genome.fa.s1547.2.7.7.80.10.50.1000.20.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: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  10425128

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   

This is table  20  of  51  ( 6083 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)
3938558--3938654	47	2.1	47	96	0	176	41	7	7	44	1.59
3940715--3940769	23	2.4	23	93	0	92	41	12	23	21	1.88
3942540--3942577	18	2.1	18	90	9	60	78	5	10	5	1.06
3942566--3942606	15	2.7	15	84	0	55	78	2	7	12	1.06
3942870--3942919	22	2.3	20	80	12	55	70	2	4	24	1.15
3942885--3942931	21	2.2	22	81	11	53	78	2	4	14	0.99
3942969--3943015	9	3.9	13	76	23	50	72	0	2	25	0.96
3942979--3943021	21	2.0	21	100	0	86	72	0	0	27	0.85
3943101--3943176	6	12.5	6	76	13	57	77	1	2	18	0.95
3943097--3943181	26	3.3	26	77	8	75	77	1	2	18	0.94
3943086--3943181	9	10.7	9	76	12	54	78	1	4	16	0.97
3947856--3947906	24	2.2	24	89	10	79	56	0	21	21	1.42
3948297--3948326	14	2.1	14	93	0	51	33	0	3	63	1.11
3949156--3949262	24	4.5	24	72	0	88	47	15	13	23	1.81
3949156--3949264	48	2.3	48	75	0	110	47	15	13	22	1.81
3950392--3950427	18	2.0	18	88	0	54	30	16	0	52	1.44
3951750--3951819	18	4.2	18	75	17	87	12	18	50	18	1.78
3951761--3951796	13	2.8	13	95	0	63	13	19	50	16	1.79
3953946--3954053	48	2.3	48	75	1	110	47	15	13	23	1.82
3955180--3955215	18	2.0	18	88	0	54	30	16	0	52	1.44
3956537--3956606	18	4.2	18	75	17	87	12	18	50	18	1.78
3956548--3956583	13	2.8	13	95	0	63	13	19	50	16	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3964823--3964931	3	35.7	3	87	3	155	35	0	0	62	1.08
3966232--3966271	18	2.2	18	90	0	62	37	2	2	57	1.26
3971611--3971652	17	2.3	19	80	12	52	80	7	4	7	1.00
3971611--3971652	18	2.3	18	88	8	59	80	7	4	7	1.00
3975025--3975193	74	2.3	74	82	7	193	34	15	19	29	1.93
3975977--3976084	53	2.1	53	85	5	148	40	15	20	23	1.90
3976440--3976494	22	2.5	22	87	0	83	34	14	14	36	1.87
3977150--3978167	75	13.4	76	90	5	1623	22	21	20	34	1.97
3977150--3978167	226	4.5	227	94	3	1716	22	21	20	34	1.97
3977929--3978099	90	1.9	90	95	0	306	31	19	17	31	1.95
3978295--3978399	3	35.7	3	86	3	151	36	0	0	61	1.09
3978512--3978614	3	35.0	3	88	3	156	36	0	0	62	1.02
3979885--3979918	17	2.1	17	88	5	52	35	2	2	58	1.28
3983594--3983652	31	1.9	31	85	0	82	38	13	13	33	1.84
3991311--3991355	13	3.5	13	81	0	54	68	13	2	15	1.30
3991480--3991523	3	14.7	3	90	0	61	27	36	4	31	1.77
3992885--3992911	6	4.5	6	100	0	54	85	0	0	14	0.61
3993613--3993656	15	2.9	16	83	10	65	40	2	0	56	1.11
3993606--3993656	15	2.9	17	77	19	52	41	1	0	56	1.10
3993643--3993696	12	4.9	11	89	10	76	46	0	0	53	1.00
3993650--3993694	2	23.5	2	91	8	76	46	0	0	53	1.00
4001878--4002040	82	2.0	81	98	1	317	32	25	12	29	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4002444--4002586	72	2.0	71	98	1	277	34	19	14	30	1.92
4002609--4003149	115	4.8	115	92	3	877	34	13	19	32	1.91
4002936--4003134	107	1.9	106	94	1	353	33	13	21	31	1.92
4005619--4005673	22	2.5	22	87	0	83	36	9	12	41	1.75
4006188--4006510	165	2.0	166	86	1	461	35	13	11	39	1.81
4006514--4006852	76	4.5	76	96	1	601	23	21	20	34	1.96
4006980--4007029	3	16.7	3	79	8	57	40	2	0	58	1.10
4007030--4007067	2	19.0	2	100	0	76	50	0	0	50	1.00
4008449--4008524	11	6.5	11	71	18	57	30	3	2	63	1.26
4015986--4016517	115	4.8	115	91	5	848	33	13	20	32	1.92
4018940--4018993	22	2.5	22	87	3	83	37	9	12	40	1.76
4019818--4020587	75	10.4	76	90	6	1208	22	21	21	34	1.96
4020721--4020757	15	2.4	16	90	4	58	40	2	0	56	1.13
4020755--4020788	2	17.5	2	93	6	61	50	0	0	50	1.00
4022042--4022080	17	2.3	18	82	13	55	23	7	0	69	1.14
4024018--4024224	48	4.3	47	84	7	231	31	14	24	28	1.95
4024018--4024197	95	1.9	97	84	9	244	31	14	25	28	1.95
4024135--4024335	113	1.8	110	91	3	330	31	18	22	27	1.97
4024114--4024603	159	3.1	158	93	4	832	33	17	22	27	1.96
4024247--4024389	46	3.0	48	87	7	204	33	18	22	25	1.96
4024125--4024591	155	3.0	156	94	3	800	32	17	22	27	1.96
4024411--4024529	48	2.6	47	89	4	179	32	17	21	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4024586--4024617	16	2.0	16	93	0	55	37	9	21	31	1.85
4024501--4024728	64	3.6	63	79	9	284	32	17	20	28	1.96
4024476--4024731	128	2.0	126	94	1	449	34	16	21	28	1.95
4024691--4024824	48	2.8	48	91	0	223	33	17	20	28	1.95
4024602--4024902	160	1.9	160	96	0	557	34	16	22	26	1.95
4038204--4038232	14	2.0	15	93	6	51	75	0	10	13	1.04
4040464--4040512	16	3.0	16	81	3	62	65	2	0	32	1.04
4041609--4041646	20	1.9	20	88	0	58	21	26	10	42	1.85
4041949--4042021	25	3.0	25	90	4	114	49	2	0	47	1.15
4041948--4042018	12	5.9	12	68	6	54	46	2	0	50	1.16
4045565--4046232	205	3.3	204	88	5	896	32	11	18	37	1.86
4048381--4048459	41	2.0	41	84	2	106	37	12	17	31	1.88
4049592--4049638	22	2.1	22	92	0	76	31	14	10	42	1.80
4050213--4050341	41	3.2	40	75	14	138	31	23	17	27	1.96
4050142--4050394	83	3.1	82	83	3	267	34	21	14	29	1.93
4050251--4050402	42	3.7	42	69	15	127	32	21	16	29	1.95
4053809--4053844	2	18.0	2	88	0	54	47	2	2	47	1.31
4055595--4055647	21	2.5	21	93	0	97	13	24	3	58	1.51
4057564--4057604	21	1.9	21	85	14	57	60	0	2	36	1.10
4058677--4058721	20	2.2	20	96	0	81	44	17	11	26	1.82
4060632--4060664	17	1.9	17	93	0	57	75	3	6	15	1.11
4060630--4060682	25	2.2	24	86	6	72	71	3	9	15	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4067162--4067210	12	3.9	13	75	20	50	69	4	6	20	1.27
4067163--4067215	25	2.2	24	86	6	72	71	3	7	16	1.24
4067795--4068379	292	2.0	292	99	0	1161	31	11	13	43	1.81
4069149--4069179	2	15.5	2	100	0	62	48	0	0	51	1.00
4072815--4072861	19	2.4	19	83	13	60	46	4	17	31	1.67
4072815--4072862	20	2.5	20	86	10	64	47	4	16	31	1.65
4075335--4075363	14	2.1	14	93	6	51	6	6	6	79	1.06
4075396--4075442	17	2.9	17	84	12	55	53	0	0	46	1.00
4076052--4076168	57	2.1	57	100	0	234	16	27	15	41	1.88
4076462--4076512	21	2.5	20	78	9	57	19	23	27	29	1.98
4076855--4077384	201	2.6	202	85	2	685	33	21	13	32	1.91
4076855--4077447	201	3.0	199	80	4	665	34	21	12	31	1.91
4082146--4082199	17	3.2	17	89	0	81	20	11	33	35	1.88
4082154--4082205	17	3.1	17	88	0	77	17	13	30	38	1.88
4083288--4083378	36	2.5	36	80	7	103	24	14	27	34	1.94
4085604--4085952	43	8.1	43	83	3	283	25	16	24	33	1.95
4085606--4085885	130	2.2	129	81	2	312	25	15	25	33	1.95
4085779--4085942	84	1.9	85	86	3	233	20	20	24	34	1.96
4086358--4086425	21	3.2	21	89	0	100	4	33	20	41	1.72
4086411--4086441	9	3.4	9	100	0	62	0	41	22	35	1.54
4086436--4086491	12	4.9	12	76	12	55	1	32	25	41	1.66
4086411--4086476	21	3.3	21	83	6	75	1	36	24	37	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4086427--4086486	21	2.9	21	85	5	77	1	33	26	38	1.67
4093696--4093750	22	2.5	22	93	0	92	41	25	5	27	1.77
4093747--4093792	21	2.1	22	92	4	76	45	10	10	32	1.74
4094415--4094498	43	2.0	42	81	11	100	30	17	14	36	1.90
4095834--4096022	41	4.6	41	88	2	274	31	18	15	34	1.92
4095838--4096022	82	2.3	82	92	2	302	30	18	15	35	1.93
4096069--4096192	41	3.0	42	74	15	130	25	20	17	36	1.94
4096070--4096198	42	3.1	42	74	17	133	24	18	18	37	1.93
4097161--4097243	33	2.5	34	82	5	107	18	1	13	67	1.29
4097161--4097247	34	2.6	33	83	5	113	17	1	13	67	1.29

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