genome.fa.s4117.2.7.7.80.10.50.1000.6.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: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2456583

Tables:   1   2   3   4   5   6   7   8   9   

This is table  6  of  9  ( 1080 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)
1449434--1449726	143	2.0	143	99	0	577	28	18	25	26	1.98
1449960--1450072	60	1.9	60	81	3	138	39	13	9	37	1.77
1451100--1451157	30	1.9	30	92	0	98	24	27	27	20	1.99
1451857--1451900	17	2.6	17	77	0	52	59	0	0	40	0.98
1453637--1453682	20	2.3	20	96	0	83	6	28	41	23	1.79
1453737--1453883	60	2.4	62	93	5	244	41	0	2	56	1.11
1453878--1453939	19	3.3	19	78	15	58	37	1	0	61	1.06
1462053--1462086	17	2.0	17	88	0	50	26	32	17	23	1.97
1463511--1463600	23	3.9	23	77	2	90	13	8	18	58	1.60
1463527--1463585	24	2.5	23	81	5	73	10	10	20	59	1.58
1463606--1463640	14	2.5	14	90	0	52	17	11	11	60	1.59
1468229--1468301	31	2.3	32	81	6	87	12	5	21	60	1.52
1468557--1468598	22	2.0	21	86	13	59	66	4	4	23	1.30
1470736--1470765	5	6.0	5	92	0	51	23	0	0	76	0.78
1472326--1472384	29	2.0	29	86	3	82	67	1	5	25	1.20
1472434--1472502	36	2.0	34	82	5	84	55	0	1	43	1.08
1474048--1474207	60	2.7	59	81	11	182	41	5	19	33	1.75
1474068--1474221	59	2.6	59	79	11	163	44	5	18	31	1.73
1474919--1474960	6	7.0	6	100	0	84	16	50	16	16	1.79
1487301--1487391	44	2.0	45	87	2	130	48	23	15	13	1.80
1496256--1496355	51	2.0	51	93	0	173	45	16	12	27	1.82
1496982--1497016	18	2.0	18	88	5	54	65	0	31	2	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1498425--1498456	2	16.0	2	100	0	64	50	0	0	50	1.00
1503852--1503887	18	1.9	19	88	5	56	63	0	33	2	1.08
1513912--1513953	2	21.0	2	100	0	84	50	0	0	50	1.00
1514819--1514851	3	11.3	3	93	6	59	30	0	0	69	0.88
1515129--1515169	21	2.0	21	90	0	64	31	48	12	7	1.68
1518335--1518394	31	1.9	32	89	3	95	58	6	11	23	1.57
1519394--1519434	22	2.0	20	85	9	55	14	4	19	60	1.51
1522935--1522994	18	3.4	17	74	21	61	25	25	11	38	1.89
1522926--1522978	17	3.1	17	70	24	56	28	26	9	35	1.87
1522925--1523002	35	2.2	35	90	0	129	28	26	8	35	1.87
1526034--1526097	34	1.9	33	83	3	83	59	4	1	34	1.28
1531252--1531439	96	2.0	96	94	2	333	25	16	14	43	1.86
1544804--1544917	59	1.9	60	80	8	135	33	3	5	57	1.38
1549907--1549980	26	2.8	26	67	20	64	64	4	6	24	1.35
1552025--1552235	110	1.9	111	94	0	370	46	9	6	37	1.61
1552963--1553003	2	20.5	2	100	0	82	48	0	0	51	1.00
1556071--1556149	28	2.9	28	77	15	76	46	15	3	34	1.63
1562737--1562770	15	2.3	15	89	0	50	44	0	20	35	1.52
1562826--1562853	11	2.5	11	100	0	56	57	0	0	42	0.99
1569363--1569409	16	2.7	18	83	9	53	21	2	8	68	1.27
1579556--1579640	42	2.0	42	100	0	170	18	15	18	47	1.83
1586412--1586465	3	18.0	3	88	7	83	0	31	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1587594--1587678	43	2.0	43	100	0	170	37	28	3	30	1.74
1587954--1588047	31	3.0	31	89	3	136	36	15	10	37	1.83
1595008--1595038	4	7.8	4	100	0	62	51	22	0	25	1.48
1595133--1595179	22	2.1	22	84	7	60	46	2	2	48	1.25
1597061--1597109	23	2.1	23	100	0	98	18	12	30	38	1.87
1597663--1597964	121	2.4	125	88	5	434	29	12	12	46	1.78
1598738--1598781	17	2.6	17	85	0	61	18	15	36	29	1.92
1603624--1603833	43	4.8	43	74	5	136	30	20	17	31	1.96
1614288--1614317	5	6.0	5	100	0	60	80	0	0	20	0.72
1636015--1636115	49	2.1	49	96	0	184	20	39	13	25	1.90
1638952--1639016	23	2.9	22	70	6	58	21	21	9	47	1.78
1643240--1643406	8	20.9	8	73	4	113	38	17	21	22	1.93
1643240--1643503	16	16.0	16	69	10	111	37	18	21	23	1.94
1643240--1643503	32	8.0	32	71	12	142	37	18	21	23	1.94
1643247--1643446	40	5.0	40	77	4	172	36	16	22	25	1.94
1644577--1644642	8	8.6	8	74	15	50	54	1	0	43	1.09
1644546--1644654	53	2.0	53	82	8	132	51	0	0	46	1.13
1644550--1644614	22	3.1	20	82	10	76	52	0	0	47	1.00
1644561--1644610	14	3.3	14	78	15	55	48	0	0	52	1.00
1644698--1644751	26	2.2	25	81	15	60	48	1	1	48	1.23
1644718--1644788	35	2.0	36	81	13	85	47	1	2	47	1.25
1644789--1644833	23	2.0	23	90	0	72	53	2	0	44	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1644789--1644841	23	2.5	21	77	14	63	54	1	0	43	1.11
1646764--1646794	14	2.2	14	94	0	53	3	12	25	58	1.50
1648737--1648765	14	2.0	15	93	6	51	58	0	13	27	1.36
1651775--1651872	48	2.0	49	96	2	180	35	22	6	35	1.79
1652063--1652106	2	22.0	2	100	0	88	50	0	0	50	1.00
1653111--1653223	31	3.7	30	74	10	86	43	7	6	42	1.59
1653353--1653409	2	29.0	2	96	3	107	49	0	0	50	1.00
1653752--1653804	23	2.3	23	76	0	61	16	15	7	60	1.57
1655634--1656033	102	3.9	101	88	2	543	16	29	27	27	1.97
1658661--1658802	18	7.9	18	88	3	162	23	8	33	33	1.85
1658661--1658801	36	3.9	36	86	3	187	23	8	34	34	1.85
1661541--1661578	19	2.0	19	100	0	76	26	15	10	47	1.78
1665363--1665480	60	2.0	60	89	0	182	27	29	23	18	1.98
1667051--1667092	18	2.3	18	80	16	50	61	2	0	35	1.09
1668044--1668069	2	13.0	2	100	0	52	50	0	0	50	1.00
1672079--1672108	13	2.2	14	94	5	53	23	0	0	76	0.78
1673468--1673621	69	2.2	69	98	0	299	22	20	23	33	1.97
1675998--1676031	17	1.9	18	88	5	52	70	2	0	26	1.01
1675999--1676050	24	2.1	25	82	3	61	67	3	3	25	1.25
1678447--1678535	41	2.2	41	95	2	162	34	2	5	57	1.35
1679978--1680025	23	2.2	21	88	7	69	50	2	0	47	1.12
1689434--1689475	18	2.3	19	87	4	59	57	0	2	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1691660--1691699	20	2.0	20	90	9	64	17	17	25	40	1.91
1691706--1691760	20	2.8	20	75	10	67	29	14	29	27	1.95
1692176--1692203	11	2.5	11	100	0	56	35	17	25	21	1.95
1698916--1698954	20	2.0	20	94	0	69	12	25	41	20	1.88
1698991--1699032	20	2.1	20	90	0	66	16	21	38	23	1.93
1699247--1699302	21	2.9	19	79	12	69	46	10	12	30	1.76
1699247--1699303	18	2.9	19	80	12	71	45	12	12	29	1.78
1703516--1703572	28	2.0	29	96	3	107	21	24	0	54	1.45
1705420--1705471	26	2.0	26	88	7	79	30	3	3	61	1.32
1711741--1711784	22	2.1	21	83	8	54	11	25	40	22	1.87
1712067--1712118	21	2.6	19	81	6	68	19	25	40	15	1.90
1712067--1712111	21	2.1	21	91	0	72	17	26	42	13	1.86
1713803--1713841	18	2.1	18	85	9	51	51	10	5	33	1.58
1713857--1713894	19	2.1	18	90	9	60	42	7	5	44	1.56
1722996--1723048	13	3.8	13	86	13	79	60	13	9	16	1.58
1723038--1723082	10	4.6	10	83	2	56	60	15	11	13	1.60
1723501--1723569	33	2.1	33	100	0	138	37	13	14	34	1.85
1729377--1729508	60	2.2	60	89	4	196	31	18	18	31	1.95
1732674--1732705	2	16.0	2	93	0	55	46	0	0	53	1.00
1736116--1736272	64	2.4	65	79	6	178	33	19	18	28	1.95
1736776--1736831	22	2.5	22	82	0	67	17	23	30	28	1.97
1743009--1743164	64	2.4	65	80	11	187	35	18	18	27	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1743669--1743724	22	2.5	22	82	0	76	17	28	28	25	1.98
1744676--1744713	12	2.9	14	88	11	62	42	23	15	18	1.89
1748589--1748626	19	2.1	18	90	9	60	42	7	5	44	1.56
1748760--1748814	26	2.2	26	90	3	85	20	27	43	9	1.81
1749868--1749905	2	19.5	2	83	5	51	2	44	0	52	1.14
1750703--1750741	16	2.5	15	87	8	51	43	15	2	38	1.60
1750992--1751046	26	2.2	26	93	3	94	20	27	45	7	1.77
1752100--1752145	2	23.5	2	91	4	76	0	47	0	52	1.00
1753856--1753889	5	6.8	5	86	0	50	79	0	2	17	0.86
1754719--1754758	12	3.3	12	92	0	62	47	25	12	15	1.80

Tables:   1   2   3   4   5   6   7   8   9