genome.fa.s260.2.7.7.80.10.50.1000.19.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: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5583615

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   

This is table  19  of  26  ( 3102 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)
3851502--3851657	72	2.2	72	80	6	192	44	19	12	24	1.84
3853751--3853780	13	2.3	13	94	0	51	16	23	43	16	1.87
3855898--3856018	24	5.0	24	75	10	104	43	17	14	24	1.86
3855898--3856012	48	2.4	49	82	8	130	42	17	14	25	1.87
3859711--3859771	13	4.3	13	73	18	59	18	19	44	18	1.87
3859711--3859775	31	2.1	31	88	0	94	16	18	46	18	1.85
3861672--3861712	2	20.5	2	100	0	82	51	0	0	48	1.00
3861926--3862043	24	4.9	24	84	5	148	40	18	13	27	1.88
3861906--3862057	72	2.1	71	79	6	171	44	17	11	26	1.84
3864473--3864532	13	4.2	13	76	19	66	18	21	43	16	1.88
3864473--3864536	31	2.1	31	90	0	101	17	20	45	17	1.86
3864478--3864519	18	2.3	18	83	0	57	16	21	45	16	1.86
3866018--3866145	67	1.9	67	91	0	211	31	14	23	31	1.94
3866086--3866647	81	6.9	81	84	1	687	35	12	21	30	1.91
3869160--3869202	2	21.5	2	100	0	86	51	0	0	48	1.00
3871366--3871909	81	6.7	81	88	0	793	36	13	22	28	1.92
3873517--3874067	134	4.1	134	82	3	640	31	19	19	28	1.97
3875692--3876135	38	11.3	38	76	8	345	40	15	18	25	1.90
3875692--3876135	80	5.6	76	79	7	365	40	15	18	25	1.90
3875939--3876021	42	2.1	38	86	10	114	39	16	20	22	1.92
3876450--3876577	65	2.0	65	84	3	168	32	15	17	34	1.91
3881291--3881329	20	2.0	20	90	10	62	30	25	0	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3881467--3881734	81	3.3	81	84	5	346	29	22	10	38	1.86
3881501--3881741	81	3.0	81	89	0	376	29	21	10	38	1.87
3885363--3885402	21	2.0	20	90	5	62	65	0	2	32	1.06
3886193--3886318	45	2.8	47	82	8	136	31	23	4	39	1.76
3886423--3886584	40	4.1	40	93	0	279	33	25	17	24	1.96
3892940--3892969	13	2.3	13	94	0	51	36	26	20	16	1.93
3893453--3893578	47	2.8	45	85	5	164	30	22	7	39	1.82
3893683--3893804	40	3.0	40	98	0	235	33	27	16	22	1.95
3899196--3899275	36	2.2	38	93	4	137	17	16	18	47	1.83
3910634--3911089	41	11.1	41	83	4	474	28	19	16	34	1.94
3910634--3911089	84	5.6	82	82	4	474	28	19	16	34	1.94
3910634--3911089	125	3.7	123	81	4	494	28	19	16	34	1.94
3913691--3913717	2	13.5	2	100	0	54	51	0	0	48	1.00
3913891--3913927	16	2.3	16	95	0	65	21	8	35	35	1.83
3915024--3915232	43	4.9	44	80	5	205	26	22	18	32	1.97
3915107--3915233	42	3.0	43	85	3	175	24	25	18	30	1.98
3915011--3915233	85	2.6	84	78	8	227	25	21	19	33	1.97
3919951--3919990	20	2.0	21	85	5	55	65	0	5	30	1.14
3920998--3921077	35	2.3	35	88	0	115	18	8	36	36	1.82
3921312--3921348	17	2.2	17	95	0	65	43	5	2	48	1.40
3929875--3929942	26	2.6	26	92	0	118	30	17	32	19	1.95
3940002--3940036	18	2.0	17	88	5	52	11	25	25	37	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3942688--3942738	23	2.3	22	80	9	68	39	23	15	21	1.92
3949574--3949637	23	2.8	23	77	17	78	31	26	21	20	1.98
3950097--3950148	19	2.6	19	81	9	59	19	34	15	30	1.93
3953660--3953701	21	2.0	21	85	4	57	33	16	23	26	1.96
3957071--3957127	30	1.9	30	85	3	80	14	5	3	77	1.08
3957069--3957128	18	3.3	17	71	19	50	15	5	3	76	1.08
3958285--3958311	11	2.5	11	100	0	54	55	0	37	7	1.28
3963864--3963904	20	2.0	20	90	0	64	43	0	0	56	0.99
3965039--3965074	2	18.0	2	100	0	72	50	0	0	50	1.00
3965076--3965223	15	10.4	14	68	22	53	18	7	0	73	1.10
3965086--3965221	18	7.6	16	71	18	83	17	6	0	75	1.06
3965086--3965198	28	4.2	25	75	19	102	17	6	0	76	0.99
3965089--3965198	8	12.5	8	74	19	69	18	6	0	75	1.01
3965131--3965225	14	6.8	14	73	12	61	20	6	1	72	1.12
3965094--3965218	5	26.2	5	65	26	58	17	7	0	74	1.09
3965094--3965221	37	3.5	36	76	20	108	17	7	0	74	1.09
3965270--3965309	16	2.5	16	87	0	62	5	5	10	80	1.02
3965275--3965316	21	1.9	22	85	9	59	4	4	9	80	0.99
3965323--3965356	13	2.5	14	90	4	52	17	0	8	73	1.08
3967845--3967879	3	11.3	3	93	6	61	37	0	0	62	0.95
3967843--3967879	19	2.0	20	84	10	51	40	0	0	59	0.97
3969274--3969312	19	2.1	19	85	4	53	53	2	2	41	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3970838--3970909	36	2.0	36	91	0	117	38	19	15	26	1.91
3971537--3971577	21	2.0	21	85	0	55	19	17	9	53	1.70
3971577--3971629	20	2.7	19	78	18	63	18	13	9	58	1.61
3976637--3976816	75	2.4	75	82	3	211	32	16	23	28	1.96
3978063--3978141	22	3.6	22	87	3	106	35	13	11	39	1.81
3978777--3979013	42	5.5	42	80	4	285	29	24	20	25	1.99
3978771--3979014	86	2.8	86	94	0	416	28	24	20	26	1.99
3979189--3979238	3	16.3	3	95	4	91	36	0	0	64	0.94
3979663--3979691	12	2.4	12	100	0	58	58	41	0	0	0.98
3983874--3984040	64	2.6	64	92	3	266	36	20	13	29	1.91
3984127--3984467	109	3.1	109	89	0	520	35	25	13	25	1.92
3985159--3985206	2	25.5	2	80	19	59	45	0	2	52	1.12
3986309--3986344	18	1.9	19	88	5	56	38	0	0	61	0.96
3986329--3986369	19	2.2	19	86	0	55	19	2	0	78	0.87
3986400--3986434	2	17.5	2	100	0	70	48	0	0	51	1.00
3986537--3986641	9	11.6	8	71	20	59	16	5	1	76	1.07
3986577--3986645	14	4.9	14	77	15	61	18	5	1	73	1.10
3986565--3986649	29	3.0	27	78	10	89	17	7	1	74	1.11
3986554--3986635	24	3.5	23	77	11	67	18	6	1	74	1.09
3986539--3986645	14	7.6	14	70	21	55	16	5	1	75	1.08
3986714--3986764	16	3.1	16	82	2	66	9	3	3	82	0.93
3986694--3986777	21	3.7	22	78	12	73	11	8	2	77	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3986701--3986791	33	2.8	31	76	15	94	13	7	3	75	1.14
3988812--3988877	32	2.1	32	94	0	114	37	13	4	43	1.65
3990443--3990487	24	2.0	23	86	8	65	33	22	4	40	1.74
3990597--3990676	29	2.8	28	73	7	70	21	17	1	60	1.44
3998908--3999046	35	3.9	35	77	5	136	35	16	17	30	1.93
3998933--3999032	36	2.8	35	80	5	112	34	15	19	32	1.92
4000090--4000142	27	2.0	27	92	0	88	28	15	15	41	1.87
4003033--4003169	35	3.9	34	69	11	98	37	16	17	28	1.91
4007200--4007312	35	3.2	35	75	7	111	34	18	18	28	1.95
4007175--4007314	71	2.0	71	86	0	199	32	19	19	28	1.96
4010943--4011008	33	2.0	33	100	0	132	24	15	27	33	1.95
4015219--4015282	27	2.4	27	92	5	103	31	17	10	40	1.84
4015235--4015302	27	2.5	27	78	4	66	33	19	5	41	1.75
4015853--4015889	19	1.9	19	94	0	65	32	21	27	18	1.97
4018394--4018464	2	35.5	2	91	0	115	46	1	1	50	1.18
4019425--4019638	107	2.0	107	100	0	428	26	18	19	35	1.95
4021661--4021729	27	2.5	27	95	2	120	44	20	15	18	1.86
4022515--4022654	35	4.0	36	74	8	119	24	20	17	37	1.93
4026754--4026884	35	3.7	36	79	5	142	27	15	17	39	1.90
4028309--4028356	20	2.3	21	89	7	71	47	12	6	33	1.66
4029618--4029847	115	2.0	115	95	0	415	28	19	21	30	1.97
4033715--4033756	15	2.6	16	77	14	50	61	9	4	23	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4036312--4036336	7	3.6	7	100	0	50	48	12	0	40	1.40
4040581--4040632	16	3.2	16	70	20	54	51	19	5	23	1.67
4040582--4040646	32	2.0	32	96	0	121	49	21	7	21	1.74
4041196--4041261	18	3.7	18	97	0	123	37	25	18	18	1.93
4041322--4041365	16	2.8	15	83	10	52	25	20	38	15	1.92
4046850--4046914	32	2.0	32	90	0	103	49	23	6	21	1.72
4048818--4048880	23	2.7	23	97	0	117	19	39	17	23	1.92
4049225--4049294	24	2.9	24	87	4	70	10	15	27	47	1.77
4049235--4049288	14	4.1	14	81	18	80	7	14	27	50	1.70
4049236--4049310	24	3.1	24	88	0	69	10	14	22	52	1.73

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