genome.fa.s9001.2.7.7.80.10.50.1000.16.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: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4740655

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   

This is table  16  of  24  ( 2777 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)
3287022--3287193	20	8.6	20	69	3	76	26	22	13	37	1.92
3287044--3287193	60	2.5	60	81	2	167	26	22	14	36	1.93
3287292--3287349	22	2.6	22	89	5	82	24	44	6	24	1.77
3287356--3287390	16	2.2	16	89	0	52	28	5	0	65	1.15
3288142--3288224	24	3.5	24	89	0	112	25	19	16	38	1.92
3290796--3290928	20	6.9	20	76	13	127	45	22	10	21	1.82
3290805--3290910	54	2.0	54	83	3	133	46	22	10	20	1.81
3290990--3291043	20	2.7	20	82	0	63	22	12	22	42	1.87
3293367--3293478	21	5.3	21	84	2	118	30	14	33	22	1.93
3293367--3293478	42	2.7	41	84	2	134	30	14	33	22	1.93
3293809--3293978	21	8.1	21	79	7	184	32	34	11	21	1.89
3293809--3293978	63	2.7	63	86	0	241	32	34	11	21	1.89
3294078--3294246	42	4.0	42	88	0	239	27	13	36	23	1.92
3294078--3294236	84	1.9	84	93	0	273	26	13	36	23	1.92
3295623--3295689	20	3.3	20	78	0	80	44	20	11	22	1.84
3295674--3295716	14	3.1	14	96	0	77	46	27	13	11	1.78
3295683--3295762	34	2.4	34	89	0	124	48	21	13	16	1.80
3295654--3295750	48	2.0	48	85	0	131	46	22	12	18	1.82
3296126--3296172	16	3.1	16	90	6	71	21	0	53	25	1.46
3296201--3296279	37	2.1	38	92	2	133	30	10	45	13	1.77
3296380--3296462	20	4.2	20	75	7	71	38	13	21	26	1.90
3296381--3296556	40	4.4	40	74	2	140	38	13	21	27	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3296381--3296538	60	2.6	58	77	10	165	38	13	20	27	1.90
3296401--3296557	60	2.6	59	74	11	147	40	12	21	26	1.88
3296585--3296627	21	2.1	21	86	4	61	25	13	18	41	1.88
3300194--3300230	18	2.0	19	89	5	58	21	64	8	5	1.40
3301046--3301089	2	22.0	2	100	0	88	50	0	50	0	1.00
3302815--3302862	19	2.5	19	100	0	96	35	12	20	31	1.90
3303286--3303399	45	2.6	44	87	2	156	34	9	20	35	1.85
3303321--3303425	14	7.1	14	70	14	68	33	9	20	37	1.85
3303286--3303430	44	3.3	44	83	3	166	34	8	20	36	1.84
3303501--3303576	23	3.3	23	71	0	62	17	26	21	35	1.95
3304416--3304480	23	2.8	23	83	0	94	33	24	24	16	1.96
3305182--3305249	35	1.9	35	85	5	93	25	19	16	39	1.91
3309043--3309177	21	6.3	20	76	13	101	38	28	10	22	1.87
3309026--3309159	43	3.1	43	91	0	196	37	26	11	23	1.90
3309026--3309095	22	3.2	22	73	18	83	37	25	12	24	1.91
3309026--3309139	21	5.3	22	73	13	103	38	26	11	23	1.89
3309043--3309177	64	2.1	64	82	10	161	38	28	10	22	1.87
3315775--3315814	21	1.9	21	89	0	62	25	40	25	10	1.86
3316998--3317045	16	3.0	15	80	14	60	14	0	27	58	1.37
3317002--3317035	17	2.0	17	94	0	59	14	0	29	55	1.40
3317606--3317649	23	2.0	23	81	4	54	50	11	2	36	1.51
3318679--3318753	22	3.5	20	80	10	78	28	30	17	24	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3320299--3320344	3	14.7	3	86	8	56	36	0	0	63	0.95
3320299--3320344	19	2.4	19	92	0	74	36	0	0	63	0.95
3321782--3321921	28	4.9	28	78	12	83	15	8	0	75	1.09
3321806--3321921	9	12.2	10	68	21	54	14	6	0	77	1.02
3321812--3321909	20	4.8	21	72	20	66	16	6	1	76	1.04
3321804--3321921	28	4.2	28	80	14	127	14	7	0	77	1.03
3321851--3321935	28	3.1	28	89	1	109	11	10	0	77	0.99
3326904--3326995	21	4.3	21	75	13	98	35	29	11	22	1.90
3326887--3326977	43	2.1	43	85	0	119	36	25	12	26	1.91
3327493--3327546	22	2.5	22	82	11	60	27	24	22	25	2.00
3331223--3331253	13	2.3	14	94	5	55	61	0	0	38	0.96
3334537--3334593	25	2.3	24	84	3	69	75	3	3	17	1.09
3335832--3335904	3	23.3	3	83	5	83	61	1	1	35	1.13
3335832--3335904	30	2.4	29	86	8	94	61	1	1	35	1.13
3336673--3337077	106	3.7	106	86	7	567	21	17	26	34	1.96
3336935--3336967	12	2.8	12	100	0	66	27	12	27	33	1.92
3336829--3337073	118	2.1	118	96	0	445	21	18	26	33	1.96
3341135--3341160	12	2.2	12	100	0	52	46	0	7	46	1.31
3341235--3341350	10	11.6	10	71	17	53	73	2	3	20	1.10
3342383--3342444	3	20.0	3	83	3	70	61	1	0	37	1.06
3342769--3343006	123	1.9	123	85	3	325	27	15	24	31	1.96
3343830--3343883	3	17.0	3	84	7	63	62	1	1	33	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3344999--3345106	53	2.1	52	89	1	162	37	4	20	37	1.73
3349097--3349129	2	16.5	2	100	0	66	48	0	0	51	1.00
3349386--3349420	2	17.5	2	100	0	70	48	0	0	51	1.00
3349755--3349799	23	2.0	23	86	0	63	13	15	13	57	1.65
3350225--3350271	19	2.5	19	77	16	53	36	2	0	61	1.08
3350950--3350994	21	2.1	21	100	0	90	40	26	20	13	1.89
3352718--3352770	13	4.1	14	75	20	53	66	1	20	11	1.33
3358968--3359024	29	2.0	29	96	0	105	63	14	5	17	1.48
3360523--3360571	18	2.7	18	90	0	80	32	30	20	16	1.94
3366542--3366597	21	2.5	22	78	18	62	30	0	16	53	1.43
3366984--3367024	21	2.0	21	90	0	64	29	17	17	36	1.92
3367105--3367156	18	2.9	18	88	0	68	17	17	32	32	1.93
3368890--3368985	39	2.5	39	94	0	174	43	1	37	17	1.56
3369077--3369103	11	2.5	11	100	0	54	25	0	0	74	0.83
3369666--3369705	2	20.0	2	100	0	80	50	0	0	50	1.00
3370022--3370134	39	2.9	39	81	10	124	42	12	4	40	1.62
3370523--3370581	30	1.9	31	83	10	77	49	0	1	49	1.11
3372923--3373007	42	2.0	42	93	0	143	31	10	28	29	1.90
3376820--3376942	42	2.9	42	81	7	115	24	16	8	50	1.73
3376839--3376942	42	2.4	43	82	9	133	23	17	8	50	1.73
3376864--3377061	108	1.8	109	82	7	260	23	18	7	50	1.71
3376932--3376975	23	1.9	23	81	9	54	27	22	0	50	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3376955--3377107	44	3.7	40	74	17	118	27	18	5	49	1.69
3387199--3387289	24	3.8	24	82	5	112	25	12	20	41	1.87
3387164--3387280	48	2.4	49	87	4	157	25	11	18	44	1.83
3387192--3387296	24	4.4	24	80	4	86	26	11	20	41	1.86
3387405--3387499	43	2.2	43	92	3	156	16	9	36	36	1.82
3395837--3395878	18	2.3	18	91	0	66	30	40	7	21	1.80
3395845--3395879	18	1.9	18	100	0	70	34	34	8	22	1.85
3401960--3402049	26	3.4	26	72	10	76	53	1	1	44	1.15
3402718--3402799	27	3.1	25	78	13	76	56	1	1	41	1.15
3402736--3402828	27	3.5	26	79	7	82	51	1	3	44	1.24
3401576--3403079	756	2.0	731	88	5	2201	41	7	7	42	1.62
3403084--3403192	39	2.8	39	70	13	107	43	3	13	39	1.62
3405381--3405407	13	2.1	13	100	0	54	22	0	0	77	0.76
3408326--3408391	27	2.4	27	94	0	114	39	16	16	27	1.90
3416035--3416209	38	4.6	39	87	3	232	36	15	20	27	1.93
3416018--3416204	77	2.5	76	86	2	250	36	14	21	27	1.92
3418154--3418230	31	2.5	31	78	2	82	27	29	27	15	1.96
3418107--3418230	63	2.0	63	80	6	144	25	28	28	17	1.98
3419119--3419158	17	2.4	17	86	0	53	17	22	37	22	1.94
3419152--3419219	19	3.5	19	87	2	82	27	27	25	19	1.98
3421023--3421048	13	2.0	13	100	0	52	61	23	0	15	1.33
3426425--3426461	19	1.9	19	100	0	74	27	29	27	16	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3426451--3426491	17	2.4	17	83	0	55	17	21	39	21	1.93
3426487--3426536	9	5.1	10	74	13	50	28	30	22	20	1.98
3426485--3426536	20	2.7	19	87	3	68	26	28	25	19	1.98
3431481--3431509	6	4.8	6	100	0	58	51	13	0	34	1.42
3431606--3431648	14	3.1	14	81	15	54	76	0	2	20	0.89
3431601--3431651	10	5.1	11	86	9	58	76	0	1	21	0.88
3434774--3434830	23	2.5	23	79	0	69	14	24	10	50	1.73
3437207--3437441	126	1.9	126	96	0	434	38	11	12	37	1.78
3440188--3440284	40	2.4	42	81	8	112	54	1	3	41	1.23
3440258--3440299	14	2.9	15	78	7	50	54	0	2	42	1.13

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