genome.fa.s8488.2.7.7.80.10.50.1000.26.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: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12876159

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   

This is table  26  of  54  ( 6450 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)
6370362--6370412	23	2.2	23	85	0	66	33	19	7	39	1.81
6371222--6371250	15	1.9	15	100	0	58	41	20	24	13	1.89
6374094--6374169	29	2.6	29	78	0	89	36	13	23	26	1.91
6375828--6375866	13	2.8	13	88	11	51	35	0	2	61	1.10
6387633--6387671	21	1.9	20	84	5	51	28	15	20	35	1.93
6391173--6391464	117	2.5	117	90	2	444	31	33	16	18	1.93
6392398--6392559	29	5.6	29	88	2	202	39	22	4	33	1.74
6392575--6392649	18	3.9	18	73	17	62	13	21	45	20	1.84
6392585--6392651	13	5.0	13	72	25	59	14	20	46	17	1.84
6392584--6392636	23	2.3	23	90	0	79	11	20	47	20	1.81
6392603--6392649	18	2.6	18	86	0	76	12	23	46	17	1.82
6392574--6392661	41	2.2	40	81	2	104	18	22	40	18	1.91
6399941--6400053	60	1.9	58	87	3	163	36	17	19	26	1.94
6400533--6400576	20	2.2	20	91	0	70	9	11	20	59	1.59
6400525--6400593	24	3.0	23	75	16	63	8	11	20	59	1.58
6400928--6400952	13	1.9	13	100	0	50	56	4	8	32	1.47
6401229--6401269	20	2.0	20	100	0	82	29	14	4	51	1.63
6401626--6401687	31	2.0	31	93	0	106	50	8	9	32	1.65
6401634--6401697	31	2.1	31	87	0	92	53	7	6	32	1.55
6402775--6402807	13	2.5	13	90	9	50	42	0	18	39	1.50
6409786--6409845	22	2.7	22	92	0	102	23	28	21	26	1.99
6440485--6441119	320	2.0	315	98	1	1225	29	17	25	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6446437--6446536	2	50.0	2	100	0	200	50	0	0	50	1.00
6447667--6447815	65	2.3	66	91	3	248	22	30	20	26	1.99
6447808--6447854	21	2.3	20	88	3	67	21	25	21	31	1.98
6448207--6448250	21	2.1	21	91	0	70	29	0	15	54	1.42
6448736--6448797	17	3.4	17	73	16	61	40	0	11	48	1.39
6448758--6448801	23	2.0	23	81	4	54	40	0	9	50	1.34
6449026--6449093	13	5.3	13	71	15	52	45	5	2	45	1.42
6451215--6451555	49	7.0	49	95	0	610	41	0	11	46	1.46
6451522--6451554	14	2.4	14	90	5	50	39	3	15	42	1.62
6451638--6451672	11	3.1	12	88	12	56	51	0	5	42	1.25
6451689--6451891	26	7.9	26	84	5	198	44	1	9	43	1.47
6451730--6451824	3	32.7	3	72	6	52	51	2	6	40	1.39
6451782--6451827	9	5.2	9	84	5	67	54	0	8	36	1.32
6451786--6451818	17	1.9	17	93	0	57	51	0	9	39	1.34
6451694--6451962	14	20.8	13	69	20	149	43	2	8	45	1.46
6451939--6451980	17	2.5	17	80	0	57	40	0	2	57	1.12
6451860--6452040	54	3.4	54	79	14	171	40	3	6	49	1.45
6452989--6453033	23	2.0	23	86	0	63	55	2	4	37	1.32
6454343--6454390	22	2.1	23	92	3	80	41	10	2	45	1.50
6454337--6454444	30	3.9	28	77	22	113	45	10	1	42	1.48
6454343--6454423	22	3.3	22	72	27	74	43	12	1	43	1.50
6454642--6454681	21	1.9	21	100	0	80	57	15	0	27	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6454709--6454763	18	3.4	18	65	31	52	52	9	0	38	1.33
6454783--6454854	38	2.0	36	86	13	103	50	8	0	41	1.33
6454773--6454828	29	2.0	28	83	13	71	44	8	0	46	1.34
6455021--6455058	9	4.2	9	83	10	51	65	2	0	31	1.06
6455249--6455284	11	3.2	11	84	7	54	36	19	22	22	1.95
6455359--6455442	29	2.9	28	87	7	114	16	29	28	25	1.97
6455462--6455582	60	2.0	60	96	0	224	23	41	21	13	1.88
6459328--6459382	20	2.7	21	71	5	58	32	9	25	32	1.87
6462451--6462494	23	1.9	23	81	9	54	54	13	6	25	1.63
6471637--6471724	22	4.0	22	74	12	65	30	19	25	25	1.98
6474704--6474855	79	2.0	77	94	3	270	28	6	8	55	1.55
6478415--6478458	18	2.4	18	92	0	79	22	27	40	9	1.84
6478673--6478704	15	2.1	15	94	0	55	0	21	0	78	0.76
6479006--6479048	16	2.7	16	100	0	86	18	18	58	4	1.56
6479135--6479202	3	22.7	3	91	5	111	66	1	0	32	1.01
6479512--6480191	113	6.0	113	89	3	872	31	18	12	37	1.88
6479512--6480152	229	2.8	225	86	5	871	31	18	12	37	1.88
6480977--6481577	83	7.3	83	89	4	885	35	21	13	28	1.92
6480983--6481577	165	3.6	166	91	2	941	35	21	13	28	1.92
6480977--6481575	248	2.4	248	92	2	999	35	21	13	28	1.92
6482337--6482386	19	2.6	19	100	0	100	54	4	6	36	1.44
6482337--6482399	19	3.5	18	91	6	76	52	6	6	34	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6482732--6482810	18	4.5	19	73	20	75	1	17	0	81	0.77
6482733--6482809	7	11.1	7	78	10	79	1	15	0	83	0.72
6482743--6482804	16	3.7	16	82	16	72	1	14	0	83	0.71
6482735--6482804	35	2.0	36	91	8	117	1	15	0	82	0.73
6491109--6491161	16	3.4	16	75	12	56	45	3	0	50	1.19
6491114--6491160	16	2.9	16	78	12	60	44	2	0	53	1.12
6491315--6491371	28	2.0	28	83	12	73	63	0	0	36	0.95
6492249--6492280	15	2.1	15	94	0	55	0	21	0	78	0.76
6492710--6492773	3	21.7	3	96	3	121	67	0	0	32	0.91
6502953--6503000	2	24.0	2	100	0	96	50	0	0	50	1.00
6504696--6504732	18	2.2	17	90	9	58	10	5	32	51	1.60
6506882--6506932	25	2.0	26	88	11	79	41	19	5	33	1.76
6512178--6512260	2	41.5	2	95	4	150	49	1	0	49	1.08
6513935--6513971	18	2.2	17	90	9	58	10	5	32	51	1.60
6524123--6524567	220	2.0	222	98	1	867	33	13	11	41	1.80
6527404--6527526	21	5.8	21	72	14	58	59	1	1	37	1.17
6527442--6527500	23	2.8	20	75	20	59	59	0	1	38	1.08
6527454--6527522	23	3.0	22	81	8	68	62	1	1	34	1.13
6531259--6531300	19	2.2	19	91	0	66	30	28	4	35	1.78
6536688--6536731	14	3.1	14	80	6	54	36	20	25	18	1.95
6540667--6540728	15	4.1	15	95	2	106	19	19	3	58	1.53
6540686--6540729	8	5.8	8	78	10	56	18	22	0	59	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6541086--6541136	23	2.2	23	85	0	66	50	3	17	27	1.63
6542052--6542082	2	15.5	2	100	0	62	51	0	0	48	1.00
6542541--6542691	37	4.1	37	75	4	126	42	9	18	29	1.81
6542778--6543005	36	6.3	36	74	6	185	48	9	14	27	1.74
6548890--6548941	23	2.3	22	90	3	77	28	26	23	21	1.99
6548935--6548983	21	2.3	21	85	0	62	34	30	14	20	1.92
6549177--6549207	12	2.5	13	94	5	55	67	6	0	25	1.14
6549537--6549674	55	2.5	55	89	0	204	31	22	17	28	1.96
6555770--6555851	23	3.7	22	79	9	87	30	26	21	20	1.98
6555771--6555884	21	5.3	21	77	14	97	29	27	20	22	1.98
6556377--6556574	55	3.6	55	80	8	190	31	23	18	26	1.97
6568777--6568821	2	22.5	2	100	0	90	51	0	0	48	1.00
6573794--6573848	19	2.6	22	78	21	64	72	1	10	14	1.19
6578291--6578346	15	3.6	15	76	9	58	44	10	12	32	1.77
6578294--6578327	17	2.0	17	88	0	50	41	8	11	38	1.73
6578516--6578568	21	2.5	21	93	0	88	28	28	22	20	1.99
6578764--6578818	13	4.2	13	75	13	58	49	12	3	34	1.59
6578804--6578902	33	3.0	33	94	1	164	45	15	7	32	1.73
6578897--6578936	21	1.9	21	94	0	71	47	7	15	30	1.72
6598913--6598978	19	3.4	19	93	2	105	36	27	27	9	1.87
6599222--6599277	27	2.1	27	93	0	94	26	12	26	33	1.92
6602467--6602530	16	4.0	16	81	0	83	45	6	23	25	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6602470--6602536	32	2.1	32	94	0	116	43	7	22	26	1.80
6604654--6604691	16	2.2	18	90	9	62	52	0	2	44	1.14
6604791--6604832	19	2.3	19	87	4	59	45	4	0	50	1.23
6607682--6607724	21	2.1	21	86	4	61	44	11	11	32	1.77
6608474--6608503	15	1.9	16	93	6	53	46	13	23	16	1.82
6609492--6609529	20	1.9	20	88	0	58	21	15	31	31	1.94
6610770--6610799	15	1.9	16	93	6	53	23	6	30	40	1.80
6618943--6618997	27	2.0	27	100	0	110	25	27	3	43	1.71
6629241--6629285	17	2.6	17	96	0	81	20	46	20	13	1.83
6629261--6629340	22	3.6	22	87	0	106	23	43	18	13	1.86

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