genome.fa.s8428.2.7.7.80.10.50.1000.17.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: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6915314

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   

This is table  17  of  30  ( 3508 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)
4025016--4025461	149	3.0	148	83	4	522	36	18	23	20	1.94
4025612--4025648	14	2.6	15	83	12	51	16	29	8	45	1.76
4025642--4025682	20	2.0	20	85	0	55	24	17	14	43	1.86
4026940--4026970	12	2.5	13	94	5	55	80	0	19	0	0.71
4026938--4027016	18	3.9	19	79	12	79	78	0	20	1	0.82
4026953--4027011	10	6.3	9	74	14	57	79	0	18	1	0.81
4026913--4027017	9	10.6	9	70	19	59	77	0	20	2	0.90
4028482--4028922	66	6.8	65	84	4	477	29	19	12	38	1.88
4028999--4029092	35	2.6	34	75	8	89	31	19	13	35	1.91
4029383--4029904	91	5.8	90	82	5	576	37	17	21	23	1.94
4029383--4029904	182	2.9	180	87	3	689	37	17	21	23	1.94
4031558--4031632	8	9.5	8	75	15	50	20	2	4	73	1.12
4031558--4031626	21	3.3	21	78	15	72	17	2	4	75	1.09
4036760--4036788	3	9.7	3	100	0	58	68	0	0	31	0.89
4038101--4038178	3	27.0	3	89	7	126	67	0	0	32	0.90
4038630--4038731	42	2.5	42	83	4	127	29	21	22	26	1.99
4038603--4039301	271	2.6	273	90	1	1091	33	20	17	29	1.95
4039181--4039276	42	2.3	42	83	5	115	32	20	20	26	1.98
4041173--4041222	9	5.8	8	80	15	55	4	14	0	82	0.82
4041173--4041221	18	2.8	17	84	9	62	4	14	0	81	0.83
4041685--4041710	11	2.4	11	100	0	52	0	19	0	80	0.71
4046345--4046398	22	2.5	22	70	11	56	42	12	0	44	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4051391--4051590	111	1.8	111	82	4	260	32	15	19	33	1.93
4058201--4058227	14	1.9	14	100	0	54	37	7	40	14	1.74
4077316--4077358	21	2.2	19	83	8	50	25	11	4	58	1.52
4091005--4091109	2	54.0	2	90	5	171	49	1	0	48	1.12
4091217--4091414	35	5.5	36	88	5	203	46	4	7	40	1.52
4091222--4091400	37	4.9	37	91	2	233	46	3	7	41	1.51
4091464--4091503	4	10.0	4	89	10	64	25	0	0	75	0.81
4091463--4091519	17	3.4	17	83	13	57	24	1	1	71	1.04
4093888--4093941	18	2.9	18	74	12	56	25	3	9	61	1.43
4093940--4093969	13	2.3	13	94	0	51	60	0	0	40	0.97
4095921--4096045	5	24.4	5	78	12	67	74	4	4	16	1.15
4096270--4096323	18	2.9	18	76	12	56	72	1	1	24	1.05
4097941--4098025	31	2.9	28	76	13	80	44	1	3	50	1.26
4098808--4098845	19	2.0	19	100	0	76	57	5	5	31	1.43
4099164--4099360	20	9.9	20	81	9	111	36	25	17	19	1.94
4099170--4099379	60	3.5	59	81	6	210	37	25	17	20	1.94
4099224--4099379	20	7.8	20	87	4	174	35	25	17	21	1.95
4099190--4099379	40	4.8	40	86	5	208	36	25	17	20	1.94
4102026--4102365	19	19.4	19	80	17	416	47	18	20	13	1.82
4102054--4102346	52	5.6	52	93	4	461	47	17	21	13	1.82
4102058--4102387	52	6.3	52	93	5	391	46	17	21	13	1.83
4102026--4102387	71	5.2	70	80	12	342	46	18	21	13	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4102394--4102495	19	5.6	19	85	12	151	14	23	17	44	1.86
4102602--4102638	14	2.6	14	91	0	65	45	21	0	32	1.52
4104467--4104556	14	5.7	14	72	23	72	43	23	24	8	1.82
4104459--4104573	33	3.5	33	96	0	212	46	20	22	9	1.79
4104481--4104578	19	5.7	19	70	22	81	44	22	22	10	1.82
4104590--4104646	14	3.7	14	75	20	60	8	24	22	43	1.81
4104604--4104692	19	4.9	19	72	15	80	11	23	21	43	1.84
4104574--4104692	33	3.4	33	88	6	157	10	22	22	44	1.82
4104781--4104851	33	2.2	33	94	0	124	47	16	23	11	1.79
4105033--4105087	22	2.5	22	81	0	74	20	16	40	23	1.91
4105229--4105422	20	9.6	20	79	5	203	19	20	24	35	1.95
4105231--4105402	60	2.8	60	84	0	236	20	19	25	34	1.96
4105228--4105543	60	5.2	60	77	8	232	20	18	25	36	1.95
4105389--4105486	20	4.8	20	77	3	79	21	18	23	36	1.95
4105389--4105545	61	2.6	60	80	7	176	19	17	25	38	1.93
4105389--4105545	41	3.9	41	70	14	110	19	17	25	38	1.93
4107026--4107083	24	2.4	24	82	8	73	10	27	36	25	1.89
4111257--4111570	157	2.0	157	99	0	619	32	20	21	26	1.98
4113497--4113563	34	1.9	35	85	14	95	25	7	13	53	1.65
4113618--4113813	30	6.6	30	83	2	198	17	12	8	61	1.54
4113804--4113853	25	2.0	25	84	7	66	14	14	12	60	1.60
4115472--4115884	202	2.0	202	97	2	763	26	11	15	47	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4117646--4117770	20	5.6	24	74	20	105	77	7	15	0	0.97
4117658--4117729	17	3.9	18	77	22	69	76	8	15	0	1.01
4117658--4117749	18	4.8	19	75	17	84	77	7	15	0	0.98
4117684--4117769	5	16.6	5	77	17	61	80	5	13	0	0.89
4117670--4117769	22	4.8	20	79	16	105	79	7	14	0	0.93
4117651--4117770	38	3.1	38	79	12	120	77	6	15	0	0.97
4117646--4117766	16	7.6	16	72	17	74	76	7	15	0	0.99
4117665--4117770	10	10.0	10	69	21	65	78	7	14	0	0.96
4118800--4118865	32	2.0	33	88	2	98	24	13	27	34	1.93
4119029--4119191	29	5.0	35	64	22	111	31	11	16	41	1.83
4119017--4119225	64	3.3	64	89	0	319	30	11	16	42	1.83
4119208--4119265	30	1.9	30	93	6	100	25	20	13	39	1.90
4119306--4119703	130	3.0	130	79	4	379	25	31	18	25	1.97
4119323--4119792	134	3.5	132	78	5	439	24	31	17	26	1.97
4119988--4120075	3	29.0	3	84	11	117	31	2	0	65	1.05
4121599--4121795	30	6.6	30	82	4	218	17	10	11	60	1.57
4121599--4121795	60	3.3	60	86	1	261	17	10	11	60	1.57
4121623--4121826	60	3.4	60	80	8	218	18	8	10	62	1.53
4121621--4121822	90	2.2	90	82	4	228	18	8	10	61	1.54
4123699--4124914	6	207.0	6	92	7	1998	49	17	0	32	1.51
4125568--4125606	20	2.0	20	89	0	60	25	15	5	53	1.62
4130867--4130909	18	2.4	18	88	0	59	72	6	2	18	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4138061--4138095	3	11.3	3	93	6	61	31	2	0	65	1.07
4138836--4138885	15	3.4	15	91	2	75	46	2	0	52	1.12
4138855--4138924	23	3.0	23	72	2	68	44	0	0	55	0.99
4138873--4138939	35	2.0	33	82	11	82	41	0	0	58	0.98
4142329--4142370	17	2.5	17	92	0	66	26	16	23	33	1.96
4143048--4143085	19	2.0	20	89	5	60	44	18	13	23	1.85
4146851--4146876	12	2.2	12	100	0	52	26	30	19	23	1.98
4150862--4151209	173	2.0	174	98	1	680	39	15	14	29	1.87
4153670--4153733	17	3.8	17	76	0	56	20	9	9	60	1.54
4153866--4153978	24	4.7	24	81	2	102	34	18	23	23	1.96
4155569--4155621	23	2.3	23	96	3	99	16	22	0	60	1.36
4157543--4157601	16	3.7	16	80	8	66	32	25	6	35	1.82
4157647--4157681	16	2.1	17	89	5	54	22	14	5	57	1.59
4157877--4157919	13	3.2	12	79	20	50	25	0	11	62	1.29
4161394--4161462	15	5.1	14	80	14	76	75	5	17	1	1.07
4161399--4161487	7	11.7	7	74	18	56	76	3	17	2	1.03
4161414--4161494	8	10.4	8	72	17	55	72	3	20	2	1.11
4163920--4164020	36	2.8	36	81	4	123	33	20	11	33	1.89
4163971--4164135	66	2.5	66	80	10	169	35	19	7	38	1.79
4164023--4164426	103	4.0	100	77	9	361	34	17	11	37	1.85
4164325--4164786	66	7.0	66	92	0	773	27	18	14	39	1.90
4164325--4164786	197	2.3	198	93	0	782	27	18	14	39	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4164341--4164805	36	13.9	35	62	15	137	28	19	13	38	1.90
4164835--4165228	139	2.8	139	84	0	484	31	28	15	24	1.96
4166381--4166634	131	1.9	132	86	5	359	22	16	15	45	1.85
4166648--4166680	2	16.5	2	100	0	66	48	0	0	51	1.00
4166760--4166825	16	4.1	16	84	3	80	31	24	6	37	1.80
4166872--4166906	16	2.1	17	89	5	54	25	14	5	54	1.62
4168259--4168319	29	2.1	30	81	3	70	34	11	3	50	1.55
4171556--4171595	21	1.9	21	94	0	71	27	17	20	35	1.95
4175713--4175805	23	4.0	23	77	0	96	20	24	21	33	1.97
4175804--4175851	24	2.0	24	83	0	60	20	20	20	37	1.95

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