genome.fa.s8027.2.7.7.80.10.50.1000.20.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: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7662336

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   

This is table  20  of  38  ( 4505 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)
4186522--4187731	198	6.0	199	85	5	1456	38	14	16	30	1.88
4187601--4187651	20	2.5	20	93	0	84	43	5	11	39	1.66
4187605--4187657	20	2.7	20	87	0	61	41	9	15	33	1.79
4189302--4189349	19	2.5	19	96	0	87	31	6	10	52	1.60
4192162--4192540	198	1.9	200	86	3	541	37	14	16	31	1.89
4192567--4192614	23	2.1	23	92	0	78	37	18	8	35	1.81
4192651--4192695	23	2.0	23	95	0	81	37	20	8	33	1.83
4192567--4192728	87	1.9	87	93	0	279	34	15	9	40	1.80
4196589--4196618	12	2.5	12	94	0	51	33	0	36	30	1.58
4198018--4198044	12	2.2	12	100	0	54	85	0	0	14	0.61
4198355--4198384	2	15.0	2	100	0	60	50	0	0	50	1.00
4206164--4206204	21	2.0	21	85	4	57	19	12	31	36	1.89
4217383--4217425	20	2.1	21	87	8	63	18	13	0	67	1.23
4217382--4217431	20	2.5	20	75	15	59	18	18	0	64	1.30
4223626--4223696	36	2.0	36	83	5	90	33	14	18	33	1.90
4227698--4228524	107	7.8	107	92	1	1355	24	26	17	30	1.97
4229874--4230043	10	16.6	10	87	12	240	10	10	0	80	0.92
4229874--4230063	20	8.9	24	73	22	119	10	10	0	79	0.94
4229892--4230043	19	7.6	20	89	10	240	9	9	0	80	0.91
4229874--4230065	53	3.8	53	91	7	326	10	9	0	79	0.93
4229874--4230068	19	11.1	18	79	16	205	10	10	0	78	0.95
4229874--4230068	29	6.4	31	83	16	175	10	10	0	78	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4229875--4230049	43	4.3	40	82	17	220	10	10	0	79	0.94
4239912--4239953	15	2.7	15	96	3	75	7	19	52	21	1.69
4242182--4242249	27	2.4	26	78	21	75	48	1	1	48	1.19
4242232--4242388	52	3.5	43	71	19	122	46	0	4	48	1.27
4242245--4242397	46	3.1	52	65	23	148	44	0	4	50	1.27
4242280--4242422	33	4.5	31	68	20	91	43	1	4	50	1.32
4242243--4242485	96	2.5	95	88	6	350	45	1	3	48	1.29
4251223--4251262	20	2.0	20	90	5	62	30	0	10	60	1.30
4251639--4251672	11	3.1	11	91	0	50	26	11	0	61	1.30
4256038--4256127	46	2.0	46	86	4	128	33	7	10	48	1.65
4258957--4259004	22	2.2	22	88	0	69	25	25	33	16	1.96
4263575--4263722	60	2.5	60	88	7	205	33	12	4	49	1.62
4264617--4264641	12	2.1	12	100	0	50	16	12	40	32	1.84
4269589--4269626	2	19.0	2	100	0	76	0	50	0	50	1.00
4272849--4273010	81	2.0	81	100	0	324	25	18	14	40	1.89
4275446--4275510	21	3.1	21	88	0	94	32	27	13	26	1.94
4275476--4275518	21	2.2	20	88	12	63	25	30	11	32	1.91
4280169--4280238	31	2.2	32	82	2	88	34	22	22	20	1.97
4281159--4281197	21	1.9	21	89	5	62	64	0	0	35	0.94
4281153--4281197	14	3.3	13	78	9	54	64	0	0	35	0.94
4281929--4281966	13	2.9	13	81	14	51	73	0	5	21	1.02
4290945--4290984	20	2.0	20	90	0	62	20	35	25	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4290988--4291027	21	1.9	21	85	10	55	25	37	25	12	1.91
4295364--4295585	35	6.5	35	71	22	134	45	8	2	43	1.47
4295399--4295577	72	2.6	71	78	17	182	44	7	2	44	1.47
4295364--4295579	34	6.4	33	72	21	146	45	8	2	43	1.46
4295603--4295713	37	2.9	39	78	6	102	49	7	1	41	1.41
4295610--4295713	38	2.7	39	79	7	115	48	6	0	44	1.35
4312664--4312717	22	2.5	22	93	0	90	27	18	22	31	1.97
4314758--4314817	32	1.9	30	83	6	75	31	16	10	41	1.81
4314861--4314891	12	2.6	12	94	0	53	16	35	9	38	1.81
4316110--4316170	24	2.8	21	75	20	61	14	31	18	36	1.91
4319796--4319836	2	20.5	2	100	0	82	48	0	0	51	1.00
4323248--4323278	16	2.0	15	93	6	53	54	12	6	25	1.62
4323331--4323363	2	16.5	2	100	0	66	51	0	0	48	1.00
4329711--4329836	60	2.1	60	80	7	139	37	12	13	36	1.83
4330501--4330580	31	2.6	31	96	2	144	46	8	11	33	1.71
4332449--4332508	24	2.5	24	81	5	68	40	10	15	35	1.80
4335597--4335637	20	2.1	20	86	4	57	26	2	2	68	1.15
4336541--4336578	19	2.0	19	100	0	76	15	31	31	21	1.94
4339647--4339694	17	2.9	16	84	9	60	33	10	12	43	1.77
4339707--4339731	13	1.9	13	100	0	50	40	24	20	16	1.91
4340749--4340815	21	3.1	21	65	4	53	50	2	14	31	1.58
4340749--4341400	43	15.2	43	74	8	422	49	5	19	25	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4340786--4341365	215	2.7	215	79	5	589	49	5	19	25	1.70
4340749--4341355	258	2.4	257	78	7	606	49	5	19	25	1.69
4340794--4341355	129	4.4	128	77	7	467	49	5	19	25	1.69
4341447--4341499	25	2.1	25	100	0	106	41	7	15	35	1.75
4342520--4342973	229	2.0	229	96	0	845	32	24	14	28	1.94
4344555--4344685	38	3.4	38	85	6	176	28	20	27	23	1.99
4344780--4344838	30	2.0	30	89	0	91	40	8	18	32	1.81
4349311--4349354	2	22.5	2	93	4	72	45	0	2	52	1.13
4349578--4349671	21	4.7	21	79	10	106	29	25	21	23	1.99
4349762--4349824	30	2.1	30	93	0	108	38	12	19	30	1.89
4351640--4351686	23	2.0	23	83	0	58	42	8	19	29	1.80
4351600--4351762	87	1.9	87	92	0	272	42	13	12	30	1.82
4351757--4352234	197	2.4	194	78	7	496	32	15	13	38	1.86
4351869--4352261	199	2.0	197	79	6	420	31	16	13	37	1.88
4352141--4352333	106	1.8	107	83	1	262	30	16	12	40	1.85
4354495--4354604	58	1.9	58	81	7	134	40	16	6	36	1.74
4354835--4354881	24	2.0	24	84	12	62	36	8	6	48	1.59
4354986--4355173	91	2.1	91	84	0	241	22	19	15	43	1.88
4355616--4355654	3	13.0	3	100	0	78	66	0	0	33	0.92
4358360--4358407	22	2.2	22	92	0	78	16	16	27	39	1.90
4358360--4358420	22	2.8	22	85	2	70	19	14	24	40	1.89
4358413--4358465	24	2.2	24	100	0	106	26	16	15	41	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4359606--4359639	4	8.5	4	100	0	68	73	0	0	26	0.83
4363116--4363141	10	2.6	10	100	0	52	19	7	11	61	1.53
4368041--4368091	20	2.5	21	78	15	61	74	5	5	13	1.19
4379018--4379131	48	2.4	48	86	2	149	39	19	14	26	1.90
4379018--4379131	24	4.8	24	80	8	115	39	19	14	26	1.90
4379049--4379148	48	2.1	48	81	7	114	42	20	15	23	1.89
4382788--4382824	19	1.9	19	100	0	74	16	43	10	29	1.82
4383746--4383802	2	28.5	2	100	0	114	49	0	0	50	1.00
4388859--4388940	43	1.9	43	92	0	137	26	14	15	42	1.86
4390961--4391007	22	2.1	23	84	4	60	42	2	2	53	1.25
4396370--4396437	22	3.1	21	72	16	57	42	4	14	38	1.66
4402546--4402607	32	1.9	32	87	6	90	16	11	12	59	1.61
4403320--4403364	21	2.2	20	84	4	54	24	20	8	46	1.78
4404639--4404755	44	2.6	42	75	15	103	73	7	17	1	1.15
4404647--4404730	27	3.1	28	81	11	86	77	5	15	1	1.02
4404689--4404728	11	3.7	11	86	3	55	85	5	10	0	0.75
4404649--4404728	32	2.4	33	82	10	101	78	6	13	1	0.99
4404674--4404746	16	4.9	14	73	20	51	78	8	13	0	0.97
4404649--4404745	32	3.0	31	72	13	79	76	7	15	1	1.06
4405581--4405638	24	2.4	23	81	13	64	36	10	3	50	1.54
4405900--4405939	16	2.5	16	83	0	53	47	25	2	25	1.64
4407616--4407674	30	2.0	30	93	0	100	32	11	13	42	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4407615--4407705	30	3.0	31	82	7	98	34	14	12	39	1.83
4407805--4408252	134	3.3	134	87	1	664	26	29	18	25	1.98
4408461--4408486	3	8.7	3	100	0	52	34	0	0	65	0.93
4410601--4410633	15	2.3	15	89	5	50	42	3	3	51	1.32
4411903--4411976	36	2.1	36	89	0	112	31	20	18	29	1.97
4420438--4420487	21	2.4	21	80	6	66	22	26	18	34	1.96
4420477--4420549	21	3.5	21	88	1	94	39	16	23	20	1.92
4420496--4420638	62	2.3	62	79	8	164	37	21	18	21	1.94
4420541--4420673	20	6.6	20	84	5	108	35	24	18	21	1.95
4420558--4420613	21	2.7	21	94	0	103	44	23	16	16	1.86

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