genome.fa.s1129.2.7.7.80.10.50.1000.27.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: 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  27  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)
5930961--5931271	131	2.4	131	78	5	333	27	17	29	25	1.97
5931319--5931563	66	3.7	66	79	8	248	40	13	18	28	1.88
5931382--5931488	32	3.1	37	66	19	93	39	13	18	28	1.88
5931319--5931563	133	1.8	134	80	6	300	40	13	18	28	1.88
5931701--5931792	34	2.6	36	79	8	98	38	11	17	32	1.86
5933571--5933615	3	15.3	3	86	13	67	66	0	0	33	0.92
5933568--5933615	23	2.1	23	92	7	80	66	0	0	33	0.92
5944719--5944762	5	8.8	5	100	0	88	40	0	0	59	0.98
5950465--5950512	20	2.5	20	86	10	64	31	16	4	47	1.65
5951865--5951933	23	3.0	23	97	0	129	33	43	5	17	1.73
5953594--5953657	6	10.0	6	81	8	56	56	0	21	21	1.43
5953595--5953657	13	4.8	13	81	13	76	55	0	22	22	1.44
5953595--5953658	25	2.5	25	82	10	76	54	0	23	21	1.45
5953593--5953657	7	10.0	7	77	15	59	55	0	21	23	1.44
5956613--5956642	15	2.1	15	93	6	53	13	10	0	76	1.01
5957468--5957544	31	2.5	31	89	0	118	22	12	15	49	1.78
5963427--5963475	22	2.2	23	79	17	59	75	4	10	10	1.17
5970351--5970423	31	2.4	31	85	0	110	53	17	9	19	1.71
5971239--5971273	16	2.2	16	89	0	52	40	2	0	57	1.14
5974097--5974137	21	2.0	21	85	9	57	46	4	9	39	1.58
5975102--5975227	2	63.0	2	95	0	225	47	0	2	50	1.14
5976917--5976947	16	1.9	16	100	0	62	22	25	25	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5979139--5979171	2	16.5	2	100	0	66	51	0	0	48	1.00
5979246--5979305	23	2.7	23	84	5	79	20	18	28	33	1.96
5984248--5984280	13	2.4	14	95	5	59	24	9	0	66	1.20
5985090--5985115	3	8.7	3	100	0	52	65	0	34	0	0.93
5988109--5988274	85	2.0	85	84	7	221	30	17	20	31	1.96
5988246--5988310	13	5.0	13	90	0	94	35	20	20	24	1.96
5988923--5988966	21	2.1	21	100	0	88	65	0	6	27	1.17
5989703--5989732	11	2.7	11	94	0	51	36	10	0	53	1.35
5998900--5998947	2	24.0	2	100	0	96	50	0	0	50	1.00
6006608--6006969	184	2.0	184	97	0	688	46	9	3	41	1.53
6024236--6024293	12	4.1	14	77	18	57	77	0	13	8	0.98
6024275--6024314	20	2.0	21	90	5	64	82	0	5	12	0.82
6024231--6024320	36	2.4	38	80	10	105	77	0	12	10	0.98
6025492--6025613	37	3.3	37	87	3	167	41	15	20	22	1.89
6025614--6026400	55	14.3	55	83	3	850	31	19	20	28	1.97
6026559--6026601	20	2.2	20	91	0	68	32	11	20	34	1.89
6032375--6032417	20	2.2	20	83	8	52	32	11	20	34	1.89
6033462--6033518	23	2.5	23	85	5	80	47	0	7	45	1.30
6043045--6043080	15	2.5	14	86	8	54	33	25	27	13	1.94
6043053--6043087	15	2.3	15	100	0	70	25	25	34	14	1.94
6043058--6043112	24	2.2	25	90	3	85	27	23	34	14	1.94
6043338--6043385	14	3.7	14	73	21	59	27	22	35	14	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6043316--6043385	24	3.0	24	89	4	99	25	22	35	15	1.94
6043329--6043393	24	2.7	24	92	0	103	27	21	33	16	1.95
6047753--6047777	10	2.5	10	100	0	50	8	0	0	92	0.40
6061230--6061254	2	12.5	2	100	0	50	48	0	0	52	1.00
6063582--6063637	20	2.8	20	94	0	94	44	26	0	28	1.54
6069014--6069100	22	4.0	21	73	18	63	39	11	11	37	1.78
6069014--6069100	44	2.0	42	80	14	97	39	11	11	37	1.78
6069038--6069109	22	3.3	22	75	7	67	41	11	11	36	1.76
6069243--6069308	20	3.3	20	89	2	89	34	4	22	37	1.75
6069651--6069689	15	2.6	15	95	0	69	23	12	15	48	1.79
6069748--6069810	33	1.9	33	83	0	81	31	15	26	25	1.96
6071397--6071858	59	7.9	58	79	7	398	30	23	11	34	1.90
6072275--6072347	20	3.6	20	85	3	92	26	32	16	24	1.96
6075185--6075266	22	3.7	21	75	14	58	39	13	12	35	1.82
6075209--6075272	24	2.8	23	80	4	76	37	12	10	39	1.78
6075246--6075299	22	2.5	22	85	11	76	42	14	7	35	1.74
6078747--6078791	21	2.2	21	80	15	58	35	11	22	31	1.89
6078754--6078793	21	2.0	21	95	5	73	35	12	20	32	1.90
6082552--6082917	131	2.8	131	84	3	450	33	10	16	39	1.82
6084833--6084866	11	3.1	11	84	16	52	29	20	8	41	1.82
6098700--6098738	21	2.0	20	90	10	62	28	17	17	35	1.94
6118386--6118418	2	17.0	2	93	6	59	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6120492--6120574	7	12.1	7	85	10	118	81	1	14	2	0.85
6120492--6120588	21	4.8	20	80	12	99	80	1	13	5	0.93
6121750--6122317	135	4.2	135	85	1	732	32	22	14	31	1.93
6121750--6122317	268	2.1	267	85	2	746	32	22	14	31	1.93
6122257--6122358	41	2.5	41	96	0	186	32	25	19	22	1.97
6124621--6124983	132	2.8	130	90	0	546	32	11	16	39	1.85
6126165--6126213	15	3.3	15	78	16	57	20	0	0	79	0.73
6135158--6135191	17	1.9	17	88	5	50	88	8	0	2	0.62
6135982--6136626	98	6.6	98	81	7	757	34	24	20	20	1.96
6136080--6136618	189	2.9	189	94	1	929	34	24	21	20	1.97
6135982--6136626	287	2.2	285	83	7	811	34	24	20	20	1.96
6137959--6138011	22	2.3	23	78	18	58	28	5	0	66	1.15
6138568--6138673	50	2.1	50	98	0	203	30	29	13	27	1.94
6139422--6139461	21	2.0	21	90	5	64	35	12	17	35	1.88
6141021--6141049	2	14.5	2	100	0	58	51	0	0	48	1.00
6142738--6142774	18	2.1	18	85	14	51	43	10	13	32	1.79
6144488--6144555	24	2.8	24	84	0	82	19	13	16	51	1.76
6149281--6149365	24	3.5	24	80	0	89	21	11	17	49	1.78
6149278--6149372	24	4.0	24	78	0	82	21	11	17	49	1.78
6150505--6150550	21	2.2	20	84	3	56	45	8	6	39	1.61
6152529--6152697	42	4.0	43	86	4	204	28	9	40	21	1.85
6152565--6152637	21	3.5	21	64	7	58	30	10	39	19	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6153638--6153706	29	2.4	29	85	0	84	36	5	21	36	1.78
6153723--6153772	24	2.0	25	85	11	68	18	6	30	46	1.73
6156315--6156423	48	2.3	48	78	0	128	20	15	16	47	1.82
6156315--6156423	24	4.5	24	75	4	103	20	15	16	47	1.82
6158419--6158522	29	3.6	29	84	1	111	27	6	24	41	1.80
6158498--6158547	25	2.0	24	85	11	66	18	8	30	44	1.78
6161102--6161208	24	4.5	24	72	0	97	22	13	16	47	1.81
6166630--6166769	64	2.2	64	83	2	174	27	18	27	26	1.98
6167088--6167902	210	3.8	210	92	2	1281	50	8	12	28	1.69
6167925--6168013	2	43.0	2	72	14	65	47	2	3	47	1.31
6167942--6168012	22	3.3	22	81	11	94	46	2	4	46	1.37
6167928--6168010	42	1.9	44	92	4	143	46	2	3	46	1.33
6167925--6168021	11	9.3	11	66	17	55	46	2	4	47	1.33
6167954--6168021	24	3.2	21	70	25	54	42	1	5	50	1.35
6168107--6168225	11	10.6	11	66	16	66	47	1	2	48	1.25
6167942--6168154	20	10.2	20	68	17	103	46	6	5	42	1.52
6168083--6168181	42	2.3	43	81	5	103	47	5	5	42	1.47
6168150--6168237	9	10.6	9	65	23	50	44	0	3	52	1.18
6168246--6168342	7	13.9	7	80	0	113	21	0	35	43	1.53
6168382--6168474	33	2.9	32	84	6	118	41	6	4	47	1.49
6168390--6168505	33	3.6	32	77	15	107	45	6	3	44	1.45
6168459--6168502	2	22.0	2	90	0	70	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6168459--6168502	12	3.7	12	96	0	79	54	0	0	45	0.99
6168459--6168987	18	28.4	18	68	18	130	44	5	5	44	1.50
6168433--6168591	42	3.7	42	74	16	130	45	6	7	40	1.58
6168588--6168992	2	193.0	2	68	18	184	43	5	4	45	1.49
6168562--6168638	33	2.4	32	83	10	95	46	6	6	40	1.55
6168750--6168818	33	2.2	32	84	10	88	46	8	7	37	1.63
6169048--6169152	9	11.7	9	70	18	76	50	6	4	38	1.50
6169036--6169312	18	15.6	18	74	13	236	46	7	5	40	1.55
6169061--6169315	51	4.8	51	83	8	305	46	7	5	40	1.54
6168776--6169210	18	22.3	20	69	19	135	46	7	4	41	1.52

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