genome.fa.s1129.2.7.7.80.10.50.1000.29.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  29  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)
6406691--6406735	20	2.3	19	84	3	54	64	2	0	33	1.06
6407200--6407228	15	1.9	15	100	0	58	79	6	13	0	0.93
6408061--6408099	19	2.1	19	90	9	62	28	0	2	69	1.02
6408126--6408167	21	2.0	20	86	4	57	38	2	2	57	1.25
6413461--6413527	23	2.8	24	84	4	91	25	16	19	38	1.92
6418039--6418105	23	2.8	24	84	4	91	25	16	19	38	1.92
6420726--6420989	137	1.9	140	86	3	383	38	7	7	46	1.62
6426303--6426334	13	2.5	13	100	0	64	6	25	15	53	1.65
6428266--6428317	22	2.4	22	96	0	95	36	30	26	5	1.80
6429564--6429985	38	10.8	39	76	15	259	44	6	3	45	1.46
6429527--6429983	76	5.8	75	73	18	287	44	6	3	45	1.46
6429674--6429850	91	2.0	90	87	7	261	44	5	3	46	1.44
6429712--6429816	55	1.9	56	88	5	162	45	5	3	44	1.45
6429768--6429951	35	5.1	35	80	12	187	46	7	3	42	1.50
6429773--6429939	71	2.3	73	84	8	218	44	7	4	43	1.52
6429825--6429987	37	4.2	39	78	10	126	45	8	3	42	1.52
6431986--6432086	49	2.1	48	82	14	118	47	3	1	46	1.32
6432057--6432160	35	3.0	35	97	0	199	43	2	2	50	1.31
6432143--6432168	11	2.4	11	100	0	52	38	0	7	53	1.30
6432186--6432275	34	2.6	36	89	8	141	44	5	7	42	1.56
6434184--6434388	13	16.6	12	62	16	53	44	4	2	48	1.35
6434192--6434547	36	9.7	36	83	9	375	44	6	2	46	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6434192--6434580	38	10.5	38	80	12	382	44	6	2	46	1.43
6434194--6434529	70	4.6	66	77	14	267	44	6	2	46	1.44
6434561--6434591	2	16.0	2	93	6	55	51	0	0	48	1.00
6436565--6436793	38	6.2	36	89	4	327	43	4	3	48	1.43
6439677--6439757	34	2.4	34	91	6	128	45	2	6	45	1.41
6439744--6439825	2	42.0	2	92	4	141	48	0	0	51	1.00
6441717--6441856	36	3.8	37	91	4	196	46	4	1	47	1.31
6441751--6441843	11	7.8	11	67	15	51	46	4	2	47	1.34
6442130--6442382	20	12.4	21	80	9	265	37	26	18	18	1.93
6442130--6442382	41	6.2	41	90	4	386	37	26	18	18	1.93
6442107--6442365	121	2.1	123	90	2	414	37	25	18	18	1.94
6442943--6443001	21	2.9	21	80	7	68	52	18	18	10	1.73
6443038--6443152	33	3.5	33	85	1	158	12	21	20	45	1.84
6444856--6445235	94	4.1	94	96	1	674	21	12	19	47	1.81
6445341--6445411	14	4.7	14	77	16	70	45	21	23	9	1.82
6445323--6445398	33	2.3	33	90	0	116	44	21	25	9	1.81
6445423--6445552	19	7.7	18	67	23	68	10	22	20	46	1.81
6445450--6445537	14	5.6	14	66	23	50	11	23	17	47	1.79
6445426--6445552	33	3.8	33	87	0	173	11	22	19	47	1.80
6445505--6445540	14	2.8	13	88	12	56	8	22	19	50	1.74
6446029--6446095	21	3.2	21	66	6	55	23	35	20	19	1.95
6445977--6446095	42	2.8	42	81	5	107	22	36	18	22	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6446137--6446519	190	2.0	190	97	0	730	26	21	26	25	1.99
6447639--6447674	14	2.6	14	95	0	63	33	0	22	44	1.53
6447781--6447847	19	3.8	19	75	18	72	44	22	22	10	1.83
6447922--6448063	20	7.8	19	70	18	88	16	21	21	40	1.91
6447981--6448008	14	2.0	14	100	0	56	14	21	21	42	1.88
6447854--6448063	106	2.0	106	88	1	314	14	22	20	41	1.89
6447856--6448056	73	2.9	66	82	10	231	14	22	20	41	1.89
6447856--6448036	33	5.3	33	83	9	236	13	23	20	42	1.88
6450563--6450616	24	2.2	24	93	0	90	40	20	18	20	1.91
6450563--6450630	24	2.8	24	84	0	64	38	20	17	23	1.93
6450742--6450775	12	2.8	12	90	0	50	14	0	29	55	1.40
6451438--6451770	20	16.5	20	76	10	257	18	18	22	40	1.91
6451438--6451709	40	6.7	38	86	6	303	19	18	22	40	1.91
6451439--6451770	121	2.7	120	83	6	404	18	18	22	40	1.91
6451438--6451770	40	8.2	40	80	8	291	18	18	22	40	1.91
6451782--6451831	19	2.5	20	83	6	66	16	14	24	46	1.83
6462323--6462369	24	2.0	24	95	0	85	29	19	14	36	1.92
6462928--6462986	7	8.0	7	74	22	50	55	0	0	44	0.99
6462937--6462989	24	2.1	26	86	6	74	54	0	0	45	0.99
6464301--6464363	26	2.5	26	82	5	76	22	12	26	38	1.90
6467710--6467771	27	2.3	27	94	0	115	17	17	40	24	1.91
6468924--6468991	28	2.3	29	80	9	68	57	8	14	19	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6469489--6469514	2	13.0	2	100	0	52	50	0	0	50	1.00
6470440--6470500	3	20.7	3	90	9	99	65	0	0	34	0.93
6470842--6471074	40	5.6	40	75	10	143	27	18	29	24	1.98
6470917--6471034	46	2.6	45	88	6	161	27	18	27	26	1.98
6471406--6471465	31	2.0	30	93	3	102	43	13	13	30	1.82
6471682--6471753	27	2.6	27	85	12	85	41	12	12	33	1.80
6472138--6472211	36	2.1	34	88	9	114	44	9	17	28	1.80
6472566--6472605	16	2.5	16	87	0	53	25	2	27	45	1.66
6472725--6472766	14	2.9	14	89	3	57	33	28	9	28	1.88
6472736--6472772	14	2.6	14	91	0	56	35	27	13	24	1.93
6478398--6478477	29	2.7	30	80	7	83	63	8	10	17	1.49
6479932--6479971	3	13.7	3	85	15	57	65	0	0	35	0.93
6479932--6479975	12	3.8	12	87	3	63	63	0	0	36	0.95
6479943--6479981	18	2.2	18	95	0	69	64	0	0	35	0.94
6480264--6480413	39	3.7	40	77	9	153	26	18	30	24	1.98
6480264--6480502	43	5.7	43	74	11	131	27	18	28	25	1.98
6481147--6481221	28	2.7	29	87	10	102	45	13	9	32	1.75
6481079--6481272	94	2.1	95	86	6	270	43	13	11	31	1.79
6481610--6481683	36	2.1	34	88	9	114	43	9	17	29	1.81
6482208--6482244	14	2.6	14	91	0	56	35	27	13	24	1.93
6487880--6487944	29	2.2	29	86	2	85	60	10	12	16	1.59
6487880--6487959	29	2.7	28	79	11	79	63	8	11	16	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6487902--6487958	29	2.0	29	89	6	89	61	7	12	19	1.53
6497561--6497613	27	2.0	27	92	7	90	54	15	3	26	1.57
6498491--6498516	9	2.9	9	100	0	52	7	0	0	92	0.39
6498900--6499308	55	7.5	54	90	4	578	31	25	16	26	1.97
6500676--6500885	7	28.9	7	72	15	106	7	19	0	73	1.06
6500670--6500885	22	9.5	21	67	16	78	7	19	0	73	1.07
6500728--6500771	13	3.3	13	81	6	52	6	18	0	75	1.02
6500679--6500782	23	4.7	22	78	12	79	4	21	0	74	1.01
6500703--6500839	8	18.4	8	74	18	77	8	16	0	75	1.04
6500822--6500865	20	2.2	20	83	0	52	6	20	0	72	1.07
6512309--6512361	27	2.0	27	92	7	90	54	15	3	26	1.57
6512581--6512623	18	2.3	18	88	8	59	53	20	0	25	1.46
6516087--6516226	70	2.0	70	95	0	253	27	7	15	50	1.71
6519473--6519590	11	10.5	11	83	5	137	24	23	20	31	1.98
6519482--6519537	12	4.8	12	77	4	69	19	19	23	37	1.94
6519447--6519590	22	6.3	22	81	7	137	25	22	21	29	1.99
6519813--6519869	16	3.6	16	100	0	114	21	26	17	35	1.95
6521022--6521094	7	10.4	7	84	0	74	20	1	36	41	1.61
6525199--6525240	23	1.9	21	85	9	57	45	2	11	40	1.54
6531917--6531949	6	5.7	6	85	7	50	18	0	0	81	0.68
6540291--6540334	20	2.2	20	87	0	61	34	0	22	43	1.54
6544145--6544185	19	2.4	16	88	12	55	65	0	17	17	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6544145--6544185	6	7.0	6	86	8	50	65	0	17	17	1.27
6546300--6546337	20	1.9	20	88	0	58	18	34	21	26	1.96
6546265--6546335	36	2.0	35	86	8	99	22	32	21	23	1.98
6546801--6546864	33	1.9	33	87	0	92	31	17	26	25	1.97
6550203--6550321	8	13.9	8	72	10	67	41	0	56	1	1.15
6550202--6550310	28	3.9	28	78	3	103	41	0	56	0	1.11
6550203--6550400	10	20.0	10	70	6	89	41	1	53	3	1.25
6550203--6550400	12	16.7	12	71	6	89	41	1	53	3	1.25
6550190--6550399	18	11.3	18	70	12	104	41	0	54	3	1.23
6550309--6550346	16	2.4	16	82	8	51	34	0	57	7	1.28

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