genome.fa.s1129.2.7.7.80.10.50.1000.74.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  74  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)
17670316--17670340	11	2.3	11	100	0	50	32	16	0	52	1.44
17671172--17671217	24	1.9	24	90	0	74	43	6	15	34	1.72
17673181--17673229	24	2.0	24	88	0	71	40	8	14	36	1.75
17674301--17674325	11	2.3	11	100	0	50	32	16	0	52	1.44
17677552--17677578	11	2.5	11	100	0	54	55	7	7	29	1.55
17678250--17678293	20	2.2	20	88	4	63	40	0	25	34	1.56
17679497--17679540	22	2.0	22	86	4	63	36	4	13	45	1.64
17680254--17680295	21	2.0	20	82	13	50	45	7	9	38	1.64
17681281--17681344	21	3.0	21	90	0	101	29	25	17	28	1.97
17698849--17698905	30	1.9	30	85	0	78	45	7	14	33	1.71
17698841--17698914	30	2.5	29	78	6	76	43	6	14	35	1.72
17699348--17699414	22	3.0	22	65	8	64	41	1	7	49	1.40
17699328--17699450	44	2.8	44	90	2	167	40	1	9	47	1.46
17699357--17699429	22	3.3	22	67	7	67	38	1	6	53	1.36
17699378--17699450	22	3.3	21	66	7	56	36	2	10	49	1.53
17708256--17708289	2	17.0	2	87	0	50	44	0	5	50	1.26
17710183--17710231	21	2.4	21	83	10	57	40	18	2	38	1.62
17721339--17721363	13	1.9	13	100	0	50	48	0	4	48	1.20
17726054--17726092	20	2.0	20	89	0	60	38	25	0	35	1.56
17730799--17730879	41	2.0	41	88	9	121	28	28	20	22	1.99
17735968--17736012	21	2.1	21	83	4	54	42	11	8	37	1.72
17751398--17751452	25	2.2	25	100	0	110	43	10	3	41	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17751858--17751944	28	3.2	28	66	18	85	41	6	6	44	1.58
17751837--17751942	52	2.0	52	100	0	212	41	7	5	45	1.56
17756958--17757133	89	2.0	89	90	2	282	44	6	10	38	1.65
17773407--17773456	26	1.9	26	87	0	73	28	20	24	28	1.99
17775265--17775338	24	3.2	24	63	24	59	32	21	9	36	1.86
17775245--17775352	45	2.4	45	92	0	171	33	23	9	34	1.86
17775442--17775570	59	2.2	59	81	0	150	28	26	17	27	1.97
17780912--17780958	18	2.5	20	86	6	62	36	17	19	27	1.93
17786946--17786989	23	2.0	23	81	4	54	18	40	11	29	1.85
17790001--17790089	24	3.7	24	87	3	117	25	17	20	35	1.95
17793542--17793634	32	3.0	31	84	3	123	34	26	13	24	1.93
17794533--17794615	32	2.6	31	77	5	103	31	8	1	59	1.35
17795292--17795345	16	3.4	16	78	0	72	25	22	11	40	1.87
17795289--17795370	32	2.6	31	83	9	103	26	23	12	37	1.90
17795362--17795414	16	3.2	16	81	2	52	30	16	5	47	1.70
17795514--17795572	18	3.1	18	71	20	57	52	1	3	42	1.28
17795516--17795575	21	3.0	21	75	15	65	50	1	3	45	1.28
17795572--17795728	22	7.2	21	73	12	81	35	8	1	54	1.40
17795577--17795728	35	4.2	36	76	15	161	34	9	1	54	1.41
17795693--17795751	22	2.6	22	86	2	73	33	13	0	52	1.41
17796782--17797040	134	1.9	135	85	3	362	31	19	14	34	1.92
17798195--17798241	25	1.9	25	82	4	60	40	4	8	46	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17803800--17803829	13	2.3	13	94	0	51	20	16	23	40	1.91
17804036--17804592	304	1.8	304	92	0	954	31	18	17	32	1.94
17805182--17805231	24	2.1	24	84	0	64	40	22	10	28	1.86
17809486--17809554	14	4.9	14	87	0	102	34	21	21	21	1.97
17809487--17809554	28	2.4	28	100	0	136	33	22	22	22	1.97
17811268--17811308	8	5.4	8	77	11	50	39	0	12	48	1.41
17810767--17811266	6	82.8	6	98	1	955	33	0	33	33	1.62
17811251--17811303	26	2.0	26	88	0	79	37	5	11	45	1.64
17811257--17811308	12	4.2	12	83	9	59	38	3	11	46	1.59
17811337--17811386	25	1.9	25	84	8	64	44	8	2	46	1.44
17811352--17811410	7	8.7	7	82	14	61	37	11	0	50	1.39
17811495--17811540	24	1.9	24	86	8	67	50	0	13	36	1.41
17812402--17812435	2	17.5	2	93	6	61	50	0	0	50	1.00
17812592--17812855	14	17.0	16	72	18	91	49	3	5	41	1.43
17812601--17812654	2	27.0	2	92	7	92	50	1	0	48	1.11
17812603--17812852	40	6.0	42	68	19	130	49	3	5	42	1.42
17812771--17812846	24	3.0	25	81	14	86	56	1	5	36	1.30
17812771--17812852	18	4.6	18	76	15	82	56	1	6	36	1.32
17818564--17818603	13	3.3	13	76	20	50	17	47	22	12	1.81
17818605--17818670	29	2.2	30	89	2	98	31	0	21	46	1.51
17819491--17819656	42	4.0	42	93	0	287	19	24	24	32	1.97
17819492--17819694	84	2.4	85	90	3	302	18	24	23	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17820202--17820450	29	8.7	29	75	10	174	34	3	13	48	1.60
17820243--17820427	28	6.6	28	71	8	99	37	4	10	47	1.59
17820235--17820432	85	2.3	85	86	3	274	35	4	11	47	1.60
17820202--17820459	57	4.5	55	71	12	162	35	3	13	47	1.61
17820390--17820466	29	2.6	31	75	19	83	38	2	15	42	1.61
17828243--17828488	42	5.8	42	86	3	334	18	23	23	34	1.96
17828243--17828488	84	2.9	84	90	3	370	18	23	23	34	1.96
17829029--17829213	85	2.2	85	92	1	300	37	3	10	49	1.53
17828996--17829448	28	16.2	27	73	14	248	36	2	13	47	1.57
17829114--17829316	103	2.0	105	90	3	322	36	2	11	48	1.55
17829023--17829401	188	2.0	190	98	1	744	36	3	12	48	1.56
17829219--17829451	85	2.7	85	88	5	321	37	3	12	47	1.56
17836462--17836575	16	7.4	16	70	20	66	49	0	11	38	1.45
17836506--17836622	24	4.9	23	73	17	89	49	2	11	35	1.53
17836548--17836579	16	2.0	16	100	0	64	56	0	6	37	1.25
17836876--17836966	22	4.0	22	74	19	55	56	3	6	34	1.42
17836820--17837146	65	5.3	61	67	21	144	54	2	6	36	1.40
17836849--17837236	8	50.1	8	73	21	176	53	2	7	35	1.43
17836809--17837073	36	7.5	36	71	17	159	52	2	7	38	1.42
17837019--17837074	27	2.0	29	86	6	80	51	1	5	41	1.35
17837107--17837152	17	2.7	17	83	6	58	58	2	2	36	1.22
17837168--17837236	29	2.3	30	87	5	104	52	1	11	34	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17836806--17837400	240	2.4	246	84	10	718	52	2	7	37	1.44
17837279--17837430	2	79.0	2	65	23	51	50	3	5	40	1.43
17837259--17837428	47	3.6	45	72	19	123	50	3	6	40	1.45
17837442--17837489	22	2.2	22	85	7	62	56	0	8	35	1.30
17836806--17837491	253	2.7	253	81	11	681	52	2	8	36	1.45
17837456--17837499	22	1.9	22	86	9	61	52	2	6	38	1.41
17837488--17837613	22	5.9	22	77	17	122	36	6	0	56	1.30
17837515--17837580	29	2.2	31	84	10	84	33	4	1	60	1.26
17837601--17837907	11	28.5	11	62	18	51	46	4	4	44	1.44
17837604--17837656	17	2.9	17	86	8	61	52	3	1	41	1.30
17837683--17837738	22	2.7	21	88	5	78	46	5	0	48	1.25
17837691--17837946	20	13.4	20	69	19	129	46	4	4	44	1.44
17837782--17837974	2	97.0	2	65	19	66	48	3	3	44	1.37
17837798--17837841	21	2.2	20	87	4	61	61	2	0	36	1.09
17837783--17838024	54	4.5	54	70	11	165	47	3	4	44	1.40
17837838--17837907	11	6.5	11	71	12	65	42	2	5	48	1.41
17837703--17837894	74	2.6	73	73	12	187	45	4	4	44	1.45
17837782--17837981	94	2.2	90	85	12	273	48	3	4	44	1.38
17837719--17837961	107	2.3	103	79	9	280	46	4	4	44	1.46
17837941--17837990	24	2.1	24	88	3	75	42	2	4	52	1.31
17837932--17837982	13	4.1	13	80	10	70	41	1	5	50	1.37
17839932--17839964	2	16.5	2	100	0	66	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)
17842727--17842758	17	2.0	17	88	11	50	25	37	0	37	1.56
17844499--17844539	13	3.1	13	89	3	55	41	7	12	39	1.70
17848243--17848415	90	1.9	89	95	1	310	38	10	6	43	1.67
17855097--17855153	26	2.2	26	90	0	87	26	14	26	33	1.94
17855254--17855300	18	2.6	17	87	9	67	48	4	14	31	1.63
17855338--17855416	25	3.0	25	83	10	79	49	1	26	22	1.58
17855445--17855509	18	3.4	18	72	12	67	29	6	16	47	1.71
17855447--17855521	39	1.9	39	100	0	150	26	6	18	48	1.73
17859079--17859136	31	1.9	30	92	3	98	36	10	20	32	1.87
17859743--17859802	25	2.4	25	86	2	86	40	30	8	21	1.83

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