genome.fa.s9579.2.7.7.80.10.50.1000.16.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: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6215474

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   

This is table  16  of  29  ( 3390 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)
2865128--2865165	17	2.2	17	90	0	58	18	23	36	21	1.95
2871036--2871185	29	5.2	29	89	1	203	39	20	5	35	1.75
2871191--2871251	17	3.6	17	73	10	63	14	22	42	19	1.88
2871191--2871251	32	2.0	30	90	6	95	14	22	42	19	1.88
2871227--2871267	19	2.2	19	86	0	55	19	26	34	19	1.96
2871229--2871286	29	2.0	29	89	0	89	18	27	32	20	1.97
2879428--2879464	7	5.1	7	90	3	56	45	0	0	54	1.00
2879434--2879501	21	3.2	20	80	12	64	48	0	2	48	1.16
2879432--2879502	22	3.2	22	80	9	74	49	0	2	47	1.16
2882683--2882768	44	2.0	44	88	0	127	19	24	17	38	1.93
2885459--2885490	2	16.0	2	100	0	64	50	0	0	50	1.00
2885645--2885751	22	5.5	21	71	22	83	47	0	1	50	1.11
2885841--2885903	22	2.6	25	71	23	62	52	1	1	44	1.20
2887096--2887388	141	2.0	144	86	4	412	48	8	5	37	1.57
2887902--2888089	59	3.2	59	80	8	195	32	18	3	45	1.67
2888175--2888309	60	2.3	59	83	6	157	37	3	25	33	1.74
2892066--2892116	21	2.5	22	81	18	65	60	0	1	37	1.08
2894034--2894058	2	12.5	2	100	0	50	52	0	0	48	1.00
2904922--2904946	13	1.9	13	100	0	50	24	16	20	40	1.91
2905642--2906018	185	2.0	185	92	1	630	45	8	3	42	1.51
2916402--2916440	20	2.0	20	89	0	60	33	17	17	30	1.94
2928176--2928205	15	1.9	16	93	6	53	33	10	30	26	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2928345--2928375	15	2.1	15	93	0	53	54	0	0	45	0.99
2932370--2932395	2	13.0	2	100	0	52	50	0	0	50	1.00
2944627--2944710	23	3.6	23	70	3	69	26	11	14	47	1.78
2944695--2944736	22	1.9	22	90	0	66	7	11	21	59	1.56
2950727--2950833	53	2.0	53	90	0	169	48	7	21	22	1.75
2951881--2952017	20	6.8	20	97	0	256	38	14	20	26	1.91
2952002--2952064	20	3.2	20	90	0	99	23	25	23	26	2.00
2952889--2952942	24	2.2	24	93	0	90	20	18	20	40	1.91
2953117--2953149	3	11.0	3	100	0	66	66	0	33	0	0.92
2955218--2955257	6	6.7	6	88	0	62	60	17	2	20	1.48
2955324--2955593	140	1.9	140	96	0	504	29	13	14	42	1.84
2955571--2955661	46	2.0	46	91	0	146	37	28	15	18	1.91
2955618--2955684	34	2.0	34	93	0	116	40	26	16	16	1.89
2955616--2955814	20	10.6	20	70	14	136	34	22	19	24	1.97
2955652--2955863	94	2.3	94	86	2	302	33	21	19	25	1.97
2955617--2955792	74	2.4	74	81	5	239	35	22	18	23	1.96
2955571--2955814	40	6.2	40	71	15	145	34	23	18	23	1.96
2955857--2955895	20	2.0	20	89	0	60	7	17	23	51	1.71
2956009--2956070	14	4.3	14	77	6	61	46	14	0	38	1.45
2957481--2957571	42	2.2	42	80	4	103	23	16	38	21	1.93
2958059--2958103	20	2.4	19	88	7	65	40	26	17	15	1.90
2960085--2960191	20	5.4	20	85	3	119	45	23	16	14	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2960556--2960619	22	3.0	22	81	4	78	21	17	40	20	1.91
2960785--2960862	20	3.9	20	81	6	95	26	19	21	32	1.97
2970930--2970988	27	2.2	27	82	11	68	44	16	16	22	1.87
2971290--2971331	22	2.0	21	85	4	57	28	23	16	30	1.96
2980739--2980794	27	2.1	27	83	6	69	30	12	1	55	1.47
2983027--2983092	34	1.9	34	81	0	78	43	6	4	45	1.49
2997662--2997693	17	1.9	16	93	6	55	40	0	9	50	1.35
3005557--3005591	16	2.1	17	94	5	63	34	25	8	31	1.86
3011801--3011839	20	1.9	20	84	5	51	41	2	7	48	1.45
3011955--3011986	2	16.0	2	100	0	64	50	0	0	50	1.00
3012094--3012146	25	2.1	25	82	6	63	64	3	0	32	1.12
3012447--3012500	28	2.0	27	82	17	67	59	3	0	37	1.15
3013808--3013880	3	24.3	3	72	5	58	58	0	1	39	1.06
3013804--3013889	36	2.3	36	84	7	102	55	0	2	41	1.12
3013822--3013880	26	2.4	25	88	5	84	57	0	1	40	1.09
3014119--3014267	45	3.3	45	90	0	217	30	18	22	28	1.97
3014164--3014388	121	1.9	121	90	0	360	32	18	21	27	1.97
3014201--3014343	76	1.9	74	84	2	187	33	20	19	26	1.96
3014050--3014554	166	3.0	166	93	2	836	31	19	21	27	1.97
3014285--3014433	45	3.3	45	91	0	226	31	17	22	28	1.96
3014330--3014630	121	2.5	121	90	1	478	33	18	20	27	1.96
3014367--3014509	76	1.9	74	84	5	189	32	19	21	25	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3014441--3014554	45	2.5	45	82	5	131	30	21	21	26	1.98
3014496--3014858	76	4.8	76	92	0	557	33	19	20	27	1.96
3014330--3014782	197	2.3	194	71	11	459	32	19	20	27	1.97
3016893--3017058	75	2.2	74	85	4	210	30	23	14	31	1.94
3023611--3023676	13	5.1	13	96	0	105	80	1	18	0	0.79
3023611--3023686	26	2.8	26	88	4	107	77	1	19	1	0.91
3027323--3027381	17	3.4	18	93	6	104	0	18	0	81	0.69
3027323--3027381	9	6.8	9	94	5	104	0	18	0	81	0.69
3027664--3027700	2	18.5	2	100	0	74	51	0	0	48	1.00
3028355--3028477	61	2.0	61	100	0	246	39	14	18	27	1.90
3029954--3030070	60	2.0	60	100	0	234	36	18	15	29	1.92
3032545--3032577	16	2.1	16	100	0	66	48	0	15	36	1.45
3035026--3035110	3	28.3	3	73	4	64	57	0	1	41	1.06
3035027--3035110	26	3.5	25	81	9	95	58	0	1	40	1.06
3036450--3036485	2	18.0	2	100	0	72	50	0	0	50	1.00
3043256--3043317	7	8.9	7	83	0	70	19	0	27	53	1.45
3043250--3043317	21	3.2	21	82	0	82	20	0	26	52	1.46
3043364--3043426	21	3.0	21	80	13	76	26	0	26	46	1.54
3043369--3043426	14	4.1	14	82	8	73	24	0	29	46	1.53
3043475--3043536	11	5.7	11	68	24	51	35	1	3	59	1.23
3056865--3057140	40	6.8	40	75	4	176	29	20	17	32	1.96
3058708--3058832	31	4.0	31	93	2	198	38	23	18	20	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3059419--3059455	19	1.9	19	100	0	74	24	32	27	16	1.96
3063229--3063353	31	4.0	31	93	2	198	38	23	18	20	1.93
3073594--3073655	23	2.7	23	89	0	88	24	22	20	32	1.98
3075443--3075490	22	2.3	22	85	7	64	35	6	4	54	1.45
3082405--3082459	24	2.3	23	93	3	92	7	12	21	58	1.59
3090694--3090762	22	3.1	22	93	0	111	30	20	21	27	1.98
3093027--3093118	31	2.9	29	76	12	76	45	2	5	46	1.38
3093215--3093267	26	2.1	25	82	10	63	54	3	5	35	1.42
3096953--3096985	12	2.6	13	95	4	59	12	18	51	18	1.76
3097358--3097391	16	2.1	16	94	0	59	32	8	26	32	1.87
3098139--3098170	15	2.1	16	94	5	57	50	18	25	6	1.70
3101432--3101460	13	2.2	13	100	0	58	13	13	58	13	1.63
3107681--3107717	19	1.9	19	94	0	65	32	29	16	21	1.95
3107734--3107815	21	4.0	20	72	13	60	25	20	19	34	1.96
3107743--3107815	21	3.5	21	83	9	78	26	21	20	31	1.98
3107824--3107950	20	6.3	20	83	5	166	26	27	21	24	1.99
3108766--3108824	24	2.5	24	91	0	91	22	18	22	37	1.94
3109014--3109050	14	2.6	14	91	4	56	51	21	21	5	1.68
3121807--3121906	29	3.4	28	75	19	96	78	1	12	9	1.03
3121845--3121906	22	2.8	20	81	15	70	80	0	12	6	0.89
3121846--3121950	47	2.2	46	81	11	124	79	0	13	6	0.98
3121791--3121938	78	1.9	78	82	9	185	77	1	13	7	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3121851--3121949	16	6.1	16	75	14	80	79	1	12	7	0.97
3123277--3123841	153	3.6	152	84	7	655	28	16	26	27	1.97
3123260--3123885	51	11.8	56	90	4	595	28	15	26	29	1.96
3128317--3128353	12	3.1	12	88	0	56	45	27	8	18	1.77
3128522--3128805	20	14.9	20	77	8	279	34	21	19	25	1.96
3128530--3128838	54	5.5	56	76	14	228	35	21	19	23	1.95
3128569--3128805	94	2.5	93	86	0	321	34	21	19	24	1.96
3128684--3128785	53	1.9	54	91	2	170	34	24	19	21	1.96
3128679--3128849	73	2.3	73	88	1	243	35	21	19	22	1.96
3128522--3128838	167	1.9	172	88	4	491	35	20	18	24	1.95

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