genome.fa.s1279.2.7.7.80.10.50.1000.16.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

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   

This is table  16  of  29  ( 3433 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)
3750046--3750104	12	4.9	12	78	14	68	54	16	13	15	1.72
3750011--3750104	48	2.0	48	87	4	136	53	15	13	17	1.74
3750041--3750104	24	2.7	24	92	0	110	54	17	12	15	1.71
3757346--3757383	19	2.0	19	94	0	67	52	7	2	36	1.45
3768045--3768109	27	2.4	27	94	0	112	32	7	27	32	1.85
3769377--3769407	14	2.2	14	100	0	62	19	6	6	67	1.35
3770184--3770241	29	2.0	30	82	3	73	29	3	6	60	1.39
3771220--3771252	16	2.1	16	100	0	66	18	12	18	51	1.76
3772954--3773144	94	2.0	94	97	0	364	28	21	16	34	1.95
3776610--3776793	93	2.0	94	96	1	343	57	7	11	22	1.59
3778788--3778878	45	2.0	46	91	2	148	27	25	19	27	1.99
3786595--3786659	30	2.2	30	100	0	130	36	20	18	24	1.94
3787522--3787560	20	2.0	20	89	0	60	30	33	15	20	1.94
3787597--3787658	26	2.2	27	77	11	72	24	27	20	27	1.99
3788405--3788442	20	2.0	20	89	5	60	44	18	21	15	1.86
3798804--3798951	59	2.5	60	83	3	174	41	4	20	33	1.73
3798858--3798972	60	1.9	61	85	5	162	44	5	19	31	1.72
3801056--3801109	18	3.1	18	81	7	58	70	1	9	18	1.23
3802267--3802310	23	2.0	22	81	4	52	68	6	0	25	1.14
3802291--3802568	5	54.6	5	71	19	145	53	4	1	41	1.28
3802290--3802671	7	51.3	7	71	18	192	53	6	1	39	1.35
3802332--3802676	84	4.0	85	76	17	272	52	6	1	39	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3802319--3802637	59	5.5	58	74	18	192	51	6	1	40	1.37
3802314--3802636	2	171.5	2	68	25	172	51	6	1	40	1.35
3802924--3803073	79	1.9	79	81	5	185	22	18	25	34	1.96
3812309--3812360	20	2.6	21	78	9	63	30	13	30	25	1.94
3812981--3813088	53	2.1	52	85	5	146	31	18	14	35	1.91
3822258--3822284	12	2.2	12	100	0	54	66	7	0	25	1.17
3824520--3824565	18	2.5	19	85	7	67	67	0	0	32	0.91
3824521--3824563	20	2.1	20	86	4	59	69	0	0	30	0.88
3824563--3824781	2	116.5	2	69	24	122	51	6	0	41	1.34
3824568--3824742	25	7.4	25	76	16	133	49	6	1	42	1.35
3824559--3824792	7	33.0	7	70	17	128	51	6	0	41	1.34
3824545--3824781	14	15.8	15	72	17	156	51	5	0	41	1.32
3824563--3824792	55	4.2	55	76	17	210	50	6	0	41	1.35
3824926--3824964	17	2.4	16	91	4	60	30	0	0	69	0.89
3826387--3826427	20	2.0	20	95	0	73	34	0	2	63	1.08
3828984--3829035	21	2.5	21	93	0	86	34	17	5	42	1.73
3829502--3829533	15	2.1	15	94	0	55	78	0	21	0	0.76
3829517--3829581	18	3.7	17	75	17	62	81	3	13	1	0.88
3829504--3829586	27	3.0	26	77	13	78	78	3	16	1	0.96
3830604--3830675	32	2.2	32	82	0	90	30	15	23	30	1.95
3831194--3831702	110	4.7	110	90	1	778	35	22	16	25	1.95
3832658--3832711	3	17.7	3	88	3	81	31	0	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3834137--3834177	20	2.0	20	95	0	73	34	0	2	63	1.08
3834266--3834295	13	2.3	13	94	0	51	30	0	0	70	0.88
3834264--3834296	7	4.9	7	88	7	50	30	0	0	69	0.88
3845576--3845649	22	3.7	20	83	15	82	31	16	24	28	1.96
3845520--3845746	95	2.4	93	83	7	269	33	15	22	28	1.94
3845691--3845764	22	3.5	22	90	3	116	35	14	22	27	1.94
3846151--3846506	79	4.5	79	95	0	606	33	13	23	29	1.93
3846233--3846580	45	8.5	45	67	21	154	33	13	25	28	1.93
3847065--3847193	68	1.9	68	82	3	161	31	10	27	31	1.89
3847447--3847568	45	2.7	45	96	0	217	50	5	23	19	1.69
3848113--3848248	71	1.9	70	94	4	238	30	11	25	31	1.92
3850766--3850810	17	2.6	17	82	6	56	31	13	11	44	1.78
3868440--3868551	45	2.5	45	94	1	190	37	8	24	29	1.86
3874304--3874378	34	2.2	35	82	2	89	28	16	9	46	1.77
3874370--3874412	17	2.6	16	78	10	50	30	18	6	44	1.76
3886583--3886672	7	13.7	7	77	13	86	81	0	3	15	0.83
3886583--3886672	26	3.5	26	83	11	114	81	0	3	15	0.83
3886593--3886672	6	12.7	6	82	12	90	81	0	3	15	0.83
3889550--3889621	37	1.9	37	86	5	101	29	9	1	59	1.38
3905350--3905403	25	2.2	25	93	0	90	27	31	29	11	1.91
3907143--3907170	14	2.0	14	100	0	56	42	21	14	21	1.88
3912324--3912372	24	2.0	24	88	0	71	61	0	28	10	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3919947--3920002	15	3.7	15	87	2	76	58	12	23	5	1.54
3925794--3925900	2	53.5	2	100	0	214	50	0	0	49	1.00
3925970--3926224	88	3.0	86	88	3	363	31	14	21	32	1.94
3927821--3927880	2	30.0	2	100	0	120	50	0	0	50	1.00
3928101--3928141	18	2.3	18	87	8	57	43	0	0	56	0.99
3928281--3928321	18	2.3	18	87	8	57	43	0	0	56	0.99
3928095--3928456	180	2.0	180	100	0	724	36	9	10	43	1.72
3929204--3929249	23	2.0	23	87	8	67	23	17	6	52	1.68
3930145--3930217	37	1.9	38	86	2	103	46	1	1	50	1.18
3930849--3931267	183	2.3	183	94	0	730	44	13	16	25	1.84
3931091--3931589	162	3.1	163	81	8	538	42	13	18	25	1.87
3931581--3931626	20	2.3	20	88	0	65	47	23	15	13	1.80
3938108--3938254	74	2.0	74	81	10	176	21	19	19	40	1.91
3939406--3939444	18	2.2	18	95	0	69	56	0	35	7	1.28
3940990--3941038	19	2.6	19	93	0	80	32	4	8	55	1.48
3941472--3942636	200	5.8	201	85	3	1505	40	13	15	30	1.86
3941472--3942635	401	2.9	397	86	3	1597	40	13	15	30	1.86
3942843--3942890	23	2.1	23	100	0	96	8	8	16	66	1.42
3944427--3944479	18	2.9	18	91	2	79	47	11	5	35	1.63
3945837--3945867	15	2.1	15	100	0	62	32	19	19	29	1.96
3947147--3947885	197	3.7	199	86	1	991	39	14	14	31	1.87
3947572--3947610	20	2.0	19	85	5	51	46	10	15	28	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3947849--3947891	22	2.0	22	86	4	61	27	9	9	53	1.63
3949504--3949547	19	2.3	19	96	0	79	31	6	9	52	1.59
3950033--3950095	27	2.3	27	91	0	90	23	26	25	23	2.00
3952339--3952857	200	2.6	199	84	3	690	39	14	14	31	1.86
3952852--3953013	87	1.9	87	92	0	270	35	11	11	42	1.76
3952936--3952980	23	2.0	23	86	0	63	42	15	8	33	1.78
3957850--3957882	15	2.2	15	94	0	57	30	15	33	21	1.94
3957861--3957903	21	2.0	21	91	8	70	27	18	32	20	1.96
3961021--3961052	9	3.6	9	95	0	55	9	6	9	75	1.20
3962850--3962891	18	2.3	18	84	11	59	28	7	14	50	1.69
3965403--3965453	21	2.4	21	84	15	70	7	7	1	82	0.92
3965403--3965453	22	2.5	20	74	20	50	7	7	1	82	0.92
3969813--3969860	19	2.5	19	93	0	78	29	4	29	37	1.76
3978791--3978838	23	2.1	23	96	0	87	52	12	22	12	1.73
3979641--3979781	30	4.7	30	77	8	117	17	29	8	44	1.78
3979641--3979781	60	2.3	60	84	2	167	17	29	8	44	1.78
3980521--3980578	14	3.9	14	78	15	55	6	36	6	50	1.56
3980539--3980687	31	4.8	31	71	17	112	10	34	9	46	1.70
3980501--3980725	93	2.4	93	90	1	335	12	30	10	46	1.75
3981015--3981316	30	10.1	30	78	5	254	21	24	10	43	1.84
3980992--3981315	90	3.6	91	78	8	308	21	24	9	43	1.83
3981715--3981779	30	2.3	27	76	10	67	44	3	1	50	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3981794--3981848	21	2.7	20	80	8	65	43	0	0	56	0.99
3981794--3981867	12	6.2	12	67	24	50	45	0	0	54	1.00
3981866--3981997	30	4.4	30	75	3	122	21	26	12	39	1.89
3982005--3982068	30	2.1	30	86	11	87	21	28	9	40	1.84
3982178--3982353	60	2.9	60	75	5	167	18	23	10	46	1.81
3982164--3982358	30	6.5	30	69	11	87	20	23	10	46	1.81
3983567--3984208	30	21.3	29	76	7	437	20	26	9	43	1.82
3984048--3984150	31	3.3	31	76	8	102	24	23	7	44	1.79
3984927--3985143	93	2.3	93	83	3	249	14	27	8	49	1.72
3985041--3985113	31	2.5	30	87	12	100	9	31	6	52	1.60

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