genome.fa.s2890.2.7.7.80.10.50.1000.17.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: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5046466

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  17  of  21  ( 2516 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)
3978954--3978995	21	2.0	20	86	4	57	45	7	9	38	1.64
3994604--3994639	17	2.1	17	90	10	56	19	8	0	72	1.10
3994619--3994747	3	42.7	3	74	13	88	25	1	6	66	1.24
3994624--3994714	32	2.8	33	76	14	91	27	2	4	65	1.23
3996780--3996814	16	2.1	18	89	10	56	42	0	8	48	1.33
3996755--3996954	105	1.9	105	87	0	292	31	11	11	46	1.75
3996644--3997090	244	1.8	244	88	0	680	32	11	10	44	1.75
3996856--3997369	139	3.7	136	81	5	505	30	12	12	43	1.80
4006079--4006117	15	2.6	15	100	0	78	35	12	10	41	1.77
4006439--4006497	29	2.0	29	90	6	93	55	0	1	42	1.09
4006440--4006523	23	3.3	24	76	18	64	52	0	1	46	1.08
4007448--4007496	23	2.1	24	85	11	66	46	2	2	48	1.25
4007441--4007509	25	2.8	24	75	22	63	47	1	1	49	1.19
4013710--4013778	31	2.2	31	82	5	77	28	26	23	21	1.99
4015109--4015134	4	6.5	4	100	0	52	50	26	0	23	1.50
4015223--4016105	139	6.3	138	82	6	880	43	13	12	30	1.82
4015223--4016118	279	3.2	278	82	5	992	43	13	12	30	1.81
4015223--4016118	418	2.1	418	80	6	996	43	13	12	30	1.81
4018266--4018397	3	45.0	3	74	14	80	63	4	3	28	1.29
4018266--4018374	20	5.4	20	75	4	94	62	5	1	30	1.28
4018588--4018960	118	3.2	118	85	3	473	24	20	16	38	1.92
4020120--4020197	9	7.7	10	72	20	56	1	15	3	79	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4020119--4020188	16	4.2	16	77	20	72	0	14	4	81	0.84
4020119--4020164	6	8.3	6	86	13	64	0	17	0	82	0.67
4020119--4020164	22	2.1	22	92	8	76	0	17	0	82	0.67
4020120--4020197	5	15.4	5	76	18	56	1	15	3	79	0.94
4025095--4025135	14	2.9	15	85	10	59	43	9	4	41	1.59
4025502--4025698	21	9.5	21	74	10	154	19	18	25	36	1.94
4025502--4025650	42	3.6	41	88	3	185	20	19	24	35	1.95
4025527--4025653	42	3.1	42	94	2	222	19	18	25	36	1.95
4025508--4025726	105	2.1	103	92	1	357	20	17	24	37	1.94
4025819--4025850	6	5.5	6	92	7	57	34	50	15	0	1.45
4026486--4026597	21	5.4	21	70	21	94	37	22	19	20	1.94
4026482--4026658	40	4.3	42	95	1	299	35	24	19	20	1.96
4026507--4026744	21	11.6	21	75	8	222	34	26	19	20	1.96
4026549--4026744	61	3.2	62	87	5	197	33	27	19	19	1.96
4039440--4039469	11	2.6	11	94	5	51	80	0	0	20	0.72
4039437--4039474	16	2.4	16	82	8	51	73	0	0	26	0.83
4039455--4039501	24	2.0	24	83	8	60	61	2	6	29	1.32
4039517--4039543	5	5.4	5	100	0	54	81	0	0	18	0.69
4040721--4041557	261	3.2	261	91	0	1311	31	20	18	29	1.97
4041451--4041514	20	3.2	20	65	20	51	29	18	21	29	1.97
4041445--4041536	42	2.2	42	88	3	132	31	19	21	27	1.97
4044558--4044605	22	2.2	22	85	7	62	2	16	0	81	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4044564--4044605	13	3.3	13	78	18	52	0	16	0	83	0.65
4046557--4046593	17	2.2	17	90	0	56	29	16	0	54	1.43
4047288--4047320	7	5.0	7	92	7	52	60	9	15	15	1.58
4052657--4052692	18	2.0	18	89	10	56	16	22	25	36	1.94
4062850--4062891	21	2.0	20	86	4	57	45	7	9	38	1.64
4066409--4066459	13	3.9	13	97	0	93	21	21	15	41	1.90
4066400--4066459	26	2.3	26	91	2	93	20	23	16	40	1.91
4069739--4069788	15	3.3	15	86	5	66	58	2	2	38	1.21
4069829--4069890	19	3.3	18	77	6	52	51	1	3	43	1.27
4078126--4078182	2	28.5	2	100	0	114	50	0	0	49	1.00
4080065--4080093	2	15.0	2	92	7	51	51	0	0	48	1.00
4080701--4080736	17	2.1	17	89	0	54	19	11	0	69	1.18
4080754--4080848	3	31.0	3	79	10	70	24	0	5	70	1.07
4080761--4080847	14	5.8	14	75	17	52	22	0	4	72	1.03
4083234--4083266	15	2.1	16	88	5	50	42	0	6	51	1.26
4083203--4083401	105	1.9	105	87	2	292	31	11	11	45	1.75
4083304--4083815	139	3.7	136	82	5	528	30	12	12	44	1.79
4090795--4090839	18	2.5	18	82	7	56	22	11	2	64	1.36
4094561--4094956	196	2.0	200	98	2	764	24	16	25	33	1.96
4096575--4096600	3	8.7	3	100	0	52	65	0	0	34	0.93
4097674--4097808	69	2.0	69	100	0	270	34	14	20	30	1.93
4098717--4098836	48	2.6	45	83	6	154	21	17	22	38	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4098706--4098857	43	3.4	43	76	8	133	23	15	23	37	1.93
4104209--4104266	29	2.0	28	87	9	82	55	0	1	43	1.10
4104244--4104292	23	2.1	24	84	3	64	48	0	0	51	1.00
4105211--4105259	23	2.1	24	85	11	66	46	2	2	48	1.25
4106203--4106279	25	3.0	25	75	3	64	50	3	1	44	1.28
4106232--4106342	39	2.9	36	73	20	93	54	2	0	42	1.21
4106230--4106319	41	2.3	40	81	9	105	52	2	1	44	1.20
4106243--4106342	38	2.6	40	76	20	97	56	3	1	40	1.22
4106308--4106353	15	3.1	15	84	9	51	60	2	0	36	1.09
4110090--4110180	45	2.0	45	100	0	182	28	24	7	39	1.83
4111314--4111361	3	15.7	3	79	12	53	58	0	2	39	1.10
4113052--4113933	139	6.3	138	82	5	906	43	13	12	30	1.81
4113187--4113941	417	1.8	418	83	5	1017	43	12	12	30	1.80
4116099--4116236	3	47.0	3	74	16	103	65	3	2	27	1.23
4116100--4116213	39	2.8	43	82	11	132	65	4	1	28	1.21
4116099--4116240	11	12.1	12	67	17	75	66	3	2	27	1.22
4116426--4116799	118	3.2	115	81	6	383	24	19	16	39	1.91
4116425--4116797	120	3.2	118	78	9	384	24	19	15	39	1.91
4117962--4118027	6	11.5	6	80	18	70	0	13	3	83	0.76
4117962--4118027	10	6.3	11	81	13	77	0	13	3	83	0.76
4117960--4118030	34	2.1	35	82	12	94	0	15	2	81	0.80
4117939--4118030	8	11.0	8	75	17	55	0	18	2	79	0.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4123002--4123042	14	2.9	15	82	17	52	43	12	4	39	1.63
4123414--4123536	42	3.0	42	93	2	205	21	20	24	34	1.97
4123465--4123587	63	1.9	65	96	3	232	19	19	24	36	1.95
4123530--4123650	40	3.0	40	92	2	197	22	19	22	36	1.95
4124264--4124295	15	2.1	15	94	0	55	3	40	15	40	1.63
4124430--4124581	21	7.4	21	77	5	150	33	25	19	21	1.97
4124403--4124493	40	2.3	40	98	0	173	36	25	18	19	1.95
4124430--4124575	61	2.4	61	92	0	247	33	26	19	21	1.97
4124466--4124581	40	2.8	42	82	5	146	32	25	19	21	1.97
4124595--4124642	21	2.3	21	96	0	87	20	20	29	29	1.98
4137169--4137198	11	2.6	11	94	5	51	80	0	0	20	0.72
4137166--4137203	16	2.4	16	82	8	51	73	0	0	26	0.83
4137245--4137271	5	5.4	5	100	0	54	81	0	0	18	0.69
4138447--4139283	261	3.2	261	89	0	1266	31	21	18	29	1.96
4139177--4139240	20	3.2	20	65	20	51	29	18	21	29	1.97
4139171--4139262	42	2.2	42	88	3	132	31	19	21	27	1.97
4142310--4142347	7	5.6	7	82	17	53	0	15	0	84	0.63
4142813--4142864	19	2.7	19	79	8	61	0	23	1	75	0.91
4144307--4144343	17	2.2	17	100	0	74	27	21	0	51	1.48
4147963--4147995	2	16.5	2	100	0	66	51	0	0	48	1.00
4149048--4149153	45	2.4	45	88	1	151	21	16	38	23	1.92
4164216--4164265	16	3.1	16	77	8	57	58	2	4	36	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4164290--4164337	19	2.4	20	83	16	64	52	2	0	45	1.12
4165250--4165297	24	2.0	24	83	4	60	33	12	4	50	1.59
4174566--4174714	3	52.7	3	75	15	131	30	3	1	65	1.17
4174581--4174684	14	8.1	13	74	19	85	26	2	0	69	1.09
4174554--4174685	59	2.4	58	81	13	154	28	3	0	66	1.14
4174587--4174712	17	6.9	18	75	17	93	28	3	1	65	1.19
4174566--4174714	26	5.8	26	75	17	132	30	3	1	65	1.17
4175352--4175817	139	3.5	126	77	14	420	30	13	13	42	1.82
4175419--4175993	139	4.2	136	79	8	545	28	13	14	43	1.83
4179597--4179756	65	2.5	65	90	1	241	33	22	15	29	1.94

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21