genome.fa.s7823.2.7.7.80.10.50.1000.17.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: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6287495

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   32   
          33   

This is table  17  of  33  ( 3920 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)
3228966--3228997	13	2.3	15	89	10	50	37	12	6	43	1.68
3229617--3229663	2	23.5	2	100	0	94	48	0	0	51	1.00
3229918--3229980	23	2.5	25	82	10	76	49	1	1	47	1.20
3230211--3230294	39	2.2	40	86	4	118	21	17	20	40	1.91
3234621--3234710	45	2.0	45	95	0	162	24	20	18	36	1.95
3234807--3235068	22	11.9	22	73	14	121	46	4	7	41	1.53
3234829--3235043	67	3.3	64	75	16	210	47	4	6	41	1.50
3234834--3234988	82	1.9	83	93	1	267	43	4	9	42	1.56
3234829--3235018	104	1.8	103	87	8	287	46	4	7	41	1.51
3234879--3234951	37	1.9	38	88	5	112	43	5	8	42	1.57
3234993--3235122	28	4.8	28	74	14	87	49	3	3	43	1.39
3235014--3235139	28	4.3	30	77	13	104	47	4	5	42	1.48
3234917--3235103	22	8.0	22	76	14	99	48	4	5	41	1.47
3235028--3235126	29	3.5	27	78	10	83	49	4	4	42	1.40
3243854--3243901	3	16.0	3	91	8	80	35	0	0	64	0.94
3243841--3243920	19	3.8	21	74	24	71	36	2	0	61	1.10
3245220--3245258	21	1.9	20	89	5	60	38	2	5	53	1.37
3246375--3246681	153	2.0	154	93	1	528	34	15	12	37	1.85
3254017--3254218	90	2.2	90	92	0	332	24	17	21	36	1.95
3254194--3254277	42	2.0	42	88	0	123	23	17	17	40	1.91
3254326--3254811	136	3.6	136	88	2	728	32	18	22	26	1.97
3255100--3255162	3	21.0	3	87	6	83	34	1	1	61	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3256489--3256524	18	2.1	17	89	5	54	38	2	5	52	1.39
3258784--3258822	20	2.0	19	90	5	60	33	17	28	20	1.96
3261984--3262036	21	2.6	20	85	5	70	37	15	15	32	1.88
3275689--3275748	30	2.0	30	100	0	120	46	16	3	33	1.64
3277033--3277162	54	2.4	54	83	2	145	30	21	17	30	1.96
3293039--3293138	30	3.5	28	82	10	121	35	12	15	38	1.84
3293221--3293324	30	3.5	30	82	3	138	40	12	10	36	1.78
3293191--3293361	60	2.8	60	76	10	186	41	9	11	38	1.73
3298410--3298458	22	2.3	22	82	10	57	46	2	0	51	1.12
3300003--3300043	20	2.0	20	95	0	73	34	24	7	34	1.83
3300064--3300095	2	16.5	2	93	6	57	50	0	0	50	1.00
3300111--3300572	182	2.5	185	82	5	544	39	10	15	34	1.81
3300448--3301123	158	4.3	158	85	1	865	38	10	14	36	1.80
3300448--3301101	315	2.1	315	86	3	940	39	9	14	36	1.79
3307044--3307068	12	2.1	12	100	0	50	8	24	8	60	1.52
3309998--3310035	20	1.9	20	88	0	58	18	26	28	26	1.98
3313836--3313875	21	1.9	21	85	10	55	35	10	2	52	1.48
3322219--3322257	18	2.2	18	85	0	51	17	2	12	66	1.35
3323787--3323834	23	2.0	25	84	8	64	41	10	0	47	1.37
3324332--3324518	92	2.0	92	96	2	349	34	8	10	46	1.69
3331532--3331589	28	2.1	27	87	3	80	56	10	12	20	1.64
3332481--3332542	31	2.0	31	93	0	106	33	20	12	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3333753--3333783	2	15.5	2	100	0	62	0	48	0	51	1.00
3341506--3341544	20	2.0	20	90	5	62	61	0	15	23	1.33
3343025--3343119	50	1.9	50	87	8	142	34	2	0	63	1.07
3343109--3343165	26	2.2	25	84	6	69	15	3	1	78	0.96
3343206--3343255	26	1.9	26	88	8	75	20	6	2	72	1.16
3344607--3344713	53	2.0	53	96	0	196	46	19	17	15	1.84
3346340--3346383	11	3.8	11	82	11	61	79	0	15	4	0.89
3346345--3346390	24	2.0	22	91	8	74	76	0	17	6	1.00
3346343--3346389	10	4.4	10	78	21	51	78	0	17	4	0.90
3347516--3347605	32	2.8	32	84	1	117	31	11	17	40	1.85
3348148--3348394	106	2.3	106	86	2	327	34	23	18	23	1.96
3348719--3348753	15	2.3	15	90	0	52	20	20	20	40	1.92
3348898--3348987	35	2.5	36	89	7	148	43	16	8	31	1.79
3350014--3350083	2	36.5	2	83	8	83	41	0	0	58	0.98
3350066--3350171	54	1.9	55	87	9	155	22	3	1	71	1.12
3350105--3350203	42	2.3	43	83	13	116	18	8	1	72	1.14
3350178--3350248	25	2.8	26	85	8	85	19	7	0	73	1.06
3351536--3351589	20	2.7	19	75	8	63	33	31	18	16	1.93
3351576--3351693	21	5.8	20	71	8	67	38	19	18	23	1.93
3351639--3351691	20	2.7	20	88	5	72	43	20	18	16	1.88
3351712--3351890	20	8.9	20	79	4	189	39	24	18	18	1.92
3351703--3351890	40	4.7	40	90	3	245	38	23	19	18	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3351643--3351893	60	4.2	60	76	8	204	39	23	19	18	1.93
3352751--3352802	24	2.2	23	86	6	77	21	19	17	42	1.89
3355355--3355492	19	7.7	19	68	19	100	46	18	21	13	1.83
3355342--3355488	33	4.3	33	80	10	177	45	19	21	13	1.84
3355488--3355574	33	2.6	33	87	0	111	16	18	20	44	1.86
3355519--3355577	19	3.4	18	68	22	54	18	18	16	45	1.85
3355684--3355720	14	2.6	14	91	0	65	45	21	0	32	1.52
3357103--3357194	42	2.2	42	80	3	105	26	17	35	20	1.95
3359157--3359218	20	3.2	20	90	4	108	50	16	22	11	1.76
3359155--3359214	19	3.1	19	90	4	102	50	16	23	10	1.75
3359155--3359242	39	2.5	35	87	10	117	48	15	22	12	1.79
3359254--3359348	19	5.2	19	79	14	119	10	23	21	45	1.82
3359852--3359983	20	6.6	20	84	1	183	18	20	25	35	1.95
3359854--3360044	40	4.8	40	84	6	242	18	19	24	37	1.94
3359851--3360044	81	2.4	81	86	4	259	18	19	24	37	1.94
3359851--3360128	20	13.8	20	76	9	143	20	19	23	37	1.94
3359912--3360128	81	2.7	81	79	9	194	20	18	22	38	1.94
3371544--3371599	25	2.3	24	87	9	78	12	12	35	39	1.81
3372952--3373030	5	15.0	5	83	9	95	45	0	0	54	0.99
3372959--3373068	15	6.9	16	70	24	90	49	0	0	49	1.13
3372953--3373031	21	3.7	21	98	1	149	46	0	0	53	1.00
3373092--3373120	12	2.3	13	94	5	51	34	0	6	58	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3374840--3374885	22	2.0	23	87	4	67	63	10	2	23	1.38
3375065--3375102	16	2.4	16	100	0	76	26	21	18	34	1.96
3376500--3376611	29	3.8	29	93	1	188	42	9	15	32	1.79
3379972--3380001	15	2.0	15	93	0	51	20	0	23	56	1.42
3381291--3381402	29	3.8	29	93	1	188	42	9	15	32	1.79
3381933--3381990	29	2.0	29	86	0	80	15	36	25	22	1.94
3382031--3382117	33	2.6	33	85	0	111	26	26	36	10	1.88
3382121--3382176	29	1.9	29	92	0	94	25	30	32	12	1.92
3385380--3385487	3	35.3	3	76	7	92	38	2	0	57	1.20
3385389--3385489	50	2.0	50	88	3	150	41	2	0	54	1.22
3386837--3386908	37	1.9	38	86	5	103	23	8	2	65	1.34
3386963--3386989	3	9.0	3	100	0	54	33	0	0	66	0.92
3389711--3389782	35	2.0	36	84	7	94	31	11	20	36	1.88
3392724--3392782	9	6.8	9	84	7	86	77	0	20	1	0.85
3392726--3392788	8	7.6	8	84	11	83	79	0	19	1	0.82
3392726--3392788	17	3.8	17	87	8	94	79	0	19	1	0.82
3392723--3392796	26	3.0	25	84	9	100	77	0	18	4	0.93
3395467--3395641	75	2.3	75	83	2	217	27	16	25	30	1.97
3396928--3397026	22	4.6	22	86	2	121	36	14	13	36	1.85
3397966--3398079	60	1.9	60	90	0	183	23	21	23	31	1.98
3398019--3398331	73	4.3	73	95	1	556	26	20	20	32	1.97
3398480--3398581	3	33.3	3	74	7	71	40	2	0	55	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3398487--3398543	23	2.6	22	81	8	62	42	1	1	54	1.21
3398475--3398537	26	2.5	25	75	12	65	42	1	1	53	1.19
3398480--3398587	41	2.7	39	81	13	114	41	2	0	54	1.21
3400025--3400054	3	10.0	3	100	0	60	33	0	0	66	0.92
3406647--3406699	26	2.1	25	96	3	97	7	13	37	41	1.72
3406654--3407056	201	2.0	202	99	0	799	26	13	25	34	1.93
3411201--3411396	81	2.4	82	85	4	252	35	18	16	30	1.93
3411201--3411448	83	3.0	82	82	6	254	33	18	16	30	1.94
3411213--3411478	83	3.2	82	80	7	195	35	18	15	30	1.92
3414172--3414233	31	2.0	31	84	6	81	19	8	9	62	1.50

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   32   
          33