genome.fa.s9070.2.7.7.80.10.50.1000.6.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: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2268343

Tables:   1   2   3   4   5   6   7   8   9   

This is table  6  of  9  ( 1013 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)
1333379--1333465	43	2.0	42	91	2	138	49	0	0	50	1.00
1333523--1333598	36	2.3	31	74	21	82	17	35	11	35	1.86
1337136--1338498	474	2.8	476	86	4	1913	43	13	17	24	1.86
1344737--1344767	16	1.9	16	93	0	53	64	3	6	25	1.33
1353331--1353516	56	3.3	55	78	3	192	27	15	16	40	1.89
1357405--1357452	16	3.1	15	76	8	51	35	4	0	60	1.16
1369369--1369457	31	2.9	30	74	9	83	38	5	8	47	1.59
1372086--1372125	10	3.8	10	81	12	53	70	2	0	27	1.01
1373387--1373443	29	2.0	29	86	6	80	50	0	5	43	1.24
1373834--1373890	10	5.5	10	83	8	60	22	3	1	71	1.10
1373828--1373890	21	3.0	20	79	9	63	23	3	3	69	1.17
1373845--1373892	11	4.5	11	80	15	55	22	4	0	72	1.01
1377779--1377858	35	2.3	35	79	12	85	53	10	7	28	1.61
1380156--1380194	18	2.2	18	95	4	71	64	0	0	35	0.94
1387492--1387526	2	17.5	2	100	0	70	48	0	0	51	1.00
1388382--1388411	7	4.3	7	100	0	60	30	0	13	56	1.37
1398087--1398120	17	1.9	18	88	5	52	47	0	0	52	1.00
1411822--1411865	21	2.1	21	91	0	70	40	2	0	56	1.11
1412240--1412303	31	2.1	30	83	11	78	46	14	0	39	1.44
1420035--1420067	16	2.1	16	100	0	66	42	9	24	24	1.83
1420129--1420351	35	6.0	35	70	15	115	25	21	15	37	1.93
1420125--1420453	77	4.3	77	88	0	469	26	20	17	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1420164--1420469	42	7.8	41	69	15	173	26	20	17	36	1.94
1420127--1420453	154	2.1	154	89	1	521	26	19	17	35	1.95
1420982--1421051	34	2.0	35	88	2	106	52	11	10	25	1.68
1422432--1422478	20	2.2	21	85	7	60	55	0	0	44	0.99
1423052--1423106	26	2.4	25	82	17	66	7	23	5	63	1.41
1428279--1428346	33	2.2	32	81	7	77	42	0	1	55	1.08
1428307--1428370	30	2.2	28	83	5	74	40	0	0	59	0.97
1428363--1428394	17	1.9	17	93	6	57	21	3	6	68	1.26
1428515--1428553	17	2.3	17	86	0	51	46	2	0	51	1.14
1430150--1430189	21	1.9	21	94	0	71	20	30	20	30	1.97
1430837--1430900	23	2.8	23	79	9	76	32	26	21	18	1.97
1431112--1431178	30	2.2	30	89	0	98	31	23	4	40	1.75
1437211--1437329	59	2.0	59	90	3	186	28	28	18	24	1.98
1437854--1437922	23	3.0	22	83	8	84	26	24	26	23	2.00
1440018--1440090	34	2.1	34	89	0	110	53	6	4	35	1.47
1442429--1442489	15	3.9	16	78	10	63	60	0	0	39	0.97
1442433--1442520	32	2.7	33	75	15	85	57	0	1	40	1.06
1449010--1449047	6	6.3	6	100	0	76	52	15	0	31	1.43
1449918--1449959	21	2.0	22	85	4	59	26	0	26	47	1.52
1461447--1461480	13	2.7	13	90	4	52	61	5	2	29	1.34
1462338--1462389	13	4.2	12	92	7	86	15	15	15	53	1.73
1462337--1462389	25	2.1	26	96	3	99	15	15	15	54	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1462338--1462389	19	2.8	19	97	2	97	15	15	15	53	1.73
1462338--1462389	6	8.3	6	91	8	86	15	15	15	53	1.73
1463088--1463149	31	2.0	31	87	6	90	38	22	19	19	1.93
1463979--1464028	24	2.1	24	85	7	66	26	2	12	60	1.43
1464502--1464538	19	1.9	19	89	10	58	18	8	0	72	1.08
1474218--1474267	24	2.1	24	85	7	66	26	2	12	60	1.43
1479813--1479934	64	1.9	64	84	3	165	27	15	20	36	1.93
1484857--1484949	24	3.9	24	72	10	82	22	12	17	47	1.81
1486017--1486062	24	1.9	24	82	8	58	36	10	8	43	1.71
1487686--1487711	12	2.2	12	100	0	52	76	0	15	7	0.99
1488934--1489006	30	2.4	30	79	2	74	34	17	10	36	1.85
1489438--1489512	37	2.0	37	82	10	91	49	4	1	45	1.29
1497991--1498015	3	8.3	3	100	0	50	68	0	32	0	0.90
1503361--1503402	21	2.0	20	86	13	59	30	0	2	66	1.04
1514708--1514783	30	2.6	30	93	2	136	27	11	6	53	1.62
1518727--1518804	20	3.9	21	78	18	87	41	23	19	16	1.90
1518680--1518804	40	3.1	40	73	19	100	37	25	16	20	1.93
1519246--1519284	20	2.0	19	85	5	51	51	23	15	10	1.73
1521427--1521525	21	4.7	21	76	9	103	24	35	19	21	1.96
1521427--1521545	42	2.8	42	81	7	134	23	36	19	20	1.95
1522893--1523032	66	2.2	62	85	7	176	31	0	17	50	1.51
1523695--1523758	24	2.7	24	78	4	76	48	10	4	35	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1523703--1523739	18	2.1	18	89	0	56	51	10	5	32	1.60
1524126--1524175	25	2.0	25	96	0	91	44	22	8	26	1.80
1524266--1524340	20	3.8	20	89	0	105	41	21	17	20	1.90
1524641--1524681	18	2.3	18	91	0	64	17	0	26	56	1.41
1524641--1524680	12	3.3	12	85	0	53	17	0	27	55	1.43
1526936--1526989	24	2.2	24	83	6	65	40	24	14	20	1.90
1527887--1527976	20	4.6	19	78	6	74	25	14	21	38	1.91
1527887--1527957	19	3.7	20	83	5	83	26	14	21	38	1.91
1530828--1530930	33	3.2	33	90	2	156	44	14	7	33	1.74
1530925--1530966	21	2.0	21	95	0	75	47	7	14	30	1.71
1547479--1547536	23	2.5	23	80	5	64	44	13	25	15	1.83
1552075--1552199	8	14.9	8	77	6	88	32	3	16	48	1.63
1552071--1552191	12	10.2	12	80	3	111	32	3	17	47	1.64
1552087--1552191	4	26.8	4	82	3	124	29	3	20	46	1.68
1556558--1556602	16	2.8	17	83	6	58	31	0	0	68	0.89
1556576--1556620	20	2.3	19	84	3	54	35	0	2	62	1.08
1556571--1556626	29	2.0	30	83	13	75	37	0	1	60	1.07
1556619--1556713	3	31.7	3	91	0	145	61	0	4	34	1.16
1557033--1557673	113	5.7	113	96	0	1104	30	18	13	36	1.90
1558341--1558788	82	5.5	82	96	0	792	37	21	13	28	1.91
1559942--1560015	10	7.1	10	79	14	69	2	16	0	81	0.81
1559938--1560012	34	2.2	35	85	7	100	2	16	0	81	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1559939--1560011	6	10.7	7	76	15	57	2	15	0	82	0.79
1570593--1570629	15	2.7	15	88	12	53	62	8	5	24	1.44
1570620--1570670	18	2.9	17	75	16	50	72	1	0	25	0.95
1572789--1572833	20	2.3	19	84	3	54	35	0	2	62	1.08
1572784--1572839	29	2.0	30	83	13	75	37	0	1	60	1.07
1572832--1572929	3	32.7	3	93	0	169	63	0	2	34	1.06
1573023--1573072	22	2.2	22	89	3	73	38	4	16	42	1.66
1573035--1573078	22	2.0	23	95	4	81	34	4	20	40	1.73
1573195--1573223	2	14.5	2	100	0	58	48	0	0	51	1.00
1578521--1578550	5	6.0	5	92	0	51	76	20	0	3	0.92
1578521--1578549	15	1.9	15	100	0	58	75	20	0	3	0.94
1583559--1583588	2	15.0	2	100	0	60	50	0	0	50	1.00
1583875--1583908	17	2.0	17	88	11	52	38	8	0	52	1.33
1588290--1588323	16	2.1	16	94	0	59	32	8	26	32	1.87
1589074--1589105	15	2.1	16	94	5	57	50	18	25	6	1.70
1593228--1593289	25	2.5	25	86	5	81	45	9	0	45	1.36
1598966--1599047	29	2.8	29	94	1	137	32	14	9	42	1.79
1600336--1600365	15	2.0	15	93	0	51	56	23	0	20	1.42
1603734--1603815	29	2.8	29	94	1	137	32	14	9	42	1.79
1606150--1606197	14	3.2	14	80	19	53	50	0	0	50	1.00
1611066--1611287	111	2.0	111	96	0	408	45	11	7	35	1.69
1611573--1611681	50	2.2	50	83	1	139	22	27	32	17	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1633201--1633883	346	2.0	346	98	0	1321	23	15	21	38	1.92
1634249--1634282	3	12.0	3	87	12	54	70	0	0	29	0.87
1634249--1634282	17	2.0	17	100	0	68	70	0	0	29	0.87
1634248--1634281	11	3.1	11	91	8	52	73	0	0	26	0.83
1635641--1635731	36	2.7	32	74	14	101	49	2	3	45	1.30
1638860--1638897	19	2.0	19	90	10	60	13	31	31	23	1.93
1639118--1639202	2	42.5	2	92	4	145	49	0	1	49	1.08
1639658--1639701	23	1.9	23	90	0	70	18	29	25	27	1.98
1639805--1639841	18	2.1	17	90	5	56	18	13	35	32	1.90
1644501--1644546	22	2.0	22	83	4	56	28	26	28	17	1.98

Tables:   1   2   3   4   5   6   7   8   9