genome.fa.s3.2.7.7.80.10.50.1000.98.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  98  of  150  ( 17918 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)
30799528--30799571	20	2.3	19	84	4	52	22	2	9	65	1.32
30804172--30804229	24	2.3	26	85	8	75	56	34	3	5	1.38
30805407--30805435	4	7.2	4	100	0	58	24	0	0	75	0.80
30807331--30807374	22	2.0	22	100	0	88	45	13	18	22	1.84
30813030--30813092	20	3.3	18	80	14	56	55	4	1	38	1.31
30813030--30813092	19	3.3	19	80	10	58	55	4	1	38	1.31
30820728--30820934	106	2.0	106	95	0	369	35	16	15	32	1.91
30847441--30847465	5	5.0	5	100	0	50	60	0	0	40	0.97
30849555--30849623	29	2.4	29	87	0	102	39	30	7	23	1.82
30853975--30854012	16	2.4	16	90	0	58	68	13	0	18	1.21
30854736--30854785	24	2.1	24	96	0	91	44	14	10	32	1.78
30855727--30855761	18	1.9	18	94	0	61	65	0	20	14	1.26
30855926--30855974	26	1.9	25	83	4	62	44	6	10	38	1.63
30856362--30856435	35	2.1	35	94	0	130	31	6	12	50	1.66
30857724--30857780	29	2.0	29	82	0	69	17	29	14	38	1.89
30857717--30857867	58	2.6	58	86	4	180	19	25	13	41	1.88
30857743--30857870	29	4.4	29	93	2	204	20	25	13	41	1.88
30869874--30869907	2	17.0	2	93	0	59	0	47	0	52	1.00
30875213--30875314	49	2.2	48	80	7	120	31	15	6	46	1.72
30878481--30878512	15	2.1	15	100	0	64	40	6	21	31	1.78
30880423--30880469	14	3.4	14	80	16	62	23	4	2	70	1.16
30884252--30884301	21	2.4	21	80	6	57	28	16	8	48	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30887163--30887248	33	2.6	33	98	0	163	31	23	25	19	1.98
30890237--30890373	69	2.0	69	92	2	231	28	10	21	38	1.88
30903606--30903647	21	2.0	21	90	4	68	47	0	2	50	1.14
30907798--30907858	21	2.8	22	80	9	72	54	1	1	42	1.20
30909230--30909277	21	2.2	22	88	3	71	20	14	8	56	1.64
30909433--30909483	17	2.8	18	76	11	50	33	0	5	60	1.21
30909424--30909478	19	2.8	19	76	10	58	34	0	3	61	1.13
30915952--30916007	29	1.9	29	85	7	78	51	3	5	39	1.42
30919301--30919371	6	11.8	6	74	16	51	4	18	1	76	1.03
30919302--30919371	27	2.6	27	78	14	74	4	18	1	75	1.04
30921201--30921444	50	4.9	50	88	4	339	22	30	20	26	1.98
30924158--30924193	16	2.2	17	90	5	56	25	13	0	61	1.33
30940772--30940802	15	2.1	15	93	0	53	32	22	12	32	1.92
30941990--30942032	21	2.0	22	86	13	63	32	18	0	48	1.48
30945308--30945367	30	2.0	31	83	9	79	41	0	38	20	1.52
30945472--30945532	30	2.0	31	90	3	97	36	0	44	19	1.51
30951013--30951063	22	2.3	22	93	0	84	31	29	0	39	1.57
30952239--30952263	7	3.6	7	100	0	50	28	0	12	60	1.32
30952622--30952660	19	2.0	21	85	10	55	28	20	20	30	1.98
30953208--30953257	21	2.4	21	80	6	57	36	34	28	2	1.69
30953360--30953540	44	4.0	43	73	14	152	43	0	12	43	1.47
30953425--30953560	25	5.7	25	74	15	137	44	0	13	41	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30953382--30953560	94	1.9	93	93	2	306	43	0	13	42	1.48
30953576--30953825	29	9.4	29	73	21	210	45	26	0	27	1.57
30953576--30953898	52	6.3	51	75	15	279	46	26	0	27	1.56
30953556--30953903	23	14.0	23	72	21	240	45	25	0	27	1.58
30953900--30954137	116	2.1	116	95	0	431	37	9	9	43	1.70
30954113--30954154	17	2.4	18	80	4	50	42	9	2	45	1.49
30957128--30957479	126	2.8	125	91	0	562	32	22	15	28	1.95
30957613--30957658	21	2.2	21	100	0	92	32	32	6	28	1.83
30958678--30958782	41	2.6	41	93	0	183	22	28	20	27	1.99
30958673--30958859	41	4.6	41	87	6	172	24	27	19	28	1.98
30959071--30959128	25	2.4	25	97	2	109	43	25	3	27	1.71
30959387--30959414	2	14.0	2	100	0	56	50	0	0	50	1.00
30972177--30972613	69	6.4	69	80	4	445	18	22	22	36	1.95
30972128--30972613	69	7.1	69	79	4	419	18	22	23	36	1.95
30972177--30972613	205	2.1	207	83	3	542	18	22	22	36	1.95
30981950--30982045	31	3.1	31	95	3	174	31	9	13	45	1.75
30984608--30985256	44	14.1	44	67	17	250	32	19	21	26	1.97
30984570--30985307	142	5.3	142	89	3	1074	32	19	21	27	1.97
30984652--30984842	98	1.9	97	82	6	233	33	19	20	25	1.97
30984797--30984984	98	1.9	97	79	6	209	33	18	20	27	1.96
30985051--30985330	129	2.2	129	93	0	479	28	20	21	30	1.98
30985098--30985299	44	4.7	45	70	10	125	30	17	22	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30992663--30992698	18	2.1	18	89	5	56	47	0	5	47	1.25
30998245--30998498	90	2.8	90	77	3	269	29	8	11	50	1.67
31002589--31002639	22	2.3	22	87	12	86	27	31	1	39	1.68
31002613--31002712	51	2.0	51	97	0	191	30	28	0	42	1.56
31002738--31002788	10	5.1	10	78	0	57	31	0	0	68	0.90
31002724--31002788	30	2.2	30	97	0	121	35	0	1	63	1.04
31004972--31005041	25	2.7	25	86	4	95	47	2	10	40	1.52
31005033--31005216	18	10.3	18	79	14	220	49	21	0	28	1.54
31005212--31005375	56	3.0	55	78	12	199	37	10	6	44	1.66
31005359--31005383	10	2.5	10	100	0	50	44	8	0	48	1.32
31008444--31008786	123	2.8	124	93	1	582	32	21	16	29	1.95
31011790--31011872	27	3.0	27	70	19	71	37	8	1	53	1.39
31011926--31012257	64	5.4	63	78	14	367	35	8	0	55	1.37
31011769--31012216	176	2.5	174	89	5	670	35	8	1	54	1.40
31017800--31017825	9	2.9	9	100	0	52	11	0	0	88	0.52
31018574--31018601	13	2.2	13	100	0	56	42	14	14	28	1.84
31022285--31022315	16	2.0	15	93	6	53	16	0	12	70	1.16
31025315--31025390	21	3.7	21	87	3	102	36	9	15	38	1.80
31025315--31025396	40	2.1	39	81	9	94	37	8	15	37	1.79
31025315--31025416	21	4.8	23	84	8	87	37	7	15	39	1.77
31025379--31025423	22	2.0	23	86	4	65	35	4	13	46	1.63
31025367--31025426	23	2.7	23	82	7	70	38	3	15	43	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31025599--31025643	23	2.0	23	81	0	54	22	0	15	62	1.33
31025869--31025904	16	2.3	16	90	4	56	27	0	0	72	0.85
31025941--31026000	23	2.7	23	84	5	70	28	3	8	60	1.42
31037410--31037460	20	2.6	19	79	14	50	23	29	7	39	1.83
31037565--31037655	33	2.8	33	82	0	119	17	34	24	24	1.96
31039039--31039105	29	2.3	29	84	0	80	31	11	22	34	1.90
31043196--31043270	36	2.1	36	100	0	150	30	9	25	34	1.87
31043873--31043910	20	1.9	20	94	0	67	21	18	13	47	1.82
31046674--31046867	39	4.9	39	85	4	239	46	19	2	31	1.63
31047306--31047411	33	3.2	33	69	21	96	40	25	5	28	1.78
31051833--31051874	20	2.2	20	86	4	59	45	11	21	21	1.84
31056783--31056857	23	3.3	23	90	0	114	33	28	21	17	1.96
31057505--31057554	2	24.5	2	95	4	91	48	0	2	50	1.12
31067406--31067450	9	4.7	10	78	15	51	62	0	0	37	0.96
31068257--31068360	49	2.1	49	87	1	147	28	8	10	51	1.66
31070112--31070144	11	2.8	12	86	4	50	48	12	3	36	1.56
31071231--31071262	14	2.3	14	94	0	55	56	0	3	40	1.15
31071617--31071657	14	2.9	14	85	7	55	58	2	0	39	1.11
31071653--31071716	19	3.4	19	68	0	65	51	3	3	42	1.33
31071640--31071713	38	1.9	38	100	0	148	52	2	2	41	1.29
31072054--31072109	28	2.0	28	100	0	112	28	0	0	71	0.86
31072095--31072177	11	7.9	11	74	17	79	40	2	0	56	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31072061--31072120	28	2.1	28	84	0	75	33	1	0	65	1.03
31072067--31072171	40	2.6	39	89	4	156	35	1	0	62	1.06
31072106--31072164	29	2.0	30	87	9	86	37	3	0	59	1.14
31072101--31072202	22	4.8	22	68	14	63	42	1	1	53	1.23
31075999--31076070	36	2.0	36	88	0	108	27	12	27	31	1.93
31081946--31082038	44	2.1	44	91	4	150	35	31	5	27	1.80
31082020--31082056	16	2.3	16	90	0	65	21	32	5	40	1.76
31086197--31086259	31	2.0	31	96	0	117	58	11	12	17	1.62
31094222--31094783	89	6.4	87	69	15	218	27	23	19	29	1.98
31094225--31094605	129	2.9	129	86	2	494	27	23	19	28	1.99

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