genome.fa.s9624.2.7.7.80.10.50.1000.16.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: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8249038

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   34   35   36   37   38   

This is table  16  of  38  ( 4514 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)
3036343--3036371	13	2.2	13	100	0	58	58	0	0	41	0.98
3036438--3036525	3	29.3	3	74	17	51	69	5	0	25	1.10
3036625--3036712	3	29.3	3	70	22	53	68	0	3	28	1.06
3036625--3036695	24	3.0	23	75	17	67	67	0	2	29	1.05
3037866--3037926	8	7.1	8	75	14	59	78	1	1	18	0.91
3037867--3037913	14	3.4	14	84	0	58	80	0	2	17	0.80
3037866--3037929	10	7.0	9	73	15	51	78	1	1	18	0.92
3037867--3037921	14	3.9	14	82	0	56	78	1	1	18	0.94
3037867--3037934	8	7.8	9	76	14	54	76	1	1	20	0.94
3037956--3038164	38	5.6	37	87	5	282	45	6	2	45	1.41
3037943--3038163	77	2.9	75	85	8	290	46	6	2	44	1.42
3038234--3038530	38	8.1	37	83	9	337	43	5	5	45	1.50
3038259--3038581	76	4.5	69	80	11	234	45	5	4	44	1.48
3038597--3038626	14	2.2	13	94	5	51	33	0	13	53	1.40
3038878--3038926	22	2.2	22	100	0	98	30	40	12	16	1.85
3039886--3039936	9	5.9	9	80	13	54	15	1	1	80	0.89
3039884--3039937	25	2.1	25	86	10	74	14	1	1	81	0.86
3039886--3039936	17	2.9	17	85	2	66	15	1	1	80	0.89
3040120--3040149	13	2.3	13	94	0	51	30	0	0	70	0.88
3045275--3045983	85	8.4	84	84	2	778	34	21	17	26	1.95
3045307--3045934	168	3.7	168	88	1	864	34	21	17	27	1.95
3046532--3046560	2	14.5	2	100	0	58	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3046569--3046820	36	6.9	37	83	13	287	44	4	6	44	1.50
3046735--3046802	31	2.2	30	84	7	82	44	5	4	45	1.48
3048269--3048311	23	1.9	22	86	13	61	11	4	6	76	1.13
3048642--3048884	40	6.1	42	84	12	302	45	4	2	46	1.39
3048642--3048961	38	8.2	38	82	13	293	44	7	2	45	1.45
3048642--3048932	77	3.7	75	80	13	279	44	6	2	45	1.44
3048944--3048984	2	21.0	2	95	5	75	51	0	0	48	1.00
3053482--3053510	12	2.3	13	94	5	51	37	0	3	58	1.15
3054156--3054197	10	4.4	10	85	11	61	7	11	0	80	0.88
3054156--3054204	18	2.8	18	87	6	66	8	12	0	79	0.93
3054216--3054365	62	2.5	59	84	7	171	25	6	0	68	1.17
3061562--3061829	123	2.2	123	84	2	342	38	22	13	26	1.90
3063218--3063260	18	2.4	18	92	0	68	20	6	0	72	1.08
3063330--3063430	5	18.8	5	70	22	55	16	5	1	75	1.10
3063361--3063437	6	12.8	6	76	15	54	16	3	1	77	0.98
3063298--3063422	42	2.9	41	75	17	121	18	7	1	72	1.15
3063361--3063436	26	3.0	25	77	11	82	17	3	1	77	0.99
3064914--3064985	30	2.4	29	80	13	83	59	0	9	30	1.29
3066539--3066721	61	3.0	61	99	0	357	38	19	3	38	1.68
3070616--3070771	64	2.4	65	84	3	208	30	21	19	27	1.98
3076311--3076391	23	3.8	21	78	13	69	25	20	22	30	1.98
3076299--3076372	23	3.3	23	76	14	91	27	21	22	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3078608--3078647	19	2.1	19	95	0	71	42	2	27	27	1.68
3079034--3079170	66	2.1	65	86	6	188	29	21	20	28	1.98
3079034--3079191	65	2.4	64	83	5	156	29	21	20	28	1.98
3085208--3085261	25	2.2	25	86	6	74	1	22	9	66	1.30
3085689--3085763	3	25.3	3	91	2	125	62	0	2	34	1.09
3086073--3086258	99	1.9	98	93	3	320	32	19	10	37	1.87
3086163--3086682	225	2.3	227	88	6	772	31	19	12	36	1.89
3086163--3086682	112	4.6	113	92	4	761	31	19	12	36	1.89
3087156--3088125	83	11.7	83	92	2	1551	37	22	12	27	1.90
3087158--3088125	165	5.9	166	94	1	1626	37	22	12	27	1.90
3087159--3088125	247	3.9	248	94	1	1690	37	22	12	28	1.90
3089393--3089459	22	3.0	22	100	0	134	26	26	26	19	1.99
3089679--3089737	30	1.9	31	89	3	93	33	23	6	35	1.82
3089752--3089823	29	2.5	29	93	0	117	38	12	9	38	1.76
3090125--3090297	69	2.5	68	84	8	210	17	27	27	27	1.98
3092707--3092858	68	2.2	68	89	3	227	17	27	27	26	1.98
3092707--3092880	68	2.6	67	86	6	210	17	27	27	27	1.98
3093997--3094034	10	3.8	10	96	0	67	0	10	0	89	0.49
3093997--3094038	11	3.8	11	90	9	68	0	11	0	88	0.53
3093997--3094038	21	2.0	22	95	4	77	0	11	0	88	0.53
3104399--3104703	154	2.0	156	96	3	566	47	8	11	32	1.70
3105530--3105582	26	2.0	26	82	7	63	41	3	11	43	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3106689--3106724	11	3.2	11	92	4	54	38	0	0	61	0.96
3106720--3106783	3	21.3	3	93	0	101	60	0	4	34	1.17
3109056--3109119	30	2.1	30	91	0	101	31	14	29	25	1.94
3110381--3110503	29	4.4	29	80	5	103	39	4	8	47	1.54
3110404--3110524	28	4.4	28	77	10	140	38	3	9	47	1.53
3110401--3110536	28	4.9	27	76	8	121	39	2	9	47	1.51
3110403--3110558	83	1.9	82	84	7	208	38	3	9	48	1.52
3111453--3111914	187	2.5	184	84	6	576	43	8	14	33	1.75
3111922--3112092	77	2.2	77	80	9	204	35	11	16	35	1.86
3112163--3112726	211	2.7	205	82	5	661	48	6	11	33	1.65
3122935--3122960	12	2.2	12	100	0	52	38	19	0	42	1.51
3127433--3127466	17	2.1	17	88	5	52	26	2	0	70	1.01
3130625--3130664	20	2.0	20	95	0	71	25	15	27	32	1.95
3132690--3132771	36	2.3	36	95	0	146	41	9	29	19	1.83
3137907--3137984	22	3.6	22	74	19	83	35	12	23	28	1.91
3140014--3140376	100	3.6	99	77	6	311	39	17	8	34	1.81
3141901--3141978	33	2.4	33	84	0	102	15	6	34	43	1.72
3144919--3145010	45	2.0	45	83	8	116	33	9	7	48	1.64
3144819--3145114	145	2.0	146	85	3	400	39	12	10	38	1.77
3144981--3145332	102	3.5	101	86	2	431	39	13	10	37	1.78
3151007--3151086	21	3.7	21	74	12	81	21	10	23	45	1.82
3151003--3151089	44	2.0	44	90	0	138	22	9	24	43	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3151740--3151772	12	2.8	12	95	0	57	27	9	39	24	1.85
3158785--3158850	12	5.2	12	77	12	60	34	3	0	62	1.11
3162987--3163465	137	3.5	135	81	4	522	25	14	31	29	1.95
3164306--3164363	19	3.1	19	100	0	116	15	25	15	43	1.86
3164494--3164520	14	1.9	14	100	0	54	3	22	0	74	0.98
3164489--3164552	24	2.6	24	78	7	58	6	15	0	78	0.95
3164492--3164579	37	2.4	36	83	9	106	6	17	0	76	1.00
3164516--3164582	27	2.4	28	85	7	84	7	16	0	76	1.01
3164499--3164578	36	2.2	35	80	12	90	7	17	0	75	1.03
3171248--3171365	42	2.8	41	80	2	128	33	21	21	23	1.97
3171639--3172045	53	7.7	53	85	4	480	37	19	10	32	1.85
3173824--3173875	19	2.6	20	78	6	61	15	21	15	48	1.81
3173859--3173915	22	2.5	22	78	18	62	5	15	5	73	1.19
3173877--3173940	27	2.4	27	82	7	69	3	15	4	76	1.08
3174194--3174229	2	18.0	2	100	0	72	50	0	0	50	1.00
3180853--3180922	19	3.8	19	73	7	72	57	2	1	38	1.23
3191037--3191075	3	12.7	3	83	5	51	35	0	2	61	1.10
3193818--3193853	16	2.2	16	90	9	56	50	16	8	25	1.73
3195531--3195578	17	2.8	17	83	0	60	22	45	14	16	1.84
3195573--3195612	20	2.0	20	90	0	62	20	20	20	40	1.92
3196165--3196220	29	1.9	29	96	0	103	16	26	23	33	1.95
3196165--3196245	29	2.8	28	86	3	90	16	24	22	37	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3202374--3202438	17	3.9	16	78	13	60	24	30	16	27	1.97
3202393--3202454	17	3.7	16	80	8	61	24	35	17	22	1.95
3203126--3203188	29	2.2	29	82	5	74	20	15	14	49	1.80
3203267--3203303	18	2.1	18	94	0	65	27	27	16	29	1.97
3206811--3206874	29	2.1	29	82	8	74	51	4	4	39	1.44
3207811--3207864	25	2.2	25	96	0	99	35	20	5	38	1.76
3209037--3209316	137	2.0	137	84	4	368	42	17	13	26	1.87
3209476--3209513	19	2.0	20	89	5	60	55	7	5	31	1.51
3210920--3211079	41	3.9	40	78	3	149	31	16	15	36	1.90
3210926--3211083	82	1.9	82	87	2	228	30	17	15	36	1.91

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   34   35   36   37   38