genome.fa.s9624.2.7.7.80.10.50.1000.23.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: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8249038

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  23  of  38  ( 4514 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)
4352952--4353277	162	2.0	162	100	0	652	31	14	16	37	1.89
4353937--4354022	44	2.0	44	81	4	102	26	20	17	34	1.95
4356503--4356555	23	2.2	23	86	6	70	37	26	5	30	1.79
4356802--4356853	21	2.5	20	78	9	59	32	0	13	53	1.40
4356830--4356892	28	2.2	30	94	5	112	30	0	12	57	1.36
4357319--4357344	4	6.5	4	100	0	52	23	0	23	53	1.46
4357386--4357444	16	3.4	16	72	20	55	38	0	11	49	1.40
4357406--4357448	22	2.0	22	81	4	52	39	0	9	51	1.34
4358787--4358896	54	2.0	54	100	0	220	38	18	25	18	1.93
4358808--4358893	27	3.2	27	63	18	70	36	16	27	19	1.93
4361023--4361066	23	1.9	23	85	0	61	54	2	4	38	1.33
4362355--4362425	30	2.4	30	92	4	117	46	14	0	39	1.44
4362355--4362445	30	3.0	30	82	10	96	43	12	1	42	1.49
4362689--4362751	29	2.3	26	78	17	74	50	6	0	42	1.27
4362749--4362807	28	2.1	29	81	15	70	40	8	0	50	1.33
4363028--4363093	23	2.9	23	88	0	96	39	15	24	21	1.91
4363037--4363093	11	5.0	11	75	8	60	40	15	22	21	1.91
4364104--4364128	2	12.5	2	100	0	50	48	0	0	52	1.00
4367799--4367879	20	3.8	20	72	12	63	22	20	29	27	1.99
4371413--4371555	70	2.0	70	97	0	268	23	30	10	35	1.89
4383171--4383204	11	3.1	11	86	0	50	8	0	8	82	0.85
4390465--4390574	40	2.8	40	91	0	166	22	12	26	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4393304--4393349	23	2.0	23	83	8	58	39	15	0	45	1.46
4393671--4393748	30	2.6	30	83	4	95	38	19	21	20	1.94
4396996--4397055	2	30.0	2	100	0	120	50	0	0	50	1.00
4397324--4397387	20	3.2	20	97	0	119	39	25	17	18	1.92
4397324--4397405	40	2.0	40	85	0	110	36	23	17	23	1.94
4397324--4397405	20	4.1	20	91	0	92	36	23	17	23	1.94
4397432--4397529	40	2.5	40	73	9	92	31	19	13	35	1.90
4397686--4397725	16	2.5	16	87	0	62	30	2	0	67	1.04
4400765--4400800	18	2.0	18	94	0	63	55	25	2	16	1.55
4401054--4401145	20	4.6	20	77	0	103	19	17	21	41	1.90
4401054--4401145	40	2.3	40	84	0	121	19	17	21	41	1.90
4401075--4401178	40	2.6	40	81	0	109	25	18	19	37	1.94
4402673--4402785	21	5.4	21	78	4	102	22	18	37	22	1.94
4402673--4402785	42	2.7	42	88	0	154	22	18	37	22	1.94
4402712--4402810	21	4.7	21	86	5	119	24	19	35	21	1.96
4402693--4402810	42	2.8	42	85	5	132	24	19	33	22	1.97
4403129--4403203	21	3.6	21	68	12	55	30	37	12	20	1.89
4403220--4403269	21	2.4	21	82	0	64	32	32	14	22	1.93
4404662--4404714	20	2.7	20	81	0	61	15	13	20	50	1.76
4405569--4405621	20	2.7	20	81	0	61	15	15	18	50	1.77
4403976--4406702	907	3.0	907	98	0	5278	35	20	16	27	1.94
4406855--4406899	22	2.0	22	86	0	63	22	20	42	15	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4407752--4407791	20	1.9	21	85	10	55	57	10	0	32	1.32
4408903--4408960	19	3.2	19	80	9	75	6	12	22	58	1.57
4410556--4410652	3	32.3	3	89	4	151	30	3	1	64	1.15
4412344--4412517	30	5.8	30	78	9	151	16	11	13	59	1.62
4412329--4412514	60	3.1	60	79	10	168	17	11	12	58	1.63
4412243--4412559	90	3.6	89	77	10	246	18	11	11	58	1.62
4416293--4416741	227	2.0	222	96	2	835	35	16	11	37	1.84
4417074--4417100	2	13.5	2	100	0	54	0	0	48	51	1.00
4418546--4418614	33	2.1	33	91	0	111	31	18	20	28	1.96
4418696--4418999	66	4.7	63	79	10	298	28	15	14	42	1.86
4418696--4418999	130	2.4	128	83	7	384	28	15	14	42	1.86
4418696--4418999	65	4.7	62	77	12	242	28	15	14	42	1.86
4419015--4419523	130	3.9	128	82	4	603	27	32	17	23	1.97
4419682--4419722	3	13.3	3	85	14	57	31	2	0	65	1.05
4420059--4420095	16	2.3	16	90	0	56	18	40	10	29	1.85
4421339--4421652	30	10.6	30	75	12	195	19	12	11	57	1.65
4421457--4421623	90	1.9	90	83	5	221	18	11	11	58	1.63
4424887--4424915	13	2.1	14	93	6	51	34	0	0	65	0.93
4428651--4428709	24	2.5	24	81	10	68	6	18	42	32	1.77
4428693--4428725	16	2.1	16	94	0	57	6	9	45	39	1.61
4428732--4429135	205	2.0	205	94	1	704	36	13	13	35	1.84
4429623--4429741	37	3.3	37	88	5	172	44	19	5	31	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4429622--4429741	35	3.3	36	89	5	181	44	20	5	30	1.72
4433574--4433692	37	3.3	37	87	5	163	44	18	5	31	1.71
4433573--4433692	35	3.3	36	88	5	172	44	19	5	31	1.72
4433591--4433720	35	3.7	35	85	8	140	41	17	7	33	1.78
4437739--4437770	16	2.0	16	93	0	55	28	6	25	40	1.79
4463721--4463833	41	2.8	41	89	5	167	19	21	21	38	1.94
4463721--4463830	19	5.5	19	69	13	69	19	21	20	38	1.94
4464436--4464512	6	13.7	6	98	1	119	0	18	53	28	1.45
4464605--4464691	38	2.2	40	91	6	142	37	21	19	20	1.94
4464605--4464670	19	3.5	19	73	8	71	39	19	19	21	1.93
4464629--4464691	19	3.0	22	68	13	69	38	23	19	19	1.93
4464631--4464698	22	3.2	22	68	15	63	36	23	20	19	1.95
4466344--4466391	3	15.7	3	79	12	53	66	2	2	29	1.14
4466347--4466399	22	2.4	21	84	9	70	67	1	3	26	1.17
4466323--4466391	19	3.6	20	78	9	81	65	2	1	30	1.16
4468012--4468036	13	1.9	13	100	0	50	44	0	16	40	1.47
4468050--4468087	18	2.1	18	90	0	58	50	0	18	31	1.47
4468999--4469045	2	23.5	2	95	0	85	46	0	0	53	1.00
4469629--4469855	54	4.2	54	86	1	276	28	18	18	34	1.95
4470304--4470342	18	2.0	18	85	14	51	28	20	5	46	1.72
4475241--4475397	54	2.9	53	78	5	154	27	20	19	33	1.96
4478735--4478764	14	2.1	15	93	6	53	63	13	10	13	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4480429--4480470	20	2.1	20	86	8	59	76	4	0	19	0.96
4482303--4482568	136	2.0	136	84	3	347	27	20	18	34	1.95
4482979--4483238	54	4.7	56	82	5	212	39	17	9	33	1.82
4483038--4483238	54	3.7	54	85	6	262	40	17	9	32	1.82
4483934--4483993	18	3.4	17	75	13	50	45	3	5	46	1.41
4483971--4484010	2	20.0	2	100	0	80	50	0	0	50	1.00
4485696--4485742	21	2.2	21	77	7	51	19	8	2	70	1.24
4490538--4490811	30	9.1	30	97	0	512	30	23	22	23	1.99
4491108--4491170	20	3.3	20	73	13	78	15	22	3	58	1.51
4491095--4491182	37	2.4	37	98	0	167	17	21	2	59	1.49
4491121--4491183	13	4.9	13	72	16	51	19	22	1	57	1.49
4495182--4495450	30	9.0	30	98	0	520	30	23	22	23	1.99
4495752--4495814	20	3.3	20	73	13	78	15	22	3	58	1.51
4495739--4495825	37	2.4	37	98	0	165	17	21	2	58	1.49
4504147--4504313	83	2.0	84	95	3	302	18	9	17	53	1.70
4516947--4517633	105	6.5	106	81	3	713	29	20	26	23	1.99
4516947--4517633	53	12.9	53	81	2	725	29	20	26	23	1.99
4517935--4517988	20	2.7	18	80	13	54	44	5	5	44	1.50
4520729--4520794	28	2.4	28	94	0	114	28	1	25	43	1.63
4521442--4521502	7	8.6	7	79	13	63	13	0	0	86	0.56
4521442--4521511	16	4.3	16	84	12	90	12	1	0	85	0.66
4521442--4521511	26	2.9	23	82	14	86	12	1	0	85	0.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4521442--4521502	1	61.0	1	73	0	50	13	0	0	86	0.56
4521442--4521502	9	7.4	8	87	8	79	13	0	0	86	0.56
4525310--4525377	29	2.5	28	75	20	72	76	7	1	14	1.07
4525339--4525383	17	2.5	18	82	17	58	73	11	2	13	1.19
4527922--4527981	31	1.9	32	86	3	86	60	1	3	35	1.23
4527986--4528027	16	2.8	16	85	7	52	71	0	4	23	1.05
4527990--4528043	23	2.3	24	87	3	74	66	0	3	29	1.09
4530707--4530759	25	2.1	26	85	3	72	52	0	9	37	1.34
4531104--4531161	27	2.1	28	84	9	75	44	15	17	22	1.86
4531250--4531291	15	3.1	14	83	16	61	47	14	16	21	1.82

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