genome.fa.s1.2.7.7.80.10.50.1000.6.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: 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  6  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)
1283212--1283249	20	1.9	20	84	10	51	50	10	7	31	1.66
1284640--1284685	23	2.0	23	91	0	74	36	21	21	19	1.95
1285278--1285342	21	3.1	21	79	0	76	30	18	18	32	1.95
1296694--1296842	58	2.6	58	95	0	271	34	20	20	24	1.97
1303155--1303240	4	23.0	4	69	13	58	50	0	0	50	1.00
1303155--1303240	6	15.3	6	75	13	58	50	0	0	50	1.00
1303155--1303235	36	2.2	36	95	0	144	49	0	0	50	1.00
1313442--1314414	488	2.0	482	95	4	1769	34	16	19	29	1.94
1314626--1314792	88	2.0	86	92	7	288	43	17	17	20	1.88
1322688--1322787	50	2.0	50	100	0	200	20	20	24	36	1.95
1323430--1323463	14	2.4	14	95	0	59	5	35	35	23	1.79
1323677--1323701	4	6.2	4	100	0	50	24	0	24	52	1.48
1329097--1329121	13	1.9	13	100	0	50	8	24	24	44	1.80
1329714--1329747	2	17.0	2	100	0	68	50	0	0	50	1.00
1337069--1337102	17	2.1	17	89	10	54	44	5	0	50	1.26
1339135--1339193	28	2.1	28	81	12	68	52	8	8	30	1.61
1340690--1340727	18	2.1	19	90	5	60	68	2	13	15	1.32
1340937--1340984	23	2.0	26	84	12	66	39	4	0	56	1.19
1342093--1342195	17	6.3	16	74	15	86	17	0	28	54	1.43
1342099--1342248	50	3.0	50	87	3	212	18	1	28	52	1.54
1342686--1342748	32	2.0	33	84	6	85	30	3	0	66	1.07
1363191--1363235	24	1.9	23	90	4	72	22	8	20	48	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1363190--1363241	24	2.2	24	82	6	70	25	7	19	48	1.75
1371517--1371561	21	2.1	21	87	0	63	31	28	24	15	1.96
1373242--1373308	22	3.0	22	91	2	107	20	26	26	25	1.99
1376414--1376458	21	2.1	21	87	0	63	31	28	24	15	1.96
1378151--1378217	22	3.0	22	95	2	116	19	26	28	25	1.99
1385141--1385190	20	2.5	20	96	0	91	48	0	0	52	1.00
1385141--1385203	20	3.1	20	88	6	74	47	1	1	49	1.20
1385423--1385448	6	4.3	6	100	0	52	69	0	0	30	0.89
1386500--1386545	17	2.6	17	82	6	56	41	0	4	54	1.20
1387271--1387308	18	2.1	18	100	0	76	15	39	5	39	1.70
1390679--1390708	2	14.5	2	93	6	51	46	3	0	50	1.18
1395965--1395999	3	11.7	3	100	0	70	0	65	0	34	0.93
1397680--1397713	17	1.9	18	88	5	52	41	5	11	41	1.66
1397822--1397862	2	20.5	2	100	0	82	51	0	0	48	1.00
1398335--1398413	27	2.9	27	92	0	122	50	16	13	18	1.78
1398345--1398421	27	2.9	27	92	0	118	53	19	10	16	1.72
1407774--1407869	36	2.7	36	86	0	138	66	0	33	0	0.92
1407771--1407868	12	8.2	12	84	0	115	66	0	33	0	0.92
1416781--1416861	34	2.4	34	100	0	162	29	17	14	38	1.90
1422052--1422095	20	2.3	19	81	14	54	65	9	6	18	1.42
1428954--1429026	31	2.4	31	85	0	101	47	8	5	38	1.56
1428999--1429058	28	2.1	28	85	11	79	46	6	5	41	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1431694--1431771	25	3.1	25	100	0	156	41	7	24	26	1.82
1453842--1453891	8	6.2	8	100	0	100	12	24	12	52	1.72
1459744--1459797	27	2.0	27	88	0	81	33	9	14	42	1.78
1460119--1460347	114	2.0	114	100	0	458	24	19	22	33	1.97
1463614--1463684	31	2.2	32	80	2	81	52	4	5	38	1.45
1464831--1464881	26	2.0	26	84	0	66	56	3	3	35	1.36
1468253--1468309	29	2.0	29	96	0	105	14	33	31	21	1.92
1468313--1468382	33	2.1	33	94	0	122	10	40	24	25	1.86
1468313--1468397	33	2.6	33	88	0	107	9	37	27	25	1.87
1468379--1468411	14	2.4	14	94	0	57	6	30	39	24	1.79
1468623--1468661	19	2.1	19	100	0	78	15	38	35	10	1.81
1471703--1471730	10	2.8	10	100	0	56	89	0	10	0	0.49
1472894--1473334	238	1.8	240	83	4	579	36	10	16	35	1.83
1473187--1473661	261	1.8	261	85	2	677	33	10	15	40	1.82
1475089--1475170	41	2.0	41	95	0	146	36	17	2	43	1.62
1487351--1487448	50	1.9	52	83	4	128	48	14	23	13	1.78
1488174--1488874	105	6.7	105	96	0	1222	33	25	18	22	1.96
1489250--1489331	41	2.0	41	95	0	146	36	17	2	43	1.62
1498483--1498796	103	3.0	103	96	0	565	28	19	29	22	1.98
1498848--1498894	23	2.0	24	83	8	60	42	4	2	51	1.33
1500859--1500913	28	2.0	28	88	0	83	30	9	18	41	1.81
1501540--1501576	17	2.2	17	95	0	65	16	18	18	45	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1505084--1505121	18	2.1	19	85	5	51	57	2	0	39	1.12
1505163--1505221	24	2.5	23	76	12	66	54	1	3	40	1.27
1507990--1508019	2	15.0	2	100	0	60	0	50	0	50	1.00
1514394--1514436	21	2.0	21	100	0	86	39	27	4	27	1.76
1516107--1516145	21	2.0	20	85	10	53	43	12	12	30	1.81
1526091--1526116	3	8.7	3	100	0	52	34	34	30	0	1.58
1526734--1526868	61	2.2	61	96	1	245	31	8	7	52	1.59
1528871--1529144	41	6.6	41	79	9	254	27	18	20	33	1.96
1528870--1529144	84	3.3	82	83	6	301	27	18	20	33	1.96
1530948--1531006	21	2.8	21	84	0	73	18	5	20	55	1.61
1530760--1531016	131	1.9	130	96	3	442	28	5	15	50	1.66
1531118--1531228	42	2.6	42	83	7	118	23	20	24	31	1.98
1531175--1531385	43	4.9	43	83	2	219	26	24	21	27	1.99
1537270--1537317	23	2.1	23	88	0	69	35	12	18	33	1.89
1537648--1537686	20	2.0	20	89	0	60	48	10	15	25	1.76
1538030--1538066	18	2.1	18	89	0	56	51	10	5	32	1.60
1538270--1538313	23	1.9	23	100	0	88	43	15	4	36	1.68
1538693--1538744	23	2.3	22	90	6	77	44	19	1	34	1.62
1538703--1538765	23	2.7	23	90	0	90	38	19	6	36	1.77
1540472--1540497	3	8.7	3	100	0	52	34	34	30	0	1.58
1541115--1541238	61	2.0	60	93	1	212	33	9	5	50	1.59
1541510--1541545	18	1.9	19	88	5	56	50	0	2	47	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1543452--1543567	33	3.6	32	79	5	108	30	7	8	53	1.60
1560231--1560289	29	2.0	29	100	0	118	23	13	13	49	1.78
1564666--1564724	29	2.0	29	100	0	118	23	13	13	49	1.78
1566557--1566597	6	6.8	6	91	0	55	41	0	9	48	1.36
1572026--1572100	37	2.0	37	97	0	141	38	20	10	30	1.86
1574655--1574714	25	2.4	25	100	0	120	28	13	23	35	1.92
1585035--1585071	15	2.5	15	90	0	56	8	67	16	8	1.40
1586523--1586579	16	3.5	16	76	11	53	77	3	7	12	1.10
1594699--1594735	3	12.3	3	94	0	65	67	0	2	29	1.04
1607501--1607793	148	2.0	148	91	2	482	48	9	7	34	1.63
1607960--1608045	35	2.4	35	86	1	118	30	1	26	41	1.63
1615027--1615065	19	2.1	19	90	9	62	43	7	5	43	1.55
1626205--1626370	82	2.0	82	100	0	332	34	12	15	37	1.85
1626557--1626598	2	21.0	2	100	0	84	50	0	0	50	1.00
1626785--1626823	20	1.9	21	84	5	53	30	7	5	56	1.49
1634902--1634956	26	2.1	26	96	0	101	47	12	3	36	1.59
1638203--1638248	16	3.1	16	70	23	55	32	8	2	56	1.42
1639142--1639177	6	6.0	6	96	0	63	63	2	0	33	1.08
1648376--1648432	30	1.9	30	85	0	78	28	8	8	54	1.61
1648724--1648757	17	2.0	17	94	0	59	14	5	47	32	1.69
1649057--1649093	2	18.5	2	100	0	74	48	0	0	51	1.00
1653207--1653265	2	29.5	2	100	0	118	50	0	0	49	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1653676--1653717	2	21.0	2	100	0	84	50	0	0	50	1.00
1659805--1659842	2	19.0	2	100	0	76	50	0	0	50	1.00
1665980--1666031	13	4.0	13	76	16	54	57	0	0	42	0.98
1668207--1668262	23	2.4	23	79	8	60	51	3	0	44	1.18
1672571--1672618	2	24.0	2	100	0	96	50	0	0	50	1.00
1675368--1675401	15	2.3	15	100	0	68	55	11	26	5	1.58
1687191--1687253	6	9.8	6	81	13	72	82	1	1	14	0.82
1687189--1687253	20	3.4	18	83	12	76	81	3	1	13	0.88
1687191--1687253	14	4.8	13	86	9	76	82	1	1	14	0.82
1689435--1689468	9	3.8	9	88	11	52	76	0	2	20	0.92

Tables:   1   2   3   4   5   6   7   8