genome.fa.s9634.2.7.7.80.10.50.1000.19.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  19  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)
4143697--4143802	45	2.3	43	81	10	122	28	18	21	31	1.97
4150044--4150126	11	7.6	11	70	20	50	71	1	4	22	1.12
4150062--4150103	17	2.5	17	84	7	50	73	0	7	19	1.05
4152590--4152628	2	19.5	2	100	0	78	51	0	48	0	1.00
4152773--4152817	4	12.2	4	90	9	62	75	0	0	24	0.80
4152774--4152806	17	1.9	17	93	0	57	75	0	0	24	0.80
4152773--4152817	13	3.1	15	81	15	58	75	0	0	24	0.80
4158895--4158947	25	2.1	26	82	3	63	18	3	3	73	1.14
4158901--4158957	25	2.3	24	79	11	62	17	3	3	75	1.09
4158975--4159025	4	13.2	4	80	12	54	23	0	1	74	0.92
4158975--4159025	16	3.3	16	84	13	63	23	0	1	74	0.92
4158926--4159071	22	6.5	22	72	17	97	20	4	2	71	1.16
4159031--4159077	24	2.0	23	87	8	67	12	12	0	74	1.07
4159038--4159102	24	2.5	26	85	14	82	12	10	0	76	1.01
4159205--4159231	3	9.0	3	100	0	54	33	0	0	66	0.92
4160719--4160752	14	2.4	14	95	0	59	50	11	32	5	1.63
4161843--4162096	96	2.6	95	88	3	357	32	18	17	31	1.94
4162975--4164090	85	13.1	85	87	0	1428	34	22	18	24	1.96
4165352--4165446	3	31.0	3	73	17	72	30	2	2	65	1.16
4165426--4165494	36	1.9	35	82	5	84	14	7	2	75	1.13
4165583--4165624	3	13.7	3	85	9	50	30	0	0	69	0.89
4165520--4165609	48	1.9	46	84	8	119	18	6	3	71	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4165823--4165869	3	15.7	3	100	0	94	31	0	0	68	0.90
4166403--4166434	14	2.3	14	100	0	64	50	21	6	21	1.71
4168994--4169058	23	2.8	23	90	4	105	36	15	3	44	1.62
4175939--4175970	11	2.9	11	100	0	64	28	0	0	71	0.86
4175996--4176047	20	2.6	20	87	6	70	50	0	0	50	1.00
4184083--4184112	13	2.2	14	94	5	53	53	3	6	36	1.44
4192254--4192345	31	3.0	31	90	3	132	25	17	21	35	1.95
4194687--4194729	20	2.2	20	86	0	59	37	16	11	34	1.85
4201289--4201331	20	2.2	20	86	0	59	37	16	11	34	1.85
4204184--4204229	20	2.2	20	84	7	56	45	4	4	45	1.43
4206062--4206090	15	1.9	15	100	0	58	44	0	0	55	0.99
4209151--4209318	36	4.7	36	96	0	302	33	15	9	41	1.79
4222099--4222135	19	1.9	19	94	0	65	32	27	5	35	1.79
4222509--4222550	21	2.0	21	85	4	57	26	33	21	19	1.97
4223352--4223412	22	2.8	22	85	5	79	24	22	22	29	1.99
4229410--4229446	19	1.9	19	94	0	65	32	27	5	35	1.79
4229429--4229479	25	2.0	25	88	7	77	25	23	9	41	1.85
4237927--4237969	16	2.6	17	74	7	52	44	0	0	55	0.99
4240464--4240498	16	2.2	16	89	0	52	51	2	0	45	1.16
4242130--4242163	14	2.4	14	90	0	50	23	38	32	5	1.79
4244224--4244252	2	14.5	2	100	0	58	48	0	0	51	1.00
4250756--4250792	18	2.1	18	94	0	65	35	16	0	48	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4253139--4253368	115	2.0	115	99	0	451	45	17	13	23	1.85
4256342--4256381	6	6.7	6	83	11	55	37	15	0	47	1.45
4256349--4256407	18	3.2	18	81	9	75	37	15	0	47	1.45
4256342--4256395	24	2.2	24	81	18	67	37	16	0	46	1.48
4258139--4258163	2	12.5	2	100	0	50	52	0	0	48	1.00
4259127--4259177	19	2.5	22	84	9	63	21	27	15	35	1.94
4262695--4262741	6	7.8	6	90	0	67	2	46	0	51	1.13
4262699--4262746	12	4.0	12	80	0	51	4	47	0	47	1.21
4264759--4264797	20	2.0	20	94	0	69	33	10	20	35	1.86
4268153--4268193	21	2.0	21	85	0	55	58	7	9	24	1.55
4272177--4272277	21	4.7	21	70	13	80	31	25	19	22	1.98
4273000--4273144	55	2.6	55	85	2	193	31	22	16	29	1.96
4276869--4277013	55	2.6	55	89	2	211	30	21	20	28	1.98
4277448--4277500	23	2.3	23	96	0	97	41	33	0	24	1.55
4278335--4278388	23	2.5	22	82	8	65	27	20	16	35	1.94
4278751--4278819	30	2.2	30	82	15	86	36	5	17	40	1.74
4278760--4278819	29	2.0	31	90	6	97	35	6	16	41	1.75
4279012--4279053	21	2.0	21	95	0	75	23	21	28	26	1.99
4279082--4279121	20	1.9	21	85	10	55	37	37	10	15	1.80
4279337--4279406	34	2.1	32	89	5	104	31	15	31	21	1.95
4280866--4280897	15	2.1	15	94	0	55	6	0	28	65	1.16
4287235--4287273	20	2.0	20	89	0	60	33	10	23	33	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4289942--4289989	19	2.4	20	82	10	62	25	31	12	31	1.92
4292131--4292330	108	1.8	111	82	9	259	41	11	10	37	1.75
4293388--4293432	19	2.4	18	82	17	56	0	17	22	60	1.37
4293980--4294034	3	17.0	3	78	14	56	61	1	3	32	1.24
4293980--4294032	10	5.4	10	80	8	56	60	1	3	33	1.26
4293980--4294032	20	2.7	20	83	13	65	60	1	3	33	1.26
4294159--4294555	151	2.7	151	93	5	659	33	22	22	22	1.97
4294159--4294555	76	5.3	76	91	6	652	33	22	22	22	1.97
4295629--4295739	53	2.1	55	86	5	156	23	19	17	39	1.92
4297878--4298317	115	3.8	115	94	1	767	32	21	13	32	1.92
4298211--4298748	174	3.1	174	98	0	1049	35	20	13	29	1.92
4305538--4305595	17	3.6	16	82	15	66	72	0	1	25	0.94
4305535--4305582	14	3.3	14	77	16	53	72	0	0	27	0.84
4307977--4308033	3	18.0	3	78	10	60	61	1	3	33	1.23
4307977--4308032	13	4.0	14	73	15	53	60	1	3	33	1.24
4307980--4308031	10	4.9	11	77	17	56	59	1	3	34	1.27
4312398--4312459	3	20.7	3	83	6	81	61	1	0	37	1.06
4312960--4313116	36	4.5	36	66	16	114	38	13	17	29	1.88
4312960--4313182	103	2.2	102	89	1	347	39	13	16	30	1.88
4313069--4313324	66	3.9	66	84	6	306	39	14	14	31	1.87
4313069--4313308	132	1.8	132	87	5	360	37	15	14	32	1.88
4321428--4321457	15	2.0	15	100	0	60	13	46	26	13	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4323960--4324026	32	2.1	33	97	2	127	35	17	19	26	1.94
4325344--4325377	17	2.0	17	100	0	68	23	5	29	41	1.78
4327012--4327050	20	2.0	20	85	10	53	23	10	2	64	1.37
4336912--4336938	14	1.9	14	100	0	54	7	22	3	66	1.33
4340419--4340512	8	12.0	8	77	17	67	78	0	11	9	0.96
4340446--4340525	39	2.1	39	86	11	96	82	0	10	7	0.84
4340439--4340486	1	48.0	1	80	0	51	89	0	6	4	0.58
4340406--4340506	31	3.3	30	76	18	93	78	0	11	9	0.97
4341435--4341917	105	4.6	105	96	0	840	36	19	22	21	1.96
4341897--4341962	20	3.3	20	67	14	55	45	12	19	22	1.83
4345160--4345184	9	2.8	9	100	0	50	44	0	12	44	1.41
4347402--4347499	23	4.2	24	90	2	85	23	16	18	41	1.89
4347414--4347501	23	3.8	23	92	1	131	23	18	19	38	1.93
4349766--4349815	25	2.0	25	88	0	73	32	6	6	56	1.48
4353307--4353361	20	2.8	20	88	0	83	40	14	16	29	1.88
4353327--4353946	182	3.4	181	90	3	921	41	13	18	26	1.88
4355912--4355966	24	2.4	23	80	11	69	45	0	7	47	1.30
4356206--4356239	9	3.8	9	84	0	50	35	8	52	2	1.47
4356202--4356239	18	2.1	18	95	0	67	34	7	52	5	1.53
4358226--4358274	19	2.6	19	96	0	89	32	2	10	55	1.45
4358722--4359889	201	5.8	200	93	0	1913	37	15	14	32	1.88
4360881--4360946	33	2.0	33	100	0	132	27	24	12	36	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4364106--4365891	198	9.0	199	86	2	2274	38	14	16	30	1.88
4365855--4365894	21	1.9	21	89	0	62	30	12	15	42	1.83
4364137--4365866	594	2.9	594	90	2	2632	39	14	16	30	1.88
4366706--4366753	19	2.5	19	96	0	87	31	6	10	52	1.60
4369400--4369895	199	2.5	198	82	3	593	39	14	14	30	1.86
4369914--4370076	87	1.9	87	92	0	272	32	15	12	39	1.84
4369998--4370042	23	2.0	23	95	0	81	37	20	8	33	1.83
4372170--4372229	31	1.9	31	93	0	102	21	28	23	26	1.99
4375447--4375478	16	1.9	17	93	6	57	43	0	15	40	1.47
4375871--4375958	32	2.9	30	84	3	122	38	9	22	29	1.85

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