genome.fa.s4117.2.7.7.80.10.50.1000.1.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  1  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)
1--7908	7	1144.9	7	95	4	13522	41	43	0	13	1.50
7906--8062	7	22.4	7	100	0	314	14	57	28	0	1.37
8060--8112	12	4.2	12	90	4	70	35	45	3	15	1.64
8109--8182	7	10.6	7	100	0	148	14	58	27	0	1.37
8102--8198	21	4.6	21	89	0	104	19	54	22	3	1.58
9922--9972	3	17.0	3	83	0	57	23	33	5	37	1.79
9926--9989	12	5.3	12	86	0	74	20	32	7	39	1.81
9926--9989	6	10.7	6	82	0	56	20	32	7	39	1.81
11485--12605	200	5.6	200	96	0	2035	31	18	14	35	1.91
17132--17198	28	2.4	28	97	0	125	44	23	2	28	1.68
17132--17205	14	5.3	14	72	16	64	44	24	4	27	1.71
17193--17273	28	2.9	29	76	7	87	44	24	2	28	1.67
17221--17289	7	9.9	7	76	6	68	42	27	2	27	1.70
17186--17230	21	2.2	20	92	4	72	42	26	2	28	1.67
17221--17289	21	3.3	20	80	6	75	42	27	2	27	1.70
17202--17292	35	2.6	35	80	3	103	42	27	2	27	1.67
17325--17373	22	2.3	22	85	3	64	46	28	8	16	1.75
17416--17594	7	25.7	7	69	5	76	40	29	4	25	1.75
17540--17579	13	2.9	14	88	7	64	42	27	2	27	1.68
17540--17601	27	2.3	27	80	8	72	41	32	1	24	1.64
33707--33735	5	5.8	5	100	0	58	0	0	58	41	0.98
37551--37587	19	1.9	19	88	0	56	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47786--48064	36	7.9	36	87	3	354	18	24	23	34	1.96
47786--48060	71	3.9	71	85	3	367	18	24	23	34	1.96
47786--48064	107	2.6	106	87	5	377	18	24	23	34	1.96
49303--49414	39	2.9	38	76	6	111	43	1	7	47	1.41
49303--49408	37	2.8	39	78	5	110	40	1	7	50	1.42
49432--49648	34	6.4	33	73	20	157	44	3	7	44	1.49
49434--49612	71	2.6	71	77	16	180	45	3	7	43	1.50
49426--49577	35	4.2	37	75	17	117	46	3	7	42	1.50
49539--49610	32	2.2	32	79	16	78	47	4	5	43	1.46
49677--49729	20	2.5	22	77	20	60	28	5	0	66	1.15
49689--49750	14	4.4	14	75	4	52	27	4	0	67	1.10
49690--49750	24	2.5	24	79	10	70	27	4	0	67	1.11
49689--49750	19	3.3	18	80	6	61	27	4	0	67	1.10
55920--56619	84	8.4	83	78	5	682	29	24	20	25	1.99
55920--56648	165	4.4	166	78	5	722	29	24	20	25	1.99
55920--56619	249	2.8	249	92	0	1098	29	24	20	25	1.99
57271--57357	39	2.2	39	85	4	113	47	1	5	45	1.34
57271--57362	37	2.4	37	84	10	107	44	1	6	47	1.36
57399--57483	35	2.5	31	77	15	98	45	3	8	42	1.51
57409--57491	34	2.4	34	80	11	91	43	4	7	44	1.53
57487--57512	11	2.4	11	100	0	52	34	0	15	50	1.45
57642--57686	16	2.9	16	87	9	58	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57643--57681	14	2.6	14	88	8	51	43	0	0	56	0.99
57676--57711	5	7.2	5	93	0	63	19	2	0	77	0.88
62404--62447	18	2.4	18	78	14	54	27	36	2	34	1.70
76601--76830	41	5.7	41	74	18	214	47	6	20	25	1.75
76636--76702	33	2.0	34	91	2	109	49	7	16	26	1.72
76673--76831	84	1.9	83	88	5	239	48	6	20	23	1.74
83702--83752	14	3.8	14	72	17	54	60	5	0	33	1.21
83708--83764	26	2.2	26	96	3	107	56	3	0	40	1.17
84801--84856	29	1.9	29	82	7	69	46	1	3	48	1.30
102600--102645	20	2.3	20	79	13	51	43	6	2	47	1.41
102689--102725	17	2.1	18	95	5	67	35	0	0	64	0.94
105936--105976	18	2.3	18	100	0	82	43	19	14	21	1.87
107835--107884	24	2.1	24	82	14	59	22	24	24	30	1.99
108396--108461	21	3.1	21	85	12	98	28	24	22	24	1.99
110776--110808	9	3.8	9	92	4	50	12	12	0	75	1.04
118833--118907	10	8.7	10	67	31	57	57	21	12	9	1.62
118839--118901	16	3.9	16	100	0	126	57	23	12	6	1.58
119969--119998	14	2.1	14	100	0	60	46	30	16	6	1.73
125943--125973	4	7.8	4	92	0	53	77	22	0	0	0.77
127652--127983	116	2.9	113	89	4	486	35	17	14	32	1.90
127880--128023	69	2.1	68	85	3	200	32	16	16	34	1.92
130739--130764	2	13.0	2	100	0	52	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)
141285--141356	24	3.0	24	67	25	62	43	13	5	37	1.68
141333--141407	35	2.1	35	90	0	114	44	18	1	36	1.59
141403--141479	35	2.2	35	83	0	100	36	0	20	42	1.53
154217--154286	12	5.8	12	85	6	97	35	17	12	34	1.88
154218--154289	36	2.0	36	91	0	117	37	18	11	33	1.86
165920--165949	2	14.5	2	93	6	51	50	0	46	3	1.18
175435--175469	18	1.9	18	88	0	52	54	0	17	28	1.43
181744--181768	12	2.1	12	100	0	50	24	32	0	44	1.54
189718--189767	16	3.1	16	73	0	55	72	0	10	18	1.12
190752--190797	21	2.2	21	92	0	74	23	19	28	28	1.98
190770--190830	21	3.0	19	77	13	59	22	19	22	34	1.97
191025--191120	39	2.5	39	92	0	156	30	18	16	34	1.93
191398--191437	20	2.0	20	100	0	80	40	5	40	15	1.68
191507--191574	21	3.4	19	72	21	66	33	17	22	26	1.96
191515--191586	21	3.4	21	73	21	78	38	20	19	20	1.93
191514--191605	42	2.2	42	96	0	166	36	22	18	21	1.95
191536--191611	21	3.6	21	71	13	66	35	25	19	19	1.95
191565--191745	90	2.0	91	85	8	244	30	18	22	28	1.98
191709--191755	21	2.2	21	96	0	85	21	23	25	29	1.99
191709--191762	21	2.6	21	90	0	72	22	22	27	27	1.99
196483--196527	23	2.0	22	86	4	63	48	4	2	44	1.35
196763--196800	16	2.4	16	86	4	51	39	7	18	34	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
202406--202451	21	2.2	20	88	3	65	78	2	0	19	0.86
215433--215479	21	2.2	21	88	7	69	14	6	10	68	1.38
222353--222392	20	2.0	19	85	9	53	50	5	10	35	1.58
226974--227065	46	2.0	46	100	0	184	32	13	26	28	1.93
245004--245058	28	1.9	28	82	10	67	61	1	0	36	1.06
246536--246660	41	3.3	40	65	25	99	30	17	20	31	1.96
247135--247308	60	2.9	59	79	7	165	31	20	6	41	1.77
257773--257805	2	16.5	2	100	0	66	51	0	0	48	1.00
259334--259405	22	3.6	20	77	20	62	66	1	8	23	1.27
259364--259404	19	2.2	19	86	8	57	63	0	12	24	1.28
261878--261921	4	10.8	4	81	13	54	20	2	2	75	1.03
263407--263442	18	2.0	18	94	0	63	25	22	30	22	1.99
263427--263549	54	2.3	54	91	2	194	22	21	26	30	1.99
266174--266241	21	3.1	22	81	12	79	32	17	27	22	1.96
283567--283647	27	3.0	27	74	12	67	44	14	6	34	1.71
283774--283814	21	1.9	22	85	5	57	34	26	24	14	1.94
283803--283834	13	2.5	13	94	0	55	21	21	40	15	1.91
299453--299544	4	23.8	4	78	14	86	2	16	0	81	0.79
299432--299544	25	4.7	24	78	14	117	2	17	0	79	0.84
299457--299536	17	4.8	17	86	7	110	2	15	0	82	0.77
299465--299545	42	1.9	42	87	9	121	2	14	0	82	0.77
300364--300433	25	2.9	25	85	10	85	27	10	12	50	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
314254--314296	20	2.1	21	95	4	79	51	11	18	18	1.76
314987--315020	16	2.2	15	89	5	50	55	8	0	35	1.31
323621--323654	17	1.9	18	88	5	52	73	2	2	20	1.09
327131--327269	16	9.0	15	83	9	149	0	16	2	81	0.79
327136--327269	7	17.6	7	83	13	126	0	16	2	81	0.79
327130--327208	1	79.0	1	71	0	59	0	13	0	86	0.58
328080--328142	25	2.6	26	85	11	82	28	11	14	46	1.78
338803--339066	42	6.5	41	76	13	251	25	20	6	47	1.74
338803--339066	119	2.2	119	83	8	327	25	20	6	47	1.74
338941--339078	43	3.4	43	74	18	125	25	21	7	45	1.77

Tables:   1   2   3   4   5   6   7   8   9