genome.fa.s9605.2.7.7.80.10.50.1000.22.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: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9158330

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   

This is table  22  of  35  ( 4090 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)
5037400--5037466	15	4.8	14	72	20	52	0	11	10	77	0.99
5037385--5037458	37	2.0	38	84	7	98	0	12	8	79	0.92
5037383--5037462	34	2.2	37	78	12	87	0	11	8	80	0.92
5037361--5037465	39	2.7	39	76	11	99	0	13	8	77	1.04
5040651--5040685	16	2.1	18	89	10	56	65	0	8	25	1.21
5040619--5040713	19	5.2	17	67	22	50	69	1	8	21	1.21
5040696--5040733	20	1.9	20	88	0	58	63	2	7	26	1.35
5040619--5040757	75	1.9	72	80	14	158	68	1	7	22	1.24
5040796--5040822	2	13.5	2	100	0	54	51	0	0	48	1.00
5040808--5040901	33	2.9	32	79	7	91	59	6	4	29	1.41
5041284--5041353	34	2.1	34	94	0	122	31	14	11	42	1.81
5041394--5041434	17	2.4	17	100	0	82	19	24	4	51	1.66
5041411--5041660	113	2.2	113	93	0	419	27	18	13	40	1.89
5041562--5041725	73	2.2	73	84	2	204	32	16	16	34	1.91
5042489--5042830	115	3.0	115	93	2	555	29	19	15	35	1.93
5044175--5044254	5	16.4	5	76	23	82	0	18	0	81	0.70
5044167--5044251	6	14.7	6	77	18	83	0	17	0	82	0.67
5044158--5044254	11	8.6	11	82	9	108	0	18	0	81	0.69
5044157--5044246	29	3.1	29	82	16	116	0	17	0	82	0.68
5044157--5044255	44	2.3	42	88	11	141	0	19	0	80	0.71
5051556--5051587	15	2.1	15	94	0	55	46	6	18	28	1.73
5054340--5054757	217	1.9	216	96	2	777	31	14	20	34	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5058302--5058336	10	3.5	10	92	0	52	51	20	5	22	1.68
5064725--5064814	45	2.0	45	100	0	180	28	20	11	40	1.86
5077005--5077045	20	2.0	20	90	0	64	21	19	21	36	1.95
5082320--5082469	75	2.0	75	100	0	300	30	10	26	32	1.90
5085593--5085696	37	2.8	37	84	4	138	40	14	15	29	1.87
5086109--5086285	68	2.6	66	73	14	155	33	4	2	58	1.33
5086164--5086217	26	2.0	27	86	10	76	37	5	0	57	1.22
5086194--5086263	19	3.5	19	71	22	54	31	2	2	62	1.24
5086549--5086573	2	12.5	2	100	0	50	48	0	0	52	1.00
5089551--5089640	46	2.0	46	89	8	139	70	10	13	6	1.34
5089551--5089620	22	3.1	22	74	11	70	70	10	12	7	1.34
5089573--5089640	22	2.9	23	78	8	84	70	8	14	5	1.31
5090228--5090304	22	3.5	22	92	0	127	38	27	12	20	1.89
5091110--5092392	106	12.1	106	90	0	1904	34	23	17	24	1.96
5092449--5093959	106	14.2	106	89	0	2218	34	23	18	23	1.96
5094032--5096235	106	21.0	106	88	3	3084	34	24	17	23	1.96
5096964--5097068	37	2.8	37	82	4	131	41	15	12	30	1.84
5097359--5097419	16	3.9	14	74	19	50	26	1	1	70	1.06
5097362--5097419	28	2.0	29	83	9	75	25	1	1	70	1.06
5097367--5097514	18	7.8	17	70	22	59	31	2	0	66	1.08
5097384--5097474	41	2.2	42	80	9	98	31	3	1	63	1.17
5097583--5097621	9	4.3	9	83	0	51	12	0	5	82	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5097583--5097621	18	2.2	18	90	0	60	12	0	5	82	0.83
5097657--5097703	18	2.7	18	87	12	64	31	0	0	68	0.90
5097629--5097697	11	6.5	11	72	18	58	34	2	0	62	1.10
5097575--5097722	12	12.2	12	71	12	52	25	2	1	70	1.08
5097671--5097735	11	5.5	11	80	12	58	18	0	0	81	0.69
5097697--5097739	9	4.9	9	91	5	70	11	0	0	88	0.52
5097673--5097764	40	2.2	41	81	7	98	17	3	0	79	0.86
5106600--5106647	18	2.7	18	77	3	53	31	0	14	54	1.41
5111524--5111594	20	3.5	20	73	7	72	29	15	19	35	1.93
5111681--5111810	61	2.1	61	90	2	199	31	16	21	30	1.96
5121679--5121717	20	2.0	20	94	0	69	35	23	10	30	1.88
5129752--5129790	20	2.0	20	89	0	60	33	23	10	33	1.88
5133405--5133615	49	4.3	49	88	1	316	24	19	14	41	1.89
5134563--5134612	3	17.0	3	87	4	66	40	0	0	60	0.97
5135891--5135963	16	4.1	17	71	25	53	26	4	4	65	1.28
5135993--5136083	47	1.9	49	82	10	118	39	4	2	53	1.33
5136002--5136096	45	2.0	47	80	6	104	41	4	2	52	1.32
5136101--5136366	144	1.8	142	83	7	340	37	7	7	46	1.62
5136891--5136949	28	2.2	26	81	6	73	35	3	0	61	1.13
5136902--5136956	26	2.0	28	86	13	80	34	3	0	61	1.13
5140223--5140254	15	2.1	15	94	0	55	25	21	6	46	1.74
5148643--5148699	21	2.6	22	94	2	98	33	17	14	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5149081--5149483	124	3.4	121	80	11	479	40	15	19	24	1.91
5152622--5152652	13	2.4	13	94	0	53	25	16	22	35	1.94
5152680--5152749	30	2.3	30	97	0	131	38	12	14	34	1.84
5152680--5152757	30	2.7	29	92	4	113	38	14	14	33	1.86
5152724--5152884	85	1.9	85	92	0	268	29	19	18	32	1.95
5152918--5152968	2	25.5	2	92	7	86	47	1	0	50	1.12
5158826--5158896	15	4.7	15	87	1	97	9	18	12	59	1.60
5160191--5160564	187	2.0	187	100	0	748	36	18	13	31	1.90
5161617--5161661	20	2.2	21	96	4	83	28	11	0	60	1.31
5169618--5169708	45	2.0	45	95	0	164	32	26	8	31	1.87
5187820--5187909	45	2.0	45	86	0	126	35	14	21	28	1.92
5188834--5188882	20	2.5	20	100	0	98	20	14	14	51	1.77
5188842--5188887	20	2.6	18	86	13	60	21	13	15	50	1.78
5190261--5190290	2	15.0	2	100	0	60	50	0	0	50	1.00
5202944--5202983	21	1.9	21	85	10	55	35	10	2	52	1.48
5208050--5208083	13	2.6	13	100	0	68	14	0	5	79	0.91
5208047--5208108	9	7.1	8	78	12	61	14	1	4	79	0.98
5208088--5208217	38	3.2	40	73	19	119	23	3	3	70	1.16
5208064--5208187	23	5.1	23	69	20	74	20	3	4	71	1.16
5208246--5208303	31	1.9	29	89	6	89	29	6	3	60	1.39
5208241--5208313	31	2.4	30	82	13	87	28	8	2	60	1.40
5208345--5208383	2	19.5	2	100	0	78	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)
5208478--5208531	27	2.0	27	82	10	65	7	9	5	77	1.11
5219622--5219661	20	2.0	20	95	0	71	20	7	30	42	1.79
5225446--5227110	836	2.0	837	96	0	3080	35	13	23	27	1.93
5231186--5231240	24	2.3	24	96	0	101	7	16	16	60	1.57
5237005--5237038	17	2.1	17	88	5	52	32	23	5	38	1.79
5247293--5247376	23	3.7	23	90	0	123	23	29	21	25	1.99
5247414--5247447	17	2.1	17	88	5	52	32	23	5	38	1.79
5248942--5249316	53	7.1	53	92	1	592	38	20	16	25	1.92
5248943--5249316	158	2.4	159	92	1	626	38	20	16	24	1.92
5249870--5249921	18	2.6	19	72	18	52	25	26	13	34	1.93
5252982--5253187	103	2.0	103	100	0	412	30	17	17	34	1.93
5261780--5261831	23	2.4	21	87	6	68	38	42	0	19	1.51
5266898--5266948	14	3.5	15	81	10	54	62	1	0	35	1.06
5266892--5266938	7	7.1	7	79	13	55	63	0	0	36	0.94
5266934--5266984	26	1.9	27	88	4	77	54	7	0	37	1.29
5266984--5267050	27	2.4	28	92	5	118	40	7	4	47	1.52
5267012--5267213	39	5.3	39	86	4	279	39	9	5	45	1.60
5267029--5267213	76	2.4	73	83	8	253	40	9	5	45	1.59
5269703--5270035	166	2.0	166	100	0	666	39	18	24	18	1.92
5275839--5275887	26	1.9	26	87	4	73	71	4	4	20	1.19
5283327--5283571	55	4.5	55	86	4	341	35	17	17	29	1.93
5290085--5290629	55	9.9	54	85	5	321	34	16	17	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5290122--5290629	110	4.6	110	92	1	761	35	16	17	30	1.92
5290142--5290629	165	3.0	164	89	3	746	34	16	18	30	1.93
5295604--5295651	18	2.9	16	84	9	53	37	2	0	60	1.09
5295619--5295651	15	2.1	16	88	5	50	39	0	0	60	0.97
5296641--5296746	50	2.1	50	100	0	212	51	1	14	32	1.52
5297281--5297309	2	14.5	2	100	0	58	0	48	0	51	1.00
5302446--5302518	38	1.9	38	97	0	137	23	15	15	46	1.83
5307584--5307617	14	2.5	14	90	4	52	52	0	0	47	1.00
5309704--5309842	69	2.0	69	82	0	170	19	17	24	38	1.93
5315316--5315370	16	3.4	17	78	9	53	56	5	7	30	1.49

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