genome.fa.s190.2.7.7.80.10.50.1000.54.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: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  14308945

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   56   57   58   59   60   61   62   

This is table  54  of  62  ( 7381 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)
12766868--12766928	23	2.7	22	80	7	77	18	31	24	26	1.97
12771888--12771948	23	2.7	23	92	0	104	18	27	27	26	1.98
12774852--12774900	23	2.1	23	100	0	98	24	26	0	48	1.51
12779044--12779096	23	2.3	23	100	0	106	24	28	0	47	1.52
12780184--12780216	2	16.5	2	93	0	57	48	0	3	48	1.17
12781984--12782019	15	2.2	18	80	19	51	22	16	5	55	1.62
12781987--12782019	17	2.1	17	88	11	52	24	15	6	54	1.63
12784935--12785000	32	2.1	32	82	5	80	30	13	15	40	1.85
12787318--12787355	20	1.9	20	88	0	58	39	2	5	52	1.38
12789247--12789325	3	27.0	3	78	10	83	31	1	2	64	1.15
12791733--12791773	10	3.8	10	82	17	55	7	9	21	60	1.52
12791855--12791887	16	2.1	16	94	0	57	6	15	21	57	1.59
12791931--12791996	30	2.2	30	97	0	123	12	19	27	40	1.87
12791939--12792008	30	2.3	30	87	4	97	18	15	21	44	1.87
12792905--12792935	16	1.9	16	93	0	53	41	0	6	51	1.27
12798741--12798784	10	4.5	10	88	2	63	0	4	9	86	0.70
12802365--12802394	13	2.3	13	94	0	51	26	0	0	73	0.84
12803726--12803897	40	4.2	40	73	13	127	28	18	17	35	1.94
12803800--12804070	83	3.3	83	78	2	269	35	16	12	34	1.87
12807720--12808003	43	6.6	42	83	3	300	27	20	19	33	1.96
12807760--12808003	129	1.9	130	87	2	357	27	21	19	31	1.97
12807720--12807992	86	3.2	85	84	4	343	27	20	19	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12808051--12808344	147	2.0	147	100	0	588	29	21	17	32	1.95
12809135--12809318	91	2.0	91	100	0	368	26	17	10	45	1.82
12818017--12818598	290	2.0	290	98	0	1128	35	16	9	39	1.81
12818584--12818728	60	2.4	61	83	4	186	43	3	21	31	1.69
12819355--12819417	31	2.0	33	87	6	94	63	1	7	26	1.31
12820415--12820486	10	7.2	10	82	16	78	70	0	0	29	0.87
12820418--12820536	42	2.9	42	84	8	131	68	0	1	29	0.99
12820412--12820546	46	2.9	47	80	14	138	68	0	1	29	1.04
12820412--12820536	41	3.1	40	81	10	132	69	0	1	28	0.98
12820563--12820691	69	1.9	68	84	9	172	44	9	4	41	1.57
12820643--12820733	38	2.4	37	83	10	112	48	7	3	40	1.48
12820643--12820876	35	6.5	35	78	9	186	44	10	3	41	1.56
12827820--12828015	45	4.4	45	83	3	234	38	10	20	30	1.86
12828618--12828649	10	3.2	10	95	0	55	53	0	9	37	1.34
12830472--12830538	21	3.2	21	89	0	98	17	23	17	40	1.91
12830509--12830627	20	5.9	20	90	1	148	36	21	17	24	1.95
12830535--12830627	20	4.7	20	94	0	159	38	21	19	20	1.93
12830614--12830696	20	4.2	20	95	0	139	28	27	19	24	1.98
12830554--12830685	40	3.3	40	82	6	117	34	24	19	21	1.96
12830514--12830627	60	1.9	61	88	1	176	35	21	18	23	1.95
12831518--12831570	24	2.2	24	89	0	79	22	16	20	39	1.92
12833985--12834055	20	3.5	20	90	3	108	36	25	19	18	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12834056--12834109	14	3.5	14	73	22	54	11	24	20	44	1.83
12834051--12834129	33	2.4	34	91	2	124	12	24	21	41	1.87
12834235--12834271	14	2.6	14	86	0	56	48	21	0	29	1.50
12835727--12835783	21	2.7	21	100	0	114	22	21	35	21	1.96
12835657--12835784	42	3.0	42	78	7	118	21	18	38	21	1.94
12836266--12836410	20	7.4	20	77	13	133	37	21	21	20	1.95
12836276--12836426	76	2.0	76	96	0	275	37	20	21	19	1.94
12836453--12836572	20	5.6	20	76	14	123	15	17	24	42	1.88
12836486--12836525	14	2.9	14	80	0	53	7	15	25	52	1.68
12836441--12836569	68	1.9	68	91	3	215	14	17	23	44	1.86
12838449--12838645	20	10.6	20	71	12	89	44	23	17	14	1.85
12838454--12838539	40	2.2	40	86	0	118	43	23	17	16	1.88
12838471--12838645	73	2.4	73	91	0	278	42	24	17	15	1.88
12838994--12839043	22	2.3	22	85	0	64	24	10	38	28	1.87
12839002--12839047	22	2.1	22	91	0	74	21	13	39	26	1.90
12839273--12839318	21	2.2	21	92	0	74	39	17	26	17	1.91
12841675--12841710	2	17.5	2	94	5	63	50	2	0	47	1.15
12841881--12841911	10	3.1	10	100	0	62	51	0	0	48	1.00
12843065--12843145	31	2.6	31	84	1	101	35	2	12	49	1.54
12846932--12846971	21	1.9	21	89	0	62	10	25	40	25	1.86
12846952--12847014	20	2.9	21	79	9	65	15	25	34	23	1.95
12854929--12855126	46	4.4	44	72	9	139	25	22	9	42	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12854949--12855076	45	2.8	45	79	3	114	25	20	11	42	1.86
12855170--12855303	68	2.0	68	92	0	223	29	26	15	28	1.96
12855642--12856700	54	19.9	54	86	2	1372	33	18	18	29	1.95
12856349--12856429	27	3.3	27	64	25	79	33	14	18	33	1.92
12860929--12861014	44	1.9	45	90	2	138	26	20	12	39	1.89
12861061--12861193	67	2.0	68	86	1	187	30	23	14	31	1.94
12861475--12861579	55	1.9	54	88	5	158	29	18	20	32	1.96
12861551--12862510	54	17.9	54	87	1	1338	33	19	18	29	1.95
12863904--12864495	199	3.0	199	82	3	706	34	10	14	40	1.81
12865687--12865722	17	2.1	17	100	0	72	36	0	11	52	1.37
12867759--12867827	23	3.0	23	71	0	57	28	21	28	20	1.98
12868385--12868490	56	1.9	55	83	9	135	23	16	22	37	1.93
12870487--12870532	18	2.7	17	90	6	67	32	8	32	26	1.87
12870580--12870608	14	2.1	14	100	0	58	13	20	6	58	1.58
12871169--12871682	221	2.4	219	91	3	813	36	28	12	23	1.90
12876136--12876199	23	2.8	23	87	0	92	28	26	26	18	1.98
12881287--12881339	20	2.7	20	100	0	106	33	11	15	39	1.83
12881115--12881522	220	1.9	215	80	6	482	29	15	13	41	1.85
12881830--12882198	20	18.5	20	84	4	449	34	26	18	20	1.96
12882871--12882917	24	2.0	24	87	8	69	25	14	21	38	1.92
12883092--12883116	12	2.1	12	100	0	50	72	0	28	0	0.86
12885422--12885747	19	18.4	19	80	15	405	47	17	20	14	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12885422--12885747	33	9.2	34	80	14	328	47	17	20	14	1.83
12885450--12885769	161	2.0	157	93	3	543	46	16	21	15	1.83
12885450--12885769	52	6.0	52	92	4	541	46	16	21	15	1.83
12885776--12885877	19	5.6	19	82	12	142	14	22	17	45	1.85
12885984--12886020	14	2.6	14	91	0	65	45	21	0	32	1.52
12886015--12886087	12	6.0	12	67	20	53	57	16	1	24	1.47
12886001--12886073	38	1.9	38	97	0	137	53	16	1	28	1.51
12887947--12888003	14	3.7	14	77	20	60	45	22	21	10	1.82
12887928--12888020	33	2.8	33	95	0	168	47	21	20	10	1.80
12887891--12888025	19	7.6	19	75	16	119	46	22	19	11	1.81
12888021--12888149	19	7.3	19	75	17	125	8	17	28	45	1.77
12888021--12888112	33	2.8	33	93	3	150	7	18	28	45	1.76
12888193--12888850	93	7.1	93	98	0	1293	46	18	12	22	1.83
12888193--12888850	185	3.5	186	98	0	1293	46	18	12	22	1.83
12888193--12888850	278	2.4	278	99	0	1307	46	18	12	22	1.83
12890556--12890645	14	5.7	14	74	23	81	42	23	25	8	1.83
12890548--12890662	33	3.5	33	95	0	212	45	20	24	9	1.81
12890555--12890667	19	6.8	18	72	23	88	43	22	24	9	1.83
12890679--12890733	14	3.6	14	73	21	56	9	25	23	41	1.83
12890663--12890733	33	2.2	33	94	0	124	8	22	25	43	1.81
12890674--12890755	33	2.5	33	89	2	119	9	25	21	42	1.84
12890686--12890774	20	4.8	20	72	19	75	12	24	19	43	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12890854--12890924	33	2.2	33	92	0	115	47	18	22	11	1.80
12891106--12891160	22	2.5	22	81	0	74	20	16	40	23	1.91
12891306--12891499	20	9.6	20	82	5	221	19	19	25	35	1.95
12891306--12891499	60	3.2	60	83	0	253	19	19	25	35	1.95
12891492--12891568	21	3.7	20	70	13	57	27	16	23	32	1.96
12891554--12891605	20	2.6	20	96	0	95	21	13	26	38	1.90
12895147--12895183	16	2.3	16	90	0	56	81	0	2	16	0.81
12897609--12897643	16	2.1	17	89	5	54	57	0	0	42	0.99
12897980--12898057	15	5.2	15	76	6	86	35	3	1	58	1.24
12898028--12898088	15	3.6	17	79	16	56	44	3	1	50	1.28

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   56   57   58   59   60   61   62