genome.fa.s1465.2.7.7.80.10.50.1000.23.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   

This is table  23  of  55  ( 6520 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)
4460882--4460937	22	2.5	22	94	0	94	32	16	12	39	1.85
4461322--4461735	113	3.7	112	89	4	599	37	14	20	27	1.92
4463643--4463699	22	2.7	19	78	21	60	33	0	3	63	1.12
4470406--4470441	18	2.0	18	88	0	54	30	5	5	58	1.44
4474482--4474542	31	1.9	32	86	3	88	49	1	6	42	1.38
4484799--4484835	19	1.9	19	94	0	65	29	32	18	18	1.96
4484861--4484954	20	4.6	20	79	7	82	26	20	21	31	1.98
4484967--4485076	20	5.4	20	82	6	150	29	28	20	21	1.98
4484942--4485080	61	2.3	61	91	0	224	31	26	20	21	1.98
4484963--4485098	61	2.2	61	86	0	191	33	25	18	22	1.97
4485238--4485296	22	2.7	22	78	0	64	18	42	11	27	1.85
4485652--4485743	20	4.7	20	84	1	96	16	18	23	41	1.90
4485710--4485753	20	2.2	20	91	0	70	11	13	20	54	1.69
4487079--4487129	18	2.8	18	93	0	84	29	43	19	7	1.79
4487732--4487912	34	4.9	38	71	14	128	38	22	20	18	1.94
4487740--4487911	74	2.3	74	88	2	256	38	22	20	18	1.94
4487732--4487907	20	9.4	20	71	15	90	38	22	20	18	1.94
4487907--4487948	19	2.2	19	91	0	66	11	16	30	40	1.85
4487916--4487952	19	1.9	19	100	0	74	5	16	29	48	1.68
4487957--4488022	20	3.3	20	85	2	80	21	16	22	39	1.92
4488009--4488053	20	2.2	20	88	0	72	20	11	17	51	1.75
4488539--4488629	21	4.3	20	73	2	65	20	36	18	24	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4488540--4488621	42	2.0	42	85	0	110	19	40	17	23	1.91
4490014--4490079	30	2.2	30	97	0	123	30	1	13	54	1.48
4490229--4490492	20	13.9	20	81	9	266	22	20	21	35	1.96
4490195--4490484	40	7.9	34	72	18	143	21	20	21	36	1.96
4490185--4490370	73	2.5	73	86	3	239	20	20	21	37	1.95
4490222--4490492	114	2.4	113	89	0	416	22	20	21	36	1.96
4493812--4493898	20	4.3	20	81	8	104	20	21	27	29	1.98
4493829--4493909	41	2.0	41	92	0	135	19	22	27	30	1.98
4493980--4494026	19	2.4	19	85	3	58	27	12	27	31	1.93
4493992--4494028	19	1.9	19	94	0	65	24	13	27	35	1.93
4496533--4496580	2	24.0	2	100	0	96	50	0	0	50	1.00
4497372--4497401	15	2.0	15	100	0	60	26	26	20	26	1.99
4499714--4499750	18	2.1	18	89	0	56	29	5	5	59	1.42
4499743--4499781	13	3.1	13	88	7	62	35	0	0	64	0.94
4501404--4501459	29	1.9	29	96	0	103	50	0	1	48	1.11
4508707--4508758	25	2.1	25	82	7	61	46	3	0	50	1.20
4510318--4510347	15	2.0	15	100	0	60	26	26	20	26	1.99
4512414--4512458	19	2.3	19	88	3	63	46	31	6	15	1.72
4516173--4516216	2	22.0	2	100	0	88	50	0	0	50	1.00
4526568--4526640	21	3.5	20	80	9	67	24	20	21	32	1.97
4526674--4526783	20	5.4	20	80	6	141	30	28	20	21	1.98
4526649--4526787	61	2.3	61	89	0	215	32	26	19	21	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4526670--4526805	61	2.2	61	85	0	182	33	25	17	22	1.96
4526938--4527017	22	3.6	22	79	0	79	20	40	16	23	1.91
4527356--4527410	19	2.8	19	80	2	74	21	20	25	32	1.97
4527398--4527440	20	2.2	20	86	0	59	11	16	20	51	1.75
4528768--4528816	18	2.7	18	90	0	71	30	44	16	8	1.76
4529479--4529601	20	6.4	20	77	11	105	34	23	20	21	1.96
4529461--4529641	34	4.9	38	70	14	119	38	22	20	19	1.94
4529480--4529585	54	2.0	54	82	0	131	35	23	21	18	1.95
4529469--4529640	74	2.3	74	87	2	247	38	21	20	19	1.94
4529534--4529636	20	5.4	20	73	13	83	40	21	20	17	1.91
4529636--4529677	19	2.2	19	91	0	66	11	16	30	40	1.85
4529645--4529681	19	1.9	19	100	0	74	5	16	29	48	1.68
4529679--4529751	20	3.7	20	83	1	85	19	16	21	42	1.89
4529738--4529782	20	2.2	20	88	0	72	20	11	17	51	1.75
4530268--4530358	21	4.3	20	73	2	65	20	36	18	24	1.95
4530269--4530350	42	2.0	42	85	0	110	19	40	17	23	1.91
4531742--4531807	30	2.2	30	97	0	123	30	1	13	54	1.48
4531957--4532240	20	14.9	20	82	8	297	22	20	22	35	1.96
4531923--4532212	40	7.9	34	72	18	143	21	20	21	36	1.96
4531913--4532098	73	2.5	73	86	3	239	20	20	21	37	1.95
4531918--4532232	94	3.4	94	78	6	291	21	20	21	36	1.96
4531950--4532237	114	2.5	113	89	0	441	21	20	21	36	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4534686--4534739	24	2.2	24	86	0	72	40	16	18	24	1.90
4535560--4535646	20	4.3	20	81	8	104	20	21	27	29	1.98
4535593--4535657	21	3.1	21	74	12	71	18	24	26	30	1.98
4535577--4535657	41	2.0	41	95	0	144	19	23	27	29	1.98
4538282--4538325	2	22.0	2	100	0	88	50	0	0	50	1.00
4539116--4539145	15	2.0	15	100	0	60	26	26	20	26	1.99
4541457--4541492	18	2.0	18	88	0	54	30	5	5	58	1.44
4543149--4543204	29	1.9	29	96	0	103	50	0	1	48	1.11
4544606--4544666	31	1.9	32	86	3	88	49	1	6	42	1.38
4556944--4556977	15	2.4	14	95	5	59	76	0	11	11	1.02
4556944--4556977	7	4.7	7	92	7	59	76	0	11	11	1.02
4556965--4556991	10	2.7	10	100	0	54	81	0	7	11	0.87
4556951--4557013	18	3.6	17	76	19	58	79	4	6	9	1.05
4558285--4559490	53	22.7	53	92	2	1940	31	18	26	24	1.97
4558285--4559490	107	11.3	107	93	1	1977	31	18	26	24	1.97
4558285--4559482	160	7.5	160	92	2	1959	31	18	25	24	1.97
4563213--4563514	44	7.0	44	82	8	352	32	18	6	42	1.75
4563391--4563478	35	2.4	37	86	7	117	35	14	5	44	1.69
4563356--4563509	81	1.9	79	92	5	256	33	16	5	44	1.70
4563666--4563832	61	2.8	60	89	2	246	30	23	12	32	1.92
4563787--4564218	177	2.4	177	85	3	516	29	22	10	37	1.88
4563787--4564209	118	3.6	118	88	2	539	30	22	10	37	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4563870--4564209	118	2.9	117	93	1	540	30	22	10	36	1.87
4563648--4564218	59	9.6	58	79	7	437	29	22	10	36	1.89
4565204--4565270	3	22.3	3	100	0	134	32	0	0	67	0.91
4567040--4567090	18	2.9	18	91	2	77	35	7	29	27	1.85
4568238--4568288	12	3.9	12	81	18	66	31	0	0	68	0.90
4568231--4568345	28	4.0	28	78	14	117	38	0	0	60	1.03
4568231--4568291	14	4.5	13	80	15	70	34	0	0	65	0.93
4568223--4568268	20	2.3	21	78	17	53	39	0	0	60	0.97
4568287--4568319	12	2.6	13	90	4	50	48	3	0	48	1.17
4568287--4568324	13	3.0	13	85	14	53	50	2	0	47	1.15
4568476--4568644	85	2.0	85	100	0	338	31	15	16	36	1.90
4572052--4572117	35	2.0	32	96	0	96	33	30	27	9	1.88
4572190--4572322	24	5.5	24	85	3	160	41	20	12	25	1.88
4572188--4572340	48	3.2	48	80	4	130	43	19	12	24	1.86
4572187--4572340	72	2.1	71	80	5	175	43	19	12	24	1.85
4577494--4577545	19	2.7	19	96	0	95	30	15	30	23	1.95
4578555--4578582	2	14.0	2	100	0	56	50	0	0	50	1.00
4578605--4578660	19	2.8	20	74	17	62	35	0	17	46	1.49
4578566--4578646	32	2.5	34	78	13	82	34	0	14	50	1.44
4586472--4586514	17	2.6	16	78	10	50	23	6	9	60	1.51
4591894--4591973	23	3.7	22	76	12	76	20	26	30	23	1.98
4600170--4600264	28	3.4	28	98	0	181	24	18	26	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4600637--4601002	29	12.6	27	77	10	173	40	9	1	49	1.41
4601007--4601086	31	2.6	31	82	4	90	50	0	7	42	1.30
4601686--4601719	17	2.0	17	100	0	68	52	11	11	23	1.70
4601811--4601883	35	2.1	35	84	5	94	49	6	17	26	1.72
4612659--4612691	3	11.0	3	100	0	66	33	0	0	66	0.92
4613703--4613735	18	1.9	17	88	11	50	36	6	15	42	1.71
4623535--4623588	11	4.7	11	79	20	58	81	7	5	5	0.98
4623534--4623589	23	2.4	23	93	3	94	80	7	5	7	1.02
4624069--4624163	44	2.2	44	100	0	190	25	15	30	28	1.96
4625807--4625861	27	2.0	28	82	13	69	23	1	7	67	1.26

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55