genome.fa.s12.2.7.7.80.10.50.1000.16.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  16  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)
4791672--4791857	22	9.0	21	72	20	133	55	12	0	32	1.37
4791672--4791857	41	4.5	41	73	17	170	55	12	0	32	1.37
4791677--4791858	83	2.2	84	77	13	198	55	12	0	32	1.37
4792028--4792061	3	11.3	3	93	0	59	0	35	0	64	0.94
4792248--4792275	14	2.0	14	100	0	56	21	57	21	0	1.41
4793759--4793827	34	2.1	34	83	8	88	40	18	4	36	1.71
4798140--4798176	10	3.8	10	89	7	58	37	0	0	62	0.96
4798142--4798188	9	5.2	9	80	10	51	40	0	0	59	0.97
4801788--4801830	21	2.0	21	100	0	86	30	18	0	51	1.47
4804182--4804237	29	1.9	29	82	7	69	30	16	16	37	1.90
4805094--4805199	42	2.5	42	92	0	167	20	31	28	19	1.97
4805207--4805266	29	2.1	28	84	6	77	45	18	13	23	1.84
4830423--4830475	25	2.1	25	89	0	79	37	13	9	39	1.77
4830652--4830697	23	2.0	23	87	8	67	32	21	28	17	1.96
4835562--4835591	11	2.7	11	89	0	51	63	6	0	30	1.20
4835575--4835615	19	2.1	20	86	4	57	65	4	7	21	1.37
4839052--4839095	5	8.4	5	82	7	52	70	2	4	22	1.17
4839473--4839498	12	2.2	12	100	0	52	38	0	15	46	1.46
4846465--4846515	20	2.7	20	87	6	70	37	5	13	43	1.69
4846903--4846935	13	2.6	13	90	4	50	0	12	3	84	0.72
4847214--4847258	3	14.7	3	81	4	54	0	24	0	75	0.80
4847217--4847276	12	4.8	12	80	11	66	0	25	0	75	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4847209--4847276	33	2.2	33	89	7	106	0	23	0	76	0.79
4847359--4847392	16	2.1	17	94	5	61	0	32	0	67	0.91
4847610--4847769	29	5.4	29	81	4	169	46	3	17	32	1.66
4848970--4849035	18	3.4	18	71	19	53	62	1	6	30	1.29
4852253--4852319	34	1.9	35	90	3	109	34	8	10	46	1.70
4852477--4852527	26	2.2	24	78	21	56	60	5	0	33	1.21
4858222--4858259	16	2.4	16	86	4	51	60	2	2	34	1.24
4859949--4859988	20	2.0	20	85	9	55	35	2	5	57	1.34
4871795--4871849	23	2.4	23	84	6	76	14	14	16	54	1.71
4879356--4879441	31	2.9	30	80	10	81	36	8	17	38	1.79
4881174--4881202	2	14.5	2	100	0	58	48	0	0	51	1.00
4883664--4883703	15	2.7	15	84	0	53	30	45	2	22	1.66
4883634--4883717	6	14.0	6	80	5	62	28	41	1	28	1.64
4883634--4883717	9	9.3	9	75	5	62	28	41	1	28	1.64
4898543--4898746	44	4.5	44	83	10	266	30	15	24	29	1.95
4898546--4898750	95	2.2	95	90	1	331	31	14	23	29	1.95
4899955--4900026	30	2.4	31	84	11	103	29	18	13	38	1.89
4900838--4900867	7	4.3	7	95	0	51	43	40	0	16	1.48
4911016--4911063	23	2.1	22	88	3	69	33	2	0	64	1.05
4913955--4913996	2	21.0	2	100	0	84	50	0	0	50	1.00
4926274--4926319	2	23.0	2	91	8	76	47	2	0	50	1.13
4933667--4933798	62	2.1	62	98	0	255	40	12	9	36	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4955061--4955094	11	2.8	12	91	8	52	35	8	11	44	1.72
4956009--4956052	22	1.9	24	86	9	65	43	2	13	40	1.57
4956141--4956429	97	3.0	97	98	0	551	42	13	11	31	1.81
4958092--4958171	27	3.0	27	79	0	97	25	22	27	25	2.00
4958471--4958508	20	1.9	20	88	0	58	36	7	10	44	1.68
4963454--4963553	34	3.2	33	67	26	90	51	12	0	37	1.39
4963446--4963564	60	2.0	60	94	0	211	53	11	0	34	1.37
4963460--4963585	60	2.1	59	86	4	155	55	11	0	32	1.41
4963815--4963885	27	2.6	27	77	0	70	19	28	25	26	1.99
4964657--4964702	3	15.3	3	100	0	92	65	0	34	0	0.93
4992674--4992816	60	2.4	59	88	2	196	47	14	15	22	1.82
4995142--4995166	13	1.9	13	100	0	50	64	4	8	24	1.38
5005701--5005727	5	5.4	5	100	0	54	77	0	22	0	0.76
5006021--5006059	19	2.0	19	85	5	51	0	38	0	61	0.96
5011874--5012003	57	2.3	56	79	15	133	35	16	10	38	1.82
5012663--5012709	4	10.8	4	86	8	58	72	4	2	21	1.12
5012663--5012709	24	2.1	24	85	14	66	72	4	2	21	1.12
5032331--5032528	97	2.1	97	97	0	371	36	18	16	29	1.92
5034171--5034240	28	2.5	27	83	4	86	24	21	15	38	1.92
5034322--5034389	22	3.0	22	79	8	82	27	29	19	23	1.98
5034322--5034385	24	2.8	22	79	9	74	29	28	20	21	1.98
5059781--5059814	2	17.0	2	100	0	68	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5062296--5062346	23	2.1	25	82	7	61	52	3	1	41	1.31
5063487--5063544	30	1.9	30	85	0	80	44	18	6	29	1.76
5064719--5064759	22	1.9	21	90	5	64	65	4	0	29	1.13
5075232--5075257	2	13.0	2	100	0	52	50	0	50	0	1.00
5092277--5092419	71	2.0	69	93	2	241	33	18	6	40	1.78
5095792--5095946	26	6.2	25	67	12	79	34	22	23	18	1.96
5095757--5095894	73	1.9	73	80	5	163	34	21	23	20	1.97
5095873--5095947	26	2.9	27	82	7	84	38	22	21	17	1.93
5096952--5096979	13	2.2	13	100	0	56	21	14	0	64	1.29
5114489--5114533	24	1.9	24	86	4	65	42	4	4	48	1.43
5120732--5120891	33	4.8	32	69	19	87	30	26	22	20	1.98
5122149--5122230	28	2.9	28	78	7	103	31	17	14	36	1.90
5122151--5122330	56	3.2	56	77	4	166	35	19	12	33	1.89
5122183--5122332	28	5.4	28	71	3	113	36	19	11	33	1.87
5122182--5122335	84	1.8	84	82	0	200	35	18	11	33	1.87
5126822--5126850	14	2.1	14	93	6	51	79	6	0	13	0.93
5136693--5136757	24	2.6	24	81	13	69	69	3	1	26	1.12
5137149--5137219	35	2.0	35	100	0	142	38	19	16	25	1.93
5142678--5142738	27	2.2	28	82	5	72	40	3	3	52	1.34
5143613--5143650	20	1.9	20	89	10	60	39	2	0	57	1.12
5143646--5143699	17	3.2	17	73	19	51	35	5	1	57	1.33
5144200--5144236	15	2.3	17	86	9	51	37	8	0	54	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5144437--5144488	24	2.1	24	85	3	68	26	3	3	65	1.27
5144539--5144582	20	2.1	21	84	12	56	18	6	11	63	1.48
5146599--5146626	8	3.5	8	100	0	56	60	0	0	39	0.97
5148701--5148746	24	1.9	24	82	8	58	43	10	17	28	1.82
5151621--5151715	32	2.9	32	75	12	88	34	0	8	56	1.29
5153474--5153522	26	1.9	25	91	4	80	20	26	20	32	1.97
5159268--5159298	5	6.4	5	92	7	55	0	19	0	80	0.71
5159253--5159298	19	2.4	19	85	7	58	2	17	4	76	1.06
5159253--5159297	14	3.2	14	87	0	63	2	17	4	75	1.07
5160110--5160181	34	2.1	34	100	0	144	25	18	8	48	1.75
5169976--5170032	6	9.5	6	76	12	55	78	0	17	3	0.88
5174511--5174569	32	1.9	31	86	6	84	30	0	6	62	1.21
5186670--5186713	23	2.0	21	86	8	61	47	2	11	38	1.52
5188106--5188146	21	2.0	21	90	9	66	51	2	4	41	1.36
5191490--5191533	22	2.0	22	100	0	88	54	13	9	22	1.67
5195728--5195868	44	3.2	43	83	3	165	31	6	23	38	1.80
5196081--5196113	2	16.5	2	93	0	57	45	3	0	51	1.16
5199813--5199843	8	3.9	8	91	0	53	41	0	0	58	0.98
5199812--5199846	16	2.2	16	100	0	70	45	0	0	54	0.99
5201294--5201352	25	2.3	27	80	16	72	45	3	23	27	1.68
5213030--5214076	421	2.5	419	90	3	1624	32	17	14	34	1.91
5216457--5216495	3	13.0	3	88	0	60	61	0	38	0	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5216457--5216495	12	3.2	12	96	0	69	61	0	38	0	0.96
5229069--5229144	9	8.4	9	79	5	82	39	23	10	26	1.87
5229069--5229144	27	2.8	27	87	0	107	39	23	10	26	1.87
5229294--5229333	18	2.2	18	86	0	53	15	5	40	40	1.68
5231244--5231296	24	2.2	24	82	0	61	60	0	15	24	1.35
5238820--5238875	29	1.9	28	82	13	69	39	1	19	39	1.62
5241187--5241325	46	3.0	46	96	0	251	35	8	26	28	1.86
5249639--5249668	2	15.0	2	100	0	60	50	0	0	50	1.00
5257964--5258106	24	6.0	24	93	0	223	20	29	30	19	1.97
5265882--5265914	14	2.4	14	94	0	57	51	15	15	18	1.77

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