genome.fa.s9624.2.7.7.80.10.50.1000.27.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  27  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)
5385202--5385252	20	2.5	20	100	0	102	41	11	19	27	1.86
5392703--5392752	20	2.5	20	83	6	57	34	12	4	50	1.58
5394621--5394723	45	2.3	45	91	1	161	45	11	19	23	1.83
5394647--5394741	45	2.1	45	82	7	113	48	9	16	25	1.76
5396379--5396418	17	2.4	17	100	0	80	55	12	7	25	1.63
5397053--5397077	8	3.1	8	100	0	50	16	24	24	36	1.94
5397598--5397653	24	2.3	24	93	0	94	30	16	14	39	1.88
5399578--5399633	18	3.2	17	79	5	58	33	17	8	39	1.81
5400613--5400692	22	3.6	22	94	0	133	27	16	30	26	1.97
5400733--5400768	18	2.1	17	94	5	63	27	11	36	25	1.90
5401092--5401526	59	7.4	59	80	6	427	35	11	24	28	1.90
5401093--5401525	177	2.4	175	82	8	491	35	11	24	28	1.90
5403592--5403651	27	2.2	27	80	11	70	36	3	6	53	1.44
5403582--5403651	27	2.6	27	72	14	65	34	4	8	52	1.51
5406526--5406568	15	2.9	15	100	0	86	55	11	0	32	1.36
5413336--5413383	18	2.7	18	96	0	87	39	8	8	43	1.65
5417247--5417285	20	1.9	20	85	15	53	25	0	28	46	1.53
5428493--5428649	76	2.1	76	98	0	305	24	15	16	42	1.88
5432579--5432643	31	2.1	31	91	0	103	33	33	9	23	1.86
5432583--5432650	31	2.2	31	86	0	91	33	32	11	22	1.90
5435418--5435517	46	2.1	47	80	7	114	39	9	16	36	1.80
5436735--5436759	5	5.0	5	100	0	50	20	60	20	0	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5436757--5436790	15	2.1	16	89	10	52	14	35	26	23	1.94
5439215--5439271	24	2.4	24	84	0	69	28	8	19	43	1.80
5441952--5442040	7	13.1	7	81	7	85	20	0	32	47	1.50
5441955--5442033	40	2.0	41	89	2	124	20	0	30	49	1.49
5441952--5442047	20	4.7	20	78	7	86	21	0	31	46	1.52
5441981--5442049	27	2.5	27	88	2	93	24	0	27	47	1.52
5442510--5442566	30	1.9	30	96	0	105	40	0	0	59	0.97
5442510--5442600	11	8.7	11	74	16	70	39	1	1	58	1.13
5442508--5442567	19	3.0	21	83	11	72	40	0	0	60	0.97
5442516--5442587	30	2.4	30	85	2	90	41	1	1	55	1.17
5443822--5443860	21	1.9	20	89	5	60	79	0	0	20	0.73
5443819--5443852	9	3.8	9	88	11	52	82	0	0	17	0.67
5445441--5445528	6	14.0	6	71	19	56	73	0	0	26	0.83
5445443--5445502	10	5.6	10	86	13	84	76	0	0	23	0.78
5445441--5445528	16	5.4	16	71	21	67	73	0	0	26	0.83
5445471--5445523	21	2.7	19	81	13	72	67	0	0	32	0.91
5445625--5445685	12	5.1	12	74	5	61	49	9	0	40	1.36
5445567--5445739	37	4.9	37	77	15	179	47	9	1	41	1.43
5445659--5445744	28	3.1	27	81	6	95	47	8	2	41	1.46
5445620--5445796	65	2.8	63	84	6	223	46	9	1	42	1.46
5445705--5445765	26	2.4	25	89	5	88	47	9	0	42	1.36
5445730--5445879	38	4.0	38	88	3	207	42	14	4	38	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5446450--5446885	45	9.7	45	91	3	628	29	21	9	39	1.85
5446489--5446969	135	3.6	135	89	2	655	28	20	10	40	1.86
5447472--5447529	22	2.8	20	87	10	89	25	31	15	27	1.96
5453201--5453619	45	9.4	45	88	1	549	29	21	9	39	1.85
5453218--5453606	135	2.9	135	91	2	631	29	21	9	39	1.85
5454045--5454104	20	2.9	20	82	5	66	28	31	13	26	1.94
5454045--5454116	20	3.5	20	80	9	65	27	29	15	27	1.96
5463572--5463609	16	2.4	16	95	0	67	31	23	15	28	1.96
5469197--5469225	15	1.9	15	100	0	58	17	6	27	48	1.72
5470003--5470063	20	2.9	21	87	7	79	18	26	34	21	1.96
5478048--5478203	65	2.4	64	82	5	163	30	21	17	29	1.97
5484017--5484074	23	2.7	21	79	10	71	27	27	20	24	1.99
5484008--5484074	21	3.1	21	77	8	80	28	26	19	25	1.99
5485648--5485705	27	2.1	27	100	0	116	25	22	13	37	1.91
5488223--5488295	16	4.4	16	71	6	56	0	21	8	69	1.14
5488709--5488749	14	2.9	15	92	7	68	39	0	0	60	0.96
5488745--5488791	3	15.7	3	95	0	85	63	0	2	34	1.06
5489017--5489447	117	3.7	116	88	3	582	28	19	12	38	1.88
5489017--5489447	233	1.8	232	85	5	602	28	19	12	38	1.88
5489406--5489599	95	2.1	93	86	1	262	27	17	16	38	1.91
5489501--5489789	113	2.6	112	95	2	515	28	19	13	38	1.90
5490441--5490664	84	2.7	84	96	3	409	37	23	14	25	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5495346--5495382	18	2.0	19	89	5	58	62	0	13	24	1.31
5504164--5504205	18	2.2	18	87	8	57	0	23	7	69	1.13
5504615--5504655	14	2.9	15	92	7	68	39	0	0	60	0.96
5504651--5504727	3	25.7	3	86	0	100	68	0	2	28	1.02
5507559--5507913	143	2.6	138	81	4	315	29	18	19	32	1.96
5509618--5509660	20	2.0	20	86	8	59	27	2	6	62	1.33
5509740--5509842	31	3.3	31	83	0	125	29	21	9	39	1.85
5509969--5510073	30	3.5	30	94	1	176	21	15	1	60	1.44
5510585--5510614	15	2.0	15	100	0	60	46	6	0	46	1.29
5510727--5510756	15	2.0	15	100	0	60	40	13	0	46	1.43
5511396--5511448	23	2.3	23	80	0	61	33	5	9	50	1.58
5511601--5511661	28	2.2	28	78	0	68	50	13	1	34	1.51
5514040--5514112	30	2.4	30	84	6	103	42	10	4	42	1.59
5514031--5514125	30	3.2	29	77	12	95	40	10	6	43	1.65
5514455--5514790	106	3.1	106	63	19	238	47	6	7	39	1.57
5514530--5514589	30	2.0	30	81	12	70	56	3	0	40	1.16
5514453--5514877	221	1.9	222	91	3	705	47	8	7	36	1.61
5516142--5516168	14	1.9	14	100	0	54	22	18	7	51	1.70
5522715--5522871	12	12.2	12	69	19	68	63	1	1	33	1.14
5522723--5523206	9	54.6	9	71	20	221	56	3	1	38	1.25
5522797--5523043	2	133.5	2	70	21	166	55	3	1	40	1.24
5522723--5523125	55	7.6	51	70	21	164	58	2	0	37	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5522812--5523117	62	4.9	61	72	18	222	56	2	0	39	1.21
5522734--5523206	56	8.2	60	70	23	190	56	3	1	38	1.26
5523049--5523117	6	11.0	6	92	4	102	63	1	0	34	1.03
5522723--5523117	17	24.6	15	70	25	130	58	2	1	37	1.19
5522717--5523130	13	29.1	14	71	22	159	58	2	0	37	1.20
5531275--5531350	21	3.5	22	81	10	61	35	17	21	26	1.95
5531295--5531350	22	2.6	22	88	8	80	35	14	23	26	1.93
5539076--5539128	23	2.3	24	80	9	65	33	24	18	22	1.97
5539094--5539149	21	2.6	21	82	5	58	33	23	19	23	1.97
5539799--5539871	21	3.5	21	94	0	119	34	24	6	34	1.82
5545978--5546022	23	2.0	23	95	0	81	28	26	22	22	1.99
5546176--5546226	21	2.4	21	96	0	93	31	23	7	37	1.83
5550926--5550995	12	5.8	12	71	6	52	51	17	14	17	1.77
5550924--5550991	24	2.8	24	76	8	66	52	16	13	17	1.74
5555547--5555600	12	4.4	12	80	13	56	68	1	0	29	1.00
5555598--5555921	2	173.5	2	70	22	208	54	3	2	40	1.28
5555582--5555914	33	10.1	31	69	23	138	54	3	2	40	1.27
5557091--5557145	23	2.3	24	81	9	60	38	9	10	41	1.72
5559675--5559717	20	2.2	20	86	0	59	30	13	20	34	1.92
5564621--5564663	20	2.2	20	86	0	59	30	13	20	34	1.92
5566888--5567450	240	2.3	242	90	1	869	30	21	11	36	1.89
5566887--5567458	81	7.1	81	87	1	799	30	21	11	36	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5568672--5568712	18	2.3	18	100	0	82	24	21	7	46	1.77
5570692--5570732	16	2.7	15	84	3	55	29	12	4	53	1.58
5570692--5570727	16	2.3	16	90	4	56	33	11	5	50	1.61
5572461--5572510	23	2.2	23	82	7	57	60	14	2	24	1.45
5575804--5575869	20	3.2	20	89	4	96	63	0	21	15	1.30
5575804--5575869	21	3.2	21	91	2	98	63	0	21	15	1.30
5582724--5582756	17	1.9	17	88	11	50	66	12	9	12	1.44
5587551--5587795	15	16.9	14	70	16	90	75	0	19	5	1.00
5587580--5587800	7	31.4	7	78	12	134	75	0	19	4	0.97
5587548--5587800	22	12.1	20	71	19	137	75	0	19	5	0.98

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