genome.fa.s1838.2.7.7.80.10.50.1000.16.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: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  3924084

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   

This is table  16  of  18  ( 2134 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)
3270915--3270993	41	1.9	41	84	7	106	63	1	1	34	1.11
3270942--3271007	30	2.2	30	88	2	96	66	0	1	31	1.01
3272758--3272876	3	39.7	3	85	6	161	36	0	0	62	1.01
3274275--3274319	2	22.5	2	86	0	63	46	0	4	48	1.22
3275768--3275792	10	2.5	10	100	0	50	8	0	0	92	0.40
3283081--3283254	70	2.4	73	81	6	194	33	16	21	28	1.95
3284516--3284573	22	2.6	22	94	0	98	31	17	15	36	1.91
3285244--3285986	73	10.0	73	93	2	1209	26	20	20	32	1.97
3286146--3286223	3	26.7	3	89	5	124	33	0	1	65	1.01
3286246--3286288	22	1.9	23	85	4	61	39	34	16	9	1.80
3286840--3286902	28	2.2	28	86	5	92	38	11	31	19	1.86
3287462--3287491	14	2.1	14	93	0	51	46	0	6	46	1.29
3294769--3294794	2	13.0	2	100	0	52	50	0	0	50	1.00
3320356--3320505	78	1.9	77	87	4	221	35	12	18	34	1.88
3321474--3321516	14	2.9	15	93	6	70	48	13	23	13	1.79
3325553--3325580	14	2.0	14	100	0	56	50	14	21	14	1.78
3326363--3326626	138	1.9	138	96	0	492	39	10	10	38	1.75
3331770--3331847	40	2.0	40	89	0	120	50	17	11	20	1.77
3340249--3340306	25	2.3	25	100	0	116	41	5	24	29	1.76
3349851--3349884	15	2.1	17	89	10	54	55	0	0	44	0.99
3353286--3353327	21	2.0	21	86	9	59	52	4	16	26	1.63
3355110--3355205	34	2.8	35	80	12	117	41	11	9	37	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3355146--3355206	17	3.5	17	77	18	63	42	13	8	36	1.74
3364218--3364377	65	2.5	66	85	5	202	30	23	18	26	1.98
3365680--3365721	21	2.0	22	81	13	52	30	28	11	28	1.92
3372358--3372398	20	2.0	21	85	4	57	17	12	29	41	1.85
3372426--3372465	21	1.9	21	90	10	64	30	12	25	32	1.92
3396109--3396165	11	5.4	11	74	16	57	56	1	0	42	1.10
3396097--3396152	25	2.3	24	81	6	69	55	1	0	42	1.10
3396094--3396171	14	5.6	14	71	17	54	52	1	0	46	1.08
3396122--3396187	31	2.1	31	82	5	78	51	1	1	45	1.19
3396210--3396244	17	2.1	17	88	0	52	25	17	25	31	1.97
3398946--3399375	37	11.8	35	76	15	269	46	3	5	44	1.44
3398946--3399375	74	5.9	72	78	12	334	46	3	5	44	1.44
3398997--3399375	37	10.5	37	82	8	392	46	3	4	45	1.41
3399361--3399427	19	3.8	17	74	23	59	31	1	4	62	1.24
3399394--3399440	19	2.5	19	89	0	67	27	2	0	70	0.99
3399401--3399442	5	8.6	5	81	5	50	23	2	0	73	0.94
3399396--3399439	24	1.9	24	90	9	74	27	2	0	70	0.99
3400515--3400541	2	13.5	2	100	0	54	48	0	0	51	1.00
3400567--3400635	18	3.6	18	68	21	50	11	4	7	76	1.12
3400563--3400653	15	5.6	16	66	22	55	13	3	7	75	1.14
3400610--3400653	18	2.5	18	85	10	56	18	0	6	75	1.02
3403382--3403564	95	1.9	95	93	0	312	31	18	19	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3404532--3405554	80	12.4	81	83	4	1176	34	23	17	24	1.96
3404532--3405578	164	6.4	164	85	3	1200	34	23	17	24	1.96
3404543--3405562	411	2.5	410	90	1	1585	34	23	17	24	1.96
3406120--3406248	35	3.6	35	79	17	142	43	3	6	46	1.46
3406118--3406487	37	10.9	34	75	16	204	45	3	4	46	1.42
3406232--3406269	2	19.5	2	94	5	69	52	0	0	47	1.00
3406128--3406359	128	1.8	129	86	8	339	44	3	5	46	1.44
3406256--3406487	37	6.5	37	84	8	286	45	3	3	46	1.39
3406256--3406523	37	7.5	37	80	9	229	45	3	4	46	1.40
3406546--3406591	5	9.4	5	83	4	58	21	2	2	73	1.04
3406544--3406591	24	2.0	23	88	4	69	22	2	2	72	1.05
3407682--3407711	2	15.5	2	93	6	53	50	0	0	50	1.00
3409496--3409636	70	2.0	71	98	1	275	29	14	17	38	1.89
3410330--3410396	33	2.0	33	100	0	134	29	23	17	28	1.97
3416091--3416167	22	3.6	22	87	6	115	46	7	16	28	1.75
3416304--3416345	14	3.2	14	83	9	54	54	7	4	33	1.49
3418748--3418953	92	2.2	92	90	1	324	33	23	12	30	1.92
3418772--3419078	164	1.9	164	89	1	481	34	24	12	28	1.92
3418864--3419025	72	2.2	72	93	0	279	33	24	13	29	1.93
3420008--3420062	24	2.4	24	81	6	69	25	16	1	56	1.50
3420265--3420426	83	2.0	82	87	6	238	41	4	9	44	1.57
3427835--3427942	43	2.5	43	87	1	146	22	20	18	38	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3432640--3432708	31	2.3	29	76	11	77	39	13	8	39	1.75
3432653--3432737	31	2.7	31	80	7	93	42	12	7	37	1.71
3433560--3433612	27	2.0	27	81	3	63	43	7	5	43	1.56
3434654--3434806	29	5.1	28	78	12	146	36	8	0	54	1.31
3434654--3434786	59	2.3	58	81	5	160	37	9	0	52	1.35
3434852--3434940	25	3.4	25	73	21	74	55	0	8	35	1.32
3434807--3435171	30	12.6	28	77	11	224	51	1	8	39	1.39
3434834--3434940	54	2.0	53	85	12	148	52	0	9	38	1.34
3434843--3435186	60	5.8	59	76	10	278	51	1	8	38	1.40
3435722--3435750	2	14.5	2	100	0	58	51	0	0	48	1.00
3436952--3437163	20	10.4	20	78	2	226	38	24	17	18	1.93
3436952--3437163	41	5.2	41	90	1	320	38	24	17	18	1.93
3437725--3437817	20	4.6	21	81	10	106	51	19	18	10	1.75
3437725--3437819	40	2.4	40	82	7	122	51	18	18	10	1.74
3437880--3437926	20	2.3	20	88	0	67	14	19	23	42	1.88
3439620--3439999	94	4.1	94	95	1	638	21	12	18	47	1.81
3440102--3440159	14	3.8	14	79	20	71	44	20	25	8	1.80
3440117--3440176	19	3.4	19	76	21	76	48	20	21	10	1.78
3440090--3440211	33	3.8	33	87	2	167	46	22	21	9	1.79
3440180--3440217	19	2.0	19	94	0	67	50	31	13	5	1.63
3440259--3440327	20	3.5	20	95	0	120	23	20	20	36	1.95
3440813--3440854	21	2.2	19	87	12	59	21	35	19	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3440838--3440929	42	2.2	42	82	3	105	25	35	17	21	1.95
3442269--3442304	14	2.6	14	90	0	54	30	0	22	47	1.52
3442487--3442593	19	5.8	19	79	12	125	15	19	16	47	1.82
3442493--3442626	34	3.8	33	79	11	133	16	21	17	44	1.87
3442487--3442635	72	2.1	72	84	2	192	16	21	17	44	1.87
3442599--3442671	20	3.6	21	85	7	98	20	19	23	36	1.95
3444673--3444706	13	2.7	13	86	4	52	8	14	23	52	1.69
3444738--3444912	87	2.0	88	96	3	327	26	25	13	34	1.93
3445892--3445937	20	2.3	20	92	7	76	23	8	19	47	1.77
3445903--3445973	20	3.5	20	84	0	79	23	16	19	39	1.92
3446066--3446257	20	9.6	20	76	6	183	19	18	25	37	1.94
3446068--3446280	61	3.5	58	76	12	189	20	17	24	37	1.94
3446093--3446257	40	4.1	41	92	1	253	19	17	24	38	1.93
3446101--3446299	81	2.5	79	86	6	249	19	17	24	38	1.93
3446269--3446318	20	2.5	20	90	6	75	18	18	20	44	1.88
3446368--3446421	20	2.7	19	69	8	54	20	18	27	33	1.96
3452961--3453000	21	1.9	21	84	0	53	27	37	25	10	1.88
3462892--3462936	21	2.1	21	88	8	65	51	6	4	37	1.49
3464488--3464528	20	2.1	19	90	4	64	7	29	14	48	1.71
3468761--3468906	60	2.4	58	80	8	159	41	10	3	43	1.56
3468975--3469125	39	3.9	38	84	5	187	43	13	5	37	1.68
3468975--3469128	78	2.0	78	87	5	222	43	13	5	37	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3469013--3469256	136	1.8	135	87	2	364	41	13	7	37	1.73
3468922--3469293	175	2.1	175	83	3	473	41	14	6	36	1.73
3469146--3469272	39	3.3	39	87	5	179	44	11	6	37	1.66
3469163--3469293	39	3.4	38	88	2	163	41	12	6	39	1.68
3470832--3470875	21	2.1	21	87	8	63	36	0	0	63	0.95
3470839--3470882	17	2.4	18	81	7	54	34	0	0	65	0.93
3475040--3475153	36	3.2	36	95	2	196	35	18	13	32	1.89
3475726--3475784	31	1.9	31	92	0	100	30	23	8	37	1.85
3479205--3479239	18	1.9	18	100	0	70	42	5	5	45	1.51
3481953--3482000	21	2.3	21	96	0	87	33	37	14	14	1.87

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18