genome.fa.s851.2.7.7.80.10.50.1000.16.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: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7304151

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   

This is table  16  of  31  ( 3618 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)
3856176--3856223	16	2.9	16	79	11	53	2	18	2	77	0.97
3856149--3856222	34	2.2	32	83	9	94	6	16	1	75	1.08
3861517--3861846	56	5.9	56	87	1	394	26	22	15	35	1.94
3861517--3861846	167	2.0	167	83	1	419	26	22	15	35	1.94
3861517--3861842	111	2.9	111	84	0	409	26	22	15	35	1.94
3872992--3873028	16	2.2	17	90	4	58	29	29	10	29	1.91
3874630--3874666	12	3.0	13	80	11	51	67	0	0	32	0.91
3884880--3884946	28	2.4	28	84	0	80	41	23	7	26	1.81
3884902--3884997	28	3.4	28	85	2	120	44	19	9	26	1.81
3885075--3885147	29	2.5	28	80	10	76	39	26	6	27	1.81
3885124--3885291	29	5.8	29	90	2	248	46	20	9	23	1.80
3885124--3885291	88	1.9	88	89	4	259	46	20	9	23	1.80
3885124--3885291	59	2.9	58	90	3	248	46	20	9	23	1.80
3885292--3885362	17	4.2	17	87	5	90	16	22	39	21	1.92
3889306--3889351	22	2.0	23	95	4	85	34	21	21	21	1.97
3889432--3889479	21	2.3	21	96	0	87	20	29	27	22	1.99
3891847--3891985	29	4.8	29	85	0	179	48	19	10	22	1.78
3892751--3892804	2	27.0	2	100	0	108	50	0	0	50	1.00
3892802--3892842	4	10.2	4	100	0	82	24	0	24	51	1.49
3897567--3897609	23	1.9	21	81	13	50	34	13	18	32	1.90
3898804--3898848	23	1.9	24	95	4	83	6	17	15	60	1.56
3900675--3900716	19	2.2	19	95	0	75	21	16	23	38	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3900952--3901040	43	2.1	43	89	0	133	34	16	20	28	1.94
3906396--3906423	2	14.0	2	100	0	56	50	0	0	50	1.00
3907998--3908173	85	2.1	85	84	4	230	30	17	21	30	1.96
3909401--3909487	20	4.1	20	77	13	84	52	16	9	21	1.71
3909420--3909507	45	2.0	45	86	0	122	51	14	10	23	1.73
3909492--3909570	20	4.0	20	81	6	79	49	15	11	24	1.77
3909401--3909570	40	4.1	40	69	8	108	50	15	10	24	1.75
3912175--3912213	18	2.3	16	83	12	51	74	7	2	15	1.15
3912176--3912213	17	2.2	17	90	4	58	76	5	2	15	1.08
3912387--3912427	2	20.5	2	100	0	82	48	0	0	51	1.00
3912569--3912609	20	2.0	22	85	9	59	56	4	2	36	1.34
3922539--3922719	47	3.8	47	88	1	272	30	19	19	29	1.97
3922539--3922728	95	2.0	93	88	2	281	30	18	20	30	1.96
3922732--3923994	249	5.1	249	91	1	1949	34	17	17	30	1.93
3922732--3923994	497	2.6	498	90	2	1992	34	17	17	30	1.93
3925096--3925216	51	2.4	51	87	1	179	21	22	19	36	1.95
3926725--3926764	10	3.9	11	78	15	50	2	15	0	82	0.77
3926719--3926768	12	4.1	12	74	20	50	2	16	0	82	0.77
3931606--3931698	45	2.1	45	81	4	107	53	12	4	29	1.58
3933235--3933309	28	2.6	28	85	2	96	16	9	46	28	1.77
3937887--3937955	32	2.1	33	89	2	104	36	20	18	24	1.95
3941389--3941426	18	2.2	18	90	4	60	36	0	5	57	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3941814--3941852	21	1.9	21	84	5	53	69	5	0	25	1.09
3949224--3949253	14	2.1	14	93	0	51	56	3	6	33	1.42
3949243--3949288	20	2.2	20	85	11	58	63	0	8	28	1.24
3949556--3949627	20	3.5	20	76	12	67	27	23	18	30	1.97
3949592--3949733	54	2.6	54	84	4	171	28	21	19	30	1.97
3949713--3949748	15	2.5	15	95	4	65	27	19	16	36	1.93
3963263--3963306	21	2.1	21	83	8	54	31	11	18	38	1.86
3963376--3963466	18	4.5	19	69	25	71	57	0	3	39	1.15
3963376--3963477	18	5.4	18	69	23	68	58	0	2	38	1.13
3963422--3963500	24	3.2	24	73	8	63	60	2	1	35	1.18
3963759--3963876	59	2.0	59	100	0	236	47	10	5	37	1.59
3965068--3965112	21	2.3	19	84	7	54	33	22	11	33	1.89
3966363--3966388	6	4.3	6	100	0	52	30	0	19	50	1.48
3973150--3973190	17	2.3	18	80	16	50	4	34	0	60	1.18
3980697--3980766	35	2.0	36	91	2	115	40	10	15	34	1.81
3987380--3987497	56	2.1	56	96	0	218	21	20	26	32	1.97
3987729--3987786	2	29.0	2	100	0	116	50	0	0	50	1.00
3994144--3994178	2	18.0	2	94	5	63	48	0	0	51	1.00
3997311--3997573	149	1.8	147	87	6	403	46	15	12	25	1.82
3997577--3997876	99	3.0	97	85	5	368	43	19	16	20	1.88
4002977--4003103	67	1.9	66	95	1	227	29	8	14	48	1.73
4010760--4011546	400	2.0	387	93	5	1348	35	14	20	28	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4020608--4020924	158	2.0	159	99	0	627	36	13	21	29	1.91
4021200--4021229	16	1.9	15	93	6	51	46	0	13	40	1.43
4024009--4024079	23	3.2	23	70	22	69	25	19	21	33	1.97
4023982--4024084	44	2.3	44	93	0	170	28	20	20	31	1.97
4024019--4024084	21	3.1	20	74	16	69	27	21	19	31	1.97
4026760--4026798	19	2.2	18	86	9	53	33	17	20	28	1.96
4030253--4030420	90	1.9	90	91	0	273	36	10	6	46	1.65
4036919--4037096	90	2.0	90	94	0	311	38	11	5	44	1.65
4038557--4039134	137	4.2	137	90	0	816	31	27	16	24	1.96
4039292--4039335	3	15.0	3	92	4	54	40	0	0	59	0.98
4039435--4039471	17	2.2	17	90	0	56	29	37	18	13	1.90
4042904--4042953	16	3.2	16	75	11	50	60	4	8	28	1.43
4043049--4043393	2	173.5	2	68	18	170	48	3	3	44	1.36
4043052--4043213	13	12.3	13	71	15	102	46	4	3	44	1.42
4043454--4043495	7	6.0	7	88	0	57	50	35	0	14	1.43
4043455--4043495	21	2.0	21	90	0	64	51	34	0	14	1.43
4043667--4043716	20	2.6	19	87	6	73	48	4	6	42	1.46
4043886--4044010	20	6.1	21	71	20	79	42	7	7	43	1.59
4044090--4044129	22	1.9	21	90	10	64	37	5	5	52	1.45
4044121--4044243	65	1.9	65	83	6	160	43	5	1	49	1.36
4044333--4044375	12	3.2	12	77	22	50	48	0	0	51	1.00
4044882--4044921	20	2.0	21	85	5	55	25	27	5	42	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4045170--4045262	6	15.5	6	70	7	55	39	40	12	6	1.69
4045167--4045210	12	3.6	12	87	3	61	36	43	11	9	1.72
4045194--4045258	18	3.7	18	74	10	62	40	41	12	6	1.67
4045233--4045274	17	2.4	18	92	4	68	45	45	7	2	1.44
4048443--4048482	11	3.5	11	83	6	53	40	7	5	47	1.54
4048733--4048786	23	2.3	24	87	3	83	46	7	1	44	1.42
4048843--4048869	13	2.1	13	100	0	54	44	0	0	55	0.99
4049787--4049928	44	3.2	44	87	4	189	28	16	24	29	1.97
4050308--4050356	21	2.3	21	79	10	64	0	38	16	44	1.48
4060306--4060654	82	4.2	82	74	8	287	31	19	17	32	1.95
4060341--4060666	42	7.9	42	67	11	145	30	19	17	32	1.95
4063922--4063997	39	1.9	39	94	0	134	55	17	13	14	1.70
4065031--4065060	3	10.0	3	100	0	60	66	0	0	33	0.92
4072922--4072998	39	1.9	39	89	7	120	45	0	2	51	1.14
4076032--4076072	21	1.9	22	90	5	66	26	19	17	36	1.94
4080421--4080890	236	2.0	231	95	3	854	30	9	15	44	1.79
4087169--4087203	18	1.9	18	94	0	61	22	17	37	22	1.94
4093975--4094019	20	2.2	21	96	4	83	60	0	0	40	0.97
4093975--4094012	11	3.6	11	86	13	62	63	0	0	36	0.95
4094010--4094034	13	1.9	13	100	0	50	44	0	0	56	0.99
4094056--4094103	22	2.1	24	84	7	64	56	4	4	35	1.38
4094659--4094703	21	2.1	21	84	8	56	26	4	24	44	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4102370--4102401	14	2.1	16	88	11	50	15	15	18	50	1.79
4102666--4102715	23	2.2	23	81	0	55	12	10	18	60	1.59
4102702--4102740	20	2.0	20	89	0	60	2	12	23	61	1.43
4102796--4102828	16	2.1	16	94	0	57	6	15	24	54	1.63
4105188--4105281	35	2.7	35	91	1	154	46	11	7	34	1.68
4105176--4105313	18	7.8	18	76	5	113	44	10	10	34	1.73
4105770--4105808	16	2.4	16	100	0	78	30	12	30	25	1.93
4107305--4107836	266	2.0	265	97	2	1014	42	18	9	29	1.81
4110931--4110964	2	17.0	2	100	0	68	50	0	0	50	1.00
4115719--4115751	16	2.0	17	88	5	50	42	0	21	36	1.53

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