genome.fa.s1129.2.7.7.80.10.50.1000.24.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  24  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)
5141895--5142209	149	2.1	149	96	1	578	34	21	16	27	1.95
5147732--5147796	31	2.1	31	82	5	78	24	9	12	53	1.67
5147943--5148013	31	2.3	31	90	0	106	22	12	16	47	1.80
5149181--5149218	15	2.5	15	83	12	51	42	0	0	57	0.98
5149178--5149241	26	2.5	25	75	9	67	51	0	0	48	1.00
5149927--5150272	183	1.9	184	95	0	622	42	2	8	47	1.46
5154683--5154981	143	2.1	144	82	9	373	37	10	17	34	1.84
5159002--5159074	11	6.8	11	72	13	55	53	10	0	35	1.36
5159002--5159083	41	2.0	41	97	0	155	54	9	0	35	1.33
5160020--5160258	45	5.3	45	83	6	252	41	20	18	19	1.90
5160005--5160256	135	1.9	135	85	5	348	39	20	17	22	1.92
5160225--5160621	38	10.2	37	79	7	362	40	16	17	25	1.91
5160225--5160621	76	5.1	76	80	4	400	40	16	17	25	1.91
5160231--5160615	194	2.0	194	86	2	531	39	17	17	25	1.91
5167375--5167558	95	1.9	96	83	7	241	33	15	21	29	1.94
5167543--5167594	20	2.5	20	82	14	54	34	13	21	30	1.92
5168005--5168498	45	11.0	45	89	2	688	40	9	18	31	1.82
5168969--5169264	38	7.6	38	80	9	328	39	16	17	26	1.91
5171471--5171542	2	36.0	2	100	0	144	50	0	0	50	1.00
5185865--5185913	17	2.9	17	78	9	55	61	2	16	20	1.44
5186036--5186078	18	2.4	18	84	11	61	6	18	2	72	1.19
5194292--5194342	16	3.2	16	75	25	54	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5198176--5198211	2	18.0	2	100	0	72	50	0	0	50	1.00
5198480--5198518	2	19.5	2	100	0	78	48	0	0	51	1.00
5205983--5206016	6	5.7	6	89	10	52	79	0	2	17	0.86
5206202--5206841	133	4.8	134	84	2	736	31	19	19	30	1.96
5206238--5206755	267	1.9	267	85	1	707	30	19	20	29	1.97
5206276--5206835	267	2.1	267	83	3	696	30	19	19	30	1.97
5206885--5207298	38	10.8	38	79	3	384	37	17	21	23	1.94
5206884--5207296	76	5.4	76	81	2	463	37	17	21	23	1.94
5206885--5207264	150	2.5	151	84	3	460	37	16	21	23	1.93
5219197--5219232	10	3.6	10	100	0	72	19	27	0	52	1.46
5221010--5221252	122	2.0	122	95	1	434	30	26	14	27	1.95
5221834--5221886	21	2.6	20	81	3	61	30	26	16	26	1.97
5222698--5222767	34	2.1	32	89	5	104	21	32	14	31	1.93
5223050--5223091	21	2.0	21	95	0	75	26	28	21	23	1.99
5223206--5223262	15	3.5	15	72	25	53	19	24	36	19	1.94
5223204--5223289	34	2.5	35	94	1	156	18	25	36	19	1.95
5223221--5223291	20	3.9	19	70	26	64	18	26	33	21	1.96
5225243--5225283	3	14.0	3	87	5	57	0	29	2	68	1.03
5226625--5226666	21	2.0	21	100	0	84	28	28	19	23	1.98
5226780--5226836	15	3.5	15	72	25	53	19	24	36	19	1.94
5226779--5226870	19	5.3	19	70	24	69	17	26	36	19	1.94
5226779--5226862	34	2.5	34	94	3	143	19	26	34	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5226847--5226889	22	2.0	22	95	0	77	11	27	39	20	1.88
5229267--5229322	21	2.7	21	82	0	67	33	25	17	23	1.96
5229313--5229389	30	2.6	29	93	2	127	27	22	23	27	1.99
5229372--5229425	21	2.6	21	82	2	74	33	25	18	22	1.97
5231489--5231528	20	2.0	21	85	5	55	25	17	10	47	1.78
5236323--5236378	20	2.6	20	80	11	58	28	21	26	23	1.99
5236912--5236982	18	3.8	18	81	7	97	18	22	32	26	1.97
5236908--5236980	38	1.9	38	94	0	128	19	23	30	27	1.98
5238808--5238840	12	2.8	12	90	0	57	42	0	48	9	1.35
5243163--5243218	20	2.6	20	80	11	58	28	21	26	23	1.99
5243748--5243801	18	2.8	20	78	15	69	18	20	29	31	1.96
5245847--5245904	30	1.9	30	82	0	71	39	6	1	51	1.39
5256086--5256146	32	1.9	32	90	6	97	57	9	14	18	1.64
5256517--5256547	15	2.1	15	93	0	53	38	12	22	25	1.90
5256822--5256882	18	3.4	18	86	6	88	39	14	36	9	1.80
5264236--5264289	24	2.2	24	100	0	108	37	11	9	42	1.73
5265174--5265231	22	2.6	22	86	10	91	67	3	0	29	1.07
5265132--5265215	33	2.5	34	76	5	91	63	3	0	33	1.12
5265174--5265243	22	3.2	20	75	20	61	65	2	1	30	1.15
5271749--5271787	20	1.9	21	89	5	62	28	17	10	43	1.82
5271736--5271796	20	2.9	21	75	7	61	26	18	11	44	1.83
5272499--5272546	21	2.3	21	92	0	78	35	16	16	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5284006--5284255	124	2.0	124	96	0	455	27	19	23	29	1.98
5286284--5286313	13	2.3	13	94	0	51	13	26	0	60	1.34
5294474--5295058	292	2.0	291	99	0	1152	28	26	17	26	1.98
5301738--5301768	16	1.9	16	93	0	53	32	19	29	19	1.96
5302054--5302097	22	2.0	22	86	8	63	2	25	4	68	1.20
5305279--5305510	85	2.7	85	78	7	195	53	6	17	21	1.67
5305279--5305510	44	5.4	44	76	9	192	53	6	17	21	1.67
5305319--5305550	44	5.5	43	74	12	178	55	7	13	23	1.63
5305363--5305550	85	2.2	84	80	10	215	57	7	12	22	1.60
5311443--5311540	47	2.1	46	84	7	126	24	19	25	30	1.98
5315731--5315801	27	2.6	27	79	0	79	30	19	35	14	1.91
5317495--5317528	9	3.9	9	84	7	52	61	2	0	35	1.11
5317480--5317529	17	3.0	17	91	2	75	60	4	2	34	1.27
5319293--5319429	60	2.3	60	94	0	247	31	10	19	37	1.87
5320508--5321122	312	2.0	312	90	2	986	36	14	10	38	1.81
5321089--5321310	111	2.0	111	100	0	444	35	20	7	36	1.80
5335238--5335293	23	2.8	18	74	23	58	12	32	23	32	1.92
5337091--5337157	10	6.0	10	71	21	53	58	19	10	11	1.62
5337091--5337174	23	3.6	23	80	3	105	59	17	9	13	1.60
5338825--5338867	22	2.0	22	86	9	61	30	13	25	30	1.94
5345498--5345569	23	3.3	23	80	14	73	15	18	16	50	1.79
5346332--5346376	22	2.1	22	84	12	58	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)
5347416--5347449	7	4.9	7	100	0	68	29	14	0	55	1.40
5350180--5350207	14	2.0	14	100	0	56	14	35	21	28	1.92
5357042--5357078	14	2.6	14	100	0	74	43	21	8	27	1.80
5365160--5365473	156	2.0	158	98	1	614	31	14	21	32	1.93
5378472--5378504	16	2.1	16	100	0	66	54	0	39	6	1.25
5383346--5383581	102	2.3	102	78	1	258	28	15	22	33	1.94
5384641--5384669	15	1.9	15	100	0	58	41	34	17	6	1.76
5385418--5385444	14	1.9	14	100	0	54	14	11	14	59	1.62
5386525--5386565	16	2.7	16	88	7	59	12	9	17	60	1.57
5389216--5389240	11	2.3	11	100	0	50	0	8	0	92	0.40
5389266--5389341	23	3.3	23	86	0	116	11	17	18	52	1.74
5389861--5389963	53	1.9	53	84	3	136	50	12	10	26	1.73
5391308--5391346	18	2.2	18	85	0	51	33	0	2	64	1.08
5393350--5393446	4	26.0	4	67	14	55	48	0	1	50	1.07
5393350--5393446	6	17.3	6	76	12	55	48	0	1	50	1.07
5398241--5398292	28	2.0	25	85	14	70	28	11	5	53	1.60
5400870--5400904	14	2.5	14	100	0	70	5	8	0	85	0.73
5406940--5407060	9	12.2	10	73	21	71	77	0	18	3	0.95
5406965--5407057	8	11.2	8	78	16	66	79	1	17	2	0.89
5406940--5407069	41	3.1	42	76	17	103	76	1	18	3	0.99
5407000--5407069	24	2.9	24	81	8	81	78	2	17	1	0.94
5406949--5407057	30	3.7	30	70	12	91	77	0	18	2	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5408056--5408099	2	23.0	2	81	9	56	43	0	0	56	0.99
5408087--5408186	40	2.7	35	80	12	92	45	3	8	44	1.48
5408124--5408401	68	3.9	67	76	17	199	44	3	5	46	1.43
5408083--5408254	68	2.4	71	83	12	201	44	2	7	45	1.44
5408193--5408569	39	10.1	39	71	21	210	46	4	5	43	1.46
5408192--5408354	37	4.1	39	74	15	120	46	4	3	46	1.38
5408192--5408543	67	4.8	78	75	18	296	46	4	5	44	1.45
5408124--5408543	147	2.9	147	79	13	404	45	4	5	44	1.47
5408426--5408539	34	3.6	31	77	13	108	46	5	5	42	1.48
5408426--5408539	33	3.6	32	79	11	119	46	5	5	42	1.48

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