genome.fa.s9634.2.7.7.80.10.50.1000.23.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   

This is table  23  of  78  ( 9351 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)
4828647--4829266	134	4.6	134	79	4	527	30	17	18	33	1.94
4829463--4829529	3	21.3	3	79	8	71	34	1	2	61	1.20
4829476--4829532	13	4.4	13	77	16	64	35	0	1	63	1.05
4829475--4829529	16	3.6	16	78	14	71	34	0	1	63	1.05
4829475--4829531	29	2.0	29	92	0	96	35	0	1	63	1.05
4829475--4829532	10	6.0	10	84	6	75	34	0	1	63	1.04
4842179--4842404	57	4.0	57	89	0	326	36	29	19	14	1.91
4847734--4847814	40	2.0	40	100	0	162	24	27	9	38	1.87
4847852--4847929	32	2.4	32	86	0	102	43	6	5	44	1.51
4848151--4848177	2	13.5	2	100	0	54	48	0	0	51	1.00
4848498--4848578	40	2.0	40	97	0	153	32	7	0	60	1.24
4848604--4848760	78	2.0	78	97	0	296	35	10	6	47	1.63
4863783--4863863	40	2.0	40	100	0	162	24	27	9	38	1.87
4863903--4863972	32	2.2	32	92	0	113	45	4	4	45	1.42
4863903--4863980	32	2.4	32	86	0	102	44	3	6	44	1.47
4864211--4864247	2	18.5	2	100	0	74	48	0	0	51	1.00
4864555--4864635	40	2.0	40	97	0	153	32	7	0	60	1.24
4864720--4864803	27	3.2	27	71	10	93	33	7	3	55	1.44
4864704--4864804	51	2.0	51	98	0	193	31	7	3	56	1.47
4866243--4866275	17	2.0	17	88	5	50	33	0	9	57	1.30
4872854--4872937	23	3.7	23	86	0	105	41	11	16	29	1.84
4873689--4873738	19	2.6	19	81	9	57	18	12	14	56	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4875286--4875325	21	1.9	21	85	10	55	42	20	2	35	1.65
4876812--4876935	11	11.6	10	68	21	65	75	0	19	4	1.00
4876809--4876983	22	8.3	21	67	17	80	75	0	18	5	1.02
4876824--4876985	7	23.1	7	74	10	82	75	0	18	5	1.04
4876824--4876936	34	3.6	33	83	10	123	76	0	18	4	1.01
4876794--4876921	17	8.2	17	68	23	77	74	1	19	4	1.08
4876833--4876982	6	23.8	6	68	23	60	75	0	18	6	1.04
4876793--4876992	105	1.9	107	85	8	284	74	1	19	5	1.06
4877914--4877969	24	2.3	24	78	6	60	33	5	1	58	1.31
4878945--4879017	38	1.9	38	82	0	92	26	20	17	35	1.95
4878927--4879142	42	5.2	42	72	9	154	28	19	15	36	1.93
4879945--4879985	20	2.0	21	85	4	57	31	12	21	34	1.91
4881848--4881893	24	1.9	24	86	8	67	21	0	52	26	1.47
4882620--4882712	20	4.6	20	77	7	71	31	12	24	31	1.93
4883645--4883687	13	3.3	13	93	0	68	18	44	20	16	1.87
4883627--4883668	18	2.3	18	87	0	57	19	45	21	14	1.85
4888826--4888885	13	4.5	13	81	8	75	15	43	23	18	1.87
4888803--4888849	18	2.6	18	89	0	76	17	46	23	12	1.82
4888858--4888908	15	3.2	16	83	13	61	15	33	23	27	1.95
4888858--4888908	8	6.4	8	82	13	61	15	33	23	27	1.95
4888858--4888908	23	2.1	25	89	7	79	15	33	23	27	1.95
4890197--4890231	18	2.0	18	88	5	54	54	0	14	31	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4899213--4899250	20	1.9	20	88	0	58	13	26	36	23	1.91
4908076--4909069	42	24.6	42	75	11	707	25	18	17	39	1.92
4908081--4908243	87	1.9	87	83	2	211	25	21	15	36	1.93
4908171--4909073	38	22.6	38	74	11	514	26	17	17	38	1.92
4908076--4909073	80	12.4	79	76	12	662	25	18	17	38	1.92
4908076--4909073	118	8.3	117	75	12	615	25	18	17	38	1.92
4909393--4909438	20	2.3	20	92	0	74	32	26	8	32	1.87
4909749--4910338	134	4.4	133	80	4	582	29	17	18	34	1.94
4910570--4910626	3	18.3	3	82	7	69	38	0	0	61	0.96
4910570--4910629	19	3.2	19	87	0	84	38	0	0	61	0.96
4910641--4910695	17	3.2	17	75	12	58	78	7	7	7	1.10
4912795--4912834	20	2.0	20	90	9	64	35	0	20	45	1.51
4933655--4933770	58	2.0	58	96	0	214	28	18	13	39	1.89
4935001--4935050	21	2.4	21	87	9	68	46	6	16	32	1.71
4939759--4939867	3	35.7	3	84	3	137	36	1	0	60	1.14
4941387--4941418	8	3.8	9	88	12	50	21	6	0	71	1.07
4944386--4944468	43	1.9	44	90	2	132	28	9	21	39	1.85
4946840--4946869	2	15.0	2	100	0	60	50	0	0	50	1.00
4947060--4947089	15	2.1	15	93	6	53	76	0	23	0	0.78
4947054--4947087	17	2.1	16	94	5	59	79	0	20	0	0.73
4951110--4951225	54	2.1	54	92	3	189	39	17	20	22	1.92
4951587--4951665	22	3.6	22	70	0	68	36	11	11	40	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4952334--4952426	47	2.0	47	100	0	186	23	23	21	31	1.99
4952368--4953556	76	15.6	76	97	0	2261	21	20	21	35	1.96
4953682--4953793	3	36.7	3	85	3	152	36	0	0	61	1.08
4956756--4956814	19	3.2	19	83	11	61	66	1	3	28	1.18
4956782--4956824	19	2.3	19	80	8	52	69	0	2	27	1.00
4957955--4958271	22	14.2	22	70	21	123	56	2	1	39	1.19
4957975--4958389	7	57.4	7	72	20	247	55	3	1	39	1.27
4957962--4958389	5	83.4	5	73	22	265	55	3	1	39	1.26
4957970--4958361	43	9.2	41	72	20	231	55	3	1	40	1.26
4957964--4958382	12	32.8	12	73	20	304	55	3	1	39	1.25
4957993--4958341	105	3.3	105	90	7	500	54	2	2	40	1.26
4957999--4958390	105	3.8	105	87	8	465	54	3	2	39	1.29
4958698--4958777	38	2.1	38	100	0	160	30	21	16	32	1.95
4964935--4965032	42	2.3	42	85	3	135	23	16	25	34	1.95
4964935--4965071	21	6.4	21	73	5	105	21	16	25	35	1.95
4966591--4966619	14	2.0	15	93	6	51	41	0	0	58	0.98
4967836--4967864	14	2.0	15	93	6	51	41	0	0	58	0.98
4968227--4968278	18	2.9	18	94	0	86	32	23	19	25	1.97
4969070--4969170	44	2.3	44	81	8	118	27	26	16	28	1.97
4969190--4969546	198	1.8	198	88	2	556	36	16	19	27	1.93
4969435--4969584	79	1.9	79	83	5	196	39	16	16	28	1.90
4969561--4969657	40	2.4	40	80	0	95	35	21	19	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4977098--4977987	443	2.0	443	98	0	1708	42	16	13	27	1.86
4978296--4978335	20	2.0	20	85	0	53	35	20	20	25	1.96
4980585--4980647	30	2.1	30	96	0	117	38	4	23	33	1.76
4981010--4981049	9	4.4	9	81	12	55	32	12	10	45	1.75
4981530--4981579	22	2.3	22	92	0	82	22	12	16	50	1.77
4981542--4981592	22	2.3	22	96	0	93	17	15	17	49	1.81
4986156--4986312	79	2.0	79	94	1	280	45	7	7	39	1.60
4986328--4986369	18	2.3	19	91	4	68	35	11	19	33	1.88
4986441--4986492	26	2.0	26	92	3	88	21	15	13	50	1.78
4994569--4994602	17	2.0	17	88	11	52	29	0	5	64	1.17
4994905--4994953	23	2.2	22	96	3	89	20	0	36	42	1.52
4994971--4995044	14	5.4	14	80	3	51	48	29	1	20	1.58
4994991--4995048	7	8.4	7	78	3	64	44	32	0	22	1.53
5001454--5001483	13	2.2	14	94	5	53	40	13	26	20	1.89
5002853--5002923	34	2.1	34	100	0	142	23	21	8	46	1.78
5005703--5005781	7	11.6	8	69	29	51	45	0	0	54	0.99
5005703--5005781	8	9.3	10	70	28	51	45	0	0	54	0.99
5005702--5005782	10	7.9	10	77	14	76	44	0	0	55	0.99
5007288--5007543	2	138.5	2	68	26	131	51	5	1	42	1.31
5007288--5007544	19	13.4	19	71	20	166	51	5	1	42	1.31
5016389--5016440	25	2.0	26	85	10	72	57	5	17	19	1.59
5016464--5016503	19	2.1	19	95	0	71	27	0	17	55	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5018646--5018687	16	2.7	16	88	3	59	78	7	9	4	1.08
5020958--5021135	5	35.6	5	69	23	69	58	3	1	36	1.24
5020973--5021207	7	33.7	7	76	14	193	54	5	1	39	1.31
5020965--5021268	22	13.3	23	70	19	153	53	7	0	38	1.35
5021068--5021207	2	74.5	2	69	28	78	50	5	1	42	1.35
5020973--5021207	75	3.3	71	79	11	198	54	5	1	39	1.31
5021084--5021280	7	28.6	7	72	16	108	49	9	1	40	1.41
5020973--5021207	3	64.2	4	68	25	91	54	5	1	39	1.31
5021050--5021281	82	2.8	80	74	14	186	50	8	0	39	1.39
5021205--5021266	20	3.2	19	86	4	79	50	16	0	33	1.45

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