genome.fa.s1129.2.7.7.80.10.50.1000.21.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   

This is table  21  of  89  ( 10573 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)
4420876--4420953	41	1.9	41	94	0	138	43	17	25	12	1.85
4420877--4420952	21	3.7	21	85	3	109	44	18	25	11	1.83
4420937--4420992	14	3.7	14	70	25	51	42	23	25	8	1.82
4420929--4421008	32	2.5	32	91	2	124	45	23	22	8	1.80
4421024--4421113	14	5.7	14	72	23	72	8	24	22	44	1.81
4421015--4421121	33	3.2	33	100	0	214	9	24	19	46	1.79
4421015--4421099	19	5.0	19	71	23	82	9	23	21	45	1.80
4422807--4423365	93	6.1	93	98	0	1063	22	12	19	45	1.84
4422807--4423365	185	3.0	186	97	1	1063	22	12	19	45	1.84
4423412--4423540	19	7.3	19	73	17	116	45	27	17	9	1.78
4423448--4423540	33	2.8	32	91	4	150	46	27	18	7	1.76
4423412--4423540	52	2.5	52	73	14	131	45	27	17	9	1.78
4423536--4423653	19	6.7	19	75	18	121	10	20	22	46	1.80
4423558--4423614	14	3.7	14	77	20	60	10	21	22	45	1.82
4423541--4423633	33	2.8	33	95	0	168	10	20	21	47	1.80
4423605--4423669	19	3.4	19	85	4	78	10	16	27	44	1.81
4425473--4425508	12	3.0	12	83	0	54	19	0	16	63	1.30
4425575--4425613	14	2.7	14	92	4	60	35	0	23	41	1.55
4425713--4425819	19	5.8	19	86	11	152	44	16	23	14	1.85
4425713--4425828	52	2.2	52	92	7	191	43	18	24	14	1.87
4425802--4425828	14	1.9	14	100	0	54	37	22	25	14	1.93
4425855--4426067	19	12.4	19	76	20	238	14	21	17	46	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4425874--4426081	33	6.2	33	76	15	223	13	22	18	46	1.83
4425834--4426040	52	4.0	52	97	2	393	14	23	16	45	1.84
4428257--4428281	12	2.1	12	100	0	50	0	28	0	72	0.86
4429157--4429246	20	4.6	20	86	5	121	20	15	22	42	1.89
4429157--4429341	40	4.8	39	82	10	168	21	18	24	34	1.96
4429157--4429341	58	3.2	58	81	7	180	21	18	24	34	1.96
4429176--4429341	20	8.6	20	83	7	177	21	19	25	32	1.97
4429328--4429380	19	2.7	20	82	11	65	11	18	24	45	1.82
4429366--4429448	21	4.0	21	73	6	78	25	16	24	33	1.96
4432028--4432068	17	2.4	17	95	0	73	36	7	14	41	1.74
4432075--4432109	17	2.1	17	94	0	61	42	2	5	48	1.41
4433841--4433868	14	2.0	14	100	0	56	21	28	7	42	1.79
4434298--4434329	8	3.9	8	92	8	55	87	0	12	0	0.54
4434298--4434329	17	1.9	17	93	6	57	87	0	12	0	0.54
4434548--4434622	35	2.1	35	90	4	116	25	14	28	32	1.95
4435735--4435886	5	29.2	5	68	16	60	73	1	7	17	1.13
4435735--4435787	12	4.2	12	81	16	54	77	0	1	20	0.87
4435734--4435787	24	2.2	24	83	6	65	75	0	1	22	0.89
4435749--4435809	23	2.5	24	79	12	72	77	0	6	16	0.98
4435948--4435973	3	8.7	3	100	0	52	69	0	0	30	0.89
4436086--4436133	2	24.5	2	95	4	89	52	0	0	47	1.00
4437925--4439140	167	7.3	167	89	1	1647	23	19	26	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4437925--4439140	84	14.6	84	87	1	1687	23	19	26	30	1.98
4441288--4441532	95	2.5	95	84	5	296	34	17	15	33	1.91
4444252--4444434	12	14.0	12	68	20	75	73	1	5	20	1.10
4444248--4444418	5	33.6	5	70	13	100	73	1	5	19	1.11
4444267--4444434	29	5.7	29	69	18	89	73	1	5	19	1.10
4444255--4444405	41	3.7	37	73	23	103	72	1	6	19	1.13
4444248--4444421	17	11.1	15	70	10	73	73	1	5	19	1.10
4444668--4444707	19	2.0	20	90	4	64	75	0	2	22	0.93
4444673--4444707	7	5.3	7	86	13	56	74	0	0	25	0.82
4444707--4444749	2	21.5	2	100	0	86	51	0	0	48	1.00
4446184--4446220	2	18.5	2	100	0	74	51	0	0	48	1.00
4452727--4452774	21	2.3	21	89	7	71	39	27	8	25	1.84
4455781--4455829	22	2.2	22	82	7	64	32	30	28	8	1.86
4456740--4456880	31	4.5	31	92	0	237	20	18	21	39	1.92
4457358--4457400	21	2.0	21	82	8	52	32	4	13	48	1.63
4463421--4463450	12	2.5	12	100	0	60	30	13	0	56	1.37
4465076--4465142	29	2.3	29	79	5	73	49	13	20	16	1.79
4467719--4467855	46	3.0	46	87	2	170	32	21	8	38	1.82
4467956--4468089	58	2.3	58	78	6	162	27	24	18	29	1.98
4468378--4468426	24	2.0	24	88	0	71	42	12	14	30	1.82
4469940--4469998	30	2.0	30	83	6	75	35	18	6	38	1.78
4471882--4471929	6	7.7	6	84	9	60	0	14	2	83	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4471882--4471929	13	3.8	12	78	10	60	0	14	2	83	0.74
4471882--4471929	19	2.5	20	80	10	64	0	14	2	83	0.74
4471880--4471929	14	3.3	14	76	17	55	0	14	2	84	0.72
4475374--4475399	3	8.7	3	100	0	52	0	0	30	69	0.89
4475398--4475534	46	3.0	46	83	8	165	33	18	6	40	1.77
4475634--4475763	58	2.2	58	81	5	172	28	24	19	27	1.98
4476048--4476096	24	2.0	24	96	0	89	44	12	12	30	1.78
4480984--4481029	21	2.2	21	84	0	56	23	8	34	32	1.86
4482979--4483034	2	30.0	2	86	13	84	48	0	0	51	1.00
4482974--4483038	15	4.1	16	88	11	98	49	0	0	50	1.00
4483026--4483087	19	3.3	19	77	4	63	54	0	0	45	0.99
4483088--4483141	12	4.6	12	83	4	74	24	48	16	11	1.79
4483212--4483264	25	2.1	25	89	6	81	22	16	37	22	1.94
4489395--4489467	32	2.4	31	93	4	121	30	20	16	32	1.95
4495049--4495076	1	28.0	1	100	0	56	0	0	0	100	0.00
4496658--4496696	20	2.0	20	90	5	62	20	15	20	43	1.88
4496729--4496780	22	2.2	24	86	6	72	36	19	15	28	1.92
4499036--4499075	21	1.9	21	94	0	71	32	12	5	50	1.62
4499072--4499170	33	3.0	33	92	1	155	32	6	15	46	1.70
4502264--4502361	43	2.3	43	98	0	187	42	15	17	24	1.87
4514113--4514158	21	2.2	21	92	0	74	19	50	15	15	1.79
4514632--4514671	13	3.0	13	82	7	53	32	27	15	25	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4515946--4516005	26	2.3	27	80	11	70	45	18	8	28	1.78
4519224--4519274	23	2.2	24	82	3	59	27	19	3	49	1.66
4521718--4521756	20	2.0	20	89	0	60	33	10	23	33	1.88
4525234--4525272	20	2.0	20	89	0	60	33	5	23	38	1.77
4534557--4534588	2	16.0	2	100	0	64	50	0	0	50	1.00
4537327--4537378	24	2.2	24	89	0	77	40	21	19	19	1.92
4537367--4537445	23	3.5	22	79	6	68	37	25	20	16	1.93
4537408--4537460	23	2.3	23	90	0	79	33	28	22	15	1.94
4538557--4538582	11	2.4	11	100	0	52	46	23	0	30	1.53
4541418--4541459	14	2.9	14	82	13	50	54	26	2	16	1.54
4543399--4543437	19	2.1	19	90	0	60	10	25	38	25	1.87
4547270--4547309	21	1.9	21	85	10	55	32	5	5	57	1.42
4551523--4551574	2	26.0	2	96	0	95	50	1	0	48	1.12
4558465--4558532	34	2.0	34	100	0	136	35	11	11	41	1.78
4559101--4559153	21	2.5	21	84	6	72	20	24	18	35	1.95
4559143--4559188	20	2.3	20	88	7	67	39	21	17	21	1.93
4559843--4559994	60	2.5	60	90	1	223	19	19	21	39	1.93
4559864--4560111	40	6.2	40	82	4	248	19	19	23	37	1.94
4559838--4560054	20	10.7	20	80	7	197	20	18	22	38	1.94
4559942--4560077	61	2.2	60	80	6	157	19	19	25	36	1.95
4560063--4560111	20	2.5	20	90	6	73	12	20	24	42	1.86
4562407--4562465	29	2.0	29	87	6	84	45	8	18	27	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4564461--4564496	18	2.0	18	100	0	72	33	50	11	5	1.61
4564831--4564879	24	2.0	25	96	4	91	59	0	0	40	0.98
4564833--4564889	24	2.4	24	88	5	80	59	0	1	38	1.08
4565621--4565711	47	1.9	48	88	2	139	35	12	13	39	1.81
4572424--4572508	34	2.5	34	78	14	86	49	2	4	43	1.36
4572428--4572631	64	3.1	68	76	11	208	45	6	7	40	1.59
4576249--4576350	34	3.0	34	78	15	111	48	3	2	45	1.36
4576293--4576413	63	1.9	63	88	5	183	45	4	7	42	1.51
4577856--4577922	20	3.4	19	77	8	71	32	20	16	29	1.95
4577858--4577935	40	2.0	40	89	5	122	32	19	14	34	1.91

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