genome.fa.s1129.2.7.7.80.10.50.1000.23.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   79   80   
          81   82   83   84   85   86   87   88   89   

This is table  23  of  89  ( 10573 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)
4884950--4884994	22	2.0	22	87	12	65	44	17	8	28	1.79
4885442--4885793	187	1.9	188	83	2	458	41	10	17	30	1.84
4885854--4886025	70	2.5	70	83	5	206	45	12	14	27	1.81
4897654--4897919	138	1.9	137	86	3	374	41	16	10	30	1.83
4899452--4899481	12	2.5	12	94	0	51	40	0	3	56	1.16
4903179--4903241	26	2.4	26	100	0	126	20	14	0	65	1.27
4903183--4903231	15	3.5	15	73	21	61	18	16	0	65	1.28
4903677--4903704	14	2.0	14	100	0	56	42	14	0	42	1.45
4908478--4908534	29	2.0	29	82	6	71	19	8	3	68	1.31
4909647--4909736	8	10.4	9	82	13	102	11	2	0	86	0.65
4909664--4909736	1	73.0	1	77	0	74	10	0	0	89	0.50
4909665--4909739	8	9.2	8	88	8	116	12	0	0	88	0.53
4909819--4910150	57	6.0	57	78	9	326	41	16	9	32	1.80
4909860--4909955	50	1.9	49	91	2	156	38	15	13	32	1.87
4909942--4910151	113	1.9	113	91	2	350	43	15	8	32	1.76
4911334--4911359	13	2.0	13	100	0	52	46	0	15	38	1.46
4911526--4911591	28	2.4	28	84	5	80	19	6	36	37	1.77
4912411--4912459	25	1.9	26	83	4	64	18	20	12	48	1.79
4933738--4933789	24	2.2	24	82	0	59	19	0	25	55	1.43
4933749--4933795	24	2.0	24	83	4	60	21	0	23	55	1.44
4935860--4935998	35	4.0	35	82	1	154	43	10	9	37	1.71
4935860--4935999	18	8.0	17	75	5	127	42	10	9	37	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4953673--4953816	18	8.2	17	81	5	171	44	11	9	34	1.74
4953674--4953818	35	4.1	35	88	2	200	44	11	9	33	1.74
4957874--4957916	21	2.0	21	82	8	52	48	9	4	37	1.56
4963042--4963486	54	8.3	53	84	5	263	33	17	16	32	1.93
4963042--4963486	108	4.1	106	82	4	498	33	17	16	32	1.93
4963043--4963487	162	2.8	161	84	1	543	33	18	16	31	1.93
4965173--4965214	20	2.1	20	100	0	84	38	28	4	28	1.77
4970016--4970352	54	6.2	54	89	0	521	32	18	17	31	1.94
4971635--4971675	20	2.0	22	90	9	68	43	12	0	43	1.41
4972755--4972796	22	1.9	22	95	0	75	28	26	21	23	1.99
4975996--4976049	21	2.8	19	81	13	74	27	9	12	50	1.71
4976262--4976318	21	2.6	22	86	8	73	26	29	21	22	1.99
4976689--4976759	34	2.1	33	84	2	88	32	15	28	23	1.95
4978519--4978548	15	1.9	16	93	6	53	40	20	3	36	1.69
4978904--4978993	31	3.0	29	81	10	101	32	14	6	46	1.70
4980688--4980729	14	3.0	14	85	0	57	26	0	21	52	1.47
4981279--4981321	21	2.0	21	86	0	59	25	23	23	27	2.00
4983295--4983410	58	2.0	58	93	0	196	37	15	17	29	1.90
4985800--4985859	24	2.5	24	75	8	68	0	35	0	65	0.93
4985810--4985896	29	3.0	27	79	15	95	0	39	0	60	0.97
4985809--4985916	26	4.1	26	73	23	75	0	41	0	58	0.98
4985845--4985918	26	3.0	26	79	14	86	0	41	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4986097--4986141	6	7.5	6	94	0	81	20	15	15	48	1.80
4988661--4989104	87	5.1	87	97	0	834	31	5	28	34	1.81
4990233--4990272	21	1.9	21	89	0	62	35	5	15	45	1.68
4996948--4997052	15	6.6	15	75	12	102	33	15	21	29	1.94
4996977--4997071	18	5.6	18	73	14	94	28	14	24	32	1.95
4996962--4997070	33	3.3	33	97	0	200	30	15	23	30	1.96
4997862--4998014	54	2.8	54	87	3	211	32	14	20	32	1.93
5001511--5001543	14	2.5	13	90	9	57	0	9	0	90	0.44
5001511--5001543	9	3.8	9	88	4	50	0	9	0	90	0.44
5014748--5014804	6	9.7	6	92	1	71	82	3	0	14	0.80
5016878--5017093	57	3.8	57	89	0	306	40	22	15	21	1.90
5016854--5017097	57	4.3	57	86	0	290	39	21	14	24	1.90
5017440--5017491	20	2.6	20	87	0	68	9	23	21	46	1.80
5017519--5017571	20	2.7	20	81	0	61	20	13	28	37	1.90
5017733--5017789	24	2.6	23	81	13	66	56	0	8	35	1.31
5017785--5017822	15	2.5	16	83	12	53	63	2	0	34	1.09
5018042--5018161	42	2.9	42	93	0	204	15	17	19	47	1.83
5018369--5018493	26	4.6	27	70	23	93	45	0	1	52	1.16
5018659--5018708	20	2.5	20	100	0	100	34	16	10	40	1.81
5018691--5018772	15	5.5	15	86	2	112	35	18	7	39	1.78
5018691--5018772	30	2.8	30	92	5	132	35	18	7	39	1.78
5018691--5018777	45	2.0	44	90	2	138	33	18	6	41	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5021292--5021830	200	2.7	200	83	5	635	33	11	20	35	1.88
5021681--5021706	13	2.0	13	100	0	52	23	7	38	30	1.83
5024660--5024836	84	2.1	84	95	0	318	40	11	18	29	1.86
5025338--5025650	46	6.8	46	92	0	504	41	15	21	21	1.89
5031933--5031992	16	3.6	18	75	24	60	58	8	1	31	1.38
5032202--5032250	25	2.0	25	95	0	89	61	18	2	18	1.45
5032908--5032983	37	2.1	37	97	0	143	40	2	7	48	1.46
5033951--5033998	9	5.3	9	82	9	53	60	0	2	37	1.09
5033936--5034014	27	2.9	26	81	12	79	59	0	2	37	1.11
5034357--5034398	3	14.0	3	100	0	84	66	0	0	33	0.92
5034708--5034742	17	1.9	19	88	11	56	31	0	0	68	0.90
5041840--5041878	15	2.6	15	83	0	51	61	7	12	17	1.54
5042302--5042374	3	24.0	3	94	2	128	64	0	1	34	1.02
5045594--5045678	34	2.5	34	96	0	152	58	0	0	41	0.98
5046624--5046701	30	2.6	30	80	8	88	47	6	1	44	1.36
5046688--5046744	2	30.0	2	75	22	52	50	1	1	45	1.22
5046653--5046744	44	2.1	42	86	4	121	48	4	1	45	1.29
5046856--5047182	69	4.7	68	75	12	236	36	9	21	32	1.86
5046923--5047182	69	3.8	68	78	8	249	36	9	21	33	1.85
5047131--5047238	56	1.9	56	86	1	155	36	10	20	33	1.86
5047198--5047311	37	3.2	36	65	12	90	35	14	18	31	1.90
5060997--5061058	32	2.0	32	87	6	92	50	9	20	19	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5065404--5065472	23	3.0	23	84	0	102	34	26	23	15	1.95
5067344--5067368	11	2.3	11	100	0	50	16	20	8	56	1.65
5067729--5068011	131	2.2	131	85	0	368	40	14	10	33	1.81
5068916--5069005	23	3.9	23	79	0	99	37	23	18	20	1.94
5075875--5075922	24	2.0	24	84	8	62	33	25	20	20	1.97
5075954--5076021	23	3.0	23	75	0	64	35	23	23	17	1.95
5082030--5082414	55	7.1	55	86	4	505	30	16	17	35	1.92
5082030--5082479	110	4.1	109	83	3	530	30	16	17	34	1.92
5083284--5083312	2	14.5	2	100	0	58	48	0	0	51	1.00
5088200--5088233	2	17.0	2	100	0	68	50	0	0	50	1.00
5092573--5092624	19	2.7	19	100	0	104	26	17	34	21	1.95
5093068--5093102	2	17.5	2	100	0	70	48	0	0	51	1.00
5097719--5097743	6	4.2	6	100	0	50	48	0	20	32	1.50
5099592--5099623	2	16.0	2	100	0	64	50	0	0	50	1.00
5099874--5100236	157	2.3	158	85	1	469	49	7	17	26	1.72
5101624--5101665	20	2.2	20	83	8	52	23	21	23	30	1.99
5104272--5104338	23	2.9	23	81	0	80	25	22	20	31	1.98
5117180--5117210	14	2.2	14	94	0	53	29	22	9	38	1.86
5117667--5117729	3	20.0	3	83	6	72	39	1	0	58	1.07
5118983--5119022	3	13.3	3	100	0	80	32	0	0	67	0.91
5119051--5119075	10	2.5	10	100	0	50	16	0	0	84	0.63
5125130--5125183	17	3.1	17	76	12	65	74	1	20	3	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5125100--5125175	24	3.1	24	76	10	64	76	1	19	2	0.98
5127527--5127589	31	2.0	31	96	0	117	33	20	15	30	1.94
5129775--5129829	22	2.5	22	93	0	101	34	10	14	40	1.81
5130342--5130669	167	2.0	165	91	2	532	36	13	12	37	1.83
5130712--5131280	73	7.8	73	96	0	1021	30	18	12	38	1.88
5132952--5133014	27	2.3	28	83	2	83	23	1	4	69	1.16
5132975--5133031	3	19.7	3	81	13	66	28	0	3	68	1.06
5136946--5136990	23	2.0	23	90	0	72	24	26	26	22	2.00
5136958--5137272	149	2.1	149	96	1	578	34	21	17	27	1.95
5141883--5141927	23	2.0	23	90	0	72	24	26	26	22	2.00

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   79   80   
          81   82   83   84   85   86   87   88   89