genome.fa.s9624.2.7.7.80.10.50.1000.20.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: 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  20  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)
3845326--3845402	3	26.7	3	77	12	81	61	0	2	36	1.10
3845642--3845715	20	3.7	20	88	0	103	25	16	27	31	1.96
3845781--3845834	20	2.7	20	85	0	63	33	18	20	27	1.96
3845566--3845834	139	1.9	139	88	3	407	30	16	18	34	1.93
3845662--3845959	119	2.5	119	88	1	445	31	16	17	33	1.93
3845879--3846034	75	2.1	75	90	0	240	32	18	19	30	1.96
3845975--3846018	20	2.2	20	83	0	52	29	27	20	22	1.99
3845775--3846132	194	1.8	194	90	0	572	32	17	17	31	1.94
3847625--3847858	51	4.6	51	80	8	244	23	20	18	38	1.94
3847626--3847872	100	2.4	105	88	5	369	23	20	19	37	1.94
3847626--3847874	50	4.8	51	81	6	261	23	20	19	36	1.95
3849351--3849415	18	3.5	19	87	8	89	3	15	0	81	0.81
3856551--3856591	12	3.2	13	80	13	50	29	29	9	31	1.89
3860114--3860182	30	2.3	30	82	2	75	37	21	4	36	1.74
3861299--3861366	31	2.2	31	91	0	109	27	16	7	48	1.72
3863476--3863615	70	2.0	70	100	0	280	24	21	11	42	1.85
3866263--3866308	24	1.9	24	90	0	74	41	10	13	34	1.79
3866844--3866904	30	2.0	31	81	9	72	36	26	4	32	1.78
3867548--3867804	123	2.1	122	97	2	489	38	22	5	34	1.77
3868151--3868218	31	2.2	31	91	0	109	26	17	8	47	1.77
3869030--3869159	21	6.1	21	74	1	89	46	23	0	28	1.58
3869051--3869111	28	2.1	29	82	8	72	49	24	1	24	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3869065--3869126	14	4.4	14	71	4	52	48	24	1	25	1.60
3869404--3869454	19	2.6	20	90	3	77	43	23	17	15	1.88
3869404--3869701	20	14.6	20	80	5	186	39	19	23	18	1.92
3869508--3869699	40	4.7	40	83	5	249	36	17	25	19	1.94
3869508--3869691	83	2.2	83	94	0	314	36	17	26	20	1.94
3869688--3869731	20	2.2	20	91	0	70	54	15	18	11	1.70
3869809--3869858	6	8.5	6	97	2	93	32	52	16	0	1.44
3870533--3870593	5	11.6	5	94	1	86	0	19	54	26	1.45
3870702--3870852	20	7.4	20	84	4	185	23	23	16	36	1.94
3870702--3870873	83	2.1	81	82	8	204	23	23	16	36	1.94
3870887--3870938	20	2.6	20	93	0	86	11	17	19	51	1.75
3870927--3870976	19	2.8	18	91	8	84	16	16	24	44	1.86
3872338--3872419	29	2.8	29	94	1	137	32	14	9	42	1.79
3876778--3876828	23	2.2	23	100	0	102	35	21	19	23	1.96
3877066--3877147	29	2.8	29	94	1	137	32	14	9	42	1.79
3879262--3879299	16	2.4	16	87	12	53	15	2	2	78	0.97
3879250--3879303	18	2.9	19	78	10	58	16	1	3	77	1.00
3879243--3879303	18	3.7	18	68	24	53	14	1	4	78	0.99
3881668--3881720	20	2.5	21	79	14	56	16	16	13	52	1.74
3882551--3882679	8	15.9	8	77	11	120	79	0	17	2	0.83
3882568--3882683	17	6.8	17	79	14	116	80	0	18	0	0.77
3882564--3882715	34	4.7	32	71	18	93	78	0	20	1	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3882564--3882715	11	13.7	11	71	16	86	78	0	20	1	0.83
3882551--3882714	38	4.3	38	72	18	119	78	0	19	2	0.87
3882582--3882710	23	5.6	22	75	18	104	79	0	20	0	0.79
3884664--3884863	60	3.5	56	74	16	180	32	9	17	40	1.82
3885730--3886171	91	4.9	91	88	2	595	37	17	21	22	1.94
3886123--3886191	22	3.4	22	68	25	69	49	14	23	13	1.78
3886113--3886210	39	2.5	39	96	0	178	46	13	21	18	1.82
3886022--3886301	130	2.2	130	90	1	436	39	15	21	22	1.91
3886141--3886203	21	3.1	21	67	28	64	46	9	26	17	1.79
3886233--3886447	116	1.9	116	85	3	292	37	17	21	23	1.94
3888284--3888322	21	1.9	20	89	5	60	38	12	0	48	1.42
3888577--3888652	31	2.5	31	85	8	93	35	13	25	26	1.92
3889660--3889750	33	3.0	29	80	13	103	24	8	7	59	1.54
3889673--3889750	29	2.5	32	87	8	108	25	10	8	55	1.63
3889902--3889944	12	3.6	12	78	9	52	16	0	4	79	0.90
3895587--3895619	16	2.1	16	100	0	66	6	12	24	57	1.57
3904328--3904402	35	2.1	35	100	0	150	37	5	28	29	1.79
3906197--3907363	399	2.9	399	91	2	1853	31	16	13	38	1.87
3907672--3907696	11	2.3	11	100	0	50	48	8	8	36	1.62
3908702--3908763	6	10.3	6	78	0	52	25	29	4	40	1.76
3908702--3908763	12	5.2	12	80	0	61	25	29	4	40	1.76
3908702--3908765	24	2.7	24	85	0	83	26	28	4	40	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3910057--3910376	160	2.0	161	99	0	633	41	5	19	33	1.75
3910832--3910881	19	2.6	19	100	0	100	30	12	26	32	1.92
3919393--3919512	64	1.9	63	82	1	150	34	21	20	24	1.97
3920692--3920762	15	4.5	15	81	10	81	26	4	40	28	1.74
3921220--3922595	200	6.9	200	79	10	1470	34	14	11	38	1.83
3921750--3921799	21	2.4	21	100	0	100	32	16	10	42	1.81
3921768--3922595	399	2.1	400	89	2	1288	34	15	11	37	1.84
3922859--3922907	19	2.6	19	96	0	89	55	10	2	32	1.45
3924456--3924530	18	4.2	18	91	0	114	0	44	0	56	0.99
3924805--3924869	21	3.1	21	95	0	112	15	32	10	41	1.81
3924953--3924985	15	2.2	15	94	0	57	15	63	3	18	1.43
3927254--3927855	182	3.3	181	88	2	839	28	16	13	40	1.87
3927680--3928045	162	2.3	162	89	0	545	28	16	13	40	1.87
3929632--3929737	52	2.0	53	96	1	196	34	20	4	39	1.74
3935483--3935535	26	2.0	27	85	10	74	45	5	1	47	1.37
3935700--3935743	16	2.7	17	86	6	65	47	27	0	25	1.52
3939032--3939195	65	2.4	67	80	11	183	40	6	5	47	1.53
3939094--3939195	35	3.0	34	68	18	86	42	4	4	48	1.46
3939051--3939223	70	2.6	67	80	14	177	42	4	5	47	1.46
3939032--3939225	68	2.9	69	78	13	185	41	5	6	46	1.52
3950842--3950903	26	2.4	26	88	0	88	24	12	46	16	1.81
3955458--3955500	12	3.4	12	83	6	50	86	2	9	2	0.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3955461--3955500	17	2.3	18	86	4	55	85	2	10	2	0.80
3955814--3955842	14	2.0	15	93	6	51	10	0	27	62	1.28
3961506--3961561	18	3.3	16	90	7	60	39	39	7	14	1.73
3961513--3961567	18	3.1	18	94	0	92	34	38	9	18	1.82
3967700--3967774	35	2.1	35	92	0	123	45	22	0	32	1.53
3967770--3967847	35	2.2	35	86	0	111	38	0	20	41	1.53
3969488--3969582	50	1.9	50	95	0	172	33	9	17	38	1.82
3970042--3970223	41	4.5	41	72	11	149	28	16	16	38	1.90
3970321--3970358	19	2.0	20	84	5	51	36	0	7	55	1.29
3972256--3972295	20	2.0	20	100	0	80	45	5	30	20	1.72
3972498--3972556	21	2.8	21	92	0	100	22	8	18	50	1.73
3977425--3977451	2	13.5	2	100	0	54	48	0	0	51	1.00
3985171--3985231	18	3.4	18	66	20	56	54	3	1	40	1.27
3986120--3986152	11	3.1	11	86	8	50	39	0	0	60	0.97
3988967--3989016	10	4.8	10	80	9	64	84	4	0	12	0.76
3988970--3989021	19	2.7	18	85	14	68	84	3	0	11	0.74
3990114--3990151	13	2.9	14	80	11	53	47	0	5	47	1.24
3990795--3990883	36	2.4	37	96	1	162	30	7	17	43	1.78
3990870--3990953	37	2.2	38	82	2	98	35	14	21	28	1.92
3990927--3990977	22	2.4	22	86	3	77	43	11	19	25	1.85
3990949--3991263	36	8.9	36	78	11	310	41	13	19	25	1.87
3991087--3991148	21	3.2	21	65	32	57	43	9	19	27	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3992596--3992889	95	3.1	95	95	1	509	34	18	15	32	1.92
3995809--3995875	23	3.2	23	62	33	60	23	28	11	35	1.91
3995793--3995893	39	2.6	39	95	0	175	23	31	10	33	1.90
3996995--3997033	11	3.5	11	86	6	60	79	0	2	17	0.84
3999122--3999146	12	2.1	12	100	0	50	44	0	0	56	0.99
4000722--4001301	123	4.7	123	91	0	910	24	18	16	40	1.90
4001316--4001466	36	4.1	37	68	7	94	36	11	19	32	1.88
4001316--4001466	73	2.1	73	88	5	225	36	11	19	32	1.88
4003515--4003745	75	3.1	74	85	5	286	29	20	16	33	1.95
4010060--4010084	12	2.1	12	100	0	50	60	16	8	16	1.58

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