genome.fa.s7984.2.7.7.80.10.50.1000.20.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: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12923621

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   

This is table  20  of  65  ( 7696 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)
3876694--3876772	31	2.5	31	89	0	122	29	30	27	12	1.93
3877894--3878026	63	2.1	63	80	5	144	33	18	24	24	1.96
3881592--3881620	15	1.9	15	100	0	58	0	34	0	65	0.93
3883653--3883714	27	2.3	27	94	0	115	38	20	14	25	1.91
3885441--3885469	2	14.5	2	100	0	58	51	0	0	48	1.00
3885489--3885667	85	2.1	86	81	7	213	30	16	21	31	1.95
3888227--3888276	23	2.1	23	85	7	64	24	18	24	34	1.96
3891852--3891881	2	15.0	2	100	0	60	50	0	0	50	1.00
3895092--3895123	16	2.0	16	100	0	64	50	12	0	37	1.41
3900658--3900696	14	2.8	14	77	14	53	38	10	12	38	1.78
3900764--3900843	25	3.2	25	78	8	83	50	0	2	47	1.14
3900803--3900859	17	3.5	17	68	18	50	42	0	1	56	1.10
3901566--3901634	23	3.0	23	80	6	59	47	0	2	49	1.16
3901793--3901853	21	2.9	21	81	11	63	54	0	1	44	1.10
3900889--3902107	612	2.0	606	94	2	2158	45	5	6	42	1.53
3906001--3906064	27	2.4	27	86	0	83	45	0	0	54	0.99
3905991--3906051	3	20.7	3	86	9	54	40	0	0	59	0.98
3907449--3907652	112	1.8	109	82	7	259	38	9	9	43	1.69
3908184--3908267	33	2.6	33	80	14	88	28	5	3	61	1.36
3911518--3911556	15	2.6	15	100	0	78	30	12	12	43	1.81
3915339--3915369	9	3.6	9	91	8	55	22	22	0	54	1.44
3918879--3918920	10	4.0	10	80	20	50	78	0	21	0	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3918878--3918921	21	2.0	21	87	12	63	79	0	20	0	0.73
3920442--3920734	113	2.6	112	89	2	426	37	16	18	26	1.92
3920643--3920820	86	2.1	86	96	0	329	32	17	19	30	1.95
3920729--3920977	113	2.2	113	86	0	327	35	14	20	30	1.91
3920530--3920933	199	2.0	199	87	0	574	35	16	19	29	1.93
3921318--3921394	36	2.1	36	83	4	93	42	0	0	57	0.99
3921318--3921381	3	21.7	3	87	9	60	40	0	0	59	0.97
3924880--3924936	3	19.0	3	88	0	87	28	0	0	71	0.86
3925200--3925242	22	2.0	22	100	0	86	11	41	18	27	1.85
3938005--3938059	12	4.6	12	84	6	67	78	1	20	0	0.85
3938004--3938076	12	5.8	12	76	19	60	76	1	21	0	0.86
3938004--3938075	26	2.8	25	80	16	85	76	1	22	0	0.86
3939146--3939393	43	5.4	45	70	12	164	25	30	19	25	1.98
3939080--3939451	141	2.6	141	94	0	645	25	29	19	25	1.98
3939598--3939669	3	24.0	3	97	0	135	31	0	0	68	0.90
3939931--3939979	22	2.2	22	96	0	89	12	42	20	24	1.86
3941184--3941216	12	2.6	13	90	4	50	27	0	0	72	0.85
3945811--3945864	20	2.7	19	75	8	63	33	31	18	16	1.93
3945811--3945926	21	5.6	21	68	7	67	33	25	19	21	1.97
3945914--3946389	20	23.5	20	73	10	213	36	24	17	21	1.95
3945963--3946205	40	6.0	41	85	4	293	37	24	18	19	1.93
3945972--3946205	81	2.9	80	83	7	287	38	24	17	19	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3946240--3946286	21	2.2	21	84	0	67	19	27	17	36	1.93
3947249--3947302	24	2.2	24	93	0	90	20	18	20	40	1.91
3949732--3949819	20	4.4	20	86	2	115	37	23	18	20	1.94
3949796--3949887	33	2.7	33	91	3	139	42	19	23	14	1.88
3949825--3949893	19	3.8	19	73	21	76	44	18	21	14	1.85
3949902--3949997	33	2.9	34	87	3	131	13	21	20	43	1.86
3950012--3950059	21	2.3	21	100	0	96	47	16	12	22	1.80
3951529--3951621	42	2.2	42	80	3	107	22	17	39	20	1.92
3952101--3952169	20	3.5	20	89	0	93	36	21	20	21	1.95
3952211--3952278	19	3.8	19	81	18	101	5	16	30	47	1.70
3952236--3952294	14	3.9	14	74	20	55	6	18	27	47	1.74
3952217--3952341	33	3.8	33	89	2	164	8	20	24	46	1.78
3952280--3952364	14	4.8	18	73	18	63	11	22	18	47	1.81
3952269--3952326	14	3.8	14	75	20	62	8	25	18	46	1.78
3952429--3952808	94	4.1	94	93	2	622	47	18	12	21	1.80
3954510--3954581	20	3.5	20	84	5	92	12	16	19	51	1.76
3955141--3955354	20	10.6	20	77	6	225	19	19	24	36	1.94
3955138--3955415	41	6.9	40	77	8	240	21	18	24	35	1.95
3955143--3955354	41	5.2	41	90	2	329	19	18	24	37	1.94
3955346--3955391	20	2.3	20	96	0	83	23	19	30	26	1.98
3955381--3955476	42	2.3	42	78	5	106	25	19	20	34	1.96
3957791--3957838	15	3.1	16	85	8	64	50	0	14	35	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3957790--3957840	16	3.4	15	81	7	59	47	0	13	39	1.43
3958871--3958928	16	3.6	16	80	2	62	8	8	24	58	1.56
3958877--3958959	32	2.6	32	80	0	85	13	8	24	54	1.66
3960199--3960262	33	1.9	33	81	6	76	56	4	0	39	1.20
3960904--3960940	19	2.0	18	94	5	65	81	5	2	10	0.96
3961214--3961251	15	2.5	15	100	0	76	34	7	18	39	1.80
3961244--3961303	20	3.0	20	97	0	111	40	10	13	36	1.78
3961470--3961534	28	2.3	27	82	15	78	50	1	1	46	1.20
3961470--3961567	31	3.2	32	76	15	84	51	2	1	45	1.19
3961587--3961630	22	2.0	23	86	4	63	54	0	0	45	0.99
3961591--3961647	21	2.6	22	81	10	64	52	0	0	47	1.00
3961527--3961647	54	2.3	51	77	19	133	50	0	0	47	1.12
3961837--3961956	42	2.9	42	91	0	204	44	17	20	18	1.87
3964002--3964050	15	3.3	15	85	0	71	10	65	16	8	1.46
3966164--3966194	16	1.9	16	93	0	53	19	12	19	48	1.81
3966673--3966706	2	17.0	2	100	0	68	50	0	0	50	1.00
3968814--3968852	20	2.0	20	85	9	55	48	0	0	51	1.00
3968828--3968888	12	5.0	12	75	11	61	49	1	0	49	1.10
3968828--3968884	25	2.2	27	84	6	73	50	1	0	47	1.11
3975506--3975909	43	9.5	43	79	3	352	35	15	22	25	1.94
3977163--3977199	11	3.3	11	92	3	56	27	54	18	0	1.44
3977162--3977196	6	6.0	6	93	6	54	28	54	17	0	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3977697--3977793	6	16.2	6	100	0	194	0	16	49	34	1.46
3977877--3977942	19	3.3	19	72	12	69	40	21	19	18	1.91
3977892--3977963	22	3.4	22	73	11	87	37	25	19	18	1.94
3977870--3977963	41	2.3	41	98	0	179	39	23	18	19	1.92
3977952--3977995	21	2.1	21	86	0	61	34	29	15	20	1.94
3979921--3979981	22	2.8	22	75	9	70	32	14	6	45	1.71
3979977--3980029	21	2.5	21	100	0	106	47	20	15	16	1.83
3981465--3981566	37	2.8	37	90	0	168	34	20	19	25	1.96
3982106--3982140	7	5.3	7	93	6	56	45	22	0	31	1.53
3983380--3983605	83	2.8	81	79	5	233	35	19	13	31	1.91
3983939--3983973	3	11.7	3	100	0	70	31	0	0	68	0.90
3993130--3993462	117	2.8	118	79	10	285	36	15	22	25	1.94
3996853--3996887	18	1.9	18	88	0	52	20	17	34	28	1.95
4005965--4006190	113	2.0	113	95	0	407	23	16	26	33	1.96
4016455--4016503	11	4.5	10	78	16	53	14	0	8	77	0.98
4016455--4016494	18	2.2	19	86	4	55	15	0	7	77	0.98
4020687--4020715	14	2.0	15	93	6	51	58	0	0	41	0.98
4021962--4022053	2	46.0	2	97	0	175	48	0	0	51	1.00
4028355--4028725	117	3.2	116	79	8	328	36	15	20	26	1.93
4034721--4034791	4	18.2	4	91	5	119	0	26	50	22	1.49
4034796--4034876	40	2.0	40	100	0	162	37	19	22	20	1.95
4035519--4035554	19	1.9	19	94	5	65	55	5	11	27	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4035588--4035966	111	3.4	111	95	0	634	45	10	11	32	1.73
4035937--4035988	20	2.6	20	90	0	77	42	15	9	32	1.79
4036530--4036582	2	26.0	2	88	11	81	49	1	1	47	1.23
4037026--4037078	28	1.9	27	84	3	70	37	1	5	54	1.35
4038366--4038424	10	5.7	10	78	7	64	62	16	10	10	1.53
4039468--4039518	10	4.7	10	80	17	57	54	23	11	9	1.66
4039458--4039534	14	6.1	13	73	25	58	55	18	14	11	1.68
4039458--4039521	24	2.7	24	90	4	103	56	20	12	10	1.66
4039921--4039961	21	2.0	21	90	0	64	24	14	29	31	1.95
4039921--4039972	21	2.5	21	84	6	52	26	13	28	30	1.94

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