genome.fa.s6.2.7.7.80.10.50.1000.159.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  159  of  168  ( 20060 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)
47568171--47568225	21	2.7	21	85	2	67	63	1	1	32	1.15
47568192--47568248	21	2.6	21	86	8	69	68	3	3	24	1.21
47571159--47571192	18	1.9	17	94	5	59	0	29	11	58	1.33
47573184--47573510	95	3.4	94	89	6	444	33	22	14	29	1.94
47575466--47575517	18	2.7	19	73	11	52	59	1	3	34	1.27
47586393--47586469	39	2.0	39	89	0	118	29	16	18	35	1.93
47594567--47594606	2	20.0	2	100	0	80	50	0	0	50	1.00
47599378--47599553	87	2.0	87	80	2	192	36	22	8	32	1.84
47599552--47599601	18	2.7	19	78	6	57	54	0	4	42	1.19
47599566--47599618	19	2.7	20	80	11	65	60	0	1	37	1.08
47599610--47599652	17	2.4	17	84	7	50	60	0	2	37	1.10
47599778--47599803	10	2.6	10	100	0	52	88	0	0	11	0.52
47599910--47599990	19	4.3	19	73	14	60	35	3	1	59	1.23
47599977--47600009	16	2.1	16	100	0	66	42	6	0	51	1.26
47600530--47600575	24	2.0	24	83	12	60	36	4	19	39	1.72
47601895--47601933	2	19.5	2	100	0	78	51	0	0	48	1.00
47603164--47603202	19	2.1	19	85	9	53	51	0	0	48	1.00
47603253--47603277	2	12.5	2	100	0	50	52	0	0	48	1.00
47605550--47605586	18	2.0	19	89	5	58	21	2	48	27	1.63
47607173--47607200	3	9.3	3	100	0	56	32	0	0	67	0.91
47611113--47611159	17	2.8	17	87	6	60	25	4	6	63	1.36
47616356--47616392	18	2.1	17	90	5	56	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47619215--47619352	31	4.6	31	67	14	92	40	12	5	42	1.64
47620820--47620854	17	2.1	17	94	0	61	45	0	0	54	0.99
47620932--47621018	38	2.3	39	84	8	115	51	4	0	43	1.22
47621566--47621594	14	2.1	14	100	0	58	65	13	6	13	1.45
47621621--47621669	11	4.5	11	89	0	80	67	24	0	8	1.18
47628363--47628411	25	2.0	24	84	11	64	40	2	20	36	1.64
47631083--47631124	15	2.8	15	85	0	57	52	19	0	28	1.46
47636539--47636571	6	5.5	6	96	0	57	12	15	54	18	1.71
47638059--47638083	7	3.6	7	100	0	50	88	0	0	12	0.53
47638686--47638752	34	1.9	35	85	8	93	11	4	4	79	1.03
47639464--47639527	32	2.0	32	90	0	101	37	10	9	42	1.73
47640173--47640210	20	1.9	20	88	0	58	13	23	26	36	1.91
47648557--47648599	22	2.0	22	100	0	86	37	13	25	23	1.92
47654733--47654788	20	2.8	20	75	2	60	39	39	7	14	1.73
47654698--47654769	26	2.7	27	79	12	85	40	37	6	15	1.74
47659078--47659116	3	13.0	3	100	0	78	66	0	0	33	0.92
47659034--47659095	29	2.1	29	82	5	72	54	6	12	25	1.62
47669806--47669859	16	3.4	16	86	0	63	42	5	20	31	1.75
47670036--47670159	58	2.1	58	88	2	178	53	3	0	43	1.17
47672219--47672350	36	3.6	36	83	6	156	6	27	12	53	1.62
47673364--47673505	69	2.0	69	85	8	189	24	8	25	41	1.83
47674625--47674708	37	2.3	36	83	8	107	41	13	11	33	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47674789--47674830	18	2.3	18	100	0	84	50	26	0	23	1.50
47674807--47674883	33	2.3	33	100	0	154	42	18	5	33	1.72
47674760--47674863	51	2.0	51	96	0	190	45	19	3	31	1.68
47677953--47678162	92	2.3	91	85	4	271	45	3	4	46	1.41
47678215--47678545	66	5.4	63	67	22	238	41	3	6	48	1.44
47678177--47678589	120	3.4	120	96	2	733	42	2	5	49	1.39
47678302--47678353	15	3.6	15	80	12	56	44	0	1	53	1.11
47678422--47678473	15	3.6	15	80	12	56	44	0	1	53	1.11
47678551--47678592	15	2.7	16	82	14	52	45	0	2	52	1.13
47678542--47678583	15	2.9	15	82	10	52	47	0	0	52	1.00
47678695--47678729	18	2.0	17	88	5	52	45	0	0	54	0.99
47678526--47678842	157	2.0	157	95	0	562	47	5	3	43	1.41
47678967--47679001	16	2.2	16	100	0	70	40	37	0	22	1.55
47680163--47680210	24	2.0	25	84	12	64	62	4	16	16	1.48
47680309--47680369	23	2.4	25	86	10	81	42	8	27	21	1.81
47680327--47680375	23	2.1	23	88	0	71	44	6	30	18	1.74
47684110--47684173	2	32.0	2	100	0	128	50	0	0	50	1.00
47693761--47693804	2	22.5	2	95	4	81	50	0	0	50	1.00
47704044--47704084	21	2.0	21	85	9	57	36	9	7	46	1.65
47707093--47707123	14	2.2	14	94	0	53	38	0	12	48	1.42
47711583--47711618	2	18.0	2	100	0	72	50	0	0	50	1.00
47712638--47712693	26	2.2	26	83	6	69	62	3	1	32	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47717645--47717725	31	2.6	31	86	3	110	39	6	4	49	1.49
47722890--47722944	23	2.4	23	84	0	74	23	16	20	40	1.91
47724021--47724059	18	2.2	17	86	13	53	33	0	20	46	1.51
47725839--47725886	21	2.3	21	86	10	71	35	12	0	52	1.40
47725960--47726041	38	2.2	38	100	0	164	35	13	4	46	1.65
47729048--47729089	22	1.9	22	85	9	59	38	2	4	54	1.34
47732390--47732437	2	24.5	2	95	4	89	50	50	0	0	1.00
47734624--47734723	42	2.4	42	91	0	155	27	28	10	35	1.89
47735598--47735631	17	2.1	17	88	5	52	32	17	0	50	1.47
47738785--47738893	44	2.5	44	92	1	193	30	14	22	32	1.94
47744847--47744936	45	2.0	45	100	0	180	22	22	6	48	1.73
47754439--47754495	20	2.9	19	84	10	71	40	0	7	52	1.28
47754445--47754511	19	3.4	18	83	8	71	35	1	7	55	1.37
47754445--47754511	20	3.4	19	85	8	73	35	1	7	55	1.37
47756280--47756304	13	1.9	13	100	0	50	24	12	16	48	1.79
47759697--47759830	57	2.3	58	80	6	155	43	15	19	21	1.88
47760904--47760939	7	5.4	7	90	9	58	88	0	11	0	0.50
47766135--47766193	9	6.4	9	81	11	66	22	10	25	42	1.84
47766141--47766196	19	2.9	19	74	15	62	19	8	25	46	1.79
47767612--47767661	2	25.0	2	100	0	100	50	0	0	50	1.00
47779328--47779361	16	2.2	15	89	5	50	64	8	11	14	1.49
47781554--47781593	14	2.6	16	84	11	57	62	2	0	35	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47782129--47782167	19	2.1	19	85	4	53	17	5	12	64	1.46
47782309--47782343	16	2.1	17	89	5	54	40	0	0	60	0.97
47782508--47782538	16	1.9	16	100	0	62	58	0	6	35	1.24
47782559--47782603	23	2.0	23	86	0	63	66	2	0	31	1.04
47794800--47794855	22	2.5	23	82	2	69	51	1	1	44	1.22
47794831--47794870	16	2.5	16	91	0	62	47	2	7	42	1.45
47794880--47795059	68	2.9	61	89	8	265	40	5	9	45	1.58
47794943--47794970	9	3.1	9	100	0	56	32	0	10	57	1.33
47794859--47795029	68	2.5	68	97	1	319	39	4	8	47	1.54
47797652--47797683	10	3.1	10	95	4	55	25	0	0	75	0.81
47798175--47798212	19	2.0	19	89	0	58	50	7	5	36	1.54
47798311--47798382	27	2.7	27	93	0	117	52	12	0	34	1.39
47798422--47798591	27	7.0	24	73	23	144	32	1	13	52	1.48
47798425--47798596	49	3.6	49	85	6	244	31	1	13	54	1.47
47798558--47798609	21	2.3	23	75	24	58	30	0	9	59	1.29
47798633--47798676	11	4.3	11	80	16	58	38	2	6	52	1.41
47798639--47798676	19	2.0	19	94	0	67	36	2	7	52	1.45
47798896--47798972	27	2.9	28	90	3	115	19	38	24	16	1.92
47802183--47802267	41	2.1	41	97	0	161	50	7	16	25	1.70
47806577--47806625	22	2.3	21	82	10	64	42	12	0	44	1.41
47807064--47807094	14	2.2	14	94	0	53	29	9	0	61	1.28
47809118--47809153	16	2.2	16	90	0	54	41	2	5	50	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47817906--47817955	23	2.2	23	82	7	57	56	16	4	24	1.57
47822234--47822304	3	23.7	3	100	0	142	67	0	0	32	0.91
47822672--47822697	3	8.7	3	100	0	52	69	30	0	0	0.89
47824833--47824931	49	2.0	49	98	0	189	33	32	10	24	1.88
47827886--47828144	128	2.0	128	97	0	491	32	18	11	37	1.87
47836126--47836172	24	2.0	24	86	0	67	34	4	17	44	1.68
47836282--47836348	31	2.2	30	97	2	125	53	7	10	28	1.62
47837646--47837677	16	2.0	16	93	0	55	31	21	12	34	1.91
47838491--47838545	2	28.5	2	85	14	80	47	0	1	50	1.11
47839278--47839346	30	2.3	30	76	2	75	52	8	1	37	1.42

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   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168