genome.fa.s8356.2.7.7.80.10.50.1000.17.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  17  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)
3374284--3374386	30	3.3	31	73	9	93	16	27	30	26	1.97
3377460--3377523	30	2.1	30	88	0	92	18	20	23	37	1.94
3381998--3382080	2	41.5	2	100	0	166	49	0	0	50	1.00
3382097--3382166	3	23.3	3	88	0	104	35	0	0	64	0.94
3385231--3385273	21	2.0	21	100	0	86	27	27	18	25	1.98
3385796--3385864	23	3.0	23	89	0	102	26	26	27	20	1.99
3385880--3386092	103	2.1	103	97	0	399	36	23	14	25	1.93
3396012--3396046	2	17.5	2	100	0	70	48	0	0	51	1.00
3400222--3400271	21	2.4	21	89	0	82	6	20	34	40	1.77
3407966--3407997	11	2.9	11	95	0	55	0	31	0	68	0.90
3408359--3408404	4	11.0	4	86	4	56	26	6	0	67	1.15
3411306--3411346	2	22.0	2	85	14	61	46	0	0	53	1.00
3411312--3411346	9	3.8	9	96	3	61	45	0	0	54	0.99
3413408--3413491	27	3.2	27	63	13	75	30	19	21	28	1.97
3413322--3413658	54	6.3	54	85	1	372	29	19	19	30	1.97
3420325--3420463	54	2.6	54	79	10	174	28	15	20	35	1.93
3420809--3420986	94	1.9	95	87	4	261	24	22	15	37	1.93
3420809--3421007	94	2.1	94	81	5	224	26	23	13	36	1.92
3421882--3421916	13	2.7	13	86	0	52	28	0	0	71	0.86
3423872--3423913	16	2.6	16	92	0	75	4	19	30	45	1.71
3423885--3424047	73	2.2	73	90	3	256	20	17	22	39	1.92
3428885--3428916	2	16.0	2	100	0	64	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3429640--3429681	14	2.9	14	92	3	66	40	0	52	7	1.29
3429642--3429697	14	3.9	14	79	9	51	42	0	50	7	1.30
3430927--3431382	185	2.5	185	84	3	587	40	12	15	31	1.85
3431496--3431745	72	3.6	70	81	7	276	30	14	12	42	1.83
3431826--3431877	21	2.5	21	96	0	95	34	15	17	32	1.91
3431826--3431878	10	5.1	10	73	8	52	35	15	16	32	1.90
3431754--3431927	93	1.9	93	81	4	217	33	13	8	44	1.74
3431754--3431949	93	2.1	93	80	5	209	34	13	8	43	1.75
3434107--3434484	196	1.9	195	88	2	562	29	12	16	41	1.86
3434381--3434496	53	2.2	53	93	0	196	31	16	14	37	1.89
3435040--3435065	13	2.0	13	100	0	52	0	0	46	53	1.00
3443693--3443766	37	2.0	37	89	0	112	27	10	8	54	1.63
3446189--3446223	17	2.0	18	88	5	54	42	5	0	51	1.25
3446565--3446623	31	1.9	31	89	3	93	38	20	18	22	1.93
3448363--3448495	22	5.8	21	73	15	95	42	3	9	45	1.52
3448427--3448479	27	2.0	26	89	7	81	50	3	5	39	1.44
3448418--3448568	47	3.0	48	77	12	155	45	4	8	41	1.55
3448369--3448552	71	2.6	67	78	14	174	42	4	9	42	1.57
3448363--3448557	25	8.1	24	70	17	104	44	4	9	42	1.57
3448561--3448619	21	2.8	20	70	10	55	47	1	6	44	1.39
3448589--3448651	28	2.2	31	77	13	71	42	1	4	50	1.32
3448630--3448674	2	22.5	2	100	0	90	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3449822--3449855	15	2.3	15	90	5	52	23	5	0	70	1.09
3449827--3449856	15	2.0	15	100	0	60	20	6	0	73	1.05
3450808--3450849	9	4.6	9	85	5	57	16	2	0	80	0.81
3452259--3452327	24	2.9	24	80	0	84	42	23	11	23	1.86
3461803--3461919	34	3.1	34	68	23	90	38	12	20	28	1.89
3461744--3461919	79	2.2	79	91	0	280	39	12	19	27	1.88
3465303--3465367	27	2.4	27	97	0	121	30	3	18	47	1.64
3466213--3466678	45	11.6	42	69	24	266	34	10	25	29	1.89
3466204--3466445	79	3.1	78	89	1	360	36	9	23	29	1.88
3466292--3466569	123	2.2	124	92	0	459	33	11	26	28	1.91
3466415--3466683	79	3.4	79	91	0	448	34	9	26	29	1.88
3466213--3466648	202	2.2	203	91	0	694	34	10	25	29	1.89
3466700--3466773	20	3.4	20	73	20	67	45	9	24	20	1.80
3466673--3466791	46	2.6	46	87	1	168	45	10	22	21	1.82
3466674--3466761	26	3.6	25	72	18	87	44	10	23	21	1.83
3468154--3468241	22	4.0	22	84	12	117	45	2	10	42	1.50
3468160--3468249	44	2.0	45	89	2	137	43	2	11	43	1.52
3468225--3468266	17	2.5	17	100	0	84	40	0	11	47	1.40
3468258--3468370	2	57.5	2	71	22	53	45	0	5	48	1.31
3468157--3468286	39	3.2	40	80	13	97	44	1	10	43	1.47
3468179--3468307	61	2.1	61	83	8	156	44	1	8	44	1.43
3468275--3468366	27	3.7	26	76	17	79	45	1	4	48	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3475387--3475532	30	4.9	29	77	9	123	15	14	8	60	1.57
3475388--3475533	60	2.4	60	80	2	168	15	14	8	61	1.55
3479228--3479283	16	3.6	16	75	20	55	78	7	10	3	1.06
3480478--3480507	15	2.0	15	93	0	51	20	30	20	30	1.97
3480533--3480716	40	4.3	41	68	17	108	26	29	17	26	1.98
3480533--3480772	130	1.9	128	90	2	365	26	31	17	25	1.97
3480533--3480890	134	2.7	128	82	7	398	26	31	15	25	1.96
3481056--3481124	3	23.7	3	77	16	74	30	2	0	66	1.06
3488428--3488487	23	2.6	22	86	5	75	21	26	28	23	1.99
3495017--3495056	21	1.9	21	89	0	62	40	5	0	55	1.22
3500320--3500359	22	1.9	21	90	10	64	27	17	22	32	1.96
3504617--3504661	24	1.9	23	81	4	54	37	0	2	60	1.09
3504640--3504715	33	2.5	32	79	12	88	43	0	0	56	0.99
3504635--3504725	32	2.8	32	74	12	87	42	0	0	57	0.99
3507027--3507133	34	3.1	34	87	0	160	52	4	4	38	1.43
3513592--3513634	20	2.2	20	87	8	61	37	18	11	32	1.87
3521969--3522039	31	2.3	31	90	0	106	32	15	11	40	1.83
3522297--3522336	21	2.0	21	90	5	64	35	0	20	45	1.51
3522727--3522768	8	5.5	8	86	11	52	28	0	0	71	0.86
3522727--3522769	14	2.9	14	89	6	59	27	0	0	72	0.85
3523600--3523652	27	1.9	28	96	3	99	32	5	5	56	1.46
3526435--3526651	53	4.1	53	87	3	292	39	13	7	39	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3527109--3527396	42	6.7	42	81	6	312	24	20	9	46	1.79
3527051--3527394	86	4.0	85	79	8	315	24	20	8	47	1.77
3527105--3527400	44	6.9	43	79	8	268	25	19	8	46	1.79
3528302--3528341	20	2.0	20	90	0	62	45	15	15	25	1.84
3530107--3530262	82	2.0	79	80	8	176	46	7	25	21	1.76
3530466--3530513	24	2.0	24	100	0	96	20	29	16	33	1.95
3532750--3532829	38	2.1	38	83	4	99	37	17	11	33	1.85
3534115--3534141	5	5.4	5	100	0	54	18	0	0	81	0.69
3534174--3534219	3	15.3	3	100	0	92	65	0	0	34	0.93
3540871--3540926	25	2.2	25	90	0	85	25	19	23	32	1.98
3544750--3544798	20	2.5	19	87	12	73	61	0	26	12	1.31
3547009--3547090	32	2.6	32	82	1	94	35	14	15	34	1.89
3547595--3547721	44	3.2	44	63	28	118	25	1	13	59	1.44
3547593--3547797	76	3.0	66	84	13	204	28	0	13	56	1.44
3547591--3547752	76	2.1	76	90	3	263	28	1	12	58	1.42
3548373--3548406	17	2.0	17	88	0	50	23	0	2	73	0.97
3551451--3551485	5	7.0	5	86	0	52	25	0	0	74	0.82
3551447--3551476	15	2.0	15	100	0	60	33	0	0	66	0.92
3553286--3553413	44	3.2	43	62	29	100	24	2	11	61	1.41
3553282--3553444	77	2.1	76	88	4	247	26	2	10	60	1.42
3554066--3554098	9	3.8	9	88	8	50	21	0	0	78	0.75
3554065--3554098	17	2.0	17	88	0	50	23	0	0	76	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3554065--3554100	13	2.8	12	91	8	54	22	0	0	77	0.76
3556103--3556149	3	15.3	3	91	8	69	70	0	0	29	0.88
3556359--3556543	84	2.2	84	85	4	248	25	19	23	30	1.98
3556651--3556815	36	4.4	37	84	5	190	37	15	21	26	1.92
3556670--3556734	21	3.4	21	64	24	61	41	13	21	23	1.89
3556651--3556796	75	2.0	75	89	4	226	39	14	20	25	1.90
3557522--3557822	110	2.8	109	86	4	396	26	18	20	34	1.95
3557979--3558019	20	2.0	20	100	0	82	39	9	19	31	1.84
3561429--3561477	25	1.9	26	83	4	64	55	6	4	34	1.44
3561862--3562027	21	7.8	21	73	16	146	19	19	24	37	1.94

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