genome.fa.s6.2.7.7.80.10.50.1000.20.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  20  of  168  ( 20060 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)
5277639--5277742	55	2.0	53	83	7	131	27	28	14	28	1.95
5279527--5279566	18	2.2	19	90	4	64	60	2	10	27	1.42
5281389--5281414	12	2.2	12	100	0	52	26	7	7	57	1.54
5281481--5281565	44	1.9	45	87	2	127	37	10	5	45	1.63
5285577--5285634	25	2.4	22	78	21	62	68	0	3	27	1.05
5285641--5285728	6	15.8	5	81	11	52	70	1	3	25	1.10
5285681--5285727	3	15.7	3	100	0	94	68	0	0	31	0.90
5285840--5285911	30	2.4	29	79	9	74	70	2	2	23	1.13
5299652--5299685	5	6.8	5	100	0	68	41	0	0	58	0.98
5312761--5312789	15	1.9	15	100	0	58	41	0	20	37	1.53
5315314--5315347	11	3.2	11	87	4	52	73	0	0	26	0.83
5324849--5324943	46	2.1	46	100	0	190	36	21	23	18	1.95
5324803--5325015	118	1.8	118	96	0	399	34	18	26	20	1.96
5324895--5325140	72	3.4	72	95	0	429	34	19	24	21	1.96
5325065--5325386	144	2.2	144	87	2	396	32	16	25	25	1.96
5325106--5325386	144	2.0	144	92	0	472	32	15	24	27	1.95
5327251--5327303	28	1.9	28	85	11	74	20	11	1	66	1.33
5328664--5328696	15	2.1	17	88	11	52	18	6	0	75	1.00
5334259--5334309	22	2.3	22	96	0	93	25	33	0	41	1.56
5334353--5334416	28	2.2	30	91	5	105	35	0	0	64	0.94
5336181--5336215	18	1.9	18	88	0	52	25	34	8	31	1.86
5336472--5336521	21	2.4	21	82	0	64	42	34	22	2	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5336710--5336925	29	7.0	29	83	13	206	45	28	1	24	1.64
5336713--5336925	34	6.8	33	81	14	220	45	28	1	24	1.64
5336736--5336925	56	3.1	57	85	10	229	45	28	1	24	1.63
5336768--5336830	27	2.5	23	77	20	72	50	25	0	23	1.49
5336790--5336925	35	4.1	35	82	13	171	44	30	2	23	1.65
5337069--5337093	10	2.5	10	100	0	50	44	8	0	48	1.32
5344504--5345311	288	2.8	288	94	1	1388	32	15	23	28	1.95
5346512--5346569	27	2.1	27	81	12	66	17	10	1	70	1.23
5346512--5346570	28	2.1	27	84	9	75	16	10	1	71	1.22
5348035--5348085	13	3.8	13	84	2	66	37	0	1	60	1.08
5348047--5348085	11	2.9	15	78	21	50	33	0	2	64	1.08
5348074--5348135	28	2.2	29	77	13	67	41	11	0	46	1.39
5348113--5348153	2	20.5	2	84	0	55	46	7	0	46	1.30
5348092--5348153	28	2.1	28	85	5	79	45	8	0	46	1.32
5350533--5350566	12	2.8	12	86	0	50	41	11	29	17	1.85
5353265--5353324	19	3.3	19	77	13	72	81	0	18	0	0.69
5353256--5353330	29	2.5	30	82	6	89	81	0	14	4	0.83
5353265--5353323	24	2.6	24	82	12	63	81	0	18	0	0.69
5353266--5353316	9	5.4	9	75	15	50	80	0	19	0	0.71
5353266--5353323	7	7.9	7	75	17	55	81	0	18	0	0.70
5353289--5353336	24	2.0	24	84	8	62	75	0	22	2	0.91
5354628--5354832	88	2.3	87	90	3	320	29	18	25	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5354724--5354963	132	1.8	132	93	1	419	29	18	25	26	1.98
5354856--5355314	88	5.2	88	72	15	349	30	18	24	26	1.98
5354691--5355052	44	8.2	43	63	22	110	30	17	25	26	1.97
5354633--5355196	220	2.6	220	91	1	900	30	17	25	26	1.97
5354809--5355636	44	18.8	44	64	19	214	29	18	25	27	1.98
5354631--5355316	220	3.1	219	85	6	734	30	17	24	27	1.98
5354944--5355777	132	6.3	132	90	0	1213	29	18	25	26	1.98
5355803--5356134	50	6.7	49	74	6	247	31	22	20	25	1.98
5355781--5356137	100	3.6	100	84	2	475	31	22	19	25	1.98
5357939--5357991	13	3.8	13	80	11	61	37	0	1	60	1.08
5357950--5357988	15	2.6	15	87	0	60	33	0	2	64	1.08
5363119--5363143	12	2.1	12	100	0	50	8	8	20	64	1.46
5364111--5364179	22	3.0	24	68	23	76	40	10	4	44	1.58
5364514--5364553	21	1.9	21	85	10	55	42	2	0	55	1.13
5364815--5364875	13	4.7	13	91	0	104	40	26	9	22	1.85
5367260--5367395	39	3.5	39	78	3	114	38	22	18	20	1.93
5367262--5367395	38	3.4	38	78	5	110	38	22	18	20	1.93
5367433--5367715	41	6.9	41	86	4	365	21	19	28	30	1.98
5371223--5371280	24	2.4	24	91	0	98	39	15	15	29	1.88
5372195--5372287	47	2.0	47	100	0	186	21	21	18	38	1.93
5372859--5372924	34	1.9	35	84	9	91	39	1	3	56	1.24
5372859--5372927	35	2.0	35	83	11	88	39	1	2	56	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5373031--5373386	43	8.3	43	86	0	444	21	16	32	30	1.95
5373479--5373521	22	2.0	22	95	0	77	41	27	20	9	1.83
5381598--5381628	9	3.4	9	90	0	53	25	12	22	38	1.90
5381682--5381718	9	4.1	9	92	0	65	45	13	10	29	1.77
5381767--5381827	30	2.0	31	87	3	88	18	44	1	36	1.59
5384242--5384756	72	7.2	72	77	4	405	31	23	13	32	1.92
5384242--5384791	217	2.5	217	81	2	516	31	22	13	32	1.93
5389771--5389822	26	2.0	26	100	0	104	38	0	23	38	1.55
5398825--5399123	50	5.8	50	87	2	391	21	30	22	25	1.99
5404062--5404118	30	1.9	28	86	10	78	38	3	12	45	1.59
5404062--5404118	29	1.9	30	85	3	80	38	3	12	45	1.59
5405066--5405098	12	2.8	12	86	13	50	6	15	0	78	0.93
5410899--5410949	26	2.0	26	84	7	68	35	0	11	52	1.38
5413660--5413693	15	2.3	15	90	10	52	55	0	5	38	1.24
5413852--5413890	16	2.5	16	83	4	53	46	0	7	46	1.31
5413849--5413964	61	1.9	61	80	7	137	40	5	8	45	1.57
5414192--5414237	7	6.6	7	78	16	51	60	10	0	28	1.30
5414156--5414333	52	3.6	51	71	16	158	45	15	3	35	1.63
5414113--5414323	95	2.2	95	85	3	271	45	14	4	35	1.65
5414192--5414237	15	3.3	15	82	11	62	60	10	0	28	1.30
5414233--5414290	21	2.8	20	80	15	73	43	13	3	39	1.61
5414406--5414577	9	20.2	9	68	15	82	44	19	2	33	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5414406--5414468	27	2.3	27	94	0	108	49	15	1	33	1.55
5414548--5414584	7	5.0	7	87	12	56	54	16	0	29	1.43
5420178--5420229	21	2.5	20	78	9	59	26	21	48	3	1.67
5420557--5420844	42	6.9	41	82	3	279	31	20	21	26	1.98
5420557--5420760	84	2.4	84	89	1	311	35	20	20	23	1.96
5420558--5420795	126	1.9	126	83	1	307	33	20	20	25	1.97
5420930--5420974	22	2.0	22	86	0	63	42	26	20	11	1.85
5421172--5421266	3	30.7	3	82	4	109	63	3	3	30	1.26
5422028--5422062	11	3.2	11	91	0	52	80	2	2	14	0.95
5422013--5422051	18	2.2	18	90	4	62	76	0	10	12	1.01
5422782--5423587	46	17.4	46	89	1	1153	32	25	16	26	1.96
5424484--5424909	108	4.1	106	83	9	496	48	8	16	26	1.75
5424694--5424885	96	2.0	96	94	1	339	47	7	17	28	1.74
5425181--5425236	12	4.9	11	81	18	62	1	16	0	82	0.76
5430031--5430064	15	2.3	15	90	10	52	55	0	5	38	1.24
5438424--5438475	21	2.5	20	78	9	59	26	21	48	3	1.67
5438803--5439048	42	5.9	41	84	5	314	34	20	21	23	1.96
5438802--5439048	126	2.0	126	89	1	379	34	20	21	23	1.96
5441455--5441489	11	3.2	11	91	0	52	80	2	2	14	0.95
5441440--5441478	18	2.2	18	90	4	62	76	0	10	12	1.01
5441875--5441918	18	2.3	19	84	11	54	18	4	0	77	0.94
5442515--5442556	23	1.9	21	90	9	66	35	45	0	19	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5442515--5442615	22	4.9	21	75	19	88	34	42	0	22	1.54
5442533--5442571	16	2.5	16	91	4	62	33	41	0	25	1.56
5443545--5443723	41	4.3	40	75	11	141	37	23	16	22	1.93
5443543--5443723	82	2.2	83	82	6	217	38	23	16	22	1.92
5446925--5446954	11	2.7	11	94	0	51	16	16	10	56	1.66
5449917--5449971	18	3.1	18	86	0	74	25	7	18	49	1.73
5450857--5450902	18	2.6	18	85	0	65	26	8	41	23	1.83
5454262--5454316	18	3.1	18	86	0	74	25	7	18	49	1.73
5455477--5455509	16	2.1	16	94	0	57	15	0	3	81	0.80
5468258--5468500	46	5.5	46	65	17	127	30	19	20	29	1.97

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   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168