genome.fa.s1840.2.7.7.80.10.50.1000.8.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: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2412736

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   

This is table  8  of  12  ( 1360 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)
1464692--1464740	23	2.1	23	88	0	71	59	14	14	12	1.62
1467894--1467959	3	21.7	3	73	14	55	34	0	1	63	1.04
1469353--1469392	2	20.0	2	100	0	80	50	0	0	50	1.00
1469828--1470065	80	3.1	80	61	28	195	32	8	11	47	1.70
1469763--1470067	152	2.0	152	100	0	610	31	9	11	46	1.73
1470365--1470456	43	2.1	43	100	0	184	45	3	17	33	1.65
1471772--1471807	6	6.0	6	93	0	54	16	22	16	44	1.86
1471773--1471808	18	2.0	18	94	0	63	16	25	16	41	1.89
1472132--1472297	84	2.0	80	95	4	296	40	13	24	21	1.89
1476493--1476527	16	2.1	18	89	10	56	65	0	8	25	1.21
1477108--1477209	34	2.9	36	89	7	172	27	14	13	44	1.83
1479313--1479412	42	2.4	42	85	5	132	23	25	22	30	1.99
1479330--1479394	22	3.0	23	65	15	57	24	21	24	29	1.99
1482616--1482650	2	17.5	2	100	0	70	51	0	0	48	1.00
1482632--1482834	108	1.9	105	81	4	235	34	15	12	36	1.86
1484085--1484177	27	3.4	27	87	0	132	30	17	13	38	1.89
1484718--1484763	18	2.6	18	96	0	83	41	36	0	21	1.54
1495989--1496035	25	1.9	24	83	12	60	40	0	4	55	1.19
1495989--1496035	24	1.9	25	86	4	69	40	0	4	55	1.19
1496061--1496096	2	19.0	2	88	11	58	50	0	0	50	1.00
1504178--1504234	16	3.5	16	76	11	62	61	7	1	29	1.32
1504798--1504898	31	3.3	31	76	8	107	37	6	8	46	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1510756--1510832	27	2.8	26	79	13	75	68	2	0	28	1.02
1510775--1510816	21	2.0	22	90	4	68	66	2	0	30	1.04
1525418--1525465	19	2.5	19	80	10	53	16	8	2	72	1.18
1528261--1528337	3	24.7	3	84	7	91	33	2	0	63	1.08
1528305--1528338	7	5.1	7	92	7	54	41	0	0	58	0.98
1532075--1532252	55	3.2	55	84	3	221	26	21	19	32	1.97
1532326--1532422	42	2.3	41	83	1	122	32	22	22	21	1.98
1532300--1533062	219	3.5	214	91	2	1195	31	20	15	31	1.94
1532759--1532859	42	2.4	41	83	3	130	30	22	22	23	1.99
1532790--1532859	20	3.5	20	67	16	54	34	21	22	21	1.97
1533100--1533252	37	4.1	38	91	4	224	19	19	20	40	1.92
1539213--1539263	20	2.5	20	96	0	93	56	11	15	15	1.66
1539883--1539979	49	2.0	49	82	8	117	35	22	10	31	1.88
1543542--1543587	19	2.4	19	96	0	83	23	45	13	17	1.83
1552478--1552565	24	3.7	24	90	0	149	23	23	21	30	1.99
1552646--1552746	35	2.9	35	98	0	193	7	32	29	29	1.86
1555815--1555898	24	3.5	24	90	0	123	22	20	21	35	1.96
1558501--1558563	23	2.7	23	87	0	99	38	19	15	26	1.92
1558626--1558667	17	2.4	17	88	4	57	35	19	11	33	1.88
1563007--1563059	16	3.4	16	81	2	54	33	7	0	58	1.26
1564457--1564521	33	1.9	34	85	14	91	26	3	3	67	1.20
1564620--1564684	3	20.7	3	96	3	103	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1564678--1564707	15	2.0	15	93	0	51	13	3	3	80	0.97
1572196--1572238	21	2.0	21	100	0	86	23	13	27	34	1.93
1572217--1572303	44	2.0	44	90	0	138	29	14	19	35	1.92
1573855--1573903	24	2.0	24	96	0	89	26	12	26	34	1.92
1576808--1578141	84	15.9	84	83	2	1501	35	21	18	24	1.95
1578751--1578798	19	2.5	20	80	6	55	33	2	2	62	1.18
1580126--1580198	19	3.9	18	74	16	69	26	5	2	65	1.27
1580363--1580402	21	1.9	21	85	10	55	7	12	2	77	1.07
1580391--1580464	11	6.9	11	71	10	55	12	2	8	77	1.09
1580458--1580498	21	2.0	21	85	0	55	9	2	12	75	1.13
1581743--1581776	2	17.0	2	100	0	68	50	0	0	50	1.00
1582334--1582375	22	1.9	22	95	0	75	26	11	7	54	1.62
1585230--1585310	31	2.6	31	96	0	144	18	19	23	38	1.93
1586005--1586045	21	2.0	21	90	0	64	26	24	24	24	2.00
1588220--1588283	27	2.4	26	84	2	83	25	15	15	43	1.86
1588217--1588284	13	5.2	13	72	10	66	23	19	16	41	1.90
1595371--1595432	29	2.2	28	85	2	79	25	29	17	27	1.98
1595395--1595432	14	2.7	14	87	0	58	26	26	18	28	1.98
1597954--1598005	13	4.0	13	87	0	77	23	21	21	34	1.97
1598162--1598193	17	1.9	16	93	6	55	50	0	0	50	1.00
1599405--1599539	44	3.0	44	92	2	216	25	12	17	44	1.84
1599559--1599589	2	15.0	2	93	6	53	48	0	3	48	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1599583--1599701	60	2.0	60	98	1	231	35	15	13	35	1.87
1603088--1603139	19	2.7	19	100	0	104	28	17	30	23	1.97
1603191--1603248	20	2.6	22	86	10	75	29	20	22	27	1.99
1603849--1603918	21	3.2	21	68	9	59	44	5	18	31	1.73
1606389--1606615	40	5.6	39	72	13	147	32	16	13	37	1.88
1608281--1608339	25	2.3	26	82	11	68	42	0	3	54	1.17
1608287--1608339	27	2.0	27	85	7	72	45	0	1	52	1.11
1608336--1608376	15	2.8	15	82	14	50	21	7	0	70	1.11
1608460--1608509	25	2.0	25	100	0	100	36	44	20	0	1.52
1609647--1609678	8	3.9	8	92	8	55	9	3	0	87	0.64
1609646--1609678	9	3.8	9	84	8	50	9	3	0	87	0.63
1609650--1609688	17	2.3	17	86	0	51	15	5	0	79	0.90
1616632--1616692	30	1.9	33	83	9	83	19	9	6	63	1.46
1616641--1616686	14	3.1	15	76	20	51	19	8	6	65	1.43
1620214--1620298	44	1.9	44	85	0	116	42	14	21	22	1.88
1621834--1621858	13	1.9	13	100	0	50	56	4	0	40	1.18
1621874--1621923	24	2.0	26	84	7	68	40	0	4	56	1.18
1621874--1621918	21	2.0	23	83	8	58	40	0	4	55	1.20
1621907--1621967	23	2.6	24	80	14	74	24	1	1	72	1.03
1622048--1622117	25	2.8	25	82	4	79	40	41	12	5	1.67
1640026--1640065	20	2.0	20	90	0	62	27	12	27	32	1.93
1641919--1641980	21	3.0	21	97	0	115	20	33	17	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1641919--1642030	21	5.3	22	88	8	112	21	28	22	27	1.99
1642680--1642716	14	2.6	14	91	4	56	51	13	5	29	1.63
1642838--1642938	31	3.2	31	63	18	82	38	24	1	34	1.67
1642782--1642974	63	3.0	63	95	0	332	37	22	1	38	1.64
1642867--1642989	23	5.6	23	71	13	107	35	20	0	43	1.58
1642930--1642992	23	2.7	23	95	0	108	33	17	0	49	1.47
1643768--1643866	26	3.9	25	72	17	62	43	0	3	53	1.16
1643835--1643876	20	2.1	20	86	0	57	47	0	0	52	1.00
1646823--1646930	38	2.7	39	80	8	103	29	23	17	29	1.97
1646851--1646930	41	1.9	43	87	5	119	30	22	18	28	1.98
1646694--1647418	236	3.1	238	86	4	963	32	16	16	34	1.92
1646694--1647390	235	2.9	237	86	5	923	33	16	16	33	1.91
1647461--1647503	17	2.7	15	79	13	50	67	4	9	18	1.36
1647980--1648210	117	2.0	117	89	0	354	38	15	22	23	1.92
1649121--1649165	22	2.2	20	84	11	56	15	0	33	51	1.44
1651391--1651424	2	17.5	2	93	6	61	52	0	0	47	1.00
1651389--1651424	17	2.1	17	100	0	72	52	0	0	47	1.00
1651393--1651422	15	2.0	15	100	0	60	53	0	0	46	1.00
1652705--1652767	34	1.9	32	87	6	90	61	3	1	33	1.21
1653668--1653832	78	2.1	77	94	4	289	44	13	1	40	1.54
1654813--1654850	20	1.9	20	94	0	67	23	13	10	52	1.71
1654864--1654979	20	5.8	20	78	11	114	17	17	25	39	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1654847--1654934	40	2.2	41	80	10	101	18	15	28	37	1.92
1654867--1654979	40	2.8	40	88	7	151	17	15	25	40	1.90
1654863--1654979	60	2.0	60	83	6	148	17	17	25	40	1.90
1654963--1655059	20	4.7	21	72	8	56	27	17	24	29	1.97
1655487--1655523	2	18.5	2	100	0	74	48	0	0	51	1.00
1661517--1661580	19	3.4	19	75	0	65	51	14	17	17	1.76
1668333--1668375	17	2.4	18	84	7	61	41	0	2	55	1.12
1668471--1668539	24	2.9	23	78	6	66	36	43	15	4	1.67
1677804--1677886	42	2.0	42	88	4	123	25	21	19	33	1.97
1678040--1678140	41	2.5	40	80	9	114	24	21	21	31	1.98

Tables:   1   2   3   4   5   6   7   8   9   10   11   12