genome.fa.s7984.2.7.7.80.10.50.1000.3.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: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12923621

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   

This is table  3  of  65  ( 7696 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)
396966--397119	15	10.3	15	75	14	90	46	3	4	44	1.42
396965--397020	18	2.9	19	87	12	71	48	3	1	46	1.30
396985--397043	18	3.3	18	79	11	68	47	3	1	47	1.29
397255--397316	19	3.3	19	80	8	81	43	0	30	25	1.55
397503--397684	2	96.0	2	66	18	77	45	2	5	46	1.38
397644--397680	11	3.5	11	92	3	58	48	0	0	51	1.00
398027--398185	2	81.5	2	67	18	77	47	2	5	45	1.38
397967--398146	99	1.8	99	91	4	301	47	2	5	44	1.38
397971--398181	99	2.1	97	84	8	264	48	2	5	44	1.38
398243--398330	7	12.6	7	71	9	63	42	38	1	18	1.58
398375--398458	13	6.8	13	66	17	54	41	7	10	40	1.67
398364--398479	60	1.9	60	98	0	223	39	6	12	41	1.69
398476--398571	21	4.5	21	75	15	72	38	5	8	47	1.56
398553--398603	15	3.3	15	71	15	50	41	3	3	50	1.39
398582--398665	43	2.1	42	81	14	99	45	4	3	46	1.41
398561--398725	65	2.6	62	78	14	162	41	4	3	50	1.39
398607--398729	29	4.3	28	72	17	85	41	4	2	51	1.36
398695--398733	11	3.5	11	83	10	53	38	2	0	58	1.12
398872--398917	20	2.3	20	88	3	67	45	4	8	41	1.55
398888--398946	2	28.0	2	76	10	55	45	5	5	44	1.47
398970--399017	19	2.6	18	81	15	62	39	8	10	41	1.69
398968--399051	34	2.4	34	80	15	100	40	7	9	42	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
399007--399091	20	4.2	21	68	23	65	41	5	7	45	1.55
399081--399117	19	1.9	19	100	0	74	35	0	10	54	1.36
399154--399215	14	4.4	14	75	18	56	46	6	1	45	1.38
399099--399262	59	2.6	62	79	13	176	42	4	3	49	1.42
399106--399307	66	3.2	64	80	13	188	43	4	2	48	1.39
400021--400056	18	2.1	17	89	5	54	58	2	0	38	1.13
400201--400239	16	2.4	16	91	0	60	33	17	28	20	1.96
402877--403121	116	2.1	118	89	1	377	36	13	19	31	1.90
407653--407832	65	2.8	63	83	6	209	28	17	24	29	1.97
407843--407900	20	2.9	20	97	0	107	24	15	29	31	1.95
407672--407881	65	3.2	64	83	8	232	28	16	23	31	1.96
410940--410981	12	3.4	12	83	3	57	21	19	19	40	1.92
411332--411398	23	2.9	23	82	4	73	50	17	7	23	1.71
415849--415917	25	2.8	25	93	0	120	24	24	10	40	1.86
418733--418774	21	2.0	21	100	0	84	38	19	9	33	1.84
422326--422388	22	3.0	21	79	4	72	36	14	12	36	1.84
422900--422938	16	2.4	16	87	8	53	15	2	2	79	0.95
425194--425266	22	3.3	22	77	11	62	38	10	12	38	1.78
430876--430917	20	2.2	20	86	4	59	30	0	30	38	1.58
430884--430922	19	2.0	20	85	5	53	28	0	33	38	1.57
432444--432541	49	2.0	47	82	7	117	46	7	17	28	1.74
436327--436353	2	13.5	2	100	0	54	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
437001--437041	20	2.0	21	86	13	59	43	0	53	2	1.13
437022--437088	12	5.3	12	81	5	62	44	1	50	2	1.26
437796--437849	28	1.9	28	84	0	72	25	12	11	50	1.74
438157--438208	17	3.2	17	84	15	74	26	0	9	63	1.25
439789--439887	50	2.0	50	84	7	130	20	27	22	30	1.98
454229--454267	2	19.5	2	100	0	78	51	0	0	48	1.00
454377--454409	17	1.9	17	88	11	50	66	0	0	33	0.92
454896--454934	20	2.0	20	84	0	51	2	35	43	17	1.63
456358--456415	24	2.4	24	88	0	80	51	10	5	32	1.58
458643--458715	31	2.4	31	85	0	101	39	12	15	32	1.84
459576--459631	20	2.8	20	97	0	103	37	23	21	17	1.94
459861--459905	20	2.2	20	96	0	81	33	44	8	13	1.75
460775--460916	70	2.0	70	90	0	221	48	13	9	28	1.73
461051--461106	25	2.2	25	87	0	76	37	28	17	16	1.91
461647--461690	20	2.2	20	87	0	61	29	29	15	25	1.96
468113--468246	54	2.5	54	86	4	173	26	16	28	29	1.97
476741--476799	7	8.0	7	74	22	50	44	0	0	55	0.99
476738--476799	24	2.4	26	81	10	74	45	0	0	54	0.99
476712--476849	72	1.9	73	85	5	190	42	5	1	50	1.33
476819--476860	20	2.2	20	91	4	68	40	2	2	54	1.26
479853--479891	20	2.0	19	85	5	51	30	2	2	64	1.21
486181--486303	55	2.2	55	85	0	165	34	14	26	25	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
486613--486723	48	2.3	48	98	1	215	43	4	0	52	1.21
486713--486746	17	1.9	18	88	5	52	58	0	2	38	1.13
488170--488214	22	2.0	23	86	4	65	80	4	13	2	0.97
500009--500034	5	5.2	5	100	0	52	61	0	38	0	0.96
500659--500702	18	2.5	17	78	10	52	29	31	6	31	1.84
501433--501477	12	3.8	12	84	0	63	24	15	17	42	1.88
501683--501730	22	2.2	22	88	0	69	58	20	8	12	1.60
505734--506061	43	7.6	42	82	7	194	34	24	23	17	1.96
505771--506064	43	6.8	43	86	3	394	33	25	23	17	1.96
508706--508764	20	3.5	17	84	13	61	30	23	25	20	1.98
508737--508764	14	2.0	14	100	0	56	35	28	21	14	1.92
511417--511444	2	14.0	2	100	0	56	50	0	0	50	1.00
511601--511659	30	2.0	30	96	0	109	27	13	38	20	1.90
511608--511672	30	2.2	30	83	5	78	27	16	35	20	1.94
516901--516934	16	2.1	16	100	0	68	38	11	20	29	1.88
520127--520162	12	3.0	12	83	0	54	16	16	16	50	1.79
524436--524503	24	2.8	24	84	4	75	20	13	13	52	1.73
526607--526643	17	2.2	17	90	0	56	13	29	29	27	1.94
528940--528975	12	3.0	12	83	0	54	16	16	16	50	1.79
528917--528987	24	3.0	24	83	4	81	22	12	15	49	1.78
533401--533436	12	3.0	12	83	0	54	16	16	16	50	1.79
533378--533448	24	3.0	24	83	4	81	22	12	15	49	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
537840--537907	24	2.8	24	86	4	84	19	14	13	52	1.73
542301--542368	24	2.8	24	86	4	84	19	14	13	52	1.73
546750--546817	24	2.8	24	86	4	84	19	14	13	52	1.73
548931--548967	17	2.2	17	95	0	65	13	32	29	24	1.93
548946--549020	32	2.3	32	73	15	75	20	25	29	25	1.99
553101--553150	22	2.4	20	83	9	64	20	26	26	28	1.99
557382--557423	20	2.0	20	86	9	57	21	28	21	28	1.99
557998--558109	41	2.7	41	72	20	133	37	7	18	36	1.79
558879--558974	24	4.0	24	91	0	129	16	11	18	53	1.73
563450--563521	24	3.0	24	81	0	90	18	12	18	51	1.76
567965--568073	24	4.5	24	75	11	89	20	13	15	50	1.78
572516--572586	24	3.0	24	82	0	97	19	9	16	53	1.71
575685--575724	17	2.4	17	86	0	53	17	30	25	27	1.97
578684--578740	24	2.4	25	74	17	66	21	17	12	49	1.79
578698--578792	24	4.0	24	79	8	86	21	11	15	51	1.75
582974--583046	24	3.0	24	83	0	101	19	9	17	53	1.71
586144--586185	17	2.5	17	84	7	59	16	28	28	26	1.97
589168--589239	24	3.0	24	87	0	108	19	11	18	51	1.75
589145--589239	48	2.0	48	81	4	111	21	11	16	50	1.76
591358--591398	17	2.4	17	91	0	64	12	26	31	29	1.92
593698--593766	24	2.9	24	84	0	93	20	11	15	52	1.74
597355--597459	48	2.2	48	83	6	124	17	16	17	49	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
597392--597461	12	5.8	12	73	6	61	15	14	18	51	1.77
597392--597462	24	3.0	24	89	0	115	16	14	18	50	1.78
597623--597654	2	16.0	2	100	0	64	50	0	0	50	1.00
601900--601973	24	3.1	24	82	0	85	20	8	16	55	1.66
602873--602947	10	6.8	12	76	17	90	25	8	30	36	1.85
602873--602947	22	3.4	22	96	0	141	25	8	30	36	1.85
605333--605365	12	2.8	12	95	0	57	27	6	33	33	1.81
602917--606750	804	4.8	806	94	1	6584	35	6	21	37	1.79
607580--607605	12	2.2	12	100	0	52	23	11	7	57	1.59
608476--608562	21	4.2	21	66	12	63	41	19	5	33	1.75

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