genome.fa.s9587.2.7.7.80.10.50.1000.16.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: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6483253

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   

This is table  16  of  29  ( 3457 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)
3509376--3509446	19	3.7	19	75	0	52	29	16	5	47	1.70
3517173--3517250	31	2.5	31	83	6	88	43	6	20	29	1.76
3518420--3518465	20	2.3	20	85	3	58	34	0	26	39	1.57
3536868--3536944	31	2.5	31	80	2	91	27	31	27	14	1.95
3536821--3536944	63	2.0	63	82	6	153	25	29	28	16	1.97
3537821--3537860	17	2.4	17	95	0	71	10	22	50	17	1.76
3537855--3537993	9	14.3	9	74	12	98	29	27	27	15	1.96
3537857--3537994	19	7.1	19	83	8	118	29	27	26	16	1.97
3537899--3537993	29	3.2	29	84	15	124	30	26	27	15	1.96
3537935--3537994	21	2.9	21	95	2	104	33	23	26	16	1.96
3539921--3539966	22	2.2	21	85	14	60	15	10	26	47	1.78
3541426--3541453	2	14.0	2	100	0	56	50	0	0	50	1.00
3542065--3542168	39	2.7	39	74	5	95	35	23	23	18	1.95
3543589--3543997	49	8.3	49	86	2	552	39	14	19	26	1.90
3543589--3543997	99	4.2	99	88	3	612	39	14	19	26	1.90
3544493--3544542	21	2.3	21	83	10	57	34	6	8	52	1.55
3547752--3547791	14	2.9	14	100	0	80	65	0	0	35	0.93
3551718--3551779	21	3.0	21	83	2	81	32	17	11	38	1.85
3551718--3551794	21	3.7	21	80	5	75	31	16	9	42	1.80
3552638--3552669	11	2.9	11	95	0	55	46	15	18	18	1.84
3553754--3553829	23	3.2	23	77	3	62	32	17	10	39	1.83
3556362--3556407	20	2.3	20	85	3	58	30	0	26	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3560155--3560196	22	2.0	21	90	4	66	42	16	16	23	1.88
3561526--3561665	30	4.7	30	68	19	96	27	17	27	28	1.97
3565151--3565290	3	46.7	3	100	0	280	33	0	0	66	0.92
3565663--3565726	25	2.9	21	71	24	51	68	1	7	21	1.23
3567045--3567083	20	2.0	20	89	0	60	33	30	15	20	1.94
3567105--3567157	22	2.4	22	87	0	70	13	18	24	43	1.86
3573723--3573772	20	2.5	20	81	12	66	28	32	22	18	1.97
3573774--3573822	22	2.2	22	89	7	73	18	26	26	28	1.98
3573832--3573871	17	2.4	17	100	0	80	45	5	12	37	1.64
3575762--3575872	36	3.2	36	65	21	101	37	17	22	22	1.94
3575732--3575872	67	2.1	67	89	2	212	36	18	21	24	1.95
3577785--3577852	23	3.0	23	74	8	68	55	13	16	14	1.69
3582293--3582470	50	3.5	50	92	0	275	15	34	33	17	1.91
3582481--3582604	49	2.5	52	88	5	175	25	25	22	26	2.00
3585880--3586100	110	2.0	111	91	2	356	47	9	7	36	1.64
3586179--3586207	14	2.1	14	100	0	58	58	0	6	34	1.25
3586762--3586822	27	2.2	28	80	8	72	70	8	16	4	1.29
3588080--3588150	28	2.5	28	93	0	115	46	5	25	22	1.73
3588292--3588342	21	2.2	24	80	10	63	45	0	5	49	1.26
3598393--3598436	19	2.4	19	92	3	72	72	0	9	18	1.10
3599272--3599362	5	17.8	5	72	20	73	74	3	5	16	1.14
3599272--3599368	11	9.4	11	73	17	75	75	4	5	15	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3599332--3599379	23	2.1	22	84	3	60	75	6	6	12	1.19
3600929--3600991	29	2.2	29	94	5	110	20	14	23	41	1.89
3602314--3602376	19	3.4	19	88	2	92	71	0	7	20	1.11
3602968--3603159	76	2.6	76	85	7	234	56	11	0	30	1.39
3603049--3603159	24	4.5	24	68	16	82	61	11	0	27	1.31
3605626--3605667	20	2.1	20	86	0	57	19	16	11	52	1.74
3612342--3612380	20	2.0	20	85	10	53	35	33	0	30	1.58
3614826--3614860	18	1.9	19	88	11	56	40	5	5	48	1.51
3622649--3622708	3	20.0	3	82	0	57	26	5	36	31	1.78
3622652--3622683	15	2.1	15	100	0	64	25	6	34	34	1.81
3625063--3625096	13	2.5	14	90	4	52	67	0	2	29	1.05
3626224--3626269	20	2.3	19	85	14	58	50	8	15	26	1.73
3638928--3639284	82	4.4	82	88	0	516	23	18	22	34	1.96
3639368--3640097	90	8.2	89	81	3	585	30	18	17	34	1.94
3639334--3640097	181	4.3	177	80	3	694	30	18	17	34	1.93
3640187--3640857	62	11.0	63	81	6	505	35	15	22	26	1.94
3640265--3640364	29	3.3	28	67	20	76	31	17	25	27	1.97
3640136--3640857	124	5.8	124	78	7	596	35	15	22	27	1.94
3640136--3640857	186	3.9	186	78	7	636	35	15	22	27	1.94
3640621--3640762	57	2.5	57	91	0	221	37	11	23	26	1.90
3642959--3643008	19	2.7	19	87	3	66	12	18	8	62	1.53
3645742--3645782	22	1.9	21	85	5	55	48	4	24	21	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3650429--3650465	3	12.3	3	94	0	65	62	0	0	37	0.96
3650464--3650492	3	9.7	3	100	0	58	34	0	0	65	0.93
3665640--3665759	2	60.5	2	96	1	224	50	0	0	49	1.00
3665864--3665897	16	2.2	15	89	5	50	38	0	0	61	0.96
3674406--3674459	22	2.6	20	78	16	65	57	11	7	24	1.58
3675707--3676145	91	4.8	91	85	1	520	25	21	14	37	1.92
3675707--3676158	182	2.5	182	84	1	573	26	21	14	37	1.92
3676671--3676813	75	1.9	72	83	4	178	39	12	18	30	1.87
3676979--3677092	36	3.2	36	82	3	122	42	9	17	30	1.81
3677025--3677105	37	2.2	37	82	2	92	45	8	14	30	1.75
3683076--3683326	129	1.9	129	88	4	373	37	15	14	33	1.88
3687678--3687739	27	2.3	27	86	10	83	41	20	8	29	1.81
3690168--3690253	44	2.0	44	92	0	145	31	22	9	37	1.86
3703655--3703692	2	18.5	2	89	5	58	47	0	2	50	1.15
3703638--3703684	19	2.3	21	85	7	62	46	2	2	48	1.25
3723073--3723127	12	4.6	12	75	22	53	12	9	9	69	1.38
3741579--3741724	65	2.3	65	84	9	201	28	21	17	32	1.96
3743882--3743919	16	2.4	16	86	8	51	36	7	5	50	1.54
3747322--3747447	57	2.2	58	85	1	164	34	4	13	46	1.64
3747287--3747435	29	5.1	29	80	4	147	36	4	12	46	1.63
3747927--3747980	2	27.0	2	96	0	99	48	0	1	50	1.11
3750152--3750190	13	3.1	13	85	7	62	33	12	5	48	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3750152--3750188	12	2.9	13	88	8	58	35	13	2	48	1.57
3752294--3752419	65	2.0	64	83	1	162	28	20	16	34	1.95
3753991--3754032	18	2.3	18	84	8	50	45	2	2	50	1.27
3755002--3755063	21	2.9	22	75	15	67	69	3	1	25	1.13
3755841--3755886	2	23.0	2	100	0	92	50	0	0	50	1.00
3756181--3756259	28	2.7	29	73	16	72	24	1	44	30	1.62
3756205--3756258	28	1.9	28	92	0	90	22	0	44	33	1.53
3756435--3756776	91	3.8	91	85	0	452	25	21	15	37	1.93
3757170--3757298	66	2.0	66	87	6	190	42	16	18	22	1.89
3757170--3757345	66	2.7	67	79	11	175	40	14	19	25	1.90
3757360--3757520	36	4.6	36	69	16	133	37	13	21	28	1.90
3757337--3757520	101	1.8	102	93	1	325	37	12	21	28	1.90
3757502--3757542	15	2.7	15	88	0	64	31	19	29	19	1.96
3757526--3757825	39	7.7	39	88	0	440	35	18	19	27	1.95
3757797--3757973	76	2.4	73	78	14	184	40	13	13	32	1.84
3757951--3758026	39	1.9	39	89	5	118	40	21	14	23	1.90
3762763--3762828	13	4.8	13	76	18	55	71	4	1	22	1.13
3762763--3762851	21	4.3	21	74	17	64	68	3	2	25	1.17
3762815--3762850	19	1.9	18	88	5	54	69	0	2	27	1.02
3763892--3763961	28	2.4	28	83	7	86	20	1	48	30	1.58
3765391--3765475	12	7.2	12	72	15	61	20	4	2	72	1.13
3765401--3765447	20	2.4	20	79	13	53	14	4	2	78	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3765498--3765580	41	2.0	43	86	9	118	26	7	3	62	1.38
3769007--3769906	84	10.9	84	82	3	1034	34	22	18	24	1.96
3769007--3769906	167	5.4	167	84	3	1014	34	22	18	24	1.96
3769007--3769907	247	3.6	247	85	2	1110	34	22	18	24	1.96
3769779--3770216	217	2.0	217	95	0	795	35	20	15	28	1.93
3771897--3772047	66	2.3	63	79	13	162	29	3	4	62	1.33
3772197--3772237	7	6.0	7	81	16	50	0	12	4	82	0.81
3772197--3772230	14	2.4	14	95	0	59	0	11	5	82	0.83
3772200--3772237	20	1.9	20	94	0	67	0	10	5	84	0.77
3772253--3772298	24	1.9	24	82	8	58	17	4	4	73	1.15

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