genome.fa.s1547.2.7.7.80.10.50.1000.3.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: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  10425128

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   

This is table  3  of  51  ( 6083 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)
375821--376399	235	2.5	235	85	3	758	27	22	13	37	1.91
377711--377779	22	3.1	22	93	0	120	27	17	26	28	1.97
377717--377788	22	3.5	19	83	14	65	22	18	29	30	1.97
380041--380582	117	4.6	118	84	3	695	28	21	13	35	1.92
380038--380581	235	2.3	233	86	4	747	28	22	13	35	1.92
380529--380646	63	1.9	62	87	1	173	27	18	12	41	1.87
380592--381069	118	4.1	119	85	1	604	27	21	13	38	1.90
382803--382966	21	8.0	21	71	16	80	5	18	0	76	0.98
382840--382970	9	14.1	9	73	18	67	3	18	0	77	0.91
382891--382968	10	8.1	10	82	10	74	1	14	0	84	0.68
382869--382957	6	15.7	6	76	20	77	3	14	0	82	0.80
382805--382964	27	5.6	27	74	15	92	5	18	0	76	0.97
382895--382965	16	4.2	17	87	7	101	1	12	0	85	0.65
382910--382966	27	2.2	26	93	3	96	1	10	0	87	0.61
382890--382957	1	68.0	1	73	0	55	0	13	0	86	0.56
385665--385922	3	87.3	3	68	17	148	63	3	4	28	1.29
385671--385852	8	21.2	8	68	20	75	64	2	3	29	1.23
385665--385920	41	6.1	41	71	19	145	63	3	4	28	1.29
385711--385849	38	3.7	37	77	16	126	66	0	4	28	1.16
394126--394164	19	2.0	20	90	5	62	41	0	0	58	0.98
394254--394352	5	18.8	5	70	17	58	41	1	1	56	1.13
394224--394353	28	4.5	29	71	25	89	40	0	3	56	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
394254--394379	26	4.8	26	72	17	93	44	0	1	53	1.15
394260--394352	23	4.0	23	74	12	75	41	1	1	55	1.14
394278--394354	8	9.6	8	70	14	52	40	1	1	57	1.15
394550--394601	22	2.4	22	93	0	86	32	9	19	38	1.84
398596--398628	4	8.2	4	93	0	57	24	3	27	45	1.68
400880--400913	17	2.0	17	100	0	68	23	35	5	35	1.79
403736--403812	3	26.7	3	87	7	106	33	1	0	64	1.01
404781--404824	21	2.1	21	87	8	63	77	0	15	6	0.97
405372--405570	51	3.9	51	85	1	245	19	13	11	55	1.67
405372--405570	103	1.9	102	82	1	245	19	13	11	55	1.67
406218--406611	131	3.0	128	87	2	511	29	11	17	41	1.85
406249--406611	129	2.8	129	86	4	480	29	11	17	41	1.85
409937--410025	7	12.7	7	67	16	51	77	0	15	6	0.97
409997--410043	18	2.5	18	86	6	58	80	0	17	2	0.80
412166--412836	241	2.8	242	86	2	933	31	16	16	35	1.92
412806--413438	260	2.4	262	79	6	725	33	15	15	35	1.90
413989--414435	134	3.3	132	82	5	515	31	19	17	31	1.95
414669--414726	3	20.0	3	85	7	75	34	1	0	63	1.04
415487--415521	1	35.0	1	88	0	52	94	0	0	5	0.32
415487--415521	10	3.5	10	92	0	61	94	0	0	5	0.32
415536--415869	166	2.0	169	97	1	638	21	20	15	43	1.88
416250--416448	51	3.9	51	89	0	299	17	12	12	57	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
417098--417493	131	3.0	131	82	3	485	31	13	15	39	1.86
420887--420943	7	8.0	7	79	16	64	54	0	0	45	0.99
420884--420943	16	3.9	15	89	10	95	53	0	0	46	1.00
420884--420945	9	6.9	9	81	18	76	53	0	0	46	1.00
420884--420945	2	34.0	2	81	18	82	53	0	0	46	1.00
424586--424722	42	3.3	42	94	0	238	23	21	19	35	1.96
428371--428437	32	2.2	32	84	10	86	34	5	0	59	1.22
428357--428437	30	2.8	28	70	23	69	30	6	1	61	1.28
428451--428495	21	2.2	21	84	7	58	24	8	0	66	1.20
428519--428586	25	2.7	26	78	15	72	25	4	4	66	1.29
428579--428620	15	2.7	15	88	3	57	23	9	2	64	1.35
428742--428791	16	3.1	16	76	18	50	18	6	4	72	1.22
438949--439076	66	1.9	66	85	3	177	56	11	21	10	1.65
439055--439111	7	7.6	7	78	9	51	78	1	17	1	0.91
439055--439105	8	6.2	8	76	13	50	78	1	17	1	0.94
441041--441086	23	2.0	24	83	12	60	39	2	10	47	1.51
441048--441100	27	2.0	25	82	13	63	37	3	9	49	1.53
442224--442282	9	6.3	9	78	18	50	22	3	3	71	1.16
442254--442311	22	2.7	21	75	19	57	29	6	0	63	1.20
443692--443743	2	27.0	2	88	7	81	48	0	1	50	1.12
445523--445594	30	2.4	30	79	9	92	25	25	12	37	1.91
445685--445717	17	1.9	17	93	0	57	45	15	0	39	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
446047--446283	114	2.0	120	94	5	423	27	25	11	34	1.91
447227--447280	17	3.0	18	83	8	74	50	1	1	46	1.23
452592--452724	60	2.2	60	82	7	155	35	12	12	39	1.82
454202--454256	24	2.3	23	81	6	65	20	20	10	49	1.78
454217--454267	24	2.2	24	86	6	70	19	17	11	50	1.76
454889--454932	2	22.0	2	100	0	88	50	0	0	50	1.00
455710--455825	21	5.6	21	67	19	73	22	17	25	35	1.95
455716--455850	42	3.3	42	91	2	211	22	17	23	36	1.95
455775--455846	21	3.4	21	69	14	67	22	15	22	40	1.91
456520--456565	23	2.0	23	95	0	83	41	17	19	21	1.90
467926--467983	26	2.3	26	87	3	82	18	15	31	34	1.93
468359--468387	15	1.9	15	100	0	58	31	20	13	34	1.92
473633--473695	26	2.5	26	84	5	85	19	15	30	34	1.93
474072--474100	15	1.9	15	100	0	58	31	20	13	34	1.92
479751--479813	26	2.5	26	84	5	85	19	15	30	34	1.93
480190--480218	15	1.9	15	100	0	58	31	20	13	34	1.92
485884--485946	26	2.5	26	84	5	85	19	15	30	34	1.93
486313--486341	15	1.9	15	100	0	58	31	20	13	34	1.92
492013--492091	26	3.0	26	88	3	115	20	11	29	39	1.87
492381--492444	31	2.1	31	96	0	119	23	14	21	40	1.90
493900--493930	14	2.1	15	94	5	55	77	0	16	6	0.97
493995--494188	39	4.9	39	87	1	255	45	23	3	27	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
497860--497912	20	2.7	20	80	8	63	32	15	30	22	1.94
498326--498579	55	4.6	55	80	3	287	37	17	16	28	1.91
498325--498579	110	2.3	110	84	2	334	37	18	16	28	1.92
498884--499104	45	4.8	45	78	6	203	45	8	19	26	1.78
498893--499031	46	2.9	49	82	8	187	47	7	19	25	1.75
498885--499059	46	3.8	45	82	6	183	48	6	18	26	1.73
499038--499255	45	4.8	44	89	2	292	38	11	22	27	1.88
506453--506688	121	1.9	122	87	0	348	13	33	30	22	1.92
512387--512430	19	2.3	19	88	7	63	18	31	29	20	1.96
512468--512688	86	2.5	87	86	5	304	33	3	17	46	1.64
512468--512688	29	7.6	29	87	3	295	33	3	17	46	1.64
514971--515014	22	2.0	21	91	4	70	31	13	25	29	1.94
515354--515684	55	6.1	55	82	3	384	34	18	19	28	1.95
515374--515684	108	2.9	108	83	3	349	34	18	19	27	1.95
515846--515979	68	2.0	68	86	0	187	29	14	26	29	1.95
516076--516253	46	3.8	45	84	10	234	48	7	19	24	1.75
516241--516453	45	4.7	45	85	2	266	38	12	22	26	1.90
528342--528379	19	2.0	19	85	10	51	18	5	21	55	1.62
534230--534378	77	1.9	79	82	5	187	40	10	6	43	1.63
536543--537981	746	1.9	747	95	0	2628	38	16	17	27	1.91
538301--538334	17	2.1	16	88	5	50	76	0	8	14	1.01
548539--548572	17	2.1	16	88	5	50	76	0	8	14	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
559954--560019	30	2.2	30	84	7	82	42	0	4	53	1.21
561144--561196	3	17.7	3	82	7	63	33	3	0	62	1.13
561132--561196	33	2.0	33	96	0	121	35	4	0	60	1.18
561410--561446	18	2.0	19	85	15	51	40	5	0	54	1.24
561699--561771	35	2.1	35	97	0	137	17	20	42	19	1.89
567053--567105	20	2.7	19	91	2	79	18	20	28	32	1.97
567056--567105	19	2.5	20	90	3	75	20	22	26	32	1.98
567015--567170	84	1.9	84	84	8	210	28	15	25	31	1.96
567133--567170	20	1.9	20	94	0	67	18	15	34	31	1.92
575749--575839	45	2.0	46	89	2	139	27	19	24	28	1.99

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