genome.fa.s9463.2.7.7.80.10.50.1000.9.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: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  3931635

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  9  of  20  ( 2327 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)
1661278--1661322	22	2.0	22	91	0	72	33	8	8	48	1.65
1661525--1661570	19	2.4	19	96	0	83	60	4	0	34	1.16
1665353--1665394	22	2.0	21	95	4	75	42	0	11	45	1.41
1665359--1665586	38	6.0	37	74	13	164	40	4	10	43	1.61
1665552--1665724	22	7.2	24	70	21	105	43	2	9	44	1.51
1665605--1665656	27	2.0	26	88	7	79	55	3	3	36	1.36
1666959--1666998	17	2.3	18	91	4	64	20	2	0	77	0.88
1666959--1667008	17	2.9	16	80	16	55	20	2	0	78	0.86
1666960--1667008	9	5.3	9	80	2	53	18	2	0	79	0.83
1670752--1670801	24	2.1	24	92	0	82	32	28	16	24	1.96
1679107--1679153	22	2.0	22	84	8	58	48	0	8	42	1.33
1679122--1679345	37	5.9	37	76	12	163	47	4	7	40	1.54
1679121--1679346	38	6.0	37	74	14	144	46	4	7	40	1.54
1679323--1679418	22	4.2	22	81	5	102	46	2	6	44	1.40
1679310--1679414	47	2.2	46	82	12	117	44	2	8	43	1.49
1679364--1679408	23	1.9	23	90	4	72	51	4	0	44	1.21
1679311--1679420	22	4.8	22	74	12	87	45	2	7	44	1.45
1679464--1679501	3	13.0	3	84	15	53	34	0	0	65	0.93
1680361--1680393	12	2.8	12	100	0	66	6	9	60	24	1.49
1680744--1680792	15	3.1	15	79	5	53	24	10	2	63	1.37
1680899--1680949	19	2.7	19	96	3	95	35	5	0	58	1.22
1682029--1682061	12	2.6	13	95	4	59	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1682029--1682089	25	2.3	25	81	13	61	34	1	0	63	1.04
1683493--1683517	12	2.1	12	100	0	50	16	8	0	76	1.02
1684281--1684310	15	2.0	15	100	0	60	33	6	0	60	1.23
1691979--1692023	20	2.2	20	88	0	63	26	20	22	31	1.98
1692006--1692099	42	2.3	41	83	1	116	25	22	23	28	1.99
1692259--1692363	42	2.5	41	85	1	138	24	21	20	32	1.98
1692274--1692351	21	3.7	21	67	13	61	26	19	21	32	1.97
1691729--1692424	277	2.6	276	85	5	752	31	17	17	33	1.94
1692254--1692367	20	5.6	20	69	10	70	24	21	21	32	1.98
1700187--1700220	5	6.8	5	100	0	68	82	0	0	17	0.67
1702782--1702822	18	2.3	18	86	0	55	53	2	17	26	1.56
1708473--1708686	2	108.0	2	64	22	62	47	3	4	44	1.40
1708478--1708568	31	3.1	31	72	25	90	47	2	2	48	1.26
1708573--1708612	13	3.4	12	86	13	57	50	7	7	35	1.59
1708580--1708623	13	3.2	13	80	6	52	50	9	4	36	1.55
1708783--1708824	17	2.4	17	81	18	50	42	0	28	28	1.56
1709041--1709255	8	26.6	8	76	9	159	0	14	48	35	1.51
1709043--1709247	10	20.1	10	79	11	166	0	14	48	36	1.50
1709051--1709243	4	48.2	4	80	2	118	0	13	49	36	1.47
1709051--1709266	14	15.0	14	79	7	157	0	15	49	35	1.48
1709352--1709389	2	19.0	2	100	0	76	50	0	0	50	1.00
1709470--1709502	7	5.0	7	85	14	52	30	42	0	27	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1709521--1709546	4	6.5	4	100	0	52	0	23	50	26	1.50
1709547--1709691	76	1.9	76	97	0	272	44	2	7	46	1.43
1709716--1709770	2	28.0	2	96	3	103	49	0	0	50	1.00
1709855--1709887	7	5.0	7	85	14	52	30	42	0	27	1.56
1709894--1709955	19	3.2	19	84	4	79	48	6	3	41	1.45
1710038--1710081	21	2.1	21	86	0	61	47	29	0	22	1.51
1710449--1710495	2	23.0	2	95	4	85	48	0	2	48	1.13
1710578--1710628	14	3.6	14	71	10	50	47	29	1	21	1.62
1710992--1711041	2	24.0	2	88	8	73	50	2	2	46	1.24
1710981--1711048	18	3.6	19	86	6	93	50	5	2	41	1.42
1711138--1711189	7	7.4	7	82	0	50	48	28	0	23	1.51
1711129--1711189	21	2.9	21	75	0	59	47	29	0	22	1.52
1711558--1711607	2	24.0	2	88	8	73	50	2	2	46	1.24
1709896--1712144	565	4.0	562	88	4	3264	43	10	8	37	1.70
1712497--1712554	22	2.5	23	81	18	68	43	1	0	55	1.10
1711829--1712755	450	2.1	451	94	1	1637	43	12	8	36	1.73
1713100--1713157	2	28.0	2	89	6	89	50	1	1	46	1.22
1713246--1713320	28	2.7	29	89	4	102	53	24	0	22	1.46
1713244--1713327	21	4.0	21	76	6	89	53	25	0	21	1.46
1713274--1713320	14	3.4	14	77	11	60	55	25	0	19	1.43
1713273--1713328	28	2.0	28	92	0	94	55	26	0	17	1.43
1713246--1713313	14	4.9	14	73	7	57	52	23	0	23	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1713701--1713742	2	21.0	2	90	9	68	50	2	0	47	1.14
1713830--1713867	7	5.4	7	81	12	51	57	26	0	15	1.38
1714096--1714151	21	2.7	21	100	0	112	39	0	0	60	0.97
1714347--1714385	16	2.4	16	91	0	60	38	15	25	20	1.92
1722306--1722425	63	1.9	64	87	1	179	43	16	12	27	1.84
1724860--1724899	21	2.0	20	85	5	53	42	0	0	57	0.98
1725197--1725268	21	3.5	21	84	1	83	33	23	20	22	1.97
1725213--1725292	21	3.8	21	79	0	88	36	22	20	21	1.95
1725213--1725313	42	2.4	42	81	3	123	33	22	18	24	1.97
1728022--1728136	51	2.3	51	87	6	162	49	8	4	37	1.54
1734882--1734963	32	2.6	32	78	3	85	36	18	12	32	1.88
1739189--1739231	15	3.0	14	83	6	50	58	0	13	27	1.37
1741995--1742652	81	8.1	81	88	1	890	32	23	10	34	1.88
1747890--1748524	81	7.9	81	89	1	947	30	23	11	34	1.90
1747890--1748524	161	4.0	161	89	2	940	30	23	11	34	1.90
1749253--1749301	21	2.6	19	84	12	57	30	26	14	28	1.95
1751492--1751585	21	4.5	21	75	9	86	31	29	17	21	1.96
1765170--1768104	990	3.0	973	96	2	5333	34	17	15	32	1.91
1775128--1775180	7	7.7	7	85	2	63	24	7	1	66	1.28
1775128--1775180	14	3.8	14	84	0	79	24	7	1	66	1.28
1775128--1775180	21	2.5	21	90	0	88	24	7	1	66	1.28
1788588--1788624	17	2.1	18	85	14	51	29	0	0	70	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1789891--1789938	21	2.3	21	85	0	60	14	18	35	31	1.91
1790325--1790375	2	25.5	2	100	0	102	50	0	0	49	1.00
1793060--1793266	111	1.9	111	88	4	319	33	18	14	33	1.91
1793449--1793484	16	2.2	17	95	5	65	55	19	0	25	1.43
1793798--1793873	22	3.6	22	69	25	74	25	22	15	36	1.93
1793800--1793878	40	2.0	40	97	0	149	22	25	15	36	1.93
1793801--1793890	40	2.2	40	92	0	144	25	24	13	36	1.92
1808631--1808689	23	2.7	22	77	15	59	71	3	6	18	1.23
1809865--1810144	141	2.0	141	87	1	400	22	15	20	42	1.89
1818336--1818512	69	2.6	69	90	1	268	26	15	10	48	1.77
1819361--1819426	30	2.2	30	89	2	98	31	22	30	15	1.95
1820283--1820318	18	1.9	19	88	5	56	25	5	19	50	1.69
1821214--1821327	48	2.4	48	86	1	156	35	14	10	39	1.81
1840666--1840717	23	2.3	23	96	0	95	57	11	7	23	1.59
1855894--1856043	21	6.8	21	71	19	119	38	22	20	20	1.94
1855894--1856052	42	3.7	42	84	11	146	37	22	19	20	1.94
1855915--1856052	42	3.2	46	91	5	184	36	23	19	20	1.95
1855946--1856058	21	5.4	21	74	16	108	35	24	20	19	1.96
1864852--1864921	31	2.3	31	79	16	83	31	7	4	57	1.45
1869071--1869169	30	3.3	29	75	2	99	61	9	16	13	1.55
1869099--1869170	29	2.4	29	76	2	81	58	8	19	13	1.61
1870553--1870598	3	15.0	3	86	13	67	67	2	0	30	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1870542--1870598	22	2.6	22	86	10	73	64	3	0	31	1.10
1870545--1870598	25	2.2	25	86	6	74	64	1	0	33	1.04
1871033--1871103	28	2.5	29	90	4	110	46	16	14	22	1.83
1871033--1871120	28	3.0	28	83	11	97	43	14	17	25	1.87
1871240--1871377	38	4.0	32	74	17	118	38	11	15	34	1.83
1871454--1871602	66	2.3	67	89	2	221	38	12	14	34	1.83
1871454--1871641	66	2.8	66	83	4	175	40	11	14	33	1.82
1871664--1871827	68	2.5	68	80	7	178	43	14	13	28	1.82
1871664--1871820	67	2.4	63	79	10	172	43	14	14	28	1.83
1871780--1871846	30	2.4	28	85	9	91	41	14	10	32	1.80

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20