genome.fa.s12.2.7.7.80.10.50.1000.18.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   

This is table  18  of  120  ( 14336 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)
5522380--5522413	16	2.0	16	88	11	50	58	0	0	41	0.98
5522610--5522640	5	6.2	5	100	0	62	38	0	0	61	0.96
5523123--5523156	17	2.0	17	100	0	68	23	11	17	47	1.81
5523261--5523300	19	2.1	19	86	9	55	50	2	17	30	1.59
5524296--5524329	15	2.3	15	94	0	59	38	20	0	41	1.53
5528121--5528154	16	2.1	16	88	0	50	32	23	11	32	1.91
5527964--5528322	188	1.9	188	98	1	693	45	13	9	32	1.75
5529780--5529907	61	2.1	61	79	7	134	38	3	11	46	1.56
5538579--5538620	11	3.8	11	78	9	50	54	0	2	42	1.13
5538575--5538619	22	2.1	22	87	4	65	57	0	2	40	1.11
5538751--5538803	22	2.5	21	85	14	65	35	1	1	60	1.19
5551475--5551528	21	2.6	21	81	0	63	29	31	9	29	1.88
5554858--5555332	104	4.6	104	94	1	785	19	20	29	30	1.97
5558111--5558142	16	2.0	16	93	0	55	25	9	12	53	1.68
5577322--5577367	15	3.1	15	77	0	56	23	10	50	15	1.75
5581003--5581031	10	3.0	10	95	5	51	72	0	0	27	0.85
5585530--5585581	24	2.2	24	86	6	70	50	5	3	40	1.45
5592688--5592735	7	6.3	7	81	13	51	64	2	4	29	1.23
5592687--5592733	25	2.0	23	87	8	67	63	2	4	29	1.25
5595546--5595587	17	2.6	16	85	14	52	33	2	0	64	1.07
5599554--5599603	22	2.3	21	86	3	64	62	2	4	32	1.25
5599552--5599623	21	3.7	19	76	9	65	66	1	4	27	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5599599--5599635	17	2.1	17	90	5	56	70	0	2	27	1.01
5600327--5600379	18	3.0	17	86	8	70	67	1	0	30	1.01
5605302--5605353	24	2.2	24	89	0	77	53	7	3	34	1.48
5607119--5607152	13	2.5	13	90	4	50	61	11	8	17	1.54
5607242--5607293	24	2.2	24	96	0	95	57	7	0	34	1.27
5608310--5608848	275	2.0	275	96	0	997	38	13	21	26	1.90
5612267--5612333	34	1.9	35	87	3	100	32	8	11	46	1.72
5613661--5613713	27	2.0	27	100	0	106	37	7	41	13	1.72
5616969--5617021	16	3.3	16	74	10	54	15	33	1	49	1.55
5622681--5622810	64	2.0	64	100	0	260	44	16	10	27	1.81
5625835--5625866	2	16.0	2	100	0	64	50	0	0	50	1.00
5638560--5638626	34	1.9	35	87	3	100	32	8	11	46	1.72
5639170--5639213	8	5.8	8	84	10	56	34	0	65	0	0.93
5639173--5639209	4	9.8	4	82	11	51	29	0	70	0	0.88
5639164--5639218	22	2.5	22	85	2	76	36	0	63	0	0.95
5648606--5648655	20	2.5	20	83	6	66	46	16	12	26	1.81
5658923--5658958	18	2.0	18	94	0	63	27	41	11	19	1.85
5660505--5660551	15	3.1	15	71	17	51	44	2	2	51	1.25
5661532--5661587	12	4.2	13	74	17	51	12	12	1	73	1.18
5662914--5662949	17	2.1	18	89	5	56	50	0	0	50	1.00
5663132--5663174	13	3.2	13	80	3	50	27	25	11	34	1.91
5663128--5663177	7	7.3	7	78	13	50	30	24	14	32	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5663629--5663721	21	4.4	21	67	14	57	63	1	2	33	1.13
5663709--5663772	32	2.0	32	84	6	85	53	0	3	43	1.16
5668444--5668484	10	4.0	10	87	3	55	34	0	19	46	1.50
5673030--5673133	51	2.0	51	100	0	208	40	7	19	32	1.80
5676228--5676276	17	2.9	17	75	0	53	69	0	28	2	1.00
5677339--5677409	21	3.4	21	82	0	88	15	15	35	33	1.89
5679875--5679989	27	4.3	27	79	5	90	28	24	12	34	1.91
5679894--5679989	27	3.6	27	86	0	120	30	21	13	34	1.92
5682667--5682754	25	3.2	25	64	27	61	45	22	7	23	1.79
5683521--5683638	45	2.6	45	89	4	168	28	22	16	32	1.95
5698339--5698611	139	2.0	139	83	4	354	25	22	15	36	1.93
5699172--5699244	35	2.1	35	82	10	87	24	8	0	67	1.18
5699680--5699747	19	3.5	19	84	15	86	55	7	1	35	1.37
5701037--5701074	15	2.4	17	82	13	53	65	0	13	21	1.26
5704521--5704587	27	2.5	27	95	0	116	31	25	32	10	1.89
5704537--5704581	15	3.2	15	72	18	51	26	31	33	8	1.87
5704657--5704700	21	2.1	21	95	0	79	29	0	11	59	1.32
5704791--5704834	16	2.8	16	82	0	61	56	2	2	38	1.24
5704867--5704939	38	1.9	38	97	0	137	39	2	4	53	1.34
5704868--5704959	38	2.4	38	87	5	125	43	3	3	50	1.34
5705044--5705155	8	13.4	8	66	19	50	50	14	0	33	1.49
5705070--5705162	19	4.9	19	70	23	72	53	12	0	33	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5705070--5705155	27	3.1	27	88	3	127	53	11	0	34	1.37
5705198--5705235	19	1.9	19	89	5	58	57	7	0	34	1.28
5705234--5705323	27	3.3	27	98	0	171	12	32	24	31	1.92
5705779--5705837	21	2.8	21	82	15	68	47	1	1	49	1.21
5706070--5706103	12	2.7	13	86	9	52	47	0	2	50	1.16
5710323--5710501	51	3.4	51	85	6	207	34	13	23	28	1.93
5710368--5710481	57	2.0	57	92	1	192	31	14	25	28	1.95
5710380--5710501	57	2.1	58	90	1	192	35	12	23	28	1.91
5713165--5713206	13	3.2	13	80	10	50	61	9	2	26	1.39
5713621--5713661	18	2.3	18	87	4	57	80	2	7	9	0.99
5714578--5714633	25	2.2	26	83	6	69	25	1	5	67	1.21
5716899--5716946	13	3.5	13	82	17	62	6	18	2	72	1.15
5718062--5718106	20	2.3	19	85	11	56	51	2	2	44	1.26
5718053--5718106	19	2.8	18	78	13	63	51	1	1	44	1.22
5718720--5718778	25	2.4	25	89	10	95	30	1	1	66	1.12
5719010--5719074	34	1.9	34	83	0	85	26	12	15	46	1.81
5729566--5729650	9	9.4	9	90	0	116	41	25	8	24	1.83
5729566--5729650	18	4.7	18	92	0	134	41	25	8	24	1.83
5736645--5736675	2	15.5	2	100	0	62	51	0	0	48	1.00
5756023--5756066	15	2.9	15	82	3	61	86	13	0	0	0.57
5756024--5756066	10	4.3	10	85	8	61	88	11	0	0	0.52
5757274--5757389	46	2.6	44	80	2	115	31	20	18	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5757323--5757513	44	4.4	44	70	13	146	30	19	20	29	1.97
5767821--5767845	6	4.2	6	100	0	50	52	0	0	48	1.00
5781252--5781301	23	2.2	23	92	0	82	30	28	12	30	1.92
5785987--5786014	2	14.0	2	100	0	56	50	0	0	50	1.00
5794284--5794339	29	2.0	28	86	10	78	50	16	3	30	1.62
5800531--5800611	24	3.4	22	74	19	65	37	20	23	18	1.94
5800640--5800694	26	2.1	26	89	0	83	38	23	20	18	1.93
5801322--5801361	20	2.0	20	85	0	53	37	15	2	45	1.59
5802436--5802487	24	2.2	24	82	0	59	50	3	1	44	1.31
5823949--5824042	37	2.6	36	81	8	109	32	22	1	43	1.60
5823949--5824043	36	2.6	35	80	12	102	32	23	1	43	1.61
5824325--5824358	17	1.9	18	88	5	52	35	23	0	41	1.55
5824732--5824765	4	8.0	4	87	12	50	0	26	0	73	0.83
5824727--5824768	9	4.7	9	85	8	59	0	26	0	73	0.83
5824728--5824765	13	2.9	13	92	0	67	0	26	0	73	0.83
5825077--5825164	31	3.0	28	77	9	88	45	2	0	52	1.13
5825087--5825132	14	2.9	15	84	15	58	47	0	0	52	1.00
5825112--5825150	12	3.4	11	80	13	51	46	2	0	51	1.14
5829608--5829636	14	2.1	14	100	0	58	13	0	6	79	0.93
5832591--5832628	20	1.9	20	88	0	58	21	2	7	68	1.28
5833238--5833270	6	5.5	6	100	0	66	15	0	0	84	0.61
5833378--5833410	17	1.9	17	93	0	57	57	0	3	39	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5835358--5835386	2	14.5	2	100	0	58	48	0	0	51	1.00
5837912--5838153	105	2.3	105	77	5	265	30	20	17	31	1.96
5838532--5838892	104	3.5	103	80	2	359	29	20	16	33	1.94
5842440--5842498	11	5.4	11	78	6	66	23	28	1	45	1.63
5842448--5842498	22	2.3	22	96	0	93	23	29	1	45	1.64
5842487--5842541	29	1.9	28	82	10	67	30	23	1	43	1.64
5842471--5842548	40	2.0	40	82	5	95	26	25	1	46	1.61
5844520--5844576	24	2.4	24	82	5	62	28	31	17	22	1.97
5847556--5847584	7	4.3	7	91	8	51	44	41	0	13	1.44
5858636--5858824	93	2.1	91	83	4	236	18	15	11	55	1.69

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   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120