genome.fa.s7960.2.7.7.80.10.50.1000.27.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: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7905731

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   

This is table  27  of  39  ( 4646 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)
5181920--5181960	21	1.9	22	85	5	57	46	2	0	51	1.14
5181879--5181953	3	25.7	3	69	15	50	38	4	1	56	1.27
5183385--5183416	3	10.7	3	100	0	64	34	0	0	65	0.93
5186062--5186150	41	2.2	41	97	0	169	41	2	24	31	1.67
5186918--5186998	43	1.9	41	82	5	99	48	3	17	30	1.64
5187234--5187294	22	2.8	22	85	9	72	29	21	26	22	1.99
5187550--5187596	18	2.6	17	78	15	51	48	2	12	36	1.53
5188006--5188064	12	5.1	12	74	14	52	18	16	25	38	1.92
5188022--5188066	21	2.1	21	91	0	72	20	20	17	42	1.90
5188828--5188871	2	22.0	2	100	0	88	50	0	0	50	1.00
5195917--5195963	23	2.0	23	91	0	76	38	8	21	31	1.83
5195937--5196083	64	2.3	64	97	0	276	42	12	14	29	1.83
5196128--5196818	198	3.5	197	83	8	818	31	14	13	40	1.86
5198571--5198633	11	5.5	11	81	10	81	46	9	7	36	1.66
5198557--5198631	36	2.1	36	100	0	150	48	10	5	36	1.61
5198571--5198630	25	2.5	24	73	26	65	48	10	6	35	1.63
5199621--5199675	6	9.2	6	91	0	65	27	30	1	40	1.67
5199621--5199675	18	3.1	18	89	0	74	27	30	1	40	1.67
5200488--5200537	2	25.0	2	100	0	100	50	0	0	50	1.00
5201352--5201919	199	3.1	178	80	8	455	32	17	14	36	1.90
5201555--5202518	200	4.9	197	81	10	1036	32	16	15	36	1.89
5202000--5202345	180	1.9	179	88	2	525	28	17	16	38	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5202870--5202918	19	2.6	19	90	6	73	55	8	6	30	1.54
5204325--5204363	18	2.2	18	95	0	69	2	41	0	56	1.13
5204614--5204657	21	2.1	21	86	0	61	13	29	13	43	1.83
5205036--5205090	24	2.5	21	76	21	58	49	3	0	47	1.19
5207084--5207575	182	2.7	181	86	1	680	27	17	13	41	1.87
5210614--5211554	159	5.9	158	84	3	907	21	22	25	31	1.98
5210615--5211521	477	1.9	477	81	4	1112	20	22	25	31	1.98
5223746--5223805	30	2.0	31	86	3	86	28	8	10	53	1.63
5224718--5224769	21	2.6	21	90	6	81	34	13	5	46	1.67
5233328--5233387	30	2.0	31	86	3	86	28	8	10	53	1.63
5234293--5234344	21	2.6	20	87	6	79	32	13	5	48	1.66
5242912--5242941	12	2.5	12	100	0	60	43	6	50	0	1.28
5256669--5256706	20	1.9	20	100	0	76	42	10	23	23	1.85
5257580--5257709	43	3.0	43	79	2	136	23	3	20	53	1.62
5267316--5267358	19	2.3	19	83	0	50	37	27	11	23	1.89
5267417--5267466	26	1.9	26	83	0	64	30	16	14	40	1.87
5267557--5267600	23	1.9	23	90	0	70	13	52	13	20	1.74
5267559--5267612	22	2.4	23	87	3	74	16	48	16	18	1.82
5268024--5268061	14	2.8	14	84	4	51	28	10	13	47	1.76
5273435--5273490	24	2.3	24	84	0	67	28	19	16	35	1.93
5273449--5273502	24	2.2	24	93	0	90	20	18	20	40	1.91
5275920--5276007	20	4.4	20	88	2	133	35	25	21	18	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5276013--5276158	19	8.4	18	66	21	82	47	18	20	13	1.82
5276051--5276138	14	5.6	14	70	23	59	44	19	23	12	1.85
5276032--5276168	33	4.2	33	93	1	222	45	19	21	13	1.84
5276291--5276327	14	2.6	14	86	0	56	48	21	0	29	1.50
5277684--5277788	42	2.5	42	76	7	115	24	20	34	20	1.96
5278268--5278354	20	4.3	20	92	0	138	39	21	18	20	1.93
5278398--5278451	19	2.8	19	88	0	81	7	16	27	48	1.73
5278442--5278499	14	3.8	14	75	20	62	10	24	20	44	1.82
5278424--5278514	33	2.8	33	90	3	141	12	21	20	45	1.84
5278399--5278484	19	4.8	19	71	18	76	9	18	23	48	1.76
5278614--5278970	94	3.8	94	93	1	590	46	17	13	22	1.82
5280659--5280717	19	3.1	19	92	0	100	47	18	20	13	1.82
5280715--5280793	33	2.4	33	91	0	122	11	21	20	46	1.81
5280770--5280869	21	4.9	21	85	3	118	12	20	17	51	1.76
5281427--5281640	20	10.6	20	79	6	243	18	18	25	37	1.93
5281429--5281640	41	5.2	41	92	1	347	18	18	25	37	1.93
5281649--5281701	20	2.7	20	85	5	72	15	18	22	43	1.87
5283615--5283695	37	2.2	37	95	4	146	28	25	25	19	1.99
5285063--5285136	31	2.4	31	88	0	121	32	9	28	29	1.88
5289490--5289570	2	42.0	2	73	20	66	46	1	3	48	1.27
5289669--5289752	19	4.5	18	75	11	71	45	0	26	28	1.54
5289652--5289714	27	2.3	27	81	5	74	49	0	22	28	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5289644--5289732	46	2.0	45	88	6	135	48	0	23	28	1.51
5289645--5289733	20	4.2	20	68	18	56	48	0	22	29	1.51
5290718--5291159	80	5.5	80	93	1	717	31	25	20	22	1.98
5296207--5296676	80	5.8	80	90	1	701	32	25	19	21	1.97
5300557--5300586	2	15.0	2	100	0	60	50	0	0	50	1.00
5300725--5300794	2	35.0	2	77	11	63	48	7	1	42	1.39
5300725--5300794	19	3.4	19	81	16	86	48	7	1	42	1.39
5300714--5300794	21	4.0	19	82	10	90	48	8	2	40	1.47
5300741--5300794	23	2.3	23	100	0	108	48	7	0	44	1.31
5300880--5300959	7	11.3	7	68	2	52	50	30	0	20	1.49
5300878--5300918	21	2.0	21	90	0	64	56	29	0	14	1.39
5300900--5300945	15	3.1	14	81	6	56	50	26	0	23	1.50
5301306--5301371	2	33.0	2	75	6	62	59	1	0	39	1.07
5300707--5301849	567	2.0	571	89	2	1747	44	11	8	35	1.71
5301451--5301492	21	2.0	20	86	4	57	57	19	4	19	1.58
5301482--5301526	7	6.4	7	80	10	56	55	24	0	20	1.43
5301480--5301521	14	3.0	14	85	0	66	54	26	0	19	1.44
5301836--5301862	13	2.1	13	100	0	54	44	0	0	55	0.99
5301994--5302044	14	3.6	14	75	15	52	50	27	0	21	1.48
5302364--5302417	2	26.0	2	88	7	81	50	1	1	46	1.23
5302500--5302578	14	5.6	14	80	8	72	51	22	0	25	1.48
5302506--5302578	21	3.5	21	71	14	53	52	21	0	26	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5302898--5302950	20	2.5	20	72	6	52	47	5	9	37	1.60
5303020--5303091	7	10.3	7	72	0	54	52	29	0	18	1.45
5303041--5303091	14	3.6	14	86	5	68	50	29	0	19	1.48
5303020--5303091	28	2.6	28	80	4	74	52	29	0	18	1.45
5303020--5303091	21	3.4	21	76	0	81	52	29	0	18	1.45
5303246--5303292	14	3.7	14	71	26	50	51	4	0	44	1.21
5303244--5303293	23	2.1	24	96	3	93	48	4	0	48	1.20
5303536--5303578	16	2.7	16	92	0	68	37	13	27	20	1.91
5304475--5304514	10	4.0	10	86	0	53	27	32	0	40	1.57
5304560--5304593	9	3.9	9	84	7	52	35	0	2	61	1.11
5304559--5304597	17	2.4	17	95	4	71	33	0	5	61	1.18
5304688--5304714	8	3.4	8	100	0	54	40	11	0	48	1.39
5308660--5308699	20	2.0	20	100	0	80	15	30	40	15	1.87
5310800--5310859	30	2.0	29	84	9	77	38	8	23	30	1.84
5311157--5311235	35	2.2	36	82	13	92	35	0	17	46	1.49
5312476--5312500	12	2.1	12	100	0	50	36	0	24	40	1.55
5324108--5324188	33	2.5	33	89	4	119	28	14	18	38	1.90
5324124--5324189	33	2.0	33	96	0	123	27	12	19	40	1.87
5324243--5324287	3	15.7	3	82	17	60	68	0	0	31	0.89
5324529--5324767	83	2.9	83	84	0	298	24	18	25	32	1.97
5324774--5324834	30	2.0	30	87	0	86	31	8	16	44	1.77
5324836--5325075	36	6.9	36	73	16	193	39	12	21	26	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5324964--5325073	36	3.0	37	94	2	204	36	13	23	26	1.92
5329929--5329974	14	3.4	14	93	3	76	63	0	0	36	0.95
5330343--5330424	33	2.5	33	85	0	119	30	13	18	37	1.89
5330478--5330518	3	13.7	3	100	0	82	68	0	0	31	0.90
5332617--5332641	11	2.3	11	100	0	50	56	8	20	16	1.65
5346450--5346487	4	9.5	4	100	0	76	23	0	0	76	0.79
5348043--5348082	2	20.0	2	100	0	80	50	0	0	50	1.00
5350784--5350846	2	31.5	2	100	0	126	49	0	0	50	1.00
5350864--5350923	31	1.9	30	83	12	77	11	23	18	46	1.81
5360769--5360811	21	2.0	21	86	0	59	30	27	25	16	1.97

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