genome.fa.s9639.2.7.7.80.10.50.1000.18.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: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  15077257

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   

This is table  18  of  62  ( 7398 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)
3875230--3875351	21	6.1	21	75	14	107	48	10	22	18	1.78
3877757--3878139	30	12.7	30	77	9	314	62	8	12	16	1.52
3877795--3878093	155	1.9	159	82	6	376	63	8	11	15	1.50
3877957--3878140	57	3.3	54	81	13	194	64	8	10	16	1.48
3877956--3878140	87	2.2	83	82	5	210	64	8	10	16	1.47
3878591--3878740	74	2.0	75	98	1	293	25	22	15	36	1.93
3879371--3879414	21	2.1	21	86	0	61	13	22	43	20	1.87
3879882--3880338	220	2.1	223	85	3	627	25	18	31	24	1.97
3880463--3880522	31	1.9	32	89	3	95	38	11	21	28	1.89
3880505--3880665	62	2.5	62	88	6	216	45	15	10	28	1.79
3880569--3880667	29	3.3	29	65	20	76	48	15	9	27	1.74
3880744--3880823	37	2.1	39	83	4	101	40	12	16	31	1.85
3881152--3881192	16	2.6	16	88	7	57	24	0	24	51	1.49
3886661--3887102	30	14.7	30	80	6	401	62	9	11	17	1.53
3886676--3887064	89	4.3	90	81	7	398	62	8	10	17	1.52
3888289--3888328	21	1.9	21	89	0	62	17	22	40	20	1.92
3888523--3888590	3	23.3	3	94	5	122	66	0	0	33	0.92
3889578--3889620	19	2.3	20	84	15	65	30	18	32	18	1.95
3890968--3891152	93	2.0	93	97	0	352	36	5	20	37	1.77
3891371--3891405	18	1.9	18	100	0	70	17	22	34	25	1.96
3894998--3895032	11	3.2	11	95	0	61	25	8	22	42	1.82
3896750--3896819	27	2.6	27	100	0	140	42	10	11	35	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3897433--3897463	9	3.4	9	90	0	53	74	0	25	0	0.82
3903327--3903371	22	2.0	22	86	0	63	37	4	13	44	1.64
3903526--3903649	59	2.1	59	86	0	167	28	20	22	28	1.99
3904681--3904766	3	28.7	3	100	0	172	67	0	0	32	0.91
3909857--3909901	22	2.0	22	86	0	63	37	4	13	44	1.64
3917083--3917162	21	3.8	21	80	6	90	26	15	26	32	1.95
3917065--3917204	42	3.3	42	84	0	172	27	15	22	35	1.94
3919825--3919899	34	2.2	34	90	0	114	53	6	18	21	1.67
3920027--3920074	13	3.7	13	100	0	96	62	0	14	22	1.32
3926436--3926478	22	2.0	22	90	0	68	30	30	18	20	1.97
3933475--3933499	13	1.9	13	100	0	50	16	0	0	84	0.63
3941765--3941824	15	3.9	15	86	2	84	13	46	26	13	1.80
3945551--3945594	16	2.8	16	92	0	79	43	13	11	31	1.80
3951441--3951496	23	2.4	23	96	0	103	42	7	41	8	1.63
3963324--3963387	24	2.7	23	81	11	76	75	0	1	23	0.90
3963326--3963434	10	9.9	11	66	24	52	70	0	5	22	1.13
3963344--3963412	21	3.2	20	82	12	68	71	1	2	24	1.09
3964570--3964610	17	2.4	17	91	0	64	24	0	46	29	1.53
3965102--3965267	66	2.7	61	85	5	226	28	13	18	39	1.89
3966000--3966238	85	2.8	85	85	1	311	27	17	20	34	1.95
3970462--3970544	30	2.7	30	90	1	103	45	19	14	20	1.85
3970476--3970544	30	2.3	30	100	0	138	49	17	15	17	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3979666--3979770	45	2.3	45	91	1	165	40	22	15	20	1.90
3990108--3990163	15	3.7	15	92	2	85	58	12	21	7	1.57
3993460--3993494	15	2.3	15	100	0	70	22	28	14	34	1.93
3993962--3994038	39	2.0	38	87	7	111	55	7	33	2	1.42
3994095--3994439	173	2.0	172	99	0	681	28	9	30	32	1.88
3996637--3996850	85	2.5	84	84	7	265	33	17	19	29	1.95
3996828--3996873	13	3.5	13	81	0	56	32	19	17	30	1.95
4013809--4013835	12	2.2	12	100	0	54	44	7	0	48	1.31
4014155--4014320	71	2.3	72	85	3	226	30	23	19	26	1.98
4016276--4016392	20	5.9	20	85	3	141	24	17	24	33	1.96
4016267--4016392	40	3.2	40	85	3	166	24	16	25	33	1.96
4016257--4016389	60	2.2	59	86	4	187	24	17	24	33	1.96
4016474--4016693	89	2.5	88	87	0	323	37	15	17	29	1.91
4016715--4017018	96	3.2	94	87	5	420	38	14	24	22	1.91
4016744--4017021	90	3.0	90	86	7	387	39	14	23	23	1.91
4017085--4017206	47	2.6	47	88	0	172	36	21	17	24	1.94
4018438--4018467	2	15.0	2	92	0	51	46	0	3	50	1.18
4019961--4020018	13	4.5	13	78	8	57	25	24	0	50	1.50
4019961--4020018	25	2.3	26	85	8	75	25	24	0	50	1.50
4020074--4020134	19	3.3	18	81	6	68	34	14	4	45	1.67
4022962--4023031	30	2.4	30	88	7	99	31	18	7	42	1.77
4025433--4025485	21	2.5	22	84	9	65	50	7	3	37	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4032192--4032312	14	8.7	14	71	15	74	14	0	40	43	1.52
4032184--4032244	28	2.2	27	77	8	68	14	0	39	45	1.45
4032192--4032265	7	10.6	7	84	11	80	14	0	40	44	1.46
4033199--4033238	2	20.0	2	100	0	80	50	0	0	50	1.00
4036096--4036143	22	2.2	22	81	3	62	43	8	10	37	1.69
4036158--4036230	23	3.2	23	94	0	119	35	6	20	36	1.80
4036233--4036272	21	2.0	20	90	5	62	35	12	2	50	1.54
4036647--4036742	23	4.2	23	98	0	183	34	8	21	35	1.84
4036158--4037127	512	1.9	512	94	0	1719	40	7	10	41	1.69
4037218--4037265	23	2.1	23	92	0	78	37	14	8	39	1.76
4039467--4039512	24	1.9	24	95	0	83	28	45	13	13	1.80
4042309--4042370	13	4.5	13	73	15	52	0	19	17	62	1.32
4043068--4043292	40	5.8	40	91	8	394	18	23	10	47	1.80
4043066--4043297	76	3.1	76	100	0	464	18	24	10	47	1.79
4043235--4044120	113	7.8	113	92	2	1422	27	19	15	38	1.92
4044422--4044522	52	1.9	52	100	0	202	34	15	13	35	1.88
4045014--4045490	83	5.6	83	87	5	688	38	23	12	26	1.90
4044962--4045490	166	3.1	173	89	5	804	37	22	12	28	1.90
4045014--4045481	258	1.8	249	89	5	731	38	23	11	26	1.89
4046637--4046696	9	7.0	8	75	24	52	0	20	0	80	0.72
4046638--4046700	23	2.7	23	81	15	85	0	19	0	80	0.70
4046637--4046701	26	2.4	28	80	12	82	0	20	0	80	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4046656--4046698	13	3.3	13	84	9	61	0	16	0	83	0.64
4046638--4046697	10	6.6	9	79	14	61	0	18	0	81	0.69
4053941--4053972	15	2.1	15	94	0	55	46	9	18	25	1.79
4058031--4058093	25	2.5	25	76	2	63	60	4	3	31	1.33
4058856--4058917	13	4.5	13	73	15	52	0	19	17	62	1.32
4059311--4059379	27	2.8	24	80	16	79	55	0	0	44	0.99
4061701--4061745	19	2.4	19	85	7	56	40	0	4	55	1.20
4063514--4063547	2	17.0	2	100	0	68	50	0	0	50	1.00
4063723--4064899	76	15.5	76	95	0	2048	35	20	20	23	1.96
4065578--4065632	22	2.5	22	90	0	92	38	14	12	34	1.84
4066000--4066109	54	2.1	52	89	3	166	21	20	17	40	1.92
4066799--4067112	157	2.0	157	98	0	610	30	18	14	37	1.90
4068489--4068674	93	2.0	93	89	2	284	35	21	13	29	1.92
4068414--4068873	206	2.2	207	94	1	798	35	21	13	30	1.91
4068691--4068966	92	3.0	93	89	2	423	36	21	13	28	1.91
4075582--4075627	19	2.4	19	79	13	51	60	0	6	32	1.22
4075571--4075635	28	2.2	28	81	10	69	58	0	7	33	1.27
4076088--4076132	19	2.4	19	85	7	56	40	0	4	55	1.20
4076487--4076522	15	2.3	15	90	4	54	69	0	2	27	1.02
4077863--4077920	2	29.0	2	96	0	107	50	0	1	48	1.11
4077927--4077968	15	2.9	15	82	3	59	54	0	2	42	1.13
4085481--4085549	32	2.1	35	91	8	117	40	10	20	28	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4086193--4086221	2	14.5	2	100	0	58	48	0	0	51	1.00
4086213--4086270	20	2.8	21	70	24	59	25	3	0	70	1.03
4086433--4086512	40	2.0	40	86	9	112	31	5	7	56	1.49
4086577--4086605	9	3.3	9	95	4	51	17	0	0	82	0.66
4086581--4086626	15	3.1	15	81	3	58	13	10	0	76	1.03
4087564--4087592	10	2.9	10	100	0	58	10	0	6	82	0.83
4087558--4087622	28	2.4	26	78	9	67	13	3	9	73	1.19
4094938--4095774	106	8.0	106	85	5	1069	34	23	18	23	1.96
4095033--4095630	302	2.0	304	90	1	948	35	23	18	23	1.96
4096258--4096329	35	2.1	35	100	0	144	40	11	20	27	1.87

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