genome.fa.s1711.2.7.7.80.10.50.1000.10.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: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4148933

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   

This is table  10  of  13  ( 1546 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)
3209521--3209568	20	2.3	21	92	3	80	18	25	41	14	1.88
3212378--3212449	30	2.4	29	83	4	90	30	15	9	44	1.78
3216279--3216326	21	2.3	21	92	0	78	43	12	8	35	1.73
3216867--3217040	54	3.2	54	94	0	294	30	13	18	37	1.90
3217011--3217072	32	1.9	32	90	0	97	24	11	20	43	1.85
3216955--3217126	86	2.0	86	93	2	292	28	12	20	38	1.88
3217041--3217335	54	5.5	54	93	0	493	32	10	18	38	1.85
3216901--3217180	140	2.0	140	93	4	476	29	11	19	39	1.87
3216867--3217234	194	1.9	194	95	0	664	30	12	19	37	1.88
3217044--3217748	54	12.6	54	78	9	459	32	10	18	38	1.84
3217041--3217737	108	6.2	108	73	13	568	33	10	17	38	1.84
3217073--3217876	402	2.0	401	96	0	1473	33	10	17	38	1.83
3219375--3219552	89	2.0	90	89	1	277	38	24	8	29	1.84
3224132--3224224	47	2.0	47	97	0	177	49	12	11	25	1.75
3224989--3225026	18	2.1	18	85	9	51	42	15	21	21	1.89
3225393--3226384	54	18.3	54	82	3	1071	34	17	18	28	1.94
3225393--3226384	164	6.1	163	83	4	1117	34	17	18	28	1.94
3225391--3226384	382	2.6	379	89	1	1431	34	17	18	28	1.94
3226525--3226854	81	4.1	81	84	2	403	39	11	20	27	1.88
3226538--3226852	161	2.0	161	84	1	416	39	12	20	28	1.89
3226871--3226920	2	25.0	2	100	0	100	50	0	0	50	1.00
3227786--3228137	178	2.0	174	96	3	652	35	16	20	27	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3230948--3231561	54	11.3	54	81	3	644	33	17	20	28	1.96
3230952--3231561	109	5.6	108	79	5	631	33	17	20	28	1.95
3231706--3232023	81	3.9	81	87	0	413	37	11	22	28	1.88
3255832--3255897	29	2.2	30	81	10	82	25	18	9	46	1.78
3259168--3259491	161	2.0	161	100	0	648	29	5	22	43	1.75
3263671--3263739	30	2.3	30	97	0	129	44	4	26	24	1.72
3268122--3268327	98	2.1	98	84	3	263	31	16	16	35	1.92
3298172--3298316	78	1.9	76	84	8	195	43	4	11	40	1.62
3298902--3299358	54	8.5	54	86	0	601	26	16	19	36	1.93
3301508--3301577	32	2.3	31	90	5	106	35	30	12	21	1.91
3305954--3306337	54	7.1	54	88	2	556	26	15	20	38	1.92
3307656--3307694	17	2.3	17	90	0	60	41	2	20	35	1.66
3317444--3317482	17	2.4	17	86	4	62	33	0	10	56	1.33
3331381--3331610	115	2.0	115	99	0	451	26	19	21	32	1.97
3333142--3333276	32	4.2	32	75	3	110	37	22	15	24	1.93
3333295--3333528	114	2.0	115	99	0	461	36	20	8	33	1.84
3334909--3334946	12	3.2	12	85	3	51	57	2	0	39	1.12
3335306--3335341	16	2.2	16	90	0	54	55	0	16	27	1.42
3335940--3336040	32	3.4	28	84	11	130	42	35	9	11	1.75
3335933--3336039	29	3.4	32	85	8	157	42	36	10	11	1.75
3336137--3336207	33	2.2	33	80	5	83	35	23	9	30	1.88
3336276--3336329	28	1.9	28	92	0	90	27	9	12	50	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3336270--3336327	28	2.2	26	81	9	71	29	8	12	50	1.69
3337518--3337567	27	1.9	27	88	8	77	42	6	0	52	1.26
3337550--3337607	25	2.3	25	84	0	80	39	1	0	58	1.08
3337884--3337919	15	2.4	15	90	9	56	75	0	2	22	0.94
3342416--3342503	25	3.4	26	80	17	96	43	3	0	53	1.17
3342485--3342542	25	2.3	25	84	0	80	39	1	0	58	1.08
3342819--3342854	15	2.4	15	90	9	56	75	0	2	22	0.94
3347597--3347699	45	2.3	45	89	1	152	22	19	12	45	1.84
3349254--3349280	14	1.9	14	100	0	54	70	22	0	7	1.12
3354233--3354309	22	3.5	22	78	5	93	24	25	24	24	2.00
3354234--3354328	44	2.2	42	87	7	129	25	22	25	27	2.00
3354233--3354328	21	4.5	20	78	11	86	25	22	25	27	2.00
3359960--3360008	19	2.7	17	84	9	53	26	20	28	24	1.99
3359980--3360124	64	2.2	65	85	6	188	25	19	25	29	1.98
3361053--3361101	20	2.5	20	86	6	64	28	26	0	44	1.54
3361063--3361102	20	2.0	20	95	0	71	27	25	0	47	1.52
3361399--3361437	19	2.1	19	95	0	69	30	17	12	38	1.88
3367147--3367294	45	3.3	44	88	2	215	22	21	10	45	1.83
3372406--3372456	24	2.1	24	85	0	66	37	11	17	33	1.86
3374872--3375055	95	1.9	95	83	4	237	23	22	13	40	1.90
3376044--3376080	19	1.9	19	88	0	56	48	2	16	32	1.60
3378531--3378578	20	2.5	19	86	3	60	70	2	0	27	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3379357--3379442	42	2.1	41	82	6	102	37	5	2	54	1.37
3381235--3381327	42	2.2	43	84	1	116	36	11	9	41	1.75
3381422--3381657	51	4.6	50	82	5	242	48	16	11	24	1.78
3381427--3381657	102	2.3	103	84	5	308	48	16	10	23	1.77
3382417--3382478	25	2.4	26	91	5	108	27	9	6	56	1.56
3382423--3382477	25	2.2	25	100	0	110	29	10	7	52	1.63
3384827--3384866	19	2.1	19	85	0	53	52	0	2	45	1.14
3386535--3386630	41	2.3	42	83	5	124	30	21	15	32	1.95
3386554--3386704	41	3.7	41	79	2	124	28	19	17	34	1.95
3388350--3388412	13	4.8	13	80	7	58	1	19	1	77	0.93
3388349--3388451	34	2.9	35	78	16	106	1	23	1	72	1.04
3388349--3388451	35	2.9	33	80	13	109	1	23	1	72	1.04
3388365--3388465	35	2.9	35	79	5	89	2	21	1	73	1.07
3394408--3394443	15	2.5	15	90	4	56	66	2	2	27	1.19
3395752--3395845	22	4.5	22	84	5	124	28	29	25	15	1.96
3396394--3396557	64	2.5	64	78	13	158	26	20	19	33	1.97
3402699--3402816	22	5.5	22	85	5	145	28	27	24	18	1.98
3402718--3402816	44	2.2	44	92	0	162	28	27	26	18	1.98
3407150--3407244	3	30.0	3	81	8	82	63	2	1	33	1.13
3407163--3407213	16	3.6	16	66	33	53	60	3	0	35	1.15
3407154--3407245	25	3.7	25	87	10	127	63	3	1	32	1.18
3407150--3407244	22	4.3	22	80	10	104	63	2	1	33	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3411799--3411836	20	1.9	20	100	0	76	26	31	7	34	1.85
3423111--3423150	4	9.8	4	94	5	71	75	0	0	25	0.81
3423726--3423853	65	2.0	65	86	9	181	57	13	1	28	1.46
3424724--3424760	3	12.3	3	100	0	74	0	32	0	67	0.91
3428638--3428685	4	11.8	4	95	4	87	75	0	0	25	0.81
3428638--3428685	25	1.9	25	100	0	96	75	0	0	25	0.81
3428641--3428684	21	2.1	21	100	0	88	77	0	0	22	0.77
3429263--3429479	65	3.1	70	82	13	243	56	12	0	29	1.43
3429319--3429478	76	2.2	75	86	5	220	56	12	1	30	1.44
3429589--3429616	10	2.8	10	100	0	56	64	0	10	25	1.26
3442886--3442955	13	5.5	13	81	3	81	80	0	17	2	0.84
3443987--3444293	83	3.7	83	94	2	512	27	13	22	37	1.91
3445029--3445672	114	5.6	112	88	4	842	36	13	20	29	1.91
3445807--3445890	3	27.7	3	95	2	150	33	1	1	64	1.09
3447286--3447330	20	2.2	21	88	4	65	37	2	2	57	1.23
3451734--3451791	18	3.5	17	76	21	52	70	0	3	25	1.03
3451749--3451794	13	3.5	14	77	11	53	73	0	0	26	0.83
3451749--3451795	8	6.0	8	76	14	53	74	0	0	25	0.82
3451842--3451884	18	2.4	18	88	7	61	72	4	4	18	1.20
3454337--3454408	28	2.6	28	100	0	144	15	25	16	43	1.87
3459784--3459839	18	3.2	17	82	9	60	76	0	3	19	0.93
3459798--3459839	8	5.0	8	83	11	57	80	0	0	19	0.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3459887--3459929	18	2.4	18	92	0	68	74	4	4	16	1.16
3460437--3460607	76	2.3	75	86	6	224	56	12	0	29	1.41
3460437--3460643	76	2.8	75	79	9	221	57	11	1	29	1.43
3461046--3461108	3	21.0	3	96	0	117	68	0	0	31	0.90
3461308--3461652	137	2.5	137	81	4	392	27	14	27	30	1.95
3462634--3462780	22	6.8	22	74	20	98	2	19	0	78	0.87
3462631--3462780	43	3.5	43	75	18	150	3	18	0	78	0.90
3462680--3462767	7	11.9	7	84	10	113	1	17	0	81	0.75
3462651--3462770	15	7.8	15	80	12	120	2	17	0	80	0.83
3462631--3462778	11	13.6	11	74	17	62	3	18	0	78	0.89

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13