genome.fa.s2660.2.7.7.80.10.50.1000.7.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: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2211860

Tables:   1   2   3   4   5   6   7   8   9   

This is table  7  of  9  ( 1072 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)
1495112--1495160	2	25.0	2	95	4	91	51	0	0	48	1.00
1497628--1497680	19	2.8	18	83	13	63	43	1	0	54	1.11
1501676--1501713	2	19.0	2	100	0	76	50	0	50	0	1.00
1510751--1510789	19	2.1	19	100	0	78	15	33	5	46	1.68
1515306--1515414	30	3.6	30	81	8	121	43	5	5	45	1.50
1518106--1518148	6	7.2	6	91	0	59	34	0	65	0	0.93
1518254--1518283	15	2.0	15	100	0	60	26	0	0	73	0.84
1525703--1525747	16	2.8	16	75	0	54	17	20	15	46	1.84
1533021--1533091	29	2.3	29	81	11	81	66	0	7	26	1.17
1536754--1536793	21	1.9	21	89	0	62	72	2	10	15	1.21
1548386--1549315	310	3.0	311	95	2	1718	33	13	13	39	1.84
1551157--1551340	102	1.8	102	88	9	286	47	14	11	26	1.78
1553362--1553405	11	4.1	12	77	22	53	54	0	0	45	0.99
1553957--1554005	23	2.1	23	82	14	57	55	14	18	12	1.69
1554192--1554229	2	19.5	2	94	5	69	47	0	0	52	1.00
1554204--1554784	297	2.0	299	90	3	924	36	12	11	38	1.80
1555420--1555486	27	2.5	27	92	0	107	11	55	8	23	1.64
1555621--1555691	21	3.4	21	72	18	67	7	61	5	25	1.43
1555616--1555934	41	8.3	41	72	18	265	8	62	4	24	1.43
1555614--1555673	20	2.9	21	76	20	72	6	63	6	23	1.43
1555583--1555848	74	3.5	76	82	10	330	8	62	4	24	1.42
1555716--1555860	21	6.4	21	69	18	78	6	64	4	24	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1555720--1555862	15	8.8	16	66	21	59	6	64	4	25	1.35
1555875--1555993	55	2.1	56	93	3	213	10	63	4	22	1.43
1555985--1556024	21	1.9	21	89	0	62	15	62	2	20	1.43
1556006--1556082	6	13.0	6	83	2	84	6	75	0	18	1.01
1556023--1556091	23	3.0	24	85	8	81	7	76	0	15	0.99
1555806--1556051	131	1.9	131	88	5	372	9	63	4	22	1.41
1556020--1556091	12	6.2	12	82	4	76	6	76	0	16	0.99
1556008--1556091	6	14.3	6	81	7	66	8	73	0	17	1.07
1559774--1559844	20	3.5	20	90	0	115	33	16	16	32	1.92
1560988--1561057	2	35.0	2	91	0	113	47	1	1	50	1.19
1563665--1563748	43	2.0	43	95	4	154	36	14	9	39	1.78
1565450--1565487	16	2.4	15	87	12	58	31	18	7	42	1.79
1566905--1566961	27	2.1	27	93	0	96	12	54	8	24	1.65
1567113--1567531	42	10.5	42	71	15	307	9	61	4	24	1.45
1567086--1567598	21	24.8	21	66	14	102	9	61	4	23	1.44
1567089--1567233	36	3.9	36	76	12	148	10	61	3	24	1.44
1567289--1567355	20	3.2	20	68	16	55	5	62	7	23	1.44
1567324--1567561	78	3.1	76	94	2	408	10	61	5	23	1.47
1567417--1567562	42	3.6	42	72	17	146	10	60	4	23	1.47
1567462--1567609	18	7.9	18	70	21	72	11	64	2	20	1.38
1567548--1567609	6	10.3	6	82	6	72	11	69	0	19	1.18
1570878--1570950	20	3.7	20	82	8	71	28	17	13	39	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1576403--1576477	25	3.1	24	71	21	66	49	1	2	46	1.24
1576524--1576639	2	60.0	2	91	6	195	50	0	0	49	1.00
1577142--1577172	16	1.9	16	93	0	53	29	6	6	58	1.48
1578004--1578060	27	2.1	27	93	0	96	12	54	8	24	1.65
1578223--1578288	21	3.1	21	72	8	62	6	63	4	25	1.37
1578291--1578350	21	2.8	22	72	20	54	8	63	3	25	1.38
1578377--1578447	21	3.4	21	75	21	78	4	64	7	23	1.36
1578180--1578456	77	3.6	78	88	3	400	7	62	4	24	1.42
1578398--1578468	21	3.4	21	75	14	83	4	66	5	23	1.31
1578441--1578502	21	3.0	21	78	0	61	9	62	3	24	1.40
1578413--1578656	77	3.1	78	95	2	438	10	61	4	23	1.47
1578629--1578700	17	3.9	19	84	12	64	12	68	0	19	1.21
1578217--1578622	196	2.1	196	93	2	692	8	61	4	24	1.45
1578639--1578700	6	10.3	6	83	13	74	11	69	0	19	1.18
1578637--1578700	17	3.6	17	83	14	76	10	70	0	18	1.16
1578639--1578697	23	2.5	24	84	13	77	10	69	0	20	1.17
1582402--1582476	20	3.8	20	94	0	132	37	16	16	30	1.90
1587225--1587268	11	4.1	12	77	22	53	54	0	0	45	0.99
1588178--1588212	2	17.5	2	100	0	70	48	0	0	51	1.00
1588687--1588727	2	20.5	2	100	0	82	48	0	0	51	1.00
1589030--1589057	2	14.0	2	100	0	56	50	0	0	50	1.00
1589690--1589742	27	2.0	27	96	0	97	11	50	11	26	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1589869--1590505	36	16.3	36	69	18	307	9	60	5	24	1.48
1589899--1590479	42	14.6	42	74	12	555	9	60	5	24	1.49
1589943--1590497	78	7.1	78	89	4	841	9	60	5	24	1.49
1590399--1590545	18	7.9	18	71	20	79	11	64	2	21	1.38
1590459--1590545	6	14.2	6	77	9	77	12	66	1	19	1.30
1603277--1603620	172	2.0	172	100	0	688	32	21	9	36	1.85
1619902--1619942	19	2.2	19	86	0	55	41	2	0	56	1.13
1634342--1634412	32	2.2	32	97	2	135	18	19	21	40	1.91
1634443--1634515	31	2.4	31	95	4	132	19	17	20	42	1.89
1634651--1634837	31	6.0	31	96	1	331	19	18	22	38	1.93
1639125--1639327	31	6.5	31	97	0	379	18	19	21	40	1.92
1639792--1639834	21	2.0	21	100	0	86	25	23	27	23	2.00
1643356--1643498	31	4.6	31	94	0	241	19	19	22	38	1.93
1646359--1646566	75	2.8	75	84	3	249	24	30	24	21	1.99
1650409--1650456	24	2.0	24	100	0	96	45	12	20	20	1.83
1652313--1652373	23	2.8	22	80	9	72	22	34	22	19	1.97
1652355--1652394	21	1.9	21	85	10	55	25	37	25	12	1.91
1654003--1654145	73	1.9	75	90	9	231	34	30	20	13	1.92
1654421--1654462	17	2.7	15	82	13	57	14	0	28	57	1.38
1654425--1654458	17	2.0	17	94	0	59	11	0	32	55	1.36
1655064--1655270	75	2.7	75	84	3	245	24	30	24	21	1.99
1663757--1663832	37	2.1	37	89	0	116	30	26	14	28	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1672492--1672750	129	2.0	130	99	0	511	30	10	11	48	1.72
1673075--1673619	256	2.1	249	87	6	765	27	11	20	40	1.87
1680201--1680235	18	1.9	18	88	0	52	22	17	11	48	1.79
1680470--1680512	12	3.4	13	78	15	54	39	0	2	58	1.11
1683283--1683315	17	1.9	17	88	11	50	63	0	3	33	1.10
1700817--1700844	2	14.0	2	100	0	56	50	0	0	50	1.00
1700907--1700982	35	2.2	35	97	0	143	36	14	19	28	1.91
1701617--1701647	14	2.2	14	94	0	53	51	16	0	32	1.44
1701606--1701647	18	2.3	18	83	0	57	50	16	0	33	1.46
1711672--1711710	20	2.0	19	85	5	51	43	17	0	38	1.50
1718164--1718408	44	5.6	44	77	8	218	24	17	8	48	1.76
1718052--1718495	87	5.1	87	76	12	324	25	17	7	50	1.71
1718077--1718495	43	9.7	44	75	10	294	25	17	7	49	1.73
1718164--1718449	132	2.2	132	87	3	402	25	17	8	48	1.75
1718164--1718487	132	2.5	132	82	7	349	25	18	8	48	1.75
1719339--1719375	2	18.5	2	100	0	74	51	0	0	48	1.00
1719375--1719402	2	14.0	2	100	0	56	50	0	50	0	1.00
1727095--1727147	20	2.6	21	84	3	72	41	1	3	52	1.30
1739209--1739242	17	2.1	16	88	5	50	76	0	8	14	1.01
1739717--1739763	24	2.0	24	83	8	60	59	10	2	27	1.42
1743079--1743122	20	2.2	20	84	4	63	65	0	15	18	1.27
1749978--1750024	24	2.0	24	83	8	60	57	14	2	25	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1755524--1755555	2	16.5	2	93	6	57	53	0	0	46	1.00
1760692--1760719	3	9.3	3	100	0	56	0	32	0	67	0.91
1763794--1763836	11	3.9	11	80	19	54	51	0	0	48	1.00
1763796--1763846	21	2.2	24	86	10	72	50	0	0	49	1.00
1770262--1770298	18	2.1	18	100	0	74	67	5	0	27	1.12
1770266--1770306	18	2.3	18	91	0	64	65	7	0	26	1.18
1770599--1770665	24	2.8	24	90	0	107	29	0	41	28	1.56
1790031--1790408	186	2.0	186	92	1	625	41	4	8	45	1.54
1792697--1792799	34	3.1	34	92	1	172	59	0	1	38	1.09
1792706--1792782	25	3.1	25	76	10	68	61	0	1	37	1.05

Tables:   1   2   3   4   5   6   7   8   9