genome.fa.s12.2.7.7.80.10.50.1000.13.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  13  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)
3805434--3805544	19	5.8	19	86	0	168	36	13	9	40	1.76
3805434--3805537	38	2.7	38	96	0	190	37	12	8	41	1.74
3808906--3808982	39	2.0	39	100	0	154	36	23	20	19	1.95
3810776--3810824	21	2.3	21	89	0	71	26	8	38	26	1.84
3810936--3810975	19	2.2	18	86	4	53	37	0	0	62	0.95
3819277--3819351	34	2.3	32	78	15	82	53	2	1	42	1.23
3826329--3826382	5	10.8	5	91	0	72	42	14	22	20	1.88
3831914--3831944	15	2.1	15	93	0	53	64	19	6	9	1.45
3832862--3832886	2	12.5	2	100	0	50	52	0	0	48	1.00
3834398--3834451	26	2.1	26	100	0	108	37	3	14	44	1.63
3837848--3837929	30	2.8	30	82	8	82	58	6	2	32	1.36
3837878--3837934	25	2.3	25	80	16	66	61	5	1	31	1.28
3837878--3837929	27	2.0	26	88	7	79	59	5	1	32	1.32
3838141--3838187	2	24.0	2	95	4	87	51	0	0	48	1.00
3838267--3838308	3	14.0	3	89	0	66	64	2	2	30	1.19
3838633--3838688	21	2.5	22	77	13	62	42	16	7	33	1.75
3844805--3844839	13	2.7	13	90	0	52	25	0	0	74	0.82
3844845--3844907	26	2.3	27	83	5	74	34	1	1	61	1.15
3846468--3846505	9	4.2	9	93	0	67	28	10	13	47	1.76
3851708--3851787	35	2.3	34	81	8	99	46	0	5	48	1.24
3851729--3851789	24	2.5	23	80	15	61	45	0	4	49	1.23
3852115--3852183	35	2.0	35	85	5	95	46	0	5	47	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3852131--3852191	24	2.5	23	80	15	61	45	0	4	49	1.23
3852246--3852277	2	16.0	2	100	0	64	50	0	0	50	1.00
3853430--3853517	39	2.2	40	79	2	97	36	5	20	37	1.76
3856328--3856406	17	4.6	17	73	16	56	29	26	22	21	1.99
3856325--3856406	34	2.4	34	77	4	94	30	26	21	20	1.98
3856736--3856764	14	2.1	14	100	0	58	34	31	0	34	1.58
3864025--3864067	16	2.6	16	77	3	50	72	4	11	11	1.27
3868693--3868735	22	2.0	22	90	0	68	9	18	27	44	1.80
3868841--3868932	42	2.2	43	86	2	123	22	22	29	25	1.99
3868902--3869046	43	3.4	43	87	3	195	19	19	29	31	1.96
3868926--3869066	43	3.3	41	80	9	140	22	22	27	26	1.99
3869034--3869197	43	3.8	43	82	4	179	29	29	18	21	1.97
3869009--3869173	86	1.9	86	81	4	199	26	29	20	23	1.99
3869545--3869656	21	5.3	21	78	4	100	6	42	16	34	1.73
3869545--3869646	42	2.4	42	79	6	116	5	43	15	35	1.71
3869628--3869774	66	2.2	66	86	4	199	13	28	18	39	1.89
3869667--3869797	66	2.0	66	86	3	183	14	25	19	41	1.89
3875176--3875249	31	2.4	31	84	4	96	39	37	1	21	1.62
3875845--3876150	113	2.7	112	84	7	386	29	25	21	23	1.99
3876080--3876222	73	1.9	75	87	5	211	25	23	25	24	2.00
3875966--3876363	188	2.1	188	80	8	456	26	25	24	23	2.00
3876093--3876256	73	2.3	72	83	7	190	27	23	23	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3897391--3897415	2	12.5	2	100	0	50	48	0	0	52	1.00
3897579--3897630	27	2.0	24	82	10	59	34	7	7	50	1.60
3906180--3906215	17	2.1	17	89	0	54	63	2	8	25	1.36
3906477--3906553	29	2.5	31	83	4	95	49	12	11	25	1.75
3924879--3924944	31	2.2	31	86	2	89	45	4	6	43	1.49
3926047--3926084	17	2.2	17	95	0	67	36	10	28	23	1.88
3928550--3928591	6	6.8	6	86	2	57	45	16	21	16	1.86
3928569--3928678	45	2.4	45	89	3	168	45	20	14	20	1.85
3933070--3933150	21	3.9	21	78	0	81	46	14	20	17	1.83
3936226--3936379	56	2.7	56	84	4	175	50	12	12	24	1.74
3936273--3936375	31	3.5	30	70	16	99	53	9	10	26	1.66
3936246--3936379	56	2.4	57	87	5	191	52	11	10	24	1.69
3936552--3936617	31	2.1	31	82	0	78	39	13	12	34	1.82
3938195--3938244	25	2.0	25	88	0	73	22	4	36	38	1.73
3941591--3941644	25	2.0	28	82	10	69	48	1	1	48	1.23
3946468--3946498	16	1.9	16	100	0	62	0	38	16	45	1.47
3953484--3953548	30	2.2	30	86	5	87	46	9	13	30	1.75
3954719--3954751	16	2.1	16	94	0	57	39	6	9	45	1.61
3954972--3954998	3	9.0	3	100	0	54	66	0	0	33	0.92
3957757--3957818	22	2.7	22	90	5	88	48	1	1	48	1.21
3957792--3957848	16	3.6	16	90	0	87	47	3	3	45	1.37
3957902--3957958	28	2.1	27	86	3	78	40	3	7	49	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3957898--3958055	83	2.0	82	85	12	220	39	4	8	48	1.53
3958102--3958148	22	2.1	22	84	7	60	57	4	2	36	1.30
3965366--3965979	49	12.5	49	69	4	351	33	22	20	22	1.97
3965366--3966063	98	7.1	98	87	1	912	33	22	20	23	1.97
3965366--3966040	197	3.4	197	90	0	965	33	22	20	23	1.97
3966091--3966289	44	4.6	43	78	7	206	28	21	25	25	1.99
3967106--3967153	3	15.7	3	95	4	87	31	2	0	66	1.03
3967331--3967359	3	9.7	3	100	0	58	31	0	0	68	0.89
3969074--3969127	26	2.1	26	96	0	99	31	7	1	59	1.36
3969085--3969130	14	3.4	14	76	11	60	30	6	0	63	1.20
3972620--3972704	26	3.5	25	77	15	97	54	4	2	38	1.34
3982367--3982391	10	2.5	10	100	0	50	60	20	8	12	1.57
3985516--3985564	25	2.0	25	100	0	98	38	8	4	48	1.52
3985970--3985995	5	5.2	5	100	0	52	38	0	0	61	0.96
3986172--3986196	12	2.1	12	100	0	50	24	36	24	16	1.94
3986357--3986424	9	7.4	9	83	3	82	41	26	10	22	1.85
3989621--3989684	21	3.0	21	97	0	119	28	28	6	37	1.81
3991746--3991816	30	2.4	30	83	9	83	45	2	7	45	1.45
4002021--4002171	75	2.0	76	94	1	268	34	15	25	24	1.94
4003336--4003454	33	3.6	33	68	6	89	30	18	25	26	1.98
4008870--4008930	31	2.0	31	90	0	95	42	16	9	31	1.81
4010730--4010771	21	2.0	21	90	9	68	4	0	42	52	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4010731--4010786	14	4.0	14	76	15	53	5	0	39	55	1.23
4010731--4010772	7	6.0	7	83	10	59	2	0	42	54	1.13
4010813--4011117	96	3.2	95	85	5	416	38	2	19	40	1.66
4011145--4011444	126	2.4	126	93	0	501	32	19	22	26	1.97
4016090--4016132	11	3.9	11	93	0	68	27	32	0	39	1.57
4017283--4017315	7	4.7	7	100	0	66	27	0	15	57	1.38
4018898--4019097	33	5.5	33	70	20	139	20	18	28	33	1.96
4018819--4019097	75	3.7	75	93	0	468	21	18	27	32	1.97
4024269--4024334	17	3.7	17	74	18	71	63	1	3	31	1.19
4024269--4024342	17	4.2	17	73	19	62	64	1	2	31	1.15
4024317--4024422	50	2.1	52	84	5	137	57	5	7	29	1.49
4026042--4026332	126	2.3	125	90	1	465	27	19	18	34	1.95
4026419--4026582	48	3.4	47	64	14	111	38	18	1	41	1.61
4026369--4026608	96	2.5	96	89	4	358	38	19	1	40	1.61
4026687--4026717	16	1.9	16	93	0	53	54	29	0	16	1.42
4031115--4031147	15	2.1	16	88	5	50	33	0	0	66	0.92
4035317--4035364	24	2.0	24	83	0	60	62	0	8	29	1.24
4035894--4035924	16	1.9	16	100	0	62	0	38	16	45	1.47
4040907--4040952	21	2.2	21	88	3	67	36	6	0	56	1.25
4042851--4042894	24	1.9	22	81	9	52	38	9	13	38	1.77
4043038--4043078	2	21.5	2	90	9	68	48	0	0	51	1.00
4047116--4047144	2	15.0	2	92	7	51	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4049294--4049367	22	3.4	22	88	0	103	28	28	14	28	1.96
4054403--4054464	31	2.0	31	93	0	106	25	8	16	50	1.72
4058727--4058761	15	2.3	15	90	0	52	48	2	8	40	1.49
4062495--4062548	19	2.9	18	81	10	56	42	0	9	48	1.35
4062495--4062534	18	2.4	17	84	12	55	47	0	7	45	1.31
4062508--4062548	20	2.1	20	86	4	57	36	0	9	53	1.34
4070019--4070048	15	2.0	15	93	0	51	30	0	0	70	0.88
4072801--4072854	21	2.4	24	79	14	62	62	3	5	27	1.34
4074171--4074196	3	8.7	3	100	0	52	34	0	0	65	0.93
4081858--4082360	150	3.3	152	85	6	678	29	11	7	51	1.64

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