genome.fa.s3.2.7.7.80.10.50.1000.17.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  17  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)
4612527--4612598	28	2.7	25	74	17	65	36	2	2	58	1.27
4613137--4613581	126	3.6	125	89	2	662	30	15	23	29	1.96
4614687--4614831	45	3.2	45	84	1	166	43	18	17	20	1.88
4617644--4617681	20	1.9	20	89	10	60	55	5	2	36	1.37
4618615--4618714	51	2.0	51	90	4	157	46	3	25	26	1.67
4618674--4618750	11	7.1	10	76	13	57	48	1	25	24	1.59
4618674--4618748	33	2.2	34	83	9	100	46	1	26	25	1.61
4618695--4618748	22	2.4	23	87	6	83	46	1	27	24	1.63
4622367--4622444	39	2.0	39	100	0	156	43	2	23	30	1.67
4625346--4625410	31	2.1	31	85	8	87	55	10	10	23	1.65
4625417--4625481	30	2.2	30	100	0	130	30	20	10	38	1.86
4626697--4627355	309	2.1	302	79	7	722	35	15	10	37	1.82
4627356--4627397	2	21.0	2	95	0	75	47	0	0	52	1.00
4628491--4628531	21	2.0	21	90	0	64	48	21	12	17	1.79
4638389--4638428	18	2.2	18	86	0	53	42	2	20	35	1.65
4642751--4642847	46	2.1	46	92	0	158	41	11	19	27	1.86
4644369--4644412	21	2.1	21	83	8	54	31	2	4	61	1.28
4644728--4644765	3	12.7	3	100	0	76	68	0	0	31	0.90
4646151--4646216	25	2.4	27	80	14	73	18	4	4	72	1.19
4658432--4658502	28	2.8	23	75	19	61	40	1	2	54	1.23
4658476--4658509	10	3.5	10	92	4	52	41	0	0	58	0.98
4659633--4659692	25	2.6	24	78	17	65	40	0	21	38	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4659638--4659718	19	4.3	19	75	18	71	39	1	20	38	1.61
4660055--4660154	45	2.2	45	82	7	123	23	16	18	43	1.88
4667007--4667084	21	3.7	21	82	0	93	50	15	17	16	1.79
4667007--4667089	42	2.0	42	83	4	105	49	14	19	16	1.80
4669108--4669161	3	18.0	3	81	14	67	31	1	1	64	1.14
4669106--4669164	8	6.8	8	81	14	64	32	1	1	64	1.13
4669086--4669182	45	2.2	43	77	14	99	27	7	1	63	1.27
4669209--4669248	3	13.3	3	100	0	80	32	0	0	67	0.91
4670841--4670898	6	8.8	6	77	20	55	18	3	1	75	1.03
4677060--4677099	16	2.5	16	88	8	55	37	0	2	60	1.11
4685765--4685798	17	2.0	17	100	0	68	29	17	23	29	1.97
4690189--4690219	2	15.5	2	100	0	62	48	0	0	51	1.00
4693853--4693933	2	40.5	2	100	0	162	0	0	49	50	1.00
4697628--4697664	20	2.0	20	89	10	60	43	5	10	40	1.63
4700197--4700315	57	2.1	58	88	1	177	43	3	4	48	1.38
4700202--4700335	57	2.4	56	81	8	155	43	2	5	48	1.40
4706135--4706164	15	1.9	16	93	6	53	23	13	0	63	1.29
4706281--4706314	14	2.4	14	90	0	50	14	0	2	82	0.79
4710297--4710352	17	3.1	17	77	20	60	67	0	32	0	0.91
4710416--4710505	17	5.5	16	78	12	78	77	0	22	0	0.76
4710413--4710479	20	3.5	20	83	15	81	76	0	23	0	0.79
4710413--4710495	27	3.1	26	76	11	87	77	0	22	0	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4710432--4710505	6	12.5	6	78	13	82	81	0	18	0	0.70
4710432--4710506	36	2.0	38	87	7	109	81	0	18	0	0.69
4710431--4710506	10	7.7	10	72	8	66	80	0	19	0	0.72
4710573--4710626	19	2.8	20	83	13	60	29	42	27	0	1.56
4710576--4710631	23	2.7	20	81	13	69	30	41	28	0	1.57
4718435--4718478	21	2.1	21	95	0	79	29	11	29	29	1.92
4718727--4718766	20	2.0	20	100	0	80	25	35	10	30	1.88
4718768--4718842	32	2.4	32	84	6	91	54	2	0	42	1.14
4718934--4718973	6	6.7	6	83	11	55	77	0	5	17	0.94
4721494--4721606	54	2.1	54	96	0	208	24	12	14	48	1.78
4721498--4721593	30	3.4	30	66	21	80	26	11	16	45	1.81
4724084--4724121	19	2.0	19	85	10	51	60	0	15	23	1.35
4724124--4724167	15	2.9	15	83	10	54	50	9	0	40	1.34
4724256--4724297	18	2.5	17	85	11	59	76	2	4	16	1.07
4724257--4724317	24	2.6	23	82	10	70	75	3	4	16	1.11
4724256--4724313	16	3.5	16	84	11	73	74	3	5	17	1.15
4724257--4724317	7	7.9	7	75	15	50	75	3	4	16	1.11
4724533--4724564	14	2.3	14	94	0	55	75	3	0	21	0.95
4731484--4731518	4	8.8	4	87	0	52	20	2	2	74	1.08
4739343--4739640	101	3.0	99	91	5	478	35	11	26	26	1.90
4741409--4741451	19	2.3	19	84	8	52	34	2	6	55	1.39
4741459--4741517	18	3.2	18	79	18	59	32	5	6	55	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4746976--4747349	7	53.7	7	70	12	137	45	33	0	20	1.55
4746977--4747349	21	17.9	21	69	12	155	45	33	0	20	1.55
4747103--4747227	22	5.9	22	68	21	63	44	33	0	22	1.53
4747214--4747280	20	3.3	20	89	2	98	53	29	0	16	1.43
4747514--4747555	21	2.0	21	82	17	52	45	35	0	19	1.50
4750282--4750374	39	2.5	37	80	7	98	27	29	22	20	1.98
4750486--4750514	13	2.3	13	94	5	51	31	3	20	44	1.68
4751723--4751774	19	2.7	19	71	14	52	34	0	13	51	1.41
4752249--4752353	41	2.6	41	96	0	192	24	17	24	33	1.96
4754535--4754594	5	11.6	5	92	7	102	58	0	0	41	0.98
4754760--4754788	12	2.4	12	100	0	58	58	0	6	34	1.25
4760836--4760869	15	2.3	15	100	0	68	32	0	38	29	1.58
4763825--4763865	20	2.0	20	100	0	82	41	9	14	34	1.79
4764661--4764713	20	2.8	18	78	18	54	58	0	0	41	0.98
4764660--4764719	32	1.9	31	90	6	95	58	0	0	41	0.98
4764709--4764760	18	2.9	17	75	11	50	61	3	1	32	1.25
4764660--4764758	37	2.9	33	80	15	89	58	2	1	38	1.16
4765841--4765903	30	2.1	31	93	3	110	28	25	6	39	1.80
4765853--4765898	15	3.0	16	68	12	51	26	26	6	41	1.80
4770205--4770258	27	2.0	27	89	7	83	24	27	14	33	1.94
4770459--4770518	30	2.0	31	86	3	86	25	18	6	50	1.71
4774598--4774714	45	2.6	45	87	0	153	29	18	23	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4774910--4774950	20	2.0	21	90	4	66	70	17	0	12	1.16
4779672--4779819	57	2.5	56	80	8	161	31	20	24	22	1.98
4781371--4781597	116	2.0	116	97	0	427	22	29	14	34	1.93
4784143--4784172	3	10.0	3	92	0	51	63	0	36	0	0.95
4784441--4784578	37	3.7	37	70	13	111	31	5	12	51	1.61
4784394--4784622	76	2.9	79	76	10	245	33	4	12	49	1.62
4784394--4784614	40	5.6	41	70	17	132	33	4	11	49	1.61
4787486--4787521	16	2.3	16	90	4	56	16	2	25	55	1.55
4789769--4790430	156	4.3	156	91	2	1036	29	9	8	52	1.64
4789778--4790430	310	2.1	309	91	2	983	29	9	8	52	1.64
4790809--4790863	5	11.0	5	76	7	58	0	32	0	67	0.91
4790803--4790863	20	3.0	20	87	0	86	0	32	0	67	0.91
4790802--4790869	19	3.5	20	75	16	70	0	33	0	66	0.92
4791589--4791868	95	2.9	95	81	8	336	38	2	17	41	1.63
4794222--4794295	34	2.2	33	90	4	112	45	6	5	41	1.53
4794411--4794462	21	2.6	20	77	14	54	3	19	42	34	1.69
4794698--4794740	18	2.4	18	84	0	50	46	9	25	18	1.79
4795388--4795419	7	4.6	7	100	0	64	56	15	0	28	1.40
4796593--4796646	11	4.9	11	78	15	58	44	0	29	25	1.54
4797776--4797831	16	3.5	16	79	13	62	46	5	16	32	1.69
4801468--4801584	40	2.9	40	97	0	216	34	23	21	21	1.97
4801635--4801751	41	2.9	41	94	0	198	17	23	32	26	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4802059--4802188	7	18.4	7	71	7	66	21	0	30	46	1.57
4802138--4802241	35	3.0	34	78	10	95	22	0	37	40	1.54
4805518--4805717	107	1.9	107	86	2	285	32	16	17	33	1.92
4810652--4810739	44	2.0	44	97	0	167	39	29	5	25	1.78
4811848--4811889	20	2.0	21	90	4	68	19	2	4	73	1.12
4813927--4813987	31	1.9	33	86	6	90	60	8	6	24	1.49
4816844--4817621	336	2.3	336	97	0	1452	32	24	10	32	1.90
4823196--4823246	2	25.5	2	100	0	102	50	0	0	49	1.00
4823639--4823700	31	2.1	30	82	17	76	29	14	8	48	1.72
4823908--4823983	25	3.0	24	75	21	75	38	22	18	21	1.94

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