genome.fa.s1129.2.7.7.80.10.50.1000.19.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   79   80   
          81   82   83   84   85   86   87   88   89   

This is table  19  of  89  ( 10573 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)
3932228--3932283	22	2.5	23	85	2	60	21	25	26	26	1.99
3936115--3936336	117	1.9	118	82	8	283	27	15	9	47	1.76
3936637--3936678	18	2.4	18	96	4	77	11	4	21	61	1.48
3937589--3937641	21	2.5	21	96	0	97	20	28	32	18	1.97
3938563--3938663	40	2.5	40	85	4	123	32	16	19	30	1.95
3938795--3939029	130	1.8	131	80	2	285	35	20	16	27	1.94
3939190--3939260	3	23.7	3	100	0	142	32	0	0	67	0.91
3944411--3944483	3	25.0	3	89	8	107	31	1	0	67	1.00
3945759--3945886	30	4.3	29	78	13	102	21	14	8	56	1.64
3946219--3946278	26	2.3	26	85	0	75	30	13	16	40	1.87
3946231--3946279	13	3.8	13	88	0	71	28	16	16	38	1.90
3946219--3946286	13	5.2	13	77	10	50	27	16	16	39	1.89
3946219--3946286	26	2.6	25	75	9	64	27	16	16	39	1.89
3946442--3946488	2	23.5	2	100	0	94	48	0	0	51	1.00
3948373--3948401	15	1.9	15	100	0	58	41	13	13	31	1.84
3949309--3949345	17	2.2	17	100	0	74	43	0	24	32	1.55
3949309--3949355	17	2.8	17	90	6	60	46	0	21	31	1.51
3950312--3950341	8	3.8	8	90	0	51	63	0	36	0	0.95
3952281--3952337	30	1.9	30	92	0	96	12	14	12	61	1.57
3954164--3954203	14	3.1	14	79	13	50	75	5	20	0	0.99
3954186--3954228	18	2.4	18	80	7	52	79	4	16	0	0.90
3954213--3954250	12	3.3	12	89	7	53	78	10	10	0	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3955724--3956054	130	2.5	130	85	1	430	25	33	16	24	1.96
3956385--3956432	3	16.7	3	87	8	73	33	2	0	64	1.05
3957743--3957814	30	2.4	29	82	11	83	18	12	9	59	1.59
3957760--3957870	30	3.7	30	78	6	109	20	13	9	55	1.66
3960821--3960857	18	2.0	19	89	5	58	18	13	0	67	1.23
3961271--3961312	19	2.2	19	100	0	84	26	4	9	59	1.48
3973465--3973523	25	2.4	25	94	0	100	33	5	35	25	1.78
3974554--3974592	20	2.0	20	89	0	60	33	0	25	41	1.56
3977717--3977777	17	3.7	16	76	6	59	50	1	3	44	1.28
3977736--3977787	18	2.9	18	75	13	54	53	0	0	46	1.00
3977972--3978005	14	2.4	14	90	0	50	64	0	0	35	0.94
3987501--3987537	2	18.5	2	94	0	65	51	2	0	45	1.15
3991161--3991356	65	3.0	64	82	8	211	26	16	23	33	1.96
3991662--3991694	13	2.5	13	100	0	66	51	0	9	39	1.34
3995365--3995489	31	4.0	31	69	8	83	26	29	27	16	1.97
3995366--3995489	63	2.0	63	82	9	155	25	29	27	16	1.97
3996359--3996410	7	7.4	7	95	0	95	26	28	26	17	1.97
3996407--3996464	5	10.8	5	78	14	62	6	22	51	18	1.70
3996400--3996464	22	3.0	22	100	0	130	9	23	49	18	1.76
3996461--3996558	19	5.2	18	83	12	117	28	29	28	13	1.94
3996461--3996578	38	3.1	38	83	13	129	29	27	27	14	1.95
3996461--3996578	29	4.1	28	81	12	116	29	27	27	14	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3996461--3996578	9	12.3	9	80	10	110	29	27	27	14	1.95
4002730--4002852	31	4.0	31	69	8	90	26	30	26	16	1.97
4002731--4002852	61	2.0	63	84	9	162	26	30	27	16	1.97
4003713--4003756	7	6.4	7	89	5	72	25	29	27	18	1.98
4003801--4003856	19	2.9	19	100	0	112	30	32	26	10	1.90
4003800--4003915	38	3.1	36	81	14	119	30	27	27	14	1.95
4003806--4003916	19	5.8	19	82	10	104	30	27	26	15	1.96
4003800--4003915	9	12.3	9	79	10	108	30	27	27	14	1.95
4009359--4009518	65	2.5	65	87	7	220	30	16	21	31	1.96
4009359--4009566	65	3.2	64	80	11	219	28	16	23	32	1.96
4011692--4011729	19	2.0	20	84	5	51	39	2	26	31	1.70
4011887--4011965	23	3.5	22	70	8	70	22	21	27	27	1.99
4015787--4015826	21	1.9	21	85	10	55	35	10	2	52	1.48
4017711--4017833	65	1.9	64	86	6	178	28	18	23	29	1.98
4017691--4017848	64	2.5	62	77	11	158	29	18	24	27	1.98
4022120--4022205	27	3.2	27	63	28	65	29	19	17	33	1.95
4021573--4022414	54	15.6	54	88	3	1131	31	20	18	29	1.96
4030057--4030123	32	2.1	32	85	0	89	34	17	8	38	1.82
4034685--4034731	15	3.1	14	80	19	51	59	0	31	8	1.27
4036701--4036746	20	2.3	19	85	14	58	26	15	8	50	1.73
4047514--4047566	19	2.8	19	85	2	72	11	18	52	16	1.73
4054364--4054433	22	3.4	21	80	16	67	32	15	21	30	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4054756--4055125	108	3.4	108	82	1	384	31	18	18	31	1.95
4054758--4055078	162	2.0	162	83	1	401	31	19	18	31	1.95
4054760--4055078	54	5.9	54	85	2	363	31	19	17	31	1.95
4054758--4055125	54	6.8	53	83	3	317	31	18	18	31	1.95
4056313--4056365	19	3.0	19	86	10	69	5	15	56	22	1.60
4057293--4057422	61	2.2	59	80	9	138	39	13	10	36	1.80
4070783--4070978	103	1.9	101	85	3	232	32	15	21	30	1.94
4071105--4071154	25	2.0	25	96	0	91	40	24	2	34	1.66
4072172--4072216	22	2.0	23	86	4	65	28	13	31	26	1.94
4072639--4072811	58	3.0	59	82	9	212	31	14	19	34	1.92
4073181--4073507	68	4.8	68	85	2	415	32	14	23	29	1.94
4073457--4073836	81	4.7	81	87	1	505	35	12	23	27	1.92
4073892--4073921	2	15.0	2	100	0	60	50	0	0	50	1.00
4077726--4077913	94	2.0	95	85	1	252	33	15	23	27	1.95
4077800--4077855	22	2.7	20	78	10	67	32	16	26	25	1.96
4078270--4078433	58	2.8	58	88	5	233	31	14	20	33	1.92
4078901--4079005	32	3.2	32	65	24	81	30	14	23	31	1.94
4078805--4079129	68	4.8	68	90	0	481	32	14	23	29	1.94
4079079--4079931	162	5.4	162	84	4	1101	36	12	24	27	1.91
4079079--4079368	81	3.6	81	88	0	393	35	12	24	27	1.92
4079390--4079931	81	6.7	81	89	1	793	36	12	23	27	1.91
4079014--4079931	311	2.9	311	86	3	1207	36	12	23	27	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4083719--4083759	15	2.8	15	85	10	50	53	0	0	46	1.00
4084495--4084534	21	2.0	21	90	5	64	57	0	2	40	1.12
4086005--4086042	17	2.2	17	95	0	67	36	10	5	47	1.61
4086538--4086610	23	3.2	23	90	0	110	34	6	20	38	1.79
4086116--4087012	489	1.8	489	94	1	1593	41	7	9	41	1.66
4087687--4087752	28	2.4	27	77	7	71	15	16	21	46	1.83
4087931--4087960	15	2.0	15	93	0	51	3	56	0	40	1.16
4089308--4089332	12	2.1	12	100	0	50	60	0	0	40	0.97
4090696--4090899	64	3.2	65	81	6	184	30	21	16	30	1.96
4108631--4108667	12	3.0	13	80	15	51	75	10	8	5	1.17
4109207--4109237	12	2.6	12	100	0	62	0	12	6	80	0.89
4119919--4120003	36	2.3	36	83	6	98	34	11	20	34	1.89
4119896--4120087	102	1.9	102	89	2	296	35	13	17	33	1.88
4120028--4120186	67	2.4	67	82	2	194	35	13	19	32	1.90
4120159--4120212	27	2.0	27	100	0	108	37	14	14	33	1.88
4120189--4120306	36	3.4	36	73	17	124	40	15	15	28	1.87
4120072--4120279	93	2.2	94	86	5	285	38	15	16	29	1.89
4120162--4120305	66	2.2	63	88	3	216	40	15	15	29	1.88
4121856--4121912	28	2.0	28	83	6	71	38	1	1	57	1.19
4124761--4124800	18	2.3	18	86	4	55	42	20	2	35	1.65
4125300--4125342	16	2.7	16	82	7	52	18	2	4	74	1.10
4125288--4125343	23	2.5	23	82	8	62	21	3	3	71	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4125498--4125538	19	2.2	19	86	0	55	39	2	0	58	1.11
4126112--4126503	182	2.2	181	78	4	389	36	12	9	40	1.76
4140048--4140092	20	2.2	20	84	0	54	31	15	28	24	1.96
4147932--4147975	21	2.1	21	82	0	52	9	43	15	31	1.79
4148515--4148549	2	17.5	2	100	0	70	48	0	0	51	1.00
4148653--4148732	41	2.0	41	97	0	151	35	2	30	32	1.71
4149098--4149257	65	2.5	63	86	6	214	30	24	19	26	1.98
4152637--4152676	21	1.9	21	89	0	62	57	10	2	30	1.45
4160113--4160153	21	2.0	21	90	0	64	53	9	2	34	1.47
4161310--4161371	29	2.1	30	82	8	74	38	14	4	41	1.67

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   79   80   
          81   82   83   84   85   86   87   88   89