479871--4479917	22	2.0	23	84	8	60	53	14	0	31	1.42
4479864--4480099	87	2.9	83	88	7	333	52	13	0	33	1.43
4479923--4479997	22	3.2	23	71	17	73	54	16	0	29	1.42
4480023--4480067	22	2.0	22	82	4	54	55	4	0	40	1.20
4480031--4480076	22	2.1	22	91	0	74	52	10	0	36	1.37
4480037--4480084	22	2.1	22	84	3	60	56	12	0	31	1.37
4480079--4480256	15	11.5	15	86	8	223	51	1	0	47	1.12
4481572--4481611	20	2.0	21	85	5	55	35	12	2	50	1.54
4481796--4481870	3	25.0	3	100	0	150	66	0	0	33	0.92
4489196--4489256	31	2.0	31	90	0	95	31	9	16	42	1.81
4493818--4493863	21	2.1	22	84	11	60	21	0	8	69	1.15
4499784--4499820	18	2.0	19	89	5	58	45	32	16	5	1.70
4499791--4499846	17	3.2	17	72	25	53	53	26	12	7	1.64
4500170--4500210	17	2.4	17	91	0	64	29	17	21	31	1.96
4506661--4506718	18	3.3	17	80	7	71	81	1	15	1	0.86
4506662--4506723	25	2.4	25	84	10	81	82	1	14	1	0.83
4507739--4508494	136	5.6	136	87	2	1083	36	15	20	27	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4507739--4508492	269	2.8	270	93	1	1242	36	15	20	27	1.93
4508445--4508515	23	3.4	22	68	22	62	43	9	28	18	1.81
4508435--4508532	40	2.5	40	93	0	169	43	9	25	21	1.82
4508295--4508670	176	2.1	176	88	0	547	37	15	21	25	1.93
4508163--4508804	312	2.1	312	88	0	960	37	16	20	26	1.93
4508475--4508875	136	3.0	134	86	3	534	35	19	18	25	1.95
4524023--4524059	18	2.0	20	84	10	51	8	5	40	45	1.56
4525375--4525440	21	3.2	21	67	4	62	16	16	25	40	1.89
4525810--4525882	28	2.6	29	93	2	121	21	34	0	43	1.53
4525817--4525882	29	2.3	28	94	2	114	22	33	0	43	1.54
4527435--4527536	42	2.5	41	81	9	134	33	22	22	21	1.97
4527214--4528451	257	4.8	258	85	3	1578	34	16	15	33	1.91
4527214--4528450	515	2.4	517	85	3	1650	34	16	16	32	1.91
4528207--4528308	42	2.5	42	80	1	107	33	20	21	24	1.97
4537973--4538017	3	14.7	3	86	13	65	33	0	2	64	1.06
4538464--4538493	13	2.3	13	100	0	60	66	6	16	10	1.41
4546989--4547514	228	2.3	228	85	4	707	32	16	16	34	1.92
4547431--4547542	42	2.7	41	79	8	118	25	19	19	35	1.95
4547513--4547567	20	2.8	20	100	0	110	20	23	21	34	1.97
4547841--4548528	267	2.6	268	83	3	816	34	21	14	29	1.93
4547844--4548545	134	5.3	134	84	2	786	34	21	14	29	1.93
4549547--4549618	25	2.8	24	85	10	99	77	0	1	20	0.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4549545--4549618	17	4.4	16	84	15	89	75	0	1	22	0.88
4549547--4549620	8	8.6	9	84	15	95	78	0	1	20	0.83
4551308--4551337	15	1.9	16	93	6	53	46	0	0	53	1.00
4556423--4556451	2	14.5	2	100	0	58	48	0	0	51	1.00
4556472--4556498	3	9.0	3	100	0	54	33	0	0	66	0.92
4556534--4556572	2	20.0	2	94	5	71	51	0	0	48	1.00
4556672--4556729	27	2.1	27	81	12	66	15	8	1	74	1.14
4556875--4556910	18	1.9	19	88	5	56	16	5	2	75	1.12
4560737--4560915	95	1.9	95	89	0	277	32	18	19	29	1.96
4562165--4562339	72	2.3	75	82	7	205	26	18	13	41	1.87

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   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78