genome.fa.s8105.2.7.7.80.10.50.1000.23.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: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5962497

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   

This is table  23  of  30  ( 3521 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)
4328862--4328897	19	1.9	19	94	5	65	22	0	5	72	1.05
4328926--4328966	20	2.0	21	85	4	57	36	2	2	58	1.24
4329600--4329624	7	3.6	7	100	0	50	68	0	0	32	0.90
4339586--4339624	16	2.5	15	88	12	60	84	0	15	0	0.62
4339586--4339626	14	2.8	15	89	10	59	80	0	19	0	0.71
4339941--4339980	16	2.5	16	88	8	55	30	7	10	52	1.62
4340775--4341069	83	3.6	83	95	0	527	26	13	23	37	1.91
4341806--4342374	113	5.0	113	91	0	881	37	14	18	29	1.90
4342684--4342765	3	27.3	3	94	0	146	34	2	0	63	1.08
4342764--4342808	22	2.1	21	84	8	56	62	2	0	35	1.08
4343227--4343306	42	1.9	41	82	2	97	65	10	25	0	1.24
4344141--4344176	19	1.9	19	94	5	65	22	0	5	72	1.05
4344205--4344245	20	2.0	21	85	4	57	36	2	2	58	1.24
4344438--4344489	17	3.1	17	70	13	54	51	0	7	40	1.30
4345576--4345651	2	38.0	2	100	0	152	50	0	0	50	1.00
4346080--4346115	14	2.6	14	95	0	63	25	27	16	30	1.97
4348729--4348761	13	2.3	15	90	10	52	39	3	18	39	1.66
4357435--4357475	21	2.0	21	85	0	55	36	2	7	53	1.42
4359126--4359255	30	4.4	29	76	3	125	19	16	9	55	1.67
4363725--4363749	2	12.5	2	100	0	50	52	0	0	48	1.00
4364995--4365269	37	7.7	37	74	13	143	32	17	11	38	1.85
4365143--4365269	36	3.5	36	89	5	186	33	21	8	36	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4365131--4365275	72	2.0	72	83	10	181	36	20	8	33	1.84
4365670--4365787	40	2.9	40	75	7	130	26	31	16	25	1.97
4365954--4365992	3	13.0	3	100	0	78	33	0	0	66	0.92
4366925--4366985	14	4.4	14	81	8	70	1	57	0	40	1.08
4366925--4366985	22	2.9	21	92	4	97	1	57	0	40	1.08
4366934--4366975	8	5.5	8	88	11	70	0	59	0	40	0.97
4367580--4367710	30	4.3	30	75	11	115	17	16	7	58	1.61
4367602--4367694	31	3.0	32	81	9	95	18	12	7	61	1.54
4367605--4367733	61	2.1	61	80	7	138	17	13	9	59	1.59
4378050--4378076	13	2.1	13	100	0	54	25	44	7	22	1.79
4382546--4382646	39	2.6	39	85	6	125	55	10	3	29	1.52
4382737--4382778	21	2.0	21	100	0	84	33	4	19	42	1.72
4387989--4388049	27	2.4	25	78	10	77	44	1	4	49	1.33
4388000--4388054	27	2.0	27	92	0	92	41	3	5	49	1.43
4388014--4388234	36	5.9	36	79	9	221	43	4	5	45	1.48
4387965--4388090	63	2.0	64	85	4	175	41	3	5	49	1.45
4388026--4388258	36	6.3	36	80	7	182	43	4	5	46	1.46
4389603--4389648	15	3.1	15	79	17	51	10	8	0	80	0.91
4389593--4389648	19	2.9	19	86	2	67	14	7	0	78	0.95
4389615--4389693	25	3.0	25	77	14	77	10	11	2	75	1.13
4394851--4395555	85	8.4	85	78	4	648	30	24	20	24	1.98
4394851--4395564	165	4.3	164	80	7	602	31	24	19	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4395568--4395924	167	2.1	167	91	0	579	28	21	20	29	1.98
4396255--4396559	36	8.2	38	80	8	209	43	3	6	46	1.46
4396318--4396342	11	2.3	11	100	0	50	40	8	8	44	1.63
4396270--4396606	74	4.6	70	81	11	315	45	3	5	45	1.44
4396684--4396727	3	14.0	3	81	9	52	29	2	0	68	1.02
4396683--4396720	19	2.0	19	100	0	76	31	5	0	63	1.17
4396684--4396731	10	5.0	10	85	7	64	29	2	0	68	1.01
4397944--4398013	9	7.3	9	80	13	52	12	8	4	74	1.20
4397980--4398012	10	3.4	10	91	4	50	15	12	6	66	1.42
4398067--4398111	2	22.5	2	100	0	90	48	0	0	51	1.00
4398137--4398178	22	2.0	22	86	9	61	21	9	0	69	1.17
4398858--4398927	3	24.0	3	77	11	74	38	0	0	61	0.96
4398859--4398953	41	2.3	40	78	10	104	38	2	0	58	1.10
4400336--4400561	120	1.9	117	81	6	276	37	8	8	45	1.65
4400528--4400576	23	2.0	25	88	7	75	46	2	0	51	1.12
4400530--4400582	23	2.4	22	78	12	63	47	3	0	49	1.19
4404425--4404456	15	2.1	15	94	0	55	25	18	9	46	1.79
4408219--4408248	9	3.4	9	90	9	53	23	13	0	63	1.29
4413238--4414247	113	9.0	113	86	2	1383	37	14	18	29	1.90
4413272--4414247	224	4.4	224	95	0	1682	38	13	18	29	1.90
4414592--4414663	3	24.7	3	78	10	78	38	0	0	61	0.96
4415955--4416180	120	1.9	118	82	6	287	36	9	9	44	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4416147--4416195	23	2.0	25	88	7	75	46	2	0	51	1.12
4423868--4423935	23	3.0	23	95	0	118	42	20	0	36	1.52
4426258--4426290	12	2.8	12	95	0	57	36	12	15	36	1.84
4433327--4433491	76	2.2	75	86	3	233	30	2	10	56	1.45
4434112--4434181	22	3.4	19	76	20	61	20	8	1	70	1.22
4439774--4439811	20	1.9	20	94	0	67	18	2	2	76	1.02
4439760--4439813	28	2.0	27	92	3	90	18	1	3	75	1.03
4440855--4440926	32	2.2	32	95	0	135	51	15	13	19	1.76
4441706--4441870	76	2.2	75	87	3	242	30	2	10	56	1.47
4441828--4441890	19	3.2	19	75	4	54	31	0	12	55	1.37
4442517--4442557	21	1.9	22	90	5	66	19	4	0	75	0.98
4446783--4446850	23	2.9	23	72	10	66	19	27	22	30	1.97
4447455--4447508	22	2.5	22	93	0	90	18	16	14	50	1.79
4447455--4447508	10	5.0	10	80	14	63	18	16	14	50	1.79
4447455--4447521	22	3.0	22	88	0	89	20	16	13	49	1.79
4457145--4457174	15	1.9	16	93	6	53	40	13	16	30	1.87
4459878--4459936	31	1.9	31	86	6	84	47	6	13	32	1.69
4460242--4460335	18	4.9	19	68	19	54	30	0	10	58	1.32
4460243--4460306	32	2.0	32	85	11	87	26	0	10	62	1.28
4460285--4460406	63	1.9	63	88	6	185	33	0	12	54	1.38
4460982--4461028	19	2.5	19	80	13	60	23	4	0	72	1.02
4461072--4461117	20	2.3	20	85	10	67	23	2	0	73	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4466021--4466091	5	13.8	5	76	15	56	22	5	0	71	1.06
4467734--4467882	19	7.4	19	70	19	79	29	0	11	59	1.33
4467793--4467917	64	2.0	63	88	4	189	30	0	12	56	1.37
4468504--4468552	19	2.6	18	81	9	62	22	4	0	73	1.00
4472542--4472596	3	17.7	3	77	7	56	58	3	7	30	1.43
4478038--4478106	2	34.5	2	100	0	138	49	0	0	50	1.00
4481867--4481927	2	30.5	2	100	0	122	49	0	0	50	1.00
4488447--4488494	18	2.6	20	81	18	68	50	0	4	45	1.21
4488480--4488525	23	2.0	24	86	4	67	39	0	4	56	1.19
4492962--4493527	139	4.1	138	77	6	502	25	15	28	30	1.96
4493590--4493834	30	7.5	30	65	21	109	37	14	18	28	1.91
4493553--4493853	133	2.3	134	93	1	516	38	14	18	28	1.90
4493553--4493853	67	4.5	67	91	0	487	38	14	18	28	1.90
4496728--4496814	29	3.0	29	75	16	74	1	19	3	75	1.00
4496744--4496809	15	4.3	15	79	11	62	0	18	3	78	0.87
4496741--4496813	22	3.3	21	76	14	67	0	19	2	78	0.88
4496741--4496813	7	9.9	7	75	21	60	0	19	2	78	0.88
4496741--4496813	36	2.0	35	84	10	94	0	19	2	78	0.88
4496767--4496825	24	2.4	25	81	16	70	1	18	5	74	1.09
4502260--4502341	23	3.6	22	77	8	85	24	25	24	25	2.00
4505005--4505126	64	1.9	65	86	8	178	30	22	18	29	1.97
4506944--4506977	13	2.6	13	100	0	68	14	38	5	41	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4509609--4509656	16	3.1	16	81	6	53	33	4	4	58	1.36
4513572--4513694	51	2.4	51	100	0	246	50	16	1	31	1.55
4520021--4520100	21	3.7	21	80	12	99	23	11	23	41	1.87
4520018--4520104	44	2.0	44	93	0	147	25	10	25	39	1.87
4525894--4526022	59	2.2	59	82	0	150	29	17	24	28	1.97
4526555--4526594	11	3.5	11	96	3	71	25	17	27	30	1.97
4529936--4530015	21	3.7	21	88	6	124	22	10	23	43	1.83
4529936--4530019	44	1.9	44	97	0	159	22	9	25	42	1.83
4532478--4532550	22	3.0	23	73	23	69	35	1	1	61	1.13
4533060--4533148	41	2.2	42	83	6	119	35	19	19	25	1.95

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