genome.fa.s3.2.7.7.80.10.50.1000.18.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  18  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)
4824481--4824511	9	3.4	9	100	0	62	41	19	0	38	1.51
4832543--4832575	11	3.1	11	86	8	50	30	0	33	36	1.58
4832545--4832586	21	2.0	21	90	0	66	35	0	23	40	1.55
4832949--4832996	25	2.0	25	91	4	80	16	27	18	37	1.92
4835327--4835377	22	2.3	22	81	18	61	60	5	5	27	1.43
4839117--4839156	18	2.2	19	86	13	57	5	37	0	57	1.21
4853497--4853532	13	2.7	13	95	4	63	50	0	16	33	1.46
4854313--4854355	18	2.4	18	76	0	50	58	2	0	39	1.11
4854702--4854735	6	5.5	6	96	3	59	2	14	0	82	0.79
4859266--4859299	16	2.1	16	94	0	59	11	35	0	52	1.38
4860426--4861068	321	2.0	321	97	0	1214	29	13	17	39	1.88
4861715--4861754	20	2.0	20	85	0	53	50	15	10	25	1.74
4862899--4862961	28	2.3	27	81	13	74	46	1	0	52	1.10
4863860--4863911	2	26.5	2	96	3	97	48	0	0	51	1.00
4869436--4870190	376	2.0	376	98	0	1467	40	17	14	27	1.89
4871332--4871384	25	2.1	25	82	6	63	28	1	16	52	1.54
4875347--4875414	31	2.2	32	79	12	79	57	2	4	35	1.34
4875566--4875590	2	12.5	2	100	0	50	52	0	0	48	1.00
4890381--4890424	18	2.4	19	92	7	81	72	0	0	27	0.85
4895779--4895836	26	2.2	26	93	0	98	36	12	10	41	1.76
4896282--4896347	35	1.9	34	90	6	107	46	10	7	34	1.67
4902304--4902349	13	3.7	13	77	11	51	54	8	10	26	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4902855--4902965	53	2.1	53	100	0	222	22	31	8	37	1.83
4906492--4906532	22	1.9	21	85	14	57	53	12	2	31	1.51
4909534--4909558	13	1.9	13	100	0	50	32	4	24	40	1.73
4911346--4911497	41	3.7	41	95	0	268	29	19	29	21	1.97
4911346--4911516	41	4.2	41	93	0	153	30	18	28	22	1.98
4914840--4914902	8	7.5	8	73	16	56	36	0	4	58	1.19
4914918--4915011	40	2.3	40	96	1	170	63	8	27	0	1.23
4916133--4916266	39	3.4	38	73	12	112	23	20	27	28	1.99
4916929--4916962	17	2.0	17	88	0	50	35	11	17	35	1.87
4920522--4920546	13	1.9	13	100	0	50	32	4	24	40	1.73
4922349--4922500	41	3.7	41	99	0	295	28	21	29	20	1.98
4924484--4924529	23	2.0	24	82	4	58	32	26	0	41	1.56
4924672--4924702	6	5.2	6	92	0	53	48	12	0	38	1.42
4925386--4925431	20	2.3	20	78	10	51	4	15	6	73	1.19
4925586--4925613	4	7.0	4	100	0	56	50	0	0	50	1.00
4935787--4935833	17	2.8	17	77	6	51	63	0	8	27	1.23
4940060--4940098	12	3.2	12	82	17	53	30	7	0	61	1.24
4940152--4940185	18	1.9	17	88	5	50	35	11	2	50	1.54
4945109--4945175	29	2.3	29	89	0	98	44	13	10	31	1.77
4945165--4945267	9	11.4	9	84	4	127	42	22	8	26	1.82
4945363--4945416	18	2.9	18	88	2	81	11	1	48	38	1.50
4946227--4946280	20	2.7	20	85	0	72	44	22	24	9	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4951154--4951191	19	2.0	19	85	10	51	71	0	26	2	1.00
4951165--4951214	24	2.1	24	85	7	66	76	0	20	4	0.95
4952704--4952762	24	2.5	24	80	0	73	20	25	30	23	1.98
4952812--4952884	27	2.7	26	83	10	94	28	17	26	27	1.98
4953355--4953422	28	2.4	28	92	0	109	16	29	23	30	1.96
4957777--4957883	54	2.0	54	88	3	162	37	14	22	25	1.93
4966639--4966685	22	2.1	23	88	4	69	10	8	2	78	1.04
4967318--4967352	2	17.5	2	100	0	70	48	0	0	51	1.00
4969547--4969591	19	2.4	19	85	7	56	26	20	8	44	1.80
4973070--4973112	21	2.0	21	100	0	86	48	9	18	23	1.76
4973756--4974856	89	12.4	89	90	1	1571	32	16	23	27	1.96
4974853--4975039	44	4.2	44	67	9	121	32	18	23	26	1.97
4975052--4975248	44	4.5	43	69	17	111	27	20	24	26	1.99
4974850--4975214	88	4.1	88	67	9	249	30	18	24	26	1.98
4974852--4975218	132	2.8	132	94	1	646	29	19	24	26	1.98
4976433--4976473	21	2.0	21	85	0	55	34	7	0	58	1.26
4976577--4976625	2	24.5	2	100	0	98	48	0	0	51	1.00
4987507--4987563	30	1.9	30	82	13	73	47	3	0	49	1.18
4988718--4988784	34	1.9	35	87	3	100	49	11	5	32	1.64
4989010--4989060	21	2.5	20	72	18	50	64	3	1	29	1.22
4990539--4990574	18	2.0	18	88	0	54	19	2	8	69	1.27
4991334--4991485	42	3.6	42	77	7	121	19	21	15	43	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4995417--4995456	16	2.7	14	85	11	53	42	5	0	52	1.23
5000199--5000237	18	2.2	17	86	4	51	48	17	7	25	1.74
5002132--5002164	16	2.1	16	100	0	66	39	30	6	24	1.79
5002689--5002714	10	2.6	10	100	0	52	26	0	7	65	1.20
5009220--5009245	11	2.4	11	100	0	52	76	0	0	23	0.78
5010007--5010061	9	5.9	9	75	8	56	30	1	3	63	1.22
5010007--5010131	19	6.8	18	70	17	80	37	1	1	59	1.17
5010011--5010117	53	2.0	52	82	8	128	40	1	1	56	1.21
5010711--5010781	37	1.9	37	83	8	92	54	1	2	40	1.23
5011170--5011199	14	2.2	13	94	5	51	30	16	0	53	1.44
5011616--5011648	7	4.7	7	92	0	57	45	0	0	54	0.99
5015376--5015405	2	15.0	2	100	0	60	50	0	0	50	1.00
5016405--5016475	36	1.9	37	83	8	92	32	19	2	45	1.65
5016463--5016506	23	1.9	22	82	17	54	38	22	0	38	1.55
5016605--5016703	23	4.3	23	93	0	153	31	24	22	22	1.98
5022574--5022612	19	2.2	17	86	9	51	5	17	2	74	1.12
5022574--5022617	18	2.4	18	85	11	54	4	20	2	72	1.13
5026563--5026618	29	1.9	29	85	7	78	30	26	30	12	1.93
5027073--5027317	26	9.4	26	77	0	202	22	14	26	37	1.92
5027078--5027302	78	2.9	77	78	2	225	21	14	27	36	1.92
5028389--5028459	22	3.3	22	84	2	90	19	21	40	18	1.91
5036552--5036589	2	19.0	2	100	0	76	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)
5036758--5036805	17	2.8	17	81	12	53	37	4	2	56	1.30
5043382--5043406	7	3.6	7	100	0	50	24	0	0	76	0.80
5044530--5044840	159	2.0	158	87	1	444	35	14	10	39	1.80
5045223--5046044	310	2.7	308	87	5	1132	35	14	11	38	1.83
5045223--5046044	158	5.3	154	86	6	1035	35	14	11	38	1.83
5059024--5059048	13	1.9	13	100	0	50	32	4	24	40	1.73
5064091--5064118	14	2.0	14	100	0	56	21	21	7	50	1.72
5065005--5065047	14	3.3	13	90	6	61	30	25	13	30	1.94
5065482--5065536	3	18.3	3	96	0	101	32	1	0	65	1.03
5065744--5065779	19	1.9	18	88	5	54	22	8	11	58	1.59
5068207--5068239	17	2.0	17	94	5	59	30	12	3	54	1.52
5069191--5069335	67	2.2	67	94	0	254	42	10	12	35	1.77
5072259--5072327	28	2.4	29	88	7	97	63	1	0	34	1.03
5091696--5091784	25	3.5	24	78	14	90	82	0	13	4	0.83
5091696--5091784	26	3.4	25	79	15	92	82	0	13	4	0.83
5091716--5091784	7	9.6	7	73	17	52	82	0	14	2	0.78
5091705--5091771	19	3.6	19	78	11	68	82	0	16	1	0.75
5091708--5091785	27	3.2	25	76	20	85	80	0	16	2	0.82
5092725--5092776	24	2.2	24	82	6	61	36	9	21	32	1.86
5093051--5093607	89	6.4	89	69	11	258	29	25	22	22	1.99
5093051--5093274	45	5.0	45	80	3	236	29	22	22	25	1.99
5093312--5093664	44	8.0	44	78	7	295	28	27	22	20	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5093401--5093664	133	2.0	133	87	0	384	28	26	23	21	1.99
5093294--5093643	89	3.9	89	82	3	375	29	27	22	21	1.99
5093864--5094243	44	8.7	43	70	13	175	31	20	19	28	1.97
5093820--5094192	129	2.8	129	84	4	437	30	21	19	27	1.98
5094895--5094919	11	2.3	11	100	0	50	44	16	16	24	1.86
5095003--5095055	26	2.0	26	100	0	106	22	0	28	49	1.50
5095986--5096010	13	1.9	13	100	0	50	28	0	16	56	1.41
5098939--5098966	14	2.0	14	100	0	56	28	35	28	7	1.84
5100469--5100510	20	2.0	21	86	4	59	38	11	0	50	1.40
5101130--5101271	73	2.0	72	88	6	216	28	20	18	32	1.96

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