genome.fa.s8356.2.7.7.80.10.50.1000.15.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: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12862612

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  15  of  56  ( 6656 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)
2944638--2944673	18	2.0	18	100	0	72	16	50	16	16	1.79
2947072--2947214	24	6.0	24	85	6	175	25	15	20	39	1.91
2949185--2949222	13	2.9	13	88	0	58	15	50	18	15	1.79
2951731--2951879	24	6.2	24	87	6	176	24	16	20	38	1.92
2951731--2951880	72	2.1	73	83	7	198	25	16	20	38	1.92
2952900--2953034	39	3.6	39	74	14	115	48	0	0	51	1.06
2952925--2953038	20	5.9	20	68	24	77	47	0	0	52	1.00
2952991--2953037	12	4.0	12	75	13	53	53	0	0	46	1.00
2952928--2953035	40	2.9	39	75	19	115	48	0	0	51	1.00
2952928--2953021	42	2.3	40	85	7	118	47	0	0	52	1.00
2953002--2953045	22	2.0	22	83	12	56	43	2	0	54	1.12
2957608--2957691	42	2.0	42	92	0	141	46	7	21	25	1.76
2958461--2958804	54	6.4	54	90	0	517	37	18	14	30	1.90
2964326--2964363	15	2.5	15	100	0	76	36	0	34	28	1.58
2974109--2974159	19	2.6	19	75	25	52	74	3	3	17	1.12
2975459--2975530	24	3.0	24	85	2	101	50	18	12	19	1.78
2975463--2975531	12	5.8	12	75	10	61	49	18	14	17	1.80
2975461--2975551	47	1.9	48	82	10	116	48	17	14	19	1.81
2976646--2976681	18	2.0	18	94	0	63	33	13	0	52	1.41
2978005--2978044	18	2.2	18	90	0	62	15	17	50	17	1.79
2977996--2978063	31	2.2	31	91	0	109	16	17	47	19	1.83
2978022--2978058	13	2.8	13	87	0	56	13	18	48	18	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2980163--2980234	24	3.0	24	83	2	92	50	18	9	22	1.76
2981356--2981390	18	1.9	18	94	0	61	31	14	0	54	1.40
2982679--2982756	8	9.5	8	72	20	56	21	25	37	15	1.93
2982689--2982722	15	2.1	16	89	10	52	23	29	35	11	1.90
2982712--2982774	13	4.5	13	72	18	54	17	22	42	17	1.89
2982722--2982756	18	1.9	18	94	0	61	17	22	42	17	1.88
2982712--2982778	31	2.2	31	86	0	89	16	20	44	17	1.86
2984755--2984826	24	3.0	24	81	2	92	50	18	11	20	1.77
2984763--2984857	12	8.2	11	71	15	66	50	20	13	15	1.78
2985900--2985934	18	1.9	18	94	0	61	31	14	0	54	1.40
2987232--2987265	15	2.1	16	89	10	52	23	29	35	11	1.90
2987255--2987286	13	2.5	13	94	0	55	15	25	43	15	1.86
2987263--2987309	18	2.6	18	86	0	67	14	21	46	17	1.83
2990561--2990809	54	4.6	54	90	0	354	40	17	12	30	1.86
3022683--3022845	76	2.2	75	82	5	186	31	2	12	53	1.51
3022995--3023025	12	2.6	12	89	0	53	9	19	3	67	1.33
3032163--3032240	35	2.2	35	86	4	104	46	6	20	26	1.75
3036851--3036896	18	2.5	19	75	10	51	28	4	34	32	1.77
3037969--3038011	11	3.8	11	81	6	50	9	9	13	67	1.42
3041594--3041628	9	3.8	9	92	3	52	14	0	5	80	0.89
3043882--3043926	12	3.8	12	100	0	90	40	8	15	35	1.79
3050931--3051119	97	1.9	97	96	0	351	28	10	14	47	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3053738--3053794	27	2.0	29	87	12	84	29	5	0	64	1.15
3056019--3056060	15	3.0	14	83	10	50	19	19	7	54	1.66
3062778--3062878	50	2.0	50	88	7	152	39	11	19	28	1.87
3063250--3063304	22	2.5	22	87	0	83	32	12	16	38	1.86
3063738--3064608	113	7.7	113	89	2	1281	37	14	18	28	1.91
3066266--3066291	7	3.7	7	100	0	52	26	0	11	61	1.30
3073654--3074111	38	12.6	34	80	12	270	47	4	5	42	1.47
3073715--3073780	28	2.5	28	88	9	95	45	3	4	46	1.38
3073735--3073794	28	2.1	28	84	6	77	50	5	3	41	1.41
3073816--3073926	25	4.5	25	72	10	102	48	4	5	41	1.46
3073915--3073975	11	5.1	11	71	24	52	45	6	8	39	1.60
3073964--3074016	27	1.9	27	85	11	72	47	3	7	41	1.50
3073741--3074111	38	9.9	37	83	9	391	48	4	5	41	1.46
3073751--3074111	74	4.9	73	78	13	362	48	4	5	41	1.46
3074104--3074143	20	2.0	20	90	0	62	35	5	15	45	1.68
3074160--3074233	22	3.4	21	74	9	69	22	1	2	72	1.04
3080660--3081139	261	1.8	258	84	4	642	33	19	20	26	1.97
3081769--3081831	26	2.4	27	81	2	74	46	4	4	44	1.45
3081699--3082020	38	9.2	37	71	20	155	44	4	8	43	1.52
3081797--3082020	38	6.2	38	76	18	212	45	4	7	41	1.54
3081835--3081937	27	3.4	27	75	22	107	46	3	7	41	1.51
3081873--3081937	27	2.4	28	92	7	109	46	4	7	41	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3081708--3082010	102	3.0	100	85	7	396	45	3	7	43	1.51
3082001--3082042	20	2.1	20	91	8	68	35	7	14	42	1.73
3082087--3082128	16	2.5	17	85	14	61	23	2	0	73	0.94
3082081--3082129	23	2.2	22	85	10	64	22	2	0	75	0.90
3083586--3083657	32	2.2	32	92	0	126	38	27	5	27	1.79
3085349--3085410	29	2.1	29	85	14	83	58	0	0	41	0.98
3086827--3086881	3	18.7	3	85	10	78	65	0	1	32	1.03
3087021--3087306	120	2.4	120	86	4	375	24	18	15	41	1.89
3087228--3087741	225	2.3	223	87	7	719	28	18	14	37	1.91
3087228--3087741	113	4.7	112	84	5	642	28	18	14	37	1.91
3087689--3087777	17	5.1	17	68	24	60	20	20	10	49	1.77
3087689--3087780	36	2.6	36	91	5	152	19	20	9	50	1.76
3087576--3087890	143	2.1	149	87	6	446	26	19	13	41	1.88
3087721--3087925	113	1.8	109	91	4	338	27	18	14	40	1.89
3088716--3089098	93	4.1	93	95	0	678	34	21	15	28	1.94
3090127--3090200	1	74.0	1	73	0	58	1	10	1	86	0.70
3090105--3090182	20	3.9	20	77	11	70	1	16	1	80	0.84
3090096--3090200	30	3.5	31	77	12	85	0	15	0	82	0.77
3097538--3097569	15	2.1	15	94	0	55	46	6	18	28	1.73
3102841--3102871	16	1.9	16	100	0	62	22	32	19	25	1.97
3103018--3103081	3	21.7	3	87	9	96	65	0	1	32	1.02
3105447--3105471	12	2.1	12	100	0	50	8	32	0	60	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3106790--3106832	21	2.0	21	81	0	50	30	30	25	13	1.94
3108302--3108504	105	1.9	105	84	0	271	23	15	22	38	1.92
3112060--3112102	21	2.0	21	86	0	59	30	27	25	16	1.97
3113573--3113774	105	1.9	105	83	2	262	24	15	21	38	1.92
3113804--3113849	24	2.0	24	86	4	67	23	26	26	23	2.00
3114789--3114904	21	5.7	21	89	6	193	29	22	18	29	1.98
3114788--3114903	39	2.9	39	92	3	187	29	22	18	29	1.98
3119824--3119849	5	5.2	5	100	0	52	0	19	57	23	1.40
3119676--3119975	156	1.9	157	91	3	498	30	15	16	37	1.90
3121594--3121640	20	2.3	20	92	0	76	48	6	21	23	1.72
3121814--3121851	15	2.4	16	86	8	51	60	5	5	28	1.40
3123992--3124053	25	2.5	25	91	0	97	30	17	12	38	1.88
3124153--3124200	3	16.0	3	78	8	53	60	2	4	33	1.27
3124432--3124637	90	2.3	92	87	3	294	26	18	27	27	1.98
3135486--3135520	9	3.8	9	88	7	52	85	5	0	8	0.73
3135735--3135759	13	1.9	13	100	0	50	80	0	0	20	0.72
3138752--3138823	25	2.9	25	93	2	119	26	15	19	38	1.91
3138919--3138969	3	17.0	3	80	8	59	60	1	3	33	1.26
3139153--3139183	15	2.1	15	93	0	53	54	0	0	45	0.99
3141249--3141303	28	2.0	28	85	0	74	38	23	3	34	1.73
3143176--3143359	102	1.8	100	85	4	262	51	7	13	27	1.68
3145093--3145810	181	3.9	181	91	1	1114	42	15	15	26	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3147690--3147738	22	2.3	21	89	3	71	53	0	6	40	1.26
3147964--3148008	18	2.6	18	82	10	58	31	6	53	8	1.58
3148380--3148415	18	2.0	18	88	0	54	63	2	19	13	1.41
3148417--3148455	18	2.2	18	100	0	78	56	0	38	5	1.22
3150011--3150059	19	2.6	19	96	0	89	32	2	10	55	1.45
3150486--3151834	199	6.8	199	91	1	2047	38	15	16	30	1.89
3153329--3153367	3	13.0	3	88	0	60	35	2	33	28	1.71
3154453--3154477	11	2.3	11	100	0	50	36	8	8	48	1.62
3154785--3154837	24	2.2	24	82	0	61	37	1	13	47	1.54
3155785--3156197	200	2.1	200	90	0	637	38	13	17	29	1.88

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56