genome.fa.s9639.2.7.7.80.10.50.1000.13.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: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  15077257

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   57   58   59   60   61   62   

This is table  13  of  62  ( 7398 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)
2957210--2957256	24	2.0	24	95	0	85	53	23	12	10	1.70
2967983--2968086	50	2.0	50	83	10	131	63	14	8	13	1.51
2969900--2969948	23	2.2	22	92	7	82	26	8	4	61	1.42
2971818--2971916	30	3.3	29	75	17	96	39	8	10	42	1.68
2973975--2974015	16	2.6	16	96	0	73	34	31	4	29	1.79
2974958--2975005	3	17.0	3	87	12	75	64	0	0	35	0.94
2974958--2975008	14	3.6	14	85	15	70	64	0	0	35	0.94
2974956--2975002	11	4.3	11	100	0	94	63	0	0	36	0.94
2975854--2975902	14	3.6	14	76	20	50	22	14	6	57	1.59
2976903--2976956	19	2.8	19	75	5	56	12	3	9	74	1.20
2976903--2976956	9	5.7	9	76	10	54	12	3	9	74	1.20
2984656--2984985	121	2.7	122	80	2	326	38	23	10	26	1.88
2986015--2986120	32	3.3	32	85	7	126	27	16	4	51	1.63
2986334--2986371	15	2.5	15	83	8	51	23	5	5	65	1.34
2986858--2986909	20	2.9	18	84	15	72	15	5	3	75	1.14
2986858--2986912	17	3.0	19	87	12	80	16	5	3	74	1.15
2990096--2990121	7	3.7	7	100	0	52	61	0	0	38	0.96
2991992--2992258	140	1.9	140	99	0	525	27	26	17	28	1.98
2992550--2992608	18	3.3	17	76	9	55	72	3	8	15	1.21
2992579--2992611	9	3.7	9	100	0	66	78	0	0	21	0.75
2992677--2992702	2	13.0	2	100	0	52	50	0	0	50	1.00
2993134--2993238	42	2.4	46	76	16	109	63	1	2	31	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2993195--2993237	18	2.5	17	81	7	52	69	2	2	25	1.12
2994239--2994902	105	6.3	105	88	3	854	21	18	26	33	1.96
2995069--2995144	36	2.1	36	90	0	116	40	15	21	22	1.90
2995156--2995232	39	2.0	39	86	0	109	40	11	20	27	1.87
2995265--2995339	39	1.9	39	83	5	98	37	13	22	26	1.91
2995044--2995362	105	3.1	104	92	2	518	36	11	20	30	1.89
2996674--2997210	183	2.9	183	95	1	961	30	21	20	27	1.98
3001755--3001793	18	2.2	18	90	4	62	66	2	5	25	1.25
3002521--3002569	15	3.3	15	79	0	53	6	48	22	22	1.72
3006916--3006967	27	1.9	27	88	0	77	25	42	7	25	1.81
3016895--3016961	23	2.9	23	95	0	116	38	7	16	37	1.77
3017169--3017237	30	2.4	30	83	16	76	20	2	14	62	1.44
3017318--3017367	23	2.2	23	85	0	64	28	26	12	34	1.92
3018205--3018267	30	2.1	30	90	0	99	41	4	12	41	1.64
3025427--3025478	23	2.3	23	80	6	72	21	40	21	17	1.91
3026183--3026222	21	1.9	21	89	0	62	37	35	0	27	1.57
3027438--3027510	24	3.1	22	79	14	67	15	1	26	57	1.46
3031481--3031641	64	2.5	63	81	9	175	32	19	20	26	1.97
3032956--3033060	22	4.8	22	92	0	183	14	24	32	28	1.94
3037658--3037830	90	1.9	89	94	1	301	45	6	9	38	1.62
3040148--3040677	263	2.0	266	97	1	1003	34	23	11	31	1.90
3042604--3042645	18	2.3	18	83	0	57	23	33	14	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3046330--3046375	21	2.2	22	84	7	60	34	13	0	52	1.40
3046495--3046539	2	23.5	2	91	8	76	51	0	0	48	1.00
3053918--3053960	22	1.9	23	85	4	61	53	6	4	34	1.49
3061133--3061165	6	5.5	6	96	0	57	0	18	51	30	1.46
3075072--3075132	20	3.0	20	73	20	63	36	11	19	32	1.88
3087097--3087170	25	3.0	25	97	0	139	28	9	8	54	1.61
3100498--3100630	68	2.0	68	93	0	230	27	29	24	19	1.98
3110074--3110125	26	2.0	26	100	0	104	30	3	19	46	1.68
3113368--3113428	3	20.7	3	96	3	115	65	0	0	34	0.93
3117321--3117446	16	7.9	16	74	3	83	47	26	12	12	1.78
3117321--3117496	32	5.5	32	76	7	135	45	27	13	13	1.81
3117321--3117461	64	2.2	63	81	5	149	47	27	12	12	1.77
3117619--3117680	9	6.6	10	74	9	51	67	3	1	27	1.15
3119241--3119298	22	2.7	22	81	5	66	72	3	10	13	1.24
3119404--3119456	22	2.4	21	81	9	61	58	13	3	24	1.51
3119421--3119526	45	2.4	45	92	4	171	53	9	3	33	1.51
3119447--3119522	23	3.3	23	67	10	75	50	9	5	35	1.57
3123711--3123907	36	5.6	36	77	14	166	46	5	5	43	1.47
3123711--3123918	35	6.0	34	79	12	183	46	5	5	42	1.50
3123766--3123918	67	2.2	69	81	11	172	45	5	5	43	1.52
3123885--3123957	25	3.0	24	88	7	103	45	4	5	45	1.45
3123886--3123970	27	3.4	25	88	6	111	45	4	3	45	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3124001--3124119	41	3.1	36	77	17	116	43	0	3	52	1.23
3124001--3124095	41	2.5	39	82	14	117	47	0	4	48	1.21
3124110--3124157	3	14.7	3	91	8	60	31	0	0	68	0.90
3124001--3124119	39	3.1	36	75	17	107	43	0	3	52	1.23
3124107--3124158	21	2.6	20	84	6	70	30	0	0	69	0.89
3129908--3129996	36	2.4	36	90	5	135	30	19	13	37	1.90
3129938--3130059	57	2.1	57	92	0	199	26	20	13	40	1.89
3129938--3130016	21	4.0	21	70	18	80	27	20	11	40	1.87
3129974--3130059	21	4.4	21	70	16	85	25	20	12	40	1.88
3129908--3130186	93	2.9	93	82	9	360	27	20	13	38	1.90
3129998--3130424	36	12.3	35	76	15	377	27	20	12	39	1.89
3129998--3130424	173	2.5	173	91	1	678	27	20	12	39	1.89
3130327--3130383	15	3.5	15	71	17	51	22	22	14	40	1.90
3130342--3130401	19	3.3	19	68	20	56	26	21	10	41	1.85
3130325--3130377	15	3.1	17	72	17	56	22	22	13	41	1.88
3130338--3130393	17	3.3	17	69	18	53	28	19	12	39	1.88
3130482--3130605	33	3.7	33	81	12	155	41	20	10	28	1.85
3131192--3131320	34	3.7	36	83	11	137	42	4	6	45	1.51
3131291--3131372	26	3.2	26	94	3	139	47	4	3	43	1.42
3131384--3131462	38	2.2	35	84	8	97	43	0	3	53	1.19
3131416--3131475	16	3.7	16	78	10	59	36	0	1	61	1.06
3131462--3131500	13	3.1	13	85	14	55	30	0	0	69	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3135133--3136664	768	2.0	761	95	3	2796	32	16	18	32	1.94
3137196--3137247	20	2.6	20	96	0	95	38	26	13	21	1.90
3137238--3137335	21	4.8	20	74	10	65	36	21	19	22	1.95
3137303--3137670	20	18.5	20	83	5	431	34	25	19	20	1.96
3138345--3138391	24	2.0	24	83	8	60	27	14	19	38	1.91
3138563--3138587	12	2.1	12	100	0	50	72	0	28	0	0.86
3140773--3141066	19	16.7	19	81	15	375	47	17	20	14	1.83
3140773--3141047	121	2.3	122	89	8	411	47	17	20	14	1.83
3140812--3141103	140	2.1	141	90	5	461	46	17	19	15	1.84
3141095--3141176	19	4.6	19	79	17	104	14	24	18	42	1.87
3141141--3141184	19	2.3	19	92	0	70	18	20	15	45	1.85
3141279--3141314	14	2.6	14	86	4	56	47	22	0	30	1.52
3143198--3143332	19	7.6	19	75	16	110	45	25	18	9	1.80
3143254--3143310	14	3.7	14	72	20	51	45	28	19	7	1.76
3143235--3143327	33	2.8	33	91	0	159	47	24	19	8	1.77
3143198--3143332	52	2.5	54	77	18	149	45	25	18	9	1.80
3143328--3143418	33	2.8	33	91	5	141	7	18	28	45	1.77
3143328--3143455	19	7.3	19	74	18	116	8	17	28	45	1.78
3143498--3144235	93	8.1	93	95	4	1362	46	19	12	21	1.83
3143498--3144235	276	2.7	277	96	2	1372	46	19	12	21	1.83
3145927--3146034	33	3.3	33	93	0	189	45	19	25	10	1.81
3145934--3146036	14	6.3	18	70	25	77	43	21	24	10	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3146057--3146111	14	3.6	14	73	21	56	9	25	23	41	1.83
3146041--3146111	33	2.2	33	94	0	124	8	22	25	43	1.81
3146052--3146133	33	2.5	33	89	2	119	9	25	21	42	1.84
3146064--3146152	20	4.8	20	72	19	75	12	24	19	43	1.85
3146465--3146519	22	2.5	22	81	0	74	20	16	40	23	1.91
3146665--3146857	20	9.6	20	82	5	219	19	19	25	35	1.95
3146665--3146857	60	3.2	60	83	0	251	19	19	25	35	1.95
3146913--3146964	20	2.6	20	96	0	95	21	13	26	38	1.90
3152333--3152371	21	2.0	20	85	10	53	23	23	23	30	1.99
3156737--3156788	23	2.3	22	80	6	59	57	13	7	21	1.61

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   57   58   59   60   61   62