genome.fa.s9634.2.7.7.80.10.50.1000.9.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   

This is table  9  of  78  ( 9351 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)
1871109--1871137	9	3.3	9	95	4	51	79	0	0	20	0.74
1872501--1872556	3	18.0	3	92	7	94	66	0	0	33	0.92
1872576--1872672	36	2.7	36	83	0	104	24	39	4	31	1.74
1872650--1872766	45	2.6	46	87	5	168	24	47	4	23	1.70
1880443--1880511	34	2.0	34	86	5	95	26	42	14	17	1.87
1882376--1882419	21	2.0	23	91	8	74	22	27	13	36	1.92
1883798--1883870	20	3.6	21	78	8	80	28	16	30	24	1.96
1883745--1883966	94	2.3	93	79	11	220	31	14	25	28	1.95
1884265--1884854	59	10.0	59	89	0	885	34	11	22	32	1.89
1888471--1888545	18	4.1	18	81	6	96	25	30	24	20	1.98
1888470--1888544	38	2.0	38	94	0	132	25	30	24	20	1.98
1889796--1889853	20	2.6	22	89	10	84	25	22	20	31	1.98
1889841--1889981	64	2.2	63	83	5	176	25	23	18	32	1.97
1891229--1891268	20	2.1	19	90	4	62	20	17	0	62	1.33
1893210--1893247	20	1.9	20	88	0	58	23	28	23	23	1.99
1894518--1894555	20	1.9	20	88	0	58	26	21	21	31	1.98
1894567--1894703	64	2.2	63	84	4	168	27	21	17	33	1.96
1916456--1916499	23	1.9	23	86	9	63	56	2	0	40	1.11
1917213--1917253	20	2.0	20	95	0	73	34	0	2	63	1.08
1918048--1918098	11	4.7	11	78	11	52	72	9	0	17	1.11
1918098--1918143	21	2.1	22	88	11	69	32	4	2	60	1.28
1920842--1920875	2	17.5	2	93	6	61	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1920834--1920873	17	2.4	17	91	0	62	47	2	2	47	1.29
1920843--1920872	15	2.0	15	100	0	60	46	0	0	53	1.00
1920842--1920874	17	1.9	17	100	0	66	48	0	0	51	1.00
1921565--1922654	214	5.3	214	88	7	1537	51	8	12	28	1.68
1922750--1922936	19	9.6	19	68	16	82	44	6	6	41	1.58
1922738--1922813	19	3.8	19	77	11	64	46	2	6	44	1.43
1922738--1922811	38	1.9	39	88	2	114	45	2	6	44	1.44
1922899--1922936	11	3.5	11	88	0	58	50	2	2	44	1.30
1922942--1922995	17	3.1	17	81	2	63	46	0	3	50	1.19
1922974--1923032	22	2.5	24	81	13	77	44	1	5	49	1.34
1923080--1923136	29	2.0	28	80	12	73	40	5	0	54	1.23
1923080--1923174	40	2.4	39	83	13	113	42	4	1	52	1.27
1923161--1923228	29	2.4	28	78	11	75	48	5	5	39	1.52
1923180--1923238	29	2.0	29	86	0	82	47	6	10	35	1.64
1923244--1923311	18	3.7	18	77	14	75	41	11	7	39	1.70
1923243--1923303	20	3.2	19	74	25	65	40	9	6	42	1.64
1923252--1923366	20	6.2	18	68	28	57	39	9	6	44	1.64
1923278--1923380	29	3.7	30	72	25	109	37	9	6	45	1.64
1923262--1923396	53	2.6	49	77	17	139	39	8	5	45	1.60
1923128--1923375	91	2.9	87	78	11	251	42	8	6	43	1.60
1923277--1923395	51	2.3	49	88	8	175	37	9	5	47	1.60
1923334--1923423	18	4.8	18	75	15	76	41	7	4	46	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1923988--1924130	64	2.2	65	83	6	175	30	26	19	23	1.98
1924102--1924150	19	2.6	19	84	9	57	24	28	20	26	1.99
1926119--1926174	21	2.7	21	74	17	55	51	7	17	23	1.70
1931909--1931937	14	2.0	15	93	6	51	6	3	27	62	1.37
1934138--1934166	12	2.4	12	100	0	58	0	41	31	27	1.56
1935377--1935423	24	2.0	23	84	12	60	34	6	4	55	1.45
1935795--1935834	21	1.9	21	89	0	62	10	25	40	25	1.86
1943953--1944083	51	2.6	49	79	12	142	48	4	3	42	1.41
1944160--1944198	16	2.4	16	91	0	60	33	17	28	20	1.96
1948371--1948498	37	3.4	36	87	8	177	17	39	14	28	1.90
1948693--1948799	3	35.3	3	71	17	62	63	0	33	1	1.11
1948685--1948774	23	3.7	25	71	26	77	63	1	33	2	1.14
1948710--1948797	19	4.5	19	79	12	97	64	0	34	1	1.01
1948727--1948811	13	6.4	13	73	4	62	65	0	31	2	1.05
1952493--1952552	20	2.9	20	90	5	84	16	26	35	21	1.95
1956563--1956610	20	2.5	20	80	6	55	22	16	8	52	1.71
1958883--1958994	56	2.0	56	92	3	190	31	6	25	37	1.81
1959826--1959865	21	1.9	21	85	10	55	17	30	35	17	1.93
1961275--1961660	40	9.4	41	83	4	370	27	17	18	35	1.94
1964250--1964560	43	7.2	42	82	5	297	25	21	19	33	1.97
1964250--1964560	86	3.6	86	82	3	358	25	21	19	33	1.97
1967072--1967164	29	3.0	29	78	9	87	2	25	1	70	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1974674--1974980	154	2.0	153	98	1	589	36	19	17	26	1.94
1977126--1977172	3	16.0	3	86	4	69	70	0	29	0	0.88
1977131--1977165	17	2.1	17	94	0	61	68	0	31	0	0.90
1977126--1977171	23	2.0	23	100	0	92	69	0	30	0	0.89
1978188--1978687	127	4.0	127	90	1	745	29	25	18	26	1.98
1978188--1978670	253	1.9	254	90	1	781	29	25	18	26	1.98
1994445--1994493	2	24.5	2	100	0	98	48	0	0	51	1.00
1994549--1994588	19	2.2	18	90	4	62	32	0	2	65	1.06
1997510--1997668	81	1.9	83	86	8	227	42	11	12	32	1.79
1997692--1998184	197	2.5	199	83	5	630	29	15	15	39	1.88
1998011--1998330	168	1.9	172	82	5	407	31	11	14	42	1.81
2000785--2000832	18	2.6	19	86	3	71	52	12	2	33	1.51
2002126--2002695	200	2.9	194	88	5	822	31	15	13	39	1.86
2004864--2004914	21	2.4	21	93	0	84	45	19	13	21	1.85
2004663--2005101	223	2.0	224	87	3	645	31	17	13	37	1.88
2004885--2005644	200	3.8	198	85	4	979	31	16	14	37	1.89
2004886--2005644	400	1.9	400	88	2	1137	31	16	14	37	1.89
2006002--2006046	19	2.4	19	88	0	63	60	4	2	33	1.29
2007787--2007853	33	2.0	33	97	0	125	23	46	0	29	1.53
2010271--2010759	176	2.7	181	86	5	706	28	15	14	41	1.87
2011280--2011321	12	3.6	12	77	3	50	47	7	2	42	1.43
2012376--2012412	19	1.9	19	89	10	58	24	0	5	70	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2012418--2012493	25	3.1	24	80	12	75	15	7	1	75	1.10
2012418--2012519	25	4.1	24	72	14	73	19	5	0	73	1.09
2012424--2012519	49	1.9	50	83	10	126	19	5	1	73	1.08
2012549--2012590	14	2.9	15	77	22	54	16	0	4	78	0.91
2014305--2014348	18	2.4	18	88	7	63	11	13	9	65	1.46
2015559--2015624	22	3.0	22	97	0	123	24	27	27	21	1.99
2015572--2015612	13	3.5	13	75	25	54	24	26	26	21	2.00
2017223--2017262	21	1.9	21	84	0	53	17	22	30	30	1.97
2020281--2020345	21	3.0	22	93	4	114	24	27	26	21	1.99
2021520--2021552	2	16.5	2	93	0	57	48	0	3	48	1.17
2021600--2021638	16	2.4	16	83	12	53	38	17	5	38	1.72
2021987--2022026	20	2.0	20	85	0	53	17	22	30	30	1.97
2025486--2026269	84	9.4	84	83	4	865	30	25	20	23	1.98
2025486--2026269	252	3.1	251	88	3	1073	30	25	20	23	1.98
2028003--2028032	14	2.1	14	100	0	60	20	6	0	73	1.05
2027974--2028082	48	2.3	46	77	16	105	20	7	0	71	1.15
2032552--2032576	1	25.0	1	100	0	50	0	0	100	0	0.00
2033094--2033145	2	26.5	2	96	3	97	51	0	0	48	1.00
2033343--2033383	20	2.0	21	95	4	75	51	4	0	43	1.23
2034450--2034568	45	2.6	45	81	5	125	26	8	21	42	1.81
2045571--2045625	27	2.0	27	92	0	92	70	10	14	3	1.28
2045605--2045646	18	2.3	18	91	0	75	83	0	16	0	0.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2045582--2045685	27	3.8	27	77	10	95	78	3	15	1	0.98
2045582--2045689	18	5.9	17	73	10	63	79	3	14	1	0.95
2047931--2048156	114	2.0	114	90	0	353	33	15	19	31	1.93
2049709--2049863	54	2.9	54	91	0	247	37	16	23	22	1.94
2050229--2050283	22	2.5	22	84	0	74	36	14	12	36	1.84
2050683--2051591	113	7.9	113	87	4	1169	39	14	18	27	1.90
2051720--2051783	31	2.1	31	85	5	85	37	0	1	60	1.06
2051721--2051776	23	2.5	22	85	8	69	39	0	1	58	1.08
2053085--2053124	21	1.9	21	85	10	55	32	5	2	60	1.32
2057732--2057792	21	3.2	21	68	29	64	42	19	4	32	1.73

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78