genome.fa.s9462.2.7.7.80.10.50.1000.26.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: 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  26  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)
5311458--5311497	20	1.9	21	85	10	55	37	37	10	15	1.80
5313755--5313801	22	2.1	22	96	0	85	55	8	2	34	1.42
5313960--5314050	31	3.0	31	96	3	168	32	6	18	41	1.76
5314231--5314272	21	2.0	21	95	0	75	23	21	28	26	1.99
5314300--5314339	20	1.9	21	85	10	55	37	37	10	15	1.80
5316584--5316630	22	2.1	22	96	0	85	55	8	2	34	1.42
5316781--5316870	31	3.0	30	95	4	164	33	6	18	41	1.77
5317053--5317094	21	2.0	21	95	0	75	23	21	28	26	1.99
5317122--5317161	20	1.9	21	85	10	55	37	37	10	15	1.80
5317370--5317439	33	2.1	33	84	5	88	34	14	30	21	1.93
5319372--5319419	22	2.1	22	92	3	78	58	8	2	31	1.39
5319575--5319671	31	3.2	31	94	5	164	35	7	17	40	1.77
5319847--5319887	20	2.0	21	90	4	66	21	21	29	26	1.99
5319916--5319955	20	1.9	21	85	10	55	37	37	10	15	1.80
5323027--5323144	15	7.9	15	69	18	68	79	2	6	11	1.01
5323036--5323119	41	2.0	42	86	6	118	82	3	4	9	0.94
5323027--5323168	57	2.5	55	82	8	151	78	4	7	9	1.06
5323140--5323182	19	2.3	18	84	15	52	79	11	6	2	1.02
5323028--5323191	57	3.1	52	75	18	142	78	4	6	10	1.09
5324173--5324207	12	2.9	12	100	0	70	85	0	14	0	0.59
5324204--5324256	15	3.5	15	76	5	54	71	0	0	28	0.86
5324215--5324249	11	3.0	12	87	8	54	71	0	0	28	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5324209--5324253	18	2.4	18	82	13	56	68	0	0	31	0.89
5324706--5324781	2	38.0	2	100	0	152	50	0	0	50	1.00
5324989--5325054	24	2.7	25	77	13	75	78	3	6	12	1.04
5325033--5325071	17	2.2	17	86	4	51	79	0	7	12	0.93
5325005--5325091	28	3.1	26	76	15	77	78	2	9	10	1.06
5326492--5326561	33	2.1	34	83	2	88	47	8	0	44	1.34
5326636--5326773	72	1.9	74	86	4	199	49	8	2	39	1.46
5326625--5326811	36	5.2	35	76	9	144	45	10	2	41	1.52
5326636--5326826	75	2.6	74	81	6	192	47	9	3	39	1.52
5326804--5326846	23	2.0	23	86	9	63	46	2	4	46	1.36
5326804--5326847	21	2.0	21	82	13	52	47	2	4	45	1.35
5329173--5329253	42	1.9	42	87	5	119	29	7	19	43	1.78
5330853--5331310	54	8.5	54	87	2	607	32	18	15	33	1.92
5339468--5339855	54	7.2	54	86	2	512	30	18	17	33	1.94
5347496--5347534	16	2.4	16	91	4	60	61	5	10	23	1.48
5352555--5352591	16	2.3	16	90	0	56	13	5	18	62	1.50
5356323--5356370	25	1.9	25	86	0	69	18	27	43	10	1.82
5358071--5358179	53	2.1	53	89	0	164	25	16	17	40	1.90
5363401--5363541	76	1.9	76	95	0	255	26	17	14	40	1.89
5363551--5363805	39	6.6	39	85	0	314	31	16	15	37	1.89
5363821--5363935	59	1.9	59	89	6	180	31	26	13	28	1.93
5370169--5370399	39	6.0	39	88	0	304	29	11	22	36	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5389026--5389075	24	2.2	24	85	7	68	36	8	8	48	1.62
5390062--5390138	30	2.4	32	82	6	86	45	3	15	35	1.65
5391797--5391854	29	2.0	29	83	6	73	25	20	8	44	1.80
5392297--5392334	20	1.9	20	100	0	76	52	13	7	26	1.67
5393146--5393177	2	16.0	2	100	0	64	50	0	0	50	1.00
5395054--5395102	25	1.9	26	83	4	64	55	10	2	32	1.45
5397279--5397337	29	2.0	29	90	0	91	35	1	1	61	1.16
5397342--5397381	20	2.0	20	90	0	62	65	2	2	30	1.19
5397454--5397500	23	2.0	24	83	4	60	48	2	0	48	1.13
5399097--5399166	34	2.1	34	94	0	122	32	14	11	41	1.81
5399769--5399808	20	1.9	22	90	10	66	72	0	20	7	1.08
5400609--5400657	21	2.5	20	78	12	57	63	6	0	30	1.19
5400968--5401088	56	2.2	56	95	0	215	24	23	14	37	1.92
5401133--5401291	85	1.9	85	85	2	221	31	20	15	32	1.93
5401165--5401359	85	2.3	85	81	0	210	31	20	11	36	1.89
5402145--5402180	8	4.5	8	100	0	72	66	0	22	11	1.22
5405883--5405944	20	3.0	20	83	2	70	20	19	12	46	1.83
5405893--5405964	21	3.5	21	86	1	92	23	20	9	45	1.81
5408932--5409072	10	13.7	10	78	16	60	80	1	14	4	0.94
5408963--5409070	11	10.3	11	81	10	86	82	1	12	2	0.86
5408962--5409113	16	8.9	17	76	15	104	78	1	14	5	0.98
5408961--5409102	34	4.2	32	71	17	94	79	1	14	4	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5408979--5409070	40	2.4	39	84	10	118	84	2	10	2	0.79
5408962--5409094	10	13.5	10	77	14	73	79	1	14	4	0.95
5409002--5409094	25	3.6	27	72	15	70	79	1	13	5	0.96
5408979--5409066	1	88.0	1	70	0	59	85	2	10	2	0.78
5411224--5411248	12	2.1	12	100	0	50	0	40	32	28	1.57
5429079--5429111	13	2.5	13	100	0	66	33	6	42	18	1.75
5433836--5433977	37	3.9	37	89	4	218	47	18	17	16	1.83
5433836--5433977	73	1.9	73	90	5	225	47	18	17	16	1.83
5435376--5435414	2	19.5	2	100	0	78	48	0	0	51	1.00
5436243--5436627	115	3.3	116	82	1	450	39	16	21	22	1.92
5436065--5436454	207	1.9	210	85	3	547	39	16	21	22	1.92
5439145--5439227	41	2.1	40	93	6	143	21	15	15	46	1.83
5439519--5439642	39	3.2	39	91	2	189	50	8	8	32	1.65
5445237--5445315	21	3.8	21	84	3	106	18	21	27	31	1.97
5457052--5457260	76	2.8	77	87	3	282	24	32	23	19	1.98
5463018--5463078	23	2.9	21	87	7	79	21	34	26	18	1.96
5465304--5465375	30	2.3	30	95	4	126	41	2	18	37	1.65
5465685--5465895	76	2.8	77	86	3	275	24	32	23	19	1.98
5469255--5469289	16	2.2	16	89	0	52	80	2	8	8	1.01
5469653--5469677	13	1.9	13	100	0	50	40	16	20	24	1.91
5471447--5471480	13	2.6	13	90	0	59	44	20	17	17	1.87
5476901--5476926	2	13.0	2	100	0	52	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5483293--5483318	3	8.7	3	100	0	52	65	0	0	34	0.93
5484352--5484405	20	2.7	19	75	8	63	33	31	18	16	1.93
5484392--5484524	20	6.5	21	73	15	91	36	22	18	21	1.95
5484455--5484746	20	14.5	20	80	7	252	38	23	18	19	1.94
5485444--5485477	12	2.8	12	90	0	50	55	29	0	14	1.40
5485603--5485656	24	2.2	24	90	0	81	22	18	20	38	1.93
5488052--5488104	20	2.7	20	96	0	97	32	20	22	24	1.98
5488111--5488157	20	2.4	20	96	3	87	48	17	19	14	1.81
5488058--5488173	53	2.2	54	87	1	162	39	18	24	17	1.92
5488175--5488217	19	2.2	20	91	4	70	13	23	18	44	1.86
5488319--5488355	14	2.6	14	86	0	56	48	21	0	29	1.50
5489702--5489768	21	3.2	21	68	4	55	19	20	35	23	1.95
5489702--5489824	42	2.9	41	78	7	104	21	18	37	21	1.94
5491784--5491882	19	5.1	19	81	4	117	46	18	21	14	1.83
5491878--5491930	19	2.8	19	91	0	79	9	16	22	50	1.74
5491889--5491985	20	4.8	20	79	8	90	13	17	19	49	1.79
5492548--5492741	20	9.6	20	78	6	176	19	18	24	38	1.93
5492548--5492741	40	4.8	41	87	1	266	19	18	24	38	1.93
5492548--5492763	41	5.3	41	81	7	158	19	18	24	37	1.94
5492750--5492820	20	3.7	19	81	14	83	14	18	22	45	1.85
5496932--5496991	21	2.9	21	79	0	66	25	18	26	30	1.98
5499574--5500433	167	5.1	167	78	4	732	34	15	17	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5499575--5500430	335	2.5	333	78	5	823	34	15	17	32	1.91
5499574--5500452	169	5.2	167	78	5	695	34	15	17	32	1.91
5502678--5502726	24	2.0	24	100	0	98	48	16	16	18	1.81
5503480--5503549	15	4.7	15	72	0	50	27	0	14	58	1.36
5504299--5504369	19	3.8	19	75	17	78	22	21	35	21	1.96
5504299--5504366	36	1.9	35	91	5	111	23	17	36	22	1.94
5504507--5504566	30	2.0	30	90	6	95	46	13	6	33	1.69
5504669--5504720	20	2.5	21	84	9	54	51	3	13	30	1.58
5504678--5504734	19	2.9	19	85	10	71	52	7	12	28	1.64
5505052--5505116	26	2.5	27	90	5	100	40	7	9	43	1.65

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