genome.fa.s1465.2.7.7.80.10.50.1000.16.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

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   

This is table  16  of  55  ( 6520 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)
3077440--3077465	13	2.0	13	100	0	52	23	0	15	61	1.33
3077598--3077624	14	1.9	14	100	0	54	7	22	29	40	1.81
3078894--3078930	18	2.1	18	89	0	56	51	10	5	32	1.60
3079313--3079364	25	2.1	25	96	0	95	42	21	7	28	1.80
3082032--3082079	24	2.0	24	91	0	78	37	20	20	20	1.95
3082207--3082240	12	2.8	12	90	0	50	14	0	29	55	1.40
3083050--3083123	20	3.7	20	77	10	78	29	8	25	36	1.85
3083131--3083177	20	2.3	20	85	0	67	23	17	21	38	1.93
3093638--3093715	38	2.1	38	100	0	156	32	7	17	42	1.78
3093642--3093705	22	3.2	22	62	25	59	32	9	17	40	1.81
3094391--3094440	21	2.4	21	80	9	66	28	2	14	56	1.49
3095812--3095841	15	2.0	15	93	0	51	33	10	26	30	1.89
3099657--3099707	22	2.4	22	87	6	70	31	13	25	29	1.94
3100033--3100483	59	7.6	59	94	0	767	32	13	19	33	1.91
3102666--3102734	23	3.0	22	79	8	75	30	24	24	20	1.99
3102957--3103016	31	2.0	30	83	9	77	36	23	3	36	1.71
3108849--3108886	20	1.9	19	94	5	67	39	10	21	28	1.86
3108886--3109060	94	1.9	94	80	11	207	34	16	22	26	1.95
3109017--3109090	22	3.5	22	88	3	98	33	14	24	27	1.94
3109401--3110138	59	12.5	59	90	0	1102	32	14	18	33	1.92
3120686--3120754	32	2.1	33	84	7	88	21	8	37	31	1.84
3121008--3121189	91	2.0	91	95	0	328	31	18	19	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3123015--3123068	20	2.7	20	85	0	63	27	29	16	25	1.97
3131998--3132034	6	6.2	6	100	0	74	16	0	83	0	0.64
3134511--3134622	42	2.8	40	75	9	102	52	2	7	37	1.43
3135250--3135347	18	5.2	18	68	18	74	33	19	5	41	1.73
3135235--3135348	38	3.0	38	98	0	219	34	20	5	40	1.75
3142497--3142629	39	3.4	39	84	0	167	18	27	21	31	1.97
3143069--3143138	2	35.0	2	100	0	140	50	0	0	50	1.00
3150678--3150792	20	5.6	21	74	9	69	26	22	19	32	1.97
3150742--3150808	20	3.3	20	77	10	73	35	19	20	23	1.95
3150727--3150808	41	2.0	41	83	4	103	32	19	19	28	1.96
3154222--3154265	20	2.3	19	84	4	52	38	20	20	20	1.94
3154249--3154329	14	4.9	17	69	25	66	44	18	23	13	1.85
3154249--3154360	33	3.4	33	97	0	206	44	18	24	12	1.84
3154249--3154340	19	5.4	19	69	24	87	46	18	21	13	1.82
3154355--3154416	19	3.3	19	88	4	72	14	17	22	45	1.85
3154366--3154417	19	2.7	19	93	0	77	11	19	21	48	1.80
3154382--3154426	19	2.4	19	84	0	54	15	17	17	48	1.81
3154524--3154560	14	2.6	14	91	0	65	45	21	0	32	1.52
3155924--3156016	42	2.2	42	81	5	107	24	16	37	21	1.93
3156410--3156487	33	2.4	33	93	0	129	48	20	19	11	1.79
3156426--3156490	19	3.7	19	68	19	50	47	21	18	12	1.81
3156496--3156591	19	4.9	19	79	7	95	7	18	21	52	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3156502--3156597	39	2.5	38	87	3	129	8	19	19	52	1.71
3156688--3157059	94	4.1	94	91	3	582	47	18	12	21	1.81
3156688--3157059	187	2.0	181	90	4	586	47	18	12	21	1.81
3158743--3158864	20	6.8	19	64	23	59	45	16	22	14	1.84
3158798--3158864	33	2.0	33	91	0	107	47	17	22	11	1.80
3158865--3158935	19	3.7	19	86	1	97	11	19	23	45	1.83
3159477--3159567	20	4.5	20	81	2	119	20	18	19	40	1.91
3164303--3164333	2	15.5	2	100	0	62	51	0	0	48	1.00
3164405--3164446	13	3.2	13	89	0	57	40	7	19	33	1.78
3177886--3177985	24	4.2	24	74	5	94	47	17	14	22	1.82
3177879--3177987	48	2.3	48	77	0	119	48	16	13	21	1.80
3180470--3180501	13	2.5	13	100	0	64	12	25	46	15	1.81
3180464--3180541	18	4.2	18	91	5	111	14	19	48	17	1.81
3180478--3180542	18	3.6	18	95	0	112	10	18	50	20	1.76
3182666--3182765	24	4.2	24	74	5	94	47	17	14	22	1.82
3182659--3182767	48	2.3	48	77	0	119	48	16	13	21	1.80
3185228--3185260	13	2.5	13	90	0	57	15	21	45	18	1.85
3185236--3185313	18	4.6	18	72	15	76	15	15	48	20	1.81
3185234--3185307	31	2.4	31	93	0	121	18	14	47	18	1.83
3185254--3185289	13	2.8	13	91	0	54	19	13	47	19	1.83
3192369--3192416	24	2.0	24	87	0	69	33	12	2	52	1.51
3194297--3194368	37	1.9	37	100	0	144	25	19	23	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3213180--3213247	35	1.9	35	87	0	100	26	17	20	35	1.95
3214693--3214754	29	2.2	29	94	2	108	30	27	12	29	1.93
3215559--3216380	3	283.7	3	85	9	1131	63	0	35	0	0.95
3217591--3217660	36	1.9	36	88	5	106	48	5	14	31	1.67
3219160--3219201	21	2.0	21	95	0	75	26	28	23	21	1.99
3225978--3226028	21	2.4	21	90	0	84	15	29	25	29	1.96
3226545--3226609	34	1.9	34	93	0	112	49	7	7	35	1.60
3226802--3226926	63	2.0	63	85	3	171	37	20	0	40	1.59
3227184--3227534	117	3.0	117	91	0	578	31	23	23	21	1.98
3230718--3230759	21	2.0	21	85	0	57	50	0	0	50	1.00
3231361--3231476	61	1.9	61	83	1	153	26	31	23	18	1.97
3231682--3231720	2	20.5	2	89	10	64	51	0	0	48	1.00
3231682--3231733	10	5.1	10	86	11	54	53	0	0	46	1.00
3231708--3231748	18	2.2	19	86	4	57	63	0	2	34	1.08
3231723--3231775	23	2.3	24	81	12	67	67	0	3	28	1.07
3231768--3231829	25	2.4	26	94	5	117	69	0	6	24	1.12
3242187--3242237	14	3.6	14	81	5	50	70	3	5	19	1.24
3242408--3242516	52	2.1	51	83	5	130	63	1	9	25	1.34
3244512--3244663	79	1.9	78	81	1	178	21	21	21	35	1.96
3245158--3245308	78	1.9	78	83	2	196	19	20	24	35	1.96
3245244--3245450	106	2.0	106	88	1	308	20	17	26	35	1.95
3246560--3246619	11	5.5	11	78	9	61	0	16	1	81	0.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3246571--3246613	8	5.4	8	78	10	52	0	16	2	81	0.79
3246560--3246620	9	6.3	9	72	20	52	0	16	1	81	0.76
3246564--3246618	17	2.8	21	76	15	64	0	18	1	80	0.81
3246560--3246620	21	3.2	20	77	13	74	0	16	1	81	0.76
3246596--3246717	63	2.0	63	90	1	192	12	22	11	54	1.69
3246658--3246682	13	1.9	13	100	0	50	4	8	0	88	0.64
3246604--3246731	63	2.0	62	84	1	166	14	21	13	51	1.75
3253592--3253637	17	2.4	20	79	13	53	19	23	21	34	1.96
3256088--3256132	13	3.4	13	81	6	54	71	2	4	22	1.15
3257635--3257663	2	14.5	2	100	0	58	48	0	0	51	1.00
3271234--3271350	12	9.1	12	70	19	60	79	1	16	2	0.93
3271232--3271340	22	5.0	22	75	17	79	78	1	16	2	0.95
3271231--3271350	26	4.6	26	75	19	90	79	1	16	2	0.93
3271236--3271364	69	1.9	68	85	10	183	77	1	18	2	0.96
3272722--3273058	76	4.4	75	82	7	376	32	16	11	40	1.84
3272943--3273098	37	4.1	37	73	7	116	31	16	13	38	1.88
3273039--3273526	39	12.5	39	88	1	656	28	18	17	35	1.93
3273567--3273751	59	3.2	59	72	9	180	27	28	14	29	1.95
3277439--3277484	21	2.2	21	84	0	56	32	0	21	45	1.52
3277454--3277497	21	2.1	21	83	8	54	34	0	20	45	1.51
3279305--3279513	76	2.8	76	93	2	341	26	1	12	58	1.44
3287602--3287887	76	3.8	76	96	0	520	27	1	11	59	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3287719--3287780	32	2.0	31	84	9	81	27	0	9	62	1.26
3300835--3300916	22	3.7	22	83	0	119	30	24	19	25	1.98
3306644--3306979	37	9.2	37	74	9	246	30	19	10	39	1.85
3306659--3306979	72	4.4	72	80	5	317	30	19	11	39	1.86
3306662--3306979	144	2.2	146	83	7	389	29	19	11	39	1.86
3307182--3307229	20	2.4	20	100	0	96	29	18	14	37	1.91
3308144--3308189	18	2.3	21	85	10	62	36	6	0	56	1.25
3319732--3319782	22	2.3	21	87	9	75	54	21	7	15	1.66
3319938--3320068	70	1.9	68	92	3	217	52	5	6	35	1.49
3319871--3320284	231	1.8	230	87	4	566	54	4	8	33	1.49

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