genome.fa.s9462.2.7.7.80.10.50.1000.30.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: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  20687664

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   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   

This is table  30  of  91  ( 10815 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)
6288314--6288355	18	2.5	17	85	11	52	14	4	0	80	0.86
6288346--6288386	22	1.9	21	89	0	55	0	19	2	78	0.87
6289680--6289715	14	2.5	14	90	4	54	47	0	19	33	1.50
6297906--6297994	29	3.0	29	79	9	99	37	19	6	37	1.78
6304279--6304329	22	2.4	22	83	9	61	19	21	7	50	1.72
6308278--6308345	21	3.3	21	67	8	59	39	1	4	54	1.30
6308265--6308352	40	2.2	40	89	4	133	38	1	3	56	1.23
6308265--6308324	21	3.0	20	65	15	52	38	0	1	60	1.07
6315211--6315256	23	2.0	23	87	4	67	36	15	17	30	1.91
6317518--6317559	21	2.0	21	95	0	75	30	14	7	47	1.71
6317554--6317656	33	3.2	33	91	2	165	32	6	15	45	1.72
6318708--6319285	74	7.9	73	85	2	723	38	15	11	33	1.84
6323134--6324041	459	2.0	459	99	0	1807	31	20	13	35	1.91
6332423--6332575	77	2.0	79	83	10	199	43	5	9	42	1.59
6340333--6340638	130	2.4	127	85	6	413	50	5	12	31	1.61
6354412--6354494	27	3.1	27	96	0	148	36	21	15	26	1.94
6358414--6358683	130	2.1	129	92	2	461	33	8	13	45	1.73
6361848--6361873	13	2.0	13	100	0	52	46	30	7	15	1.74
6369935--6370068	32	4.4	32	69	21	108	39	3	11	44	1.59
6369933--6370043	56	2.0	56	90	0	177	41	3	13	41	1.62
6377066--6377107	20	2.1	20	95	0	75	14	16	21	47	1.82
6382406--6382445	21	1.9	21	89	0	62	32	20	12	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6382704--6382752	23	2.1	23	100	0	98	34	12	18	34	1.88
6385656--6385839	96	1.9	96	80	0	215	40	19	11	28	1.87
6386843--6386910	26	2.6	26	81	11	77	22	2	22	52	1.60
6391022--6391069	21	2.3	21	96	0	87	18	45	10	25	1.81
6397325--6397375	13	3.6	14	87	10	61	29	23	21	25	1.99
6398156--6398208	3	17.7	3	100	0	106	32	0	0	67	0.91
6399140--6399244	36	2.9	36	90	4	158	48	13	4	33	1.63
6408864--6409437	81	7.1	81	87	1	722	37	10	20	32	1.87
6414910--6415725	81	10.1	81	88	1	1199	35	10	21	31	1.88
6417148--6417187	19	2.1	19	90	0	62	25	47	20	7	1.75
6417940--6418267	54	6.1	54	85	1	426	30	17	20	31	1.96
6418599--6418672	20	3.7	20	88	1	94	25	29	12	32	1.92
6424382--6424818	54	8.1	54	86	1	545	29	16	19	34	1.94
6425344--6425394	20	2.5	20	96	0	93	23	21	15	39	1.92
6426151--6426193	6	7.0	6	81	5	50	72	2	0	25	0.97
6426152--6426193	19	2.3	18	91	4	66	73	2	0	23	0.94
6432255--6432319	22	3.0	22	86	2	87	30	15	33	20	1.93
6434906--6434958	21	2.5	21	100	0	106	33	18	15	32	1.92
6434969--6435020	20	2.6	20	100	0	104	30	17	26	25	1.97
6435440--6435606	59	2.8	59	88	0	246	31	11	19	37	1.88
6436038--6438344	46	49.1	46	80	11	2281	42	12	23	21	1.87
6436063--6437221	26	50.6	25	63	24	320	42	13	23	21	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6436052--6438240	66	32.1	66	66	23	439	42	12	23	21	1.87
6436046--6438287	20	98.6	20	65	25	481	42	12	23	21	1.87
6437679--6437902	26	9.5	26	66	23	138	41	12	23	21	1.88
6437773--6438222	26	18.6	25	64	25	168	42	12	22	22	1.87
6438250--6438325	20	3.5	20	69	19	62	39	10	26	23	1.87
6445965--6446044	25	3.2	25	100	0	160	30	7	27	35	1.84
6451915--6452525	55	11.1	55	88	0	846	28	22	14	34	1.94
6451829--6452525	110	6.4	110	86	2	886	28	22	14	33	1.94
6453809--6453843	16	2.1	17	94	5	63	0	17	0	82	0.66
6453796--6453858	30	2.1	29	82	8	74	3	17	0	79	0.86
6458287--6458328	19	2.3	19	95	4	77	47	16	14	21	1.82
6463153--6463276	50	2.5	50	93	0	203	37	26	5	30	1.80
6463153--6463263	25	4.4	25	88	0	177	38	27	5	28	1.78
6464858--6464947	2	45.5	2	97	2	173	50	0	0	50	1.00
6469052--6469104	23	2.3	23	86	0	70	18	22	24	33	1.97
6473471--6473512	19	2.2	19	91	0	66	35	9	16	38	1.81
6475724--6475762	20	2.0	20	84	0	51	30	23	12	33	1.92
6484276--6484314	20	2.0	20	89	0	60	33	23	10	33	1.88
6484857--6484896	21	1.9	21	94	0	71	22	22	25	30	1.99
6490628--6490674	18	2.7	18	93	3	78	31	8	31	27	1.87
6496977--6497063	31	2.8	33	77	15	94	28	5	1	64	1.24
6497010--6497057	15	3.1	15	73	5	51	27	4	2	66	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6497037--6497080	18	2.5	17	85	10	61	27	0	2	70	0.99
6497047--6497117	13	5.2	13	74	19	56	32	1	2	63	1.18
6497803--6497842	20	1.9	22	90	10	66	50	2	0	47	1.14
6497838--6497887	20	2.4	21	83	9	59	28	2	2	68	1.12
6498340--6498366	4	6.8	4	100	0	54	22	0	0	77	0.76
6504943--6504974	9	3.6	9	91	0	55	21	21	0	56	1.43
6508505--6508589	7	13.3	6	71	19	57	78	0	14	7	0.94
6508512--6508580	23	3.2	23	92	8	110	79	0	14	5	0.90
6508527--6508559	16	2.1	16	88	11	50	81	0	15	3	0.80
6508516--6508579	12	5.4	12	71	22	55	81	0	15	3	0.82
6508567--6508602	15	2.3	16	95	4	65	75	0	13	11	1.06
6508933--6509012	18	4.0	20	73	15	58	28	7	3	60	1.42
6510318--6510829	122	4.4	119	76	14	465	39	14	18	26	1.90
6510318--6510829	234	2.2	234	88	2	751	39	14	18	26	1.90
6512292--6512355	31	2.1	29	85	5	83	28	7	1	62	1.32
6512335--6512377	18	2.4	17	85	11	59	27	0	2	69	1.00
6512426--6512499	33	2.1	33	80	14	78	43	2	0	54	1.14
6518179--6518273	44	2.2	44	94	0	163	46	6	6	41	1.54
6518286--6518328	20	2.2	20	87	8	61	46	4	0	48	1.22
6520807--6520838	2	16.0	2	100	0	64	50	0	0	50	1.00
6521310--6521348	19	2.1	19	85	0	51	15	33	30	20	1.94
6532965--6533016	6	8.3	6	76	16	52	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6532982--6533016	14	2.5	14	95	0	61	62	0	0	37	0.95
6533219--6533263	2	23.5	2	78	17	51	46	0	2	51	1.13
6533224--6533268	22	2.0	22	84	16	58	48	0	2	48	1.13
6533368--6533417	20	2.4	21	83	10	66	46	2	6	46	1.39
6533451--6533550	12	8.2	12	76	19	84	41	1	1	57	1.12
6533462--6533541	2	43.5	2	73	20	68	41	1	1	56	1.15
6533462--6533541	9	8.7	10	73	20	68	41	1	1	56	1.15
6533451--6533550	19	5.4	18	80	16	98	41	1	1	57	1.12
6533451--6533551	39	2.8	36	82	14	118	40	0	0	57	1.12
6533455--6533550	10	9.6	10	79	15	78	40	1	1	57	1.13
6542442--6542487	15	3.1	15	84	9	58	47	0	2	50	1.13
6542517--6542559	17	2.6	17	96	3	79	46	0	6	46	1.30
6542606--6542654	20	2.4	21	80	13	57	46	2	6	44	1.39
6542616--6542653	20	1.9	20	88	0	58	44	2	7	44	1.47
6542630--6542691	29	2.1	29	85	11	83	43	1	9	45	1.46
6542687--6542754	13	4.7	16	72	25	62	35	0	0	64	0.94
6542690--6542754	19	3.7	19	78	15	77	33	0	0	66	0.92
6542692--6542756	22	3.1	22	83	14	77	32	0	0	67	0.91
6542698--6542763	19	3.1	22	72	18	59	36	0	0	63	0.95
6546485--6546533	25	2.0	25	83	0	62	48	0	0	51	1.00
6546493--6546535	20	2.2	20	91	8	70	51	0	0	48	1.00
6546791--6546841	21	2.4	22	81	12	61	68	0	3	27	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6549218--6549739	160	3.3	160	84	1	706	26	13	19	40	1.89
6551779--6551827	23	2.1	24	88	3	73	55	0	2	42	1.11
6551779--6551828	24	2.0	24	88	3	73	54	0	2	44	1.11
6551860--6551891	14	2.3	14	94	0	55	37	0	0	62	0.95
6552115--6552174	28	2.2	26	85	5	75	31	0	1	66	1.01
6552397--6552439	3	14.3	3	85	9	61	30	2	0	67	1.03
6555239--6555465	36	6.3	35	81	5	213	31	24	8	35	1.86
6555280--6555465	72	2.6	72	87	2	241	33	24	9	32	1.87
6555289--6555487	72	2.8	71	83	3	193	33	24	9	33	1.87
6555859--6556092	71	3.3	70	82	4	265	34	24	20	20	1.97

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   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91