genome.fa.s9634.2.7.7.80.10.50.1000.25.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   

This is table  25  of  78  ( 9351 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)
5143635--5143724	39	2.3	38	94	1	153	45	21	20	13	1.84
5143720--5143764	19	2.4	19	92	0	72	8	15	26	48	1.74
5144320--5144413	20	4.7	20	77	2	80	23	17	24	35	1.95
5144402--5144497	41	2.3	41	94	3	140	19	23	17	38	1.93
5144402--5144494	20	4.6	20	79	4	105	19	24	18	37	1.94
5145201--5145254	26	2.1	26	82	0	63	38	5	7	48	1.55
5146035--5146068	17	2.0	17	88	0	50	58	2	0	38	1.13
5146483--5146514	11	2.9	11	95	0	55	78	15	6	0	0.95
5147286--5147320	18	1.9	18	88	0	52	51	2	2	42	1.31
5151809--5151863	21	2.6	21	76	0	65	23	40	29	7	1.81
5158060--5158180	42	2.9	42	89	0	179	38	8	14	38	1.77
5158309--5158367	28	2.1	28	90	0	91	59	10	8	22	1.56
5158722--5158776	28	2.0	28	92	7	94	43	16	21	18	1.88
5161206--5161260	26	2.1	26	82	0	65	40	5	10	43	1.63
5161360--5161423	28	2.2	30	86	5	87	53	0	1	45	1.10
5162073--5162114	3	14.0	3	100	0	84	33	0	0	66	0.92
5165661--5165696	14	2.6	14	90	0	54	16	16	11	55	1.68
5167273--5167341	30	2.2	30	82	15	86	36	5	17	40	1.74
5167282--5167341	29	2.0	30	90	6	95	35	6	16	41	1.75
5167556--5167595	21	1.9	21	94	0	71	32	17	27	22	1.96
5170734--5170802	30	2.2	30	85	15	95	34	5	17	42	1.73
5170743--5170802	30	2.0	30	93	6	104	33	6	16	43	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5170996--5171036	21	2.0	21	85	9	57	34	17	24	24	1.96
5174667--5174815	38	3.9	38	88	2	212	28	20	14	35	1.93
5174776--5175059	62	4.5	62	74	14	229	28	20	15	35	1.93
5174776--5175063	129	2.3	125	81	4	337	28	20	15	36	1.93
5175203--5175599	36	11.0	36	88	1	526	40	18	18	22	1.92
5175576--5176054	102	4.7	102	85	1	557	30	19	18	31	1.95
5177055--5177089	18	1.9	18	88	0	52	51	2	2	42	1.31
5181571--5181625	21	2.6	21	76	0	65	23	40	29	7	1.81
5197345--5197451	31	3.4	32	77	13	105	34	17	17	29	1.94
5199350--5199491	75	1.9	76	86	1	205	21	17	11	48	1.79
5204431--5204469	20	2.0	20	100	0	78	46	7	10	35	1.67
5207805--5207842	15	2.4	16	82	13	51	44	0	0	55	0.99
5208004--5208061	20	2.9	20	94	0	98	25	17	5	51	1.65
5209325--5209393	23	3.0	24	77	14	72	36	24	17	21	1.95
5211459--5211539	16	4.9	16	88	5	90	39	23	11	25	1.88
5211468--5211539	8	8.8	8	90	6	117	38	23	12	25	1.90
5211719--5214172	4	627.0	4	90	6	4006	24	0	26	48	1.53
5214443--5214571	4	33.0	4	75	16	119	49	20	1	28	1.58
5214443--5214662	12	18.0	12	80	12	126	48	12	0	38	1.47
5214559--5214671	2	58.5	2	86	6	162	48	2	0	47	1.21
5215926--5215956	16	1.9	16	93	0	53	51	22	9	16	1.73
5217144--5217298	64	2.4	64	82	4	170	31	18	21	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5217910--5217952	22	2.0	23	90	9	72	39	27	13	18	1.89
5218816--5218863	3	16.0	3	100	0	96	66	0	33	0	0.92
5221050--5221163	22	5.1	22	72	13	90	35	27	19	17	1.94
5221054--5221163	21	4.9	21	68	15	60	36	25	20	18	1.94
5222111--5222159	20	2.5	20	96	0	89	26	14	18	40	1.89
5228787--5228868	2	40.5	2	97	2	155	50	0	1	48	1.08
5235840--5235915	36	2.1	36	95	0	134	17	26	26	30	1.97
5238953--5239013	25	2.6	23	80	10	68	13	18	14	54	1.72
5238949--5239013	23	2.8	22	77	13	67	12	16	13	56	1.66
5239482--5239622	65	2.2	66	82	5	171	53	2	2	41	1.27
5239786--5239826	10	3.8	10	82	17	55	43	0	0	56	0.99
5239791--5239831	13	3.2	13	80	13	50	51	0	0	48	1.00
5239786--5239867	25	3.4	24	78	6	85	46	2	2	48	1.28
5240265--5240357	25	3.5	25	76	15	89	50	2	1	46	1.20
5240368--5240429	12	5.2	12	77	9	56	46	0	0	53	1.00
5242315--5242346	2	16.0	2	100	0	64	50	0	0	50	1.00
5247464--5247502	2	19.5	2	100	0	78	51	0	0	48	1.00
5251020--5251062	16	2.7	16	100	0	86	32	18	11	37	1.87
5254284--5254312	12	2.4	12	100	0	58	31	10	24	34	1.89
5254296--5254423	57	2.2	59	85	2	170	40	4	16	38	1.69
5254504--5254580	23	3.3	23	78	8	86	19	22	24	33	1.97
5254538--5254617	24	3.4	24	79	5	83	21	22	23	32	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5259439--5259465	14	1.9	14	100	0	54	55	0	14	29	1.40
5260275--5260329	27	2.0	29	92	7	96	38	7	14	40	1.74
5260287--5260417	57	2.3	58	77	4	140	41	3	16	38	1.66
5260491--5260633	23	6.2	23	94	0	232	20	27	24	27	1.99
5260626--5260688	24	2.7	24	82	2	74	23	23	22	30	1.99
5270358--5270413	29	1.9	29	89	7	87	32	23	3	41	1.71
5270571--5270682	60	1.9	59	90	1	179	42	3	16	37	1.65
5271901--5272000	30	3.4	29	83	9	121	58	10	15	17	1.63
5273276--5273319	3	14.3	3	85	4	61	63	2	0	34	1.07
5273286--5273330	12	3.4	14	85	14	60	62	4	0	33	1.15
5273283--5273340	15	3.7	16	81	9	66	60	3	0	36	1.14
5273288--5273340	25	2.1	25	83	13	65	60	3	0	35	1.15
5273545--5273647	43	2.5	40	74	12	95	20	19	35	24	1.95
5273706--5274086	132	2.9	131	86	1	494	26	17	30	25	1.97
5274441--5274506	33	2.0	33	93	0	114	30	18	15	36	1.91
5275552--5275647	11	8.5	11	74	8	59	4	16	7	71	1.24
5284134--5284214	20	3.8	20	78	12	72	25	32	22	19	1.98
5284155--5284214	23	2.7	22	80	12	61	21	33	23	21	1.97
5288044--5288144	30	3.4	29	81	6	105	57	8	15	17	1.63
5289397--5289454	3	18.7	3	79	13	55	62	5	0	32	1.18
5299288--5299321	16	2.1	16	94	0	59	29	20	29	20	1.98
5306803--5306871	23	3.0	23	84	0	102	30	26	26	17	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5310307--5310344	12	3.0	13	85	14	53	36	7	2	52	1.45
5311824--5311867	20	2.2	21	88	8	65	20	0	20	59	1.39
5320055--5320118	24	2.7	24	97	0	119	29	20	12	37	1.89
5330638--5330672	18	1.9	18	100	0	70	17	22	34	25	1.96
5331907--5332722	408	2.0	406	92	1	1350	36	18	17	27	1.94
5333574--5333599	12	2.2	12	100	0	52	50	11	7	30	1.67
5336656--5336755	2	49.5	2	97	2	191	50	1	0	49	1.07
5337067--5337135	23	3.0	23	84	0	102	30	26	26	17	1.97
5342174--5342253	42	1.9	41	84	2	106	28	16	6	48	1.70
5342281--5342344	32	2.0	32	96	0	119	43	17	3	35	1.65
5342844--5342909	20	3.3	20	85	8	98	42	25	15	16	1.87
5342819--5342931	40	2.8	40	85	9	133	39	24	15	19	1.91
5342898--5342989	19	4.7	19	82	8	96	34	21	13	30	1.91
5342844--5343015	40	4.4	40	75	10	122	36	22	15	26	1.93
5342963--5343009	18	2.5	19	82	6	60	29	23	14	31	1.95
5346507--5346555	20	2.5	20	93	0	89	40	18	20	20	1.91
5346665--5346713	25	2.0	25	91	0	80	28	8	18	44	1.78
5347076--5347130	24	2.3	25	81	9	69	32	5	14	47	1.67
5347095--5347131	18	2.1	18	89	0	56	32	5	10	51	1.60
5347087--5347139	24	2.2	24	86	0	70	35	3	13	47	1.61
5350099--5350217	21	5.7	21	74	6	98	21	19	34	24	1.96
5352771--5352821	22	2.3	22	96	0	93	19	15	45	19	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5352937--5353012	40	1.9	40	94	0	134	18	14	25	42	1.88
5352933--5353011	20	4.0	20	79	0	104	17	16	25	40	1.90
5353029--5353084	20	2.8	21	78	8	71	28	12	32	26	1.93
5359058--5359108	15	3.4	15	83	0	66	39	5	15	39	1.72
5359056--5359124	30	2.3	29	90	2	102	43	7	14	34	1.73
5359497--5359661	27	6.0	28	71	17	107	50	1	0	47	1.13
5359503--5359563	25	2.3	26	81	16	72	47	1	0	50	1.10
5359496--5359640	56	2.6	54	78	13	134	48	1	0	48	1.14
5359613--5359661	17	2.9	17	76	11	57	59	0	0	40	0.98
5359593--5359661	33	2.1	33	84	10	88	53	0	1	44	1.09

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   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78