genome.fa.s1.2.7.7.80.10.50.1000.7.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: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2159989

Tables:   1   2   3   4   5   6   7   8   

This is table  7  of  8  ( 891 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)
1689434--1689468	13	2.6	13	90	4	52	77	0	2	20	0.90
1690999--1692071	105	10.3	105	90	4	1543	21	17	26	33	1.96
1690999--1692071	205	5.2	205	91	2	1599	21	17	26	33	1.96
1690999--1692071	310	3.4	310	89	4	1549	21	17	26	33	1.96
1692680--1693053	65	5.5	65	72	11	216	39	11	20	28	1.88
1692793--1693073	36	8.0	35	78	12	272	40	14	19	25	1.90
1692741--1693047	138	2.2	137	85	1	418	39	13	19	27	1.89
1692935--1693107	36	4.8	36	85	4	172	39	16	20	23	1.91
1693974--1694024	22	2.3	22	96	0	93	25	11	27	35	1.91
1694647--1694696	21	2.4	22	83	9	70	0	16	8	76	1.02
1694653--1694705	23	2.4	22	84	6	72	0	15	5	79	0.91
1697682--1697715	9	3.8	9	88	11	52	76	0	2	20	0.92
1697681--1697715	13	2.6	13	90	4	52	77	0	2	20	0.90
1698181--1698215	2	17.5	2	93	0	61	51	2	0	45	1.16
1698213--1698255	18	2.5	17	81	7	52	69	2	2	25	1.12
1698215--1698253	14	2.8	13	88	11	51	71	2	2	23	1.10
1699440--1699536	40	2.4	39	86	10	126	57	16	8	17	1.62
1701942--1701999	17	3.4	17	92	0	98	17	24	41	17	1.90
1701909--1701952	7	6.4	7	94	5	81	25	29	29	15	1.96
1709199--1709239	17	2.4	17	87	0	64	17	21	41	19	1.90
1709233--1709303	19	3.7	20	88	5	101	26	29	25	18	1.98
1709235--1709303	9	7.1	10	76	12	72	27	30	23	18	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1716596--1716655	30	2.0	30	93	0	102	45	10	10	35	1.71
1718801--1718938	70	2.0	69	81	5	161	34	13	13	37	1.85
1735148--1735444	146	2.0	148	96	3	555	20	24	18	37	1.94
1735397--1735496	48	2.1	48	100	0	200	23	30	12	35	1.91
1736657--1736707	24	2.1	24	82	7	59	54	1	0	43	1.11
1736668--1736713	24	1.9	25	91	8	78	50	2	0	47	1.13
1737533--1737573	14	2.9	14	96	0	73	7	34	34	24	1.83
1744174--1744235	29	2.1	29	96	0	115	32	17	12	37	1.88
1744392--1744449	29	2.0	28	83	9	73	36	1	1	60	1.17
1746356--1746380	2	12.5	2	100	0	50	52	0	0	48	1.00
1747968--1748042	29	2.5	30	86	4	125	20	37	29	13	1.90
1750353--1750395	2	21.5	2	100	0	86	48	0	0	51	1.00
1755254--1755295	19	2.2	19	83	8	50	61	0	0	38	0.96
1755527--1755575	21	2.5	19	81	12	62	28	14	36	20	1.92
1757454--1758043	197	3.0	197	97	1	1141	31	25	15	27	1.96
1759208--1759256	2	24.5	2	100	0	98	48	0	0	51	1.00
1761161--1761214	25	2.1	25	80	16	65	44	1	3	50	1.30
1761162--1761214	27	2.0	28	85	10	76	43	1	3	50	1.30
1777710--1777781	37	1.9	38	89	10	114	52	19	15	12	1.74
1777710--1777781	36	1.9	39	89	10	116	52	19	15	12	1.74
1785648--1785808	80	2.0	80	91	7	265	33	11	13	41	1.80
1797597--1797645	2	24.5	2	100	0	98	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)
1800811--1800835	13	1.9	13	100	0	50	12	8	0	80	0.92
1800875--1800932	29	2.0	29	82	0	71	20	3	10	65	1.38
1803428--1803477	16	3.1	16	82	0	73	4	14	38	44	1.63
1815934--1816001	30	2.3	30	89	0	109	11	35	16	36	1.85
1815987--1816045	27	2.2	28	81	9	77	28	32	5	33	1.79
1835820--1835884	32	2.0	32	100	0	130	21	21	9	47	1.78
1835833--1835885	16	3.3	16	70	19	56	22	24	5	47	1.73
1839972--1840002	15	2.1	15	100	0	62	6	35	12	45	1.68
1840430--1840489	22	2.8	21	74	20	61	53	0	0	46	1.00
1856488--1856512	12	2.1	12	100	0	50	16	8	0	76	1.02
1861363--1861425	27	2.3	27	88	0	90	30	14	14	41	1.85
1870710--1870767	2	29.0	2	100	0	116	50	0	0	50	1.00
1872699--1872821	27	4.6	27	96	2	223	39	0	3	56	1.15
1875467--1875613	31	4.7	31	87	0	168	30	15	18	35	1.92
1875467--1875599	62	2.1	63	87	1	187	30	15	18	35	1.93
1876156--1876453	77	4.0	78	70	17	306	28	2	12	56	1.48
1876183--1876471	142	2.0	144	95	4	521	30	2	14	52	1.53
1877758--1877929	85	2.0	85	100	0	344	36	18	16	28	1.93
1879489--1879529	18	2.3	18	95	0	73	34	34	14	17	1.90
1884790--1884837	6	8.0	6	100	0	96	33	16	0	50	1.46
1884836--1884926	6	15.5	6	93	5	98	24	58	17	0	1.39
1884840--1884926	12	7.4	12	89	7	108	22	58	18	0	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1884927--1884962	5	7.4	5	96	3	65	36	22	41	0	1.54
1885454--1885528	6	12.5	6	100	0	150	0	16	50	33	1.45
1885621--1885677	21	2.7	21	100	0	114	24	28	24	22	2.00
1885667--1885724	20	2.9	19	82	14	64	32	20	20	25	1.97
1885688--1885781	21	4.5	21	72	7	84	25	20	22	31	1.98
1885661--1885781	62	2.0	62	83	3	154	28	19	21	30	1.98
1893164--1893260	47	2.1	47	100	0	194	54	20	2	22	1.55
1893253--1893294	21	2.0	21	95	4	77	54	23	11	9	1.66
1895943--1895981	6	6.5	6	100	0	78	15	0	0	84	0.62
1899630--1899667	19	2.0	19	100	0	76	47	0	15	36	1.46
1899715--1899746	2	16.0	2	100	0	64	50	0	0	50	1.00
1904955--1905019	24	2.6	26	73	9	62	67	0	6	26	1.13
1906144--1906194	9	5.3	9	80	13	57	68	0	1	29	1.00
1906351--1906396	23	2.0	23	86	0	65	45	13	2	39	1.55
1908613--1908660	18	2.7	18	77	9	53	41	0	6	52	1.27
1923287--1923505	29	7.6	29	78	8	194	37	18	5	38	1.74
1923502--1923534	17	1.9	17	93	0	57	12	21	45	21	1.84
1924853--1924909	18	3.2	18	87	0	78	31	28	3	36	1.74
1940275--1940451	60	3.0	60	81	0	201	31	26	4	37	1.76
1940607--1940702	31	3.2	31	67	14	74	35	7	21	35	1.82
1946341--1946383	20	2.2	20	91	0	68	34	27	18	18	1.95
1947111--1947265	31	5.0	31	88	3	224	21	20	21	36	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1949984--1950024	20	2.0	20	85	0	55	26	29	26	17	1.97
1950741--1950924	31	6.0	31	89	5	277	20	20	22	36	1.95
1950999--1951048	25	2.0	25	100	0	100	28	20	20	32	1.97
1952912--1953058	64	2.3	65	82	6	176	30	25	21	22	1.99
1953871--1953932	23	2.7	23	92	0	106	20	25	25	27	1.99
1956668--1956708	18	2.3	18	82	0	55	46	19	21	12	1.82
1959019--1959078	30	2.0	30	93	0	102	36	10	10	43	1.72
1962450--1962778	20	16.2	20	86	9	436	41	23	19	15	1.90
1962871--1962999	6	21.5	6	100	0	258	33	50	16	0	1.45
1963492--1963626	6	22.5	6	100	0	270	0	16	50	33	1.45
1963722--1964089	40	9.1	40	85	6	426	16	19	22	41	1.90
1963722--1964089	20	18.2	20	79	13	346	16	19	22	41	1.90
1969512--1969541	9	3.3	9	90	0	51	76	0	0	23	0.78
1969852--1969878	14	1.9	14	100	0	54	77	0	22	0	0.76
1992792--1992969	89	2.0	89	82	5	218	42	19	11	26	1.85
1997450--1997482	17	2.0	17	88	5	50	48	0	6	45	1.27
1997542--1997591	15	3.3	15	74	20	50	48	6	4	42	1.46
1998579--1998643	20	3.2	20	75	12	78	35	18	23	23	1.96
1998550--1998663	21	5.6	20	68	19	65	31	24	21	22	1.98
1998550--1998663	41	2.8	41	84	5	158	31	24	21	22	1.98
1998673--1998740	21	3.2	21	80	0	82	27	25	20	26	1.99
1999026--1999171	21	6.8	21	83	9	170	39	20	19	20	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1999026--1999168	65	2.2	64	86	8	195	39	20	18	20	1.93
2007047--2007163	62	1.9	61	98	1	225	17	22	45	14	1.85
2008789--2008829	21	2.0	21	90	9	66	48	2	0	48	1.14
2010929--2010972	21	2.1	21	87	8	63	45	0	2	52	1.13
2010935--2010972	11	3.5	11	82	7	51	50	0	2	47	1.15
2026298--2026343	23	1.9	23	82	8	56	56	4	6	32	1.45
2027769--2027941	60	2.9	59	82	7	181	42	7	20	29	1.80
2028027--2028198	59	2.9	59	78	10	147	30	22	5	41	1.76
2028330--2028470	60	2.3	59	82	7	151	41	6	20	31	1.77
2040100--2040204	52	2.0	52	100	0	210	34	18	24	22	1.96

Tables:   1   2   3   4   5   6   7   8